Unraveling the Genetic Architecture of Peanut pod-related traits via Genome-Wide Association Study

Abstract Peanut (Arachis hypogaea L.) is a significant oilseed and food crop worldwide. Key factors affecting yield and quality include seed weight, hull weight, pod volume, and the ratio of seed weight to hull weight. This research aimed to elucidate the genetic underpinnings of peanut seed weight, hull weight, pod volume, and the ratio of seed weight to hull weight through genome-wide association studies (GWAS). A diverse population of 104 peanut varieties was utilized, and a high-density SNP dataset was generated through haplotype screening and genotype correction. A total of 40 single nucleotide polymorphisms (SNPs) significantly associated with peanut pod-related traits were identified through GWAS analysis, with 12 SNPs linked to seed weight, 12 associated with hull weight, 10 to the ratio of seed weight/hull weight(SW/HW), and 6 to pod volume. Notably, the loci identified for seed weight and hull weight were entirely identical. In 2013, three SNPs(AX-176804770, AX-147254843, and AX-177639117) were co-localized for the three traits: the seed weight, hull weight, and SW/HW. In 2015, only one SNP (AX-176810349) was co-localized for these traits. Based on these sites, 264 candidate genes were selected, with 84, 84, 76, and 20 genes related to seed weight, hull weight, SW/HW, and pod volume, respectively, and all of the genes are associated with plant growth. My research focuses on four key traits: seed weight, hull weight, pod volume, and the ratio of seed weight to hull weight. This study not only provides valuable insights into the genetic basis of these four traits but also serves as a resource of candidate genes aimed at enhancing peanut quality and facilitating genetic breeding efforts.