Screening of wild and cultivated rice in IRRI germplasm collection revealed that majority have in... more Screening of wild and cultivated rice in IRRI germplasm collection revealed that majority have intermediate apparent amylose content. It appears that ancient farmers selected rice based on texture of the lower amylose varieties, considering that the majority of rice consumers today prefer intermediate to soft-textured rice. Furthermore, 30% seems to be the natural upper natural limit of amylose levels in wild-type rice. If this is the case, the rich biodiversity of rice has been subjected to the bottleneck of domestication to select for grains that have superior cooking and eating but not nutritional or satiating qualities considering that the majority of rice consumers today eat rice three times a day. On the other hand, the amylose content of available rice mutants with deficient SBEIIb or an over-expressed GBSSI also revealed amylose levels of around 35% which is significantly lower by comparison with other high amylose cereals, whose amylose content ranges from 70–90%. Hence, to...
1 Western Sydney University: Australian Centre for Research on Separation Science, School of Scie... more 1 Western Sydney University: Australian Centre for Research on Separation Science, School of Science, 260A Victoria Rd, Parramatta 2150, Sydney, Australia 2 ARC ITTC for Functional Grains: Graham Centre – Charles Sturt University, Boorooma St, North Wagga Wagga 2650, Wagga Wagga, Australia 3 Department of Chemistry and Biotechnology: Swinburne University of Technology, John St, Hawthorn 3122, Melbourne, Australia
Rice is one of the staple foods which serves as the major source of carbohydrate in the human die... more Rice is one of the staple foods which serves as the major source of carbohydrate in the human diet. A typical milled rice grain is mainly composed of starch of up to 80-90%, with an average of 6-8% proteins and some trace amounts of dietary fiber. Although cooked white rice can elicit variable glycemic response, a portion of rice starch may evade digestion in the human small intestine. The digested portion of rice can be estimated and characterized in vitro based on starch digestion extent and rate (kinetics). The indigestible portion of starch can also be quantified. This chapter will present micro-scale methods to quantify rice starch digestion rate and extent based on the sugar fractions released after treating the samples with digestive enzymes.
Increasing paddy yield in rice does not directly translate to enhancing food security because sig... more Increasing paddy yield in rice does not directly translate to enhancing food security because significant decrease in grain yield can happen during postharvest processing of the rice paddy. In parallel with enhancing paddy yield, improving the milling quality of rice is essential in ensuring food security by mitigating the impact of significant losses during the postharvest processing of rice grains. From an industrial standpoint, maximizing the milling recovery of whole grain polished rice is crucial in fetching higher revenues to rice farmers. Significant advances in rice postharvest processing technology have been achieved which are geared toward reducing the incidence of fissures and chalkiness to increase head rice yield (HRY) in rice. The genetic bases of kernel development and grain dimension are also characterized. In addition to these advancements, an integrated phenotyping suite to simultaneously characterize phenotypes related to milling quality will help in screening for breeding lines with high HRY. Toward this goal, modern imaging tools and computer algorithms are currently being developed for high-throughput characterization of rice milling quality. With the availability of more sophisticated, affordable, automated, and nondestructive phenotyping methods of milling quality, it is envisioned that significant improvement in HRY will be made possible to ensure rice food security in the future.
Transcriptome analysis reflects the status quo of transcribed genetic code present in the form of... more Transcriptome analysis reflects the status quo of transcribed genetic code present in the form of mRNA, which helps to infer biological processes and unravel metabolic status. Despite the increasing adoption of RNA-Seq technique in recent years, transcriptome analysis using the microarray platform remains the gold standard technique, which offers a simpler, more cost-effective, and efficient method for high-throughput gene expression profiling. In this chapter, we described a streamlined transcriptomic analyses pipeline employed to study developing rice grains that can also be applied to other tissue samples and species. We described a novel RNA extraction method that obviates the problem introduced by high-starch content during rice grain development that usually leads to reduction in RNA yield and quality. The detailed procedure of microarray analysis involved in cDNA synthesis, cRNA labeling, microarray hybridization, slide scanning, feature extraction to QC validation has been described. The description of a newly developed Indica- and Japonica-specific microarray slides developed from the genome information of subpopulation to study gene expression of 60,000 genes has been highlighted. The downstream bioinformatics analyses including expression QTL mapping and gene regulatory network analyses were mentioned.
