Chao Zhou: Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China. zhouchao@ctgu.edu.cn. ORCID
Xiaoyun Liu: Institute for Interdisciplinary Research, Jianghan University, Wuhan, 430056, China.
Hanlin Zhou: Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China.
Sijia Wang: Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China.
Zhu Yuan: Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China.
Yonghong Zhang: Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, 442000, China.
Sanhe Li: Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
Aiqing You: Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
Lei Zhou: Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China. yutianzhou@gmail.com.
Zhengquan He: Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China. zhq_he@163.com.
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.
