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Genome-Wide Analysis and Expression Patterns of NAC Transcription Factor Family Under Different Developmental Stages and Abiotic Stresses in Chinese Cabbage

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Abstract

NAC (NAM, ATAF1/2 and CUC2) proteins represent a major plant-specific transcription factor (TF) family and are expressed in various developmental stages and tissues. In this study, 204 NAC genes, including 17 membrane-bound TFs, were identified in the Brassica rapa (Chinese cabbage) genome. The gene structure and motif compositions obtained suggest that the BrNAC gene family is classified broadly into eight groups. The predicted Chinese cabbage NAC genes were distributed in ten chromosomes at various densities but mainly in chromosomes 3 and 10 (14 and 14 %, respectively). A comprehensive analysis of NAC family genes in Chinese cabbage, rice and Arabidopsis was also performed. Phylogenetic analysis of BrNACs, along with their Arabidopsis and rice counterparts, divided the proteins into two major groups (A and B) and 19 subgroups. Homologous, paralogous, and orthologous searches of Chinese cabbage and Arabidopsis revealed gene loss during genome triplication in Chinese cabbage. Finally, the expression of 55 selected Chinese cabbage BrNAC genes was analyzed under different developmental stages and abiotic stress conditions (heat, cold, ABA, GA, and PEG). The selected genes were classified into three types (constitutive expression, no-expression, and period-specific expression) according to their expression profiles, which indicate that the NAC genes are involved in various aspects of the physiological and developmental processes of Chinese cabbage. Under different abiotic stress conditions, several members of BrNACs were upregulated by various abiotic stresses. Our study provides a very useful reference for functional analysis of members of BrNAC gene family in Chinese cabbage.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (31330067 and 31301782), the National High Technology Research and Development Program of China (863 Program, No. 2012AA100101), the Fundamental Research Funds for the Central Universities of China (KYZ201111), the Natural Science Foundation of Jiangsu Province (BK20130673).

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  1. College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China

    Tongkun Liu, Xiaoming Song, Weike Duan, Zhinan Huang, Gaofeng Liu, Ying Li & Xilin Hou

  2. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

    Tongkun Liu, Xiaoming Song, Weike Duan, Zhinan Huang, Gaofeng Liu, Ying Li & Xilin Hou

  3. Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing, 210095, China

    Tongkun Liu, Xiaoming Song, Weike Duan, Zhinan Huang, Gaofeng Liu, Ying Li & Xilin Hou

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  1. Tongkun Liu
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Correspondence to Xilin Hou.

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Tongkun Liu and Xiaoming Song contributed equally to this work.

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Liu, T., Song, X., Duan, W. et al. Genome-Wide Analysis and Expression Patterns of NAC Transcription Factor Family Under Different Developmental Stages and Abiotic Stresses in Chinese Cabbage. Plant Mol Biol Rep 32, 1041–1056 (2014). https://doi.org/10.1007/s11105-014-0712-6

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