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Recent Advances in Horticultural Plant Genomics
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Recent Advances in Horticultural Plant Genomics

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 34242

Special Issue Editors

Dr. Zhongxiong Lai

E-Mail Website
Guest Editor
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: horticultural crops; genomics; tissue culture；molecular biology; germplasm; somatic embryogenesis
Prof. Dr. Yuling Lin

E-Mail Website
Guest Editor
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: genomics and biotechnology; plant tissue culture; non-coding RNA; molecular biology; somatic embryogenesis
Special Issues, Collections and Topics in MDPI journals
Dr. Yuqiong Guo

E-Mail Website
Guest Editor
College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: tea processing; tea biotechnology; tea biochemistry; genomics; molecular biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Whole-genome sequencing of plants and animals has developed rapidly over the past 20 years. With the development of sequencing technologies and the reduction of sequencing costs, more and more plant genomes have been sequenced and many results have been obtained, especially with the advent and applications of second- and third-generation sequencing technologies and Hi-C technologies, which have made sequencing  a reality in many complex plant genomes. By the end of 2022, more than 400 plant genome sequences have become available, most of them of horticultural plants. The development and applications of sequencing technologies has not only reduced the time and cost of whole-genome sequencing, but has also brought the study and understanding of plants to the whole-genome level, providing a new perspective on understanding gene structure, composition, and function, gene regulation, and species evolution at the molecular level. With advances in high-throughput sequencing technology, multiomics, such as pan-genomics,  transcriptomics and genome-wide non-coding RNAs, have been rapidly developed. Genomic research tools are widely used in horticultural plants such as fruit trees, vegetables, flowers, tea plants and Chinese herbs for molecular breeding and analysis of growth and development patterns, providing a new perspective on horticultural plant research, which would assist greater  understanding of the evolutionary histories of plant species and provide genomic resources for molecular studies on the economically important traits of horticultural plants.

Dr. Zhongxiong Lai
Prof. Dr. Yuling Lin
Dr. Yuqiong Guo
Guest Editors

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Keywords

  • genomics
  • non-coding RNA
  • transcriptomics

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21 pages, 3964 KiB  
Article
Emission and Transcriptional Regulation of Aroma Variation in Oncidium Twinkle ‘Red Fantasy’ Under Diel Rhythm
by Yan Chen, Shengyuan Zhong, Lan Kong, Ronghui Fan, Yan Xu, Yiquan Chen and Huaiqin Zhong
Plants 2024, 13(22), 3232; https://doi.org/10.3390/plants13223232 (registering DOI) - 17 Nov 2024
Abstract
Oncidium hybridum is one of the important cut-flowers in the world. However, the lack of aroma in its cut-flower varieties greatly limits the sustainable development of the Oncidium hybridum cut-flowers industry. This paper is an integral investigation of the diel pattern and influencing [...] Read more.
Oncidium hybridum is one of the important cut-flowers in the world. However, the lack of aroma in its cut-flower varieties greatly limits the sustainable development of the Oncidium hybridum cut-flowers industry. This paper is an integral investigation of the diel pattern and influencing factors of the aroma release of Oncidium Twinkle ‘Red Fantasy’. GC-MS analysis revealed that the release of 3-Carene peaked at 10:00, while Butyl tiglate and Prenyl senecioate did so at 14:00, with a diel rhythm. By analyzing the correlation network between aroma component synthesis and differentially expressed genes, 15 key structural genes were detected and regulated by multiple circadian rhythm-related transcription factors. Cluster-17371.18_TPS, Cluster-65495.1_TPS, Cluster-46699.0_TPS, Cluster-60935.10_DXS, Cluster-47205.4_IDI, and Cluster-65313.7_LOX were key genes in the terpenoid and fatty acid derivative biosynthetic pathway, which were co-expressed with aroma release. Constant light/dark treatments revealed that the diurnal release of 3-Carene may be influenced by light and the circadian clock, and Butyl tiglate and Prenyl senecioate may be mainly determined by endogenous circadian clock. Under constant light treatment, the TPS, DXS, IDI, and LOX genes seem to lose their regulatory role in the release of aroma compounds from Oncidium Twinkle ‘Red Fantasy’. Under constant dark treatment, the TPS genes were consistent with the release pattern of 3-Carene, which may be a key factor in regulating the diel rhythm of 3-Carene biosynthesis. These results laid a theoretical foundation for the study of floral transcriptional regulation and genetic engineering technology breeding of Oncidium hybridum. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
►▼ Show Figures

Figure 1

Figure 1
<p>The emission patterns of three floral scent compounds—3-Carene, Butyl tiglate, and Prenyl senecioate—in <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’ under normal photoperiod (under 12 h light/12 h dark). (<b>a</b>) Overlapping analysis of 3-Carene ion current in samples at different time points within 24 h. The abscissa represents the retention time (min), and the ordinate represents the ion current intensity. (<b>b</b>) The emission patterns of 3-Carene from <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’ flowers within 48 h. (<b>c</b>) Overlapping analysis of Butyl tiglate ion current in samples at different time points within 24 h. The abscissa represents the retention time (min), and the ordinate represents the ion current intensity. (<b>d</b>) The emission patterns of Butyl tiglate from <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’ flowers within 48 h. (<b>e</b>) Overlapping analysis of Prenyl senecioate ion current in samples at different time points within 24 h. The abscissa represents the retention time (min), and the ordinate represents the ion current intensity. (<b>f</b>) The emission patterns of Prenyl senecioate from <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’ flowers within 48 h. Each treatment was conducted in triplicate with three technical repeats. Values are mean ± SD. Different lowercase letters indicate a statistically significant difference (<span class="html-italic">p</span> &lt; 0.05).</p> Full article ">Figure 2
<p>Transcriptomic analysis of <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’ at different time points within 24 h (under 12 h light/12 h dark). (<b>a</b>) Principal component analysis (PCA) plot showed overall differences among six groups (2:00, 6:00, 10:00, 14:00, 18:00, and 22:00) and the variability between intra-group samples. (<b>b</b>) Heatmap of differentially expressed genes (DEGs) sorted by K-means clustering across the samples collected at different time points. The numbers 1, 2, and 3 with each sample represented number of replicates. (<b>c</b>) Eight K-means clusters (Clusters 1–8) showed differential expression trends of DEGs at different time points. (<b>d</b>) KEGG enrichment analysis of DEGs in Cluster 4. The red boxes indicate metabolic pathways related to aroma rhythm release. (<b>e</b>) KEGG enrichment analysis of DEGs in Cluster 6. The red boxes indicate metabolic pathways related to aroma rhythm release. (<b>f</b>) KEGG enrichment analysis of DEGs in Cluster 8. The red boxes indicate metabolic pathways related to aroma rhythm release.</p> Full article ">Figure 3
<p>Overview of metabolites and DEGs in the biosynthesis pathways of fatty acid derivative and terpenoid in <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’. (<b>a</b>) The DEGs of Cluster 6 were enriched in the fatty acid derivative biosynthesis pathway. <span class="html-italic">9-lipoxygenase</span> (<span class="html-italic">9-LOX</span>), <span class="html-italic">13-lipoxygenase</span> (<span class="html-italic">13-LOX</span>), <span class="html-italic">9-hydroperoxide lyase</span> (<span class="html-italic">9-HPL</span>), <span class="html-italic">13-hydroperoxide lyase</span> (<span class="html-italic">13</span>-<span class="html-italic">HPL</span>), <span class="html-italic">alcohol dehydrogenase</span> (<span class="html-italic">ADH</span>), <span class="html-italic">allene oxide synthase</span> (<span class="html-italic">AOS</span>), and <span class="html-italic">alcohol acyltransferase</span> (<span class="html-italic">AAT</span>). The black dashed boxes represent genes enriched in the LOX pathway, and the red fonts represent differentially expressed genes. (<b>b</b>) The DEGs of Cluster 4 and Cluster 8 were enriched in the terpenoid biosynthesis pathway. <span class="html-italic">Acetyl</span>-<span class="html-italic">CoA acetyltransferase</span> (<span class="html-italic">AACT</span>), <span class="html-italic">hydroxymethylglutaryl</span>-<span class="html-italic">CoA synthase</span> (<span class="html-italic">HMGS</span>), <span class="html-italic">hydroxymethylglutaryl</span>-<span class="html-italic">CoA reductase</span> (<span class="html-italic">HMGR</span>), <span class="html-italic">mevalonate kinase</span> (<span class="html-italic">MVK</span>), <span class="html-italic">mevalonate phosphate decarboxylase</span> (<span class="html-italic">MPD</span>), <span class="html-italic">phosphomevalonate kinase</span> (<span class="html-italic">PMK</span>), <span class="html-italic">isopentenyl phosphate kinase</span> (<span class="html-italic">IPK</span>), <span class="html-italic">mevalonate diphosphate decarboxylase</span> (<span class="html-italic">MPDC</span>), <span class="html-italic">isopentenyl diphosphate isomerase</span> (<span class="html-italic">IDI</span>), <span class="html-italic">farnesyl pyrophosphate synthase</span> (<span class="html-italic">FPPS</span>), <span class="html-italic">terpenoid synthase</span> (<span class="html-italic">TPS</span>), <span class="html-italic">1-deoxy-D-xylulose 5-phosphate synthase</span> (<span class="html-italic">DXS</span>), <span class="html-italic">1-deoxy-D-xylulose 5-phosphate reductoisomerase</span> (<span class="html-italic">DXR</span>), <span class="html-italic">2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase</span> (<span class="html-italic">MCT</span>), <span class="html-italic">4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol kinase</span> (<span class="html-italic">CMK</span>), <span class="html-italic">2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase</span> (<span class="html-italic">MECPS</span>), <span class="html-italic">4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase</span> (<span class="html-italic">HDS</span>), <span class="html-italic">isoprenyl diphosphate synthase</span> (<span class="html-italic">IDS</span>), <span class="html-italic">geranylgeranyl pyrophosphate synthase</span> (<span class="html-italic">GGPPS</span>), and <span class="html-italic">geranyl diphosphate synthase</span> (<span class="html-italic">GPPS</span>). The black dashed boxes represent genes enriched in the MVA and MEP pathway, and the red fonts represent differentially expressed genes.</p> Full article ">Figure 4
<p>Establishment of weighted gene co-expression network analysis (WGCNA) modules of the differentially expressed genes (DEGs) at different time points. (<b>a</b>) Hierarchical clustering tree of the co-expression modules. The major tree branches constituted 10 distinct co-expression modules. (<b>b</b>) The gene expression patterns of the Blue, Red, Yellow, and Brown modules in WGCNA. The upper part was the clustering heatmap of genes within this module, with red indicating high expression and green indicating low expression. The lower part showed the expression patterns of module feature values in different samples. (<b>c</b>) Co-expression network of the genes from the Blue module. The red circles represent the key hub genes enriched in fatty acid derivative biosynthesis pathway, and the blue circles represent aroma synthesis related transcription factors (TFs). (<b>d</b>) Co-expression network of the genes from the Red module. The red circles represent the key hub genes enriched in terpenoid biosynthesis pathway, and the blue circles represent aroma synthesis related TFs. The red font represents TFs that were differentially enriched in the “Circadian rhythm-plant” pathway. (<b>e</b>) Co-expression network of the genes from the Brown module. The red circles represent the key hub genes enriched in terpenoid biosynthesis pathway, and the blue circles represent aroma synthesis related TFs. (<b>f</b>) Co-expression network of the genes from the Yellow module. The red circles represent the key hub genes enriched in terpenoid biosynthesis pathway, and the blue circles represent aroma synthesis related TFs. The red font represents TFs that were differentially enriched in the “Circadian rhythm-plant” pathway. The networks were visualized by Cytoscape (v3.5.1) software.</p> Full article ">Figure 5
<p>Relative expression of structural genes <span class="html-italic">Cluster-17371.18_TPS</span>, <span class="html-italic">Cluster-65495.1_TPS</span>, <span class="html-italic">Cluster-46699.0_TPS</span>, <span class="html-italic">Cluster-60935.10_DXS</span>, <span class="html-italic">Cluster</span>-<span class="html-italic">47205.4_IDI</span>, and <span class="html-italic">Cluster-65313.7_LOX</span> in <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’ flowers within 48 h (under 12 h light/12 h dark). Each treatment was conducted in triplicate with three technical repeats. Values are mean ± SD. Different lowercase letters indicate a statistically significant difference (<span class="html-italic">p</span> &lt; 0.05).</p> Full article ">Figure 6
<p>Analysis of aroma release pattern of <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’ under constant light and constant dark treatments. (<b>a</b>) The emission patterns of three floral scent compounds from <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’ flowers within 48 h under constant light. (<b>b</b>) The emission patterns of three floral scent compounds from <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’ flowers within 48 h under constant dark. Different lowercase letters indicate a statistically significant difference (<span class="html-italic">p</span> &lt; 0.05).</p> Full article ">Figure 7
<p>Analysis of aroma synthesis genes expression of <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’ under constant light and constant dark treatments. (<b>a</b>) Relative expression of structural genes <span class="html-italic">Cluster-17371.18_TPS, Cluster-65495.1_TPS</span>, <span class="html-italic">Cluster-46699.0_TPS, Cluster-60935.10_DXS</span>, <span class="html-italic">Cluster-47205.4_IDI</span>, and <span class="html-italic">Cluster-65313.7_LOX</span> in <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’ flowers within 48 h under constant light. (<b>b</b>) Relative expression of structural genes <span class="html-italic">Cluster-17371.18_TPS, Cluster-65495.1_TPS</span>, <span class="html-italic">Cluster-46699.0_TPS, Cluster-60935.10_DXS</span>, <span class="html-italic">Cluster-47205.4_IDI</span>, and <span class="html-italic">Cluster-65313.7_LOX</span> in <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’ flowers within 48 h under constant dark. Each treatment was conducted in triplicate with three technical repeats. Values are mean ± SD. Different lowercase letters indicate a statistically significant difference (<span class="html-italic">p</span> &lt; 0.05).</p> Full article ">Figure 8
<p>Schematic model of the mechanism by which the circadian rhythm regulates the aroma release of <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’. The main aroma compounds of <span class="html-italic">Oncidium</span> Twinkle ‘Red Fantasy’ were 3-Carene, Butyl tiglate, and Prenyl senecioate. 3-Carene were mainly released at 10:00, while Butyl tiglate and Prenyl senecioate were mainly released at 14:00. <span class="html-italic">DXS</span>, <span class="html-italic">CMK</span>, <span class="html-italic">IDI</span>, <span class="html-italic">TPS</span>, and <span class="html-italic">LOX</span> were key genes in the terpenoid or fatty acid derivative biosynthetic pathway, which were co-expressed with aroma release. Under the treatment of constant light or dark, the aroma release maintained a circadian rhythm.</p> Full article ">
19 pages, 15466 KiB  
Article
Transcriptomic Analysis Reveals the Mechanism of Color Formation in the Peel of an Evergreen Pomegranate Cultivar ‘Danruo No.1’ During Fruit Development
by Xiaowen Wang, Chengkun Yang, Wencan Zhu, Zhongrui Weng, Feili Li, Yuanwen Teng, Kaibing Zhou, Minjie Qian and Qin Deng
Plants 2024, 13(20), 2903; https://doi.org/10.3390/plants13202903 - 17 Oct 2024
Viewed by 545
Abstract
Pomegranate (Punica granatum L.) is an ancient fruit crop that has been cultivated worldwide and is known for its attractive appearance and functional metabolites. Fruit color is an important index of fruit quality, but the color formation pattern in the peel of [...] Read more.
Pomegranate (Punica granatum L.) is an ancient fruit crop that has been cultivated worldwide and is known for its attractive appearance and functional metabolites. Fruit color is an important index of fruit quality, but the color formation pattern in the peel of evergreen pomegranate and the relevant molecular mechanism is still unknown. In this study, the contents of pigments including anthocyanins, carotenoids, and chlorophyll in the peel of ‘Danruo No. 1’ pomegranate fruit during three developmental stages were measured, and RNA-seq was conducted to screen key genes regulating fruit color formation. The results show that pomegranate fruit turned from green to red during development, with a dramatic increase in a* value, indicating redness and anthocyanins concentration, and a decrease of chlorophyll content. Moreover, carotenoids exhibited a decrease–increase accumulation pattern. Through RNA-seq, totals of 30, 18, and 17 structural genes related to anthocyanin biosynthesis, carotenoid biosynthesis and chlorophyll metabolism were identified from differentially expressed genes (DEGs), respectively. Transcription factors (TFs) such as MYB, bHLH, WRKY and AP2/ERF were identified as key candidates regulating pigment metabolism by K-means analysis and weighted gene co-expression network analysis (WGCNA). The results provide an insight into the theory of peel color formation in evergreen pomegranate fruit. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
►▼ Show Figures

