title: Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L.).
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.
authors.affiliation: National Research Centre on Plant Biotechnology, New Delhi, India; CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India.
authors.forename: Charu
authors.initials: C
authors.lastname: Lata
authors.affiliation: National Institute of Plant Genome Research, New Delhi, India.
authors.forename: Awdhesh Kumar
authors.initials: AK
authors.lastname: Mishra
authors.affiliation: National Institute of Plant Genome Research, New Delhi, India.
authors.forename: Mehanathan
authors.initials: M
authors.lastname: Muthamilarasan
authors.affiliation: National Institute of Plant Genome Research, New Delhi, India.
authors.forename: Venkata Suresh
authors.initials: VS
authors.lastname: Bonthala
authors.affiliation: National Institute of Plant Genome Research, New Delhi, India.
authors.forename: Yusuf
authors.initials: Y
authors.lastname: Khan
authors.affiliation: National Institute of Plant Genome Research, New Delhi, India.
authors.forename: Manoj
authors.initials: M
authors.lastname: Prasad
mesh_terms: D000222:Adaptation, Physiological; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D032983:Setaria Plant / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors