State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.
BMC Plant Biol. 2019 Mar 13;19(1):102. doi: 10.1186/s12870-019-1691-4.
Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus. But they are difficult to grow for commercial seed production due to serious seed shattering. We conducted a comparative transcriptome analysis of abscission zone to find possible transcription changes associated with seed shattering, explore candidate genes involved in seed shattering and identify candidate gene-based EST-SSR markers for germplasm evaluation.
cDNA libraries from abscission zone (AZ) and non-abscission zone (NAZ) tissues of E. nutans were constructed and sequenced. A total of 111,667 unigenes were annotated and 7644 differentially expressed transcripts (DETs) were predicted, corresponding to 6936 up-regulated in AZ and 708 down-regulated in NAZ. We identified 489 candidate genes related to transcription factor, cell wall hydrolysis or modification, hydrolase activity, phytohormone signaling and response, lignin biosynthesis, and signal transduction or protein turnover. Eleven similar candidate genes involved in polygalacturonase activity, hydrolase activity, and mitogen-activated protein kinase were up-regulated in the abscission zone of the two Elymus species, suggesting these genes may have specific function for abscission zone development and seed shattering. A total of 67 polymorphic EST-SSR markers were developed and characterized based on the sequences of these candidate genes. Fourteen polymorphic EST-SSR primers were finally used to study genetic diversity in 48 E. nutans genotypes with contrasting seed shattering habit. The dendrogram based on molecular data showed that most accessions with similar seed shattering degree tended to group together.
The expression data generated from this study provides an important resource for future molecular biological research. Many DETs were associated with abscission zone development, and EST-SSR loci related to candidate genes may have potential application in identifying trait-associated markers in E. nutans in the future.
垂穗披碱草和西伯利亚披碱草是披碱草属的两种重要牧草。但由于种子严重破碎，它们难以进行商业种子生产。我们对离区进行了比较转录组分析，以寻找可能与种子破碎相关的转录变化，探索涉及种子破碎的候选基因，并鉴定基于候选基因的 EST-SSR 标记用于种质评估。
构建并测序了垂穗披碱草离区（AZ）和非离区（NAZ）组织的 cDNA 文库。共注释了 111667 个 unigenes，并预测了 7644 个差异表达转录本（DETs），对应于 AZ 上调的 6936 个和 NAZ 下调的 708 个。我们鉴定了 489 个与转录因子、细胞壁水解或修饰、水解酶活性、植物激素信号转导和响应、木质素生物合成以及信号转导或蛋白质周转相关的候选基因。在两个披碱草属的离区中，11 个相似的候选基因参与多聚半乳糖醛酸酶活性、水解酶活性和丝裂原激活蛋白激酶的表达上调，表明这些基因可能对离区发育和种子破碎具有特定功能。共开发和表征了 67 个基于这些候选基因序列的多态性 EST-SSR 标记。最终，使用 14 个多态性 EST-SSR 引物研究了 48 个具有不同种子破碎习性的垂穗披碱草基因型的遗传多样性。基于分子数据的聚类图显示，大多数具有相似种子破碎程度的个体倾向于聚集在一起。
本研究产生的表达数据为未来的分子生物学研究提供了重要资源。许多 DETs 与离区发育有关，与候选基因相关的 EST-SSR 位点将来可能具有鉴定垂穗披碱草相关性状标记的潜力。