Figure 1

Figure 1
<p>Coloration and pigment contents in ‘Danruo No.1’ pomegranate peel during fruit development. (<b>A</b>) Representative images of fruits at developmental stage 1 (S1), stage 2 (S2), and stage 3 (S3). (<b>B</b>) Fruit peel lightness (<span class="html-italic">L*</span> value). (<b>C</b>) Fruit peel <span class="html-italic">a*</span> value (higher value means redness and lower value means greenness). (<b>D</b>) Fruit peel <span class="html-italic">b*</span> value (higher value means yellowness and lower value means blueness). (<b>E</b>) Chlorophyll a content. (<b>F</b>) Chlorophyll b content. (<b>G</b>) Total chlorophyll content. (<b>H</b>) Anthocyanin content. (<b>I</b>) Carotenoid content. Each value represents the mean ± standard deviation of three biological replicates. Different letters above the bars indicate significant differences (<span class="html-italic">p</span> &lt; 0.05) according to one-way analysis of variance (ANOVA) followed by Tukey test.</p> Full article ">Figure 2
<p>Differentially expressed genes (DEGs) identification and KEGG analysis. Volcano plots of DEGs from S2 vs. S1 (<b>A</b>), S3 vs. S1 (<b>B</b>), and S3 vs. S2 (<b>C</b>). Horizontal coordinates indicate the fold change of gene expression between different groups, and vertical coordinates indicate the significance level of gene expression difference in the two groups. Red dots indicate upregulated genes, green dots indicate downregulated genes, and grey dots indicate insignificant genes. Top 20 metabolic pathways analyzed by KEGG enrichment for DEGs from S2 vs. S1 (<b>D</b>), S3 vs. S1 (<b>E</b>), and S3 vs. S2 (<b>F</b>). The pathways associated with pigments metabolism are highlighted in red color.</p> Full article ">Figure 3
<p>Expression patterns of the DEGs involved in anthocyanins synthesis in pomegranate peel at developmental stage 1 (S1), stage 2 (S2), and stage 3 (S3). The color scale from green to red represents the fragments per kilobase of transcript per million of fragments mapped (FPKM) values, from low to high.</p> Full article ">Figure 4
<p>Expression pattern of the DEGs involved in carotenoids synthesis in pomegranate peel at developmental stage 1 (S1), stage 2 (S2), and stage 3 (S3). The color scale from blue to red represents the fragments per kilobase of transcript per million of fragments mapped (FPKM) values from low to high.</p> Full article ">Figure 5
<p>Expression pattern of the DEGs involved in chlorophyll biosynthesis and degradation in pomegranate peel at developmental stage 1 (S1), stage 2 (S2), and stage 3 (S3). The color scale from green to red represents the fragments per kilobase of transcript per million of fragments mapped (FPKM) values from low to high.</p> Full article ">Figure 6
<p>Identification of transcription factors (TFs) regulating pigments metabolism in pomegranate peel during fruit development. (<b>A</b>) K-means analysis of DEGs identified from transcriptome sequencing. The expression profiles of genes in each cluster are represented in different colors, and the average expression levels of all genes in developmental stage 1 (S1), S2, and S3 are represented in black. (<b>B</b>) Weighted gene co-expression network analysis (WGCNA) of DEGs identified from transcriptome sequencing. Module-trait correlations and corresponding <span class="html-italic">p</span>-values in parentheses. The left panel shows the six modules with gene numbers. The color scale on the right shows the module-trait correlations from −1 (blue) to 1 (red). ‘Anthocyanin’, ‘Chlorophyll a’, ‘Chlorophyll b’, ‘Total chlorophyll’ and ‘Carotenoid’ represent the changes in corresponding substances’ concentrations. (<b>C</b>) Heatmap presenting the expression patterns of regulatory genes regulating pomegranate peel pigments metabolism during fruit development. (<b>D</b>) Correlation network between TFs’ expression and pigments’ contents; pink and blue circles represent positive and negative correlations, respectively. Purple, orange, and green lines representing the relation between TFs and anthocyanin, carotenoid, and chlorophyll, respectively.</p> Full article ">Figure 7
<p>The expressions of seven genes in pomegranate peel at developmental stage 1 (S1), S2, and S3 from transcriptome data were examined by quantitative polymerase chain reaction (q-PCR). The expression levels obtained by RNA-seq and q-PCR are shown with a line chart and histogram, respectively. Data are presented as the mean ± standard deviation of three biological replicates. Different letters above the bars indicate significant differences (<span class="html-italic">p</span> &lt; 0.05) according to one-way analysis of variance (ANOVA) followed by Tukey test. Data analyzed by qPCR (marked with gray letters) or RNA-seq (marked with red letters) were tested separately.</p> Full article ">
17 pages, 2929 KiB  
Article
Transcriptomic and Metabolomic Analysis Reveals the Potential Roles of Polyphenols and Flavonoids in Response to Sunburn Stress in Chinese Olive (Canarium album)
by Yu Long, Chaogui Shen, Ruilian Lai, Meihua Zhang, Qilin Tian, Xiaoxia Wei and Rujian Wu
Plants 2024, 13(17), 2369; https://doi.org/10.3390/plants13172369 - 25 Aug 2024
Viewed by 744
Abstract
Sunburn stress is one of the main environmental stress factors that seriously affects the fruit development and quality of Chinese olive, a tropical and subtropical fruit in south China. Therefore, the understanding of the changes in physiological, biochemical, metabolic, and gene expression in [...] Read more.
Sunburn stress is one of the main environmental stress factors that seriously affects the fruit development and quality of Chinese olive, a tropical and subtropical fruit in south China. Therefore, the understanding of the changes in physiological, biochemical, metabolic, and gene expression in response to sunburn stress is of great significance for the industry and breeding of Chinese olive. In this study, the different stress degrees of Chinese olive fruits, including serious sunburn injury (SSI), mild sunburn injury (MSI), and ordinary (control check, CK) samples, were used to identify the physiological and biochemical changes and explore the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) by using transcriptomics and metabolomics. Compared with CK, the phenotypes, antioxidant capacity, and antioxidant-related enzyme activities of sunburn stress samples changed significantly. Based on DEG-based KEGG metabolic pathway analysis of transcriptomics, the polyphenol and flavonoid-related pathways, including phenylpropanoid biosynthesis, sesquiterpenoid, and triterpenoid biosynthesis, monoterpene biosynthesis, carotenoid biosynthesis, isoflavonoid biosynthesis, flavonoid biosynthesis, were enriched under sunburn stress of Chinese olive. Meanwhile, 33 differentially accumulated polyphenols and 99 differentially accumulated flavonoids were identified using metabolomics. According to the integration of transcriptome and metabolome, 15 and 8 DEGs were predicted to regulate polyphenol and flavonoid biosynthesis in Chinese olive, including 4-coumarate-CoA ligase (4CL), cinnamoyl-CoA reductase (CCR), cinnamoyl-alcohol dehydrogenase (CAD), chalcone synthase (CHS), flavanone-3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), and anthocyanidin synthase (ANS). Additionally, the content of total polyphenols and flavonoids was found to be significantly increased in MSI and SSI samples compared with CK. Our research suggested that the sunburn stress probably activates the transcription of the structural genes involved in polyphenol and flavonoid biosynthesis in Chinese olive fruits to affect the antioxidant capacity and increase the accumulation of polyphenols and flavonoids, thereby responding to this abiotic stress. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
►▼ Show Figures

