Genome-Wide Analysis of Soybean HD-Zip Gene Family and Expression Profiling under Salinity and Drought Treatments

Abstract

BackgroundHomeodomain-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.Methods and FindingsAn 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.ConclusionsThis 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.

Genome-wide identification of pear HD-Zip gene family and expression patterns under stress induced by drought, salinity, and pathogen

“…HD-Zip subfamily I has the shortest sequences and contains only HD domain and LZ motif (Chen et al 2014). HD-Zip II proteins contain five additional conserved amino acids, Cys, Pro, Ser, Cys, and Glu, known as ''CPSCE'', which is located downstream of the LZ motif (Tron et al 2002;Chen et al 2014).…”

“…HD-Zip II proteins contain five additional conserved amino acids, Cys, Pro, Ser, Cys, and Glu, known as ''CPSCE'', which is located downstream of the LZ motif (Tron et al 2002;Chen et al 2014). Members of these two subfamilies bind similar pseudo-palindromic cis-elements, CAAT-NATTG (Sessa et al 1993;Frank et al 1998;Johannesson et al 2001).…”

“…The HD-Zip family members were widely investigated in A. thaliana (Schena and Davis 1992), Z. mays (Zhao et al 2011), O. sativa (Agalou et al 2008), P. trichocarpa (Hu et al 2012), and other species (Liu et al 2013;Chen et al 2014;Zhang et al 2014). Until now, no genome-wide research, including gene identification, genome organization, and phylogenetic analysis, has been reported in pear.…”

“…Then, aligned sequences were constructed using Clustal W of MEGA5.0 software (Tamura et al 2011) with the neighbor-jointing method. A bootstrap of 1000 replicates with pairwise deletion option was performed (Chen et al 2014). Subfamilies of the HDZip proteins of pear and apple were classified according to their phylogenetic relationships with their corresponding Arabidopsis HD-Zip proteins.…”

“…Recent comprehensive analysis of genes encoding HD-Zip proteins from other plant species, such as Populus (Hu et al 2012), peach (Zhang et al 2014), soybean (Chen et al 2014), Arabidopsis (Olsson et al 2004), maize (Zhao et al 2011), and rice (Agalou et al 2008), enabled comparison of numbers and classification of these genes among different species. For some species, the larger the genome size of the Fig.…”