Genome-wide Association Study for Yield and Yield-Related Traits in Diverse Blackgram Panel (Vigna mungo L. Hepper) Reveals Novel Putative Alleles for Future Breeding Programs

Abstract

Blackgram (Vigna mungo L. Hepper) is an important tropical and sub-tropical short-duration legume that is rich in dietary protein and micronutrients. Producing high-yielding blackgram varieties is hampered by insufficient genetic variability, absence of suitable ideotypes, low harvest index and susceptibility to biotic-abiotic stresses. Seed yield, a complex trait resulting from the expression and interaction of multiple genes, necessitates the evaluation of diverse germplasm for the identification of novel yield contributing traits. Henceforth, a panel of 100 blackgram genotypes was evaluated at two locations (Ludhiana and Gurdaspur) across two seasons (Spring 2019 and Spring 2020) for 14 different yield related traits. A wide range of variability, high broad-sense heritability and a high correlation of grain yield were observed for 12 out of 14 traits studied among all environments. Investigation of population structure in the panel using a set of 4,623 filtered SNPs led to identification of four sub-populations based on ad-hoc delta K and Cross entropy value. Using Farm CPU model and Mixed Linear Model algorithms, a total of 49 significant SNP associations representing 42 QTLs were identified. Allelic effects were found to be statistically significant at 37 out of 42 QTLs and 50 known candidate genes were identified in 24 of QTLs.

Identification of quantitative trait loci controlling flowering time in black gram (Vigna mungo [L.] Hepper)

“…The current study compared the locations of the QTLs for the flowering time detected in the current study with the candidate gene LOC106774489 at the Q.DtF.10 and found that the QTLs were located on the CN80 reference chromosomes 2, 4, 5, 6, 8 and 9, while LOC106774489 was on the CN80 reference chromosome 7. Thus, none of the QTLs detected in the current study matched the Q.DtF.10 identified by Singh et al (2022). However, notably, none of the flowering QTLs were common in the F2BGA and F2BGB populations, albeit the two populations shared the same cultivated parent, CN80.…”

“…These clearly indicated that days to flowering in black gram is a polygenic trait. The difference in the number of the QTLs for flowering detected in the current study and that in Singh et al (2022) may be due principally to: 1) differences in the methods of QTL mapping (genome-wide association versus linkage-based QTL analysis); and 2) differences in flowering time traits (days to 50% flowering and days to first flowering). The current study compared the locations of the QTLs for the flowering time detected in the current study with the candidate gene LOC106774489 at the Q.DtF.10 and found that the QTLs were located on the CN80 reference chromosomes 2, 4, 5, 6, 8 and 9, while LOC106774489 was on the CN80 reference chromosome 7.…”

“…Another QTL study of flowering time in black gram (conducted based on genome-wide association using 100 accessions grown in two locations for two seasons) in India identified an unstable QTL, Q.DtF.10, for days to 50% flowering (Singh et al, 2022). By using mungbean as the reference genome, the authors of that study postulated LOC106774489 encoding the PHD finger-like domain-containing enzyme 5B as the only candidate gene for the Q.DtF.10.…”

“…More than 7 million ha of black gram are cultivated, with India having the largest area (about 5.6 million ha) and being the largest consumer, with Myanmar having the second largest area (about 1 million ha) and being the biggest exporter (Khine et al, 2021). The seed yield of black gram in major production countries is low (only about 990 kg/ha) due to several production constrains, such as drought, insect infestation, disease infection and photo-and thermo-sensitivity (Sahu et al, 2020;Singh et al, 2022). Therefore, genetic improvement of these traits is necessary to improve the seed yield of black gram.…”

“…Up to the present, there has been only one published report on the QTLs controlling flowering time in black gram. Singh et al (2022) identified one QTL, QDtF.10, for days to 50% flowering in black gram using a small set of 100 accessions grown in two locations across two seasons in India. QDtF.10 accounted for 17-18% of the flowering time variation.…”