Endosymbiosis or symbiogenesis is a process where a cell hosts another cell that is acquired thro... more Endosymbiosis or symbiogenesis is a process where a cell hosts another cell that is acquired through phagocytosis or natural entry of the cell within its cytoplasm. Endosymbiosis has a profound effect on the survival of the host cell by conferring nutritional and/or biosynthetic advantage. Therefore, attempts of artificial endosymbiosis have become one of the most challenging projects in synthetic biology. In this paper, we review the process of endosymbiosis, its levels, requirements and mechanisms. We then review the unique cases of ‘natural endosymbiosis’. Furthermore, we describe and evaluate the recent cases of attempted artificial endosymbiosis. Subsequently, we assess the potential barriers to the possibility of endosymbiosis of highly evolved cell types such as mammalian cells that are known for their high inflexibility towards hosting potentially even the most ‘benign endosymbionts’. The paper concludes with possibilities and methodologies that may have not been evaluated or tried in the past, but may be used to increase the chance of artificial endosymbiosis of host cells such as those from mammalian origin that are not permissive to even benign endosymbionts. Artificial endosymbiosis is worth revisiting in this post-genomic, synthetic biology era because the tools and techniques currently available at our disposal have significantly advanced to make this grand challenge a possibility.
Rice grain quality encompasses complex interrelated traits that cover biochemical composition, co... more Rice grain quality encompasses complex interrelated traits that cover biochemical composition, cooking, eating, nutritional, and sensory properties. Because rice endosperm is composed mainly of starch, rice grain quality is traditionally defined by characterizing starch structure and composition, which is then subsequently correlated with functional properties of the grain. The current proxy tests routinely used to describe rice grain quality preferences are rather limited to the estimation of apparent amylose content, gelatinization temperature, and gel consistency. Additional tests that characterize starch property, viscoelasticity, grain texture, and aroma are also employed in more advanced laboratories. However, these tests are not routinely applied in breeding programs to distinguish cooking quality classes to reflect evolving consumer preference and market demand. As consumer preferences in Asia and all over the world are diverse due to varied demographics and culture, defining uniform attributes to capture regional grain quality preferences becomes more challenging. Hence, novel and innovative proxy tests are needed to characterize rice grain quality to meet the demand for consumer preferences of commercially-released cultivars. In this chapter, the current methods employed in rice grain quality monitoring are succinctly reviewed. Future prospects for improvement are identified, introducing cutting edge technologies that can facilitate high-throughput screening of rice diversity panels and breeding lines. Aside from addressing the requirements for quality improvement in the traditional inbred rice breeding programs, we also tackled the need to enhance grain quality in the hybrid rice sector.
The characterization of gene expression is dependent on RNA quality. In germinating, developing a... more The characterization of gene expression is dependent on RNA quality. In germinating, developing and mature cereal seeds, the extraction of high-quality RNA is often hindered by high starch and sugar content. These compounds can reduce both the yield and the quality of the extracted total RNA. The deterioration in quantity and quality of total RNA can subsequently have a significant impact on the downstream transcriptomic analyses, which may not accurately reflect the spatial and/or temporal variation in the gene expression profile of the samples being tested. In this protocol, we describe an optimized method for extraction of total RNA with sufficient quantity and quality to be used for whole transcriptome analysis of cereal grains. The described method is suitable for several downstream applications used for transcriptomic profiling of developing, germinating, and mature cereal seeds. The method of transcriptome profiling using a microarray platform is shown. This method is specifically designed for gene expression profiling of cereals with described genome sequences. The detailed procedure from microarray handling to final quality control is described. This includes cDNA synthesis, cRNA labelling, microarray hybridization, slide scanning, feature extraction, and data quality validation. The data generated by this method can be used to characterize the transcriptome of cereals during germination, in various stages of grain development, or at different biotic or abiotic stress conditions. The results presented here exemplify high-quality transcriptome data amenable for downstream bioinformatics analyses, such as the determination of differentially expressed genes (DEGs), characterisation of gene regulatory networks, and conducting transcriptome-wide association study (TWAS).
