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Summary: Jatropha curcas (physic nut), a non‐edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up‐regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed. [ABSTRACT FROM AUTHOR]

Mungbean (Vigna radiata (L.) Wilcz.) is an important leguminous crop cultivated mainly in Asia. Its wild relatives are considered useful genetic resources for mungbean breeding. However, the taxonomic history of mungbean and its wild relatives is complicated and some confusion is still present in recent publications. In this study, we examined the rDNA-ITS sequences and morphological characteristics of 83 gene bank accessions closely related to mungbean. As a result, we classified the 83 accessions into five species and one unclassified accession. The proper taxon name for each species was determined (Vigna grandiflora (Prain) Tateishi et Maxted, Vigna mungo (L.) Hepper, V. radiata, Vigna subramaniana (Babu ex Raizada) Raizada, and Vigna trinervia (Heyne ex Wight et Arn.) Tateishi et Maxted) based on a review of their taxonomic history and morphological comparisons between gene bank accessions and type specimens. A new taxonomic treatment is proposed and a morphological key has been prepared. In this treatment, Vigna radiata (L.) Wilcz. var. setulosa (Dalz.) Ohwi et Ohashi is treated as a synonym of Vigna radiata (L.) Wilcz. var. sublobata (Roxb.) Verdc., and Vigna hainiana Babu, Gopinathan et Sharma is a synonym of V. subramaniana. Accession ‘NI1135’ was revealed to be most closely related to, but is considerably differentiated from, mungbean (V. radiata) based on its rDNA-ITS sequences. It also has distinguishing morphological characters. Plants with similar morphologies and DNA profiles might be distributed in the Indian Himalaya. However, since only one accession is available at present, the taxonomic classification of ‘NI1135’ needs to be reconsidered in the future. [ABSTRACT FROM AUTHOR]

Yardlong bean [Vigna unguiculata (L.) Walp. ssp. unguiculata cv.-gr. sesquipedalis] is a vegetable legume crop evolved from cultivated grain cowpea (V. unguiculata ssp. unguiculata cv.-gr. unguiculata) which is domesticated from wild cowpea. It has a dramatic change in pod length and pod fiber content, and a complete loss of pod shattering, as compared to its wild progenitor. In this study, we identified quantitative trait loci (QTLs) controlling pod fiber content and pod shattering in two populations (BC1F1 and F2) derived from a cross between yardlong bean and wild cowpea. BC1F1:2 and F2:3 families were grown under field condition in which insoluble dietary fiber (cellulose, hemicelluloses and lignin) contents in mature pods, and pod shattering were evaluated. Correlation analysis showed positive relationship among the types of fiber, and between the fiber and shattering. Inclusive composite interval mapping revealed that a major QTL on linkage group 7 (LG7) controlled cellulose, hemicellulose and lignin contents in pod, and pod shattering. The other QTLs related to pod fibers on LG1 and LG4 also co-localized with the QTLs for pod shattering. Comparative genome analysis with azuki bean (Vigna angularis) suggested that the QTL region on LG7 for cellulose, hemiclellulose, lignin and pod shattering in yardlong bean contains genes encoding MYB transcription factor, MYB83, regulating biosynthesis of the three fibers, while the QTL region for cellulose and shattering of pod on LG1 harbors gene encoding cellulose synthase A7 (CESA7). These genes may be important targets for functional study to reveal major factors regulating pod fiber biosynthesis and pod shattering in yardlong bean. [ABSTRACT FROM AUTHOR]

