Genetic Mapping of Loci Controlling Grain Size in Central Asian Wheat Accessions Through GWAS and QTL Mapping

Although grain size is an important trait in Central Asian (CA) wheat breeding and industry, it remains genetically uncharacterized. We conducted GWAS and QTL mapping using a commercial wheat diversity panel (DP) and segregating population (SP). No genetic or phenotypic variation in grain width (GW) was detected in the studied panel under the conditions examined. For grain length (GL), we identified 37 significant MTAs on chromosomes 1A, 1B, 1D, 2B, 2D, 3A, 3B, 3D, 4B, 5A, 5B, 5D, 6A, 6B, 7A, 7B and 7D. The MTA on chromosome 2D (TaGL2DMTA) was identified by three GWAS models simultaneously. Two loci controlling GL, on chromosomes 2D (TaGL2DQTL) and 3A (TaGL3AQTL), were identified from QTL analysis. Loci on chromosome 2D were detected by complementary GWAS and QTL. TaGL2DMTA, TaGL2DQTL and TaGL3AQTL accounted for 12.4–15.5%, 14.5–18.3%, and 24.4–28.2% of the phenotypic variation, and increased GL by 6.8% (p = 0.0009), 2.3% (p = 0.024) and 4.0% (p = 0.0001), respectively. When these were converted to KASP markers, GL was significantly different between effective and non-effective alleles for TaGL2DMTA (p = 0.001) and TaGL3AQTL (p < 0.003). The validation of TaGL2DQTL highlighted limited effective allele distribution (~3%) in the DP. GL was positively correlated with GWT and TGW in both DP (r = 0.166/p = 0.03 and 0.526/p = 0.001, respectively) and SP (r = 0.212/p = 0.08 and 0.640/p = 0.001, respectively). Despite seasonal variation in GL, heritability was high, with H2 = 0.91 for DP and 0.93 for SP, indicating high genetic stability. Overall, these findings provide new insights into the genetic control of grain size, and highlight the identified loci as promising targets for marker-assisted selection in CA wheat breeding.