Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L.)

PLoS One. 2014 Nov 19;9(11):e113092. doi: 10.1371/journal.pone.0113092. eCollection 2014.

Abstract

The APETALA2/ethylene-responsive element binding factor (AP2/ERF) family is one of the largest transcription factor (TF) families in plants that includes four major sub-families, namely AP2, DREB (dehydration responsive element binding), ERF (ethylene responsive factors) and RAV (Related to ABI3/VP). AP2/ERFs are known to play significant roles in various plant processes including growth and development and biotic and abiotic stress responses. Considering this, a comprehensive genome-wide study was conducted in foxtail millet (Setaria italica L.). A total of 171 AP2/ERF genes were identified by systematic sequence analysis and were physically mapped onto nine chromosomes. Phylogenetic analysis grouped AP2/ERF genes into six classes (I to VI). Duplication analysis revealed that 12 (∼7%) SiAP2/ERF genes were tandem repeated and 22 (∼13%) were segmentally duplicated. Comparative physical mapping between foxtail millet AP2/ERF genes and its orthologs of sorghum (18 genes), maize (14 genes), rice (9 genes) and Brachypodium (6 genes) showed the evolutionary insights of AP2/ERF gene family and also the decrease in orthology with increase in phylogenetic distance. The evolutionary significance in terms of gene-duplication and divergence was analyzed by estimating synonymous and non-synonymous substitution rates. Expression profiling of candidate AP2/ERF genes against drought, salt and phytohormones revealed insights into their precise and/or overlapping expression patterns which could be responsible for their functional divergence in foxtail millet. The study showed that the genes SiAP2/ERF-069, SiAP2/ERF-103 and SiAP2/ERF-120 may be considered as potential candidate genes for further functional validation as well for utilization in crop improvement programs for stress resistance since these genes were up-regulated under drought and salinity stresses in ABA dependent manner. Altogether the present study provides new insights into evolution, divergence and systematic functional analysis of AP2/ERF gene family at genome level in foxtail millet which may be utilized for improving stress adaptation and tolerance in millets, cereals and bioenergy grasses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Physiological
  • Chromosome Mapping
  • Chromosomes, Plant
  • Evolution, Molecular
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Plant
  • Multigene Family
  • Phylogeny
  • Plant Proteins / genetics*
  • Plant Proteins / metabolism
  • Sequence Analysis, DNA
  • Setaria Plant / genetics
  • Setaria Plant / metabolism*
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism

Substances

  • Plant Proteins
  • Transcription Factors

Grants and funding

This work was financially supported by core grant of National Institute of Plant Genome Research, New Delhi, India, and Department of Science & Technology, Government of India through INSPIRE Faculty Award [IFA-11LSPA-01]. CL is the recipient of INSPIRE Faculty Award from Department of Science & Technology, while AKM and MM are the recipients of Research Fellowships from Council of Scientific and Industrial Research and University Grants Commission, New Delhi, respectively. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.