Population Structure and Genome‐Wide Association Analysis of Bruchid Resistance in Ethiopian Common Bean Genotypes

Abstract

The common bean (Phaseolus vulgaris L.) is among the most important grain legume crops in Africa. However, the common bean grain is heavily damaged by the Mexican bean weevil (Zabrotes subfasciatus Boheman). This study was conducted to determine the population structure and genome‐wide marker–trait associations of bruchid resistance in the common bean. The phenotypic diversity and population structure of 297 genotypes were analyzed, using the Illumina BARCBean6K_3 SNP BeadChip. The genotypes consisted of landraces, released varieties, breeding lines, and Mexican bean weevil resistant lines. A population structure analysis based on a Bayesian genotype clustering approach classified the 297 genotypes into two subpopulations, namely, Middle American and Andean. Similar population patterns were also observed using principal component analysis. The genome‐wide association study analysis identified 24 single‐nucleotide polymorphisms (SNPs) on nine chromosomes, with a significant (P < 0.05) association with the percentages of adult emergence and seed weight loss. The SNPs located on Pv4 and Pv7 were significantly (P < 0.001) associated with the two traits. Other significant SNPs were identified on other chromosomes of the common bean, but none of them was above the cutoff point (1.00 × 10−4). Therefore, further verification of the SNPs that have a significant marker–trait association at P < 0.05 will be vital, and accessions with these SNPs may be useful as parental materials.

Genome-Wide Association Study of Multi-Traits in Common Bean (Phaseolus Vulgaris L.)

“…The STRUCTURE software was set at burnin period length of 50,000 and after burn-in 50,000 Markov chain Monte Carlo (MMC) repetition were set ve times. For joint inference of population substructure, the kinship (K) set at the range of 1 to 10 with ve number of iterations runs for each (Kamfwa et al, 2015a;Tigist et al, 2019). The ideal number of sub-populations was determined using K method [57] implemented in the HARVESTER software [58].…”

“…Genome-wide association study (GWAS) has been used to determine genomic variants associated with traits of interest using recombinant inbreed line population or landraces population [15], [16]. Literatures have demonstrated that some genomic regions have been identi ed to be associated with traits, such as bruchid resistance [17], cooking time of andean diversity panel [18], agronomic traits [19], drought tolerance [20], anthracnose and angular leaf spot diseases [21] and symbiotic nitrogen xation [22] in common bean. However, there is a limited information on grain micronutrient contents of Fe and Zn as well as seed water imbibition during pre-soaking and cooking time.…”

Genome-wide Identification of Powdery Mildew Resistance in Common Bean

“…Various candidate genes or quantitative trait loci responsible for traits of interest have been identi ed using GWAS technology in different crops. For instance, in common bean several studies have reported identi cation of genomic regions and candidate genes associated with different traits for bruchid resistance [11], agronomic traits [12], drought tolerance [13], anthracnose and angular leaf spot diseases [14] and symbiotic nitrogen xation [15]. However, these studies have been conducted for different traits with different common bean cultivars in different geographical regions.…”

Genome-wide Identification of Powdery Mildew Resistance in Common Bean

“…Various candidate genes or quantitative trait loci responsible for traits of interest have been identi ed using GWAS technology in different crops. For instance, in common bean several studies have reported identi cation of genomic regions and candidate genes associated with different traits for bruchid resistance [21], agronomic traits [22], drought tolerance [23], anthracnose, angular leaf spot and Fusarium wilt diseases [24,25] and symbiotic nitrogen xation [26]. However, these studies have been conducted for different traits with different common bean cultivars in different geographical regions.…”