Polyploidy has been a prevalent process during plant evolution and it has made a major impact on the structure and evolution of plant genomes. Many important crop plants are polyploid. There is considerable interest in expression patterns of duplicated genes in polyploids. Alternative splicing (AS) is a fundamental aspect of gene expression that produces multiple final transcript types from a single type of mRNAs. The effects of abiotic stress conditions on AS in polyploids has received little attention. We conducted a global transcriptome analysis of Brassica napus, an allotetraploid derived from B. rapa (A_T) and B. oleracea (C_T), by RNA‐Seq of plants subjected to cold, heat, and drought stress treatments. Analyses of 27,360 pairs of duplicated genes revealed overall A_T subgenome biases in gene expression and C_T subgenome biases in the extent of alternative splicing under all three stress treatments. More genes increased in expression than decreased in response to the stresses. Negative correlations were found between expression levels and AS frequency for each type of AS. Cold stress produced the greatest changes in gene expression and AS. Cold‐induced AS changes were more likely to be shared with those generated by drought than by heat stress. We used homeologs of FLC and CCA1 as case studies to show the dynamics of how duplicates in a polyploid respond to cold stress. Our results suggest that divergence in gene expression and AS patterns between duplicated genes may increase the flexibility of polyploids when responding to abiotic stressors.

中文翻译：

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在高温，寒冷和干旱胁迫下多倍体甘蓝型油菜中重复基因表达和选择性剪接的全球见解

多倍体是植物进化过程中的一个普遍过程，它对植物基因组的结构和进化产生了重大影响。许多重要的农作物都是多倍体。人们对多倍体中重复基因的表达模式非常感兴趣。选择性剪接（AS）是基因表达的基本方面，可从一种类型的mRNA产生多种最终转录本类型。非生物胁迫条件对多倍体AS的影响很少受到关注。我们进行的全局转录组分析欧洲油菜，异源四倍体衍生自芜菁（A _Ť）和甘蓝（C _Ť），通过经受冷，热和干旱胁迫处理的植物的RNA‐Seq。对27,360对重复基因的分析显示，在所有三种胁迫处理下，选择性剪接的程度在基因表达中总体存在A _T亚基因组偏倚，而C _T亚基因组偏倚。表达增加的基因多于响应压力而减少的基因。在每种AS类型的表达水平和AS频率之间发现负相关。冷应激在基因表达和AS中产生了最大的变化。与干旱相比，干旱引起的AS变化更可能与干旱产生的AS变化相同。我们使用了FLC和CCA1的同源词作为案例研究，以显示多倍体中复制品如何响应冷胁迫的动力学。我们的结果表明，重复基因之间基因表达和AS模式的差异可能会增加多倍体对非生物胁迫的响应能力。