Genome-wide association studies unravel genomic regions and candidate genes associated with Aspergillus flavus resistance in peanut kernels

Key message In the present study, we identified 10 significant single nucleotide polymorphisms (SNPs), 3 stable quantitative trait loci (QTLs) and 3 potential candidate genes associated with peanut kernel resistance to Aspergillus flavus stress. Abstract Peanut ( Arachis hypogaea L.) is highly susceptible to A. flavus infection, producing highly carcinogenic aflatoxins. Breeding resistant varieties is an effective and sustainable approach to address this issue, and identifying novel genetic sources and loci underlying resistance is crucial. In this study, 353 A. hypogaea accessions were evaluated for resistance to A. flavus infection and aflatoxin production across three environments, leading to the identification of 13 accessions with stable resistance to both infection and aflatoxin production. A genome-wide association study (GWAS) was performed by integrating phenotypic data from multiple environments with 935,231 SNP markers, resulting in the detection of 10 significant marker-trait associations (MTAs). Of these, one showed consistent association with infection resistance in at least two out of three environments, and two were associated with resistance to both aflatoxin B 1 (AFB 1 ) and aflatoxin B 2 (AFB 2 ) production. Based on linkage disequilibrium (LD) decay estimates (70 kb upstream and downstream of significant SNPs), three novel stable QTLs were identified on chromosomes A03 and A05, designated qII_A05 , qAF_A03 , and qAF_A05 , and 13 candidate genes were initially selected within these QTL regions. Haplotype analysis further validated 3 key candidate genes: Arahy.7046BI.1 (encoding a PH/START domain-containing protein), Arahy.TX2FLU.1 (encoding a receptor-like kinase), and Arahy.ASR4JM.1 (encoding a TIR-NBS-LRR class disease resistance protein). These genes exhibited significant haplotype-trait associations, with favorable haplotypes showing high frequencies (85.43%–94.12%) in the germplasm pool, facilitating their direct utilization in breeding. Overall, this study uncovers key genetic loci and candidate genes governing peanut resistance to A. flavus infection and aflatoxin production, provides elite resistant germplasm resources, and offers practical insights for marker-assisted selection. The findings lay a solid foundation for accelerating the development of A. flavus -resistant peanut varieties and provide valuable genetic information for peanut breeding programs.