Elucidation of genetic variation and population structure of melon genetic resources in the NARO Genebank, and construction of the World Melon Core Collection.

Numerous genetic resources of major crops have been introduced from around the world and deposited in Japanese National Agriculture and Food Research Organization (NARO) Genebank. Understanding their genetic variation and selecting a representative subset ("core collection") are essential for optimal management and efficient use of genetic resources. In this study, we conducted genotyping-by-sequencing (GBS) to characterize the genetic relationships and population structure in 755 accessions of melon genetic resources. The GBS identified 39,324 single-nucleotide polymorphisms (SNPs) that are distributed throughout the melon genome with high density (one SNP/10.6 kb). The phylogenetic relationships and population structure inferred using this SNP dataset are highly associated with the cytoplasm type and geographical origin. Our results strongly support the recent hypothesis that cultivated melon was established in Africa and India through multiple independent domestication events. Finally, we constructed a World Melon Core Collection that covers at least 82% of the genetic diversity and has a wide range of geographical origins and fruit morphology. The genome-wide SNP dataset, phylogenetic relationships, population structure, and the core collection provided in this study should largely contribute to genetic research, breeding, and genetic resource preservation in melon.

Domestication of azuki bean and soybean in Japan: From the insight of archeological and molecular evidence.

Domestication of azuki bean and soybean has enabled them to acquire non-dormant seeds, non-shattering pods, and larger seed size. Seed remains of the Jomon period recently discovered at archeological sites in the Central Highlands of Japan (6,000-4,000 BP) suggest that the use of azuki bean and soybean and their increase in seed size began earlier in Japan than in China and Korea; molecular phylogenetic studies indicate that azuki bean and soybean originated in Japan. Recent identification of domestication genes indicate that the domestication traits of azuki bean and soybean were established by different mechanisms. Analyses of domestication related genes using DNA extracted from the seed remains would reveal further details about their domestication processes.

Domesticating Vigna stipulacea: Chromosome-Level genome assembly reveals VsPSAT1 as a candidate gene decreasing hard-seededness.

To increase food production under the challenges presented by global climate change, the concept of de novo domestication-utilizing stress-tolerant wild species as new crops-has recently gained considerable attention. We had previously identified mutants with desired domestication traits in a mutagenized population of the legume Vigna stipulacea Kuntze (minni payaru) as a pilot for de novo domestication. Given that there are multiple stress-tolerant wild legume species, it is important to establish efficient domestication processes using reverse genetics and identify the genes responsible for domestication traits. In this study, we identified VsPSAT1 as the candidate gene responsible for decreased hard-seededness, using a Vigna stipulacea isi2 mutant that takes up water from the lens groove. Scanning electron microscopy and computed tomography revealed that the isi2 mutant has lesser honeycomb-like wax sealing the lens groove than the wild-type, and takes up water from the lens groove. We also identified the pleiotropic effects of the isi2 mutant: accelerating leaf senescence, increasing seed size, and decreasing numbers of seeds per pod. While doing so, we produced a V. stipulacea whole-genome assembly of 441 Mbp in 11 chromosomes and 30,963 annotated protein-coding sequences. This study highlights the importance of wild legumes, especially those of the genus Vigna with pre-existing tolerance to biotic and abiotic stresses, for global food security during climate change.

Unique Salt-Tolerance-Related QTLs, Evolved in Vigna riukiuensis (Na+ Includer) and V. nakashimae (Na+ Excluder), Shed Light on the Development of Super-Salt-Tolerant Azuki Bean (V. angularis) Cultivars.

