Investigation Of The Adaptation In DNA Regulatory Region Based On Population Association Analysis And Construction Of Multi-omics Associated Network In Arabidopsis Thaliana

Arabidopsis thaliana is a widely used model plant,known as the "drosophila in plants".With the gradual development of molecular biology technology,more and more functional genes or variants have been excavated and applied to resistance breeding or high-yield breeding of crops.From the perspective of genetics,genomic variant is the fundamental cause of phenotypic differences between organisms,individuals of different ecotypes can often show different environmental fitness,and environmental adaptation study has become an important part of functional genomics research.In Arabidopsis thaliana,the 1001 Genomes group detected over 1000 whole genome sequences of Arabidopsis ecotypes.Some researchers have analyzed the correlations between variants(in coding region)and environments,and found some functional genes or loci for explaining environmental adaptability.However,there has been no systematic analysis for variants in non-coding region,which obviously does not accord with the important biological status of non-coding variants.For this reason,we took DNA regulatory region as research object,and carried out the analysis of gene expression association,environmental factor association,regional divergence correlation etc.In brief,we first screened out 321,194 non-rare variants in motif regions based on the pan-genome data of 1001 Genomes.The eQTL results included 5,771cis-eQTL,of which 3,663 variants positively associated with the expression of 2,068 genes,and 2,267 variations negatively associated with the expression of 1,356 genes.Then,we used a mixed linear model for environmental association analysis,combined with eQTL information and Motif disruption analysis,we finally pinpointed 41 causal variants with high credibility.We also carried out the co-occurrence analysis for variants in regulatory region,and found the widely existed synergistic effect among variants.Then,we studied the divergent evolution between Italian and Swedishpopulations,206 variants in DNA regulatory region were significantly associated with divergent evolution,and we found that chromosome 1 may play a more important role in the divergent evolution.In addition,phylogenetic analysis shows populations of Italy and Sweden do exist obvious divergence evolution in molecular level,and the temperature-related bioclimatic factors are likely the main causes.Finally,we carried out multi-omics association analysis on Arabidopsis population,identified eQTLs in rosette leaves,environment-related eQTLs,GWAS-related eQTLs,emQTLs,pathway-mQTLs and pathway-phenotype associations.Combining with phenotypic information,we conducted TWAS and EWAS analysis for 22 studies in AraPheno.In addition,we have discovered 2 new flowering-related genes through the multi-omics association network.In general,based on Multi-omics Association Analysis Strategy,we analyzed the eQTLs,variant-environment associations and regional divergent evolution for DNA regulatory variants.Combining the differential expression analysis and Motif disruption analysis,we pinpointed the association loci and found the potential causal loci.We have explored the molecular mechanism of local adaptation and divergent evolution,excavated some resistance-related and adaptation-related genes or loci.All the results will provide important theoretical basis and exploration direction for studying adaptive evolution mechanism of plants and mining resistance-related or adaptation-related genes or loci.