The development of rice that can produce slow and steady postprandial glucose in the bloodstream ... more The development of rice that can produce slow and steady postprandial glucose in the bloodstream is a response to alarmingly high global rates of obesity and related chronic diseases. However, rice grain quality programs from all over the world currently do not have access to a high-throughput method to distinguish rice breeding materials that are digested slowly. The objective of this study was to develop a high-throughput in vitro assay to screen the digestibility of cooked white rice grains and to investigate its ability to differentiate rice genotypes with a low starch digestibility rate. The digestibility rate and extent of three commercial rice genotypes with diverse GI values (Doongara, Reiziq and Waxy) were successfully differentiated using the protocol. Further investigations with eight rice genotypes indicated the percentage of starch hydrolysed at a single time point of the assay (SH-60) successfully differentiated genotypes with a low digestibility rate (the SH-60 of Doo...
Higher head rice yield (HRY), which represents the proportion of intact grains that survive milli... more Higher head rice yield (HRY), which represents the proportion of intact grains that survive milling, and lower grain chalkiness (opacity) are key quality traits. We investigated the genetic basis of HRY and chalkiness in 320 diverse resequenced accessions of indica rice with integrated single- and multi-locus genome-wide association studies using 2.26 million single-nucleotide polymorphisms. We identified novel haplotypes that underly higher HRY on chromosomes 3, 6, 8, and 11, and that lower grain chalkiness in a fine-mapped region on chromosome 5. Whole-genome sequencing of 92 IRRI breeding lines was performed to identify the genetic variants of HRY and chalkiness. Rare and novel haplotypes were found for lowering chalkiness, but missing alleles hindered progress towards enhancing HRY in breeding material. The novel haplotypes that we identified have potential use in breeding programs aimed at improving these important traits in the rice crop.
Abstract Background The current incidence of obesity and type 2 diabetes is at global epidemic le... more Abstract Background The current incidence of obesity and type 2 diabetes is at global epidemic levels. To mitigate their impact, there is a need to develop starch-containing foods that give rise to a low and stable postprandial blood glucose response by increasing the proportion of slowly-digestible and indigestible carbohydrate content. Rice is an ideal target food for such dietary intervention because it is a staple food for over half the world's population. Scope and approach The starch digestion of cooked white rice grains is usually complete or near complete upon consumption, but the rate of digestion is influenced by intrinsic food properties and extrinsic influences. This review provides an overview of the complex interplay between the starch granule and its interaction with non-starch components of the rice grain (intrinsic characteristics) as well as the effects of processing (extrinsic factors) on starch digestibility. Key findings and conclusions The intrinsic properties of white rice grains play a significant role in starch digestibility which can be further enhanced after processing, especially by gelatinisation and retrogradation. Post-harvest storage conditions of rice were found to influence starch digestibility but this effect was temperature-dependent. Limited studies investigated starch-lipid and starch-protein interactions in rice, but changes to substrate accessibility have been implicated. Improving our understanding of the effects of processing on starch digestibility can provide an effective tool for food manufacturers to regulate starch digestibility of existing rice varieties.
Rice lines with slower starch digestibility provide opportunities in mitigating the global rise i... more Rice lines with slower starch digestibility provide opportunities in mitigating the global rise in type II diabetes and related non-communicable diseases. However, screening for low glycemic index (GI) in rice breeding programs is not possible due to time and cost constraints. This study evaluated the feasibility of using in vitro cooked grain amylolysis, starch mobilization patterns during seed germination, and variation in starch structure and composition in the mature seed to differentiate patterns of starch digestibility. Mobilization patterns of total starch, resistant starch, amylose and amylopectin chains, and free sugars during seed germination revealed that the process is analogous to digestion in the human gastrointestinal tract. The combination of these biochemical markers can be used as an alternative measure to predict GI. Additionally, transcriptome analysis of stored mRNA transcripts in high and low GI lines detected differences in starch metabolism and confirmed the ...