Figure 1

Figure 1
<p>The changes of phenotypes, antioxidant capacity, and antioxidant-related enzyme activities in response to sunburn stress of Chinese olive. (<b>A</b>) The phenotype changes of samples. (<b>B</b>) The color changes of samples are represented by chromatic aberration <span class="html-italic">L</span>*, <span class="html-italic">a</span>*, <span class="html-italic">b</span>*, <span class="html-italic">c</span>*, and <span class="html-italic">h</span>* values. (<b>C</b>) The firmness changes of samples. (<b>D</b>) The T-AOC changes of samples (μmol·mL<sup>−1</sup> FW). (<b>E</b>) The content of H<sub>2</sub>O<sub>2</sub> in samples (μmol·g<sup>−1</sup> FW). (<b>F</b>) The content of MDA in samples (nmol·g<sup>−1</sup> FW). (<b>G</b>) The content of proline in samples (μg·g<sup>−1</sup> FW). (<b>H</b>) The activity changes of CAT, SOD, POD, APX, and PPO of samples (U·g<sup>−1</sup> FW). CK, MSI, and SSI indicate the samples of control check, mild sunburn injury, and serious sunburn injury, respectively. The upper- and lowercase letters on the curves represent significant differences at <span class="html-italic">p</span> value &lt; 0.01 and &lt;0.05 levels.</p> Full article ">Figure 2
<p>DEG-based enrichment analysis of KEGG metabolic pathway. (<b>A</b>–<b>C</b>) indicate the comparisons of T-CK vs. T-MSI, T-CK vs. T-SSI, and T-MSI vs. T-SSI. The red and blue colors indicate high and low q values, respectively.</p> Full article ">Figure 3
<p>DAMs identification. (<b>A</b>,<b>B</b>) indicate the cluster analysis and Venn diagram. M-CK, M-MSI, and M-SSI indicate the metabolomes of control check, mild sunburn injury, and serious sunburn injury, respectively.</p> Full article ">Figure 4
<p>Changes of DEGs and DAMs in metabolic pathway of phenylpropanoid biosynthesis of Chinese olive under sunburn stress. The pathway of phenylpropanoid biosynthesis referring to the KEGG database (<a href="https://www.kegg.jp/kegg-bin/show_pathway?map00940" target="_blank">https://www.kegg.jp/kegg-bin/show_pathway?map00940</a>) (accessed on 28 August 2023) [<a href="#B20-plants-13-02369" class="html-bibr">20</a>]. Orange and blue colors indicate high and low expression levels of DEGs, while red and green colors represent the up- and down-accumulation of DAMs, respectively. No color indicates no significant change. Squares, circles, and triangles represent the comparisons of CK vs. MSI, CK vs. SSI, and MSI vs. SSI, respectively.</p> Full article ">Figure 5
<p>Changes in DEGs and DAMs in the metabolic pathway of flavonoid biosynthesis of Chinese olive under sunburn stress. The pathway of flavonoid biosynthesis referring to the KEGG database (<a href="https://www.kegg.jp/kegg-bin/show_pathway?map00941" target="_blank">https://www.kegg.jp/kegg-bin/show_pathway?map00941</a>) (accessed on 28 August 2023) [<a href="#B20-plants-13-02369" class="html-bibr">20</a>]. Orange and blue colors indicate high and low expression levels of DEGs, while red and green colors represent the up- and down-accumulation of DAMs, respectively. No color indicates no significant change. Squares, circles, and triangles represent the comparisons of CK vs. MSI, CK vs. SSI, and MSI vs. SSI, respectively.</p> Full article ">Figure 6
<p>Changes in the content of total polyphenols (<b>A</b>) and total flavonoids (<b>B</b>) of Chinese olive fruits after sunburn stress. Upper- and lowercase letters on the curves represent significant differences at <span class="html-italic">p</span> value &lt; 0.01 and &lt;0.05 levels.</p> Full article ">Figure 7
<p>Potential regulation network of polyphenols and flavonoids in response to sunburn stress in Chinese olive.</p> Full article ">
13 pages, 3373 KiB  
Article
Characterization of bZIP Transcription Factors in Transcriptome of Chrysanthemum mongolicum and Roles of CmbZIP9 in Drought Stress Resistance
by Xuan Wang, Yuan Meng, Shaowei Zhang, Zihan Wang, Kaimei Zhang, Tingting Gao and Yueping Ma
Plants 2024, 13(15), 2064; https://doi.org/10.3390/plants13152064 - 26 Jul 2024
Viewed by 636
Abstract
bZIP transcription factors play important roles in regulating plant development and stress responses. Although bZIPs have been identified in many plant species, there is little information on the bZIPs in Chrysanthemum. In this study, bZIP TFs were identified from the leaf transcriptome [...] Read more.
bZIP transcription factors play important roles in regulating plant development and stress responses. Although bZIPs have been identified in many plant species, there is little information on the bZIPs in Chrysanthemum. In this study, bZIP TFs were identified from the leaf transcriptome of C. mongolicum, a plant naturally tolerant to drought. A total of 28 full-length bZIP family members were identified from the leaf transcriptome of C. mongolicum and were divided into five subfamilies based on their phylogenetic relationships with the bZIPs from Arabidopsis. Ten conserved motifs were detected among the bZIP proteins of C. mongolicum. Subcellular localization assays revealed that most of the CmbZIPs were predicted to be localized in the nucleus. A novel bZIP gene, designated as CmbZIP9, was cloned based on a sequence of the data of the C. mongolicum transcriptome and was overexpressed in tobacco. The results indicated that the overexpression of CmbZIP9 reduced the malondialdehyde (MDA) content and increased the peroxidase (POD) and superoxide dismutase (SOD) activities as well as the expression levels of stress-related genes under drought stress, thus enhancing the drought tolerance of transgenic tobacco lines. These results provide a theoretical basis for further exploring the functions of the bZIP family genes and lay a foundation for stress resistance improvement in chrysanthemums in the future. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Phylogenetic analysis of bZIP proteins in <span class="html-italic">C. mongolicum</span>. The CmbZIPs are shown as clusters in the leaf transcriptome of <span class="html-italic">C. mongolicum</span>. Branch support was assessed with 1000 bootstrap replicates. The support values are provided at each node. The letters with different colors outside the circle indicate the various subgroups. AtbZIPs represent the bZIPs from <span class="html-italic">A. thaliana</span>. The 11 <span class="html-italic">Chrysanthemum</span> bZIPs are displayed with their sequence IDs and names.</p> Full article ">Figure 2
<p>Conserved motif analysis of bZIP family in <span class="html-italic">C. mongolicum</span>. Conservative motifs are indicated with different colored boxes. The black line represents nonconserved sequences.</p> Full article ">Figure 3
<p>Identification of transgenic tobacco plants. (<b>A</b>) Genomic PCR for the identification of the transgenic plants. M: DL2000 marker, W: wild-type tobacco, lines 1–7: transgenic tobacco lines; uncropped gels are shown in <a href="#app1-plants-13-02064" class="html-app">Supplementary Figure S3</a>. (<b>B</b>) Transcript levels of <span class="html-italic">CmbZIP9</span> in wild-type and transgenic tobacco plants. Data are shown as mean ± SD (n = 3).</p> Full article ">Figure 4
<p>The constitutive expression of <span class="html-italic">CmbZIP9</span> in tobacco enhanced drought tolerance. (<b>A</b>) Morphology of wild-type and CmbZIP9 transgenic plants before and after 7 days of drought stress treatment. (<b>B</b>) Relative water content (RWC) before and after drought treatment for 4 and 7 d. (<b>C</b>) MDA content before and after drought treatment for 4 and 7 d. (<b>D</b>) Peroxidase (POD) activity before and after drought treatment for 4 and 7 d. (<b>E</b>) Superoxide dismutase (SOD) activity before and after drought treatment for 4 and 7 d. The numbers 2, 4, and 6 indicate T1 generations of three different transgenic lines. Asterisks represent values that are significantly different from those of the wild type (* <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.001).</p> Full article ">Figure 5
<p>Expression levels of stress-related genes in wild-type and transgenic tobacco lines before and after 7 days of drought treatment. W: wild-type tobacco; 2, 4, and 6: T1 generations in three different transgenic lines. Data are presented as mean ± SD of three independent experiments. Asterisks represent values that are significantly different from those of the wild type (* <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.001).</p> Full article ">
18 pages, 16224 KiB  
Article
Genome-Wide Identification of the CYP716 Gene Family in Platycodon grandiflorus (Jacq.) A. DC. and Its Role in the Regulation of Triterpenoid Saponin Biosynthesis
by Wuhua Zhang, Javed Iqbal, Zhihui Hou, Yingdong Fan, Jie Dong, Chengzhi Liu, Tao Yang, Daidi Che, Jinzhu Zhang and Dawei Xin
Plants 2024, 13(14), 1946; https://doi.org/10.3390/plants13141946 - 16 Jul 2024
Viewed by 920
Abstract
The main type of saponins occurring in the root of Platycodon grandiflorus (Jacq.) A. DC. are oleanolic acid glycosides. The CYP716 gene family plays a major role in catalyzing the conversion of β-amyrin into oleanolic acid. However, studies on the CYP716 genes in [...] Read more.
The main type of saponins occurring in the root of Platycodon grandiflorus (Jacq.) A. DC. are oleanolic acid glycosides. The CYP716 gene family plays a major role in catalyzing the conversion of β-amyrin into oleanolic acid. However, studies on the CYP716 genes in P. grandiflorus are limited, and its evolutionary history remains poorly understood. In this study, 22 PgCYP716 genes were identified, distributed among seven subfamilies. Cis-acting elements of the PgCYP716 promoters were mainly involved in plant hormone regulation and responses to abiotic stresses. PgCYP716A264, PgCYP716A391, PgCYP716A291, and PgCYP716BWv3 genes were upregulated in the root and during saponin accumulation, as shown by RNA-seq analysis, suggesting that these four genes play an important role in saponin synthesis. The results of subcellular localization indicated that these four genes encoded membrane proteins. Furthermore, the catalytic activity of these four genes was proved in the yeast, which catalyzed the conversion of β-amyrin into oleanolic acid. We found that the content of β-amyrin, platycodin D, platycoside E, platycodin D3, and total saponins increased significantly when either of the four genes was over expressed in the transgenic hair root. In addition, the expression of PgSS, PgGPPS2, PgHMGS, and PgSE was also upregulated while these four genes were overexpressed. These data support that these four PgCYP716 enzymes oxidize β-amyrin to produce oleanolic acid, ultimately promoting saponin accumulation by activating the expression of upstream pathway genes. Our results enhanced the understanding of the functional variation among the PgCYP716 gene family involved in triterpenoid biosynthesis and provided a theoretical foundation for improving saponin content and enriching the saponin biosynthetic pathway in P. grandiflorus. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Identification of <span class="html-italic">PgCYP716s</span> in <span class="html-italic">P. grandiflorus</span>. (<b>A</b>) Multiple sequence alignment of the CYP450 domain of the PgCYP716 gene family. The asterisk denoted identical amino acids. (<b>B</b>) Phylogenetic tree of CYP716 proteins. The evolutionary tree was constructed based on the complete amino acid sequences of CYP716 proteins via MEGA 11 with the Maximum likelihood method. Bootstrap = 1000. CYP716s identified in this research are highlighted in red, while the filled arrowheads signify those CYP716s that have been functionally characterized in this study.</p> Full article ">Figure 2
<p>Phylogenetic tree and gene structure analysis of 22 <span class="html-italic">PgCYP716</span> genes in <span class="html-italic">P. grandiflorus</span>. (<b>A</b>) The construction of a phylogenetic tree for the <span class="html-italic">PgCYP716</span> gene family. (<b>B</b>) The distribution of 10 conserved domains in the PgCYP716. A total of 10 motifs were identified, and each color represents one motif. (<b>C</b>) Gene structure analysis of <span class="html-italic">PgCYP716s</span>. (<b>D</b>) Conserved structural motifs of PgCYP716 proteins. Different colors represented different amino acids.</p> Full article ">Figure 3
<p>Chromosome localization and collinearity analysis of <span class="html-italic">PgCYP716</span> gene family in <span class="html-italic">P. grandiflorus</span>. (<b>A</b>) Chromosomal distribution of 22 <span class="html-italic">PgCYP716</span> genes in <span class="html-italic">P. grandiflorus</span>. (<b>B</b>) The collinearity analysis of the CYP716 gene family in <span class="html-italic">P. grandiflorus</span>, <span class="html-italic">A. eleta</span>, and <span class="html-italic">A. thaliana</span>. The red triangle represented the chromosomal position of <span class="html-italic">PgCYP716s</span>.</p> Full article ">Figure 4
<p>Analysis of cis-acting element in the promoter of <span class="html-italic">PgCYP716s</span>. (<b>A</b>) The number of different cis-acting elements in the <span class="html-italic">PgCYP716</span> gene promoter. (<b>B</b>) The positional distribution of different cis-acting elements in the <span class="html-italic">PgCYP716</span> gene promoter.</p> Full article ">Figure 5
<p>The expression of <span class="html-italic">PgCYP716s</span> genes based on RNA-seq. (<b>A</b>) The expression of <span class="html-italic">PgCYP716s</span> at different levels of saponin accumulation. (<b>B</b>) The changes in the expression of <span class="html-italic">PgCYP716s</span> in different tissues. (<b>C</b>) The changes in the expression of <span class="html-italic">PgCYP716s</span> under MeJA treatment.</p> Full article ">Figure 6
<p>The subcellular localization and expression analysis of <span class="html-italic">PgCYP716A264</span>, <span class="html-italic">PgCYP716A391</span>, <span class="html-italic">PgCYP716A291</span>, and <span class="html-italic">PgCYP716BWv3</span>. (<b>A</b>) <span class="html-italic">PgCYP716A264</span>, <span class="html-italic">PgCYP716A391</span>, <span class="html-italic">PgCYP716A291</span>, and <span class="html-italic">PgCYP716BWv3</span> genes encoded membrane proteins. The top, middle, and bottom represent bright, GFP, and merged fields, respectively. (<b>B</b>) Expression levels of the four genes in eight tissues. (<b>C</b>) Expression levels of the four genes under MeJA induction. Different letters indicated significant differences (<span class="html-italic">p &lt;</span> 0.05). Bar = 20 μm.</p> Full article ">Figure 7
<p>In vivo enzymatic activity assay in yeast. (<b>A</b>) Detection of the yeast products using the vanillin-perchloric acid method indicated that the four enzymes could catalyze the production of oleanolic acid from β-amyrin. The top figure shows yeast-induced products, and the bottom figure shows oleanolic acid detected using the vanillin-perchloric acid method. (<b>B</b>) Schematic representation of the construction of PgbAS1 and the yeast heterologous expression vectors with four PgCYP716s. (<b>C</b>) HPLC analysis of yeast cultures indicated that PgCYP716A264, PgCYP716A391, PgCYP716A291, and PgCYP716BWv3 could produce oleanolic acid. (<b>D</b>) A summary of the biochemical reactions catalyzed by four PgCYP716 enzymes.</p> Full article ">Figure 8
<p><span class="html-italic">PgCYP716A264</span>, <span class="html-italic">PgCYP716A391</span>, <span class="html-italic">PgCYP716A291</span>, and <span class="html-italic">PgCYP716BWv3</span> genes were functionally validated in the hairy roots of <span class="html-italic">P. grandiflorus</span>. (<b>A</b>) GFP fluorescence was detected in the hairy roots overexpressing <span class="html-italic">PgCYP716A264</span>, <span class="html-italic">PgCYP716A391</span>, <span class="html-italic">PgCYP716A291</span>, and <span class="html-italic">PgCYP716BWv3</span> genes. (<b>B</b>–<b>E</b>) Content of platycoside E, platycodin D3, β-amyrin, oleanolic acid, platycodin D, total saponin, soluble sugar, and starch in the WT and transgenic hairy roots. (<b>F</b>–<b>I</b>) qRT-PCR analysis of the expression of saponin synthesis pathway genes in overexpressed hairy roots. Asterisks indicated significant differences (<span class="html-italic">p</span> &lt; 0.05).</p> Full article ">
19 pages, 12237 KiB  
Article
Selection of Stable Reference Genes for QRT-PCR in Tree Peony ‘Doulv’ and Functional Analysis of PsCUC3
by Shuang Zhou, Chao Ma, Wenbin Zhou, Shuangcheng Gao, Dianyun Hou, Lili Guo and Guoan Shi
Plants 2024, 13(13), 1741; https://doi.org/10.3390/plants13131741 - 24 Jun 2024
Cited by 1 | Viewed by 889
Abstract
(1) Background: Tree peonies display extensive cultivar diversity due to widespread hybridization, resulting in a complex genetic architecture. This complexity complicates the selection of universal reference genes across different cultivars for qRT-PCR analyses. Paeonia suffruticosa ‘Doulv’, notable for its unique green blooms in [...] Read more.
(1) Background: Tree peonies display extensive cultivar diversity due to widespread hybridization, resulting in a complex genetic architecture. This complexity complicates the selection of universal reference genes across different cultivars for qRT-PCR analyses. Paeonia suffruticosa ‘Doulv’, notable for its unique green blooms in China, exhibits chlorosis post-flowering and features petaloid stamens and pistils. (2) Methods: Based on published literature and RNA-seq data from ‘Doulv’, nine candidate reference genes—ACT (Actin), TUB (β-Tubulin), UBC (Ubiquitin Conjugating Enzyme), UBQ (Ubiquitin), UPL (Ubiquitin Protein Ligase), PP2A (Protein Phosphatase 2A), PP2C (Protein Phosphatase 2C), MBF1A (Multiprotein Bridging Factor 1A), and GAPDH (Glyceraldehyde-3-Phosphate Dehydrogenase)—were selected. Their expression stability was assessed across various tissues and developmental stages of ‘Doulv’ flowers using qRT-PCR, with evaluations conducted via GeNorm_v3.5, NormFinder_v20, and BestKeeper_v1.0. Gene cloning and expression analyses of PsCUC3, including its subcellular localization, were performed. (3) Results: GAPDH and ACT were identified as the most stable reference genes in petaloid stamens across various developmental stages of ‘Doulv’, whereas UBC and MBF1A were optimal across different tissues. Notably, specific conserved amino acids in PsCUC3 from ‘Doulv’ diverged from those in NAM/CUC3 proteins of other species, impacting its protein structure. PsCUC3 expression analysis revealed no correlation with chlorophyll content in petaloid stamens but an association with petaloid organ development. Furthermore, PsCUC3 was predominantly localized in the nucleus. (4) Conclusions: This study comprehensively evaluated suitable reference genes using GeNorm_v3.5, NormFinder_v20, and BestKeeper_v1.0 software, establishing a robust qRT-PCR detection system for ‘Doulv’ peony. These results provide a solid experimental foundation for further research on ‘Doulv’ peony. Building on this experimental foundation, the functional analysis of the PsCUC3 gene was conducted. The findings suggest a potential association between the PsCUC3 gene and floral morphology alterations in ‘Doulv’, identifying PsCUC3 as crucial for understanding the molecular mechanisms influencing floral structure in tree peonies. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Floral characteristics of ‘Doulv’ peony. (<b>a</b>) Developmental stages of ‘Doulv’ flowers. Stage I: sepals crack open, exposing the outer petals. Stage II: inner petals become visible as the buds fluff up. Stage III: outer petals fully expand, inner petals loosen, though the innermost petals remain closed. Stage IV: inner petals expand fully, revealing the carpels. Stage V: all inner petals are fully expanded, with carpels completely exposed. Stage VI: outer petals start to dehydrate and undergo senescence. (<b>b</b>) Tissue differentiation in ‘Doulv’ flower at Stage III and Stage V. Stage III features fully expanded outer petals and loosened inner petals, while innermost petals are still closed, maintaining overall green coloration. By Stage V, all inner petals are fully expanded, and carpels are entirely exposed, with a shift from green to white in color.</p> Full article ">Figure 2
<p>The agarose gel electrophoresis map of candidate reference genes in ‘Doulv’.</p> Full article ">Figure 3
<p>Melting curve of candidate reference genes.</p> Full article ">Figure 4
<p>Paired difference analysis (V<span class="html-italic">n</span>/<span class="html-italic">n</span> + 1) of candidate reference genes by GeNorm. (<b>a</b>) Pairwise variation value (V value) of reference genes in petaloid stamens at different developmental stages of ‘Doulv’; (<b>b</b>) V value of reference genes in different tissues of ‘Doulv’ flower.</p> Full article ">Figure 5
<p>Nucleotide sequence and deduced amino acid sequence of the <span class="html-italic">PsCUC3</span> from ‘Doulv’ peony. Yellow: initiation codon and termination codon, respectively. Blue: NAC domain (23-148 aa). *: biosynthesis termination of PsCUC3 protein.</p> Full article ">Figure 6
<p>Alignment of the amino acid sequences of PsCUC3 with NAM/CUC3 proteins from 11 different plant species, including <span class="html-italic">Arabidopsis thaliana</span>. The NAC domain is highlighted in rose red. Boxes denote positions where conserved amino acids in PsCUC3 from ‘Doulv’ peony differ from those in other species.</p> Full article ">Figure 7
<p>Protein secondary structures of PsCUC3 from ‘Doulv’ peony and CfNAM from <span class="html-italic">Cephalotus follicularis</span> were predicted using SOPMA. Blue boxes highlight regions where the secondary structures of PsCUC3 and CfNAM are identical. Green and red boxes denote regions where the secondary structures of PsCUC3 have altered. h: alpha helix; e: extended strand; t: beta turn; c: random coil.</p> Full article ">Figure 8
<p>Interaction network analysis of CUC3 protein in <span class="html-italic">Arabidopsis thaliana</span>.</p> Full article ">Figure 9
<p>Chlorophyll contents and expression analysis of <span class="html-italic">PsCUC3</span>. (<b>a</b>) Chlorophyll contents and relative expression levels of <span class="html-italic">PsCUC3</span> in petaloid stamens at different developmental stages of ‘Doulv’. (<b>b</b>) Relative expression levels of <span class="html-italic">PsCUC3</span> in different tissues of ‘Doulv’ flower. Different letters indicate significant differences at <span class="html-italic">p</span> &lt; 0.05 (lower case letters) or <span class="html-italic">p</span> &lt; 0.01 (capital letters), respectively (based on the one-way ANOVA test).</p> Full article ">Figure 9 Cont.
<p>Chlorophyll contents and expression analysis of <span class="html-italic">PsCUC3</span>. (<b>a</b>) Chlorophyll contents and relative expression levels of <span class="html-italic">PsCUC3</span> in petaloid stamens at different developmental stages of ‘Doulv’. (<b>b</b>) Relative expression levels of <span class="html-italic">PsCUC3</span> in different tissues of ‘Doulv’ flower. Different letters indicate significant differences at <span class="html-italic">p</span> &lt; 0.05 (lower case letters) or <span class="html-italic">p</span> &lt; 0.01 (capital letters), respectively (based on the one-way ANOVA test).</p> Full article ">Figure 10
<p>Subcellular localization analysis of PsCUC3 protein.</p> Full article ">
18 pages, 2900 KiB  
Article
Regulatory Mechanism of Proanthocyanidins in Grape Peels Using vvi-miR828a and Its Target Gene VvMYBPA1
by Lingqi Yue, Jingjing He, Tian Gan, Songtao Jiu, Muhammad Khalil-Ur-Rehman, Kunyu Liu, Miao Bai, Guoshun Yang and Yanshuai Xu
Plants 2024, 13(12), 1688; https://doi.org/10.3390/plants13121688 - 18 Jun 2024
Viewed by 804
Abstract
Anthocyanins and proanthocyanidins are considered to be essential secondary metabolites in grapes and are used to regulate metabolic processes, while miRNAs are involved in their synthesis of anthocyanins and proanthocyanidins to regulate metabolic processes. The present research work was carried out to investigate [...] Read more.
Anthocyanins and proanthocyanidins are considered to be essential secondary metabolites in grapes and are used to regulate metabolic processes, while miRNAs are involved in their synthesis of anthocyanins and proanthocyanidins to regulate metabolic processes. The present research work was carried out to investigate the underlying regulatory mechanism of target genes in the grape cultivars ‘Italia’ and ‘Benitaka’. miRNA and transnscriptomic sequencing technology were employed to characterize both the profiles of miRNAs and the transcripts of grape peels at 10 and 11 weeks post flowering (10 wpf and 11 wpf). The results revealed that the expression level of vvi-miR828a in ‘Italia’ at 10 and 11 wpf was significantly higher than that in ‘Benitaka’. miRNA-seq analysis predicted MYBPA1 to be the target gene of vvi-miR828a. In transcriptome analysis, the expression level of the VvMYBPA1 gene in ‘Benitaka’ was significantly higher than that in ‘Italia’; in addition, the TPM values (expression levels) of VvMYBPA1 and miR828a also showed an evident negative correlation. The determination of the proanthocyanidin (PA) content in ‘Italia’ and ‘Benitaka’ peels at 11 wpf demonstrated that the PA content of ‘Benitaka’ was significantly higher than that of ‘Italia’. The outcomes of RT-qRCR analysis exhibited that the expression levels of the VdPAL, VdCHS, VdCHI, VdDFR, VdMYB5b, VdANR, and VdMYBPA1 genes related anthocyanin and proanthocyanidin pathways were reduced, while the expression levels of all of the above genes were increased after the transient expression of the VvMYBPA1 vector into grape leaves. The results of the transient overexpression experiment of vvi-miR828a before the veraison period of strawberry fruits showed that vvi-miR828a can significantly slow down the coloration of strawberries. The vvi-miR828a negatively regulates the accumulation of proanthocyanidins in grape fruits by inhibiting the expression of VvMYBPA1. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Expression proportions of small RNAs of different lengths in four samples.</p> Full article ">Figure 2
<p>Venn diagram of the number and proportion of miRNA expressions in each sample. (<b>A</b>) The expression number and proportion of all identified miRNAs in each sample. (<b>B</b>) The number of co-expressed and specifically expressed miRNAs in the ‘Italia’ and ‘Benitaka’ cultivar.</p> Full article ">Figure 3
<p>Number and cluster analysis of up-regulated and down-regulated differentially expressed miRNAs. (<b>A</b>) Pairwise comparison of differentially expressed miRNAs between different samples. (<b>B</b>) Expression clustering heat map of differentially expressed miRNAs in four samples; the red color represents a high miRNA expression, while the blue color represents a low miRNA expression.</p> Full article ">Figure 4
<p>MYBPA1 gene expression, qRT-PCR verification, and proanthocyanidin content. (<b>A</b>) VvMYBPA1 and miR828a transcriptome sequencing TPM values. (<b>B</b>) qRT-PCR detection of vvi-miR828a expression to verify the accuracy of miRNA sequencing data. (<b>C</b>) Proanthocyanidin (PA) content in the peel of ‘Italia’ (It11) and ‘Benitaka’ (Be11) cultivars at 11 weeks post flowering; ** indicates <span class="html-italic">p</span> &lt; 0.01.</p> Full article ">Figure 5
<p>Verification of vvi-miR828a and target gene <span class="html-italic">VvMYBPA1</span> using a dual-luciferase assay. (<b>A</b>) Schematic diagram of dual-luciferase vector. (<b>B</b>) Recognition sites of vvi-miR828a, target gene <span class="html-italic">VvMYBPA1</span>, and its mutant sequence mut-<span class="html-italic">VvMYBPA1</span>; the red “cta” base indicates the mutant bases. (<b>C</b>) Luc/Ren ratio (<span class="html-italic">MYBPA1</span> indicates the Luc/Ren ratio of the vvi-miR828a target sequence; mut-<span class="html-italic">MYBPA1</span> indicates the Luc/Ren ratio of the vvi-miR828a target sequence mutation; ** indicates <span class="html-italic">p</span> &lt; 0.01).</p> Full article ">Figure 6
<p>Expression levels of genes related to anthocyanin and proanthocyanidin synthesis after the transient expression of miR828a and <span class="html-italic">VvMYBPA1</span>. (<b>A</b>–<b>G</b>) These represent the expression levels of the <span class="html-italic">VdPAL</span>, <span class="html-italic">VdCHS</span>, <span class="html-italic">VdCHI</span>, <span class="html-italic">VdDFR</span>, <span class="html-italic">VdMYB5b</span>, <span class="html-italic">VdANR</span>, and <span class="html-italic">VdMYBPA1</span> genes, respectively, after transiently expressing pre-miR828a and <span class="html-italic">VvMYBPA1</span> in grape leaves for 3 days. The gray bar graph (OX-vvi-miR828a) represents the expression levels of anthocyanin and proanthocyanidin synthesis-related genes after the injection of bacterial fluid containing the vvi-miR828a vector; the black bar graph part (<span class="html-italic">OX-VvMYBPA1</span>) represents the expression level of related genes after the injection of bacterial fluid containing the <span class="html-italic">VvMYBPA1</span> vector. (<b>H</b>) PA content after the transient expression of pre-miR828a and <span class="html-italic">VvMYBPA1</span> in <span class="html-italic">Vitis davidii</span> leaves; ** indicates <span class="html-italic">p</span> &lt; 0.01, indicating significant difference, *** indicates <span class="html-italic">p</span> &lt; 0.001, indicating highly significant difference.</p> Full article ">Figure 7
<p>Transient overexpression of vvi-miR828a in strawberry fruits at the veraison stage. (<b>A</b>) Phenotypes were observed 1~6 days after the transient overexpression of vvi-miR828a. The three columns on the left represent strawberry fruits 1~6 days after the injection of a bacterial solution that contains the vvi-miR828a vector. The three columns on the right represent strawberry fruits 1~6 days after the injection of a bacterial solution that contains an empty vector. (<b>B</b>) Proanthocyanidin content in strawberry fruits after the transient overexpression of vvi-miR828a and <span class="html-italic">VvMYBPA1</span>; ** indicates <span class="html-italic">p</span> &lt; 0.01, indicating significant difference.</p> Full article ">Figure 8
<p>Fruits of ‘Italia’ and ‘Benitaka’ before and after the veraison period. (<b>A</b>) representative single fruits of ‘Italia’ at 10 weeks (10 wpf) and 11 weeks (11 wpf) post flowering. (<b>B</b>) representative single fruits of ‘Benitaka’ at 10 weeks and 11 weeks post flowering; scale bar length is equal to 6 mm.</p> Full article ">
16 pages, 4357 KiB  
Article
Genome-Wide Investigation of Class III Peroxidase Genes in Brassica napus Reveals Their Responsiveness to Abiotic Stresses
by Obaid Ullah Shah, Latif Ullah Khan, Sana Basharat, Lingling Zhou, Muhammad Ikram, Jiantao Peng, Wasi Ullah Khan, Pingwu Liu and Muhammad Waseem
Plants 2024, 13(7), 942; https://doi.org/10.3390/plants13070942 - 25 Mar 2024
Cited by 2 | Viewed by 1475
Abstract
Brassica napus (B. napus) is susceptible to multiple abiotic stresses that can affect plant growth and development, ultimately reducing crop yields. In the past, many genes that provide tolerance to abiotic stresses have been identified and characterized. Peroxidase (POD) proteins, members [...] Read more.
Brassica napus (B. napus) is susceptible to multiple abiotic stresses that can affect plant growth and development, ultimately reducing crop yields. In the past, many genes that provide tolerance to abiotic stresses have been identified and characterized. Peroxidase (POD) proteins, members of the oxidoreductase enzyme family, play a critical role in protecting plants against abiotic stresses. This study demonstrated a comprehensive investigation of the POD gene family in B. napus. As a result, a total of 109 POD genes were identified across the 19 chromosomes and classified into five distinct subgroups. Further, 44 duplicate events were identified; of these, two gene pairs were tandem and 42 were segmental. Synteny analysis revealed that segmental duplication was more prominent than tandem duplication among POD genes. Expression pattern analysis based on the RNA-seq data of B. napus indicated that BnPOD genes were expressed differently in various tissues; most of them were expressed in roots rather than in other tissues. To validate these findings, we performed RT-qPCR analysis on ten genes; these genes showed various expression levels under abiotic stresses. Our findings not only furnish valuable insights into the evolutionary dynamics of the BnPOD gene family but also serve as a foundation for subsequent investigations into the functional roles of POD genes in B. napus. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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Figure 1

