A Wheat 660K SNP array based high-density genetic map facilitates QTL mapping of flag leaf related traits in wheat

Abstract Flag leaf plays an important role in photosynthetic capacity and yield potential in wheat. In this study, we used a recombinant inbred line (RIL) population containing 188 lines derived from a cross between Lankao86 (LK86) and Ermangmai (EMM) to construct a genetic map using the Wheat 660K single nucleotide polymorphism (SNP) array. The high-density genetic map contains 122,620 SNP markers spanning 5,185.06 cM. It shows good collinearity with the physical map of Chinese Spring, and anchors multiple sequences of previously unplaced scaffolds (ChrUn) onto chromosomes. Based on the high-density genetic map, we identified seven and twelve quantitative trait loci (QTL) for flag leaf length (FLL) and width (FLW) across eight environments, respectively. Among them, three QTL for FLL and one for FLW are major and stably express in more than five environments. The physical distance between the flanking markers for QFll.igdb-3B is only 444 kb containing eight high confidence genes. These results suggested that we could directly map the candidate genes in a relatively small region by the high-density genetic map constructed with the Wheat 660K array. Furthermore, the identification of environmentally stable QTL for flag leaf morphology laid a foundation for the following gene cloning and flag leaf morphology improvement.