RNA-Seq Analysis of Diverse Rice Genotypes to Identify the Genes Controlling Coleoptile Growth during Submerged Germination.
RNA-Seq Analysis of Diverse Rice Genotypes to Identify the Genes Controlling Coleoptile Growth during Submerged Germination.
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DOI：
10.3389/fpls.2017.00762
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发表时间：
2017
影响因子：
5.6
通讯作者：
Tung CW
中科院分区：
文献类型：
--
作者：
Hsu SK;Tung CW
发芽阶段在水下生长的不同水稻品种的胚芽鞘伸长率各不相同。与敏感品种相比，耐淹水稻表现出显着的胚芽鞘伸长，以便从表面吸收氧气（O2），从而有更好的机会生存水分胁迫。我们进行了 RNA-seq 分析，以研究在水下表现出不同胚芽鞘伸长率的六种水稻基因型的 7 天芽转录组动态。这使我们能够鉴定参与光合作用、脂质代谢、糖酵解、厌氧发酵、激素合成、细胞壁生长和伸长的基因，并证明这些基因在基因型内部和基因型之间受到差异性调节。此外，除了确定等位基因变异如何影响厌氧发芽外，我们还比较了六种基因型的表达模式和基因组序列；这使我们能够发现一些基因在敏感品种的编码区中存在从小到大的缺失。这些结构变化可以解释数据集中转录本的缺失，以及敏感品种未能对淹没做出反应的原因。根据这些结果，我们假设转录调控增强了胚芽鞘的伸长。尽管这是未来研究的一个领域，但这项研究的结果预计将有助于水稻直播育种。
The rate of coleoptile elongation varies between different rice varieties that are grown under water during the germination stage. Compared to sensitive varieties, submergence-tolerant rice exhibits substantial coleoptile elongation in order to uptake oxygen (O2) from the surface and thus have a better chance to survive water stress. We conducted RNA-seq analysis in order to investigate 7-day-old shoot transcriptome dynamics in six rice genotypes that exhibit different coleoptile elongation rates under water. This enabled us to identify the genes involved in photosynthesis, lipid metabolism, glycolysis, anaerobic fermentation, hormone synthesis, cell wall growth and elongation, and to demonstrate that these genes are differentially regulated within, and between, genotypes. Further, in addition to determining how allelic variation affects anaerobic germination, we compared the expression patterns and genomic sequences of six genotypes; this enabled us to discover that some genes carry small-to-large deletions in the coding region of sensitive varieties. These structural variations may explain the absence of transcripts in the dataset, as well as the failure of sensitive variety to respond to submergence. On the basis of these results, we hypothesize that transcriptional regulation enhances coleoptile elongation. Although this is an area for future research, the outcome of this study is expected to facilitate rice breeding for direct-seeding.