Sequence Variation Analysis Of Glutamine Synthetase Gene Gln1-3 And Gln1-4 And Its Association With Grain Yield Related Traits In Maize (Zea Mays L.)

Maize is an important cereal crop in food supply, economic income and feed crop supply in China. Maize yield is one of the most complex quantitative traits and influenced by many factors. In general, rich functional genetic variation for grain yield existed in maize germplasm. Identification of these functionally favorable alleles contributes to developing functional markers, and thus facilitates the development of new germplasm and hybrids by marker-assisted selection. Glutamine synthetase gene Glnl-3 and Glnl-4 are members of Glutamine synthetase （GS） gene family that encoded the isozyme expressed in stalk and ear of maize, closely related to the grain yield and grain size.In this study, we selected a natural population with 87 maize inbred lines as experimental materials. Based on the target sequence capture platform technology of NimbleGen, the target sequence of gene Glnl-3 and Glnl-4 were re-sequenced and its nucleotide polymorphisms and haplotype diversity were further identified. Meanwhile, combining the measured data of grain-yield related traits of the materials cultivated in Qingdao and Sanya, favorable allelic variations related to grain yield were identified through employing the association analysis of candidate genes. The results are as follows:1、Sequence polymorphism analysis showed that,136 SNPs and 95 Indels were identified in Gln1-3 gene among 87 maize elite inbred lines, including 7 SNPs in gene coding sequence; and 158 SNPs and 69 Indels occurred within Glnl-4 gene, including 20 SNPs in gene coding sequence. Although the frequency of polymorphism in coding region is much higher than that of intron regions, the SNPs in the coding region classified the two genes into 7 haplotypes and 19 haplotypes, respectively. Numerous polymorphic sites in maize gene Gln1-3 and Glnl-4 locus were in linkage disequilibrium that decayed with increasing physical distance.2、Three SNP sites in Glnl-3 gene were significantly associated with yield related traits, where SNP₂14（C/T） was significantly associated with grain thickness; SNP 44（A/C） was significantly associated with trait ear weight; SNP₈49（C/A） was significantly associated with trait grain length, kernel weight per ear and ear weight. Whereas eight significant associations between coding sequence polymorphism of Glnl-4 and some phenotypic traits were identified in two environments. Of them, five polymorphism sites were identified to be associated significantly with four traits in Sanya environment, including grain length, grain width, ear diamerter and length of bare tip; and five polymorphism sites were identified significantly to be associated with six traits in Qingdao environment, including cob diameter, ear diamerter, length of bare tip, row number, grain length and grain width. One nonsynonymous site SNP₃50（T/C） resulting amino acid variation（P/L）, was significantly associated with grain length in both Sanya and Qingdao with contribution of 5.44% and 6.25%, respectively.