The Scale of Population Structure in Arabidopsis thaliana

Abstract

The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales.

Genome-Wide Association Mapping of Fertility Reduction upon Heat Stress Reveals Developmental Stage-Specific QTLs in Arabidopsis thaliana

“…A collection consisting of 285 natural accessions of Arabidopsis thaliana (Supplemental Data Set 1) selected to capture most of the genetic variation present within the species (Platt et al, 2010) and genotyped with ;215k SNP markers (Affymetrix SNP-tilling array Atsnptile1; Atwell et al, 2010;Li et al, 2010) was obtained from the ABRC Stock Center (Baxter et al, 2010).…”

Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis

“…10C). Arabidopsis can outcross 3% of the time in environments with natural populations (Platt et al 2010), generating hybrids in which CNVs can be formed from reshuffling much more frequently compared with de novo mutation.…”

“…Although Arabidopsis is a predominantly self-pollinating plant, 3% outcrossing still allows gene transfer among different accessions (Platt et al 2010). When the population faces the challenges of changes in the external environment, some hybrids that possess newly generated genotypes might confer better adaptation and out-compete others.…”

Genomic Conflicts that Cause Pollen Mortality and Raise Reproductive Barriers inArabidopsis thaliana

“…Geographic isolation in distinct refugia is predicted to be a major factor favoring the divergence between accessions, corroborated by the highly significant genetic differentiation (F ST ) values between Italian and Central Asian accessions (Beck et al 2008). Sha groups with other accessions from Central Asia in a highly differentiated cluster (Nordborg et al 2005;Platt et al 2010;Simon et al 2012;Brennan et al 2014). Mr-0 clusters with some Mediterranean and Cape Verde accessions (Simon et al 2012), and its genetic structure is very different from all other accessions (Nordborg et al 2005).…”