Genome-wide association studies for phenological and agronomic traits in mungbean (Vigna radiata L. Wilczek)

Abstract

Mungbean (Vigna radiata L. Wilczek) is one of the important warm-season food legumes, contributing substantially to nutritional security and environmental sustainability. The genetic complexity of yield-associated agronomic traits in mungbean is not well understood. To dissect the genetic basis of phenological and agronomic traits, we evaluated 153 diverse mungbean genotypes for two phenological (days to heading and days to maturity) and eight agronomic traits (leaf nitrogen status using SPAD, plant height, number of primary branches, pod length, number of pods per plant, seeds per pod, 100-seed weight, and yield per plant) under two environmental conditions. A wide array of phenotypic variability was apparent among the studied genotypes for all the studied traits. The broad sense of heritability of traits ranged from 0.31 to 0.95 and 0.21 to 0.94 at the Delhi and Ludhiana locations, respectively. A total of 55,634 genome-wide single nucleotide polymorphisms (SNPs) were obtained by the genotyping-by-sequencing method, of which 15,926 SNPs were retained for genome-wide association studies (GWAS). GWAS with Bayesian information and linkage-disequilibrium iteratively nested keyway (BLINK) model identified 50 SNPs significantly associated with phenological and agronomic traits. In total, 12 SNPs were found to be significantly associated with phenological traits across environments, explaining 7%-18.5% of phenotypic variability, and 38 SNPs were significantly associated with agronomic traits, explaining 4.7%-27.6% of the phenotypic variability. The maximum number of SNPs (15) were located on chromosome 1, followed by seven SNPs each on chromosomes 2 and 8. The BLAST search identified 19 putative candidate genes that were involved in light signaling, nitrogen responses, phosphorus (P) transport and remobilization, photosynthesis, respiration, metabolic pathways, and regulating growth and development. Digital expression analysis of 19 genes revealed significantly higher expression of 12 genes, viz. VRADI01G08170, VRADI11G09170, VRADI02G00450, VRADI01G00700, VRADI07G14240, VRADI03G06030, VRADI02G14230, VRADI08G01540, VRADI09G02590, VRADI08G00110, VRADI02G14240, and VRADI02G00430 in the roots, cotyledons, seeds, leaves, shoot apical meristems, and flowers. The identified SNPs and putative candidate genes provide valuable genetic information for fostering genomic studies and marker-assisted breeding programs that improve yield and agronomic traits in mungbean.

Keywords: GBS; GWAS; agronomic traits; candidate genes; mungbean; phenological traits.

Figure 1

Frequency distribution patterns of phenological [days to 50% flowering (DF50), days to 100% flowering (DF100), and days to maturity (DM)] and eight agronomic traits (nitrogen status using SPAD chlorophyll meter, plant height (PH), primary branch (PB), pod length (PL), pod number (PN), seeds per pod (SPP), 100-seed weight (100SW), and yield per plant (YPP)) exhibiting normal distribution.

Figure 2

LD decay was measured in an association panel of 126 mungbean genotypes. LD was estimated between 15,926 SNP markers over the 126 mungbean accessions, and the squared correlations of allele frequencies (r ²) of the mungbean population decreased to half of its maximum value at approximately 68 kb physical distance.

Figure 3

Population structure and kinship matrix similarity analysis of 126 mungbean genotypes. (A) Accession arrangement was based on the order of heat-map kinship similarity result. (B) Phylogenetic tree representing the genetic relations among 126 mungbean genotypes. (C) Population structure plot of the two subpopulations represented by K1 and K2 for subpopulations 1 and 2, respectively. (D) Delta K plot showing the best peak at K = 2.

Figure 4

Principal component analyses (PCA) using 15,926 high-quality GBS-based SNPs assigned to 126 mungbean genotypes in two populations (1 and 2).

Figure 5

Manhattan (left) and quantile–quantile (Q-Q) (right) plots of various phenological and agronomic traits for (A) Delhi and (B) Ludhiana.

Figure 6

Chromosomal location of the 50 significant marker-trait associations identified for phenological and agronomic traits in mungbean genotypes.