Comprehensive Genome-Wide Survey, Genomic Constitution and Expression Profiling of the NAC Transcription Factor Family in Foxtail Millet (Setaria italica L.)

Abstract

The NAC proteins represent a major plant-specific transcription factor family that has established enormously diverse roles in various plant processes. Aided by the availability of complete genomes, several members of this family have been identified in Arabidopsis, rice, soybean and poplar. However, no comprehensive investigation has been presented for the recently sequenced, naturally stress tolerant crop, Setaria italica (foxtail millet) that is famed as a model crop for bioenergy research. In this study, we identified 147 putative NAC domain-encoding genes from foxtail millet by systematic sequence analysis and physically mapped them onto nine chromosomes. Genomic organization suggested that inter-chromosomal duplications may have been responsible for expansion of this gene family in foxtail millet. Phylogenetically, they were arranged into 11 distinct sub-families (I-XI), with duplicated genes fitting into one cluster and possessing conserved motif compositions. Comparative mapping with other grass species revealed some orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of genes. The evolutionary significance as duplication and divergence of NAC genes based on their amino acid substitution rates was understood. Expression profiling against various stresses and phytohormones provides novel insights into specific and/or overlapping expression patterns of SiNAC genes, which may be responsible for functional divergence among individual members in this crop. Further, we performed structure modeling and molecular simulation of a stress-responsive protein, SiNAC128, proffering an initial framework for understanding its molecular function. Taken together, this genome-wide identification and expression profiling unlocks new avenues for systematic functional analysis of novel NAC gene family candidates which may be applied for improvising stress adaption in plants.

Comprehensive analysis of NAC transcription factors in diploid Gossypium: sequence conservation and expression analysis uncover their roles during fiber development

“…We identified 143 NAC genes in G. arboreum and 145 in G. raimondii by analyzing the NAC TF structure domain. Comprehensive analyses revealed that members of the NAC-TF family varied both in monocots or dicots (Ji et al, 2003;Rushton et al, 2008;Shen et al, 2009;Hu et al, 2010;Finn et al, 2011;Lee et al, 2012;Puranik et al, 2013;Shah et al, 2013;Shang et al, 2013;Zhu et al, 2013;Cao et al, 2015;You et al, 2015), for example, the distribution of NAC-TFs in dicots ranges from 79 in C. paraya to 187 in E. grandis. However, compared to the ~105 NAC-TFs in A. thaliana, C. papaya, and T. cacao, which belong to the malvid family, diploid cotton shows a significantly higher number of NAC-TFs.…”

“…They also play an important role in plant development, and are involved in osmotic stress and various plant developmental processes. In recent years, genomic analyses of the NAC gene family have been conducted in angiosperms such as Arabidopsis thaliana (Ooka et al, 2003), Oryza sativa (Fang et al, 2008;Nuruzzaman et al, 2010), Vitis vinifera (Wang et al, 2013), Populus trichocarpa (Hu et al, 2010), Glycine soja , Setaria italic (Puranik et al, 2013), Gossypium raimondii (Shang et al, 2013), and Musa acuminata (Cenci et al, 2014). As one of the largest groups of plant transcription factors (TFs), the NAC-TF family consists of several genes in plants.…”

“…For example, there are 105 TF genes in Arabidopsis (Ooka et al, 2003), 140 genes in rice (Fang et al, 2008;Nuruzzaman et al, 2010), 101 genes in soybean (Pinheiro et al, 2009), 163 in poplar (Hu et al, 2010), and 145 in G. raimondii (Shang et al, 2013). The gene structure, phylogeny, expression, and functional diversification of the NAC-TF family have been systematically examined (Ooka et al, 2003;Fang et al, 2008;Zhang et al, 2008;Pinheiro et al, 2009;Nuruzzaman et al, 2010;Hu et al, 2010;Wang et al, 2013;Puranik et al, 2013;Shang et al, 2013;Cenci et al, 2014) Genomic analyses indicate that segmental duplications have significantly contributed to the expansion of the NAC gene family in specific angiosperms (Fang et al, 2008;Nuruzzaman et al, 2010;Hu et al, 2010;Wang et al, 2013;Shang et al, 2013;Singh et al, 2013). Expression analyses have also provided insight into the functional divergence among members of the NAC gene family (Hu et al, 2010;Lee et al, 2012;Wang et al, 2013;Shang et al, 2013;Singh et al, 2013;Hussey et al, 2015).…”

Advances in Omics for Enhancing Abiotic Stress Tolerance in Millets

“…Most of the above candidate genes from millet crops are transcription factors (TFs) as they can regulate the expression of downstream stress responsive genes and thus play important role in imparting stress tolerance. Of note, several candidate TFs including AP2/ERFs, NAC, C 2 H 2 zinc finger and MYB were analyzed in foxtail millet to identify suitable candidate genes which can be used for further characterization using transgene-based approaches towards engineering stress resistance (Lata et al, 2014;Puranik et al, 2013;Muthamilarasan et al, 2014b;Muthamilarasan et al, 2014c). In addition to TFs, several stress-responsive genes such as WD40, Dicer-like (DCL), Argonaute (AGO) and RNAdependent RNA polymerases (RDR) have been studied in foxtail millet to identify potential candidate genes for downstream characterization (Mishra et al, 2014;Yadav et al, 2014c).…”

“…Extensive genome-wide investigation and expression profiling studies of various TF families such as AP2/ERFs, NAC, C 2 H 2 zinc finger and MYB (Lata et al, 2014;Puranik et al, 2013;Muthamilarasan et al, 2014b;Muthamilarasan et al, 2014c) and stress responsive genes such as WD40, DCL, AGO and RDR polymerases and ALDH (Mishra et al, 2014;Yadav et al, 2014c;Zhu et al, 2014) have also been carried out in foxtail millet for analyzing gene families implicated in stress tolerance, identifying suitable candidate genes and delineating gene regulatory networks and molecular cross talks for abiotic stress responses.…”