Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage (Brassica rapa)
Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage (Brassica rapa)
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DOI：
10.1038/s41438-019-0212-9
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发表时间：
2019-12-01
影响因子：
8.7
通讯作者：
Bonnema, Guusje
中科院分区：
文献类型：
--
作者：
Sun, XiaoXue;Basnet, Ram Kumar;Bonnema, Guusje
大白菜植株在形成叶球之前经历幼苗和莲座阶段。大白菜植物在其幼苗阶段类似于小白菜植物，但在其莲座期，大白菜的叶子分化，因为它们的尺寸增加，叶柄变短。为了了解在叶球形成中起作用的分子途径，分析了两个大白菜基因型和一个小白菜基因型在幼叶发育过程中的转录本丰度。这两种大白菜在早熟性、叶片大小和形状、叶片数量、叶球形状等方面存在差异。全基因组转录组分析清楚地分开了所有三种基因型的幼苗阶段，以及来自小白菜的后期阶段，来自两种大白菜的后期发育阶段（莲座、折叠和抽穗）。通过加权相关网络分析和欧氏距离的系统聚类，得到了两种大白菜与小白菜不同的基因簇。三个簇包括基因型和发育阶段的影响，而两个簇只表现出基因型效应的转录丰度的基因。这包括高度富集MapMan类光合作用的发育阶段簇的基因型，在中国白菜的莲座和折叠期间具有高表达，并且在不暴露于光的抽穗内叶中具有低表达。其他聚类包含MapMan分类Cell中的许多基因，再次显示了小白菜和两种大白菜之间的差异。我们讨论了这与大白菜和小白菜叶片生长的差异，特别是在莲座期。总的来说，两个非常不同的中国白菜与小白菜在植物发育过程中的叶片之间的转录组的比较允许识别与叶球形成相关的特定基因类别。
Chinese cabbage plants go through seedling and rosette stages before forming their leafy head. Chinese cabbage plants resemble pak-choi plants at their seedling stage, but in their rosette stage the leaves of Chinese cabbage differentiate, as they increase in size with shorter petioles. In order to understand the molecular pathways that play a role in leafy head formation, transcript abundance of young emerging leaves was profiled during development of two Chinese cabbage genotypes and a single pak-choi genotype. The two Chinese cabbages differed in many aspects, among others earliness, leaf size and shape, leaf numbers, and leafy head shape. Genome-wide transcriptome analysis clearly separated the seedling stages of all three genotypes together with the later stages from pak-choi, from the later developmental stages of both Chinese cabbages (rosette, folding, and heading). Weighted correlation network analysis and hierarchical clustering using Euclidean distances resulted in gene clusters with transcript abundance patterns distinguishing the two Chinese cabbages from pak-choi. Three clusters included genes with transcript abundance affected by both genotype and developmental stage, whereas two clusters showed only genotype effects. This included a genotype by developmental stage cluster highly enriched with the MapMan category photosynthesis, with high expression during rosette and folding in Chinese cabbages and low expression in the heading inner leaves that are not exposed to light. The other clusters contained many genes in the MapMan categories Cell, showing again differences between pak-choi and both Chinese cabbages. We discuss how this relates to the differences in leaf blade growth between Chinese cabbage and pak-choi, especially at the rosette stage. Overall, comparison of the transcriptome between leaves of two very different Chinese cabbages with pak-choi during plant development allowed the identification of specific gene categories associated with leafy head formation.