Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA.
Theor Appl Genet. 2019 Aug;132(8):2295-2308. doi: 10.1007/s00122-019-03355-8. Epub 2019 May 16.
We report rampant homoeologous exchanges in progenies of a newly synthesized rice segmental allotetraploid and demonstrate their consequences to changes of gene expression and alternative splicing. Allopolyploidization is recurrent across the tree of angiosperms and known as a driving evolutionary force in both plants and animals. A salient feature of allopolyploidization is the induction of homoeologous exchange (HE) events between the constituent subgenomes, which may in turn cause changes in gene expression, transcript alternative splicing, and phenotypic novelty. However, this issue has been poorly studied, largely because lack of a system in which the exact parentage donating the subgenomes is known and the HE events are occurring in real time. Here, we employed whole-genome re-sequencing and RNA-seq-based transcriptome profiling in four randomly chosen progeny individuals (at the 10th-selfed generation) of segmental allotetraploids that were constructed by colchicine-mediated whole-genome doubling of F1 hybrids between the two subspecies (japonica and indica) of Asian cultivated Oryza sativa. We show that rampant HE events occurred in these tetraploid individuals, which converted most of the otherwise heterozygous genomic regions into a homogenized state of one parental subgenome. We demonstrate that genes within these homogenized genomic regions in the tetraploids showed high frequencies of altered expression and enhanced alternative splicing relative to their counterparts in the corresponding diploid parents in the embryo tissue. Intriguingly, limited overlaps between the differentially expressed genes and the differential alternative spliced genes were identified, which were partitioned to distinctly enriched gene ontology terms. Together, our results indicate that HE is a major mechanism to rapidly generate novelty in gene expression and transcriptome diversity, which may facilitate phenotypic innovation in nascent allopolyploids and relevant to allopolyploid crop breeding.
我们报道了新合成的水稻片段异源四倍体后代中猖獗的同源重组交换，并证明了它们对基因表达和选择性剪接变化的影响。异源多倍化在被子植物的进化树上反复出现，是动植物进化的驱动力之一。异源多倍化的一个显著特征是组成亚基因组之间同源重组交换（HE）事件的诱导，这可能导致基因表达、转录物选择性剪接和表型新颖性的变化。然而，这个问题研究得还不够充分，主要是因为缺乏一个系统，其中确切的亚基因组供体亲本是已知的，并且 HE 事件正在实时发生。在这里，我们采用全基因组重测序和基于 RNA-seq 的转录组谱分析，对通过秋水仙素介导的两个亚种（粳稻和籼稻）亚洲栽培稻 F1 杂种全基因组加倍构建的片段异源四倍体的四个随机选择的后代个体（第 10 次自交代）进行研究。我们表明，这些四倍体个体中发生了猖獗的 HE 事件，这些事件将大多数原本杂合的基因组区域转化为一个亲本亚基因组的同质化状态。我们证明，在四倍体中，这些同质化基因组区域内的基因表现出高频改变表达和增强选择性剪接的现象，与相应二倍体亲本在胚胎组织中的基因相比。有趣的是，在差异表达基因和差异选择性剪接基因之间，我们确定了有限的重叠，这些重叠被划分到明显富集的基因本体论术语中。总之，我们的研究结果表明，HE 是快速产生基因表达和转录组多样性新颖性的主要机制，这可能有助于新生异源多倍体的表型创新，与异源多倍体作物的育种相关。
