Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers

Schmid, Karl; Törjék, Ottó; Meyer, Rhonda C.; Schmuths, Heike; Hoffmann, Matthias H.; Altmann, Thomas

doi:10.1007/s00122-006-0212-7

Cited by 113 publications

(146 citation statements)

References 45 publications

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“…However, this does not seem to have been the case in A. thaliana, relative to A. lyrata, which might be due to a population expansion following the evolution of selfing (Wright et al 2002). In addition, A. thaliana seems to have a more complicated population structure than would be expected for a self-fertilizing annual, suggesting that its effective population size might not be as small as previously thought (Nordborg et al 2005;Schmid et al 2006). …”

Section: Mechanisms Of Change In Genome Sizementioning

confidence: 76%

The shrunken genome of Arabidopsis thaliana

et al. 2008

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This paper examines macro and micro-level patterns of genome size evolution in the Brassicaceae. A phylogeny of 25 relatives of Arabidopsis thaliana was reconstructed using four molecular markers under both parsimony and Bayesian methods. Reconstruction of genome size (C value) evolution as a discrete character and as a continuous character was also performed. In addition, size dynamics in small chromosomal regions were assessed by comparing genomic clones generated for Arabidopsis lyrata and for Boechera stricta to the fully sequenced genome of A. thaliana. The results reveal a sevenfold variation in genome size among the taxa investigated and that the small genome size of A. thaliana is derived. Our results also indicate that the genome is free to increase or decrease in size across these evolutionary lineages without a directional bias. These changes are accomplished by insertions and deletions at both large and small-scales occurring mostly in intergenic regions, with repetitive sequences and transposable elements implicated in genome size increases. The focus upon taxa relatively closely related to the model organism A. thaliana, and the combination of complementary approaches, allows for unique insights into the processes driving genome size changes.

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Section: Mechanisms Of Change In Genome Sizementioning

confidence: 76%

The shrunken genome of Arabidopsis thaliana

et al. 2008

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“…We believe this difference is most likely due to recombination that occurred in the production of the F 5 plants. Due to their typically low rate of outcrossing (27), A. thaliana populations and stock accessions are mainly homozygous (35), and genetic variation among populations is highly structured (36). Interlocus associations are common within geographical areas (29,36), which may cause coadaptation of multiple genes and the overestimation of the effect of specific candidate genes.…”

Section: Discussionmentioning

confidence: 99%

“…Due to their typically low rate of outcrossing (27), A. thaliana populations and stock accessions are mainly homozygous (35), and genetic variation among populations is highly structured (36). Interlocus associations are common within geographical areas (29,36), which may cause coadaptation of multiple genes and the overestimation of the effect of specific candidate genes. It is also possible that FRI explains a smaller proportion of the variation in flowering time here than in other studies due to the particular environmental conditions used.…”

Section: Discussionmentioning

confidence: 99%

Antagonistic pleiotropic effects reduce the potential adaptive value of the FRIGIDA locus

