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.
Highlights
Plants frequently confront numerous environmental stresses which affect their growth and productivity
The Hidden Markov Model (HMM) BLAST identified a total of 186 APETALA2/ethylene-responsive element binding factor (AP2/ethylene responsive TF (ERF)) protein sequences from foxtail millet
Fifteen proteins were found to be splice variants of primary transcripts, removal of which led to the identification of a total of 171 putative SiAP2/ERF proteins (Table S2) which represents approximately 0.4407% of all annotated genes (38801 genes total) in the Setaria genome [3] which is very similar to those present in poplar (0.4390%) and rice (0.4315%) approximately 0.10% smaller than that of Arabidopsis (0.5481%) [7,8,18,53,54]
Summary
Plants frequently confront numerous environmental stresses which affect their growth and productivity. The availability of foxtail millet genome sequence has encouraged plant biology researchers to work towards deciphering its structural and functional genomics that may give new insights for its stress response and adaptation mechanisms and eventually support crop improvement programmes to ensure sustainable food security [6]. Among various TF families, the ethylene responsive TF (ERF) family plays an important role in plant growth and development and enables them to adapt to changing environmental conditions, and it is important to understand molecular functions of these genes in order to improve plant adaptability and productivity under varied ambiance/environmental changes
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