Key message
This paper reports fine mapping of
qCLS
for resistance to Cercospora leaf spot disease in mungbean and identified
LOC106765332
encoding TATA-binding-protein-associated factor 5 (TAF5) as ...the candidate gene for the resistance
Cercospora leaf spot (CLS) caused by the fungus
Cercospora canescens
is an important disease of mungbean. A QTL mapping using mungbean F
2
and BC
1
F
1
populations developed from the “V4718” (resistant) and “Kamphaeng Saen 1” (KPS1; susceptible) has identified a major QTL controlling CLS resistance (
qCLS
). In this study, we finely mapped the
qCLS
and identified candidate genes at this locus. A BC
8
F
2
KPS1 × (KPS1 × V4718) population developed in this study and the F
2
(KPS1 × V4718) population used in a previous study were genotyped with 16 newly developed SSR markers. QTL analysis in the BC
8
F
2
and F
2
populations consistently showed that the
qCLS
was mapped to a genomic region of ~ 13 Kb on chromosome 6, which contains only one annotated gene,
LOC106765332
(designated “
VrTAF5
”), encoding TATA-binding-protein-associated factor 5 (TAF5), a subunit of transcription initiation factor IID and Spt-Ada-Gcn5 acetyltransferase complexes. Sequence comparison of
VrTAF5
between KPS1 and V4718 revealed many single nucleotide polymorphisms (SNPs) and inserts/deletions (InDels) in which eight SNPs presented in eight different exons, and an SNP (G4,932C) residing in exon 8 causes amino acid change (S250T) in V4718. An InDel marker was developed to detect a 24-bp InDel polymorphism in
VrTAF5
between KPS1 and V4718. Analysis by RT-qPCR showed that expression levels of
VrTAF5
in KPS1 and V4718 were not statistically different. These results indicated that mutation in
VrTAF5
causing an amino acid change in the VrTAF5 protein is responsible for CLS resistance in V4718.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Mungbean is a socioeconomically important legume crop in Asia that is currently in high demand by consumers and industries both as dried beans and in plant-based protein foods. Marker-assisted and ...genomics-assisted breeding are promising approaches to efficiently and rapidly develop new cultivars with improved yield, quality, and resistance to biotic and abiotic stresses. Although mungbean was at the forefront of research at the dawn of the plant genomics era 30 years ago, the crop is a “slow runner” in genome research due to limited genomic resources, especially DNA markers. Significant progress in mungbean genome research was achieved only within the last 10 years, notably after the release of the VC1973A draft reference genome constructed using next-generation sequencing technology, which enabled fast and efficient DNA marker development, gene mapping, and identification of candidate genes for complex traits. Resistance to biotic stresses has dominated mungbean genome research to date; however, research is on the rise. In this study, we provide an overview of the past progress and current status of mungbean genomics research. We also discuss and evaluate some research results to provide a better understanding of mungbean genomics.
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.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Cercospora leaf spot (CLS) caused by
Cercospora canescens
is an important disease of cowpea (
Vigna unguiculata
). A previous study using an F
2
population CSR12906 (susceptible) × IT90K-59-120 ...(resistant) identified a major QTL
qCLS9.1
for resistance to CLS. In this study, we finely mapped and identified candidate genes of
qCLS9.1
using an F
3:4
population of 699 individuals derived from two F
2:3
individuals segregating at
qCLS9.1
from the original population. Fine mapping narrowed down the
qCLS9.1
for the resistance to a 60.6-Kb region on cowpea chromosome 10. There were two annotated genes in the 60.6-Kb region;
Vigun10g019300
coding for NAD-dependent malic enzyme 1 (NAD-ME1) and
Vigun10g019400
coding for dynamin-related protein 1C (DRP1C). DNA sequence analysis revealed 12 and 2 single nucleotide polymorphisms (SNPs) in the coding sequence (CDS) and the 5′ untranslated region and TATA boxes of
Vigun10g019300
and
Vigun10g019400
, respectively. Three SNPs caused amino acid changes in NAD-ME1 in CSR12906, N299S, S488N and S544N. Protein prediction analysis suggested that S488N of CSR12906 may have a deleterious effect on the function of NAD-ME1. Gene expression analysis demonstrated that IT90K-59-120 and CSR12906 challenged with
C. canescens
showed different expression in both
Vigun10g019300
and
Vigun10g019400
. Taken together, these results indicated that
Vigun10g019300
and
Vigun10g019400
are the candidate genes for CLS resistance in the cowpea IT90K-59-120. Two derived cleaved amplified polymorphic sequence markers were developed to detect the resistance alleles at
Vigun10g019300
and
Vigun10g019400
in IT90K-59-120.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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 F
2
population developed from the cross between Ambemohor × 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.
