Biology subjects

Somta, P.

Publications and source records attributed to Somta, P..

4 recordsLinked to original sources

bioRxiv2025

A wild genome of the underutilized legume lablab (Lablab purpureus) reveals the genetic basis of domestication

BackgroundWith global food security threatened by climate change and the growing global population, underutilized crops offer sustainable solutions for diversifying current agricultural systems. Lablab (Lablab purpureus) is a highly versatile, climate-resilient underutilized legume native to Africa and widely, but locally, cultivated in Asia with untapped potential for sustainable agriculture. However, the lack of wild genome resource prevents a comprehensive genome utilization research for this underutilized crop. This paper presents the first chromosome-scale genome of wild lablab with its complete gene annotation and provides comprehensive population genomic analyses of its evolution and domestication by resequencing a panel of wild and domesticated accessions. ResultsThe genome was assembled into a total size of 478.2 Mb with a scaffold N50 of 39.7 Mb, and 96.4% (460.8 Mb) of the scaffolds anchored to 11 pseudochromosomes, the haploid chromosome number of lablab. We demonstrated that domestication was likely in Africa with several subsequent instances of transportation into Asia. Our analyses identified selective sweeps resulting from domestication as well as pseudogenes associated with yield-related traits and stress tolerance, representing candidate genes for further validation and targets for future breeding programs. ConclusionsOur genomic resource for wild lablab delineated its domestication history and identified key genes and pseudogenes under selection, bridging the gap between its untapped wild diversity and breeding for improved stress resilience and yield in underutilized legumes. This offers genomic and genetic insights for crop improvement of lablab.

evolutionary biology↗

bioRxiv2024

Diurnal regulation of SOS Pathway and Sodium Excretion Underlying Salinity Tolerance of Vigna marina

Vigna marina (Barm.) Merr. is adapted to tropical marine beaches and has an outstanding tolerance to salt stress. Given there are growing demands for cultivating crops in saline soil or with saline water, it is important to understand how halophytic species are adapted to the saline environments. Here we revealed by positron emitting tracer imaging system (PETIS) that V. marina actively excretes sodium from the root during the light period but not in the dark period. The following whole genome sequencing accompanied with forward genetic study identified a QTL region harboring SOS1, encoding plasma membrane Na+/H+ antiporter, which was associated with not only salt tolerance but also ability of sodium excretion. We also found the QTL region contained a large structural rearrangement that suppressed recombination across [~]20 Mbp, fixing multiple gene loci potentially involved in salt tolerance. RNA-seq and promoter analyses revealed SOS1 in V. marina was highly expressed even without salt stress and its promoter shared common cis-regulatory motifs with those exhibiting similar expression profile. Interestingly, the cis-regulatory motifs seemed installed by a transposable element (TE) insertion. Though not identified by genetic analysis, the transcriptome data also revealed SOS2 transcription was under diurnal regulation, explaining the pattern of sodium excretion together with up-regulated expression of SOS1. Furthermore, we demonstrated that, under a condition of mild salt stress, the plants with the diurnally regulated SOS pathway outperformed those with the constitutively activated one.

plant biology↗

bioRxiv2019

Genetic factor for twisting legume pods identified by fine-mapping of shattering-related traits in azuki bean and yard-long bean

Legumes have evolved a unique manner of seed dispersal in that the seed pods explosively split open with helical tension generated by sclerenchyma on the endocarp. During domestication, azuki bean (Vigna angularis) and yard-long bean (Vigna unguiculata cv-gr. Sesquipedalis) have reduced or lost the sclerenchyma and lost the shattering behavior of seed pods. Here we performed fine-mapping with back-crossed populations and narrowed the candidate genomic region down to 4 kbp in azuki bean and 13 kbp in yard-long bean. Among genes located in these regions, we found MYB26 genes encoded truncated proteins in both the domesticated species. We also found in azuki bean and other legumes that MYB26 is duplicated and only the duplicated copy is expressed in seed pods. Interestingly, in Arabidopsis MYB26 is single copy and is specifically expressed in anther to initiate secondary wall thickening that is required for anther dehiscence. These facts indicated that, in legumes, MYB26 has been duplicated and acquired a new role in development of pod sclerenchyma. However, pod shattering is unfavorable phenotype for harvesting and thus has been selected against by human.

genetics↗

bioRxiv2018

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 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 a previous linkage map of V. vexillata and linkage maps of other four Vigna species demonstrated several macro translocations 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. Tuber traits were controlled by five QTLs with similar effect locating on different linkage groups. 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.

genomics↗