Scarcelli

Cheverud

Schaal

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

113

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Although the occurrence of epistasis and pleiotropy is widely accepted at the molecular level, its effect on the adaptive value of fitness-related genes is rarely investigated in plants. Knowledge of these features of a gene is critical to understand the molecular basis of adaptive evolution. Here we investigate the importance of pleiotropy and epistasis in determining the adaptive value of a candidate gene using the gene FRI (FRIGIDA), which is thought to be the major gene controlling flowering time variation in Arabidopsis thaliana. The effect of FRI on flowering time was analyzed in an outbred population created by randomly mating 19 natural accessions of A. thaliana. This unique population allows the estimation of FRI effects independent of any linkage association with other loci due to demographic processes or to coadapted genes. It also allows for the estimation of pleiotropic effects of FRI on fitness and inflorescence architecture. We found that FRI explains less variation in flowering time than previously observed among natural accessions, and interacts epistatically with the FLC locus. Although early flowering plants produce more fruits under spring conditions, and nonfunctional alleles of FRI were associated with early flowering, variation at FRI was not associated with fitness. We show that nonfunctional FRI alleles have negative pleiotropic effects on fitness by reducing the numbers of nodes and branches on the inflorescence. We propose that these antagonistic pleiotropic effects reduce the adaptive value of FRI, and helps explain the maintenance of alternative life history strategies across natural populations of A. thaliana.Arabidopsis thaliana ͉ FLC ͉ flowering time ͉ pleiotropy ͉ gene-by-environment interaction D espite decades of research, we still know surprisingly little about the molecular basis of adaptation (but see refs. 1 and 2). To understand the genetic basis of adaptive evolution it is necessary to combine knowledge of the molecular basis of fitness-related traits with information about how selection acts on the available genetic variation (1). A number of candidate genes underlying adaptive traits have been identified in studies by using QTL analysis or forward genetic approaches (3-5). The role of candidate genes on past adaptive evolution is then often investigated by looking at rates and patterns of nucleotide substitution for evidence of past selection. Although a number of studies have shown that the rate of synonymous-to-nonsynonymous substitution in candidate genes is compatible with natural selection (6-8), demographic dynamics also can cause departure from the neutral expectation (9, 10). Thus, direct evidence for selection at the molecular level is ultimately needed, and such data are still very limited.Determining the adaptive value of candidate genes is further complicated by the fact that the relationship between genotype and fitness is complex and results from the combination and/or interaction of multiple traits and genes. Consequently, understanding the relationship b...

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“…Because many demographic factors can affect patterns of nucleotide polymorphism in a way similar to the effects of selection, methods that can differentiate the effects of these forces are necessary before inferences can be made about their relative importance. Indeed, several recent studies have detected genome-wide departures from predictions of equilibrium neutral models in standard tests of selection (see Ford, 2002 for a review of such tests), presumably because of the effects of population genetic structure and demography (Andolfatto and Przeworski, 2000;Nordborg et al, 2005;Schmid et al, 2005Schmid et al, , 2006. Although application in more traditional ecological settings is limited, three recent papers have used alternative approaches to distinguish between demographic and selective forces in shaping human polymorphism levels Stajich and Hahn, 2005;Williamson et al, 2005), and some generalizations appear to be emerging.…”

Section: What Is Population Genomics?mentioning

confidence: 99%

Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits

2007

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A central challenge in evolutionary biology is to identify genes underlying ecologically important traits and describe the fitness consequences of naturally occurring variation at these loci. To address this goal, several novel approaches have been developed, including 'population genomics,' where a large number of molecular markers are scored in individuals from different environments with the goal of identifying markers showing unusual patterns of variation, potentially due to selection at linked sites. Such approaches are appealing because of (1) the increasing ease of generating large numbers of genetic markers, (2) the ability to scan the genome without measuring phenotypes and (3) the simplicity of sampling individuals without knowledge of their breeding history. Although such approaches are inherently applicable to non-model systems, to date these studies have been limited in their ability to uncover functionally relevant genes. By contrast, quantitative genetics has a rich history, and more recently, quantitative trait locus (QTL) mapping has had some success in identifying genes underlying ecologically relevant variation even in novel systems. QTL mapping, however, requires (1) genetic markers that specifically differentiate parental forms, (2) a focus on a particular measurable phenotype and (3) controlled breeding and maintenance of large numbers of progeny. Here we present current advances and suggest future directions that take advantage of population genomics and quantitative genetic approaches -in both model and non-model systems. Specifically, we discuss advantages and limitations of each method and argue that a combination of the two provides a powerful approach to uncovering the molecular mechanisms responsible for adaptation.

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Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers

Cited by 113 publications

References 45 publications

The shrunken genome of Arabidopsis thaliana

The shrunken genome of Arabidopsis thaliana

Antagonistic pleiotropic effects reduce the potential adaptive value of the FRIGIDA locus

Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits

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