Genome-wide association study identifies loci, beneficial alleles, and candidate genes for cadmium tolerance in castor (Ricinus communis L.)

Cadmium (Cd) is a phytotoxic element that may impede oilseed production. Breeding of Cd-tolerant cultivars is an imperative that can subsequently be used for phytoremediation of Cd-contaminated soils. Hence, to identify marker-trait associations and mine for candidate genes that confer Cd tolerance in castor, genome-wide association study (GWAS) for seven Cdtolerance-related traits was performed using a naturalized population of 175 castor accessions genotyped by 143 polymorphic simple sequence repeat markers. The results showed that there was a wide variation of Cd among the seven traits in the 175 castor accessions. A total of 27 significant (-log(10)P> 1.5) marker loci were detected to be associated with all the seven traits for Cd tolerance, and the phenotypic variance explained by these loci varied from 5.63 similar to 20.47 %. Mining of beneficial alleles revealed 29 and 181 alleles that contributed prominently to Cd tolerance and sensitivity, respectively, which would be useful for breeding Cd-tolerant cultivars. Eight novel putative candidate genes involved in stress responses and developmental processes were detected within the major loci. Gene expression analyses using the quantitative real-time polymerase chain reaction method on six selected candidate genes showed that all the genes were highly expressed in the tolerant and sensitive accessions under Cd stress, signifying their potential role in enhancing stress tolerance or responses. This study represented the first attempt to GWAS mapping and identification of novel genes in castor under Cd stress. Our results may facilitate the study of the molecular and genetic basis of Cd tolerance and the cloning of candidate Cd-tolerance genes and cultivars, which could be useful for remediation of Cd-contaminated environments.