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Published on: October 17, 2017
The pattern of polymorphism in Arabidopsis thaliana
Magnus Nordborg1, Tina T Hu, Yoko Ishino
1Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA. magnus@usc.edu
Arabidopsis thaliana exhibits worldwide genetic variation, with rapid decay of linkage disequilibrium. Despite deviations from neutral models, this weed is a valuable model for evolutionary genomics research.
Area of Science:
- Plant genetics
- Population genetics
- Evolutionary biology
Background:
- Arabidopsis thaliana is a widely distributed selfing weed.
- Understanding its genetic variation is crucial for evolutionary functional genomics.
Purpose of the Study:
- To resequence short fragments in 96 Arabidopsis thaliana individuals.
- To analyze patterns of genetic polymorphism and linkage disequilibrium.
- To assess the fit of data to neutral evolutionary models.
Main Methods:
- Resequencing of 876 short DNA fragments.
- Sampling of 96 individuals from stock centers and natural populations.
- Analysis of genetic variation, linkage disequilibrium, and population structure.
Main Results:
- Polymorphism patterns largely align with sexually reproducing species, despite selfing.
- Linkage disequilibrium rapidly decays within 50 kb.
- Genome-wide excess of rare alleles and high inter-regional variation observed, deviating from neutral models.
- Polymorphism levels correlate negatively with gene density and positively with segmental duplications.
Conclusions:
- Arabidopsis thaliana displays significant population structure and isolation by distance.
- Deviations from neutral models suggest a role for selection.
- Genome-wide surveys are needed to infer natural selection from polymorphism data.
- The data support Arabidopsis thaliana's utility as a model for evolutionary functional genomics.
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