Population epigenomics of Swedish Arabidopsis
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Magnus Nordborg
PROVIDER: E-GEOD-65685 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Plants display remarkable developmental and phenotypic plasticity in order to adapt to their environment. It has long been postulated that epigenetics plays a key role in these processes, but with one or two exceptions, solid evidence for the role of epigenetic variation in these processes is lacking. A key impediment to understanding these processes is the lack of information on the extent of epigenetic variation and how it relates to genetic and phenotypic variation in natural population, both over the lifecycle of an individual, and over evolutionary time. Here we show that genetic variants under selection in the north of Sweden appear to drive variation in DNA methylation, which in turn is highly correlated with local climate. Selective sweeps and genetic variants associated with adaptation to the local environment have previously been identified within the Swedish Arabidopsis population. Our finding that they harbour variants responsible for climate associated epigenetic variation strongly supports the role of epigenetic processes in local adaptation. These findings provide a basis for further dissecting the role of epigenetics in local adaptation at the molecular level
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Project description:In Arabidopsis thaliana a high rate of spontaneous epigenetic variation can occur in the DNA methylome in the absence of genetic variation and selection. It has been of great interest, whether natural epigenetic variation is subject to selection and contributes to fitness and adaptation in selective environments. We compared the variation in selected phenotypic traits, genome-wide cytosine DNA methylation and gene expression in two Arabidopsis recombinant inbred lines, which had undergone five generations of selection in experimental landscapes relative to their genetically identical ancestors. Selected populations exerted significant differences in flowering time and the number of branches and fruits, differences that were maintained over two to three generations in the absence of selection. We identified 4,629 and 5,158 differentially methylated cytosines which were overrepresented in genes that regulate flowering time, epigenetic processes, development and morphogenesis. Differentially methylated genes were enriched in differentially expressed genes. Thus, epigenetic variation is subject to selection and may play an important role in the adaptive response of populations in rapidly changing natural environments. Genomic DNA was extracted from whole-plant above-ground tissue of individual 25-day-old plants with the Qiagen DNeasy kit (Qiagen). DNA from two randomly chosen CVL39 individuals from ancestral (A3) lines and from 7 selected (S3) lines that had experienced 5 generations of selection in the three replicated dynamic landscapes (2xD1, 3xD5,2xD6) was sequenced (paired-end, 100 bp) using the Illumina Highseq 2000 Instrument. Single nucleotide polymorphisms and TE insertions were mapped with respect to the recombinant reference genome and compared between selected and ancestral lines.
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Project description:We used custom Nimblegen microarrays representing whole-larval transcriptomes for two species (Erynnis propertius [this submission] and Papilio zelicaon [submitted seperately]) to assess gene expression differences affecting tolerance to climatic regimes. Many individuals were sourced from populations from the northern periphery and center of the species' (shared) range; these were each divided into groups treated under peripheral and central climate regimes, resulting in 4 experimental groups for each species (Peripheral Source, Peripheral treatment; Peripheral Source, Central Treatment; Central Source, Peripheral Treatment; Central Source, Central Treatment). Using technical microarray replicates allowed us to use ANOVA to identify genes whose expression may underlie local adaptation to climate (i.e., those showing an interaction term between source and population). Abstract: Population differences may determine geographic range shifts and adaptive evolution under climate change. Local adaptation in peripheral populations could preclude or slow range expansions, and populations with different genetic make-up could have distinct trajectories that produce complex spatial patterns of population change. To investigate the genetic extent of local responses to climate change, we exposed poleward-periphery and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared whole-transcriptome expression. We found significant expression differences between populations in both species. In addition, several hundred genes including genes involved in energy metabolism and oxidative stress responded in a localized fashion in the species that exhibits greater population structure and local adaptation. Expression levels of these genes are most divergent in the same environment in which we previously detected phenotypic divergence in metabolism. By contrast, we found no localized genes in the species with higher gene flow, reflecting the lack of previously observed local adaptation. These results suggest that population differences do not generalize easily, even for related species living in the same climate, but some taxa deserve population-level consideration when predicting the effects of climate change.
