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Genome-wide analysis of primary auxin-responsive Aux/IAA gene family in maize (Zea mays. L.)


The phytohormone auxin is important in various aspects of organism growth and development. Aux/IAA genes encoding short-lived nuclear proteins are responsive primarily to auxin induction. Despite their physiological importance, systematic analysis of Aux/IAA genes in maize have not yet been reported. In this paper, we presented the isolation and characterization of maize Aux/IAA genes in whole-genome scale. A total of 31 maize Aux/IAA genes (ZmIAA1 to ZmIAA31) were identified. ZmIAA genes are distributed in all the maize chromosomes except chromosome 2. Aux/IAA genes expand in the maize genome partly due to tandem and segmental duplication events. Multiple alignment and motif display results revealed major maize Aux/IAA proteins share all the four conserved domains. Phylogenetic analysis indicated Aux/IAA family can be divided into seven subfamilies. Putative cis-acting regulatory DNA elements involved in auxin response, light signaling transduction and abiotic stress adaption were observed in the promoters of ZmIAA genes. Expression data mining suggested maize Aux/IAA genes have temporal and spatial expression pattern. Collectively, these results will provide molecular insights into the auxin metabolism, transport and signaling research.

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We are grateful to editors and reviewers for their helpful comments. We also thank Dr. Yidan Ouyang (Huazhong Agricultural University) for her help in HMM analysis. This work was supported partly by the Nature Science Foundation of Universities in Jiangsu Province (No. 09KJB180010) and the High-Level Personnel Foundation of Yangzhou University (No. nxy5286).

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Correspondence to Yijun Wang.

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Multiple alignment of maize Aux/IAA proteins. Regions I, II, III and IV limited by black boxes represented four conserved domains of Aux/IAA proteins. Two NLSs and one βαα motif were indicated by bidirectional arrows. Phosphorylation sites were emphasized by filled triangles. Identical amino acids were highlighted by filled black columns. Positions of Aux/IAA proteins were showed by figures at both sides of sequences (TIFF 1116 kb)


Phylogeny of Aux/IAA proteins. The phylogenetic tree indicated the relationship of maize, rice and Arabidopsis Aux/IAA proteins. Twelve paris of maize/rice Aux/IAA proteins were in the same clade of the phylogenetic tree. Contrarily, no maize/Arabidopsis Aux/IAA proteins were in the same clade of the dendrogram. Evolutional branches of maize/rice co-orthologs were marked in red in figure (TIFF 74 kb)

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Wang, Y., Deng, D., Bian, Y. et al. Genome-wide analysis of primary auxin-responsive Aux/IAA gene family in maize (Zea mays. L.). Mol Biol Rep 37, 3991–4001 (2010).

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  • Maize
  • Auxin
  • Aux/IAA gene family
  • Bioinformatic analysis