Rice lines with slower starch digestibility provide opportunities in mitigating the global rise i... more Rice lines with slower starch digestibility provide opportunities in mitigating the global rise in type II diabetes and related non-communicable diseases. However, screening for low glycemic index (GI) in rice breeding programs is not possible due to time and cost constraints. This study evaluated the feasibility of using in vitro cooked grain amylolysis, starch mobilization patterns during seed germination, and variation in starch structure and composition in the mature seed to differentiate patterns of starch digestibility. Mobilization patterns of total starch, resistant starch, amylose and amylopectin chains, and free sugars during seed germination revealed that the process is analogous to digestion in the human gastrointestinal tract. The combination of these biochemical markers can be used as an alternative measure to predict GI. Additionally, transcriptome analysis of stored mRNA transcripts in high and low GI lines detected differences in starch metabolism and confirmed the ...
A deeper understanding of the regulation of starch biosynthesis in rice (Oryza sativa) endosperm ... more A deeper understanding of the regulation of starch biosynthesis in rice (Oryza sativa) endosperm is crucial in tailoring digestibility without sacrificing grain quality. In this study, significant association peaks on chromosomes 6 and 7 were identified through a genomewide association study (GWAS) of debranched starch structure from grains of a 320 indica rice diversity panel using genotyping data from the high-density rice array. A systems genetics approach that interrelates starch structure data from GWAS to functional pathways from a gene regulatory network identified known genes with high correlation to the proportion of amylose and amylopectin. An SNP in the promoter region of Granule Bound Starch Synthase I was identified along with seven other SNPs to form haplotypes that discriminate samples into different phenotypic ranges of amylose. A GWAS peak on chromosome 7 between LOC_Os07g11020 and LOC_Os07g11520 indexed by a nonsynonymous SNP mutation on exon 5 of a bHLH transcript...
Screening of wild and cultivated rice in IRRI germplasm collection revealed that majority have in... more Screening of wild and cultivated rice in IRRI germplasm collection revealed that majority have intermediate apparent amylose content. It appears that ancient farmers selected rice based on texture of the lower amylose varieties, considering that the majority of rice consumers today prefer intermediate to soft-textured rice. Furthermore, 30% seems to be the natural upper natural limit of amylose levels in wild-type rice. If this is the case, the rich biodiversity of rice has been subjected to the bottleneck of domestication to select for grains that have superior cooking and eating but not nutritional or satiating qualities considering that the majority of rice consumers today eat rice three times a day. On the other hand, the amylose content of available rice mutants with deficient SBEIIb or an over-expressed GBSSI also revealed amylose levels of around 35% which is significantly lower by comparison with other high amylose cereals, whose amylose content ranges from 70–90%. Hence, to...
1 Western Sydney University: Australian Centre for Research on Separation Science, School of Scie... more 1 Western Sydney University: Australian Centre for Research on Separation Science, School of Science, 260A Victoria Rd, Parramatta 2150, Sydney, Australia 2 ARC ITTC for Functional Grains: Graham Centre – Charles Sturt University, Boorooma St, North Wagga Wagga 2650, Wagga Wagga, Australia 3 Department of Chemistry and Biotechnology: Swinburne University of Technology, John St, Hawthorn 3122, Melbourne, Australia
Rice is one of the staple foods which serves as the major source of carbohydrate in the human die... more Rice is one of the staple foods which serves as the major source of carbohydrate in the human diet. A typical milled rice grain is mainly composed of starch of up to 80-90%, with an average of 6-8% proteins and some trace amounts of dietary fiber. Although cooked white rice can elicit variable glycemic response, a portion of rice starch may evade digestion in the human small intestine. The digested portion of rice can be estimated and characterized in vitro based on starch digestion extent and rate (kinetics). The indigestible portion of starch can also be quantified. This chapter will present micro-scale methods to quantify rice starch digestion rate and extent based on the sugar fractions released after treating the samples with digestive enzymes.
