title: Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression.
abstract: Polyploidy, or whole-genome duplication (WGD), serves as a key innovation in plant evolution and is an important genomic feature for all eukaryotes. Neopolyploids have to overcome difficulties in meiosis, genomic alterations, changes of gene expression, and epigenomic reorganization. However, the underlying mechanisms for these processes are poorly understood. One of the most interesting aspects is that genome doubling events increase the dosage of all genes. Unlike allopolyploids entangled by both hybridization and polyploidization, autopolyploids, especially artificial lines, in relatively uniform genetic background offer a model system to understand mechanisms of genome-dosage effects. To investigate DNA methylation effects in response to WGD rather than hybridization, we produced autotetraploid rice with its diploid donor, Oryza sativa ssp. indica cv. Aijiaonante, both of which were independently self-pollinated over 48 generations, and generated and compared their comprehensive transcriptomes, base pair-resolution methylomes, and siRNAomes. DNA methylation variation of transposable elements (TEs) was observed as widespread in autotetraploid rice, in which hypermethylation of class II DNA transposons was predominantly noted in CHG and CHH contexts. This was accompanied by changes of 24-nt siRNA abundance, indicating the role of the RNA-directed DNA methylation pathway. Our results showed that the increased methylation state of class II TEs may suppress the expression of neighboring genes in autotetraploid rice that has obtained double alleles, leading to no significant differences in transcriptome alterations for most genes from its diploid donor. Collectively, our findings suggest that chromosome doubling induces methylation variation in TEs that affect gene expression and may become a "genome shock" response factor to help neoautopolyploids adapt to genome-dosage effects.
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100039, China; College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China;
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
authors.forename: Yuan
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100039, China;
authors.forename: En-Hua
authors.initials: EH
authors.lastname: Xia
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100039, China;
authors.forename: Qiu-Yang
authors.initials: QY
authors.lastname: Yao
authors.affiliation: State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources, South China Agricultural University, Guangzhou 510642, China.
authors.forename: Xiang-Dong
authors.initials: XD
authors.lastname: Liu
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Lgao@mail.kib.ac.cn.
authors.forename: Li-Zhi
authors.initials: LZ
authors.lastname: Gao
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics*; D004171:Diploidy; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000166:cytology / Q000235:genetics*; D010641:Phenotype; D011123:Polyploidy; D034741:RNA, Small Interfering / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements; D034741:RNA, Small Interfering
keywords: autotetraploid rice; gene expression; genome-dosage effect; methylome; transposable elements