Gene

Common wheat

Biology

Coding region

Single-nucleotide polymorphism

Genetics

Genotype

Locus (genetics)

Haplotype

Chromosome

Theoretical and Applied Genetics

The OsGW2 gene is involved in rice grain development, influencing grain width and weight. Its ortholog in wheat, TaGW2, was considered as a candidate gene related to grain development. We found that TaGW2 is constitutively expressed, with three orthologs expressing simultaneously. The coding sequence (CDS) of TaGW2 is 1,275 bp encoding a protein with 424 amino acids, and has a functional domain shared with OsGW2. No divergence was detected within the CDS sequences in the same locus in ten varieties. Genome-specific primers were designed based on the sequence divergence of the promoter regions in the three orthologous genes, and TaGW2 was located in homologous group 6 chromosomes through CS nulli-tetrasomic (NT). Two SNPs were detected in the promoter region of TaGW2-6A, forming two haplotypes: Hap-6A-A (−593A and −739G) and Hap-6A-G (−593G and −769A). A cleaved amplified polymorphic sequence (CAPS) marker was developed based on the −593 A-G polymorphism to distinguish the two haplotypes in TaGW2-6A. This gene was fine mapped 0.6 cM from marker cfd80.2 near the centromere in a recombinant inbred line (RIL) population. Two hundred sixty-five Chinese wheat varieties were genotyped and association analysis revealed that Hap-6A-A was significantly associated with wider grains and higher one-thousand grain weight (TGW) in two crop seasons. qRT-PCR revealed a negative relationship between TaGW2 expression level and grain width. The Hap-6A-A frequencies in Chinese varieties released at different periods showed that it had been strongly positively selected in breeding. In landraces, Hap-6A-A is mainly distributed in southern Chinese wheat regions. Association analysis also indicated that Hap-6A-A not only increased TGW by more than 3 g, but also had earlier heading and maturity. In contrast to Chinese varieties, Hap-6A-G was the predominant haplotype in European varieties; Hap-6A-A was mainly present in varieties released in the former Yugoslavia, Italy, Bulgaria, Hungary and Portugal.

Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.)