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Molecular evolution and gene expression differences within the HD-Zip transcription factor family of Zea mays L.

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Abstract

Homeodomain-leucine zipper (HD-Zip) transcription factors regulate developmental processes and stress responses in plants, and they vary widely in gene number and family structure. In this study, 55 predicted maize HD-Zip genes were systematically analyzed with respect to their phylogenetic relationships, molecular evolution, and gene expression in order to understand the functional diversification within the family. Phylogenetic analysis of HD-Zip proteins from Zea mays, Oryza sativa, Arabidopsis thaliana, Vitis vinifera, and Physcomitrella patens showed that they group into four classes. We inferred that the copy numbers of classes I and III genes were relatively conserved in all five species. The 55 maize HD-Zip genes are distributed randomly on the ten chromosomes, with 15 segmental duplication and 4 tandem duplication events, suggesting that segmental duplications were the major contributors in the expansion of the maize HD-Zip gene family. Expression analysis of the 55 maize HD-Zip genes in different tissues and drought conditions revealed differences in the expression levels and patterns between the four classes. Promoter analysis revealed that a number of stress response-, hormone response-, light response-, and development-related cis-acting elements were present in their promoters. Our results provide novel insights into the molecular evolution and gene expression within the HD-Zip gene family in maize, and provide a solid foundation for future functional study of the HD-Zip genes in maize.

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Acknowledgments

We thank all our collaborators who made the work on HD-Zip transcription factors a rewarding experience. We would like to thank the members of the Bioinformatics Center of Northwest A&F University for their useful input. This work was supported by the National Natural Science Foundation of China (31471505).

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Authors and Affiliations

  1. State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China

    Hude Mao

  2. College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China

    Lijuan Yu, Zhanjie Li, Hui Liu & Ran Han

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  1. Hude Mao
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Mao, H., Yu, L., Li, Z. et al. Molecular evolution and gene expression differences within the HD-Zip transcription factor family of Zea mays L.. Genetica 144, 243–257 (2016). https://doi.org/10.1007/s10709-016-9896-z

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