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<p>The phylogenetic tree of <span class="html-italic">B. napus</span> and <span class="html-italic">A. thaliana</span> POD proteins. The maximum likelihood phylogenetic tree was constructed using MEGA 11 with 1000 bootstrap replicates. The phylogenetic tree was clustered into 5 subclades (A–E). A distinct color represents each subclade.</p> Full article ">Figure 2
<p>Gene structure of <span class="html-italic">POD</span> genes in <span class="html-italic">B. napus</span>. (<b>a</b>) The phylogenetic tree shows all the <span class="html-italic">BnPOD</span> genes in the five subclades. (<b>b</b>) Conserved motif analysis conducted using MEME Suite. A total of 10 motifs were predicted. (<b>c</b>) The domain organization of <span class="html-italic">BnPODs</span>. (<b>d</b>) Exon–intron organization of <span class="html-italic">BnPODs</span>. The A, B, C, D and E represent each subclades.</p> Full article ">Figure 3
<p>The analysis of the <span class="html-italic">BnPOD</span> promoter regions. The 2 kb sequences of the <span class="html-italic">BnPOD</span> gene-promoter regions were extracted from and analyzed using the PlantCARE database.</p> Full article ">Figure 4
<p>Circos plot of <span class="html-italic">POD</span> gene duplication in <span class="html-italic">B. napus</span>. The different colors represent the genes found in different (A–E subclades) subgroups, and the lines in the middle show segmental and tandem duplications between different chromosomes.</p> Full article ">Figure 5
<p>Dual synteny plots between (<b>a</b>) <span class="html-italic">B. napus</span> and <span class="html-italic">A. thaliana</span>, (<b>b</b>) <span class="html-italic">B. napus</span> and <span class="html-italic">B. rapa</span>, and (<b>c</b>) <span class="html-italic">B. napus</span> and <span class="html-italic">B. oleracea</span> genomes, with orthologous <span class="html-italic">POD</span> genes shown with red connecting lines.</p> Full article ">Figure 6
<p>A network illustration of the regulatory associations among the putative miRNAs and <span class="html-italic">BnPOD</span> genes. The red color indicates the miRNA complimentary site with the position of <span class="html-italic">BnPODs</span> gDNAs.</p> Full article ">Figure 7
<p>Tissue/organ-specific expression patterns of <span class="html-italic">BnPOD</span> genes in <span class="html-italic">B. napus</span> according to in silico RNA-seq data. DAF; days after flowering.</p> Full article ">Figure 8
<p>Expression patterns of selected <span class="html-italic">BnPODs</span> subjected to different abiotic stresses. The data are presented with ±standard errors. Statistically significant differences are denoted by asterisks * <span class="html-italic">p</span> ≤ 0.05. CK, control; D, drought; C, cold; S, salt; H, heat; Cd, cadmium; numbers 2, 4, and 6 indicate time intervals of 2 h, 4 h, and 6 h, respectively. The samples at 0 h were used as a control (CK).</p> Full article ">
19 pages, 8521 KiB  
Article
Analysis of the UDP-Glucosyltransferase (UGT) Gene Family and Its Functional Involvement in Drought and Salt Stress Tolerance in Phoebe bournei
by Hengfeng Guan, Yanzi Zhang, Jingshu Li, Zhening Zhu, Jiarui Chang, Almas Bakari, Shipin Chen, Kehui Zheng and Shijiang Cao
Plants 2024, 13(5), 722; https://doi.org/10.3390/plants13050722 - 4 Mar 2024
Cited by 2 | Viewed by 1791
Abstract
Uridine diphosphate glycosyltransferases (UDP-GTs, UGTs), which are regulated by UGT genes, play a crucial role in glycosylation. In vivo, the activity of UGT genes can affect the availability of metabolites and the rate at which they can be eliminated from the body. UGT [...] Read more.
Uridine diphosphate glycosyltransferases (UDP-GTs, UGTs), which are regulated by UGT genes, play a crucial role in glycosylation. In vivo, the activity of UGT genes can affect the availability of metabolites and the rate at which they can be eliminated from the body. UGT genes can exert their regulatory effects through mechanisms such as post-transcriptional modification, substrate subtype specificity, and drug interactions. Phoebe bournei is an economically significant tree species that is endemic to southern China. Despite extensive studies on the UGT gene family in various species, a comprehensive investigation of the UGT family in P. bournei has not been reported. Therefore, we conducted a systematic analysis to identify 156 UGT genes within the entire P. bournei genome, all of which contained the PSPG box. The PbUGT family consists of 14 subfamilies, consistent with Arabidopsis thaliana. We observed varying expression levels of PbUGT genes across different tissues in P. bournei, with the following average expression hierarchy: leaf > stem xylem > stem bark > root xylem > root bark. Covariance analysis revealed stronger covariance between P. bournei and closely related species. In addition, we stressed the seedlings with 10% NaCl and 10% PEG-6000. The PbUGT genes exhibited differential expression under drought and salt stresses, with specific expression patterns observed under each stress condition. Our findings shed light on the transcriptional response of PbUGT factors to drought and salt stresses, thereby establishing a foundation for future investigations into the role of PbUGT transcription factors. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Chromosomal distribution and duplication of <span class="html-italic">PbUGT</span> genes.</p> Full article ">Figure 2
<p>Conserved motif of the <span class="html-italic">PbUGT</span> gene family. Different colors correspond to different types of motifs with the numbers 1–10.</p> Full article ">Figure 2 Cont.
<p>Conserved motif of the <span class="html-italic">PbUGT</span> gene family. Different colors correspond to different types of motifs with the numbers 1–10.</p> Full article ">Figure 3
<p>Phylogenetic tree of two plants’ <span class="html-italic">UGT</span> proteins. The different colored arcs represent the UGT protein subfamilies. The tree was built using 156 PbUGTs from <span class="html-italic">Phoebe bournei</span>, 122 AtUGTs from <span class="html-italic">Arabidopsis thaliana</span>.</p> Full article ">Figure 4
<p>Expression heatmap of the <span class="html-italic">PbUGT</span> family in different organ and tissues. Differences in gene expression changes are shown by color, with warmer colors indicating higher expression.</p> Full article ">Figure 5
<p>Synteny analysis of <span class="html-italic">UGT</span> genes among <span class="html-italic">Phoebe bournei</span>, <span class="html-italic">Arabidopsis thaliana</span>, <span class="html-italic">Populus trichocarpa</span>, and <span class="html-italic">Cinnamomum camphora</span>. The two rings in the middle represent the gene density of each chromosome, the gray lines represent the collinearity, and the red lines represent the highlighted collinearity of <span class="html-italic">UGT</span> genes.</p> Full article ">Figure 6
<p>Distribution and collinearity analysis of <span class="html-italic">PbUGT</span> genes. The two rings in the middle represent the gene density of each chromosome, the gray lines represent the collinearity, and the red lines represent the highlighted collinearity of <span class="html-italic">UGT</span> genes.</p> Full article ">Figure 7
<p>Enrichment analysis of stress-, hormone-, and light-responsive cis-elements in the promoter regions of the <span class="html-italic">PbUGT</span> gene family. Differences in the number of cis-elements are indicated by color, with darker colors indicating more cis-elements.</p> Full article ">Figure 8
<p>Expression profile of <span class="html-italic">PbUGT</span> genes responding to salt and drought stresses tested using RT-qPCR. (<b>A</b>) The relative gene expression levels under salt (10% NaCl) treatments for the same periods (0, 4, 6, 8,12 h). Control seedlings were treated with distilled water. (<b>B</b>) The relative gene expression levels under drought (10% PEG) treatments for the same periods (0, 4, 6, 8,12 h). Control seedlings were treated with distilled water. (* <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.0005, **** <span class="html-italic">p</span> &lt; 0.0001).</p> Full article ">
22 pages, 5894 KiB  
Article
Genome-Wide Analysis of Aux/IAA Gene Family in Artemisia argyi: Identification, Phylogenetic Analysis, and Determination of Response to Various Phytohormones
by Conglong Lian, Jinxu Lan, Rui Ma, Jingjing Li, Fei Zhang, Bao Zhang, Xiuyu Liu and Suiqing Chen
Plants 2024, 13(5), 564; https://doi.org/10.3390/plants13050564 - 20 Feb 2024
Cited by 4 | Viewed by 1456
Abstract
Artemisia argyi is a traditional herbal medicine plant, and its folium artemisia argyi is widely in demand due to moxibustion applications globally. The Auxin/indole-3-acetic acid (Aux/IAA, or IAA) gene family has critical roles in the primary auxin-response process, with extensive involvement in plant [...] Read more.
Artemisia argyi is a traditional herbal medicine plant, and its folium artemisia argyi is widely in demand due to moxibustion applications globally. The Auxin/indole-3-acetic acid (Aux/IAA, or IAA) gene family has critical roles in the primary auxin-response process, with extensive involvement in plant development and stresses, controlling various essential traits of plants. However, the systematic investigation of the Aux/IAA gene family in A. argyi remains limited. In this study, a total of 61 Aux/IAA genes were comprehensively identified and characterized. Gene structural analysis indicated that 46 Aux/IAA proteins contain the four typical domains, and 15 Aux/IAA proteins belong to non-canonical IAA proteins. Collinear prediction and phylogenetic relationship analyses suggested that Aux/IAA proteins were grouped into 13 distinct categories, and most Aux/IAA genes might experience gene loss during the tandem duplication process. Promoter cis-element investigation indicated that Aux/IAA promoters contain a variety of plant hormone response and stress response cis-elements. Protein interaction prediction analysis demonstrated that AaIAA26/29/7/34 proteins are possibly core members of the Aux/IAA family interaction. Expression analysis in roots and leaves via RNA-seq data indicated that the expression of some AaIAAs exhibited tissue-specific expression patterns, and some AaIAAs were involved in the regulation of salt and saline-alkali stresses. In addition, RT-qPCR results indicated that AaIAA genes have differential responses to auxin, with complex response patterns in response to other hormones, indicating that Aux/IAA may play a role in connecting auxin and other hormone signaling pathways. Overall, these findings shed more light on AaIAA genes and offer critical foundational knowledge toward the elucidation of their function during plant growth, stress response, and hormone networking of Aux/IAA family genes in A. argyi. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Chromosome distribution mapping of Aux/IAA gene family in <span class="html-italic">A. argyi</span>.</p> Full article ">Figure 2
<p>Collinear prediction and sequence similarity analysis of the Aux/IAA genes in <span class="html-italic">A. argyi</span>. (<b>A</b>): Mapping of collinear prediction of the AaIAA family genes in <span class="html-italic">A. argyi</span>. Black lines show AaIAA paralogs, red maths indicates chromosome numbers. (<b>B</b>): Visualising sequence similarity of the AaIAA genes in <span class="html-italic">A. argyi</span>. Different colored ribbons represent different levels of similarity, blue ≤ 50%, green ≤ 75%, orange ≤ 99%, red &gt; 99%. (<b>C</b>): Collinear prediction of the Aux/IAA family genes between <span class="html-italic">A. thaliana</span> and <span class="html-italic">A. argyi</span>. Red lines show the collinear events.</p> Full article ">Figure 3
<p>Gene structure, conserved motif, conserved domains, and promoter <span class="html-italic">cis</span>-element analysis of the Aux/IAA family genes in <span class="html-italic">A. argyi</span>. (<b>A</b>) Exon–intron organization of <span class="html-italic">A. argyi</span> Aux/IAA genes. (<b>B</b>) Conserved motif analysis of <span class="html-italic">A. argyi</span> Aux/IAA proteins. (<b>C</b>) The amino acid sequence of four typical conserved domains. (<b>D</b>) <span class="html-italic">Cis</span>-element analysis in the promoters of <span class="html-italic">A. argyi</span> Aux/IAA genes.</p> Full article ">Figure 4
<p>GO annotation of the Aux/IAA gene family in <span class="html-italic">A. argyi</span>.</p> Full article ">Figure 5
<p>Phylogenetic investigation of Aux/IAA proteins in <span class="html-italic">A. argyi</span> and <span class="html-italic">A. thaliana</span>. The phylogenetic tree was developed using MEGA software (Version: 6.06) and the neighbor-joining method with 1000 bootstraps. Each Aux/IAA group (1 to 13) is indicated by a specific color. AaIAAs in <span class="html-italic">A. argyi</span> are indicated by a solid circle dot, and AtIAAs in <span class="html-italic">Arabidopsis</span> are indicated by a star.</p> Full article ">Figure 6
<p>Prediction analysis of Aux/IAA protein interaction in <span class="html-italic">A. argyi</span>. Different line colors indicate the type of interaction evidence.</p> Full article ">Figure 7
<p>Expression profiles of AaIAA genes in the leaves and roots of <span class="html-italic">A. argyi</span> in response to salt and saline-alkali stresses based on RNA-seq data. (<b>A</b>) The expression profiles of <span class="html-italic">AaIAA</span> genes in the leaves and roots of <span class="html-italic">A. argyi</span>; FPKM data were normalized by Z-score; the bar chart shows the log<sub>2</sub>FC values of root vs. leaf. (<b>B</b>) Expression profiles of AaIAA genes in response to salt and saline–alkali stresses in leaves. (<b>C</b>) Expression profiles of AaIAA genes in response to salt and saline–alkali stresses in roots. The log<sub>2</sub>(FPKM values) data were normalized by Z-score. R: root, L: leaf, CK: control group, ST: salt treatment, SAT: saline–alkali treatment. Each set had three replicates.</p> Full article ">Figure 8
<p>Expression profiles of AaIAA genes under various hormonal treatments. (<b>A</b>) IAA treatment. (<b>B</b>) ABA treatment. (<b>C</b>) SA treatment. (<b>D</b>) MeJA treatment. Error bars represent standard error of the mean; data shown are means ± SE. Letters “a,b,c…” indicate significant differences at <span class="html-italic">p</span> &lt; 0.05.</p> Full article ">
15 pages, 4137 KiB  
Article
Functional and Transcriptome Analysis Reveal Specific Roles of Dimocarpus longan DlRan3A and DlRan3B in Root Hair Development, Reproductive Growth, and Stress Tolerance
by Qilin Tian, Xiying Xie, Ruilian Lai, Chunzhen Cheng, Zihao Zhang, Yukun Chen, Xu XuHan, Yuling Lin and Zhongxiong Lai
Plants 2024, 13(4), 480; https://doi.org/10.3390/plants13040480 - 7 Feb 2024
Cited by 1 | Viewed by 1321
Abstract
Ran GTPases play essential roles in plant growth and development. Our previous studies revealed the nuclear localization of DlRan3A and DlRan3B proteins and proposed their functional redundancy and distinction in Dimocarpus longan somatic embryogenesis, hormone, and abiotic stress responses. To further explore the [...] Read more.
Ran GTPases play essential roles in plant growth and development. Our previous studies revealed the nuclear localization of DlRan3A and DlRan3B proteins and proposed their functional redundancy and distinction in Dimocarpus longan somatic embryogenesis, hormone, and abiotic stress responses. To further explore the possible roles of DlRan3A and DlRan3B, gene expression analysis by qPCR showed that their transcripts were both more abundant in the early embryo and pulp in longan. Heterologous expression of DlRan3A driven by its own previously cloned promoter led to stunted growth, increased root hair density, abnormal fruits, bigger seeds, and enhanced abiotic stress tolerance. Conversely, constitutive promoter CaMV 35S (35S)-driven expression of DlRan3A, 35S, or DlRan3B promoter-controlled expression of DlRan3B did not induce the alterations in growth phenotype, while they rendered different hypersensitivities to abiotic stresses. Based on the transcriptome profiling of longan Ran overexpression in tobacco plants, we propose new mechanisms of the Ran-mediated regulation of genes associated with cell wall biosynthesis and expansion. Also, the transgenic plants expressing DlRan3A or DlRan3B genes controlled by 35S or by their own promoter all exhibited altered mRNA levels of stress-related and transcription factor genes. Moreover, DlRan3A overexpressors were more tolerant to salinity, osmotic, and heat stresses, accompanied by upregulation of oxidation-related genes, possibly involving the Ran-RBOH-CIPK network. Analysis of a subset of selected genes from the Ran transcriptome identified possible cold stress-related roles of brassinosteroid (BR)-responsive genes. The marked presence of genes related to cell wall biosynthesis and expansion, hormone, and defense responses highlighted their close regulatory association with Ran. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Relative expression levels of <span class="html-italic">DlRan3A</span> and <span class="html-italic">DlRan3B</span> in different tissues, developing zygotic embryos and pulp in longan. (<b>a</b>) Relative expression of <span class="html-italic">DlRan3A</span> and <span class="html-italic">DlRan3B</span> in different tissues (updated from Chen [<a href="#B16-plants-13-00480" class="html-bibr">16</a>]). R: root; St: stem; L: leaf; LB: leaf bud; FB: floral bud; A: alabastrum; MF: male flower; F: filament; An: anther; FF: female flower; YF: young fruit; RF: ripe fruit; P: pulp; S: seed; bar = 5 mm. (<b>b</b>) Relative expression of <span class="html-italic">DlRan3A</span> and <span class="html-italic">DlRan3B</span> during zygotic embryo development. Longan zygotic embryos from stage S1 to S7 were collected from 16 June to 12 July in 2015, every four or every five days; bar = 10 mm. (<b>c</b>) Relative expression of <span class="html-italic">DlRan3A</span> and <span class="html-italic">DlRan3B</span> in different sizes of longan pulp. Longan pulp from stage S1 to S4 were collected in August 2015; bar = 10 mm.</p> Full article ">Figure 2
<p>Phenotype of transgenic tobaccos. (<b>a</b>) The entire phenotypes of transgenic tobaccos. WT and T2 lines of P35S_A, PA_A, P35S_B, and PB_B (45 d) are displayed in the graph from left to right. (<b>b</b>) The phenotype of transgenic tobacco roots (21 d). WT and T2 lines of P35S_A and PA_A are displayed in the graph from left to right. The upper images illustrate the transgenic tobaccos germinated and vertically cultivated on MS medium for 21 d, and the lower images illustrate the 21-day-cultivated tobacco roots stained with propidium iodide, as observed under a confocal microscope (bar = 100 μm). (<b>c</b>) The phenotypes of flowers, fruits, and seeds of transgenic tobaccos. The WT and T2 lines of P35S_A and PA_A are displayed in the graph from left to right (bar = 5 mm).</p> Full article ">Figure 3
<p>Abiotic stress tolerance of transgenic tobaccos. Graphics related to the WT and T2 lines of P35S_A, PA_A, P35S_B, and PB_B are displayed from left to right; a control group without any treatment and the treatment groups belonging to 100 mM NaCl, 200 mM mannitol, 10 μM ABA, 35 °C heat, and 15 °C cold stresses are displayed from top to bottom.</p> Full article ">Figure 4
<p>Validation of RNA-seq results by qPCR. The corresponding gene ID is mentioned at the top of each graph. The columns represent the relative expression levels measured by qPCR using <span class="html-italic">NbEF1a</span> as a reference gene, and the red lines portray the FPKM change from RNA-seq.</p> Full article ">
18 pages, 9289 KiB  
Article
Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species
by Huiyue Ji, Junnan Liu, Yineng Chen, Xinyi Yu, Chenlu Luo, Luxi Sang, Jiayu Zhou and Hai Liao
Plants 2024, 13(4), 468; https://doi.org/10.3390/plants13040468 - 6 Feb 2024
Cited by 2 | Viewed by 1347
Abstract
Heat shock protein 20 (HSP20) serves as a chaperone and plays roles in numerous biological processes, but the codon usage bias (CUB) of its genes has remained unexplored. This study identified 140 HSP20 genes from four cruciferous species, Arabidopsis thaliana, Brassica napus [...] Read more.
Heat shock protein 20 (HSP20) serves as a chaperone and plays roles in numerous biological processes, but the codon usage bias (CUB) of its genes has remained unexplored. This study identified 140 HSP20 genes from four cruciferous species, Arabidopsis thaliana, Brassica napus, Brassica rapa, and Camelina sativa, that were identified from the Ensembl plants database, and we subsequently investigated their CUB. As a result, the base composition analysis revealed that the overall GC content of HSP20 genes was below 50%. The overall GC content significantly correlated with the constituents at three codon positions, implying that both mutation pressure and natural selection might contribute to the CUB. The relatively high ENc values suggested that the CUB of the HSP20 genes in four cruciferous species was relatively weak. Subsequently, ENc exhibited a negative correlation with gene expression levels. Analyses, including ENc-plot analysis, neutral analysis, and PR2 bias, revealed that natural selection mainly shaped the CUB patterns of HSP20 genes in these species. In addition, a total of 12 optimal codons (ΔRSCU > 0.08 and RSCU > 1) were identified across the four species. A neighbor-joining phylogenetic analysis based on coding sequences (CDS) showed that the 140 HSP20 genes were strictly and distinctly clustered into 12 subfamilies. Principal component analysis and cluster analysis based on relative synonymous codon usage (RSCU) values supported the fact that the CUB pattern was consistent with the genetic relationship at the gene level and (or) species levels. These results will not only enrich the HSP20 gene resource but also advance our understanding of the CUB of HSP20 genes, which may underlie the theoretical basis for exploration of their genetic and evolutionary pattern. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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Graphical abstract

