Genome Wide Association Mapping of Root Traits in the Andean Genepool of Common Bean (Phaseolus vulgaris L.) Grown With and Without Aluminum Toxicity

Abstract

Common bean is one of the most important grain legumes for human diets but is produced on marginal lands with unfavorable soil conditions; among which Aluminum (Al) toxicity is a serious and widespread problem. Under low pH, stable forms of Al dissolve into the soil solution and as phytotoxic ions inhibit the growth and function of roots through injury to the root apex. This results in a smaller root system that detrimentally effects yield. The goal of this study was to evaluate 227 genotypes from an Andean diversity panel (ADP) of common bean and determine the level of Al toxicity tolerance and candidate genes for this abiotic stress tolerance through root trait analysis and marker association studies. Plants were grown as seedlings in hydroponic tanks at a pH of 4.5 with a treatment of high Al concentration (50 μM) compared to a control (0 μM). The roots were harvested and scanned to determine average root diameter, root volume, root surface area, number of root links, number of root tips, and total root length. Percent reduction or increase was calculated for each trait by comparing treatments. Genome wide association study (GWAS) was conducted by testing phenotypic data against single nucleotide polymorphism (SNP) marker genotyping data for the panel. Principal components and a kinship matrix were included in the mixed linear model to correct for population structure. Analyses of variance indicated the presence of significant difference between genotypes. The heritability of traits ranged from 0.67 to 0.92 in Al-treated and reached similar values in non-treated plants. GWAS revealed significant associations between root traits and genetic markers on chromosomes Pv01, Pv04, Pv05, Pv06, and Pv11 with some SNPs contributing to more than one trait. Candidate genes near these loci were analyzed to explain the detected association and included an Al activated malate transporter gene and a multidrug and toxic compound extrusion gene. This study showed that polygenic inheritance was critical to aluminum toxicity tolerance in common beans roots. Candidate genes found suggested that exudation of malate and citrate as organic acids would be important for Al tolerance. Possible cross-talk between mechanisms of aluminum tolerance and resistance to other abiotic stresses are discussed.

New Age of Common Bean

“…Genome-wide association studies (GWAS) have become a widely accepted strategy for studying traits of importance to agriculture, thanks to the introduction of NGS-based SNP markers to decipher genotype-phenotype associations in many species [48]. Recently, a number of GWAS studies on diseases [49][50][51][52], abiotic stress [53,54], agronomic traits [55][56][57], cooking time and culinary quality traits [58] and root traits [59,60] have been conducted on common beans. In addition, the GWAS results can serve as a basis for understanding the genetic architecture of the nutritional properties of bean seeds, with the aim of increasing the macro-and micronutrient content in the bean breeding program [61].…”

Natural variation of respiration-related traits in plants

“…The homolog of this gene was subsequently characterized in a GWAS study to be responsible for fruit malate content in tomato ( Tieman et al, 2017 ; Ye et al, 2017 ). Other studies on Al tolerance in lentil and common bean resulted in the identification of a major QTL for malate secretion and candidate gene including the Al-activated malate transporter and a multidrug and toxic compound extrusion gene in lentil and common bean, respectively ( Ambachew and Blair, 2021 ; Singh et al, 2021 ).…”

Genetic Augmentation of Legume Crops Using Genomic Resources and Genotyping Platforms for Nutritional Food Security

“…Different QTLs were also identified for various abiotic stress tolerant genes through the GWAS technique. The GWAS was for the identification of candidate genes for root traits associated with aluminium toxicity in common bean [ 69 ]. In the study, a significant association of SNPs was detected between the root traits of common bean and the toxic compound extrusion gene and aluminium, which activated the malate transporter gene for tolerance to aluminium toxicity.…”