Key message: Sequence analysis revealed that an SNP (A1855G) in CsBADH of cucumber accession PK2011T202 causes amino acid change in a highly conserved motif, Y163C. Gene mapping showed association between the SNP and the fragrance. Abstract: Pandan-like fragrance is a value-added trait in several food crops such as rice, vegetable soybean and sorghum. The fragrance is caused by the volatile chemical 2-acetyl-1-pyrroline (2AP). Mutation(s) in betaine aldehyde dehydrogenase 2 ( BADH2; also known as aminoaldehyde dehydrogenase 2) gene causes defective BADH2 and results in biosynthesis of 2AP. Recently, cucumber cultivars possessing pandan-like fragrance were discovered in Thailand. In this study, we report an association between CsBADH and the fragrance in cucumber accession 'PK2011T202'. Gene expression analysis of CsBADH in leaves of PK2011T202 and '301176' (non-fragrant) at various growth stages revealed that CsBADH was expressed in both accessions. Sequence comparison of CsBADH showed that PK2011T202 possesses a single base substitution (A1855G) in exon 5 which causes an amino acid change in a highly conserved motif of BADH, Y163C. Single nucleotide-amplified polymorphism markers were developed to detect the SNP polymorphism between the wild-type and fragrance alleles. Since CsBADH is located on chromosome 1, quantitative trait locus (QTL) mapping was conducted for this chromosome using an F and a backcross populations developed from the cross between PK2011T202 and 301176. QTL analysis in both populations showed that the major QTL for fragrance, qFgr, was co-localized with the CsBADH. We concluded that the defect function of CsBADH is responsible for fragrance in cucumber PK2011T202. [ABSTRACT FROM AUTHOR]

Vigna reflexo-pilosa, which includes a neglected crop, is the only one tetraploid species in genus Vigna. The ancestral species that make up this allotetraploid species have not conclusively been identified, although previous studies suggested that a donor genome of V. reflexo-pilosa is V. trinervia. In this study, 1,429 azuki bean EST-SSR markers were developed of which 38 EST-SSR primer pairs that amplified one product in diploid species and two discrete products in tetraploid species were selected to analyze 268 accessions from eight taxa of seven Asian Vigna species including V. reflexo-pilosa var. glabra, V. reflexo-pilosa var. reflexo-pilosa, V. exilis, V. hirtella, V. minima, V. radiata var. sublobata, V. tenuicaulis and V. trinervia to identify genome donor of V. reflexo-pilosa. Since both diploid and tetraploid species were analyzed and each SSR primer pair detected two loci in the tetraploid species, we separated genomes of the tetraploid species into two different diploid types, viz. A and B. In total, 445 alleles were detected by 38 EST-SSR markers. The highest gene diversity was observed in V. hirtella. By assigning the discrete PCR products of V. reflexo-pilosa into two distinguished genomes, we were able to identify the two genome donor parents of créole bean. Phylogenetic and principal coordinate analyses suggested that V. hirtella is a species complex and may be composed of at least three distinct taxa. Both analyses also clearly demonstrated that V. trinervia and one taxon of V. hirtella are the genome donors of V. reflexo-pilosa. Gene diversity indicates that the evolution rate of EST-SSRs on genome B of créole bean might be faster than that on genome A. Species relationship among the Vigna species in relation to genetic data, morphology and geographical distribution are presented. [ABSTRACT FROM AUTHOR]

Waterlogging is severe abiotic stress during mung bean (Vigna radiata (L.) R. Wilczek var. radiata) production. Waterlogging impacts yield loss for the legume crop by around 40%-70%, depending on the severity and duration of the waterlogging. In total, 107 collected mung bean varieties were evaluated under managed waterlogging. The F2 population from crossing between waterlogging-tolerant and -susceptible mung bean varieties were screened under waterlogging conditions. Morphological responses to the waterlogging were recorded. Correlation and path coefficient analyses were used to identify essential traits for waterlogging tolerance and seed yield potential under water stress. Mung bean varieties in clusters 5 and 6 were high waterlogging tolerance with survival rates of 66.66% and 61.11%, respectively. Of 199 F2 lines from crossings between the Kamphaeng Sean2 and W162, 20 lines presented high waterlogging tolerance. The injury score was negatively correlated with the number of leaves at the final date of waterlogging (-0.845) and 1 wk after terminating the waterlogging (-0.885). At the final date of waterlogging condition, the number of leaves and leaf greenness stability index directly affected leaf injury at -0.5928 and -0.4385. One week after waterlogging termination, only the number of leaves affected the leaf injury at -0.8599. The number of leaves directly affected seed yield components at 0.6534 and higher than the direct effect of the other traits. Thus, the number of leaves was a suitable morphological parameter along with the injury score for selecting waterlogging tolerance. The number of leaves was a suitable parameter for selecting high seed yield potential under waterlogging conditions. [ABSTRACT FROM AUTHOR]

