Functional markers developed from TaGS3, a negative regulator of grain weight and size, for marker-assisted selection in wheat

The Ta GS3 homoeologous genes(homoeologs) located on chromosomes 7 A, 4 A, and7 D in hexaploid wheat were cloned. Relative expression analysis of the three Ta GS3 homoeologs revealed that the expression levels of Ta GS3-4 A and Ta GS3-7 D in developing grains were higher than that of Ta GS3-7 A. Genetic evidence showed that Ta GS3 was a negative regulator of grain weight and grain size. Fifteen polymorphic sites and five haplotypes were detected in Ta GS3-4 A. Two molecular markers were developed to distinguish the five haplotypes. Association analysis using 260 accessions from Chinese wheat mini-core collection(MCC) indicated that Ta GS3-4 A affected thousand grain weight(TGW) and grain length(GL). HAP-4 A-1 and HAP-4 A-2 were favorable haplotypes that increased TGW and GL and had undergone strong selection during domestication of wheat. In addition, interaction of the Ta GS3-4 A and Ta GS3-7 D homoeologs had significant additive effects on the grain traits. Hap-4 A-1/Hap-7 D-2 was the best haplotype combination in increasing TGW and GL. The frequencies and geographic distributions of favorable Ta GS3 haplotypes among 1388 wheat accessions from worldwide sources provided clues for selection of yield-related traits. Our findings demonstrated that Ta GS3-4 A had significant effects on TGW and GL. Marker-assisted selection of HAP-4 A-1/2 combined with HAP-7 D-2 has potential to increase wheat yields.