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Background   TaGW2-6A , cloned in earlier research, strongly influences wheat grain width and TKW. Here, we mainly analyzed haplotypes of  TaGW2-6B  and their effects on TKW and interaction with haplotypes at  TaGW2-6A.Results  About 2.9 kb of the promoter sequences of  TaGW2-6B  and  TaGW2-6D  were cloned in 34 bread wheat cultivars. Eleven SNPs were detected in the promoter region of  TaGW2-6B,  forming 4 haplotypes, but no divergence was detected in the  TaGW2-6D  promoter or coding region. Three molecular markers including CAPS, dCAPS and ACAS, were developed to distinguish the  TaGW2-6B  haplotypes. Haplotype association analysis indicated that  TaGW2-6B  has a stronger influence than  TaGW2-6A  on TKW, and  Hap-6B-1  was a favored haplotype increasing grain width and weight that had undergone strong positive selection in global wheat breeding. However, clear geographic distribution differences for  TaGW2-6A  haplotypes were found;  Hap-6A-A  was favored in Chinese, Australian and Russian cultivars, whereas  Hap-6A-G  was preferred in European, American and CIMMYT cultivars. This difference might be caused by a flowering and maturity time difference between the two haplotypes.  Hap-6A-A  is the earlier type. Haplotype interaction analysis between  TaGW2-6A  and  TaGW2-6B  showed additive effects between the favored haplotypes.  Hap-6A-A/Hap-6B-1  was the best combination to increase TKW. Relative expression analysis of the three  TaGW2  homoeologous genes in 22 cultivars revealed that  TaGW2-6A  underwent the highest expression.  TaGW2-6D  was the least expressed during grain development and  TaGW2-6B  was intermediate. Diversity of the three genes was negatively correlated with their effect on TKW.    Conclusions  Genetic effects, expression patterns and historic changes of haplotypes at three homoeologous genes of  TaGW2  influencing yield were dissected in wheat cultivars. Strong and constant selection to favored haplotypes has been found in global wheat breeding during the past century. This research also provides a valuable case for understanding interaction of genes that control complex traits in polyploid species.

Homologous haplotypes, expression, genetic effects and geographic distribution of the wheat yield gene TaGW2