High Resolution Mapping Improved Detectability and Resolution of QTLs for Grain Protein Content and Yield Related Traits in Tetraploid Wheat

High throughput SNP markers and advanced genetic and QTL mapping tools were used in this study to improve the detectability and resolution of QTLs in the complex genome of tetraploid wheat. We have reanalyzed QTLs for grain productivity and quality after genotyping our RIL population derived from Triticum durum var. Langdon X Triticum dicoccoides (G18-16) with wheat 15K SNP array (TraitGenetics). A new linkage map was constructed based on >4,000 polymorphic SNPs using MultipointULD software package (MultiQTL LTD).  The assembled map is significantly shorter than our previous SSR map (1,836 cM vs. 2,317 cM) and the average distance of between adjacent markers is much shorter (1.3 cM vs. 7.5 cM).  This map exposed new chromosomal regions that were not present in the older map, including the complete arm of chromosome 4BS. A total of 26 QTLs were mapped for yield related traits (LOD 3.6 - 29.7) and 13 QTLs for grain protein content (GPC) (LOD 3.2 - 11.2). Our new ultra-dense genetic map improved the resolution of previous QTLs (e.g. higher LOD and percentage of explained variation (PEV), and reduced the interval length), and detected novel QTLs, not present in the previous map. These new loci included a QTL for GPC on chromosome 4BS and 5 QTLs for yield related traits on chromosomes 2A, 5A, 3B, 3A, and 7A. The new map described here will facilitate marker assisted introgression and map-based cloning of wild emmer wheat genes underlying these traits.