Key message: QTL-seq, linkage mapping, and whole-genome resequencing revealed a new locus (qCLS5.1) controlling Cercospora canescens resistance in mungbean and Receptor-like protein 12 (RLP12) genes as candidate genes for the resistance. Cercospora leaf spot (CLS) disease, caused by Cercospora canescens, is a common disease of mungbean (Vigna radiata). In this study, the genetics of CLS resistance was investigated in a new source of resistance (accession V2817) and the resistance was finely mapped to identify candidate genes. F2 and F2:3 populations of the cross V1197 (susceptible) × V2718 and a BC1F1 population of the cross V1197 × (V1197 × V2817) were used in this study. Segregation analysis suggested that the resistance is controlled by a single dominant gene. QTL-seq using F2 individuals revealed that a single QTL (designated qCLS5.1) on chromosome 5 controlled the resistance. The qCLS5.1 was confirmed in the F2:3 and BC1F1 populations by QTL analysis. Fine mapping using 978 F2 individuals localized qCLS5.1 to a 48.94 Kb region containing three tandemly duplicated Receptor-like protein 12 (RLP12) genes. Whole-genome resequencing and alignment of V1197 and V2817 revealed polymorphisms causing amino acid changes and premature stop codons in the three RLP12 genes. Collectively, these results show that qCLS5.1 is a new locus for CLS resistance in mungbean, and a cluster of RLP12 genes are candidate genes for the resistance. The new locus qCLS5.1 will be useful for molecular breeding of durable CLS-resistant mungbean cultivars. [ABSTRACT FROM AUTHOR]

• Vigna radiata Mildew locus O 12 (VrMLO12) gene locates in the same region with QTL conferring powdery mildew (PM) resistance in mungbean RUM5. • VrMLO12 sequencing analysis revealed two SNPs causing amino acid changes in VrMLO12 protein, a MLO clade II protein, in RUM5. • Gene mapping revealed association between VrMLO12 and powdery mildew resistance in RUM5. • This is the first report showing association between MLO Clade II and powdery mildew resistance in plants. Loss/reduction of function of Mildew Locus O (MLO) genes clade V and MLO clade IV has been shown to be responsible for powdery mildew (PM) resistance in several plant species. Mungbean (Vigna radiata) genome possesses 18 MLO genes, VrMLO1 - VrMLO18. A previous study using mungbean F 2 and BC 1 F 1 populations derived from a cross between "CN60″ (susceptible) and "RUM5″ (resistance) demonstrated that QTL qPMRUM5−3 is a major QTL for PM resistance caused by Erysiphe polygoni and is the same with major QTL qPMV4718−3 that confers PM resistance in "V4718″ (resistance). In this study, bioinformatics analysis revealed VrMLO12 locates in the qPMRUM5−3 region. Fine mapping in the F 2 and BC 1 F 1 populations using newly developed DNA markers including gene-specific markers demonstrated association between VrMLO12 and the PM resistance. Sequence analyses of VrMLO12 revealed that compared to susceptible mungbeans, RUM5 and V4718 possess SNPs in exon 10 and exon 13. The SNPs caused amino acid changes of VrMLO12, A387S and A476 G, respectively. The change occurred in transmembrane 6 domain and calmodulin binding domain (CaMBD) of the VrMLO12 protein, respectively. qRT-PCR showed that transcript expression level of VrMLO12 in RUM5 challenged with and without by E. polygoni was significantly higher than that in CN60. Phylogenetic analysis revealed that in contrast to previous findings that MLO proteins associated with PM resistance belong to MLO clade V and MLO clade IV, VrMLO12 belongs to MLO clade II. The result suggested that VrMLO12 may function differently from the other MLOs that associated with PM susceptibility. Our findings provide insight into the PM resistance in mungbean and tools for mungbean breeding. [ABSTRACT FROM AUTHOR]

Cercospora leaf spot (CLS) disease and bruchids are the common disease and insect pest causing yield loss in mung bean (Vigna radiata (L.) R. Wilczek). ‘KUML4’ is an improved mung bean cultivar grown in Thailand having high yield, early and highly synchronous maturity, large seed size, but susceptible to CLS disease and bruchids. This study was conducted to improve ‘KUML4’ through introgression of VrTAF5 for CLS resistance and VrPGIP2 for bruchid (Callosobruchus maculatus) resistance from landrace mung bean accessions ‘V4718’ and ‘V2808’, respectively, by marker-assisted backcrossing (MABC). In the MABC, foreground selections were performed using VrTAF5- and VrPGIP2-specific markers. The BC3F3 pyramided lines with KUML4 background carrying both VrTAF5 and VrPGIP2 genes were developed and evaluated for agronomic and yield-related traits, CLS resistance, and bruchid resistance. Three BC3F3 lines, KUML4-2020-21, KUML4-2020-23, and KUML4-2020-60, exhibiting superior agronomic and yield-related traits, CLS resistance, and bruchid resistance than ‘KUML4’ were successfully obtained via MABC. Under the CLS outbreak, these lines showed 248.5%-331.7% higher seed yield than ‘KUML4’. The lines expressed nearly perfect resistance to bruchid (< 5% seeds damaged). These lines can be developed into new resistant mung bean cultivars in the future. [ABSTRACT FROM AUTHOR]

