The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China.
BMC Genomics. 2019 Apr 11;20(1):287. doi: 10.1186/s12864-019-5632-2.
The trihelix gene family is a plant-specific transcription factor family that plays important roles in plant growth, development, and responses to abiotic stresses. However, to date, no systemic characterization of the trihelix genes has yet been conducted in wheat and its close relatives.
We identified a total of 94 trihelix genes in wheat, as well as 22 trihelix genes in Triticum urartu, 29 in Aegilops tauschii, and 31 in Brachypodium distachyon. We analyzed the chromosomal locations and orthology relations of the identified trihelix genes, and no trihelix gene was found to be located on chromosome 7A, 7B, or 7D of wheat, thereby reflecting the uneven distributions of wheat trihelix genes. Phylogenetic analysis indicated that the 186 identified trihelix proteins in wheat, rice, B. distachyon, and Arabidopsis were clustered into five major clades. The trihelix genes belonging to the same clades usually shared similar motif compositions and exon/intron structural patterns. Five pairs of tandem duplication genes and three pairs of segmental duplication genes were identified in the wheat trihelix gene family, thereby validating the supposition that more intrachromosomal gene duplication events occur in the genome of wheat than in that of other grass species. The tissue-specific expression and differential expression profiling of the identified genes under cold and drought stresses were analyzed by using RNA-seq data. qRT-PCR was also used to confirm the expression profiles of ten selected wheat trihelix genes under multiple abiotic stresses, and we found that these genes mainly responded to salt and cold stresses.
In this study, we identified trihelix genes in wheat and its close relatives and found that gene duplication events are the main driving force for trihelix gene evolution in wheat. Our expression profiling analysis demonstrated that wheat trihelix genes responded to multiple abiotic stresses, especially salt and cold stresses. The results of our study built a basis for further investigation of the functions of wheat trihelix genes and provided candidate genes for stress-resistant wheat breeding programs.
三螺旋框基因家族是一类植物特异性转录因子家族，在植物生长、发育和非生物胁迫响应中发挥着重要作用。然而，迄今为止，尚未对小麦及其近缘种进行系统的三螺旋框基因分析。
我们共鉴定到小麦中 94 个三螺旋框基因，在节节麦中鉴定到 22 个，在粗山羊草中鉴定到 29 个，在拟南芥中鉴定到 31 个。我们分析了鉴定到的三螺旋框基因的染色体定位和同源关系，没有发现小麦 7A、7B 或 7D 染色体上存在三螺旋框基因，这反映了小麦三螺旋框基因的不均匀分布。系统发育分析表明，在小麦、水稻、拟南芥和粗山羊草中鉴定到的 186 个三螺旋框蛋白聚类为 5 个主要分支。属于同一分支的三螺旋框基因通常具有相似的基序组成和外显子/内含子结构模式。在小麦三螺旋框基因家族中鉴定到 5 对串联重复基因和 3 对片段重复基因，从而验证了这样一种假设，即在小麦基因组中发生的染色体内基因重复事件比在其他禾本科物种中更为频繁。利用 RNA-seq 数据分析了鉴定到的基因在冷胁迫和干旱胁迫下的组织特异性表达和差异表达谱，并通过 qRT-PCR 验证了 10 个选定的小麦三螺旋框基因在多种非生物胁迫下的表达谱，发现这些基因主要响应盐胁迫和冷胁迫。
本研究在小麦及其近缘种中鉴定到三螺旋框基因，发现基因重复事件是小麦三螺旋框基因进化的主要驱动力。我们的表达谱分析表明，小麦三螺旋框基因响应多种非生物胁迫，特别是盐胁迫和冷胁迫。本研究的结果为进一步研究小麦三螺旋框基因的功能奠定了基础，并为耐盐小麦育种计划提供了候选基因。
