Genetic Basis For Local Adaptation Of Actinidia Eriantha Based On DNA Methylation Sequencing Technology

In heterogeneous environments,spatially varying selection is known to induce adaptation to local environments,resulting in local adaptation.Local adaptation is the result of the interaction of environment,phenotype and genotype.In recent years,it has been found that not only genetic variation,but also epigenetic variation plays an important role in local adaptation.It is known that DNA methylation is the clearest and most important epigenetic modification.This study explores the possible evolutionary mechanism of DNA methylation involved in local adaptation by studying the genome-wide DNA methylation of the wild populations of Actinidia eriantha.The results of this study provide a theoretical reference for understanding of the adaptive evolutionary mechanism of plant adaptation to environmental climate change.Actinidia eriantha is endemic to China,which is widely distributed and has strong adaptability to different types of environments.In this study,we used bisulfite-sequencing(BS)combined with the reference genome of A.eriantha to construct a single-base resolution methylation map of A.eriantha,based on 13 samples collected from 13 populations.The genome-wide methylation level of A.eriantha was about 8%.For different sequence backgrounds,the methylation degree was the highest in CG(25.30%),the lowest in CHH(4.56%),and the CHG was in between(13.38%).There was a large difference in methylation level among functional components in the genome of A.eriantha,which may be related to methylation regulation on gene expression.The methylation patterns of the chromosomes were similar among the samples.Although the methylation level was different among samples,the extent of methylation level change was basically the same for the same location on the chromosomes.In addition,samples with similar genetic backgrounds and close spatial distances have more similar genomic methylation patterns.A total of 1176162 single methylation variants(SMVs)were obtained from 13 samples by methylation calling.The methylation data of each SMV site and 5 bioclimatic variables(bio2: mean diurnal range,bio4: temperature seasonality,bio8: mean temperature of wettest quarter,bio16: precipitation of wettest quarter,bio19: precipitation of coldest quarter)were analyzed by univariate linear regression analysis,where F-statistic was used to determine the significance.SMVs that were significantly associated with each environmental factor were identified.Then,these SMVs were mapped to the A.eriantha genome to discover the potentially related genes.There were about 3,000 genes anchored to each bioclimatic variable,and most of these genes were linked to more than one bioclimatic factor.Many of these genes were related to the stress response genes of plants to environmental changes,among which some have been reported to be closely related to local adaptation,such as ESK1,MYB4,and the WRKY transcription factor family.In addition,GO enrichment function analysis showed that genes were highly enriched in stress reactions such as catalytic activity and binding.In the KEGG enrichment pathway analysis,the metabolic pathway with the largest number of gene enrichment was metabolic pathway.Overall,in this study,a single-base resolution methylation map of the whole genome of A.eriantha was obtained.There were significant differences in genome-wide DNA methylation patterns among the populations of A.eriantha.The genes significantly associated with bioclimatic variables,suggest that these genes may play an important role in the local adaptation.Thus,DNA methylation may be involved in the local adaptation of A.eriantha.The results of this study provide new evidences for the adaptive evolution of A.eriantha.