QTL Mapping and Candidate Gene Analysis of Grain Size and Weight in Synthetic Hexaploid Wheat-Derived Lines

Synthetic hexaploid wheat (SHW) contains abundant genetic variation, and is the important breeding resource for enhancing genetic diversity of common wheat. Grain size, including thousand-grain weight (TGW), grain length (GL), grain width (GW), grain area (GA), aspect ratio (AR), and factor from density (FFD), is closely related with grain yield and quality in wheat. In the research, Quantitative Trait Loci (QTL) analyses were carried out for a mapping population of 284 F 2 plants derived from a cross between two sister lines derived from synthetic hexaploid wheat in order to identify genomic regions affecting grain size. The linkage map based on 1671 polymorphic Diversity arrays technology (DArT) markers detected 17 QTLs for six grain size traits on chromosomes 1A, 1B, 1D, 3B, 4A, 5A, 5B, and 7D. These QTL explained 3.8–12.4% of the phenotypic variation. For the thousand-grain weight (TGW) loci, TraesCS1B01G144800 and TraesCS1B01G145800 were prioritized within QTgw.nwipb-1B , while TraesCS5A01G111700 , encoding a WD40 repeat-containing protein, was identified as a high-confidence candidate within QTgw.nwipb-5A . Notably, TraesCS1B01G144800 showed pronounced grain-preferential expression, supporting its potential involvement in grain development. For the grain-length QTL QGl.nwipb-3B , TraesCS3B01G232800 , encoding an IAA-amino acid hydrolase ILR1, and TraesCS3B01G227700 , encoding a cyclin family protein, were prioritized based on their potential roles in auxin homeostasis and cell-cycle regulation, respectively. Haplotype analysis further revealed favorable haplotypes of TraesCS1B01G144800 , TraesCS1B01G145800 , TraesCS5A01G111700 , and TraesCS3B01G232800 that were significantly associated with increased TGW or GL. These results provide new insights into the genetic regulation of wheat grain morphology and identify valuable alleles for marker-assisted selection and molecular breeding.