Haplotype, molecular marker and phenotype effects associated with mineral nutrient and grain size traits of TaGS1a in wheat

Glutamine synthetase (GS) is a key enzyme in the formation of the amino acid glutamine during N assimilation. The characterization of GS genes and the development of functional markers are important for marker-assisted selection (MAS) in wheat breeding programs. In the present study, the full-length genomic DNA (gDNA) sequence of TaGS1a was obtained from 60 wheat varieties. TaGS1a comprises 3415 bp and has eleven exons and ten introns. Nine single nucleotide polymorphisms (SNPs) and two insertions and deletions of DNA segments (InDels) were detected in introns, resulting two haplotypes: Hap 1 and Hap 2. A cleaved amplified polymorphic sequence (CAPS) marker was developed to distinguish the two haplotypes. The TaGS1a-CAPS marker was located on chromosome 6D using Chinese Spring nullisomic-tetrasomic lines, and mapped at 2.5 cM from the SSR marker barc1121b in a RIL population. The completely corresponding results between quantitative trait locus (QTL) analysis and association analysis suggested that the TaGS1a gene had functions for grain size traits, including thousand grain weight (TGW), grain width (GW), grain height (GH), GL/GW ratio (GLW), factor form density (FFD), grain area (GA) and grain volume (GV) during maturity stage, and for the ratio of root/shoot for dry weight and nitrogen, phosphorus, potassium contents (RSDW, RSNC, RSPC and RSKC) during seedling stage.