| Epigenetic modification,which is widely existing in organisms,could modulate gene expression without altering the underlying DNA sequence and result in phenotype variation.Epigenetic variation can occur spontaneously or plastically in response to environment stimulates thus could play an important role in plants coping with new and heterogeneous environments.If these epigenetic variation are adaptive and can be transmitted stably across generations,they may provide raw materials for natural selection to act upon and impact on evolutionary trajectories.The evolutionary role of epigenetic mechanisms in response to environment could be particularly relevant for asexually reproducing plants.Alligator weed(Alternanthera philoxeroides)is native to South America and now become invasive species in many countries.Alligator weed populations in China are dominated by asexual reproduction and show very little genetic variation,but it occurs in a broad geographic distribution.Therefore,it is presumed that epigenetic variation may play an important role for alligator weed adapting to highly heterogeneous habitats and climatic regimes.However,the epigenetic differentiation among contrasting habitats and its stability in alligator weed remain largely unknown,and to some extent restrict our understanding of the invasion mechanisms of this invasive plant.In this study,integrative approaches involving field monitoring,multi-generation cultivation experiments,genome-wide DNA methylation analysis and next-generation sequencing techniques were conducted aiming to identify the genetic and epigenetic variation of alligator weed populations in China,investigate the stability of epigenetic variation and its association with climate factors,test the hypothesis that differentiation of alligator weed in response to diverse habitats is directly correlated with epigenetic variation,and explore the contribution of epigenetic variation in successful invasion process of alligator weed.Six natural populations were chosen to encompass the climate gradient experienced by alligator weed in China,including Kunming,Nanchang,Guilin,Nanning,Wuhan and Ji’nan.Genetic diversity and Genome-wide methylation of each population were profiled by using AFLP and MSAP markers respectively.The field sampling was repeated twice to collect temporal samples at the same locations to assess the stability of epigenetic variation among years in natural populations.By using the asexual materials from the natural populations,multi-generation cultivation were conducted in garden and growth chamber for 4 years.Samples of 5 generations were selected and examined by MSAP,and DNA samples were sequenced along with the samples of natural populations by m SLAF-seq to investigate the dynamics of epigenetic variation.Finally,environmental association analysis were performed with climate data from World Clim in order to test the correlation between epigenetic variation and climate factors.The main results are as follows:(1)In natural alligator weed populations,the genetic variation was extremely low but the epigenetic variation was relatively high.AFLP analysis revealed that the values of both the percentage of polymorphic loci(P%)and Shannon’s information index(I)were close to zero at population level.There was no significant genetic differentiation among populations.In contrast,the epigenetic diversity was nearly twentyfold higher than that of genetic diversity,with the percentage of polymorphic loci(epi-P%)and Shannon’s information index(epi-I)ranging from 2.60-9.29% and 0.017-0.067,respectively.AMOVA suggested significant epigenetic differentiation among populations.(2)Epigenetic differentiation among populations was relatively stable in the field while the epigenetic diversity and differentiation decreased significantly with time in common environments.The repeated measurements of natural populations in field suggested no significant difference between two measurements in epigenetic variation patterns.The two temporal samples from the same site occupied highly similar positions in the PCo A space.In contrast,the epigenetic diversity within population significantly reduced during the garden and growth chamber experiments.Loci statistics showed increasing numbers of shared epi-loci and decreasing numbers of varied epi-loci among populations,meanwhile six populations showed increasing convergence with time in the PCo A space.Only a few epi-loci could be stably transmitted across generations and the stability was largely dependent on time scale and genome context.(3)Epigenetic variations were significantly related to climate variables.At population level,the results of the distance-based redundancy analysis(db RDA)showed that the epigenetic variation patterns were significantly related to five climate variables.In addition,both Bayscan and Sambada analysis highlighted that at least 10 epi-loci were significantly associated with climate variables.The results of this study suggest that high level epigenetic variation and significant epigenetic differentiation in the natural alligator weed populations can be directly related to its response to diverse habitats when the genetic diversity is low.We found that epigenetic variation were both plastic and stable.This kind of mechanism could be benefit for alligator weed to coping with environment change.The epigenetic loci which were found associated with climate variables may have adaptive significance.In conclusion,our findings support the hypothesis that differentiation of alligator weed in response to diverse habitats is directly correlated with epigenetic variation.The observed epigenetic variation in this study is likely to give alligator weed a highly flexible adaptive mechanism that can protect plant population from environmental stress in a heterogeneous environment thus may guarantee vigorous invasiveness to this invader. |
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