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Functional & Integrative Genomics

, Volume 14, Issue 3, pp 531–543 | Cite as

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

  • Mehanathan Muthamilarasan
  • Venkata Suresh Bonthala
  • Awdhesh Kumar Mishra
  • Rohit Khandelwal
  • Yusuf Khan
  • Riti Roy
  • Manoj PrasadEmail author
Original Paper

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.

Keywords

Foxtail millet (Setaria italicaC2H2 type of zinc finger transcription factors Genome-wide Expression profiling Phylogeny Physical map Comparative mapping 

Notes

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.

Supplementary material

10142_2014_383_MOESM1_ESM.pdf (153 kb)
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)
10142_2014_383_Fig9_ESM.gif (275 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)

10142_2014_383_MOESM2_ESM.tif (384 kb)
High resolution image (TIFF 383 kb)
10142_2014_383_MOESM3_ESM.doc (32 kb)
Supplementary Table S1 Details of primers used for quantitative real-time PCR. (DOC 32 kb)
10142_2014_383_MOESM4_ESM.xls (52 kb)
Supplementary Table S2 Characteristic features of 124 C2H2-type of zinc finger protein encoding genes in foxtail millet. (XLS 52 kb)
10142_2014_383_MOESM5_ESM.xls (58 kb)
Supplementary Table S3 Summary of functional domains present in 124 SiC2H2 proteins revealed through PROSITE and InterProScan. (XLS 58 kb)
10142_2014_383_MOESM6_ESM.xls (26 kb)
Supplementary Table S4 List of predicted miRNAs targeting SiC2H2 transcripts (Setaria italica miRNAs are given in bold). (XLS 26 kb)
10142_2014_383_MOESM7_ESM.xls (45 kb)
Supplementary Table S5 Details of SiC2H2 transcription factor-based markers. (XLS 45 kb)
10142_2014_383_MOESM8_ESM.xls (38 kb)
Supplementary Table S6 Blast2GO annotation details of SiC2H2 protein sequences. (XLS 37 kb)
10142_2014_383_MOESM9_ESM.xls (1008 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)
10142_2014_383_MOESM10_ESM.xls (27 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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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Mehanathan Muthamilarasan
    • 1
  • Venkata Suresh Bonthala
    • 1
  • Awdhesh Kumar Mishra
    • 1
  • Rohit Khandelwal
    • 1
  • Yusuf Khan
    • 1
  • Riti Roy
    • 1
  • Manoj Prasad
    • 1
    Email author
  1. 1.National Institute of Plant Genome Research (NIPGR)New DelhiIndia

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