Genome-Wide Association Study Identifies Novel Loci and Candidate Genes Regulating Seed Size-Related Traits in Peanut (Arachis hypogaea L.)

Seed size-related traits are pivotal determinants of yield and appearance quality in peanut breeding programs. This study aimed to (1) investigate the genetic diversity and population structure of 120 peanut accessions (including landraces, cultivated varieties, and introduced germplasm) through genome-wide resequencing, and (2) identify key genomic regions and candidate genes associated with seed size-related traits using Genome-wide association studies (GWAS) and haplotype analysis. The population relationship and the evolution of peanuts using a large-scale single nucleotide polymorphism (SNP) dataset generated from the genome-wide resequencing of 120 peanut accessions was explored. GWAS and haplotype analysis were employed to identify regions and candidate genes associated with seed size-related traits. GWAS and haplotype analysis identified a novel region associated with HSW and SW on chr14, and a haplotype that was more dominant in HSW and SW. Two candidate genes were screened by combining LD decay distance, SNP variation information and gene function annotations.