Zombi pea (Vigna vexillata) is a legume crop that is resistant to several biotic and abiotic stresses. Callosobruchus maculatus and Callosobruchus chinensis are serious stored-insect pests of legume crops. We constructed a high-density linkage map and performed quantitative trait loci (QTLs) mapping for resistance to these insect species in zombi pea. An F2 population of 198 individuals from a cross between 'TVNu 240' (resistant) and 'TVNu 1623' (susceptible) varieties was used to construct a linkage map of 6,529 single nucleotide polymorphism markers generated from sequencing amplified fragments of specific loci. The map comprised 11 linkage groups, spanning 1,740.9 cM, with an average of 593.5 markers per linkage group and an average distance of 0.27 cM between markers. High levels of micro-synteny between V. vexillata and cowpea (Vigna unguiculata), mungbean (Vigna radiata), azuki bean (Vigna angularis) and common bean (Phaseolus vulgaris) were found. One major and three minor QTLs for C. chinensis resistance and one major and one minor QTLs for C. maculatus resistance were identified. The major QTLs for resistance to C. chinensis and C. maculatus appeared to be the same locus. The linkage map developed in this study will facilitate the identification of useful genes/QTLs in zombi pea. [ABSTRACT FROM AUTHOR]

Vigna vexillata (zombi pea) is an underutilized legume crop considered to be a potential gene source in breeding for abiotic stress tolerance. This study focuses on the molecular characterization of mechanisms controlling waterlogging tolerance using two zombi pea varieties with contrasting waterlogging tolerance. Morphological examination revealed that in contrast to the sensitive variety, the tolerant variety was able to grow, maintain chlorophyll, form lateral roots, and develop aerenchyma in hypocotyl and taproots under waterlogging. To find the mechanism controlling waterlogging tolerance in zombi pea, comparative transcriptome analysis was performed using roots subjected to short-term waterlogging. Functional analysis indicated that glycolysis and fermentative genes were strongly upregulated in the sensitive variety, but not in the tolerant one. In contrast, the genes involved in auxin-regulated lateral root initiation and formation were expressed only in the tolerant variety. In addition, cell wall modification, aquaporin, and peroxidase genes were highly induced in the tolerant variety under waterlogging. Our findings suggest that energy management and root plasticity play important roles in mitigating the impact of waterlogging in zombi pea. The basic knowledge obtained from this study can be used in the molecular breeding of waterlogging-tolerant legume crops in the future. [ABSTRACT FROM AUTHOR]

Soil salinity is a major abiotic stress in agricultural production, as it hampers the growth and development of crop plants. Developing crop cultivars with salinity/salt tolerance is a major goal in many plant breeding programs. This study aimed to identify quantitative trait locus (QTL) that controls salt tolerance in the wild zombi pea (Vigna vexillata) accession "AusTRCF 322105." For QTL analysis, a BC1F2 population resulting from the cross between salt-susceptible TVNu240 and TVNu240 × AusTRCF 322105 was used. A genetic linkage map was constructed for the BC1F2 population, consisting of 15 linkage groups and using 296 SNP markers. The map spanned 2889.9 cM in total length. Plant leaf wilt and plant survival were evaluated by subjecting the BC1F2 population to a hydroponic condition with 250 mM NaCl to assess salt tolerance at the seedling stage. QTL analysis revealed that two QTLs, qSaltol_3.1 and qSaltol_7.1, control both leaf wilt and plant survival. These two QTLs explained 23–27% and 11–15% of the trait variation. Exploration of the physical genome region revealed that qSaltol_3.1 is located near genes encoding methionine sulfoxide reductase and protein L-isoaspartate O-methyltransferase that are involved in oxidative stress resistance. In contrast, qSaltol_7.1 is located near genes encoding 3-ketoacyl-CoA synthase, L-type lectin domain containing receptor kinase VII.1, lipoxygenase 3, CBS domain-containing protein 5, NAC25 protein, and asparagine synthetase (ASNS) that have been found to be associated with salt tolerance. Nonetheless, qSaltol_3.1 and qSaltol_7.1 are novel QTLs identified for salt tolerance in the zombi pea. [ABSTRACT FROM AUTHOR]