Wild relatives of crops have the potential to improve food crops, especially in terms of improving abiotic stress tolerance. Two closely related wild species of the traditional East Asian legume crops, Azuki bean (Vigna angularis), V. riukiuensis "Tojinbaka" and V. nakashimae "Ukushima" were shown to have much higher levels of salt tolerance than azuki beans. To identify the genomic regions responsible for salt tolerance in "Tojinbaka" and "Ukushima", three interspecific hybrids were developed: (A) azuki bean cultivar "Kyoto Dainagon" × "Tojinbaka", (B) "Kyoto Dainagon" × "Ukushima" and (C) "Ukushima" × "Tojinbaka". Linkage maps were developed using SSR or restriction-site-associated DNA markers. There were three QTLs for "percentage of wilt leaves" in populations A, B and C, while populations A and B had three QTLs and population C had two QTLs for "days to wilt". In population C, four QTLs were detected for Na+ concentration in the primary leaf. Among the F2 individuals in population C, 24% showed higher salt tolerance than both wild parents, suggesting that the salt tolerance of azuki beans can be further improved by combining the QTL alleles of the two wild relatives. The marker information would facilitate the transfer of salt tolerance alleles from "Tojinbaka" and "Ukushima" to azuki beans.

Molecular Analysis of Genetic Diversity and Structure of the Lablab (Lablab purpureus (L.) Sweet) Gene Pool Reveals Two Independent Routes of Domestication.

In this study, genetic diversity and structure of 474 cultivated and 19 wild lablab (Lablab purpureus) accessions. were determined using 15 nuclear and 6 chloroplast SSR markers. The overall gene diversity was relatively low (0.3441). Gene diversity in the wild accessions (0.6059) was about two-folds greater than that in the cultivated accessions. In the wild accessions, gene diversity was greatest in the southern Africa, followed by East Africa. In the cultivated accessions, gene diversity was highest in the eastern Africa. The results suggested that South Africa is the center of origin and East Africa is the center of domestication of lablab. Different cluster analyses showed that 2-seeded-pod cultivated accessions (ssp. uncinatus) were clustered with wild accessions and that 4-(6)-seeded-pod cultivated accessions (ssp. purpureus and bengalensis) were intermingled. UPGMA tree suggested that ssp. purpureus and bengalensis were domesticated from 4-seeded-pod wild accessions of southern Africa. Haplotype network analysis based on nuclear SSRs revealed two domestication routes; the ssp. uncinatus is domesticated from 2-seeded-pod wild lablab (wild spp. uncinatus) from East Africa (Ethiopia), while the ssp. purpureus and bengalensis are domesticated from 4-seeded-pod wild lablab from Central Africa (Rwanda). These results are useful for understanding domestication and revising classification of lablab.

Same Locus for Non-shattering Seed Pod in Two Independently Domesticated Legumes, Vigna angularis and Vigna unguiculata.

Loss of pod shattering is one of the most important domestication-related traits in legume crops. The non-shattering phenotypes have been achieved either by disturbed formation of abscission layer between the valves, or by loss of helical tension in sclerenchyma of endocarp, that split open the pods to disperse the seeds. During domestication, azuki bean (Vigna angularis) and yard-long bean (Vigna unguiculata cv-gr. Sesquipedalis) have reduced or lost the sclerenchyma and thus the shattering behavior of seed pods. Here we performed fine-mapping with backcrossed populations and narrowed the candidate genomic region down to 4 kbp in azuki bean and 13 kbp in yard-long bean. Among the genes located in these regions, we found MYB26 genes encoded truncated proteins in azuki bean, yard-long bean, and even cowpea. As such, our findings indicate that independent domestication on the two legumes has selected the same locus for the same traits. We also argue that MYB26 could be a target gene for improving shattering phenotype in other legumes, such as soybean.

QTL Mapping for Agronomic and Adaptive Traits Confirmed Pleiotropic Effect of mog Gene in Black Gram [Vigna mungo (L.) Hepper].

