On the cover

Genetic resources of azuki bean (Vigna angularis) conserved in the NARO Genebank. The scale on the ruler is in millimeters (mm). Azuki bean is widely cultivated in Asia and has been introduced to other continents as a cash crop in recent decades. To develop a better understanding of azuki bean and its potential genetic resources, we have compiled information by adding recent publications on their morphology, historical taxonomic treatments, species origin, gene pool concept, geographical and ecological habitats, and stress tolerances. These genetic resources are expected to be used as breeding material against biotic and abiotic stresses (This issue, p. 295–310).

(Y. Takahashi: Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO))

Asian rice (Oryza sativa L.) was domesticated from wild rice (O. rufipogon Griff.). During rice domestication, the wild characteristic of seed-shattering behaviour was suppressed, enabling an efficient harvest with increased yield. Rice, a stable food for humans, is one of the most important crops consumed by billions of people, especially in Asian countries. With advances in molecular genetic studies, genes or loci involved in reduced seed shattering via the inhibition of abscission layer formation have been identified. The mutations alone showed no inhibitory effect on abscission layer formation in the wild rice O. rufipogon, but their combination enabled a stepwise change in the degree of seed shattering, which may be associated with advances in harvesting tools. In the early stages of rice domestication, the closed panicle formation and slight inhibition of the abscission layer resulted in complementary effects that increased harvesting efficiency. Furthermore, common and distinct loci were found to contribute to reduced seed shattering in groups of rice cultivars, indicating that mutations at seed-shattering loci are important information for tracing the process of rice domestication.

This review compiles information on the morphology, historical taxonomic treatments, species origin, gene pool concept, geographical and ecological habitats, and stress tolerance of the azuki bean (Vigna angularis) and related species. Willdenow (1802) first described the azuki bean in the genus Dolichos, and Ohwi and Ohashi (1969) finally transferred it to the genus Vigna. The genus Vigna is currently divided into five subgenera: Ceratotropis, Haydonia, Lasiospron, Plectrotropis, and Vigna. The subgenus Ceratotropis includes the moth bean in section Aconitifoliae; the mungbean and black gram in section Ceratotropis; and the azuki bean, rice bean, and creole bean in section Angulares. The wild species in section Angulares generally possess larger standard petal with more prominent appendage, keel petal with longer pocket, pistil with longer style beak compared with those of species in sections Aconitifoliae and Ceratotropis, and characterized by glabrous mature pod, smooth seed coat, hypogeal germination seed, and cordate primary leaves with petiole. Section Angulares currently consists of 13 species. The taxa that cross readily with the azuki beans included in the primary genepool are the wild azuki bean V. angularis var. nipponensis, V. nepalensis, V. tenuicaulis, V. hirtella, V. minima, V. nakashimae, and V. riukiuensis. These wild species are expected to be used as breeding material against biotic and abiotic stresses.

To explore the molecular mechanism behind maize grain quality and use of different gene stacking to improve the nutritional quality of grain, marker-assisted selection (MAS) was used to select three recessive mutant lines containing o2o16wx, along with the double-recessive mutant lines containing o2o16, o2wx, and o16wx. The resulting seeds were taken for transcriptome sequencing analysis 18 days after pollination (DAP). Results: Compared with the recurrent parent genes, in the lysine synthesis pathway, the gene pyramiding lines (o2o16wx, o2wx, and o16wx) revealed that the gene encoding aspartate kinase (AK) was up-regulated and promoted lysine synthesis. In the lysine degradation pathway, ‘QCL8010_1’ (o2o16wx) revealed that the gene encoding saccharopine dehydrogenase (LKR/SDH) was down-regulated. In addition, the gene pyramiding lines (o2o16wx, o2o16, and o16wx) indicated that the gene encoding 2-oxoglutarate dehydrogenase E1 component (OGDH) was down-regulated, inhibiting the degradation of lysine. In the tryptophan synthesis pathway, the genes encoding anthranilate synthase (AS), anthranilate synthase (APT), and tryptophan synthase (TS) were up-regulated (in o2o16wx, o2o16, o2wx, and o16wx), and promote tryptophan synthesis. In the tryptophan degradation pathway, it was revealed that the genes encoding indole-3-producing oxidase (IAAO) and indole-3-pyruvate monooxygenase (YUCCA) were down-regulated. These results provide a reference for revealing the mechanism of the o2, o16, and wx with different gene pyramiding to improve grain quality in maize.