Increasing paddy yield in rice does not directly translate to enhancing food security because sig... more Increasing paddy yield in rice does not directly translate to enhancing food security because significant decrease in grain yield can happen during postharvest processing of the rice paddy. In parallel with enhancing paddy yield, improving the milling quality of rice is essential in ensuring food security by mitigating the impact of significant losses during the postharvest processing of rice grains. From an industrial standpoint, maximizing the milling recovery of whole grain polished rice is crucial in fetching higher revenues to rice farmers. Significant advances in rice postharvest processing technology have been achieved which are geared toward reducing the incidence of fissures and chalkiness to increase head rice yield (HRY) in rice. The genetic bases of kernel development and grain dimension are also characterized. In addition to these advancements, an integrated phenotyping suite to simultaneously characterize phenotypes related to milling quality will help in screening for breeding lines with high HRY. Toward this goal, modern imaging tools and computer algorithms are currently being developed for high-throughput characterization of rice milling quality. With the availability of more sophisticated, affordable, automated, and nondestructive phenotyping methods of milling quality, it is envisioned that significant improvement in HRY will be made possible to ensure rice food security in the future.
Transcriptome analysis reflects the status quo of transcribed genetic code present in the form of... more Transcriptome analysis reflects the status quo of transcribed genetic code present in the form of mRNA, which helps to infer biological processes and unravel metabolic status. Despite the increasing adoption of RNA-Seq technique in recent years, transcriptome analysis using the microarray platform remains the gold standard technique, which offers a simpler, more cost-effective, and efficient method for high-throughput gene expression profiling. In this chapter, we described a streamlined transcriptomic analyses pipeline employed to study developing rice grains that can also be applied to other tissue samples and species. We described a novel RNA extraction method that obviates the problem introduced by high-starch content during rice grain development that usually leads to reduction in RNA yield and quality. The detailed procedure of microarray analysis involved in cDNA synthesis, cRNA labeling, microarray hybridization, slide scanning, feature extraction to QC validation has been described. The description of a newly developed Indica- and Japonica-specific microarray slides developed from the genome information of subpopulation to study gene expression of 60,000 genes has been highlighted. The downstream bioinformatics analyses including expression QTL mapping and gene regulatory network analyses were mentioned.
Endosymbiosis or symbiogenesis is a process where a cell hosts another cell that is acquired thro... more Endosymbiosis or symbiogenesis is a process where a cell hosts another cell that is acquired through phagocytosis or natural entry of the cell within its cytoplasm. Endosymbiosis has a profound effect on the survival of the host cell by conferring nutritional and/or biosynthetic advantage. Therefore, attempts of artificial endosymbiosis have become one of the most challenging projects in synthetic biology. In this paper, we review the process of endosymbiosis, its levels, requirements and mechanisms. We then review the unique cases of ‘natural endosymbiosis’. Furthermore, we describe and evaluate the recent cases of attempted artificial endosymbiosis. Subsequently, we assess the potential barriers to the possibility of endosymbiosis of highly evolved cell types such as mammalian cells that are known for their high inflexibility towards hosting potentially even the most ‘benign endosymbionts’. The paper concludes with possibilities and methodologies that may have not been evaluated or tried in the past, but may be used to increase the chance of artificial endosymbiosis of host cells such as those from mammalian origin that are not permissive to even benign endosymbionts. Artificial endosymbiosis is worth revisiting in this post-genomic, synthetic biology era because the tools and techniques currently available at our disposal have significantly advanced to make this grand challenge a possibility.
