Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

Long, Quan; Rabanal, Fernando A.; Meng, Dong; Huber, Christian D.; Farlow, Ashley; Platzer, Alexander; Zhang, Qingrun; Vilhjálmsson, Bjarni J.; Korte, Arthur; Nizhynska, Viktoria; Voronin, Viktor; Korte, Pamela; Sedman, Laura; Mandáková, Terezie; Lysak, Martin A.; Seren, Ümit; Hellmann, Ines; Nordborg, Magnus

doi:10.1038/ng.2678

Cited by 369 publications

(457 citation statements)

References 45 publications

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“…Differentiation for neutral genetic markers exhibits a pattern of isolation by distance over broad scales (Beck et al, 2008), and reduced neutral genetic variation in northern populations is consistent with genetic drift because of population bottlenecks during range expansion following Pleistocene glaciations (Beck et al, 2008). A pattern of reduced genetic variation in northern compared with southern populations has also been reported within Scandinavia (Lewandowska-Sabat et al, 2010;Long et al, 2013). Both the selfing mating system of Arabidopsis and the demographic history of populations from northern Scandinavia suggest a potential role for genetic drift in shaping genetic variation underlying fitness.…”

Section: Introductionmentioning

confidence: 78%

Heterosis and outbreeding depression in crosses between natural populations of Arabidopsis thaliana

2015

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Understanding the causes and architecture of genetic differentiation between natural populations is of central importance in evolutionary biology. Crosses between natural populations can result in heterosis if recessive or nearly recessive deleterious mutations have become fixed within populations because of genetic drift. Divergence between populations can also result in outbreeding depression because of genetic incompatibilities. The net fitness consequences of between-population crosses will be a balance between heterosis and outbreeding depression. We estimated the magnitude of heterosis and outbreeding depression in the highly selfing model plant Arabidopsis thaliana, by crossing replicate line pairs from two sets of natural populations (C ↔ R, B ↔ S) separated by similar geographic distances (Italy ↔ Sweden). We examined the contribution of different modes of gene action to overall differences in estimates of lifetime fitness and fitness components using joint scaling tests with parental, reciprocal F 1 and F 2 , and backcross lines. One of these population pairs (C ↔ R) was previously demonstrated to be locally adapted, but locally maladaptive quantitative trait loci were also found, suggesting a role for genetic drift in shaping adaptive variation. We found markedly different genetic architectures for fitness and fitness components in the two sets of populations. In one (C ↔ R), there were consistently positive effects of dominance, indicating the masking of recessive or nearly recessive deleterious mutations that had become fixed by genetic drift. The other set (B ↔ S) exhibited outbreeding depression because of negative dominance effects. Additional studies are needed to explore the molecular genetic basis of heterosis and outbreeding depression, and how their magnitudes vary across environments.

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Section: Introductionmentioning

confidence: 78%

Heterosis and outbreeding depression in crosses between natural populations of Arabidopsis thaliana

2015

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“…We considered four subpopulations: 298 Swedish accessions [Swedish RegMap (Horton et al 2012;Long et al 2013)], 204 French accessions [French RegMap (Horton et al 2012;Brachi et al 2013)], 350 accessions from the HapMap population (Li et al 2010), and a subset of 250 accessions that we refer to as the structured RegMap (accession IDs are given in Supporting Information, Table S1). The structured RegMap accessions were chosen to have large differences in genetic relatedness (i.e., variation in kinship coefficients, across pairs of accessions).…”

Section: Genotypic Datamentioning

confidence: 99%

“…We considered four subpopulations: 298 Swedish accessions [Swedish RegMap (Horton et al 2012;Long et al 2013 structured RegMap (accession IDs are given in Supporting Information, Table S1). The structured RegMap accessions were chosen to have large differences in genetic relatedness (i.e., variation in kinship coefficients, across pairs of accessions).…”

