QTL Detection for Kernel Size and Weight in Bread Wheat (Triticum aestivum L.) Using a High-Density SNP and SSR-Based Linkage Map

High-density genetic linkage maps are essential for precise mapping quantitative trait loci (QTL) in wheat (<i>Triticum aestivum</i> L.). In this study, a high-density genetic linkage map consisted of 6312 SNP and SSR markers was developed to identify QTL controlling kernel size and weight, based on a recombinant inbred line (RIL) population derived from the cross of Shixin828 and Kenong2007. Seventy-eight putative QTL for kernel length (KL), kernel width (KW), kernel diameter ratio (KDR), and thousand kernel weight (TKW) were detected over eight environments by inclusive composite interval mapping (ICIM). Of these, six stable QTL were identified in more than four environments, including two for KL (<i>qKL-2D</i> and <i>qKL-6B.2</i>), one for KW (<i>qKW-2D.1</i>), one for KDR (<i>qKDR-2D.1</i>) and two for TKW (<i>qTKW-5A</i> and <i>qTKW-5B.2</i>). Unconditional and multivariable conditional QTL mapping for TKW with respect to TKW component (TKWC) revealed that kernel dimensions played an important role in regulating the kernel weight. Seven QTL-rich genetic regions including seventeen QTL were found on chromosomes 1A (2), 2D, 3A, 4B and 5B (2) exhibiting pleiotropic effects. In particular, clusters on chromosomes 2D and 5B possessing significant QTL for kernel-related traits were highlighted. Markers tightly linked to these QTL or clusters will eventually facilitate further studies for fine mapping, candidate gene discovery and marker-assisted selection (MAS) in wheat breeding.