Increasing the oil content is a key objective in peanut breeding programs.  Accurate identification of quantitative trait loci (QTLs) with linked markers for oil content can facilitate marker-assisted selection for high-oil breeding.  In this study, a high-density bin map was constructed by resequencing a recombinant inbred line (RIL) population (ZH16×J11) consisting of 295 lines.  The bin map contained 4,212 loci and had a total length of 1,162.3 cM.  Ten QTLs for oil content were identified in six linkage groups.  Notably, two of these QTLs, qOCB03.1 and qOCB06.1, were consistently detected in a minimum of three environments and explained up to 13.62% of the phenotypic variation.  They have not been reported in previous studies and thus are novel QTLs.  The combination of favorable alleles from qOCB03.1 and qOCB06 in the RIL population could increase oil content across multiple environments from 1.50 to 2.46%.  Two insertions/deletions (InDels) markers linked to qOCB03.1 and qOCB06.1 were developed, and their association with oil content was validated in another RIL population (ZH10×ICG12625) with diverse phenotypes.  In addition, the high-resolution map allowed for the precise positioning of qOCB03.1 and qOCB06.1 within a 1.77 Mb interval on chromosome B03 and a 1.51 Mb interval on chromosome B06, respectively.  The annotation of genomic variants, analysis of transcriptome sequencing, and evaluation of the allelic effects in 292 peanut varieties revealed two candidate genes associated with oil content for each of the two QTLs.  The candidate genes identified in this study can enable the map-based cloning of key genes controlling oil content in peanut.  Furthermore, these novel and stable QTLs and their tightly linked markers are valuable for marker-assisted breeding for greater oil content in peanut.

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.