Graphical abstract
Full article ">Figure 1
<p>The codon usage indices of <span class="html-italic">HSP20</span> genes in four cruciferous species. (<b>A</b>) ENc, GC1, GC2, GC3, and GC3s indicators. (<b>B</b>) Aromo, CAI, CBI, FOP, and Gravy indicators.</p> Full article ">Figure 2
<p>ENc-GC3s plot of <span class="html-italic">HSP20</span> genes in four species. The black line represents the expected curve when the codon usage bias is determined only by mutation pressure. (<b>A</b>) <span class="html-italic">A. thaliana</span>; (<b>B</b>) <span class="html-italic">B. napus</span>; (<b>C</b>) <span class="html-italic">B. rapa</span>; and (<b>D</b>) <span class="html-italic">C. sativa</span>.</p> Full article ">Figure 3
<p>Parity rule 2 plot analysis of HSP20 genes in four species (GC bias on the x-axis and AT bias on the y-axis). The center point at 0.5 represents A = T and G = C, which means that there is no codon usage deviation between the two DNA strands. (<b>A</b>) <span class="html-italic">A. thaliana</span>; (<b>B</b>) <span class="html-italic">B. napus</span>; (<b>C</b>) <span class="html-italic">B. rapa</span>; and (<b>D</b>) <span class="html-italic">C. sativa</span>.</p> Full article ">Figure 4
<p>Neutrality plot between GC12 (the mean GC content at the first and second positions) and GC3 (GC content at the third codon position). (<b>A</b>) <span class="html-italic">A. thaliana</span>; (<b>B</b>) <span class="html-italic">B. napus</span>; (<b>C</b>) <span class="html-italic">B. rapa</span>; and (<b>D</b>) <span class="html-italic">C. sativa</span>.</p> Full article ">Figure 5
<p>Pearson correlation analysis of codon usage indices in four cruciferous species. The color changing from red to blue represents an increasing correlation index. (<b>A</b>) <span class="html-italic">A. thaliana</span>; (<b>B</b>) <span class="html-italic">B. napus</span>; (<b>C</b>) <span class="html-italic">B. rapa</span>; and (<b>D</b>) <span class="html-italic">C. sativa</span>. * and *** represented statistical significance of <span class="html-italic">p</span> &lt; 0.05 and <span class="html-italic">p</span> &lt; 0.001, respectively.</p> Full article ">Figure 6
<p>The relationship between FPKM and ENc. The FPKM values of <span class="html-italic">HSP20</span> genes under (<b>A</b>) normal, (<b>B</b>) salinity, and (<b>C</b>) drought conditions were applied for calculation. The FPKM values of <span class="html-italic">HSP20</span> genes used in (<b>D</b>) represented the sum total of those under normal, drought, and salt conditions.</p> Full article ">Figure 7
<p>RSCU analysis of <span class="html-italic">HSP20</span> genes in four cruciferous species. (<b>A</b>) <span class="html-italic">A. thaliana</span>; (<b>B</b>) <span class="html-italic">B. napus</span>; (<b>C</b>) <span class="html-italic">B. rapa</span>; and (<b>D</b>) <span class="html-italic">C. sativa</span>.</p> Full article ">Figure 8
<p>The phylogenetic analysis based on CDS of <span class="html-italic">HSP20</span> genes in four cruciferous species.</p> Full article ">Figure 9
<p>The PCA plots of first axis against second axis. (<b>A</b>) Points for <span class="html-italic">HSP20</span> genes classified by species. (<b>B</b>) Points for <span class="html-italic">HSP20</span> genes classified by subfamilies.</p> Full article ">
18 pages, 6427 KiB  
Article
Identification and Validation of the miR156 Family Involved in Drought Responses and Tolerance in Tea Plants (Camellia sinensis (L.) O. Kuntze)
by Shengjing Wen, Chengzhe Zhou, Caiyun Tian, Niannian Yang, Cheng Zhang, Anru Zheng, Yixing Chen, Zhongxiong Lai and Yuqiong Guo
Plants 2024, 13(2), 201; https://doi.org/10.3390/plants13020201 - 11 Jan 2024
Cited by 1 | Viewed by 1756
Abstract
The microRNA156 (miR156) family, one of the first miRNA families discovered in plants, plays various important roles in plant growth and resistance to various abiotic stresses. Previously, miR156s were shown to respond to drought stress, but miR156s in tea plants (Camellia sinensis [...] Read more.
The microRNA156 (miR156) family, one of the first miRNA families discovered in plants, plays various important roles in plant growth and resistance to various abiotic stresses. Previously, miR156s were shown to respond to drought stress, but miR156s in tea plants (Camellia sinensis (L.) O. Kuntze) have not been comprehensively identified and analyzed. Herein, we identify 47 mature sequences and 28 precursor sequences in tea plants. Our evolutionary analysis and multiple sequence alignment revealed that csn-miR156s were highly conserved during evolution and that the rates of the csn-miR156 members’ evolution were different. The precursor sequences formed typical and stable stem–loop structures. The prediction of cis-acting elements in the CsMIR156s promoter region showed that the CsMIR156s had diverse cis-acting elements; of these, 12 CsMIR156s were found to be drought-responsive elements. The results of reverse transcription quantitative PCR (RT-qPCR) testing showed that csn-miR156 family members respond to drought and demonstrate different expression patterns under the conditions of drought stress. This suggests that csn-miR156 family members may be significantly involved in the response of tea plants to drought stress. Csn-miR156f-2-5p knockdown significantly reduced the Fv/Fm value and chlorophyll content and led to the accumulation of more-reactive oxygen species and proline compared with the control. The results of target gene prediction showed that csn-miR156f-2-5p targeted SQUAMOSA promoter binding protein-like (SPL) genes. Further analyses showed that CsSPL14 was targeted by csn-miR156f-2-5p, as confirmed through RT-qPCR, 5′ RLM-RACE, and antisense oligonucleotide validation. Our results demonstrate that csn-miR156f-2-5p and CsSPL14 are involved in drought response and represent a new strategy for increasing drought tolerance via the breeding of tea plants. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Statistics of plants’ miR156 sequences alongside multiple sequence alignment of csn-miR156s. (<b>A</b>) Numeric distribution of miR156s in 55 plant species; the height of the column indicates their quantity. (<b>B</b>) Classification and multiple sequence alignment of miR156 family members in <span class="html-italic">Camellia sinensis</span>.</p> Full article ">Figure 2
<p>Location of the csn-MIR156 family in the ‘Tieguanyin’ genome. (<b>A</b>) Location of csn-miR156s’ precursor sequences on chromosomes. The different colors in the chromosomes represent gene density. (<b>B</b>) The position of mature csn-miR156s on precursors. The blue arrow represents the mature sequence, and the yellow capsule represents the precursor sequence.</p> Full article ">Figure 3
<p>Phylogenetic tree of plants’ MIR156 sequences. vvi. <span class="html-italic">Vitis vinifera</span>; smo. <span class="html-italic">Selaginella moellendorffii</span>; osa. <span class="html-italic">Oryza sativa</span>; csn. <span class="html-italic">Camellia sinensis</span>; ath. <span class="html-italic">Arabidopsis thaliana</span>; gma. <span class="html-italic">Glycine max</span>; mtr. <span class="html-italic">Medicago truncatula</span>; nta. <span class="html-italic">Nicotiana tabacum</span>; bna. <span class="html-italic">Brassica napus</span>; pab. <span class="html-italic">Picea abies</span>; ppt. <span class="html-italic">Physcomitrella patens</span>.</p> Full article ">Figure 4
<p>Promoter analysis of <span class="html-italic">CsMIR156</span> genes in <span class="html-italic">C. sinensis</span>.</p> Full article ">Figure 5
<p>Expression patterns of csn-miR156s under different degrees of drought. CK: normal water supply; T1: mild drought stress, T2: moderate drought stress, and T3: severe drought stress. Data are the means of three independent replicates ± standard deviation (SD). Different lowercase letters indicate significant differences (<span class="html-italic">p</span> &lt; 0.05); different uppercase letters indicate highly significant differences (<span class="html-italic">p</span> &lt; 0.01).</p> Full article ">Figure 6
<p>Csn-miR156f-2-5p plays a role in the drought tolerance of tea plants. (<b>A</b>) Expression levels of csn-miR156f-2-5p control (sODN) and csn-miR156f-2-5p-knockdown (AsODN) tea plants. (<b>B</b>) Phenotypes of the control (sODN) and csn-miR156f-2-5p-knockdown (AsODN) tea plants after 0 h and 24 h of being subjected to drought conditions. (<b>C</b>,<b>D</b>) DAB (<b>C</b>) and NBT (<b>D</b>) staining of csn-miR156f-2-5p-knockdown (AsODN) and sODN tea leaves subjected to 15% PEG at 0 h and 24 h. (<b>E</b>,<b>F</b>) Phenotype of damage (<b>E</b>) and <span class="html-italic">Fv/Fm</span> values (<b>F</b>) of csn-miR156f-2-5p-knockdown (AsODN) and sODN tea leaves subjected to 15% PEG after 0 h and 24 h that were used to assess drought stress resistance. Blue indicates a normal state of the photosynthetic apparatus, while green and yellow indicate damage to photosystem II due to drought. (<b>G</b>,<b>H</b>) Total chlorophyll (<b>G</b>) and proline content (<b>H</b>) of csn-miR156f-2-5p-knockdown (AsODN) and sODN tea leaves subjected to 15% PEG after 0 h and 24 h (* <span class="html-italic">p</span> &lt; 0.05 and ** <span class="html-italic">p</span> &lt; 0.01).</p> Full article ">Figure 7
<p>Expression patterns of targets during subjection to different degrees of drought. Data are the means of three independent replicates ± standard deviation (SD). Different lowercase letters indicate significant differences (<span class="html-italic">p</span> &lt; 0.05); different uppercase letters indicate highly significant differences (<span class="html-italic">p</span> &lt; 0.01).</p> Full article ">Figure 8
<p>Verification of the relationship between csn-miR156f-2-5p and <span class="html-italic">CsSPL14</span>. (<b>A</b>) <span class="html-italic">CsSPL14</span> cleavage sites of csn-miR156f-2-5p, as identified using 5′RLM-RACE. (<b>B</b>) Knockdown of csn-miR156f-2-5p (miR156f-2-5p-KD) with AsODN and incubation, with a solution containing sense oligonucleotide (sODN) serving as a control. (<b>C</b>) RT-qPCR verification of csn-miR156f-2-5p knockdown (KD) and changes in the expression levels of <span class="html-italic">CsSPL14</span> after 0 h, 12 h, and 24 h of incubation (** <span class="html-italic">p</span> &lt; 0.01).</p> Full article ">Figure 9
<p>The potential drought tolerance mechanisms of csn-miR156f-2-5p-<span class="html-italic">CsSPL14</span> in tea plants.</p> Full article ">
17 pages, 11224 KiB  
Article
Analysis of the Genetic Diversity in Tea Plant Germplasm in Fujian Province Based on Restriction Site-Associated DNA Sequencing
by Lele Jiang, Siyi Xie, Chengzhe Zhou, Caiyun Tian, Chen Zhu, Xiaomei You, Changsong Chen, Zhongxiong Lai and Yuqiong Guo
Plants 2024, 13(1), 100; https://doi.org/10.3390/plants13010100 - 28 Dec 2023
Cited by 3 | Viewed by 1567
Abstract
Fujian province, an important tea-producing area in China, has abundant tea cultivars. To investigate the genetic relationships of tea plant cultivars in Fujian province and the characteristics of the tea plant varieties, a total of 70 tea cultivars from Fujian and other 12 [...] Read more.
Fujian province, an important tea-producing area in China, has abundant tea cultivars. To investigate the genetic relationships of tea plant cultivars in Fujian province and the characteristics of the tea plant varieties, a total of 70 tea cultivars from Fujian and other 12 provinces in China were subjected to restriction site-associated DNA sequencing (RAD-seq). A total of 60,258,975 single nucleotide polymorphism (SNP) sites were obtained. These 70 tea plant cultivars were divided into three groups based on analyzing the phylogenetic tree, principal component, and population structure. Selection pressure analysis indicated that nucleotide diversity was high in Southern China and genetically distinct from cultivars of Fujian tea plant cultivars, according to selection pressure analysis. The selected genes have significant enrichment in pathways associated with metabolism, photosynthesis, and respiration. There were ten characteristic volatiles screened by gas chromatography–mass spectrometry (GC–MS) coupled with multivariate statistical methods, among which the differences in the contents of methyl salicylate, 3-carene, cis-3-hexen-1-ol, (E)-4-hexen-1-ol, and 3-methylbutyraldehyde can be used as reference indicators of the geographical distribution of tea plants. Furthermore, a metabolome genome-wide association study (mGWAS) revealed that 438 candidate genes were related to the aroma metabolic pathway. Further analysis showed that 31 genes of all the selected genes were screened and revealed the reasons for the genetic differences in aroma among tea plant cultivars in Fujian and Southern China. These results reveal the genetic diversity in the Fujian tea plants as well as a theoretical basis for the conservation, development, and utilization of the Fujian highly aromatic tea plant cultivars. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Population structure of 70 tea plant cultivars. (<b>a</b>) Effective-RF chromosome distribution map. (<b>b</b>) Cross-validation of K values. (<b>c</b>) Stacked diagram of tea plant community structure at K = 2, K = 3, and K = 4.</p> Full article ">Figure 2
<p>(<b>a</b>) Principal component analysis (PCA) of 70 tea plant cultivars; (<b>b</b>) The PCA of the overlapping segment in figure (<b>a</b>); (<b>c</b>) Phylogenetic tree of 70 tea plant cultivars; (<b>d</b>) Phylogenetic tree of tea plant cultivars in Fujian province. AH: Anhui; FJ: Fujian; GD: Guangdong; GX: Guangxi; GZ: Guizhou; HB: Hubei; HN: Hunan; JX: Jiangxi; SC: Sichuan; SX: Shaanxi; TW: Taiwan; YN: Yunnan; ZJ: Zhejiang; NF: Northern Fujian; EF: Eastern Fujian; SF: Southern Fujian; WF: Western Fujian.</p> Full article ">Figure 3
<p>PCA of volatile and orthogonal projections to latent structures discriminant analysis (OPLS-DA) of volatiles in fresh tea leaves. (<b>a</b>) A hierarchical clustering analysis (HCA) heatmap of volatiles of 70 tea plants; (<b>b</b>) PCA of volatile in fresh tea leaves; (<b>c</b>) OPLS-DA score plot; (<b>d</b>) Permutation test plot; (<b>e</b>) The variable importance in the project (VIP) of 27 volatiles; (<b>f</b>) HCA plot (EF: Eastern Fujian; ZJ: Zhejiang; NF: Northern Fujian; HN: Hunan; TW: Taiwan; AH: Anhui; HB: Hubei; JX: Jiangxi; GX: Guangxi; GD: Guangdong; SF: Southern Fujian; WF: Western Fujian; YN: Yunnan; SC: Sichuan; GZ: Guangzhou; SX: Shaanxi).</p> Full article ">Figure 4
<p>(<b>a1</b>–<b>a10</b>) Manhattan plots of α-farnesene association analysis (<b>a1</b>); <span class="html-italic">cis</span>-2-penten-1-ol association analysis (<b>a2</b>); 3-carene association analysis (<b>a3</b>); (Z)-linalool oxide association analysis (<b>a4</b>); (<span class="html-italic">E</span>,<span class="html-italic">E</span>)-2,4-hexadienal association analysis (<b>a5</b>); (<span class="html-italic">E</span>)-4-hexen-1-ol association analysis (<b>a6</b>); (<span class="html-italic">E</span>)-linalool oxide association analysis (<b>a7</b>); hexanal association analysis (<b>a8</b>); <span class="html-italic">cis</span>-3-hexen-1-ol association analysis (<b>a9</b>); methyl salicylate association analysis (<b>a10</b>); The blue and red dotted lines show significant associations between SNPs and metabolites value. (<b>b1</b>–<b>b10</b>) Quantile–Quantile (Q–Q) plots of the five traits in the same order with Manhattan plots showing the expected null distribution of <span class="html-italic">p</span>-value assuming no associations. The red line represents the predicted value and the blue dot represents the observed value, which can show the difference between the predicted value and the observed value.</p> Full article ">
20 pages, 3242 KiB  
Article
Analysis of Characteristics in the Macro-Composition and Volatile Compounds of Understory Xiaobai White Tea
by Mengcong Zhang, Chengzhe Zhou, Cheng Zhang, Kai Xu, Li Lu, Linjie Huang, Lixuan Zhang, Huang Li, Xuefang Zhu, Zhongxiong Lai and Yuqiong Guo
Plants 2023, 12(24), 4102; https://doi.org/10.3390/plants12244102 - 7 Dec 2023
Cited by 2 | Viewed by 1793
Abstract
Understory planting affects the growth environment of tea plants, regulating the tea plant growth and the formation of secondary metabolites, which in turn affects the flavor of Xiaobai white tea. The present research adopted biochemical composition determination, widely targeted volatilities (WTV) analysis, multivariate [...] Read more.
Understory planting affects the growth environment of tea plants, regulating the tea plant growth and the formation of secondary metabolites, which in turn affects the flavor of Xiaobai white tea. The present research adopted biochemical composition determination, widely targeted volatilities (WTV) analysis, multivariate statistical analysis, and odor activity value (OAV) analysis to analyze the characteristics in the macro-composition and volatile compounds of understory white tea. The sensory evaluation results indicated that understory Xiaobai white tea (LWTs) was stronger than ordinary Xiaobai white tea (PWTs) in terms of the taste of smoothness, sweetness, and thickness as well as the aromas of the flower and sweet. Understory planting reduced light intensity and air temperature, increased air humidity, organic matter, total nitrogen, and available nitrogen contents, which improved the growth environment of tea plants. The phytochemical analysis showed that the water-extractable substances, caffeine, flavonoids, and soluble sugar contents of understory tea fresh-leaf (LF) were higher than those of ordinary fresh-leaf (PF). The phytochemical analysis showed that the free amino acids, theaflavins, thearubigins, water-extractable substances, and tea polyphenols contents of LWTs were significantly higher than those of PWTs, which may explain the higher smoothness, sweetness, and thickness scores of LWTs than those of PWTs. The 2-heptanol, 2-decane, damasone, and cedar alcohol contents were significantly higher in LWTs than in PWTs, which may result in stronger flowery and sweet aromas in LWTs than in PWTs. These results provide a firm experimental basis for the observed differences in the flavor of LWTs and PWTs. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>(<b>A</b>) Light intensity, air temperature, and air humidity, (<b>B</b>) the content of organic matter, total nitrogen, total phosphorus, total potassium, available nitrogen, available phosphorus, available potassium, and pH. The various superscripts show significant differences (<span class="html-italic">p</span> &lt; 0.05).</p> Full article ">Figure 2
<p>(<b>A</b>) The content of water-extractable substances, free amino acids, caffeine, tea polyphenols, flavonoids, soluble sugar, theaflavins, thearubigins, and theabrownines, (<b>B</b>) Correlation between macroscopic components and major environmental factors. The various superscripts show significant differences (<span class="html-italic">p</span> &lt; 0.05). The symbols * and ** indicate statistical significance at <span class="html-italic">p</span> &lt; 0.05 and <span class="html-italic">p</span> &lt; 0.01, respectively. The sample information of fresh leaves is shown in <a href="#plants-12-04102-t001" class="html-table">Table 1</a>.</p> Full article ">Figure 3
<p>(<b>A</b>) The appearance and infusion colors of PWTs and LWTs; (<b>B</b>) Spider plots for the taste profiles of PWTs and LWTs; (<b>C</b>) Spider plots for the aroma profiles of PWTs and LWTs.</p> Full article ">Figure 4
<p>The content of water-extractable substances, free amino acids, caffeine, tea polyphenols, flavonoids, soluble sugar, theaflavins, thearubigins, and theabrownines. The symbols * and ** indicate statistical significance at <span class="html-italic">p</span> &lt; 0.05 and <span class="html-italic">p</span> &lt; 0.01, respectively. Undergrowth-picked was referred to as L, and ordinary-picked was called P.</p> Full article ">Figure 5
<p>(<b>A</b>) The OPLS-DA scores for the non-volatile components; (<b>B</b>) Permutation test plots of the non-volatile components; (<b>C</b>) The variable importance in the project (VIP) of the non-volatile components. Undergrowth-picked was referred to as L, and ordinary-picked was called P.</p> Full article ">Figure 6
<p>(<b>A</b>) The ratio of volatile components; (<b>B</b>) Venn diagram for different groups of key volatile components in BLP2 vs. BLL2, ZLP1 vs. ZLL1, ZLP2 vs. ZLL2, SLP1 vs. SLL1, SLP2 vs. SLL2, BLP1 vs. BLL1; (<b>C</b>) The content of top ten volatile components. Undergrowth-picked was referred to as L, and ordinary-picked was called P. The symbols * and ** indicate statistical significance at <span class="html-italic">p</span> &lt; 0.05 and <span class="html-italic">p</span> &lt; 0.01, respectively.</p> Full article ">Figure 7
<p>(<b>A</b>) PLSR analysis between the aroma properties and the characteristic volatile metabolites (OAVs &gt; 1) of PWTs. X. 39 volatile metabolites (OAVs &gt; 1); Y. aroma properties; (<b>B</b>) PLSR analysis between the aroma properties and the characteristic volatile metabolites (OAVs &gt; 1) of LWTs. X. 39 volatile metabolites (OAVs &gt; 1); Y. aroma properties. The serial numbers in the figure correspond to substances in the <a href="#app1-plants-12-04102" class="html-app">Supplementary Table S4</a>.</p> Full article ">Figure 8
<p>Four key differential volatile metabolites. The symbols * and ** indicate statistical significance at <span class="html-italic">p</span> &lt; 0.05 and <span class="html-italic">p</span> &lt; 0.01, respectively. Undergrowth-picked was referred to as L, and ordinary-picked was called P.</p> Full article ">
16 pages, 6741 KiB  
Article
Transcriptome Analysis Reveals Fruit Quality Formation in Actinidia eriantha Benth
by Peiyu Wang, Xin Feng, Jinlan Jiang, Peipei Yan, Zunwen Li, Weihong Luo, Yiting Chen and Wei Ye
Plants 2023, 12(24), 4079; https://doi.org/10.3390/plants12244079 - 6 Dec 2023
Viewed by 1320
Abstract
Actinidia chinensis Planch. is a fruit tree originating from China that is abundant in the wild. Actinidia eriantha Benth. is a type of A. chinensis that has emerged in recent years. The shape of A. eriantha is an elongated oval, and the skin [...] Read more.
Actinidia chinensis Planch. is a fruit tree originating from China that is abundant in the wild. Actinidia eriantha Benth. is a type of A. chinensis that has emerged in recent years. The shape of A. eriantha is an elongated oval, and the skin is covered with dense, non-shedding milk-white hairs. The mature fruit has flesh that is bright green in colour, and the fruit has a strong flavour and a grass-like smell. It is appreciated for its rich nutrient content and unique flavour. Vitamin C, sugar, and organic acids are key factors in the quality and flavour composition of A. eriantha but have not yet been systematically analysed. Therefore, we sequenced the transcriptome of A. eriantha at three developmental stages and labelled them S1, S2, and S3, and comparisons of S1 vs. S2, S1 vs. S3, and S2 vs. S3 revealed 1218, 4019, and 3759 upregulated differentially expressed genes and 1823, 3415, and 2226 downregulated differentially expressed genes, respectively. Furthermore, the upregulated differentially expressed genes included 213 core genes, and Gene Ontology enrichment analysis showed that they were enriched in hormones, sugars, organic acids, and many organic metabolic pathways. The downregulated differentially expressed genes included 207 core genes, which were enriched in the light signalling pathway. We further constructed the metabolic pathways of sugars, organic acids, and vitamin C in A. eriantha and identified the genes involved in vitamin C, sugar, and organic acid synthesis in A. eriantha fruits at different stages. During fruit development, the vitamin C content decreased, the carbohydrate compound content increased, and the organic acid content decreased. The gene expression patterns were closely related to the accumulation patterns of vitamin C, sugars, and organic acids in A. eriantha. The above results lay the foundation for the accumulation of vitamin C, sugars, and organic acids in A. eriantha and for understanding flavour formation in A. eriantha. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>(<b>A</b>) The three developmental stages of <span class="html-italic">A. eriantha</span> fruit, S1: fruit at 180 days after flowering, S2: fruit at 210 days after flowering, S3: fruit at 240 days after flowering. (<b>B</b>) Principal component analysis of three fruit samples based on gene expression profiles.</p> Full article ">Figure 2
<p>DEGs during <span class="html-italic">A. eriantha</span> maturation. (<b>A</b>–<b>C</b>) Volcano plot of DEGs between the three stages of <span class="html-italic">A. eriantha</span> ripening. (<b>D</b>) Number of DEGs. (<b>E</b>,<b>F</b>) Statistics of the core upregulated and downregulated DEGs.</p> Full article ">Figure 3
<p>Schematic diagram of the <span class="html-italic">A. eriantha</span> Vc metabolic pathway. (<b>A</b>) Metabolite and gene expression profiles of Vc synthesis in <span class="html-italic">A. eriantha</span>. <span class="html-italic">AO</span>: L-ascorbate oxidase; <span class="html-italic">APX</span>: L-ascorbate peroxidase; <span class="html-italic">DHAR</span>: dehydroascorbate reductase; <span class="html-italic">GDH</span>: L-galactose dehydrogenase; <span class="html-italic">GGP</span>: GDP-L-galactose phosphorylase; <span class="html-italic">GLDH</span>: L-galactono-1,4-lactone dehydrogenase; <span class="html-italic">GME</span>: GDP-D-mannose-3,5-epimerase; <span class="html-italic">GMP</span>: GDP-D-mannose pyrophosphorylase; <span class="html-italic">GPP</span>: L-galactose-1-phosphate phosphatase; <span class="html-italic">MDHAR</span>: monodehydroascorbate reductase; <span class="html-italic">PGI</span>: glucose-6-phosphate isomerase; <span class="html-italic">PMI</span>: mannose-6-phosphate isomerase; <span class="html-italic">PMM</span>: phosphomannomutase, <span class="html-italic">Alase</span>: aldonolactonase; <span class="html-italic">GalUR</span>: D-galacturonate reductase. Blue arrows indicate the L-galactose pathway, green arrows indicate the galacturonate pathway, and yellow arrows indicate the recycling pathway. (<b>B</b>) Determination of Vc content during <span class="html-italic">A. eriantha</span> development. Differential analysis was performed using the LSD method with <span class="html-italic">p</span> &lt; 0.05.</p> Full article ">Figure 4
<p>Analysis of expression patterns of related genes in different Vc synthesis pathways in <span class="html-italic">A. eriantha</span>. (<b>A</b>) L-galactose pathway, (<b>B</b>) galacturonate pathway, (<b>C</b>) recycling pathway. Asterisks indicate significant difference.</p> Full article ">Figure 5
<p>Schematic diagram of the <span class="html-italic">A. eriantha</span> glucose metabolism pathway. (<b>A</b>) Pathway of sucrose, fructose, and glucose metabolism in <span class="html-italic">A. eriantha</span>. <span class="html-italic">SUS</span>: sucrose synthase, <span class="html-italic">A/N-INVc</span>: invertase, <span class="html-italic">HXK</span>: hexokinase, <span class="html-italic">FRK</span>: fructokinase, <span class="html-italic">AGPase</span>: ADP-glucose pyrophosphorylase, <span class="html-italic">HKL</span>: hexokinase-like, <span class="html-italic">FKL</span>: fructokinase-like. (<b>B</b>) Determination of total sugar, sucrose, fructose, and glucose contents in <span class="html-italic">A. eriantha</span>. Letters indicate significant difference.</p> Full article ">Figure 6
<p>Quantitative analysis of genes related to glucose metabolism in <span class="html-italic">A. eriantha</span>. Asterisks indicate significant difference.</p> Full article ">Figure 7
<p>Schematic diagram of organic acid metabolism pathways in <span class="html-italic">A. eriantha</span>. (<b>A</b>) Metabolic pathways of malic acid and citric acid in <span class="html-italic">A. eriantha</span>. <span class="html-italic">CS</span>: citrate synthase, ICDH: isocitrate dehydrogenase, <span class="html-italic">ALMT</span>: AL-activated malate transporter, <span class="html-italic">MDH</span>: malate dehydrogenase, <span class="html-italic">NAD-ME</span>: malic enzyme. (<b>B</b>) Determination of titratable acid, malic acid, and citric acid in <span class="html-italic">A. eriantha</span>. Letters indicate significant difference. (<b>C</b>) Analysis of the expression patterns of two <span class="html-italic">NAD-ME</span> genes during the maturation process of <span class="html-italic">A. eriantha</span>. Asterisks indicate significant difference.</p> Full article ">
14 pages, 5180 KiB  
Article
Transcriptome Analysis Reveals Candidate Genes Involved in Gibberellin-Induced Fruit Development in Rosa roxburghii
by Xiaolong Huang, Xiaoai Wu, Guilian Sun, Yu Jiang and Huiqing Yan
Plants 2023, 12(19), 3425; https://doi.org/10.3390/plants12193425 - 28 Sep 2023
Cited by 5 | Viewed by 1440
Abstract
Gibberellins (GAs) play indispensable roles in the fruit development of horticultural plants. Unfortunately, the molecular basis behind GAs regulating fruit development in R. roxburghii remains obscure. Here, GA3 spraying to R. roxburghii ‘Guinong 5’ at full-bloom promoted fruit size and weight, prickle [...] Read more.
