Abstract: Glutamine synthetase gene family, the core elements of in vivo nitrogen use efficiency (NUE) and nitrogen recycle, encodes enzymes catalyzing the nitrogen assimilation from ammonium ion into protein in higher plant. Gln1-3 is a member of GS family that encodes the cytosolic isozyme expressed in mesophyll cells of maize (Zea mays L.). The knowledge about the genomic se-quence of the gene is the premise for the natural alleles, functional studies, and molecular marker development. In the present study, 4 571 bp of genomic region of Gln1-3 was sequenced using a maize inbred line Liaobai 371 with PCR walking strategy.
The 3 062 bp coding region of the gene was comprised of ten exons that were separated by nine introns. Totally, six out of nine
splice sites followed splicing mechanism with conserved GU sequences at 5′ donor sites and AG at 3′ acceptor sites. The se-
quence has been submitted to GenBank (Accession No.: EU338535) and annotated in details. Encoded GS1 protein, molecular
weight of 39.2 kD, is comprised of 356 amino acids. Its isoelectric point (pI) is 5.202. Conserved domain searching results showed that the region from exon 2 to exon 6 at amino-terminal was an ammonium ion binding domain, and exon 8 and exon 9 at carboxyl terminal consisted of an ATPase domain to fulfill the synthesis activity. A total of 364 sites of natural variation at impor-tant and target region of Gln1-3 gene were identified among 50 maize inbred lines, and 313 (86%) sites of the total (364) were SNP variations. The results provide a good basis for analyzing the key candidate genes associated with NUE and grain yield under different nitrogen supplies levels.

Key words: Maize, Gln1-3, Functional domain, SNP, Nitrogen use efficiency, Association analysis