Data from: Segmental allotetraploidy generates extensive homeologous expression rewiring and phenotypic diversity at the population level in rice

Allopolyploidization, i.e., concomitant merging and doubling of two or more divergent genomes in a common nucleus/cytoplasm, is known to instantly alter genome-wide transcriptome dynamics, a phenomenon referred to as “transcriptomic shock”. However, the immediate effects of transcriptomic alteration in generating phenotypic diversity at the population level remain under-investigated. Here, we employed the MassARRAY-based Sequenom platform to assess and compare orthologous, allelic, and homeologous gene expression status in two tissues (leaf and root) of a set of randomly chosen individuals from populations of parental rice subspecies (indica and japonica), in vitro “hybrids” (parental mixes), reciprocal F1 hybrids and reciprocal tetraploids at the 5th-selfed generation (S5). We show that hybridization and whole genome duplication (WGD) have opposing effects on allelic and homeologous expression in the F1 hybrids and tetraploids, respectively. Whereas hybridization exerts strong attenuating effects on allelic expression differences in diploid hybrids, WGD augments the intrinsic parental differences and generates extensive and variable homeolog content which triggers diversification in expression patterning among the tetraploid plants. Coupled with the vast phenotypic diversity observed among the tetraploid individuals, our results provide experimental evidence in support of the notion that allopolyploidy catalyzes rapid phenotypic diversification in higher plants. Our data further suggest that largely stochastic homeolog content reshuffling rather than alteration in total expression level may be an important feature of evolution in young segmental allopolyploids, which underlies rapid expression diversity at the population level.

异源多倍化（allopolyploidization）指两个或多个趋异基因组在同一细胞核/细胞质中伴随融合与加倍的过程，已知其会立即改变全基因组范围的转录组动态变化，该现象被称为“转录组震荡（transcriptomic shock）”。然而，转录组改变在种群水平产生表型多样性的直接效应仍未得到充分研究。本研究依托基于MassARRAY的Sequenom平台，对亲本水稻亚种（籼稻和粳稻）、体外“杂种”（亲本混合样本）、正反交F1杂种以及自交第5代（S5）正反交四倍体的种群中随机选取的个体的两个组织（叶片和根系），开展直系同源基因、等位基因及部分同源基因的表达状态评估与比较分析。研究发现，杂交与全基因组复制（whole genome duplication, WGD）分别对F1杂种和四倍体的等位基因与部分同源基因表达产生相反的调控效应。在二倍体杂种中，杂交会显著减弱等位基因表达差异；而全基因组复制则会放大亲本固有的表达差异，并产生广泛且可变的部分同源基因组分，进而引发四倍体植株间表达模式的多样化。结合在四倍体个体中观察到的丰富表型多样性，本研究结果为“异源多倍化可推动高等植物快速表型多样化”这一观点提供了实验证据。本研究数据进一步表明，相较于总表达水平的改变，大范围随机的部分同源基因组分重排（stochastic homeolog content reshuffling）可能是年轻节段异源多倍体进化的重要特征，这也是种群水平快速产生表达多样性的基础。