Gibberellins (GAs) play indispensable roles in the fruit development of horticultural plants. Unfortunately, the molecular basis behind GAs regulating fruit development in R. roxburghii remains obscure. Here, GA3 spraying to R. roxburghii ‘Guinong 5’ at full-bloom promoted fruit size and weight, prickle development, seed abortion, ascorbic acid accumulation, and reduction in total soluble sugar. RNA-Seq analysis was conducted to generate 45.75 Gb clean reads from GA3- and non-treated fruits at 120 days after pollination. We obtained 4275 unigenes belonging to differently expressed genes (DEGs). Gene ontology and the Kyoto Encyclopedia of Genes and Genomes displayed that carbon metabolism and oxidative phosphorylation were highly enriched. The increased critical genes of DEGs related to pentose phosphate, glycolysis/gluconeogenesis, and citrate cycle pathways might be essential for soluble sugar degradation. Analysis of DEGs implicated in ascorbate revealed the myoinositol pathway required to accumulate ascorbic acid. Finally, DEGs involved in endogenous phytohormones and transcription factors, including R2R3 MYB, bHLH, and WRKY, were determined. These findings indicated that GA3-trigged morphological alterations might be related to the primary metabolites, hormone signaling, and transcription factors, providing potential candidate genes that could be guided to enhance the fruit development of R. roxburghii in practical approaches. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Exogenous gibberellin applications influenced the fruit development of <span class="html-italic">R. roxburghii</span>. (<b>A</b>) The morphology of fruits at 60 DAP (days after pollination) and 120 DAP after gibberellin (GA<sub>3</sub>) spraying. Bar = 1 cm. (<b>B</b>) Effects of GA<sub>3</sub> on fruit weight, fruit shape index, seed number, prickle length, concentration of total soluble sugar, and L-ascorbic acid contents. Values were Mean ± S. D. from at least twenty fruits. The asterisk indicates a significant difference. “*”: <span class="html-italic">p</span> &lt; 0.05; “**”: <span class="html-italic">p</span> &lt; 0.01.</p> Full article ">Figure 2
<p>Characterization of the unigenes of <span class="html-italic">R. roxburghii</span> fruit transcriptome. (<b>A</b>) Statistics of the length distribution of assembled unigenes. (<b>B</b>) E-value distribution of the homology search of unigenes against the non-redundant (Nr) database. (<b>C</b>) Similarity distribution of the unigenes for each unique sequence. (<b>D</b>) Nr annotated species distribution similar to <span class="html-italic">R. roxburghii</span> fruit transcriptome.</p> Full article ">Figure 3
<p>Global analysis of differentially expressed genes in response to gibberellins. (<b>A</b>) Volcano plot of DEGs expressed genes with the cutoff (|log2(fold change)| ≥ 2 and an adjusted <span class="html-italic">p</span>-value &lt; 0.001). (<b>B</b>) Most significant GO functions (<b>C</b>) COG function annotations of DEGs expressed in <span class="html-italic">R. roxburghii</span> fruits.</p> Full article ">Figure 4
<p>KEGG pathway enrichment of DEGs. (<b>A</b>) Statistical analysis of annotated genes in KEEG pathways, (<b>B</b>) scatterplot of KEEG pathway for DEGs.</p> Full article ">Figure 5
<p>Expression profiles of DEGs related to primary metabolism of <span class="html-italic">R. roxburghii</span> fruit. The pathways of glycolysis/gluconeogenesis, citrate cycle (TCA), and pentose phosphate pathways were outlined and expression levels of candidate DEGs were listed using a heatmap. Bars represent the scale of the FPKM of each gene, as indicated by the red and blue rectangles.</p> Full article ">Figure 6
<p>Expression profiles of DEGs related to ascorbate metabolism and hormone signaling of <span class="html-italic">R. roxburghii</span> fruit. (<b>A</b>) The DEGs involved in the ascorbate pathway are listed. (<b>B</b>) Heatmap of DEGs-influenced ascorbate. (<b>C</b>) The simple sketch of hormone signaling pathways. (<b>D</b>) Heatmap of DEGs implicated in endogenous hormone signaling pathways. The enzymes in the red shadow represent up-regulated, whereas those in the green shadow indicate down-regulated.</p> Full article ">Figure 7
<p>GA<sub>3</sub> promoted the expression levels of most transcription factors.</p> Full article ">Figure 8
<p>The qRT-PCR verification of DEGs. (<b>A</b>) The boxplot reveals the comparison of expression levels by RNA-seq and qRT-PCR. (<b>B</b>) Correlation analysis of qPCR (2<sup>−ΔΔCt</sup>) and RNA-Seq results (RPKM). Log<sub>2</sub>fold change of RNA-seq (<span class="html-italic">y</span>-axis) and qRT-PCR (<span class="html-italic">x</span>-axis) were listed. The asterisk indicates a significant difference. “**”: <span class="html-italic">p</span> &lt; 0.01.</p> Full article ">
13 pages, 6500 KiB  
Article
Transcriptome and Metabolome Reveal Sugar and Organic Acid Accumulation in Rosa roxburghii Fruit
by Liyao Su, Tian Zhang, Min Wu, Yan Zhong and Zongming (Max) Cheng
Plants 2023, 12(17), 3036; https://doi.org/10.3390/plants12173036 - 24 Aug 2023
Cited by 5 | Viewed by 1617
Abstract
Sugars and organic acids significantly impact fruit sensory quality, but their accumulation patterns and regulatory mechanisms during the development of Rosa roxburghii fruit are still unclear. We utilized transcriptomics and metabolomics to investigate genes related to sugar and organic acid metabolism in Rosa [...] Read more.
Sugars and organic acids significantly impact fruit sensory quality, but their accumulation patterns and regulatory mechanisms during the development of Rosa roxburghii fruit are still unclear. We utilized transcriptomics and metabolomics to investigate genes related to sugar and organic acid metabolism in Rosa roxburghii. Metabolomics data revealed that sucrose, glucose and fructose were the primary sugars, whereas citric acid and malic acid were the primary organic acids in Rosa roxburghii fruit. We constructed the metabolic pathways of major sugars and organic acids in Rosa roxburghii and identified five key genes involved in sugar and organic acid synthesis. In addition, we identified a module containing 132 transcription factors that was significantly associated with sucrose, citric acid and malic acid. Based on quantitative polymerase chain reaction (qPCR), we identified 13 transcription factors involved in sugar and organic acid metabolism, including the transcription factor RrANL2 and the sucrose synthase gene RrSUS3. Further yeast one-hybrid and dual luciferase assays showed that RrANL2 could bind to the promoter of RrSUS3 to increase its expression. These results provide new insights into the metabolism of sugars and organic acids in Rosa roxburghii fruit. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Analysis of differentially expressed genes and differentially accumulated metabolites. (<b>A</b>) The five developmental stages of <span class="html-italic">Rosa roxburghii</span> fruit. (<b>B</b>–<b>E</b>) KEGG enrichment of differentially accumulated metabolites and differentially expressed genes at different stages.</p> Full article ">Figure 2
<p>Sugar (<b>A</b>) and organic acid (<b>B</b>) content in five developmental stages of <span class="html-italic">Rosa roxburghii</span> fruit. a, b, c and d indicate significant difference (LSD, <span class="html-italic">p</span> &lt; 0.05). Tartaric acid content was negligible compared with other acids. Therefore, we did not determine statistical significance.</p> Full article ">Figure 3
<p>Sugar and organic acid biosynthetic pathways. SUS: sucrose synthase; A-N-INVC: invertase; HXK: hexokinase; FRK: fructokinase; AGPase: ADP-glucose pyrophosphorylase; AMY: α-amylase; BMY: β-amylase; PK: pyruvate kinase; CS: citrate synthase; ICDH: isocitrate dehydrogenase; ALMT: AL-activated malate transporter; MDH: malate dehydrogenase; ME: malic enzyme; PECP: phosphoenolpyruvate carboxylase.</p> Full article ">Figure 4
<p>Relative expression of six genes involved in sugar and organic acid metabolism during <span class="html-italic">Rosa roxburghii</span> fruit development. Asterisk indicates significant difference (LSD, <span class="html-italic">p</span> &lt; 0.05).</p> Full article ">Figure 5
<p>Weighted gene co-expression network analysis (WGCNA) of transcription factors. (<b>A</b>) Relationships of gene modules to sugars and organic acids. (<b>B</b>) Expression profiles of transcription factors with FPKM values &gt; 10 in the brown module. (<b>C</b>) Classification of transcription factors that were upregulated during <span class="html-italic">Rosa roxburghii</span> fruit development.</p> Full article ">Figure 6
<p>Relative expression of 14 transcription factors involved in sugar and organic acid metabolism. Asterisk indicates significant difference (LSD, <span class="html-italic">p</span> &lt; 0.05).</p> Full article ">Figure 7
<p>Validation of transcription factor activity. (<b>A</b>) Validation of the interaction of 14 transcription factors with the RrSUS promoter. The 3-AT concentration was 50 µM. (<b>B</b>,<b>C</b>) Transient expression in tobacco leaves to verify the LUC activity of transcription factors. Asterisk indicates significant difference (LSD, <span class="html-italic">p</span> &lt; 0.01).</p> Full article ">
21 pages, 3351 KiB  
Article
Structural and Functional Analysis of the MADS-Box Genes Reveals Their Functions in Cold Stress Responses and Flower Development in Tea Plant (Camellia sinensis)
by Juan Hu, Qianqian Chen, Atif Idrees, Wanjun Bi, Zhongxiong Lai and Yun Sun
Plants 2023, 12(16), 2929; https://doi.org/10.3390/plants12162929 - 13 Aug 2023
Cited by 4 | Viewed by 2214
Abstract
MADS-box genes comprise a large family of transcription factors that play crucial roles in all aspects of plant growth and development. However, no detailed information on the evolutionary relationship and functional characterization of MADS-box genes is currently available for some representative lineages, such [...] Read more.
MADS-box genes comprise a large family of transcription factors that play crucial roles in all aspects of plant growth and development. However, no detailed information on the evolutionary relationship and functional characterization of MADS-box genes is currently available for some representative lineages, such as the Camellia plant. In this study, 136 MADS-box genes were detected from a reference genome of the tea plant (Camellia sinensis) by employing a 569 bp HMM (Hidden Markov Model) developed using nucleotide sequencing including 73 type I and 63 type II genes. An additional twenty-seven genes were identified, with five MIKC-type genes. Truncated and/or inaccurate gene models were manually verified and curated to improve their functional characterization. Subsequently, phylogenetic relationships, chromosome locations, conserved motifs, gene structures, and gene expression profiles were systematically investigated. Tea plant MIKC genes were divided into all 14 major eudicot subfamilies, and no gene was found in Mβ. The expansion of MADS-box genes in the tea plant was mainly contributed by WGD/fragment and tandem duplications. The expression profiles of tea plant MADS-box genes in different tissues and seasons were analyzed, revealing widespread evolutionary conservation and genetic redundancy. The expression profiles linked to cold stress treatments suggested the wide involvement of MADS-box genes from the tea plant in response to low temperatures. Moreover, a floral ‘ABCE’ model was proposed in the tea plant and proved to be both conserved and ancient. Our analyses offer a detailed overview of MADS-box genes in the tea plant, allowing us to hypothesize the potential functions of unknown genes and providing a foundation for further functional characterizations. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Phylogenetic relationship of type II MADS-box proteins. The maximum likelihood (ML) phylogenetic tree of MADS-box proteins from tea plant, <span class="html-italic">Arabidopsis</span>, and grape was constructed using FastTree with the GTR+CAT model. Tea plant genes are marked with blue stars. The subfamilies are presented in different colors. At, <span class="html-italic">A. thaliana</span>; Vvi, <span class="html-italic">Vitis vinifera</span>, Cs, <span class="html-italic">C. sinensis</span>.</p> Full article ">Figure 2
<p>Phylogenetic relationship, gene structure analysis, and motif compositions of MADS-box genes in the tea plant. (<b>A</b>) A total of 136 full-length sequences of CsMADS protein were used to build a neighbor-joining tree, with 1000 bootstrap replicates. (<b>B</b>) Conserved motif patterns were identified in tea plant MADS-box proteins using the MEME webserver. Different motifs are represented by different colors. (<b>C</b>) The exon–intron structures of <span class="html-italic">CsMADS</span>. Green blocks represent exons, and gray lines indicate introns. The size scale is indicated at the bottom.</p> Full article ">Figure 3
<p>Chromosomal locations for the tea plant <span class="html-italic">MADS-box</span> gene family. Genes were mapped onto 14 chromosomes. The gene density of each chromosome was calculated with TBtools and is visualized by gradient colors from blue (low level) to red (high level). Tandem duplicates are linked with red curves.</p> Full article ">Figure 4
<p>Synteny blocks of <span class="html-italic">CsMADS</span> genes in tea plant chromosomes. Gray lines indicate syntenic gene arrangements in the genome of the tea plant, while orange lines link gene pairs derived from segmental duplications or whole genome duplications.</p> Full article ">Figure 5
<p>Expression patterns of tea plant MADS-box genes in different tissues (root, stem, bud, leaf, and flower) and seasons (spring, summer, autumn, and winter). (<b>A</b>) Clustering heatmap of type II <span class="html-italic">CsMADS</span> expression profiles. The three major expression groups are marked as A, B, and C, and roman numbers below/above the horizontal line represent further subdivided modules. (<b>B</b>) Clustering heatmap of type I C<span class="html-italic">sMADS</span> expression profiles. Genes and tissues are listed in <a href="#app1-plants-12-02929" class="html-app">supplementary Table S5</a>. The TPM values were adopted for the relative gene expression levels and were normalized by genes (log2TPM). The color scale bar is provided at the top-left corner.</p> Full article ">Figure 6
<p>Expression analysis of <span class="html-italic">CsMADS</span> in response to cold stress. (<b>A</b>) Expression analysis of <span class="html-italic">CsMADS</span> in response to cold stress in fish leaf (FL) and two-leaf-and-one-bud (TAB) tissues. (<b>B</b>) Expression analysis of <span class="html-italic">CsMADS</span> in response to cold acclimation. The TPM values were adopted for the relative gene expression level and normalized by gene (log2TPM). The color scale bar is located at the top.</p> Full article ">Figure 7
<p>Expression profiles of ABC(D)E genes in the four whorls of the flower and a proposed floral ABCE model for the tea plant. (<b>A</b>) Heatmap of expression patterns of tea plant A-, B-, C-, D-, and E-class genes in floral organs (sepals, petals, pistils, and stamens) of three developmental stages. “FS” stands for flower stage, “se” for sepals, “pe” for petals, “pi” for pistils, and “st” for stamens (<b>B</b>) A floral model for the tea plant built according to the expression patterns described in <a href="#plants-12-02929-f007" class="html-fig">Figure 7</a>A and the expected functions of detected MADS-box genes. “*” represent that putative gene function was different from expectation due to expression split.</p> Full article ">Figure 8
<p>RT-qPCR verification of 16 ABCE model genes. The left y-axis represents the relative expression of the RT-qPCR results and the right y-axis stands for the FPKM value from the RNA-seq results. The blue solid line represents the TPM value, and the orange dashed line is the relative expression.</p> Full article ">
17 pages, 9709 KiB  
Article
Genome-Wide Identification of the MPK Gene Family and Expression Analysis under Low-Temperature Stress in the Banana
by Zhengyang Fan, Bianbian Zhao, Ruilian Lai, Huan Wu, Liang Jia, Xiaobing Zhao, Jie Luo, Yuji Huang, Yukun Chen, Yuling Lin and Zhongxiong Lai
Plants 2023, 12(16), 2926; https://doi.org/10.3390/plants12162926 - 12 Aug 2023
Cited by 1 | Viewed by 1801
Abstract
Mitogen-activated protein kinases (MAPKs and MPKs) are important in the process of resisting plant stress. In this study, 21, 12, 18, 16, and 10 MPKs were identified from Musa acuminata, Musa balbisiana, Musa itinerans, Musa schizocarpa, and Musa textilis [...] Read more.
Mitogen-activated protein kinases (MAPKs and MPKs) are important in the process of resisting plant stress. In this study, 21, 12, 18, 16, and 10 MPKs were identified from Musa acuminata, Musa balbisiana, Musa itinerans, Musa schizocarpa, and Musa textilis, respectively. These MPKs were divided into Group A, B, C, and D. Phylogenetic analysis revealed that this difference in number was due to the gene shrinkage of the Group B subfamily of Musa balbisiana and Musa textilis. KEGG annotations revealed that K14512, which is involved in plant hormone signal transduction and the plant–pathogen interaction, was the most conserved pathway of the MPKs. The results of promoter cis-acting element prediction and focTR4 (Fusarium oxysporum f. sp. cubense tropical race 4) transcriptome expression analysis preliminarily confirmed that MPKs were relevant to plant hormone and biotic stress, respectively. The expression of MPKs in Group A was significantly upregulated at 4 °C, and dramatically, the MPKs in the root were affected by low temperature. miR172, miR319, miR395, miR398, and miR399 may be the miRNAs that regulate MPKs during low-temperature stress, with miR172 being the most critical. miRNA prediction and qRT-PCR results indicated that miR172 may negatively regulate MPKs. Therefore, we deduced that MPKs might coordinate with miR172 to participate in the process of the resistance to low-temperature stress in the roots of the banana. This study will provide a theoretical basis for further analysis of the mechanism of MPKs under low-temperature stress of bananas, and this study could be applied to molecular breeding of bananas in the future. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Phylogenetic analysis of the <span class="html-italic">MPK</span> gene family in <span class="html-italic">Arabidopsis thaliana</span> (At), <span class="html-italic">Musa acuminata</span> (Ma), <span class="html-italic">Musa balbisiana</span> (Mb), <span class="html-italic">Musa itinerans</span> (Mi), <span class="html-italic">Musa schizocarpa</span> (Ms), and <span class="html-italic">Musa textilis</span> (Mt).</p> Full article ">Figure 2
<p>The number of <span class="html-italic">MPK</span> subfamily members.</p> Full article ">Figure 3
<p>Collinearity analysis of the <span class="html-italic">MPK</span> gene family in bananas. The rings from the outside to the inside represent gene density, GC content, unknown base content, and pseudochromosomes. (<b>a</b>) Collinearity analysis of <span class="html-italic">Musa acuminata</span>. The colorful lines indicate the collinearity between the <span class="html-italic">MaMPK</span>s. (<b>b</b>) The 3–10 MB region of the Chr04 of <span class="html-italic">Musa acuminata.</span> (<b>c</b>) Collinearity analysis of <span class="html-italic">Musa balbisiana</span>. The colorful lines indicate the collinearity between the <span class="html-italic">MbMPK</span>s. (<b>d</b>) The 3–10 MB region of the Chr04 of <span class="html-italic">Musa balbisiana</span>. (<b>e</b>) Collinearity analysis of <span class="html-italic">Musa schizocarpa.</span> The colorful lines indicate the collinearity between the <span class="html-italic">MsMPK</span>s. (<b>f</b>) The 3–10 MB region of the Chr04 of <span class="html-italic">Musa schizocarpa</span>.</p> Full article ">Figure 3 Cont.
<p>Collinearity analysis of the <span class="html-italic">MPK</span> gene family in bananas. The rings from the outside to the inside represent gene density, GC content, unknown base content, and pseudochromosomes. (<b>a</b>) Collinearity analysis of <span class="html-italic">Musa acuminata</span>. The colorful lines indicate the collinearity between the <span class="html-italic">MaMPK</span>s. (<b>b</b>) The 3–10 MB region of the Chr04 of <span class="html-italic">Musa acuminata.</span> (<b>c</b>) Collinearity analysis of <span class="html-italic">Musa balbisiana</span>. The colorful lines indicate the collinearity between the <span class="html-italic">MbMPK</span>s. (<b>d</b>) The 3–10 MB region of the Chr04 of <span class="html-italic">Musa balbisiana</span>. (<b>e</b>) Collinearity analysis of <span class="html-italic">Musa schizocarpa.</span> The colorful lines indicate the collinearity between the <span class="html-italic">MsMPK</span>s. (<b>f</b>) The 3–10 MB region of the Chr04 of <span class="html-italic">Musa schizocarpa</span>.</p> Full article ">Figure 4
<p>Collinearity analysis of the <span class="html-italic">MPK</span> gene family in <span class="html-italic">Musa acuminata</span>, <span class="html-italic">Musa balbisiana,</span> and <span class="html-italic">Musa schizocarpa</span>. The red lines mark the <span class="html-italic">MPK</span> gene pairs in bananas.</p> Full article ">Figure 5
<p>The type of <span class="html-italic">MPK</span> gene family in KEGG. One protein sequence may correspond to multiple entries.</p> Full article ">Figure 6
<p>Prediction analysis of <span class="html-italic">MPKs</span> promoter cis-acting elements in <span class="html-italic">Musa acuminata</span> (<b>a</b>), <span class="html-italic">Musa itinerans</span> (<b>b</b>), <span class="html-italic">Musa balbisiana</span> (<b>c</b>), <span class="html-italic">Musa schizocarpa</span> (<b>d</b>), and <span class="html-italic">Musa textilis</span> (<b>e</b>). The color depth of the square represents the number of cis-acting elements.</p> Full article ">Figure 7
<p>The interaction network between miRNAs and <span class="html-italic">MaMPKs</span>. The yellow rectangles represent genes, and the other ellipses represent miRNAs. The orange and red ellipses represent miRNAs that regulate three genes simultaneously. The pink, blue, green, and purple ellipses represent miRNAs that regulate one gene. This interaction network was visualized using Cytoscape.</p> Full article ">Figure 8
<p>The expression of miR172 under low-temperature stress. Uppercase and lowercase letters indicate a significant difference at <span class="html-italic">p</span> &lt; 0.01 and 0.05.</p> Full article ">Figure 9
<p>Expression patterns of <span class="html-italic">MPKs</span> under biotic and abiotic stress. (<b>a</b>) <span class="html-italic">Fusarium oxysporum</span> f. sp. <span class="html-italic">cubense</span> tropical race 4 (<span class="html-italic">Foc</span>TR4)-infected bananas at 0, 1, 4, and 7 days. (<b>b</b>) Bananas were treated at 0 °C, 4 °C, 13 °C, and 28 °C for 24 h. Red represents high expression and dark blue represents low expression.</p> Full article ">Figure 10
<p>The expression analysis of Group A under low-temperature stress. Uppercase and lowercase letters indicate a significant difference at <span class="html-italic">p</span> &lt; 0.01 and 0.05.</p> Full article ">Figure 11
<p>The expression of <span class="html-italic">MaMPKs</span> in different tissues. Red represents high expression and white represents low expression. These cartoon heat maps were visualized using TBtools.</p> Full article ">
15 pages, 2866 KiB  
Article
Characterization of Carotenoid Cleavage Oxygenase Genes in Cerasus humilis and Functional Analysis of ChCCD1
by Chunzhen Cheng, Rui Yang, Lu Yin, Jianying Zhang, Limin Gao, Rong Lu, Yan Yang, Pengfei Wang, Xiaopeng Mu, Shuai Zhang, Bin Zhang and Jiancheng Zhang
Plants 2023, 12(11), 2114; https://doi.org/10.3390/plants12112114 - 26 May 2023
Cited by 7 | Viewed by 1829
Abstract
Carotenoid cleavage oxygenases (CCOs) are key enzymes that function in degrading carotenoids into a variety of apocarotenoids and some other compounds. In this study, we performed genome-wide identification and characterization analysis of CCO genes in Cerasus humilis. Totally, nine CCO genes could [...] Read more.
Carotenoid cleavage oxygenases (CCOs) are key enzymes that function in degrading carotenoids into a variety of apocarotenoids and some other compounds. In this study, we performed genome-wide identification and characterization analysis of CCO genes in Cerasus humilis. Totally, nine CCO genes could be classified into six subfamilies, including carotenoid cleavage dioxygenase 1 (CCD1), CCD4, CCD7, CCD8, CCD-like and nine-cis-epoxycarotenoid dioxygenase (NCED), were identified. Results of gene expression analysis showed that ChCCOs exhibited diverse expression patterns in different organs and in fruits at different ripening stages. To investigate the roles of ChCCOs in carotenoids degradation, enzyme assays of the ChCCD1 and ChCCD4 were performed in Escerichia coli BL21(DE3) that can accumulate lycopene, β-carotene and zeaxanthin. The prokaryotic expressed ChCCD1 resulted in obvious degradation of lycopene, β-carotene and zeaxanthin, but ChCCD4 did not show similar functions. To further determine the cleaved volatile apocarotenoids of these two proteins, headspace gas chromatography/mass spectrometer analysis was performed. Results showed that ChCCD1 could cleave lycopene at 5, 6 and 5′, 6′ positions to produce 6-methy-5-hepten-2-one and could catalyze β-carotene at 9, 10 and 9′, 10′ positions to generate β-ionone. Our study will be helpful for clarifying the roles of CCO genes especially ChCCD1 in regulating carotenoid degradation and apocarotenoid production in C. humilis. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Phylogenetic analysis results (<b>A</b>) of CCO proteins from <span class="html-italic">Cerasus humilis</span> (Ch), <span class="html-italic">P. persica</span> (Pp), <span class="html-italic">Fragaria vesca</span> (Fv), <span class="html-italic">Solanum Lycopersicum</span> (Sl), <span class="html-italic">Oryza sativa</span> (Os) and <span class="html-italic">Arabidopsis thaliana</span> (At), and nucleotides (<b>B</b>) and proteins (<b>C</b>) similarity analysis results of ChCCOs. CCD1, CCD4, CCD-like, CCD8, CCD7 and NCED are six subfamilies of CCOs. Red stars in A represent <span class="html-italic">C. humilis</span> CCD members. In B and C: the redder the color, the higher the similarity; the greener the color, the lower the similarity.</p> Full article ">Figure 2
<p>Protein–protein interaction network for ChCCOs based on the <span class="html-italic">Prunus persica</span> protein database.</p> Full article ">Figure 3
<p>Heatmap for the transcriptome data-based expression analysis of <span class="html-italic">ChCCOs</span> in the fruit, leaf, kernel, rhizome and root of <span class="html-italic">C. humilis</span>. For heatmap drawing, log<sub>2</sub>(FPKM + 1) values of <span class="html-italic">ChCCO</span> genes were used. The redder the color, the higher the gene’s expression, and white represents no expression.</p> Full article ">Figure 4
<p>Quantitative real-time PCR analysis results of <span class="html-italic">ChCCOs</span> in fruits at four different ripening stages. (<b>A</b>–<b>F</b>) represents expression analysis result for <span class="html-italic">ChCCD-like-a</span>, <span class="html-italic">ChCCD1</span>, <span class="html-italic">ChCCD4</span>, <span class="html-italic">ChCCD8</span>, <span class="html-italic">ChNCED1</span> and <span class="html-italic">ChNCED5</span>, respectively. DAF: days after flowering. The different letters above the columns represent significant differences at <span class="html-italic">p</span> &lt; 0.05 level.</p> Full article ">Figure 5
<p>Functional analysis results of ChCCD1 and ChCCD4 proteins. (<b>A</b>) The influences of ChCCD1 and ChCCD4 expression on the color changes of <span class="html-italic">E. coli</span> strains that can accumulate lycopene (carrying pACCRT-EIB vector), β-carotene (carrying pACCAR16ΔcrtX vector) and zeaxanthin (carrying pACCAR25ΔcrtX vector); CK: control bacteria with no IPTG addition. (<b>B</b>) ChCCD1 can cleave lycopene into 6-methyl-5-heptene-2-one. (<b>C</b>) ChCCD1 can cleave β-carotene into β-ionone.</p> Full article ">Figure 6
<p>GC-MS detection results of the ChCCD1 cleaved volatile products of lycopene and β-carotene in <span class="html-italic">E. coli.</span> (<b>A</b>,<b>B</b>) for the cleaved volatile products of lycopene and β-carotene, respectively; (<b>C</b>,<b>D</b>) fragments pattern for 6-methy-5-hepten-2-one and β-ionone, respectively. Blue circles in (<b>A</b>) and (<b>B</b>) represent starting and ending time points of peak.</p> Full article ">
21 pages, 4940 KiB  
Article
Genome-Wide Identification, Expression and Stress Analysis of the GRAS Gene Family in Phoebe bournei
by Jiarui Chang, Dunjin Fan, Shuoxian Lan, Shengze Cheng, Shipin Chen, Yuling Lin and Shijiang Cao
Plants 2023, 12(10), 2048; https://doi.org/10.3390/plants12102048 - 21 May 2023
Cited by 3 | Viewed by 1908
Abstract
GRAS genes are important transcriptional regulators in plants that govern plant growth and development through enhancing plant hormones, biosynthesis, and signaling pathways. Drought and other abiotic factors may influence the defenses and growth of Phoebe bournei, which is a superb timber source [...] Read more.
GRAS genes are important transcriptional regulators in plants that govern plant growth and development through enhancing plant hormones, biosynthesis, and signaling pathways. Drought and other abiotic factors may influence the defenses and growth of Phoebe bournei, which is a superb timber source for the construction industry and building exquisite furniture. Although genome-wide identification of the GRAS gene family has been completed in many species, that of most woody plants, particularly P. bournei, has not yet begun. We performed a genome-wide investigation of 56 PbGRAS genes, which are unequally distributed across 12 chromosomes. They are divided into nine subclades. Furthermore, these 56 PbGRAS genes have a substantial number of components related to abiotic stress responses or phytohormone transmission. Analysis using qRT-PCR showed that the expression of four PbGRAS genes, namely PbGRAS7, PbGRAS10, PbGRAS14 and PbGRAS16, was differentially increased in response to drought, salt and temperature stresses, respectively. We hypothesize that they may help P. bournei to successfully resist harsh environmental disturbances. In this work, we conducted a comprehensive survey of the GRAS gene family in P. bournei plants, and the results provide an extensive and preliminary resource for further clarification of the molecular mechanisms of the GRAS gene family in P. bournei in response to abiotic stresses and forestry improvement. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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Figure 1