Organ size and architecture of plants are important traits affecting crop yield and agronomic practices. An induced mutant, multiple-organ gigantism (MOG), of black gram (Vigna mungo) has been obtained, which shows gigantic leaves, fruit, seed, and architecture (plant height) but lower number of pods per plant. These traits are a pleiotropic effect of a single recessive gene, mog. In this study, we investigated variation of 16 agronomic and adaptive traits in a recombinant inbred line (RIL) population derived from a cross between the MOG mutant (V. mungo var. mungo) and wild black gram (V. mungo var. silvestris) accession TC2210 and identified quantitative trait loci (QTLs) controlling those traits to gain a better understanding of the effect of the mog gene on breeding. The results showed that most of the traits (100-seed weight, leaf size, and plant height) showed moderate narrow-sense heritability (h 2) (45-65%), while pod size and seed length (SDL) showed high h 2 (>75%) and pod dehiscence (shattering), and seed width (SDW) and days to flowering showed low h 2 (<35%). The QTLs for the traits were mapped onto a high-density linkage map developed for the RIL population. Inclusive composite interval mapping identified 42 QTLs in total for the 16 traits with number of QTLs per trait ranging from one to six. Major QTLs for the MOG phenotypes were clustered on linkage group (LG) 6, confirming the pleiotropic effect of the mog gene. Effect of the mog gene/QTL for the MOG phenotypic variations was not high, ranging from about 15% in plant height to 40% in leaf size. For 100-seed weight, which is the most interesting trait, the mog gene/QTL contributed about 30% of the total trait variation and showed an additive effect of only 0.51 g, which is only about 1.5-fold higher than that of the other five QTLs detected for this trait. These results indicated that mog gene expression is highly affected by environment and the effect of the gene toward organ size and plant height is not extraordinarily high. Implications of the findings of this study and exploiting of the MOG mutant in breeding were also discussed.

Whole genome sequencing data of Vigna nakashimae var. Ukushima and G418.

Vigna nakashimae is one of the closely related species of Vigna angularis (Adzuki bean). Two strain of 'Ukushima' and 'G418' were identified as salt tolerance strains in Vigna nakashimae from gene bank collection. F2 populations from an inter- or intra-specific cross between the sensitive and tolerant strains are useful for the detection of salt tolerance QTL in Vigna nakashimae. Although Vigna angularis reference genome is available and useful for genetic analysis by genotyping-by-sequencing/RADseq in closely related species, it is not enough for isolation of responsible genes. To reveal sequence variation in Vigna nakashimae "Ukushima" and "G418", the whole genome sequencing was performed using Illumina HiSeq X Ten system (411,174,986 and 478,116,282 read). NGS data was deposited in the DNA Data Bank of Japan (DDBJ) under accession number DRA009307.

Domesticating Vigna Stipulacea: A Potential Legume Crop With Broad Resistance to Biotic Stresses.

Though crossing wild relatives to modern cultivars is a usual means to introduce alleles of stress tolerance, an alternative is de novo domesticating wild species that are already tolerant to various kinds of stresses. As a test case, we chose Vigna stipulacea Kuntze, which has fast growth, short vegetative stage, and broad resistance to pests and diseases. We developed an ethyl methanesulfonate-mutagenized population and obtained three mutants with reduced seed dormancy and one with reduced pod shattering. We crossed one of the mutants of less seed dormancy to the wild type and confirmed that the phenotype was inherited in a Mendelian manner. De novo assembly of V. stipulacea genome, and the following resequencing of the F2 progenies successfully identified a Single Nucleotide Polymorphism (SNP) associated with seed dormancy. By crossing and pyramiding the mutant phenotypes, we will be able to turn V. stipulacea into a crop which is yet primitive but can be cultivated without pesticides.

Development of an SNP-based high-density linkage map and QTL analysis for bruchid (Callosobruchus maculatus F.) resistance in black gram (Vigna mungo (L.) Hepper).

