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

key messageA high-density genetic map containing 122,620 SNP markers was constructed, which facilitated the identification of eight major flag leaf-related QTL in relatively narrow intervals. The flag leaf plays an important role in photosynthetic capacity and yield potential in wheat. In this study, we used a recombinant inbred line population containing 188 lines derived from a cross between 'Lankao86' (LK86) and 'Ermangmai' to construct a genetic map using the Wheat 660 K single-nucleotide polymorphism (SNP) array. The high-density genetic map contains 122,620 SNP markers spanning 5185.06 cM. It shows good collinearity with the physical map of Chinese Spring and anchors multiple sequences of previously unplaced scaffolds onto chromosomes. Based on the high-density genetic map, we identified seven, twelve, and eight quantitative trait loci (QTL) for flag leaf length (FLL), width (FLW), and area (FLA) across eight environments, respectively. Among them, three, one, and four QTL for FLL, FLW, and FLA are major and stably express in more than four environments. The physical distance between the flanking markers for QFll.igdb-3B/QFlw.igdb-3B/QFla.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 660 K 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.