Rice grain quality encompasses complex interrelated traits that cover biochemical composition, co... more Rice grain quality encompasses complex interrelated traits that cover biochemical composition, cooking, eating, nutritional, and sensory properties. Because rice endosperm is composed mainly of starch, rice grain quality is traditionally defined by characterizing starch structure and composition, which is then subsequently correlated with functional properties of the grain. The current proxy tests routinely used to describe rice grain quality preferences are rather limited to the estimation of apparent amylose content, gelatinization temperature, and gel consistency. Additional tests that characterize starch property, viscoelasticity, grain texture, and aroma are also employed in more advanced laboratories. However, these tests are not routinely applied in breeding programs to distinguish cooking quality classes to reflect evolving consumer preference and market demand. As consumer preferences in Asia and all over the world are diverse due to varied demographics and culture, defining uniform attributes to capture regional grain quality preferences becomes more challenging. Hence, novel and innovative proxy tests are needed to characterize rice grain quality to meet the demand for consumer preferences of commercially-released cultivars. In this chapter, the current methods employed in rice grain quality monitoring are succinctly reviewed. Future prospects for improvement are identified, introducing cutting edge technologies that can facilitate high-throughput screening of rice diversity panels and breeding lines. Aside from addressing the requirements for quality improvement in the traditional inbred rice breeding programs, we also tackled the need to enhance grain quality in the hybrid rice sector.
The characterization of gene expression is dependent on RNA quality. In germinating, developing a... more The characterization of gene expression is dependent on RNA quality. In germinating, developing and mature cereal seeds, the extraction of high-quality RNA is often hindered by high starch and sugar content. These compounds can reduce both the yield and the quality of the extracted total RNA. The deterioration in quantity and quality of total RNA can subsequently have a significant impact on the downstream transcriptomic analyses, which may not accurately reflect the spatial and/or temporal variation in the gene expression profile of the samples being tested. In this protocol, we describe an optimized method for extraction of total RNA with sufficient quantity and quality to be used for whole transcriptome analysis of cereal grains. The described method is suitable for several downstream applications used for transcriptomic profiling of developing, germinating, and mature cereal seeds. The method of transcriptome profiling using a microarray platform is shown. This method is specifically designed for gene expression profiling of cereals with described genome sequences. The detailed procedure from microarray handling to final quality control is described. This includes cDNA synthesis, cRNA labelling, microarray hybridization, slide scanning, feature extraction, and data quality validation. The data generated by this method can be used to characterize the transcriptome of cereals during germination, in various stages of grain development, or at different biotic or abiotic stress conditions. The results presented here exemplify high-quality transcriptome data amenable for downstream bioinformatics analyses, such as the determination of differentially expressed genes (DEGs), characterisation of gene regulatory networks, and conducting transcriptome-wide association study (TWAS).
The development of rice that can produce slow and steady postprandial glucose in the bloodstream ... more The development of rice that can produce slow and steady postprandial glucose in the bloodstream is a response to alarmingly high global rates of obesity and related chronic diseases. However, rice grain quality programs from all over the world currently do not have access to a high-throughput method to distinguish rice breeding materials that are digested slowly. The objective of this study was to develop a high-throughput in vitro assay to screen the digestibility of cooked white rice grains and to investigate its ability to differentiate rice genotypes with a low starch digestibility rate. The digestibility rate and extent of three commercial rice genotypes with diverse GI values (Doongara, Reiziq and Waxy) were successfully differentiated using the protocol. Further investigations with eight rice genotypes indicated the percentage of starch hydrolysed at a single time point of the assay (SH-60) successfully differentiated genotypes with a low digestibility rate (the SH-60 of Doo...
Higher head rice yield (HRY), which represents the proportion of intact grains that survive milli... more Higher head rice yield (HRY), which represents the proportion of intact grains that survive milling, and lower grain chalkiness (opacity) are key quality traits. We investigated the genetic basis of HRY and chalkiness in 320 diverse resequenced accessions of indica rice with integrated single- and multi-locus genome-wide association studies using 2.26 million single-nucleotide polymorphisms. We identified novel haplotypes that underly higher HRY on chromosomes 3, 6, 8, and 11, and that lower grain chalkiness in a fine-mapped region on chromosome 5. Whole-genome sequencing of 92 IRRI breeding lines was performed to identify the genetic variants of HRY and chalkiness. Rare and novel haplotypes were found for lowering chalkiness, but missing alleles hindered progress towards enhancing HRY in breeding material. The novel haplotypes that we identified have potential use in breeding programs aimed at improving these important traits in the rice crop.