Black gram (Vigna mungo var. mungo) is an important pulse crop in Asia. The cowpea weevil (Callosobruchus maculatus) is a stored-seed insect pest (seed weevil/bruchid) that causes serious postharvest losses in pulse crops, including black gram. In this study, we constructed a high-density linkage map for black gram and identified quantitative trait loci (QTLs) for C. maculatus resistance. A recombinant inbred line (RIL) population of 150 lines from a cross between BC48 [cultivated black gram (var. mungo); bruchid-susceptible] and TC2210 [wild black gram (var. silvestris); bruchid-resistant] were used to construct a linkage map of 3,675 SNP markers from specific-locus amplified fragment sequencing. The map comprised 11 linkage groups spanning 1,588.7 cM with an average distance between adjacent markers of 0.57 cM. Seeds of the RIL population grown in 2016 and 2017 were evaluated for C. maculatus resistance through two traits; the percentage of damaged seeds (PDS) and infestation severity progress (AUDPS). Inclusive composite interval mapping identified three QTLs each for PDS and AUDPS. Two QTLs, qVmunBr6.1 and qVmunBr6.2, mapped about 10 cM apart on linkage group 6 were common between PDS and AUDPS. Comparative genome analysis revealed that qVmunBr6.1 and qVmunBr6.2 are new loci for C. maculatus resistance in Vigna species and that genes encoding a lectin receptor kinase and chitinase are candidates for qVmunBr6.2. The high-density linkage map constructed and QTLs for bruchid resistance identified in this study will be useful for molecular breeding of black gram.

Construction of genetic linkage map and genome dissection of domestication-related traits of moth bean (Vigna aconitifolia), a legume crop of arid areas.

The moth bean (Vigna aconitifolia), possibly the most primitive crop of the genus Vigna, is a highly drought- and heat-resistant legume grown in arid areas. Moth bean domestication involved phenotypic changes, including reduction of seed dormancy and pod shattering, increased organ size, and earlier flowering and maturity. However, the genetics of the domestication process in moth bean is not known. In this study, we constructed a genetic linkage map for moth bean and used the map to identify quantitative trait loci (QTL) for domestication-related traits of an F2 population of 188 individuals produced from a cross of wild moth bean (TN67) and cultivated moth bean (ICPMO056). The genetic linkage map comprised 11 linkage groups (LG) of 172 simple sequence repeat markers and spanned a total length of 1016.8 centiMorgan (cM), with an average marker distance of 7.34 cM. A comparative genome analysis showed high genome synteny between moth bean and mungbean (Vigna radiata), adzuki bean (Vigna angularis), rice bean (Vigna umbellata), and yardlong bean (Vigna unguiculata). In total, 50 QTLs and 3 genes associated with 20 domestication-related traits were identified. Most of the QTLs belonged to five LGs (1, 2, 4, 7, and 10). Key traits related to domestication such as seed dormancy and pod shattering were controlled by large-effect QTLs (PVE > 20%) with one or two minor QTLs, whereas all other traits were controlled by one-seven minor QTLs, apart from seed weight, which was controlled by one major and seven minor QTLs. These results suggest that a small number of mutations with large phenotypic effects have contributed to the domestication of the moth bean. Comparative analysis of QTLs with related Vigna crops revealed that there are several domestication-related large-effect QTLs that had not been used in moth bean domestication. This study provides a basic genetic map and identified genome regions associated with domestication-related traits, which will be useful for the genetic improvement of the moth bean and related Vigna species.

QTL analysis of domestication syndrome in zombi pea (Vigna vexillata), an underutilized legume crop.

