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Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

文献类型： 外文期刊

作者： Xu, Jing 1 ; Chen, Guo 1 ; Hermanson, Peter J. 3 ; Xu, Qiang 1 ; Sun, Changshuo 1 ; Chen, Wenqing 1 ; Kan, Qiuxin 1 ; Li, 1 ;

作者机构： 1.Huazhong Agr Univ, Natl Key Lab Crop Genet Improvement, Wuhan 430070, Hubei, Peoples R China

2.Xinjiang Acad Agr Sci, Inst Nucl & Biol Technol, Urumqi 830091, Peoples R China

3.Univ Minnesota, Dept Plant & Microbial Biol, St Paul, MN 55108 USA

关键词： DNA methylation; Gene expression; Phenotypic diversity; Maize

期刊名称：GENOME BIOLOGY （ 影响因子：13.583； 五年影响因子：17.433 ）

ISSN： 1474-760X

年卷期： 2019 年 20 卷 1 期

页码：

收录情况： SCI

摘要： Background DNA methylation can provide a source of heritable information that is sometimes entirely uncoupled from genetic variation. However, the extent of this uncoupling and the roles of DNA methylation in shaping diversity of both gene expression and phenotypes are hotly debated. Here, we investigate the genetic basis and biological functions of DNA methylation at a population scale in maize. Results We perform targeted DNA methylation profiling for a diverse panel of 263 maize inbred genotypes. All genotypes show similar levels of DNA methylation globally, highlighting the importance of DNA methylation in maize development. Nevertheless, we identify more than 16,000 differentially methylated regions (DMRs) that are distributed across the 10 maize chromosomes. Genome-wide association analysis with high-density genetic markers reveals that over 60% of the DMRs are not tagged by SNPs, suggesting the presence of unique information in DMRs. Strong associations between DMRs and the expression of many genes are identified in both the leaf and kernel tissues, pointing to the biological significance of methylation variation. Association analysis with 986 metabolic traits suggests that DNA methylation is associated with phenotypic variation of 156 traits. There are some traits that only show significant associations with DMRs and not with SNPs. Conclusions These results suggest that DNA methylation can provide unique information to explain phenotypic variation in maize.

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