QTL analysis of seed weight and seed dormancy in black gram (Vigna mungo [L.] Hepper)

Abstract

Importance of the work: Black gram is a scientifically important orphan crop with little research published on the molecular breeding of this legume. Seed weight is a key trait contributing to seed yield. Seed dormancy can be exploited to reduce pre-harvest sprouting. Objectives: To identify the quantitative trait loci (QTLs) controlling black gram seed weight and seed dormancy. Materials & Methods: Two F 2 populations developed from a cross between cultivated (Chai Nat 80 [CN80]) and wild black gram (PI213017 or TVNu1076) were grown under field conditions. The F 2 populations were determined for seed weight and seed dormancy. Single nucleotide polymorphism-based linkage maps previously constructed for the two population were used for QTL analysis. Candidate genes were identified using the reference genome sequence of CN80. Results: The broad-sense heritability (H 2 ) calculated for seed weight was 65.23-73.71%, while that for seed dormancy was 81.53-99.80%. In total, 10 QTLs on 7 linkage groups (LGs) were detected for seed weight and three QTLs on two LGs were detected for seed dormancy. Depending on the population, QTLs explained between 5.07% (qSd100wt7.1+) and 34.20% (qSd100wt10.2+) of the seed weight variation, and between 10.18% (qSdwa6.1-) and 43.81% (qSdwa6.2-) of the seed dormancy variation. Candidate genes of various functions were identified for these two traits. Main finding: Novel QTLs and candidate genes controlling seed weight and seed dormancy were identified for black gram. One of the candidate genes, WVD2-LIKE 4 for seed weight, appeared to be an ortholog with a candidate gene for the same trait in mungbean.

Genetics, genomics, and breeding of black gram [Vigna mungo (L.) Hepper]

“…The QTL for the MOG phenotype was also reported to contribute approximately 30% PVE for seed weight ( Somta et al., 2020 ). In another study, QTLs for seed weight were identified using two F 2 populations derived from crossing between cultivated and wild black grams in which 10 QTLs on seven linkage groups (LGs) were detected in total for the seed weight ( Lomlek et al., 2023 ). The QTLs explained between 5.07% ( qSd100wt7.1+ ) and 34.20% ( qSd100wt10.2+ ) of the weight variation, depending on the population.…”

“…The QTLs explained between 5.07% ( qSd100wt7.1+ ) and 34.20% ( qSd100wt10.2+ ) of the weight variation, depending on the population. Genes encoding for pentatricopeptide repeat (RPP)-containing protein, WRKY46 , glutathione S -transferase U9, NAC domain-containing protein 100, calcineurin B-like protein (CBL)-interacting protein kinase, cyclin-D6-1, kinesin, histidine phosphotransfer protein, AUXIN RESPONSE FACTOR 2A, and WAVE-DAMPENED2 (WVD2)-like 4 protein are candidate genes for seed weight QTLs ( Lomlek et al., 2023 ). Two minor QTLs for pod dehiscence, qPdt3.1− and qPdt5.1− , on LGs 3 and 5, respectively, with ≤10% PVE and a single QTL with large effect controlling approximately 20% PVE for seed dormancy were also reported in black gram ( Somta et al., 2020 ).…”

“…In addition, using the same populations and linkage maps as that reported by Suamuang et al (2023), 10 QTLs were detected for seed weight, and three were detected for seed dormancy. Depending on populations, QTLs explained between 5.07% (qSd100wt7.1+) to 34.20% (qSd100wt10.2+) of the seed weight variation and 10.18% (qSdwa6.1−) to 43.81% (qSd100wt6.2 −) of the seed dormancy variation (Lomlek et al, 2023). Several candidate genes were identified including WVD2-LIKE 4 for seed weight that appeared to be an ortholog with a candidate gene for the seed weight in mungbean.…”