Zombi pea (Vigna vexillata (L.) A. Rich) is an underutilized crop belonging to the genus Vigna. Two domesticated forms of zombi pea are cultivated as crop plants; seed and tuber forms. The cultivated seed form is present in Africa, while the cultivated tuber form is present in a very limited part of Asia. Genetics of domestication have been investigated in most of cultivated Vigna crops by means of quantitative trait locus (QTL) mapping. In this study, we investigated genetics of domestication in zombi pea by QTL analysis using an F2 population of 139 plants derived from a cross between cultivated tuber form of V. vexillata (JP235863) and wild V. vexillata (AusTRCF66514). A linkage map with 11 linkage groups (LGs) was constructed from this F2 population using 145 SSR, 117 RAD-seq and 2 morphological markers. Many highly segregation distorted markers were found on LGs 5, 6, 7, 8, 10 and 11. Most of the distorted markers were clustered together and all the markers on LG8 were highly distorted markers. Comparing this V. vexillata linkage map with linkage maps of other four Vigna species demonstrated several genome rearrangements in V. vexillata. QTL analysis for 22 domestication-related traits was investigated by inclusive composite interval mapping in which 37 QTLs were identified for 18 traits; no QTL was detected for 4 traits. Number of QTLs detected in each trait ranged from 1 to 5 with an average of only 2.3. Five QTLs for tuber width and three QTLs for tuber weight. Interestingly, 2 QTLs each for tuber width and tuber weight detected on LG2 and LG4 were located at similar position and wild allele increased tuber width and weight. This indicated wild germplasm having small tuber have potential to increase yield of large tuber cultivated type. Large-effect QTLs (PVE > 20%) were on LG4 (pod length), LG5 (leaf size and seed thickness), and LG7 (for seed-related traits). Comparison of domestication-related QTLs of the zombi pea with those of cowpea (Vigna unguiculata), azuki bean (Vigna angularis), mungbean (Vigna radiata) and rice bean (Vigna umbellata) revealed that there was conservation of some QTLs for seed size, pod size and leaf size between zombi pea and cowpea and that QTLs associated with seed size (weight, length, width and thickness) in each species were clustered on same linkage.

Genetic Dissection of Azuki Bean Weevil (Callosobruchus chinensis L.) Resistance in Moth Bean (Vigna aconitifolia [Jaqc.] Maréchal).

The azuki bean weevil (Callosobruchus chinensis L.) is an insect pest responsible for serious postharvest seed loss in leguminous crops. In this study, we performed quantitative trait locus (QTL) mapping of seed resistance to C. chinensis in moth bean (Vigna aconitifolia [Jaqc.] Maréchal). An F2 population of 188 plants developed by crossing resistant accession 'TN67' (wild type from India; male parent) and susceptible accession 'IPCMO056' (cultivated type from India; female parent) was used for mapping. Seeds of the F2 population from 2014 and F2:3 populations from 2016 and 2017 were bioassayed with C. chinensis, and the percentage of damaged seeds and progress of infestation severity were measured. Segregation analysis suggested that C. chinensis resistance in TN176 is controlled by a single dominant gene, designated as Rcc. QTL analysis revealed one principal and one modifying QTL for the resistance, named qVacBrc2.1 and qVacBrc5.1, respectively. qVacBrc2.1 was located on linkage group 2 between simple sequence repeat markers CEDG261 and DMB-SSR160 and accounted for 50.41% to 64.23% of resistance-related traits, depending on the trait and population. Comparative genomic analysis suggested that qVacBrc2.1 is the same as QTL Brc2.1 conferring C. chinensis resistance in wild azuki bean (V. nepalensis Tateishi and Maxted). Markers CEDG261 and DMB-SSR160 should be useful for marker-assisted selection for C. chinensis resistance in moth bean.

Diversity of Drought Tolerance in the Genus Vigna.

Wild relatives of crop plants are thought as reservoir of prominent genetic resources for abiotic stress tolerance. However, insufficient information on genetic variation and phenotypic traits restricts their use for crop breeding. This study focused on wild species of genus Vigna (family Fabaceae) originated from highly humid to arid regions. To clarify the diversity of drought tolerance during the vegetative stage, 69 accessions, including 15 domesticated, and 54 wild accessions, were evaluated under two drought conditions of non-terminal and terminal stresses. In the non-terminal drought condition, the plants were grown in pipes of different heights where surface soil water content decreased faster in pipes with greater height. Relative shoot biomass was used for tolerance evaluation and we identified 19 drought tolerant accessions. Almost of them were wild accessions showing higher relative shoot biomass than that in the domesticated accessions. Domesticated species were mostly classified as drought susceptible but could be improved using tolerant conspecific wild ancestors with cross-compatibility. The tolerance was related with higher plant water status presumably due to small water consumption. However, the variation of drought tolerance could not be explained by simple tolerance factor alone, and other tolerance mechanisms such as deep rooting and increasing in root biomass were found in the tolerant accessions. In the terminal drought condition, the plants were grown in small pots, and the watering was stopped to expose them extreme and rapid soil water scarcity. The tolerance was evaluated as the number of days until wilting. However, the accessions found to be tolerant in the pot experiment were not the same as those in the pipe experiment. In this condition, plant water status was not related with the length of days to wilting. This indicates that different mechanisms are necessary for adaptation to each of the non-terminal and terminal drought conditions. Many accessions were tolerant to one of the conditions, although we identified that some accessions showed tolerance in both experiments. The great diversity in drought tolerance in the genus Vigna might serve to both improve crop drought tolerance and understand the mechanisms of adaptation in drought-prone environments.