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Project description:We used custom Nimblegen microarrays representing whole-larval transcriptomes for two species (Papilio zelicaon [this submission] and Erynnis propertius [submitted seperately]) to assess gene expression differences affecting tolerance to climatic regimes. Many individuals were sourced from populations from the northern periphery and center of the species' (shared) range; these were each divided into groups treated under peripheral and central climate regimes, resulting in 4 experimental groups for each species (Peripheral Source, Peripheral treatment; Peripheral Source, Central Treatment; Central Source, Peripheral Treatment; Central Source, Central Treatment). Using technical microarray replicates allowed us to use ANOVA to identify genes whose expression may underlie local adaptation to climate (i.e., those showing an interaction term between source and population). Abstract: Population differences may determine geographic range shifts and adaptive evolution under climate change. Local adaptation in peripheral populations could preclude or slow range expansions, and populations with different genetic make-up could have distinct trajectories that produce complex spatial patterns of population change. To investigate the genetic extent of local responses to climate change, we exposed poleward-periphery and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared whole-transcriptome expression. We found significant expression differences between populations in both species. In addition, several hundred genes including genes involved in energy metabolism and oxidative stress responded in a localized fashion in the species that exhibits greater population structure and local adaptation. Expression levels of these genes are most divergent in the same environment in which we previously detected phenotypic divergence in metabolism. By contrast, we found no localized genes in the species with higher gene flow, reflecting the lack of previously observed local adaptation. These results suggest that population differences do not generalize easily, even for related species living in the same climate, but some taxa deserve population-level consideration when predicting the effects of climate change. Previously we sequenced and assembled whole larval transcriptome ESTs sourced from pooled central-population individuals subjected to environmental stressors (see O'Neil et al., 2008). From these assemblies custom Nimblegen microarrays were designed (Nimblegen, Inc.), representing 34,609 putative gene sequences for E. propertius (submitted separately) and 25,735 putative gene sequences for P. zelicaon (this submission). Probe designs sought 5 representative 60mer probes for E.propertius and 4 representative probes for P. zelicaon. Messenger RNA was was sampled from multiple individuals of each experimental group and pooled before being converted to cDNA and hybridized to technical replicate microarrays. Three technical replicates for each experimental group were used, for a total of 12 microarrays (per species). Microarray data were log2 transformed and quintile-normalized (Bolstad et al. 2003) on a per-species basis.
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Project description:We used custom Nimblegen microarrays representing whole-larval transcriptomes for two species (Erynnis propertius [this submission] and Papilio zelicaon [submitted seperately]) to assess gene expression differences affecting tolerance to climatic regimes. Many individuals were sourced from populations from the northern periphery and center of the species' (shared) range; these were each divided into groups treated under peripheral and central climate regimes, resulting in 4 experimental groups for each species (Peripheral Source, Peripheral treatment; Peripheral Source, Central Treatment; Central Source, Peripheral Treatment; Central Source, Central Treatment). Using technical microarray replicates allowed us to use ANOVA to identify genes whose expression may underlie local adaptation to climate (i.e., those showing an interaction term between source and population). Abstract: Population differences may determine geographic range shifts and adaptive evolution under climate change. Local adaptation in peripheral populations could preclude or slow range expansions, and populations with different genetic make-up could have distinct trajectories that produce complex spatial patterns of population change. To investigate the genetic extent of local responses to climate change, we exposed poleward-periphery and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared whole-transcriptome expression. We found significant expression differences between populations in both species. In addition, several hundred genes including genes involved in energy metabolism and oxidative stress responded in a localized fashion in the species that exhibits greater population structure and local adaptation. Expression levels of these genes are most divergent in the same environment in which we previously detected phenotypic divergence in metabolism. By contrast, we found no localized genes in the species with higher gene flow, reflecting the lack of previously observed local adaptation. These results suggest that population differences do not generalize easily, even for related species living in the same climate, but some taxa deserve population-level consideration when predicting the effects of climate change. Previously we sequenced and assembled whole larval transcriptome ESTs sourced from pooled central-population individuals subjected to environmental stressors (see O'Neil et al., 2008). From these assemblies custom Nimblegen microarrays were designed (Nimblegen, Inc.), representing 34,609 putative gene sequences for E. propertius (this submission) and 25,735 putative gene sequences for P. zelicaon (submitted seperately). Probe designs sought 5 representative 60mer probes for E.propertius and 4 representative probes for P. zelicaon. Messenger RNA was was sampled from multiple individuals of each experimental group and pooled before being converted to cDNA and hybridized to technical replicate microarrays. Three technical replicates for each experimental group were used, for a total of 12 microarrays (per species). Microarray data were log2 transformed and quintile-normalized (Bolstad et al. 2003) on a per-species basis.
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