Genome-wide association analysis identifies novel genetic loci and candidate genes associated with seed dormancy in cultivated peanut.

key messageTwo significant regions on chromosomes A03 and A04, along with the candidate gene Arahy.5SR8FF, were identified to be associated with seed dormancy in peanut through GWAS. Two KASP markers were developed and validated, demonstrating their potential for use in marker-assisted breeding. Seed dormancy is a crucial trait that can influence both peanut yield and quality. In this study, a genome-wide association analysis (GWAS) was conducted using 353 peanut accessions with diverse genetic backgrounds from various global regions. The germination index was evaluated across multiple years and environments to identify genomic loci regulating seed dormancy. Phenotypic evaluation revealed extensive variation in seed dormancy within these accessions. The broad-sense heritability was greater than 0.89, and both genotype and genotype-by-environment interactions showed significant effects. Numerous SNPs on chromosomes A02, A03, A04, A05, A07, A09, A11, and A19 were identified significantly associated with seed dormancy, with particularly consistent and stable associations on chromosomes A03 and A04. By integrating mutation type, expression level, allele mining, and gene function analysis, the gene Arahy.5SR8FF, encoding HECT-type E3 ubiquitin-protein ligases, was considered as the key candidate for regulating seed dormancy in peanut. Additionally, two significant SNPs on chromosomes A03 and A04 were validated and developed into KASP markers, providing valuable tools for marker-assisted breeding of peanut varieties with desired dormancy level.