Multiple organ gigantism caused by mutation in VmPPD gene in blackgram (Vigna mungo).

Seed size is one of the most important traits in leguminous crops. We obtained a recessive mutant of blackgram that had greatly enlarged leaves, stems and seeds. The mutant produced 100% bigger leaves, 50% more biomass and 70% larger seeds though it produced 40% less number of seeds. We designated the mutant as multiple-organ-gigantism (mog) and found the mog phenotype was due to increase in cell numbers but not in cell size. We also found the mog mutant showed a rippled leaf (rl) phenotype, which was probably caused by a pleiotropic effect of the mutation. We performed a map-based cloning and successfully identified an 8 bp deletion in the coding sequence of VmPPD gene, an orthologue of Arabidopsis PEAPOD (PPD) that regulates arrest of cell divisions in meristematic cells. We found no other mutations in the neighboring genes between the mutant and the wild type. We also knocked down GmPPD genes and reproduced both the mog and rl phenotypes in soybean. Controlling PPD genes to produce the mog phenotype is highly valuable for breeding since larger seed size could directly increase the commercial values of grain legumes.

Diversity and Evolution of Salt Tolerance in the Genus Vigna.

Breeding salt tolerant plants is difficult without utilizing a diversity of wild crop relatives. Since the genus Vigna (family Fabaceae) is comprised of many wild relatives adapted to various environmental conditions, we evaluated the salt tolerance of 69 accessions of this genus, including that of wild and domesticated accessions originating from Asia, Africa, Oceania, and South America. We grew plants under 50 mM and 200 mM NaCl for two weeks and then measured the biomass, relative quantum yield of photosystem II, leaf Na+ concentrations, and leaf K+ concentrations. The accessions were clustered into four groups: the most tolerant, tolerant, moderately susceptible, and susceptible. From the most tolerant group, we selected six accessions, all of which were wild accessions adapted to coastal environments, as promising sources of salt tolerance because of their consistently high relative shoot biomass and relative quantum yield. Interestingly, variations in leaf Na+ concentration were observed between the accessions in the most tolerant group, suggesting different mechanisms were responsible for their salt tolerance. Phylogenetic analysis with nuclear DNA sequences revealed that salt tolerance had evolved independently at least four times in the genus Vigna, within a relatively short period. The findings suggested that simple genetic changes in a few genes might have greatly affected salt tolerances. The elucidation of genetic mechanisms of salt tolerances in the selected accessions may contribute to improving the poor salt tolerance in legume crops.

Genotypic difference in (137)Cs accumulation and transfer from the contaminated field in Fukushima to azuki bean (Vigna angularis).

The screening of mini-core collection of azuki bean accessions (Vigna angularis (Willd.) Ohwi & Ohashi) for comparative uptake of (137)Cs in their edible portions was done in field trials on land contaminated by the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident. Ninety seven azuki bean accessions including their wild relatives from a Japanese gene bank, were grown in a field in the Fukushima prefecture, which is located approximately 51 km north of FDNPP. The contamination level of the soil was 3665 ± 480 Bq kg(-1) dry weight ((137)Cs, average ± SD). The soil type comprised clay loam, where the sand: silt: clay proportion was 42:21:37. There was a significant varietal difference in the biomass production, radiocaesium accumulation and transfer factor (TF) of radiocaesium from the soil to edible portion. Under identical agricultural practice, the extent of (137)Cs accumulation by seeds differed between the accessions by as much as 10-fold. Inter-varietal variation was expressed at the ratio of the maximum to minimum observed (137)Cs transfer factor for seeds ranged from 0.092 to 0.009. The total biomass, time to flowering and maturity, and seed yield had negative relationship to (137)Cs activity concentration in seeds. The results suggest that certain variety/varieties of azuki bean which accumulated less (137)Cs in edible portion with preferable agronomic traits are suitable to reduce the (137)Cs accumulation in food chain on contaminated land.

