Genome-wide analysis of spatiotemporal expression patterns during rice leaf development.
Genome-wide analysis of spatiotemporal expression patterns during rice leaf development.
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DOI：
10.1186/s12864-021-07494-5
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发表时间：
2021-03-09
期刊：
影响因子：
4.4
通讯作者：
Itoh JI
中科院分区：
文献类型：
--
作者：
Miya M;Yoshikawa T;Sato Y;Itoh JI
水稻叶片沿近端至远端轴由叶片、鞘和叶鞘交界区三个不同的区域组成。每个区域都有独特的形态和功能，但每个区域发展背后的遗传程序却知之甚少。为了充分阐明水稻叶片的发育，发现具有独特功能的基因，探索这三个区域发育过程中的全基因组转录谱至关重要。在这项研究中，我们使用了微阵列分析来分析水稻叶片中基因表达的时空模式，该分析使用了水稻叶片在广泛发育阶段取样的解剖部分。各区域的动态变化表明，在组织分化的整个过程中，转录组发生了巨大的变化，叶片和鞘的转录组在成熟阶段差异较大。对水稻叶片表达模式的聚类分析揭示了可能参与水稻叶片发育的特定生物学过程的基因群。此外，我们利用转录组数据和原位杂交相结合，发现了可能参与水稻叶片发育的新基因，并在高分辨率下分析了它们的空间表达模式。我们成功地鉴定了多个在水稻或草叶组织中表现出局部表达的基因。虽然已经阐明了几种植物叶片发育的遗传机制，但由于形态和发育差异，将这些信息直接应用于水稻和禾本科植物是不合适的。我们的分析不仅提供了对水稻叶片发育的见解，而且还提供了作为基因发现宝贵资源的表达谱。本研究鉴定的基因和基因簇为进一步研究水稻叶片独特的发育机制提供了基础。在线版本包含补充材料，可在10.1186/s12864-021-07494-5获得。
Rice leaves consist of three distinct regions along a proximal-distal axis, namely the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, but the genetic programs underlying the development of each region are poorly understood. To fully elucidate rice leaf development and discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions. In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages. The dynamics in each region revealed that the transcriptomes changed dramatically throughout the progress of tissue differentiation, and those of the leaf blade and sheath differed greatly at the mature stage. Cluster analysis of expression patterns among leaf parts revealed groups of genes that may be involved in specific biological processes related to rice leaf development. Moreover, we found novel genes potentially involved in rice leaf development using a combination of transcriptome data and in situ hybridization, and analyzed their spatial expression patterns at high resolution. We successfully identified multiple genes that exhibit localized expression in tissues characteristic of rice or grass leaves. Although the genetic mechanisms of leaf development have been elucidated in several eudicots, direct application of that information to rice and grasses is not appropriate due to the morphological and developmental differences between them. Our analysis provides not only insights into the development of rice leaves but also expression profiles that serve as a valuable resource for gene discovery. The genes and gene clusters identified in this study may facilitate future research on the unique developmental mechanisms of rice leaves. The online version contains supplementary material available at 10.1186/s12864-021-07494-5.
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