Identification of novel QTLs for resistance to late leaf spot in peanut by SNP array and QTL-seq analyses

Late leaf spot disease (LLS) is one of the most important diseases that cause severe yield losses in peanut. Peanut has various sources of resistance to LLS, so the identification of resistant quantitative trait loci (QTLs) and the development of related molecular markers are of great importance for the breeding of LLS-resistant peanut. In this study, 173 individual lines of a recombinant inbred line (RIL) population and the 48K SNP array for genotyping were used to construct a high-density genetic map with 1,475 bin markers and 20 linkage groups. A total of 11 QTLs were obtained through QTL analysis using the constructed genetic map. Among them, the stable major QTL qLLS.LG02 was identified on linkage group 2 in all six environments, with the phenotypic variation explained (PVE) ranging from 15.57 to 31.09%. QTL-seq technology was also employed for a QTL analysis of LLS resistance. As a result, 14 QTL loci related to LLS resistance were identified using the G prime algorithm. Notably, the physical positions of qLLS02 and qLLS03 coincided with those of qLLS.LG02 and qLLS.LG03, respectively. Gene annotation analysis within the 14 QTL intervals from QTL-seq revealed a total of 163 nucleotide-binding site–leucine-rich repeat (NBS-LRR) disease resistance genes, accounting for 22.86% of all resistance (R) genes in the peanut genome and showing a 4.26-fold enrichment with a P-value of 5.19e–57. Within the QTL region qLLS02 of the resistant parent Mi-2, there was a 5 Mb structural variation (SV) interval containing 81 NBS-LRR genes. A PCR diagnostic marker was developed, and validation data suggested that this SV might lead to gene deletion or replacement with other genes. This SV has the potential to enhance peanut resistance to LLS. The results of this study have significant implications for improving peanut breeding for LLS resistance through the development of associated molecular markers.