Key message: The major QTL Sdp1.1+ controlling seed dormancy in cowpea was finely mapped, and two CCoAOMT1 genes were identified as candidate genes for the dormancy. Seed dormancy in wild cowpea may be useful in breeding cultivated cowpea with pre-harvest sprouting resistance. A previous study identified a major quantitative trait locus (QTL) for seed dormancy, Sdp1.1+ , using the population of the cross between cultivated cowpea 'JP81610' and wild cowpea 'JP89083.' However, the molecular basis of seed dormancy in cowpea is not yet known. In this study, we aimed to finely map the locus Sdp1.1+ and identify candidate gene(s) for it. Germination tests demonstrated that the seed coat is the major factor controlling seed dormancy in the wild cowpea JP89083. Microscopic observations revealed that wild cowpea seeds, unlike cultivated cowpea seeds, possessed a palisade cuticle layer. Fine mapping using a large F2 population of the cross JP81610 × JP89083 grown in Thailand revealed a single QTL, Sdp1.1+ , controlling seed dormancy. The Sdp1.1+ was confirmed using a small F2 population of the same cross grown in Japan. The Sdp1.1+ was mapped to a 37.34-Kb region containing three genes. Two closely linked genes, Vigun03g278900 (VuCCoAOMT1a) and Vigun03g290000 (VuCCoAOMT1b), located 4.844 Kb apart were considered as candidate genes for seed dormancy. The two genes encoded caffeoyl coenzyme A O-methyltransferase 1 (CCoAOMT1). DNA sequencing and alignment of VuCCoAOMT1a and VuCCoAOMT1b between JP89083 and JP81610 revealed a single nucleotide polymorphism (SNP) causing an amino acid change in VuCCoAOMT1a and several SNPs leading to six amino acid changes in VuCCoAOMT1b. Altogether, these results indicate that VuCCoAOMT1a and VuCCoAOMT1b are candidate genes controlling physical seed dormancy in the wild cowpea JP89083. [ABSTRACT FROM AUTHOR]

Aroma is an important trait that can enhance the product value in several crops. Pandan-like fragrance resulting from accumulation of 2-acetyl-1-pyrroline (2AP) is one of the pleasant aromas in food crops which is caused by null or missense mutations in betaine aldehyde dehydrogenase 2 (BADH2) gene. In addition, betaine aldehyde aehydrogenase 1 (BADH1) has shown to be associated with aroma in rice. In this study, we investigated the genetics controlling coconut juice-like fragrance in inflorescence of sorghum cultivar ‘Ambemohor’. 2AP analysis in seeds revealed that Ambemohor possessed no 2AP. An F2 population developed from the cross between Ambemohor 9 KU630 (nonfragrant) segregated into a ratio of 3 (fragrant) : 1 (nonfragrant), suggesting that the coconut juice-like fragrance in Ambemohor is controlled by a single dominant gene, designated ‘Aro’. Bulked segregant analysis suggested that the gene controlling fragrance in Ambemohor is located on sorghum chromosome 6. Quantitative trait locus (QTL) analysis identified a major QTL, qAro6.1, for the fragrance located on chromosome 6 between markers SB3567 and SB3570. Bioinformatics analysis revealed that SB3567 and SB3570 were 217.8 kb apart and there were 29 annotated genes in this region including BADH1. Sequence analysis revealed that BADH1 sequences in Ambemohor and KU630 differed in size, but their coding sequences (CDS) were of same size. CDS alignment revealed four single-nucleotide polymorphisms (SNPs) between Ambemohor and KU630 in which two SNPs caused amino change in BADH1 of Ambemohor. These results suggested that BADH1 is a candidate gene for the coconut juice-like fragrance in Ambemohor. [ABSTRACT FROM AUTHOR]