The Pattern of Polymorphism in Arabidopsis thaliana

By Magnus Nordborg, T. Hu, Y. Ishino, Jinal Jhaveri, C. Toomajian, Honggang Zheng, E. Bakker, P. Calabrese, J. Gladstone, Rana Goyal and 14 more. PLoS Biology, 2005

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We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/34f1b798f6af3c95094f9a2898342a8d02fdaee0

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Citations in the corpus

Applications of Linkage Disequilibrium and Association Mapping in Crop Plants (2007, neutral): “In Arabidopsis (Nordborg et al. 2005), natural samples were collected from around the world but because of strong population structure and selfing, these samples in many respects behave more like families for association mapping purposes (Aranzana et al.”
Genome-wide association study of 107 phenotypes in a common set of Arabidopsis thaliana inbred lines (2010, neutral): “The genotyped sample (Supplementary Table 1) includes a core set of 95 lines 4 for which a wide variety of phenotypes were available, plus a second set of 96 for which many phenotypes related to flowering were available 5 .”
A QTL Cluster for Plant Architecture and Its Ecological Significance in Asian Wild Rice (2007, background): “…a significant linkage disequilibrium persists only within 50 kb or 100 kb in predominantly self-pollinated plants such as Arabidopsis and rice, suggesting the occurrence of more frequent recombination in self-pollinated plants than previously expected (Garris et al. 2003, Nordborg et al. 2005).”
Natural selection on protein-coding genes in the human genome (2005, neutral): “01151 8 32 (10) 159 (83) mRNA transcription 0.”
Quaternary range dynamics of ecologically divergent species (Edraianthus serpyllifolius and E. tenuifolius, Campanulaceae) within the Balkan refugium (2011, methodology): “Similarity among results of different runs for the same K was calculated according to Nordborg et al. (2005) using structure-sum-2009 (http://www2.uit.no/ikbViewer/page/ansatte/ organisasjon/ansatte/person?p_document_id=41186&p_dimension_ id=88165&p_lang=2).”
Genomic Consequences of Outcrossing and Selfing in Plants (2008, background): “Keywords: inbreeding, genome evolution, recombination, transposable elements, genome size, deleterious mutation.”
On the Relevance and Control of Leaf Angle (2010, background): “Development of fast high throughput methods such as hypocotyl assays provides an excellent platform for (suppressor) mutant screens or for extensive Genome Wide Association mapping (GWA) approaches which in particular requires large sets of accessions to be screened (Nordborg et al., 2005; Nordborg ”
Demographic fate of Arabidopsis thaliana cohorts of autumn‐ and spring‐germinated plants along an altitudinal gradient (2012, background): “…and evolutionary model system because the species inhabits a wide range of anthropic and wild environments (Sharbel, Haubold & Mitchell-Olds 2000; Nordborg et al. 2005; Ostrowski et al. 2006; Schmid et al. 2006; Beck, Schmuths & Schaal 2008; François et al. 2008; Picó et al. 2008; Platt et al.…”
Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. (2009, methodology): “We compared the TE SFS with the SFS for A. thaliana sSNPs, utilizing a genome-wide nucleotide sequence data set consisting of 876 fragments of 500– 800 bp sequenced in the same 48 individuals that made up our TE frequency panel (Nordborg et al. 2005).”
Development of a Research Platform for Dissecting Phenotype–Genotype Associations in Rice (Oryza spp.) (2010, background): “…for heterotic groups in maize (Matsuoka et al. 2002), 0.087–0.290 for US wheat germplasm collection (Chao et al. 2007), 0.37– 0.86 for Ethiopian and other barley populations (Saisho and Purugganan 2007) and 0.20–0.88 for Arabidopsis thaliana population (He et al. 2007; Nordborg et al. 2005).”
Loss of Self‐Incompatibility and Its Evolutionary Consequences (2008, background): “However, species-wide variation in A. thaliana remains quite high (Nordborg et al. 2005), reflecting its broad geographic range and large species-wide population size.”
Genetic association mapping and genome organization of maize. (2006, background): “The complex evolutionary and breeding history in maize [31,32 ] and other species [22,35] has undoubtedly created both population structure and complex familial relationships.”