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C2H2 type of zinc finger transcription factors in foxtail millet define response to abiotic stresses

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Abstract

C2H2 type of zinc finger transcription factors (TFs) play crucial roles in plant stress response and hormone signal transduction. Hence considering its importance, genome-wide investigation and characterization of C2H2 zinc finger proteins were performed in Arabidopsis, rice and poplar but no such study was conducted in foxtail millet which is a C4 Panicoid model crop well known for its abiotic stress tolerance. The present study identified 124 C2H2-type zinc finger TFs in foxtail millet (SiC2H2) and physically mapped them onto the genome. The gene duplication analysis revealed that SiC2H2s primarily expanded in the genome through tandem duplication. The phylogenetic tree classified these TFs into five groups (I–V). Further, miRNAs targeting SiC2H2 transcripts in foxtail millet were identified. Heat map demonstrated differential and tissue-specific expression patterns of these SiC2H2 genes. Comparative physical mapping between foxtail millet SiC2H2 genes and its orthologs of sorghum, maize and rice revealed the evolutionary relationships of C2H2 type of zinc finger TFs. The duplication and divergence data provided novel insight into the evolutionary aspects of these TFs in foxtail millet and related grass species. Expression profiling of candidate SiC2H2 genes in response to salinity, dehydration and cold stress showed differential expression pattern of these genes at different time points of stresses.

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Acknowledgments

This work was financially supported by the core grant of National Institute of Plant Genome Research (NIPGR), New Delhi, India. Mr. Mehanathan Muthamilarasan and Mr. Awdhesh Kumar Mishra acknowledge the awards of Research Fellowship from University Grants Commission and Council of Scientific and Industrial Research, New Delhi, India, respectively. The authors also thank Mr. Subodh Verma, NIPGR for his timely assistance.

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  1. National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India

    Mehanathan Muthamilarasan, Venkata Suresh Bonthala, Awdhesh Kumar Mishra, Rohit Khandelwal, Yusuf Khan, Riti Roy & Manoj Prasad

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  1. Mehanathan Muthamilarasan
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  2. Venkata Suresh Bonthala
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  3. Awdhesh Kumar Mishra
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  4. Rohit Khandelwal
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Corresponding author

Correspondence to Manoj Prasad.

Additional information

Mehanathan Muthamilarasan and Venkata Suresh Bonthala contributed equally to this work.

Electronic supplementary material

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Supplementary Figure S1

Intron-exon positions of 124 C2H2-type of zinc finger protein encoding genes of foxtail millet. Exons and introns are represented by green boxes and black lines, respectively. (PDF 153 kb)

Supplementary Figure S2

Distribution of C2H2-type of zinc finger protein in sequenced plant genomes. The data was retrieved from Plant Transcription Factor Database (http://planttfdb.cbi.pku.edu.cn/). (GIF 274 kb)

High resolution image (TIFF 383 kb)

Supplementary Table S1

Details of primers used for quantitative real-time PCR. (DOC 32 kb)

Supplementary Table S2

Characteristic features of 124 C2H2-type of zinc finger protein encoding genes in foxtail millet. (XLS 52 kb)

Supplementary Table S3

Summary of functional domains present in 124 SiC2H2 proteins revealed through PROSITE and InterProScan. (XLS 58 kb)

Supplementary Table S4

List of predicted miRNAs targeting SiC2H2 transcripts (Setaria italica miRNAs are given in bold). (XLS 26 kb)

Supplementary Table S5

Details of SiC2H2 transcription factor-based markers. (XLS 45 kb)

Supplementary Table S6

Blast2GO annotation details of SiC2H2 protein sequences. (XLS 37 kb)

Supplementary Table S7

Summary of cis-acting regulatory elements present in the upstream sequences of all the 124 C2H2-type of zinc finger proteins. (XLS 1008 kb)

Supplementary Table S8

The Ka/Ks ratios and estimated divergence time for orthologous SiC2H2 proteins between foxtail millet, sorghum, maize and rice. (XLS 27 kb)

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Muthamilarasan, M., Bonthala, V.S., Mishra, A.K. et al. C2H2 type of zinc finger transcription factors in foxtail millet define response to abiotic stresses. Funct Integr Genomics 14, 531–543 (2014). https://doi.org/10.1007/s10142-014-0383-2

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