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.

Keywords: abiotic stress; citrate and malate transporters; hydroponic culture; root traits; single nucleotide polymorphism markers.

FIGURE 1

Identification of common bean genotypes from the Andean diversity panel (ADP) with low percent reduction of total root length and Low percent increase in average root diameter (ARD).

FIGURE 2

Principal component analysis for common bean genotypes from the Andean diversity panel (ADP) based on the single nucleotide polymorphism (SNP) dataset pruned for the criteria of non-linkage disequilibrium (LD).

FIGURE 3

Manhattan and QQ plots of genome wide association study (GWAS) results of Average root diameter (A), Number of root forks (B), number of root links (C), Root surface area (D), Root volume (E), and Total root length (F), where single nucleotide polymorphism (SNP) loci are ordered by physical position and grouped by chromosome. The black dash line indicates the genome wide significance threshold. The SNP loci highlighted in red were significant with a given trait at p-values lower than the Bonferroni corrected significance cut-off value for number of independent tests which was p = 1 × 10^{– 5}.