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Genome-wide analysis of the WRKY gene family in cotton

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Abstract

WRKY proteins are major transcription factors involved in regulating plant growth and development. Although many studies have focused on the functional identification of WRKY genes, our knowledge concerning many areas of WRKY gene biology is limited. For example, in cotton, the phylogenetic characteristics, global expression patterns, molecular mechanisms regulating expression, and target genes/pathways of WRKY genes are poorly characterized. Therefore, in this study, we present a genome-wide analysis of the WRKY gene family in cotton (Gossypium raimondii and Gossypium hirsutum). We identified 116 WRKY genes in G. raimondii from the completed genome sequence, and we cloned 102 WRKY genes in G. hirsutum. Chromosomal location analysis indicated that WRKY genes in G. raimondii evolved mainly from segmental duplication followed by tandem amplifications. Phylogenetic analysis of alga, bryophyte, lycophyta, monocot and eudicot WRKY domains revealed family member expansion with increasing complexity of the plant body. Microarray, expression profiling and qRT-PCR data revealed that WRKY genes in G. hirsutum may regulate the development of fibers, anthers, tissues (roots, stems, leaves and embryos), and are involved in the response to stresses. Expression analysis showed that most group II and III GhWRKY genes are highly expressed under diverse stresses. Group I members, representing the ancestral form, seem to be insensitive to abiotic stress, with low expression divergence. Our results indicate that cotton WRKY genes might have evolved by adaptive duplication, leading to sensitivity to diverse stresses. This study provides fundamental information to inform further analysis and understanding of WRKY gene functions in cotton species.

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Acknowledgments

We thanks for the National Basic Research Program of China (Grant No. 2010CB126006) and the China Agriculture Research System (Grant No. CARS-18) providing the financial support for this project. We are grateful to the researchers who submitted the microarray data to the public expression databases. We are also grateful to all of the members of our laboratories who completed the expression profiling. We also thanks for EVans Ondati to help us revise the language.

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The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

    Lingling Dou, Xiaohong Zhang & Shuxun Yu

  2. State Key Laboratory in Cotton Biology, Cotton Research Institute, P. R. Chinese Academy of Agriculture Sciences (CAAS), Anyang, 455000, Henan, People’s Republic of China

    Lingling Dou, Xiaohong Zhang, Chaoyou Pang, Meizhen Song, Hengling Wei, Shuli Fan & Shuxun Yu

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Communicated by S. Hohmann.

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438_2014_872_MOESM1_ESM.tif

Supplementary material 1 (TIFF 118435 kb) Phylogenetic relationships between all species investigated in this study. The tree was constructed by the simplified phylogeny of species investigated in this study. The total number of WRKY proteins found in each species is indicated on the right of each species

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Dou, L., Zhang, X., Pang, C. et al. Genome-wide analysis of the WRKY gene family in cotton. Mol Genet Genomics 289, 1103–1121 (2014). https://doi.org/10.1007/s00438-014-0872-y

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