High Density Genetic and Bin Mapping for Dissecting Disease Resistance Quantitative Trait Loci in Peanut

Mapping and identification of quantitative trait loci (QTLs) are important for efficient marker-assisted breeding and for analysis of the molecular mechanisms regulating traits. Diseases such as leaf spots and Tomato spotted wilt virus (TSWV) cause significant loses to peanut growers. Previously, two recombinant inbred line (RIL) populations derived from SunOleic 97R × NC94022 and Tifrunner × GT-C20, were developed and used for developing SSR-based genetic maps and identification of QTLs for oil content and disease resistance. However, these QTLs cover large segments of the physical map, limiting their utility in marker development and breeding. To generate a high density linkage map and fine map these QTLs, we performed whole genome re-sequencing (WGRS) for these RILs including parental genotypes. Tifrunner was sequenced to 60X coverage, and the other three parental genotypes were sequenced to 10-12X coverage. A total of ~3 Tb of data was generated by sequencing 261 RILs (143 S-lines and 118 T-lines) at 2-5X coverage. The mapping of parental and population sequencing data achieved alignment of 74-77% of the total reads to the ancestor diploid reference genomes of cultivated peanut. Genome-wide variations, including SNP, InDel and other types of variation, could be detected. Alignment and SNP identification is underway after which a high density genetic map will be constructed, and recombination breakpoints identified for use in QTL analyses. This combination of bin mapping-based QTL and gene enrichment analyses will assist in identifying candidate genes for disease resistance and other important agronomic traits.