Genomic DNA Sequence, Gene Structure, Conserved Domains, and Natural Alleles of Gln1-4 Gene in Maize

Abstract

Gln1-4 is one of the important members of glutamine synthetase (GS) gene family. The objectives of this study were to isolate the genomic DNA (gDNA) sequence of Gln1-4, to analyze structure, conserved domains, and natural allelic variations of the gene, and to found a basis for association analysis of the functional sites associated with nitrogen use efficiency in maize ( Zea mays L.). PCR walking strategy was applied to isolate the gDNA sequence of Gln1-4 and its flanking sequences. A total of 3724 bp gDNA sequence of Gln1-4 was assembled from the maize inbred line Mo17. The full length of the coding region was 2858 bp, which comprised of 10 exons separated by 9 introns. All the 18 splicing sites were the conserved sequence of GU at the 5′ donor sites and AG at the 3′ acceptor sites. This sequence was submitted to GenBank under the accession number EU369651. Gln1-4 encodes a GS protein with the molecular weight of 39.2 kD, which was composed of 356 amino acids. The isoelectric point was 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 to exon 9 at carboxyl terminal consisted of an ATPase activity domain. Compared with Gln1-3, Gln1-4 was highly conserved in DNA sequence, amino acid sequence, gene structure, and conserved domains with a 98.31% identity of amino acid sequence. A total of 318 types of natural DNA variation at the important and target region of Gln1-4 gene were identified among 52 maize inbred lines, of which 90% was single nucleotide polymorphisms (242) and small indels (45). The analysis of the functional sites associated with nitrogen use efficiency of Gln1-4 should focus on the binding and catalyzing domains and the splicing sites.