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Genome-wide identification of the class III aminotransferase gene family in rice and expression analysis under abiotic stress

ATIII gene family in japonica and indica rice

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Abstract

Aminotransferases are pyridoxal 5′-phosphate-dependent enzymes that play crucial roles in plant growth, development, and responses to abiotic stress. The class III aminotransferase family (ATIII family) is an important subfamily. However, no characterization of rice ATIII genes has been previously reported. Using available rice genome sequence information, we identified 12 japonica and 13 indica ATIII genes that were randomly localized on chromosomes 2, 3, 4, 5, 7, 8, and 11. Information provided by the Plant Genome Duplication Database revealed that four japonica and four indica ATIII genes are the results of segmental duplications, and two japonica and six indica genes resulted from tandem duplications. A phylogenetic analysis of the ATIII genes in japonica, indica and Arabidopsis enabled the classification of the genes into six different groups, and the characteristics were established before the monocot-dicot and japonica–indica split. An analysis of the Ka/Ks, divergence time and average indel length suggested the diverse selection styles of the duplicated gene pairs. Gene structure and motif analyses revealed that the ATIII gene family has experienced extensive divergence. Real-time PCR was performed to examine the expression pattern of the japonica ATIII genes in response to various abiotic stresses including drought, salt, and cold. The results suggested that most of the genes were differentially up- or down-regulated in rice seedlings in response to at least one stress factor, which indicates the key role of the rice ATIII gene family in responding to abiotic stresses. These results provide a basis for elucidating the roles of the ATIII genes and their further functional analysis under abiotic stresses.

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Acknowledgments

This work was supported by the Tackle Key Program in Science and Technology of the Science and Technology Ministry (2011BAD35B02-01) and supported by the Program in Science and Technology of the Science and Technology Ministry (2011BAD16B11).

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  1. Agricultural College, Northeast Agricultural University, No. 59, Mucai Street, Gongbin Road, Xiangfang, Harbin, 150030, Heilongjiang, People’s Republic of China

    Jian Sun, Dong-Wei Xie, Hong-Wei Zhao & De-Tang Zou

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  1. Jian Sun
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  2. Dong-Wei Xie
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Correspondence to De-Tang Zou.

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Sun, J., Xie, DW., Zhao, HW. et al. Genome-wide identification of the class III aminotransferase gene family in rice and expression analysis under abiotic stress. Genes Genom 35, 597–608 (2013). https://doi.org/10.1007/s13258-013-0108-2

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