Zhou Chao, Liu Xiaoyun, Li Xinglei, Zhou Hanlin, Wang Sijia, Yuan Zhu, Zhang Yonghong, Li Sanhe, You Aiqing, Zhou Lei, He Zhengquan
Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China.
Institute for Interdisciplinary Research, Jianghan University, Wuhan, 430056, China.
Rice (N Y). 2021 Aug 4;14(1):72. doi: 10.1186/s12284-021-00515-7.
Evolutionarily, polyploidy represents a smart method for adjusting agronomically important in crops through impacts on genomic abundance and chromatin condensation. Autopolyploids have a relatively concise genetic background with great diversity and provide an ideal system to understand genetic and epigenetic mechanisms attributed to the genome-dosage effect. However, whether and how genome duplication events during autopolyploidization impact chromatin signatures are less understood in crops. To address it, we generated an autotetraploid rice line from a diploid progenitor, Oryza sativa ssp. indica 93-11. Using transposase-accessible chromatin sequencing, we found that autopolyploids lead to a higher number of accessible chromatin regions (ACRs) in euchromatin, most of which encode protein-coding genes. As expected, the profiling of ACR densities supported that the effect of ACRs on transcriptional gene activities relies on their positions in the rice genome, regardless of genome doubling. However, we noticed that genome duplication favors genic ACRs as the main drivers of transcriptional changes. In addition, we probed intricate crosstalk among various kinds of epigenetic marks and expression patterns of ACR-associated gene expression in both diploid and autotetraploid rice plants by integrating multiple-omics analyses, including chromatin immunoprecipitation sequencing and RNA-seq. Our data suggested that the combination of H3K36me2 and H3K36me3 may be associated with dynamic perturbation of ACRs introduced by autopolyploidization. As a consequence, we found that numerous metabolites were stimulated by genome doubling. Collectively, our findings suggest that autotetraploids reshape rice morphology and products by modulating chromatin signatures and transcriptional profiling, resulting in a pragmatic means of crop genetic improvement.
从进化角度来看，多倍体是一种通过影响基因组丰度和染色质凝聚来调控作物重要农艺性状的巧妙方式。同源多倍体具有相对简洁的遗传背景且多样性高，为理解基因组剂量效应所导致的遗传和表观遗传机制提供了理想系统。然而，在作物中，同源多倍体化过程中基因组复制事件是否以及如何影响染色质特征尚不清楚。为解决这一问题，我们从二倍体祖先种籼稻93-11培育出了一个同源四倍体水稻品系。利用转座酶可及染色质测序技术，我们发现同源多倍体在常染色质中导致更多的可及染色质区域（ACR），其中大多数编码蛋白质编码基因。正如预期的那样，ACR密度分析表明，ACR对转录基因活性的影响取决于它们在水稻基因组中的位置，与基因组加倍无关。然而，我们注意到基因组加倍有利于基因ACR成为转录变化的主要驱动因素。此外，我们通过整合包括染色质免疫沉淀测序和RNA测序在内的多组学分析，探究了二倍体和同源四倍体水稻植株中各种表观遗传标记之间的复杂相互作用以及ACR相关基因表达的模式。我们的数据表明，H3K36me2和H3K36me3的组合可能与同源多倍体化引入的ACR动态扰动有关。因此，我们发现基因组加倍刺激了大量代谢产物的产生。总体而言，我们的研究结果表明，同源四倍体通过调节染色质特征和转录谱重塑水稻形态和产物，从而为作物遗传改良提供了一种实用手段。
