DNA methylation plays an important role in plant development and environmental responses. Natural variation for DNA methylation can be coupled with or without genetic changes. The extent to which DNA methylation is dependent upon genetic variations is of great interest. A research on the causes and consequences of natural DNA methylation variation in maize was recently published in Genome Biology. This study identified thousands of regions with differential DNA methylation (DMRs) among maize inbred lines, investigated the genetic basis of DMRs, and provided evidence for the functional consequences of DNA methylation on gene expression and metabolic traits. This is a collaborative work between Huazhong Agricultural University and University of Minnesota.
In the past few years, the development of high-throughput genotyping technology has greatly accelerated crop genetic improvement. A large number of SNPs can be used to build models to predict phenotypes and perform genomic selection. The prerequisite for this practice is that phenotypic variation is determined by DNA sequence variation. However, under many circumstances, DNA sequence variation can only explain part of heritability for many traits. There is still a considerable part of heritability that cannot be explained and was called "missing heritability". How to detect and utilize this part of heritability is a major challenge for geneticists and breeders. Epigenetic variation refers to mitotically and/or meiotically heritable changes in gene expression that occur without a change in DNA sequence, including chromatin modifications such as DNA methylation. Previous research suggests that there is a huge amount of variation in DNA methylation between different maize genotypes. However, it’s hard to study DNA methylation variation at population leveldue to the lack of effective high-throughput and low-cost DNA methylation detection technologyin a genome with high complexity.
In this study, researchers employed the SeqCap technology that was developed in an earlier study by this group to enrich for specific genomic regions (Li et al., Nucleic Acids Research, 2015, 43: e81). Compared to previous study, more regions were carefully selected based on previous researches on DNA methylation in maize. These regions not only are most likely to have variation in DNA methylation and affect gene expression, but also can be effectively detected among different maize inbreds which show dramatic DNA sequence variation. With this, DNA methylation was analyzed in a panel of 263 maize lines from tropical, subtropical and temperate regions. Thousands of DMRs were identified. In combination with about 1 million SNPs, gene expression data in two tissues (leaf and kernel) and metabolic traits in kernels, the genetic basis of DNA methylation variation and its effect on phenotypic variationwas thoroughly investigated. Interestingly, the researchersfound that >60% of DMRs arenot associated with DNA sequence variations. They also found that DNA methylation can affect gene expression and this effect is dependent upon tissue and sequence contexts. In addition, association analysis between DMRs and metabolic traits found that about 16% of the traits were significantly associated with DMRs. It is interesting to note that >50% of the DMRs associated with traits were not associated with SNPs, and some traits were only associated with DMRs and not with SNPs. These results provided evidence that DNA methylationc an carry unique genetic information.
This study systematically analyzed the genetic basis of DNA methylation variation and proved that DNA methylation can regulate gene expression and phenotypes, providing new support to explain the missing heritability. This is the first study to analyze DNA methylation variation and its function in a crop at the population level.
Professor Qing Li from Huazhong Agricultural University and Professor Nathan Springer from University of Minnesota are the co-corresponding authors. Ph.D. students Jing Xu and Guo Chen are the co-first authors. Professor Jianbing Yan and Professor Lin Li from Huazhong Agricultural University participated in this work. This research was supported by funds including The National Key Research and Development Program of China, the Huazhong Agricultural University Scientific & Technological Self-innovation Foundation, and the Fundamental Research Funds for the Central Universities.
Link：https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1859-0?utm_source=wechat&utm_medium=social&utm_content=organic&utm_campaign=BSCN_2_CZ_GB_WeChat_Nov
