DNA methylation variation in soybean domestication improvement.

Crop domestication is one of the most important events in agricultural development.
through the continuous domestication and improvement of wild crops, humans have been able to obtain modern crops that meet the needs of production and life.
domestication and improvement process is the process of selecting the genome diversity of crop groups.
the current research on crop domestication improvement mainly focuses on the selection of genetic variation, in the DNA level identification of a large number of domestication selection interval.
However, in addition to genetic variation, epigenetics also plays a very important role in the growth and development of plants.
so far, the role of epigenetic variation in crop domestication and improvement has been rarely reported.
the Tian Zhixi Research Group of the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences conducted an over-sequencing analysis of 302 soybean varieties and conducted a detailed study of the DNA selection interval (DNA selecit regionon, DSR) during soybean domestication improvement (Zhou et al., 2015 Nature Biotechnology).
on this basis, in order to explore the role of epigenetic variation in the process of crop domestication and improvement, the members of the research team studied the most extensive DNA methylation in epigenetic signals, and sequenced and analyzed the whole genome methylation of 45 soybean varieties, including 9 wild species, 12 farm species and 24 cultivated species.
: DNA methylation variation in soybean domestication improvement.
A: DNA differential methylation interval (DMR) identification in soybean domestication and improvement process; B: DMR has high genetic diversity; C: DMR is associated with genetic variation; D: Genes that overlap with "independent" CG-DMR in the domestication process are enriched in carbohydrate metabolism.
by comparing methylation levels between subgroups, the researchers identified the difference methylation intervals (Methylly DifferentialDed Regions, DMRs) that changed in levels of DNA methylation in 4,248 and 1,164 DNA methylation levels, respectively, during the domestication process from wild to farm species and in the improvement of farm species to cultivation, respectively.
by comparing the DNA horizontal selection interval DSR, it is found that DMR and DSR are two completely different selection intervals, which are significantly different in length, with little overlap, no correlation in chromosome distribution, large differences in genomic structure composition, and Significantly high nucleotide polymorphism.
the results suggest that the selection of soybean domestication improvement process estochers at epigenetic levels and DNA levels appear to be independently carried out.
further, to determine whether the choice of DNA methylation is indeed independent of the choice of DNA levels, the researchers analyzed the association of DMR with the genetic variationarounds around it (siRNA, TE variants, and SNP) and found that only 22.54 percent of DMR can be interpreted by genetic variation, suggesting that most of the DMR in soybean domestication improvement is indeed the result of dna methylation is independently selected, and they are not by-products of genetic variation.
analyzing the functions of these "independent" DMRs that are not associated with genetic variation, it was found that genes that overlapped with "independent" DMR, in particular the "independent" CG-DMR during domestication, were significantly enriched in the carbohydrate pathway and encoded all key regulatory enzymes in the pathway.
discovery provides important evidence for the biological role of DNA methylation in soybean domestication.
the study for the first time at the group level to analyze the role of epigenetics in crop domestication, to prove that DNA methylation can play a role in crop domestication independent of DNA variation, suggesting that epigenetic variation can indeed serve as a new genetic resource for the cultivation of better crops.
related paper was published online September 10 in the journal Genome Biology (DOI: 10.1186/s13059-018-1516-z).
Tian Zhixi Research Group, Ph.D. Shen Wei is the first author of this article, and Tian Zhixi is the communication author of this article.
the research was supported by the National Natural Science Foundation of China and the Chinese Academy of Sciences' Class A strategic pilot science and technology special funding.
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