Figure 1
<p>Phylogenetic tree of PbGRAS, AtGRAS and OsGRAS proteins. The different-colored arcs indicate subfamilies of the GRAS family. The tree was constructed using the 56 PbGRAs identified in <span class="html-italic">P. bournei</span>, the 34 AtGRAs identified in <span class="html-italic">A. thaliana</span> and the 60 OsGRAs identified in <span class="html-italic">O. sativa</span> by using MEGA11 with the bootstrap 1000 times.</p> Full article ">Figure 2
<p>Genomic positions, duplication events and syntenic relationships of <span class="html-italic">PbGRAS</span> genes. The green and red blocks in the middle represent the gene density of each chromosome. Those genomes deriving from segmental replication events are linked by colored lines, and the gray lines denote synthetic blocks in the <span class="html-italic">P. bournei</span> genome. The genes in purple, blue, red, and yellow are those with tandem replication.</p> Full article ">Figure 3
<p>Analysis of homology between the <span class="html-italic">P. bournei</span> genome and plant genomes of <span class="html-italic">A. thaliana</span> and <span class="html-italic">O. sativa</span>. Gray lines symbolize pairs of genomes between homologous blocks, and red lines represent adjacent <span class="html-italic">PbGRAS</span> gene pairs. The orange lines emphasize the synthesized GRAS gene pairs in the three species.</p> Full article ">Figure 4
<p>Phylogenetic relationship, motif pattern, and gene structure of <span class="html-italic">PbGRAS</span> genes. (<b>a</b>) Phylogenetic tree of <span class="html-italic">PbGRAS</span>. (<b>b</b>) The motifs of PbGRAS. Motifs 1–10 are displayed in different colored boxes. The protein length can be estimated using the scale at the bottom. (<b>c</b>) Gene structure of <span class="html-italic">PbGRAS</span> genes. Green boxes indicate exons (CDS), black lines indicate introns, and yellow boxes indicate 5′ and 3′ untranslated regions.</p> Full article ">Figure 5
<p>The multiple sequence alignment in <span class="html-italic">PbGRAS7</span>, <span class="html-italic">PbGRAS10</span>, <span class="html-italic">PbGRAS14</span>, <span class="html-italic">PbGRAS16</span>, and <span class="html-italic">PbGRAS40</span> using Jalview software. The “*” under the conservation in the first line of the annotation indicates the highest similarity, and the number is the output score of the degree of conservatism. In sequence alignment, amino acid alignment of A, I, L, M, F, W, V, C is shown in blue, R, K in red, N, Q, S, T in green, E and D in magenta, G in orange, H, Y in cyan, and P in yellow.</p> Full article ">Figure 6
<p>Predicted cis-acting elements in the promoter regions of <span class="html-italic">PbGRAS</span> genes. On the left is the ML phylogenetic tree (bootstrap replications: 1000) with branches labeled with bootstrap values. The one on the right is the promoter position (−2000 bp). The cis-acting regulatory elements in the promoter were categorized into 19 types with different colors. The lower axis denotes the quantity of each cis-acting element.</p> Full article ">Figure 7
<p>Expression profiling of <span class="html-italic">PbGRAS</span>. The expression of <span class="html-italic">PbGRAS</span> in five different tissues. The redder the color block, the higher the expression level, and the whiter the color, the lower the expression.</p> Full article ">Figure 8
<p>Expression of <span class="html-italic">PbGRAS</span> genes in <span class="html-italic">P. bournei</span> in response to drought, salt and temperature stresses was tested by means of qRT-PCR. (<b>a</b>) Relative gene expression levels at the same time points (4, 6, 8, 12, and 24 h) under treatments with a nutrient solution of 10% PEG simulating a drought environment. The control group was processed in distilled water. (<b>b</b>) Relative gene expression levels under the treatment with 10% NaCl nutrient solution immersion. The control group was processed in distilled water. (<b>c</b>) Relative gene expression levels at low temperature (10 °C) and for the control (25 °C). (<b>d</b>) Relative gene expression levels at high temperature (40 °C) and for the control (25 °C). (** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.0005, **** <span class="html-italic">p</span> &lt; 0.0001).</p> Full article ">

