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Genome-wide identification and characterisation of F-box family in maize

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Abstract

F-box-containing proteins, as the key components of the protein degradation machinery, are widely distributed in higher plants and are considered as one of the largest known families of regulatory proteins. The F-box protein family plays a crucial role in plant growth and development and in response to biotic and abiotic stresses. However, systematic analysis of the F-box family in maize (Zea mays) has not been reported yet. In this paper, we identified and characterised the maize F-box genes in a genome-wide scale, including phylogenetic analysis, chromosome distribution, gene structure, promoter analysis and gene expression profiles. A total of 359 F-box genes were identified and divided into 15 subgroups by phylogenetic analysis. The F-box domain was relatively conserved, whereas additional motifs outside the F-box domain may indicate the functional diversification of maize F-box genes. These genes were unevenly distributed in ten maize chromosomes, suggesting that they expanded in the maize genome because of tandem and segmental duplication events. The expression profiles suggested that the maize F-box genes had temporal and spatial expression patterns. Putative cis-acting regulatory DNA elements involved in abiotic stresses were observed in maize F-box gene promoters. The gene expression profiles under abiotic stresses also suggested that some genes participated in stress responsive pathways. Furthermore, ten genes were chosen for quantitative real-time PCR analysis under drought stress and the results were consistent with the microarray data. This study has produced a comparative genomics analysis of the maize ZmFBX gene family that can be used in further studies to uncover their roles in maize growth and development.

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Acknowledgments

This work was supported by the National Natural Science Foundation (Grant No. 31000121) and the National Basic Research Program (Grant No. 2012CB114200) in China.

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Authors and Affiliations

  1. State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People’s Republic of China

    Fengjuan Jia, Bingjiang Wu, Hui Li, Jinguang Huang & Chengchao Zheng

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  1. Fengjuan Jia
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  2. Bingjiang Wu
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  3. Hui Li
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  4. Jinguang Huang
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  5. Chengchao Zheng
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Corresponding author

Correspondence to Chengchao Zheng.

Additional information

Communicated by S. Hohmann.

F. Jia and B. Wu contributed equally to the study.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 1166 kb) Fig. S1 Sequence alignment of all maize F-box motifs

438_2013_769_MOESM2_ESM.ppt

Supplementary material 2 (PPT 135 kb) Fig. S2 Phylogenetic relationships between Arabidopsis, rice and maize F-box genes

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Supplementary material 3 (DOC 24 kb) Fig. S3 The preference number of maize F-box proteins in different subcellular fraction

Supplementary material 4 (XLS 204 kb) Table S1 List of maize F-box proteins

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Supplementary material 5 (XLS 554 kb) Table S2a Analysis of the promoter regions of ZmFBX genes. Table S2b Summary of motifs in promoter regions of ZmFBX genes

Supplementary material 6 (XLS 17 kb) Table S3 List of ZmFBX genes changed in repsonse to abiotic stress

Supplementary material 7 (XLS 26 kb) Table S4 Expression of ZmFBX genes in response to abotic stress

Supplementary material 8 (XLS 14 kb) Table S5 Sequences of the primers used in the quantitative real-time PCR analysis

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Supplementary material 9 (XLS 20 kb) Table S6 Ka/Ks analysis and estimated divergence time for the duplicated ZmFBX paralogs

Supplementary material 10 (XLS 49 kb) Table S7 Subcellular localization of maize F-box proteins

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Jia, F., Wu, B., Li, H. et al. Genome-wide identification and characterisation of F-box family in maize. Mol Genet Genomics 288, 559–577 (2013). https://doi.org/10.1007/s00438-013-0769-1

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  • DOI: https://doi.org/10.1007/s00438-013-0769-1

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