A Journey from a SSR-based Low Density Map to a SNP-based High Density Map for Identification of Disease Resistance Quantitative Trait Loci in Peanut

摘要

Mapping and identification of quantitative trait loci (QTLs) are important for efficient markerassisted breeding. Diseases such as leaf spots and Tomato spotted wilt virus (TSWV) cause significant loses to peanut growers. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 through coordination of international efforts in genome research beginning with molecular marker development, improvement of map resolution and coverage, and the release of two diploid wild peanut species' genomes in 2014. At the same time, we initiated two recombinant inbred line (RIL) populations, derived from Tifrunner × GT-C20 (T) and SunOleic 97R × NC94022 (S), in 2005, and used them for construction of genetic maps and identification of QTLs for oil content and disease resistance using SSR markers in the early years since 2009. However, these QTL regions cover large segments of the physical map. To generate a high density genetic map and to fine map the SSR-based QTLs, we performed whole genome re-sequencing (WGRS) for these RILs and parental lines. Tifrunner was sequenced to 60X coverage, and the other three parents were sequenced to 10-30X coverage. A total of 261 RILs (118 T-lines and 143 S-lines) were resequenced to 2-5X coverage. For the "T" population, a total of 18,000 SNPs were called initially using a newly developed SNP-calling pipeline and 10,500 high quality SNPs were used for construction of a high density genetic map resulting in 9957 SNPs and 3038 cM in length. This genetic map has been improved from 239 SSR markers to 418 SSR markers to 9957 SNPs. This map has also been used for analysis of QTL which have been improved, such as, from QTL_qTSWV1 with 12.9% phenotypic variation explained (PVE) to qTSWV_T10_A04_1 with 14.4% PVE with SSR-based maps to qTSWV_A03_110 with 21.6% PVE using the SNP-based map. For ELS and LLS, the QTLs have been improved from qELS_T10_A03_2 with 11.5% PVE to qELS_A03_25 with 46.5% PVE , and qLLS_T11_A06_1 with 15.12% PVE based on SSR map to qLLS_B05_85 with 48.55% PVE on the SNP map. This high density map will be used for the tetraploid reference genome assembly, and for possible map-based cloning.