Revealing the Key Genetic Basis of Late Leaf Spot Resistance in Peanut by Combining QTL Mapping, QTL-seq and RNA-seq

Late leaf spot (LLS) is the most widespread and destructive fungal disease affecting peanut worldwide, yet relatively little is known about its genetic basis. In this study, QTL mapping using a 1327-bin map (derived from 9533 SNP/InDel markers) and multi-environment phenotypic data repeatedly detected two major LLS-resistance QTLs on chromosomes A02 and B06 in the Zhonghua 5 × ICGV 86699 recombinant inbred line (RIL) population. QTL-seq analysis confirmed qLLSA02, and integration of both mapping methods narrowed the A02 interval to a 1.0-3.4 Mb region. Transcriptome profiling identified thousands of differentially expressed genes. Through systematic investigation of variants, functional annotation, expression patterns, allelic effects and comparative genomics within this target region, we identified 10 LLS resistance candidate genes and further prioritised two of these as the most promising candidates. Two kompetitive allele-specific PCR (KASP) markers were developed from SNPs of the two priority candidate genes, showing a strong correlation between genotype and LLS phenotype. Pathway analysis revealed that flavonoid biosynthesis, plant hormone signal transduction, and plant-pathogen interaction pathways are involved in the response to LLS infection. This study provided insights into the genetic and molecular mechanisms underlying LLS resistance in peanut, and the two developed KASP markers can facilitate LLS resistance peanut breeding.