Genome-wide marker-trait association analysis in a core set of Dolichos bean germplasm

Abstract

Association mapping (AM), an alternative method of quantitative trait loci (QTL) discovery, exploits historic linkage disequilibrium (LD) present in natural populations. AM is effective in self-pollinated crops such as Dolichos bean as LD extends over longer genomic distance driven-by low rate of recombination and thereby requiring fewer markers for exploring marker-traits associations. A core set of Dolichos bean germplasm consisting of 64 accessions was evaluated for nine quantitative traits (QTs) during 2014 and 2015 rainy seasons and genotyped using 234 simple sequence repeats (SSR) markers. Substantial diversity was observed among the core set accessions at loci controlling QTs and 95 of the 234 SSR markers were found polymorphic. The structure analysis and low magnitude of fixation indices suggested weak population structure, which in-turn indicated the low possibility of false discovery rates in the marker-QTs association. The marker allele's scores were regressed onto phenotypes at nine QTs following general linear model and mixed linear model for exploring marker-QTs associations. Significantly higher number of SSR markers was found associated with genomic regions controlling nine QTs. A few of the markers such as KT Dolichos (KTD) 200 for days to 50% flowering, KTD 273 for fresh pod yield per plant and KTD 130 for fresh pods per plant explained ≥10% of the trait variations. The study could also identify a few SSR markers such as KTD 273, KTD 271 and KTD 130 linked to multiple traits. These linked SSR markers are suggested for validation for their use in marker-assisted Dolichos bean improvement programmes.

Developments and Prospects in Imperative Underexploited Vegetable Legumes Breeding: A Review

“…A set of 234 SSRs (mostly in-house designed) were used in association with mapping for identifying genetic control of days to 50% flowering, fresh pod number per plant, and fresh pod weight per plant. Three markers, namely, KTD 200, KTD 130, and KTD 273 were found to be associated with traits, respectively explaining more than 10 percent of phenotypic variation in each case [ 83 ].…”

Recent developments in Lablab purpureus genomics: A focus on drought stress tolerance and use of genomic resources to develop stress‐resilient varieties

“…This phenomenon of gene regulation has been formerly studied through molecular markers. However, the development of marker technology has been slower in Lablab and some other legumes than in cereal crops to the point of recognizing them as “orphan crops” (Dhaliwal et al, 2020; Vaijayanthi et al, 2018). In their steps of advancement, the first group of markers, amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), and random amplification of polymorphic DNA (RAPD), was employed to understand the diversity and genetic characterization.…”

“…In their steps of advancement, the first group of markers, amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), and random amplification of polymorphic DNA (RAPD), was employed to understand the diversity and genetic characterization. The second group, namely, sequence‐based markers including single nucleotide polymorphism (SNPs), microsatellite or simple sequence repeats (SSRs), and expressed sequence tags (ESTs), was utilized in mapping studies (Dholakia et al, 2019; Kamotho et al, 2016; Keerthi et al, 2018; Kimani et al, 2012; Konduri et al, 2000; Rai et al, 2018a; Sserumaga et al, 2021; Vaijayanthi et al, 2018). Despite their applications in Lablab, there has been little utilization of these markers to improve drought tolerance.…”

“…It is also a common problem in other Lablab‐growing areas in Africa. Although in India HA3 and HA4 Lablab varieties have been developed to overcome this challenge of flower dropping (Ramesh & Byre Gowda, 2016), genomic improvement of our cultivars based on already available resources (Ramtekey et al, 2019) would create a permanent solution (Rai et al, 2018b; Vaijayanthi et al, 2018).…”