Exploring The Genetic Mechanism Of Arabidopsis Local Adaption By Multi-omics Integration

Plant local adaptation can be achieved through its genetic variation,including the co-regulation of genomes,transcriptome and epigenetics at multiple omics levels,which will increase its fitness in the local environment.To identify the underlying mechanisms of genome-wide range local adaptation in Arabidopsis thaliana,we conducted integrative analysis of 620 strains of Arabidopsis ecotype of genome,transcriptome and methylome multi-omics data generated by “1001Genome” project and identified genetic variations associated with various environmental factors.The results showed that the average temperature of the coldest season of Bio11,the lowest temperature of the coldest month of Bio6,the average temperature of the driest season of Bio9 and the one-year average temperature of Bio1 were the main climatic factors affecting the divergent evolution of Arabidopsis populations on a global scale.Then,through eQTL and emQTL analysis,we found that changes in the DNA regulatory regions near the genes and changes in different methylation levels may have a regulatory effect on gene expression.Fourteen SNPs and twenty-six DNA methylation sites were identified,which are involved in regulating the expression of two functional genes related to cold domestication(CBF1 and AT4G39130)and two functional genes related to flower development(REM1 and LSU4).Through the calculation of pathway activity,low temperature environment samples of unsaturated fatty acid synthesis and metabolism and other lipid metabolism pathways activity are significantly enhanced.At the same time,the activity of the MAPK signaling pathway is significantly increased in the low temperature environment,activating downstream transcription factors and cold-resistant gene responses.These pathways enhanced the cold tolerance of Arabidopsis.In the long-term evolutionary process,the genetic variation that is conducive to individual adaptation to the local climate environment is positively selected,which may be the potential mechanism of multi-level participation in the regulation of local adaptation evolution of Arabidopsis thaliana.In conclusion,we have found some new genetic variations in environmental adaptation and provided some insights into their potential functions in local climate adaptation,providing important theoretical basis for the study of plant stress tolerance and adaptation.