Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress

Abstract

BackgroundThe homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). Findings in these species suggest HD-Zip genes as high priority candidates for crop improvement.ResultsIn this study we have identified members of the HD-Zip gene family in soybean cv. ‘Williams 82’, and characterized their expression under dehydration and salt stress. Homology searches with BLASTP and Hidden Markov Model guided sequence alignments identified 101 HD-Zip genes in the soybean genome. Phylogeny reconstruction coupled with domain and gene structure analyses using soybean, Arabidopsis, rice, grape (Vitis vinifera), and Medicago truncatula homologues enabled placement of these sequences into four previously described subfamilies. Of the 101 HD-Zip genes identified in soybean, 88 exist as whole-genome duplication-derived gene pairs, indicating high retention of these genes following polyploidy in Glycine ~13 Mya. The HD-Zip genes exhibit ubiquitous expression patterns across 24 conditions that include 17 tissues of soybean. An RNA-Seq experiment performed to study differential gene expression at 0, 1, 6 and 12 hr soybean roots under dehydration and salt stress identified 20 differentially expressed (DE) genes. Several of these DE genes are orthologs of genes previously reported to play a role under abiotic stress, implying conservation of HD-Zip gene functions across species. Screening of HD-Zip promoters identified transcription factor binding sites that are overrepresented in the DE genes under both dehydration and salt stress, providing further support for the role of HD-Zip genes in abiotic stress responses.ConclusionsWe provide a thorough description of soybean HD-Zip genes, and identify potential candidates with probable roles in dehydration and salt stress. Expression profiles generated for all soybean genes, under dehydration and salt stress, at four time points, will serve as an important resource for the soybean research community, and will aid in understanding plant responses to abiotic stress.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-950) contains supplementary material, which is available to authorized users.

A homolog of Class IV HD-Zip transcription factors, EsHdzip1, confers drought resistance in tobacco via enhanced the capacity of water conserving and absorbing

“…Overexpression of some HD-Zip genes have been shown to confer abiotic stress tolerance by activating the expression of stress-responsive gene and/or promoting the ABA biosynthesis (Yu et al 2008;Belamkar et al 2014;Chen et al 2014). Therefore, to better understand the physiological roles of HD-Zip transcription factors during abiotic stress, it was of much importance to develop abiotic stresstolerant plants by engineering manipulation.…”

“…Many studies have reported that some members of transcription factor family such as AP2, NAC, NF-Y, and HD-Zip are involved in abiotic stress-mediated responses and play pivotal regulatory roles in the stress tolerance in plants Nakashima et al 2012;Belamkar et al 2014;Chen et al 2014). During the early phase of plant acclimation to drought stress, the stress signals are transduced to trigger the expression of a large number of stress-responsive genes (Kim et al 2002;Harb et al 2010).…”

“…A novel transcription factor NF-YC1 from Bermudagrass was reported to enhance the tolerance of transgenic rice to drought and salinity (Chen et al 2014). Recently, increased evidences have shown that some members of HD-Zip transcription factors play important roles in mediating abiotic stress responses in plants (Cabello and Chan 2012;Zhao et al 2014;Belamkar et al 2014). HD-Zip proteins are a large family of plant-specific transcription factors (Schena and Davis 1992).…”

Expression of Heat Shock Proteins by Heat Stress in Soybean

“…Because of the low cost and high capacity of data, RNA-sequencing (RNA-seq) has been using to measuring differentially expressed genes (DEGs) in response to stress (Marioni et al 2008;Wang et al 2009;Anders and Huber 2010;Rapaport et al 2013). It was also used to reveal differential expressed transcriptome in rice under cold conditions (Shen et al 2014), HD-Zip transcription factors in soybean under salt stress (Belamkar et al 2014) and regulated genes in Brassica juncea under drought stress and high temperature (Bhardwaj et al 2015).…”

Genetic diversity andin vitroassessment of salt tolerance responses and associated changes in gene expression of male poplar (Populus) trees

“…Transcription factors (TFs) are important regulatory proteins, and play significant roles in the plant response and adaptation to different types of abiotic stresses (Jeong, Volny, & Lukowitz, 2012;Lee, Park, Yoon, Choi, & Eo, 2013;Lindemose, O'Shea, Jensen, & Skriver, 2013). HD-Zip genes are plant-specific transcriptional factors that play crucial roles in Populus tree development and response to environmental stresses such as water deficit and salt stress (Belamkar et al, 2014;Du, Mansfield, & Groover, 2009;Elhiti & Stasolla, 2009;Hu et al, 2012;Lee et al, 2013;Robischon, Du, Miura, & Groover, 2011). As Populus species are dioecious, male clones in some of the Populus species tend to have longer internodes, higher plant dry weight and heavier wood as compared to the female clones (Gyulai et al, 2015;Khosla & Deol, 1984).…”