SummaryArabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

The plant Arabidopsis thaliana occurs naturally in many different habitats throughout Eurasia. As a foundation for identifying genetic variation contributing to adaptation to diverse environments, a 1001 Genomes Project to sequence geographically diverse A. thaliana strains has been initiated. Here we present the first phase of this project, based on population-scale sequencing of 80 strains drawn from eight regions throughout the species' native range. We describe the majority of common small-scale polymorphisms as well as many larger insertions and deletions in the A. thaliana pan-genome, their effects on gene function, and the patterns of local and global linkage among these variants. The action of processes other than spontaneous mutation is identified by comparing the spectrum of mutations that have accumulated since A. thaliana diverged from its closest relative 10 million years ago with the spectrum observed in the laboratory. Recent species-wide selective sweeps are rare, and potentially deleterious mutations are more common in marginal populations

SUMMARY The epigenome orchestrates genome accessibility, functionality and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation and co-expression modules. Physical maps for nine of the most diverse genomes reveals how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Currently, genetic variation is probably the most important basic resource for plant biology. In addition to the variation artificially generated by mutants in model plants, naturally occurring genetic variation is extensively found for most species, including Arabidopsis. In many cases, natural variation present among accessions is multigenic, which has historically hampered its analysis. However, the exploitation of this resource down to the molecular level has now become feasible, especially in model species like Arabidopsis, where several genes accounting for natural variation have already been identified. Dissecting this variation requires first a quantitative trait locus (QTL) analysis, which in Arabidopsis has proven very effective by using recombinant inbred lines (RILs). Second, identifying the particular gene and the nucleotide polymorphism underlying QTL is the major challenge, and is now feasible by combining high-throughput genetics and functional genomic strategies. The analysis of Arabidopsis natural genetic variation is providing unique knowledge from functional, ecological, and evolutionary perspectives. This is illustrated by reviewing current research in two different biological fields: flowering time and plant growth. The analysis of Arabidopsis natural variation for flowering time revealed the identity of several genes, some of which correspond to genes with previously unknown function. In addition, for many other traits such as those related to primary metabolism and plant growth, Arabidopsis QTL analyses are detecting loci with small effects that are not easily amenable by mutant approaches, and which might provide new insights into the networks of gene regulation.