Citation: Belamkar, V., Weeks, N.T., Bharti, A.K., Farmer, A.D., Graham, M.A., Cannon, S.B. 2014. Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. Biomed Central (BMC) Genomics. 15:950. DOI:10.1186/1471-2164-15-950.
Interpretive Summary: Soybeans yields can be severely decreased by drought, heat stress and saline soil conditions. All of these stresses are likely to increase with climate change and intensification of agriculture: drought and heat stress due to higher temperatures and saline soil conditions due to salts left in the soil during irrigation or by incursion of salty water in coastal areas. Breeding progress towards plants that are more resilient to these environmental stresses can be speeded by an understanding of genes that help control plant responses to these kinds of stresses. The research in this paper describes a set of related genes in soybean that respond to salt and desiccation. These findings are supported by reports of similar functions of genes in this "gene family" in other species, such as corn, rice and the genetic model plant Arabidopsis. The results of this work will be useful to plant breeders and researchers working to produce soybean varieties that are more tolerant to climate and environmental stresses.
Technical Abstract: The 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 well 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 various species suggest HD-Zip genes as high priority candidates for crop improvement. In 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 ~10 Mya. The HD-Zip genes exhibit both ubiquitous and tissue-specific expression patterns across 14 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 numerous 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. We provide a thorough description of soybean HD-Zip genes, and identify candidates with roles in dehydration and salt stress. Expression profiles generated for all soybean genes, under dehydration and salt stress, at four different time points, will serve as an important resource for the soybean research community, and will aid in understanding plant responses to abiotic stress.