Abstract Background The current incidence of obesity and type 2 diabetes is at global epidemic le... more Abstract Background The current incidence of obesity and type 2 diabetes is at global epidemic levels. To mitigate their impact, there is a need to develop starch-containing foods that give rise to a low and stable postprandial blood glucose response by increasing the proportion of slowly-digestible and indigestible carbohydrate content. Rice is an ideal target food for such dietary intervention because it is a staple food for over half the world's population. Scope and approach The starch digestion of cooked white rice grains is usually complete or near complete upon consumption, but the rate of digestion is influenced by intrinsic food properties and extrinsic influences. This review provides an overview of the complex interplay between the starch granule and its interaction with non-starch components of the rice grain (intrinsic characteristics) as well as the effects of processing (extrinsic factors) on starch digestibility. Key findings and conclusions The intrinsic properties of white rice grains play a significant role in starch digestibility which can be further enhanced after processing, especially by gelatinisation and retrogradation. Post-harvest storage conditions of rice were found to influence starch digestibility but this effect was temperature-dependent. Limited studies investigated starch-lipid and starch-protein interactions in rice, but changes to substrate accessibility have been implicated. Improving our understanding of the effects of processing on starch digestibility can provide an effective tool for food manufacturers to regulate starch digestibility of existing rice varieties.
Rice lines with slower starch digestibility provide opportunities in mitigating the global rise i... more Rice lines with slower starch digestibility provide opportunities in mitigating the global rise in type II diabetes and related non-communicable diseases. However, screening for low glycemic index (GI) in rice breeding programs is not possible due to time and cost constraints. This study evaluated the feasibility of using in vitro cooked grain amylolysis, starch mobilization patterns during seed germination, and variation in starch structure and composition in the mature seed to differentiate patterns of starch digestibility. Mobilization patterns of total starch, resistant starch, amylose and amylopectin chains, and free sugars during seed germination revealed that the process is analogous to digestion in the human gastrointestinal tract. The combination of these biochemical markers can be used as an alternative measure to predict GI. Additionally, transcriptome analysis of stored mRNA transcripts in high and low GI lines detected differences in starch metabolism and confirmed the ...
Rice lines with slower starch digestibility provide opportunities in mitigating the global rise i... more Rice lines with slower starch digestibility provide opportunities in mitigating the global rise in type II diabetes and related non-communicable diseases. However, screening for low glycemic index (GI) in rice breeding programs is not possible due to time and cost constraints. This study evaluated the feasibility of using in vitro cooked grain amylolysis, starch mobilization patterns during seed germination, and variation in starch structure and composition in the mature seed to differentiate patterns of starch digestibility. Mobilization patterns of total starch, resistant starch, amylose and amylopectin chains, and free sugars during seed germination revealed that the process is analogous to digestion in the human gastrointestinal tract. The combination of these biochemical markers can be used as an alternative measure to predict GI. Additionally, transcriptome analysis of stored mRNA transcripts in high and low GI lines detected differences in starch metabolism and confirmed the ...
A deeper understanding of the regulation of starch biosynthesis in rice (Oryza sativa) endosperm ... more A deeper understanding of the regulation of starch biosynthesis in rice (Oryza sativa) endosperm is crucial in tailoring digestibility without sacrificing grain quality. In this study, significant association peaks on chromosomes 6 and 7 were identified through a genomewide association study (GWAS) of debranched starch structure from grains of a 320 indica rice diversity panel using genotyping data from the high-density rice array. A systems genetics approach that interrelates starch structure data from GWAS to functional pathways from a gene regulatory network identified known genes with high correlation to the proportion of amylose and amylopectin. An SNP in the promoter region of Granule Bound Starch Synthase I was identified along with seven other SNPs to form haplotypes that discriminate samples into different phenotypic ranges of amylose. A GWAS peak on chromosome 7 between LOC_Os07g11020 and LOC_Os07g11520 indexed by a nonsynonymous SNP mutation on exon 5 of a bHLH transcript...
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Papers by Vito Butardo