Identification of QTL for Grain Traits and Plant Height Using the Recombinant Inbred Line Population Derived from the Cross of Zhongke 331 × Nongda 399

Improving wheat yield is essential to meet the increasing demand for food production. This study aims to identify quantitative trait loci (QTL) associated with grain traits and plant height (PH) in winter wheat, using a recombinant inbred line (RIL) population derived from a cross between Zhongke 331 and Nongda 399. The RIL population was genotyped using the 16K GenoBaits Wheat single nucleotide polymorphism (SNP) array. A genetic linkage map was established, comprising 14,868 SNPs and spanning 3846.91 cM, with an average interval of 1.11 cM between markers. These SNPs were categorized into 3463 SNP bin markers, with 1653, 1508, and 302 located in the A, B, and D sub-genomes, respectively. QTL analysis for thousand-grain weight (TGW), grain length (GL), grain width (GW), and PH revealed 61 QTL influencing these traits across six environments. Loci <i>qPH-4B.1</i> and <i>qPH-4D.1</i> were consistently detected in five environments. QTL clusters with pleiotropic effects that regulate multiple grain traits were identified on chromosomes 4B and 4D. Furthermore, the combination of <i>qPH-4B.1</i> and <i>qPH-4D.1</i> resulted in a reduced plant height compared to the presence of either locus alone, indicating an additive effect between these loci.