Genome-wide analysis of soybean HD-Zip gene family and expression profiling under salinity and drought treatments

• Published in: PloS one Vol. 9; no. 2; p. e87156
• Main Authors: Chen, Xue, Chen, Zhu, Zhao, Hualin, Zhao, Yang, Cheng, Beijiu, Xiang, Yan
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 03.02.2014; Public Library of Science (PLoS)
• Subjects: Agriculture; Amino Acid Sequence; Amino acids; Arabidopsis; Arabidopsis - genetics; Base Sequence; Biological evolution; Biology; Biotechnology; Cell division; Chromosome Mapping; Chromosomes; Chromosomes, Plant - genetics; Cladistic analysis; Cluster Analysis; Corn; Deoxyribonucleic acid; Divergence; DNA; DNA binding proteins; Drought; Droughts; Evolutionary genetics; Gene duplication; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant - drug effects; Genes; Genetic Variation; Genome, Plant - genetics; Genomes; Genomics; Glycine max; Glycine max - genetics; High definition television; Homeobox; Homeodomain Proteins - classification; Homeodomain Proteins - genetics; Laboratories; Landscape architecture; Leucine; Leucine zipper proteins; Leucine Zippers - genetics; Molecular biology; Molecular Sequence Data; Oligonucleotide Array Sequence Analysis; Oryza; Oryza - genetics; Phylogenetics; Phylogeny; Plant growth; Plant Proteins - classification; Plant Proteins - genetics; Polymerase chain reaction; Profiling; Proteins; Reproduction (copying); Reverse Transcriptase Polymerase Chain Reaction; Salinity; Salinity effects; Sodium Chloride - pharmacology; Soybeans; Stresses; Tissues; Transcription factors
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0087156

Homeodomain-leucine zipper (HD-Zip) proteins, a group of homeobox transcription factors, participate in various aspects of normal plant growth and developmental processes as well as environmental responses. To date, no overall analysis or expression profiling of the HD-Zip gene family in soybean (Glycine max) has been reported. An investigation of the soybean genome revealed 88 putative HD-Zip genes. These genes were classified into four subfamilies, I to IV, based on phylogenetic analysis. In each subfamily, the constituent parts of gene structure and motif were relatively conserved. A total of 87 out of 88 genes were distributed unequally on 20 chromosomes with 36 segmental duplication events, indicating that segmental duplication is important for the expansion of the HD-Zip family. Analysis of the Ka/Ks ratios showed that the duplicated genes of the HD-Zip family basically underwent purifying selection with restrictive functional divergence after the duplication events. Analysis of expression profiles showed that 80 genes differentially expressed across 14 tissues, and 59 HD-Zip genes are differentially expressed under salinity and drought stress, with 20 paralogous pairs showing nearly identical expression patterns and three paralogous pairs diversifying significantly under drought stress. Quantitative real-time RT-PCR (qRT-PCR) analysis of six paralogous pairs of 12 selected soybean HD-Zip genes under both drought and salinity stress confirmed their stress-inducible expression patterns. This study presents a thorough overview of the soybean HD-Zip gene family and provides a new perspective on the evolution of this gene family. The results indicate that HD-Zip family genes may be involved in many plant responses to stress conditions. Additionally, this study provides a solid foundation for uncovering the biological roles of HD-Zip genes in soybean growth and development.