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A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling

文献类型： 外文期刊

作者： Zhou, Chao 1 ; Liu, Xiaoyun 2 ; Li, Xinglei 3 ; Zhou, Hanlin 1 ; Wang, Sijia 1 ; Yuan, Zhu 1 ; Zhang, Yonghong 4 ; Li, Sa 1 ;

作者机构： 1.China Three Gorges Univ, Biotechnol Res Ctr, Key Lab Gorges Reg Plant Genet & Germplasm Enhanc, Yichang 443002, Peoples R China

2.Jianghan Univ, Inst Interdisciplinary Res, Wuhan 430056, Peoples R China

3.Bioacme Biotechnol Co Ltd, Wuhan 430056, Peoples R China

4.Hubei Univ Med, Hubei Key Lab Wudang Local Chinese Med Res, Shiyan 442000, Peoples R China

5.Hubei Acad Agr Sci, Food Crops Inst, Hubei Key Lab Food Crop Germplasm & Genet Improve, Wuhan 430064, Peoples R China

关键词： Rice; Autopolyploid; Accessible chromatin regions; Transcriptional regulation; Epigenetic marks

期刊名称：RICE （ 影响因子：4.783； 五年影响因子：5.23 ）

ISSN： 1939-8425

年卷期： 2021 年 14 卷 1 期

页码：

收录情况： SCI

摘要： 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.

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