Genome-Wide Association Studies Revealed the Genetic Loci and Candidate Genes of Pod-Related Traits in Peanut (Arachis hypogaea L.)

Cultivated peanut (Arachis hypogaea L.) is one of the most important oilseed crops worldwide. Pod-related traits, including pod length (PL), pod width (PW), ratio of PL to PW (PL/W) and 100-pod weight (100-PW), are crucial factors for pod yield and are key target traits for selection in peanut breeding. However, the studies on the natural variation and genetic mechanism of pod-related traits are not clear in peanut. In this study, we phenotyped 136 peanut accessions for four pod-related traits in two consecutive years and genotyped the population using a re-sequencing technique. Based on 884,737 high-quality single nucleotide polymorphisms (SNPs), genome-wide association studies (GWAS) were conducted for four pod-related traits using a fixed and random model uniform cyclic probability (FarmCPU) model. The results showed that a total of 36 SNPs were identified by GWAS, among which twenty-one, fourteen and one SNPs were significantly associated with PL, PL/W and 100-PW, respectively. The candidate regions where the four peak SNPs (10_76084075, 11_138356586, 16_64420451, and 18_126782541) were located were used for searching genes, and nineteen candidate genes for pod-related traits were preliminarily predicted based on functional annotations. In addition, we also compared the expression patterns of these nineteen candidate genes in different tissues of peanut, and we found that eight genes were specifically highly expressed in tender fruit, immature pericarp, or seed, so we considered these genes to be the potential candidate genes for pod-related traits. These results enriched the understanding of the genetic basis of pod-related traits and provided an important theoretical basis for subsequent gene cloning and marker-assisted selection (MAS) breeding in peanut.