Comparative transcriptomics identifies differences in the regulation of the floral transition between Arabidopsis and Brassica rapa cultivars
Comparative transcriptomics identifies differences in the regulation of the floral transition between Arabidopsis and Brassica rapa cultivars
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DOI：
10.1101/2020.08.26.266494
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发表时间：
2020-08
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通讯作者：
A. Calderwood;Jo Hepworth;S. Woodhouse;L. Bilham;D. M. Jones;Eleri H Tudor;Mubarak Ali;C. Dean;R. Wells;J. Irwin;Richard J. Morris
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作者：
A. Calderwood;Jo Hepworth;S. Woodhouse;L. Bilham;D. M. Jones;Eleri H Tudor;Mubarak Ali;C. Dean;R. Wells;J. Irwin;Richard J. Morris
花期转换的时机影响生殖和产量，然而它在作物中的调控仍然知之甚少。在这里，我们使用RNA-Seq来确定和比较模式物种拟南芥和近缘作物油菜在花期转换过程中的基因表达动态。对不同物种之间基因表达随时间的直接比较表明，相似性很小，这可能导致不同的基因调控网络在发挥作用。然而，这些差异可以通过基因表达谱的同步，通过曲线注册在很大程度上得到解决。我们发现不同的基因需要不同的注册功能，这表明拟南芥和油菜没有共同的‘发育时间’可以通过基因表达来定位。相反，不同基因的表达模式以不同的速度进行。我们发现，共同调控的基因在物种之间的同步性方面表现出类似的变化，这表明类似的基因调节子网络结构可能是活跃的，它们之间的连接不同。对拟南芥和油菜以及两个油菜材料之间花转换调控的详细比较表明，关键的花整合基因SOC1的调节模式不同，即使在相同的环境条件下，油菜材料的花转换也是由不同的途径触发的。我们的研究加深了对长日照快速循环甘蓝型油菜开花时间调控网络的机械性理解，并强调了注册方法对于比较发育基因表达数据的重要性。
The timing of the floral transition affects reproduction and yield, however its regulation in crops remains poorly understood. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. A direct comparison of gene expression over time between species shows little similarity, which could lead to the inference that different gene regulatory networks are at play. However, these differences can be largely resolved by synchronisation, through curve registration, of gene expression profiles. We find that different registration functions are required for different genes, indicating that there is no common ‘developmental time’ to which Arabidopsis and B. rapa can be mapped through gene expression. Instead, the expression patterns of different genes progress at different rates. We find that co-regulated genes show similar changes in synchronisation between species, suggesting that similar gene regulatory sub-network structures may be active with different wiring between them. A detailed comparison of the regulation of the floral transition between Arabidopsis and B. rapa, and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways, even when grown under the same environmental conditions. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa under long days and highlights the importance of registration methods for the comparison of developmental gene expression data.