Fine mapping of the major QTL qLLS.A02.1 and identification of a novel NBS-LRR gene cluster associated with late leaf spot resistance in peanut (Arachis hypogaea L.)

Late leaf spot (LLS) is a major foliar disease that significantly reduces yield and compromises the quality of peanut (Arachis hypogaea L.). To identify genes conferring LLS resistance, a recombinant inbred line (RIL) population of 257 lines from a cross between the susceptible cultivar Baisha 1016 and the resistant germplasm ICGV 86699 was analyzed using whole-genome resequencing. A high-density genetic map was constructed with 4908 bin markers, leading to the identification of 19 quantitative trait loci (QTL) for LLS resistance. A major QTL, qLLS.A02.1, was consistently detected on chromosome A02 across six environments, explaining up to 37.49% of the phenotypic variance. Fine mapping delimited the qLLS.A02.1 locus to a 319 kb region flanked by KASP markers S4 and S5, which contained a cluster of ten NBS-LRR genes. Validation in 266 accessions confirmed a significant association of these flanking markers with LLS resistance. Transcriptome analysis revealed that four NBS-LRR genes within the cluster were specifically upregulated in the resistant parent. This study provides valuable genetic resources and molecular markers for breeding LLS-resistant peanut varieties.