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24 pages, 1433 KiB  
Review
Exploiting Brassica rapa L. subsp. pekinensis Genome Research
by Faujiah Nurhasanah Ritonga, Zeyu Gong, Yihui Zhang, Fengde Wang, Jianwei Gao, Cheng Li and Jingjuan Li
Plants 2024, 13(19), 2823; https://doi.org/10.3390/plants13192823 - 9 Oct 2024
Viewed by 840
Abstract
Chinese cabbage, Brassica rapa L. subsp. pekinensis is a crucial and extensively consumed vegetable in the world, especially Eastern Asia. The market demand for this leafy vegetable increases year by year, resulting in multiple challenges for agricultural researchers worldwide. Multi-omic approaches and the [...] Read more.
Chinese cabbage, Brassica rapa L. subsp. pekinensis is a crucial and extensively consumed vegetable in the world, especially Eastern Asia. The market demand for this leafy vegetable increases year by year, resulting in multiple challenges for agricultural researchers worldwide. Multi-omic approaches and the integration of functional genomics helps us understand the relationships between Chinese cabbage genomes and phenotypes under specific physiological and environmental conditions. However, challenges exist in integrating multi-omics for the functional analysis of genes and for developing potential traits for Chinese cabbage improvement. However, the panomics platform allows for the integration of complex omics, enhancing our understanding of molecular regulator networks in Chinese cabbage agricultural traits. In addition, the agronomic features of Chinese cabbage are significantly impacted by the environment. The expression of these agricultural features is tightly regulated by a combination of signals from both the internal regulatory network and the external growth environment. To comprehend the molecular process of these characteristics, it is necessary to have a prior understanding of molecular breeding for the objective of enhancing quality. While the use of various approaches in Chinese cabbage is still in its early stages, recent research has shown that it has the potential to uncover new regulators both rapidly and effectively, leading to updated regulatory networks. In addition, the utilization of the efficient transformation technique in conjunction with gene editing using CRISPR/Cas9 will result in a reduction in time requirements and facilitate a more precise understanding of the role of the regulators. Numerous studies about Chinese cabbage have been conducted in the past two decades, but a comprehensive review about its genome still limited. This review provides a concise summary of the latest discoveries in genomic research related to Brassica and explores the potential future developments for this species. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Term co-occurrence map of Chinese cabbage studies using VOSviewer software version 1.620 (<a href="https://www.vosviewer.com/" target="_blank">https://www.vosviewer.com/</a>). VOSviewer analysed text mining and bibliometric of scientific papers by observing the outputs of term (keyword) co-occurrence analysis. Studies about Chinese cabbage from 2010–2020 relate to biotic and abiotic stresses, head formation, and multi-omics (accessed: 30 September 2024).</p> Full article ">Figure 2
<p>Interaction network analysis of genes related to leafy head formation in Chinese cabbage by using STRING. The interaction network has significantly more interactions than expected. This means that 21 <span class="html-italic">A. thaliana</span> proteins have more interactions among themselves, indicating the proteins are at least partially biologically connected as a group. The line colour is related to the type of interaction. The green line shows gene neighbourhood, the pink line means experimentally determined, the black line presents co-expression, the dark blue line indicates gene co-occurrence, and the blue line indicates protein homology. (For more interpretation of the colour codes in this figure legend, the reader is referred to the web version of this network analysis (<a href="https://string-db.org/cgi/network?taskId=bZ8uTOvikcqY&amp;sessionId=bYgYPvAH4fiB" target="_blank">https://string-db.org/cgi/network?taskId=bZ8uTOvikcqY&amp;sessionId=bYgYPvAH4fiB</a> (accessed: 30 September 2024)).</p> Full article ">
27 pages, 2972 KiB  
Review
Multi-Omics Research Accelerates the Clarification of the Formation Mechanism and the Influence of Leaf Color Variation in Tea (Camellia sinensis) Plants
by Yan-Gen Fan, Ting-Ting Zhao, Qin-Zeng Xiang, Xiao-Yang Han, Shu-Sen Yang, Li-Xia Zhang and Li-Jun Ren
Plants 2024, 13(3), 426; https://doi.org/10.3390/plants13030426 - 31 Jan 2024
Cited by 3 | Viewed by 1848
Abstract
Tea is a popular beverage with characteristic functional and flavor qualities, known to be rich in bioactive metabolites such as tea polyphenols and theanine. Recently, tea varieties with variations in leaf color have been widely used in agriculture production due to their potential [...] Read more.
Tea is a popular beverage with characteristic functional and flavor qualities, known to be rich in bioactive metabolites such as tea polyphenols and theanine. Recently, tea varieties with variations in leaf color have been widely used in agriculture production due to their potential advantages in terms of tea quality. Numerous studies have used genome, transcriptome, metabolome, proteome, and lipidome methods to uncover the causes of leaf color variations and investigate their impacts on the accumulation of crucial bioactive metabolites in tea plants. Through a comprehensive review of various omics investigations, we note that decreased expression levels of critical genes in the biosynthesis of chlorophyll and carotenoids, activated chlorophyll degradation, and an impaired photosynthetic chain function are related to the chlorina phenotype in tea plants. For purple-leaf tea, increased expression levels of late biosynthetic genes in the flavonoid synthesis pathway and anthocyanin transport genes are the major and common causes of purple coloration. We have also summarized the influence of leaf color variation on amino acid, polyphenol, and lipid contents and put forward possible causes of these metabolic changes. Finally, this review further proposes the research demands in this field in the future. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Proteins and genes involved in chlorophyll synthesis pathway. Next to the arrow, the word above represents the protein name, and the corresponding gene name is below. GluRS, glutamyl-tRNA synthetase; GluTR, glutamyl-tRNA reductase; GSA-AM, glutamate-1-semialdehyde 2,1-aminomutase; PBGS, porphobilinogen synthase; HMBS, hydroxymethylbilane synthase; UROS, uroporphyrinogen-III synthase; UROD, uroporphyrinogen decarboxylase; CPOX, coproporphyrinogen III oxidase; PPOX, protoporphyrinogen III oxidase; MgCh, magnesium chelatase; MgPMT, magnesium-protoporphyrin O-methyltransferase; MgPEC, magnesium-protoporphyrin IX monomethyl ester (oxidative) cyclase; DVR, divinyl chlorophyllide a 8-vinyl-reductase; POR, protochlorophyllide reductase; NOL, chlorophyll(ide) b reductase; CAO, chlorophyllide a oxygenase; ChlG, chlorophyll/bacteriochlorophyll a synthase; CLH, chlorophyllase; HCAR, hydroxymethyl chlorophyll a reductase; SGR, magnesium dechelatase; PAO/ACD1, pheophorbide a oxygenase; ACD2, red chlorophyll catabolite reductase; PPD, pheophorbidase.</p> Full article ">Figure 2
<p>The synthesis process of flavonoids and anthocyanins. The yellow textboxes represent the flavonols, the pale green textboxes represent the catechins, and the purple textboxes represent the decorated anthocyanins. PAL, phenylalanine ammonia lyase; C4H, cinnamate-4-hydroxylase; 4CL, 4-coumarate: CoA ligase; CHS chalcone synthase; CHI chalcone isomerase; F3H, flavanone 3-hydroxylase; F3′H, flavonol 3′-hydroxylase; F3′5′H, flavonol 3′5′-hydroxylase; FLS, flavonol synthase; DFR, dihydroflavonol 4-reductase; LAR, leucoanthocyanidin reductase; ANS/LDOX, leucoanthocyanidin dioxygenase; ANR, anthocyanin reductase; UGT, UDP-glucose: flavonol-3-O-glycosyltransferase.</p> Full article ">Figure 3
<p>Red/green frameless arrows represent a promoting/inhibitory effect, while red/green framed arrows represent an increase/decrease in substances. Substances surrounded with a dashed outline are in a free state. Compared to green varieties, chlorotic varieties are hindered in chlorophyll synthesis and degradation under strong light or low-temperature conditions, resulting in imbalanced carbon (C) and nitrogen (N) metabolism and reduced flavonoid content in the chlorotic leaves. Excess free nitrogen promotes the accumulation of free amino acids in chlorotic leaves. On the other hand, the loss of chloroplast structure and degradation of photosynthetic-chain-related proteins further increase the content of free amino acids in chlorotic leaves. In addition, the synthesis of fatty acids has also increased in chlorotic varieties. In purple varieties, low temperature or strong light enhances the expression of flavonoid-pathway-related genes, promoting the synthesis of more anthocyanins.</p> Full article ">
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