The introgression of heterologous genomes through interspecific hybridization offers a great opportunity to expand the gene pool of crops, thereby broadening the traits that can be targeted for improvement. The introgression of C genomic regions carrying desirable traits from Brassica napus (AACC) into the diploid B. rapa (AA) via homoeologous recombination (HR) has been commonly used. However, the precise identification of HR sites remains a significant challenge, limiting the practical application of genome introgression via HR in breeding programs. Here, we developed an indicator named ‘Dosage-score’ from the coverage depth of next-generation sequencing reads. Then, Dosage-score analysis applied to both in BC₁F₁ individuals obtained by backcrossing B. rapa to F₁ progeny (B. rapa × B. napus) and in the parental lines, and successfully identified the precise HR sites resulting from F₁ meiosis as well as those that were native in the parental B. napus genome. Additionally, we introgressed the C6 segment from HR identified by Dosage-score analysis into B. rapa genome background, revealing gene expression on the added segment without noticeable phenotypic change. The identification of HR by Dosage-score analysis will contribute to the expansion of the gene pool for breeding by introgression of heterologous genomes in Brassica crops.

The vascular bundle system in the panicle neck of rice (Oryza sativa L.) connects the culm to the panicle and transports assimilates. The number of vascular bundles in the panicle neck (VBN) is correlated with the diameter of the panicle neck (DPN), but there are few reported QTLs for DPN. We conducted quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from a cross between ‘Asominori’ and ‘IR24’ and detected three QTLs—qDPN5, qDPN6, and qDPN11—on chromosomes 5, 6, and 11. The qDPN5, qDPN6, and qDPN11 were in the same position as the QTLs for VBN reported in previous studies. Within the RILs, there was a significant positive correlation between DPN and VBN. In segregating populations, each QTL had a distinct effect on both values. Analysis of chromosome segment substitution lines showed that qDPN5 and qDPN11 affected DPN and qDPN6 affected VBN. Through substitution mapping, we narrowed down the region of qDPN5 and qVBN5.2 to 960 kbp between KNJ8 Indel385 and RM18926, and the region of qVBN6 to 750 kbp between C5 Indel5756 and KNJ8 Indel493. Due to the weak effect of qDPN6 in the ‘IR24’ genetic background, the location of qDPN6 could not be determined.

Tomatoes have the highest agricultural production among vegetables in Japan and worldwide. Japanese large-sized fresh-market tomatoes have a unique breeding history that differs from that of other countries, represented by pink-colored and juicy fruits with a good taste and flavor. We performed whole-genome resequencing of 150 Japanese large-sized fresh-market tomato cultivars released from the 1940s to the 2000s to unveil how breeding selection has changed the genome of Japanese tomato cultivars and provide a genomic basis for future Japanese tomato breeding. The genomic population structure of the cultivars was highly correlated with the year of release. Comparison between the agronomic performance and release year of the cultivars reflected trends in recent breeding selection: an increase in fruit sugar content and a decrease in yield performance. Multiple selection signatures were detected on all the tomato chromosomes. One of the selection signatures was related to the introgression of a resistance gene (Tm-2) from a wild relative. Interestingly, some of the putative QTLs detected by genome-wide association studies did not co-localize with the selection signatures, indicating that the genetic diversity of Japanese tomato cultivars still has the potential for genetic improvement of agronomic performance.

Turnip mosaic virus (TuMV) poses a major threat to Brassica crops like Chinese cabbage, causing significant economic losses. A viable and effective strategy to manage such diseases is by improvement of genetic-based viral resistance. To achieve this, it is important to have detailed and wide-ranging genetic resources, necessitating genetic exploration. To identify useful TuMV resistant genetic resources, we screened geographically and genetically diverse resources including over 90 accessions from the Tohoku Univ. Brassica Seed Bank against eleven TuMV isolates phylogenetically classified into five clusters. Two USA accessions exhibited no or only slight symptoms with no virus protein detected in virus-inoculated and non-inoculated upper leaves, suggesting an extreme resistance to all tested TuMV isolates. Through sequencing and dCAPS analysis of eukaryotic translation initiation factor (eIF4E/eIFiso4E) in the 95 B. rapa accessions, several amino acid substitutions were observed on the dorsal surface and cap-binding sites of eIF4E/eIFiso4E proteins, with three of them significantly associated with resistance/susceptibility responses. When exploring co-infection using TuMV and cucumber mosaic virus (CMV), the TuMV susceptible accession died, but TuMV resistance was retained in the TuMV resistant accession. It suggested that the broad-spectrum resistance in the two USA accessions is a highly valuable resources for Brassica breeding.

