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Acta Agron Sin ›› 2009, Vol. 35 ›› Issue (6): 983-991.doi: 10.3724/SP.J.1006.2009.00983

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

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

WU Yong-Sheng12,LI Xin-Hai1,HAO Zhuan-Fang1,ZHANG Shi-Huang1,XIE Chuan-Xiao1*   

  1. 1Institute of Crop Sciences,Chinese Academy of Agricultural Sciences/Natiomal Key Facilities for Crop Gene Resource and Genetic Improvement,Beijing 100081,China;2Guangxi Maize Research Institute,Nanning 530227,China
  • Received:2008-10-30 Revised:2009-03-23 Online:2009-06-12 Published:2009-04-16
  • Contact: XIE Chuan-Xiao，E-mail:cxxie@caas.net.cn;Tel:010-82105853

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Abstract:

Maize (Zea mays L.) cultivars with improved nitrogen use efficiency would be beneficial for low-input production systems and for environment since it would reduce the surface water pollution and the nitrate leaching into underground water. Glutamine synthetase genes families are the core elements for nitrogen assimilation and metabolism in maize plants. The objectives of this study were to isolate the genomic DNA sequence of Gln1-4, which is one of the important members of glutamine synthetase gene family, to analyze the gene structure, conserved domains and natural allelic variations and so that was to found basis for association analysis of the functional sites related to nitrogen use efficiency in maize. PCR walking strategy was applied to isolate the gDNA sequence of Gln1-4 and its flanking sequence. The gene structure was analyzed by aligning gDNA sequence and its’ mature mRNA sequence. The conserved domains were obtained by searching Conserved Domain Database (CDD) at NCBI. The natural allelic variations were evaluated by resequencing and aligning DNA sequences among 52 inbreds. A total of 3 724 bp gDNA sequence of Gln1-4 of Mo17 was assembled. The full length of the coding region was 2 858 bp, which was comprised of ten exons separated by nine introns. All 18 splicing sites were the conserved sequence of GU at 5' donor sites and AG at 3' acceptor sites. The sequence has been submitted to GenBank (Accession No.: EU369651) and annotated in details. Gln1-4 encodes a GS protein with molecular weight of 39.2 kD, which was comprised of 356 amino acids. Its isoelectric point (pI) 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. As compared with Gln1-3, the DNA sequence, amino acid sequence, gene structure and conserved domains for Gln1-4 were highly conserved with a 98.31% identity of amino acid sequence. A total of 318 types of natural DNA variation at important and target region of Gln1-4 gene were identified among 52 maize inbred lines, of which 242 was SNPs and 45 was small indels, comprising 90% of the total allelic variations. The analysis of the functional sites gene associated with nitrogen use efficiency of Gln1-4 in maize should focus on binding and catalyzing domains and splicing sites.

Key words: Maize, Gln1-4, Conserved Functional domain, Natural allelic variation, Nitrogen use efficiency


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