Whole genome-wide association study reveals genetic insights into leaf spot disease resistances and seed germination/dormancy in peanut.

Peanut (Arachis hypogaea L.) is an important crop in the world, serving as a key source of edible oil and protein. Comprehensive genomic and phenotypic analyses were conducted on 87 accessions from the U.S. peanut mini-core collection using 217 Gb of high-quality resequencing data to identify the candidate genes and markers that underlie the leaf spot resistance and seed dormancy in peanuts. A total of 87,726 SNPs were identified and mapped across 20 chromosomes, revealing a higher SNP density in the B subgenome (35.55 SNPs/Mb) compared to the A subgenome (33.26 SNPs/Mb). Phylogenetic, population structure, and principal component analyses consistently partitioned the accessions into three distinct gene pools designated as Group 1, 2, and 3. Group 1, comprising primarily Arachis hypogaea, included 28 genotypes; Group 2, mainly fastigiata types, comprised 18 accessions; while Group 3, displaying the highest diversity, contained mixed genotypes from the other groups. Linkage disequilibrium analysis indicated an LD decay distance of approximately 63.1 kb, confirming that the marker density was sufficient for GWAS. Significant SNP associations at a suggestive threshold of p< 1.14 × 10-1 were identified for leaf spot, seed germination and dormancy agronomic traits. As a result, three candidate genes were identified: Ah11g381400, homologous to Arabidopsis ATE1, was associated with early leaf spot resistance; Ah16g445600, a homolog of ERF34, was linked to late leaf spot resistance; and Ah19g214100, homologous to ICE1, emerged as a central regulator affecting both germination and dormancy. These findings provide actionable targets for marker-assisted selection to enhance disease resilience and seed quality in breeding programs.