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/细胞质中发生伴随融合与加倍的过程，已知其会快速改变全基因组转录组动态，这一现象被称为“转录组冲击（transcriptomic shock）”。然而，转录组改变在群体水平上产生表型多样性的直接效应仍研究不足。本研究采用基于MassARRAY的Sequenom平台，对从水稻亲本亚种籼稻（indica）与粳稻（japonica）、体外“杂种”（亲本混合样本）、正反交F1杂种以及第五代自交正反交四倍体（S5）的各群体中随机选取的一批个体的两种组织（叶片与根）的直系同源基因（orthologous gene）、等位基因（allelic gene）及部分同源基因（homeologous gene）的表达状态进行评估与比较。研究结果显示，杂交与全基因组复制（WGD）分别对二倍体杂种和四倍体的等位基因及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强化亲本固有表达差异，并产生广泛且可变的部分同源基因组成，进而引发四倍体植株间表达模式的多样化。结合在四倍体个体间观测到的丰富表型多样性，本研究结果为“异源多倍化可促进高等植物快速表型多样化”这一观点提供了实验证据。此外，本研究数据还表明，相较于总表达水平的改变，主要由随机过程介导的部分同源基因组成重排或许是年轻片段型异源多倍体进化的重要特征，这一特征构成了群体水平快速表达多样性的基础。