Green rice leafhopper (GRH, Nephotettix cincticeps Uhler) is a serious insect pest of rice in the temperate regions of Asia. Myanmar has a high genetic diversity and is located at the center of the origin of rice. To understand the genetic architecture of GRH resistance in Myanmar indica rice landraces, a genome-wide association study (GWAS) was performed using a diversity panel collected from diverse geographical regions. Phenotypic variation in GRH resistance was associated with three genomic regions, MTA4, MTA5, and MTA11, located on chromosomes 4, 5, and 11, respectively. MTA4 and MTA5 were adjacent to the known resistance genes GRH6 and GRH1. Analysis of haplotypes and linkage disequilibrium blocks revealed that the haplotypes HapGRH6A, HapGRH1A, and HapMTA11A mainly explained GRH resistance. Map-based cloning revealed that GRH6 was highly induced by GRH infestation and conferred resistance by inhibiting the sucking of phloem sap. The distribution of resistance haplotypes revealed that accessions harboring major resistance haplotypes (HapGRH6A and HapGRH1A) were mainly distributed in Southern Myanmar, and HapMTA11A was mainly responsible for GRH resistance in mountainous areas of Myanmar. Our findings could facilitate the elucidation of the molecular mechanism of GRH resistance and provide essential haplotype-based genetic information for the development of GRH-resistant rice cultivars.

Hokkaido-specific malting barley varieties have been developed to improve the grain yield, disease resistance, malting quality, and brewing quality. In this report we describe the breeding and evaluation of brewing quality of a hulled two-row malting barley (Hordeum vulgare L.) variety ‘Satuiku 5 go’ lacking lipoxygenase-1 (LOX-1-less). ‘Satuiku 5 go’ was evaluated in the joint field trials for malting barley in Hokkaido from 2016 to 2018. ‘Satuiku 5 go’ exhibited 11% higher grain yield and 7.6 cm shorter plant height than the control variety, ‘Ryohfu’. However, the disease severity of Fusarium head blight (FHB) in ‘Satuiku 5 go’ was higher than in ‘Ryohfu’. For malting quality, ‘Satuiku 5 go’ exhibited higher diastatic power, soluble nitrogen content, and fine extract content, and lower wort β-glucan content than ‘Ryohfu’. 100-litter pilot scale brewing trials were conducted with ‘Satuiku 5 go’ and ‘Satuiku 2 go’ as a control variety, also a LOX-1-less variety, and no clear differences were observed.

‘Hisui no Kaori’ is the first lettuce (Lactuca sativa L.) cultivar characterized by a sweet fragrance, attributed to 2-acetyl-1-pyrroline with the same compound as in fragrant rice and soybean cultivars, as well as edible leaves and stem. Field cultivation trials established optimal planting distances at 30 cm between seedlings, with a fertilizer requirement of N = 150 kg/ha. ‘Hisui no Kaori’ exhibited minimal stem burst as well as resistance to soft rot disease, proving easier to cultivate compared with prominent stem-type cultivars. Field cultivation tests at different altitudes and incubator tests revealed that an air temperature exceeding 20°C is pivotal for the development of the sweet fragrance. ‘Hisui no Kaori’ displayed moderately resistance to Fusarium wilt race 1 and highly resistance to race 2. In lettuce, discoloration is known to occur at the cut surface due to mechanical wounding. In a cut leaf test, ‘Hisui no Kaori’ was classified as having delayed discoloration. Overall, ‘Hisui no Kaori’ is expected to contribute to the expanding potential and the increasing market price of lettuce. This work represents a pioneering effort to open up the fragrant type of lettuce.