Novel Genetic Resources in the Genus Vigna Unveiled from Gene Bank Accessions.

The genus Vigna (Fabaceae) consists of five subgenera, and includes more than 100 wild species. In Vigna, 10 crops have been domesticated from three subgenera, Vigna, Plectrotropis, and Ceratotropis. The habitats of wild Vigna species are so diverse that their genomes could harbor various genes responsible for environmental stress adaptation, which could lead to innovations in agriculture. Since some of the gene bank Vigna accessions were unidentified and they seemed to be novel genetic resources, these accessions were identified based on morphological traits. The phylogenetic positions were estimated based on the DNA sequences of nuclear rDNA-ITS and chloroplast atpB-rbcL spacer regions. Based on the results, the potential usefulness of the recently described species V. indica and V. sahyadriana, and some wild Vigna species, i.e., V. aconitifolia, V. dalzelliana, V. khandalensis, V. marina var. oblonga, and V. vexillata, was discussed.

The Vigna Genome Server, 'VigGS': A Genomic Knowledge Base of the Genus Vigna Based on High-Quality, Annotated Genome Sequence of the Azuki Bean, Vigna angularis (Willd.) Ohwi & Ohashi.

The genus Vigna includes legume crops such as cowpea, mungbean and azuki bean, as well as >100 wild species. A number of the wild species are highly tolerant to severe environmental conditions including high-salinity, acid or alkaline soil; drought; flooding; and pests and diseases. These features of the genus Vigna make it a good target for investigation of genetic diversity in adaptation to stressful environments; however, a lack of genomic information has hindered such research in this genus. Here, we present a genome database of the genus Vigna, Vigna Genome Server ('VigGS', http://viggs.dna.affrc.go.jp), based on the recently sequenced azuki bean genome, which incorporates annotated exon-intron structures, along with evidence for transcripts and proteins, visualized in GBrowse. VigGS also facilitates user construction of multiple alignments between azuki bean genes and those of six related dicot species. In addition, the database displays sequence polymorphisms between azuki bean and its wild relatives and enables users to design primer sequences targeting any variant site. VigGS offers a simple keyword search in addition to sequence similarity searches using BLAST and BLAT. To incorporate up to date genomic information, VigGS automatically receives newly deposited mRNA sequences of pre-set species from the public database once a week. Users can refer to not only gene structures mapped on the azuki bean genome on GBrowse but also relevant literature of the genes. VigGS will contribute to genomic research into plant biotic and abiotic stresses and to the future development of new stress-tolerant crops.

A Homoploid Hybrid Between Wild Vigna Species Found in a Limestone Karst.

Genus Vigna comprise several domesticated species including cowpea and mungbean, and diverse wild species. We found an introgressive hybrid population derived from two wild species, Vigna umbellata and Vigna exilis, in Ratchaburi district, Thailand. The hybrid was morphologically similar to V. umbellata but habituated in a limestone rock mountain, which is usually dominated by V. exilis. Analyzing simple sequence repeat loci indicated the hybrid has undergone at least one round of backcross by V. umbellata. We found the hybrid acquired vigorous growth from V. umbellata and drought tolerance plus early flowering from V. exilis, and thus has taken over some habitats of V. exilis in limestone karsts. Given the wide crossability of V. umbellata, the hybrid can be a valuable genetic resource to improve drought tolerance of some domesticated species.