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

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.

背景：同源域-亮氨酸拉链（Homeodomain-leucine zipper, HD-Zip）蛋白属于一类同源框转录因子，参与植物正常生长发育的多个环节以及环境胁迫响应。截至目前，尚未见针对大豆（Glycine max）HD-Zip基因家族的全基因组分析或表达谱研究的报道。
方法与结果：本研究通过对大豆基因组的系统检索与分析，共鉴定得到88个HD-Zip家族候选基因。基于系统发育分析，这些基因被划分为I至IV共4个亚家族。各亚家族内部的基因结构与基序组成相对保守。88个基因中有87个不均匀地分布于20条染色体上，共检测到36个片段重复（segmental duplication）事件，表明片段重复是HD-Zip基因家族扩张的重要驱动因素。通过对非同义替换率与同义替换率比值（Ka/Ks）的分析发现，HD-Zip家族的重复基因在复制事件后基本经历了纯化选择，功能分化受到限制。表达谱分析显示，80个基因在14种组织中呈现差异化表达；另有59个HD-Zip基因在盐胁迫与干旱胁迫处理下表现出表达差异，其中20个旁系同源基因对的表达模式近乎一致，另有3个旁系同源基因对在干旱胁迫下出现了显著的表达分化。针对筛选出的12个大豆HD-Zip基因的6个旁系同源基因对，分别在干旱与盐胁迫条件下开展定量实时荧光逆转录PCR（Quantitative real-time RT-PCR, qRT-PCR）验证，结果证实了这些基因的胁迫诱导表达模式。
结论：本研究全面梳理并解析了大豆HD-Zip基因家族，为该家族的进化研究提供了全新视角。研究结果表明，HD-Zip家族基因可能广泛参与植物的胁迫响应过程。此外，本研究为解析HD-Zip基因在大豆生长发育中的生物学功能奠定了坚实的理论基础。