Genome-Wide Dissection of Early and Late Leaf Spot Resistance in Advanced Peanut Backcross Lines Carrying Introgressions from Arachis stenosperma and Arachis batizocoi

Early and late leaf spot (ELS and LLS), caused by Passalora arachidicola and Nothopassalora personata, are major constraints to peanut (Arachis hypogaea L.) production. Durable resistance in cultivated germplasm remains limited due to the crop’s narrow genetic base. Wild Arachis species represent an important but underutilized source of resistance. This study aimed to identify and prioritize wild introgressions associated with foliar disease resistance in advanced peanut backcross lines derived from the induced allotetraploid BatSten1 (Arachis batizocoi × A. stenosperma)4x. A population of advanced backcross lines carrying reduced wild genome content (~5% to ~1% across advancement) was evaluated through four years of field trials for LLS severity and yield, complemented by detached-leaf bioassays to dissect resistance components for both ELS and LLS. Genome-wide SNP genotyping, combined with mixed-model analysis and association mapping, identified introgressed regions influencing disease response. Genome-wide association studies (GWAS) detected loci on chromosomes A06 and A09 associated with LLS resistance, explaining approximately 25% and 11% of phenotypic variation, respectively, with evidence of additive effects between loci. Component-level analyses further revealed both resistance- and susceptibility-associated introgressions. Although tomato spotted wilt virus (TSWV) incidence was evaluated in field trials, exploratory GWAS did not detect significant marker–trait associations, indicating that genetic components associated with this trait were not resolved under the conditions tested. Overall, these results expand the understanding of the genetic architecture of leaf spot resistance beyond traditional donor sources and provide a framework for prioritizing beneficial wild introgressions while minimizing linkage drag in peanut pre-breeding programs.