Section: Genotypic Datamentioning

confidence: 99%

Marker-Based Estimation of Heritability in Immortal Populations

et al. 2014

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Heritability is a central parameter in quantitative genetics, from both an evolutionary and a breeding perspective. For plant traits heritability is traditionally estimated by comparing within-and between-genotype variability. This approach estimates broad-sense heritability and does not account for different genetic relatedness. With the availability of high-density markers there is growing interest in marker-based estimates of narrow-sense heritability, using mixed models in which genetic relatedness is estimated from genetic markers. Such estimates have received much attention in human genetics but are rarely reported for plant traits. A major obstacle is that current methodology and software assume a single phenotypic value per genotype, hence requiring genotypic means. An alternative that we propose here is to use mixed models at the individual plant or plot level. Using statistical arguments, simulations, and real data we investigate the feasibility of both approaches and how these affect genomic prediction with the best linear unbiased predictor and genome-wide association studies. Heritability estimates obtained from genotypic means had very large standard errors and were sometimes biologically unrealistic. Mixed models at the individual plant or plot level produced more realistic estimates, and for simulated traits standard errors were up to 13 times smaller. Genomic prediction was also improved by using these mixed models, with up to a 49% increase in accuracy. For genome-wide association studies on simulated traits, the use of individual plant data gave almost no increase in power. The new methodology is applicable to any complex trait where multiple replicates of individual genotypes can be scored. This includes important agronomic crops, as well as bacteria and fungi.KEYWORDS marker-based estimation of heritability; GWAS; genomic prediction; Arabidopsis thaliana; one-vs. two-stage approaches N ARROW-SENSE heritability is an important parameter in quantitative genetics, determining the response to selection and representing the proportion of phenotypic variance that is due to additive genetic effects (Jacquard 1983;Ritland 1996;Visscher et al. 2006Visscher et al. , 2008Holland et al. 2010;Sillanpaa 2011). This definition of heritability goes back to Fisher (1918) and Wright (1920) almost a century ago. In plant species for which replicates of the same genotype are available (inbred lines, doubled haploids, clones), a different form of heritability, broadsense heritability, is traditionally estimated by the intraclass correlation coefficient for genotypic effects, using estimates for within-and between-genotype variance. Broad-sense heritability is also referred to as repeatability and gives the proportion of phenotypic variance explained by heritable (additive) and nonheritable (dominance, epistasis) genetic variance.With the arrival of high-density genotyping there is growing interest in marker-based estimation of narrow-sense heritability (WTCCC 2007;Yang et al. 2010Yang et al. , 2011Vatti...

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“…In the first of these papers, Long et al [69] There are a variety of approaches that can be used to sample a large number of genetic markers distributed across a genome without requiring whole-genome sequencing (e.g. Genotype by sequencing [66], RADseq [67], multiplexed genotype sequencing [68], sequence capture).…”

Section: Box 1: How Many Sweeps In Sweden?mentioning

confidence: 99%

Advances and limits of using population genetics to understand local adaptation

Tiffin

Ross‐Ibarra

2014

Preprint

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Local adaptation is an important process shaping within species diversity. In recent years, population genetic analyses, which complement organismal approaches in advancing our understanding of local adaptation have become widespread. Here we focus on using population genetics to address some key questions in local adaptation: What traits are involved? What environmental variables are most important? Does local adaptation target the same genes in related species? Do loci responsible for local adaptation exhibit tradeoffs across environments? After discussing these questions we highlight important limitations to population genetic analyses including challenges with obtaining high quality data, deciding which loci are targets of selection, and limits to identifying the genetic basis of local adaptation.

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Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

Cited by 369 publications

References 45 publications

Heterosis and outbreeding depression in crosses between natural populations of Arabidopsis thaliana

Heterosis and outbreeding depression in crosses between natural populations of Arabidopsis thaliana

Marker-Based Estimation of Heritability in Immortal Populations

Advances and limits of using population genetics to understand local adaptation

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