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DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Lablab (Lablab purpureus (L.) Sweet) is a legume crop widely cultivated in tropical and subtropical regions of Africa and Asia. In this study, we assessed genetic diversity and population structure ...of 299 individuals of subspecies purpureus and bengalensis of lablab from Thailand using 13 simple sequence repeat (SSR) markers. The SSR markers detected only 34 alleles in total with a mean of 2.6 alleles per locus. Overall gene diversity was 0.360. Gene diversity (HE) and allelic richness (AR) in different geographic regions was comparable. Similarly, both HE and AR between subspecies purpureus and bengalensis were similar. STRUCTURE and neighbor-joining (NJ) analyses revealed that the 299 individuals were clustered into two major groups. In contrast, principal coordinate analysis (PCoA) revealed admixture of the lablab germplasm. STRUCTURE, NJ and PCoA analyses also revealed that the subspecies purpureus and bengalensis are not genetically differentiated. Although the number of individuals from the west of Thailand was small and all of them were collected from the same province, they possessed comparable gene diversity with those from the other geographic regions. These results demonstrated that there is moderately low genetic diversity of lablab in Thailand and the west of the country possesses high diversity of lablab.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Root-knot nematodes (RKNs; Meloidogyne spp.) are becoming a serious problem in legume production. This study identified Vigna genotypes exhibiting resistance to M. incognita (RKN) and characterized ...the modes of the resistance to M. incognita. In total, 279 accessions from 21 Vigna species were screened for resistance based on a galling index (GI) and an egg mass index (EI). Seven accessions were highly resistant to RKN with GI≤25, namely JP74716 (V. mungo var. mungo; cultivated black gram), JP107881 (V. nepalensis), JP229392 (V. radiata var. sublobata; wild mungbean), AusTRCF118141 (V. unguiculata subsp. unguiculata; cultivated cowpea), AusTRCF306385 (V. unguiculata subsp. unguiculata), AusTRCF322090 (V. vexillata var. vexillata; wild zombi pea) and JP235929 (V. vexillata var. vexillata). JP229392 and AusTRCF322090 were the most resistant accessions having EI values of 18.74 and 1.88, respectively. Continuous culture of M. incognita on both JP229392 and AusTRCF322090 resulted in a weakness in pathogenic ability for this RKN. The resistance in JP229392 and AusTRCF322090 to RKN appeared to be antibiosis that was associated with reduced nematode penetration, retardation of nematode development and impeding giant cell formation. The Vigna germplasm resistance to RKN identified in this study could be utilized as gene sources for the development of RKN-resistant Vigna cultivars.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Winged bean Psophocarpus tetragonolobus (L.) DC. is a vegetable legume crop. The center of origin, diversity and domestication of this crop are not known. In this study, we assessed the genetic ...diversity and population structure of 457 accessions of winged bean collected from six geographical regions (North, Northeast, East, West, and central, and South) in Thailand using 14 simple sequence repeat (SSR) markers. In total, the SSR markers detected only 55 alleles with an average of 3.9 alleles per locus. Observed heterozygosity was relatively high (0.15) and overall gene diversity was moderate (0.487). Gene diversity, allelic richness and observed heterozygosity in the six regions were comparable, while the estimated out-crossing rate was relatively high (16.4%). STRUCTURE analysis grouped the 457 winged bean accessions into three sub-populations. Neighbor-joining (NJ) analysis grouped all the accessions into two major clusters. Genetic groups identified by both STRUCTURE analysis and NJ analysis were unrelated to geographical origins. Principal coordinate analysis revealed no clear clustering of the winged bean accessions. Although genetic groups were not unrelated to geographical origins, most of the winged bean accessions with long pods (30 cm or higher in length) or having purple seed coats or purple young pods were grouped together. This suggested that the winged beans with long pods or with purple seed or purple young pods may have a single origin. Altogether, these results demonstrated that the genetic diversity of winged bean in Thailand was moderate with high genetic admixture. We argue that the high genetic admixture of the winged bean in Thailand is due to seed migration and relatively high outcrossing rate.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The adzuki bean (Vigna angularis (Ohwi) Ohwi and Ohashi) is an important grain legume of Asia. It is cultivated mainly in China, Japan and Korea. Despite its importance, few genomic resources are ...available for molecular genetic research of adzuki bean. In this study, we developed EST-SSR markers for the adzuki bean through next-generation sequencing. More than 112 million high-quality cDNA sequence reads were obtained from adzuki bean using Illumina paired-end sequencing technology, and the sequences were de novo assembled into 65,950 unigenes. The average length of the unigenes was 1,213 bp. Among the unigenes, 14,547 sequences contained a unique simple sequence repeat (SSR) and 3,350 sequences contained more than one SSR. A total of 7,947 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats (99.0%) as the most abundant motif class, followed by AG/CT (68.4%), AAG/CTT (30.0%), AAAG/CTTT (26.2%), AAAAG/CTTTT (16.1%), and AACGGG/CCCGTT (6.0%). A total of 500 SSR markers were randomly selected for validation, of which 296 markers produced reproducible amplicons with 38 polymorphic markers among the 32 adzuki bean genotypes selected from diverse geographical locations across China. The large number of SSR-containing sequences and EST-SSR markers will be valuable for genetic analysis of the adzuki bean and related Vigna species.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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