Discovery of the genomic region and candidate gene for qELSB02.1, a novel and stable major QTL associated with peanut early leaf spot resistance

• Bulked segregant RNA-Seq identified a novel and stable major early leaf spot resistance QTL qELSB02 . 1 . • Linkage analysis and substitution mapping fine-mapped qELSB02 . 1 into a 465 Kb genomic region. • Gene and protein characterization confirm AhELSR1 as the most probable candidate gene. • Allelic variation analysis of AhELSR1 revealed four haplotypes using 244 global accessions. • A diagnostic marker was developed and validated via peanut germplasm and gene introgression. Early leaf spot (ELS) is one of peanut’s prominent and widespread foliar fungal diseases, causing severe yield losses and forage quality deterioration in South China. Discovery of the genomic region and the underlying candidate gene controlling ELS resistance will promote progress in resistance breeding and facilitate uncovering its genetic basis. In this study, a major genomic region, qELSB02 . 1 , was identified using a bulked segregant RNA-Seq (BSR-seq) approach in a RIL population derived from a cross between a susceptible cultivar ZH10 and a resistant line ICG12625. It was further confirmed via simple sequence repeat genetic map-based linkage analysis, explaining 20.13-35.27% of the phenotypic variation. Using a partial genetic map and a segregation mapping population, qELSB02 . 1 was fine-mapped into a 465 kb genomic region by linkage analysis and substitution mapping. Furthermore, an NB-ARC-LRR gene ( Arahy . V6I7WA ) was identified as the most probable candidate gene for qELSB02 . 1 and was named Arachis hypogaea ELS resistance 1 ( AhELSR1 ) based on functional annotation, sequence variation analysis, expression profiling, and protein structure prediction. Allelic variation analysis using 244 global peanut germplasm accessions identified four haplotypes, providing valuable clues for understanding ELS resistance evolution mediated by AhELSR1 . Five SNPs, located in the first exon of AhELSR1 , altering four encoding amino acids, were used to develop a diagnostic marker. The marker was further validated using diverse peanut germplasm and through introgression of AhELSR1 into a susceptible cultivar. Our results provide new insights into the genetic basis of ELS resistance regulation and benefit the breeding efforts for developing improved cultivars with enhanced ELS resistance.