ArticleProceedings of the National Academy of Sciences of the United States of America2007
Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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85 citing papers in PubMed, 160 citations in OpenAlex.
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- The evolution of metabolism: How to test evolutionary hypotheses at the genomic level.Computational and structural biotechnology journal · 2020Review
- Comparative analysis of metabolome of rice seeds at three developmental stages using a recombinant inbred line population.The Plant journal : for cell and molecular biology · 2019Article
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- Evidence for Adaptive Introgression of Disease Resistance Genes Among Closely RelatedG3 (Bethesda, Md.) · 2017Article
- Genomic variations and distinct evolutionary rate of rare alleles in Arabidopsis thaliana.BMC evolutionary biology · 2016Article
- Genome Wide Association Mapping in Arabidopsis thaliana Identifies Novel Genes Involved in Linking Allyl Glucosinolate to Altered Biomass and Defense.Frontiers in plant science · 2016Article
- The Defense Metabolite, Allyl Glucosinolate, Modulates Arabidopsis thaliana Biomass Dependent upon the Endogenous Glucosinolate Pathway.Frontiers in plant science · 2016Article
- Microarray-based large scale detection of single feature polymorphism in Gossypium hirsutum L.Journal of genetics · 2015Article
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- Investigation of the multifunctional gene AOP3 expands the regulatory network fine-tuning glucosinolate production in Arabidopsis.Frontiers in plant science · 2015Article
- The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification.BMC genomics · 2014Article
- Patterns of divergence of a large family of nodule cysteine-rich peptides in accessions of Medicago truncatula.The Plant journal : for cell and molecular biology · 2014Article
- Genomic variability as a driver of plant-pathogen coevolution?Current opinion in plant biology · 2014Review
25 more citing papers are in PubMed but not listed here.
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15 authors at 8 institutions in 4 countries.
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Abstract
We used hybridization to the ATH1 gene expression array to interrogate genomic DNA diversity in 23 wild strains (accessions) of Arabidopsis thaliana (arabidopsis), in comparison with the reference strain Columbia (Col). At <1% false discovery rate, we detected 77,420 single-feature polymorphisms (SFPs) with distinct patterns of variation across the genome. Total and pair-wise diversity was higher near the centromeres and the heterochromatic knob region, but overall diversity was positively correlated with recombination rate (R(2) = 3.1%). The difference between total and pair-wise SFP diversity is a relative measure contrasting diversifying or frequency-dependent selection, similar to Tajima's D, and can be calibrated by the empirical genome-wide distribution. Each unique locus, centered on a gene, has a diversity and selection score that suggest a relative role in past evolutionary processes. Homologs of disease resistance (R) genes include members with especially high levels of diversity often showing frequency-dependent selection and occasionally evidence of a past selective sweep. Receptor-like and S-locus proteins also contained members with elevated levels of diversity and signatures of selection, whereas other gene families, bHLH, F-box, and RING finger proteins, showed more typical levels of diversity. SFPs identified with the gene expression array also provide an empirical hybridization polymorphism background for studies of gene expression polymorphism and are available through the genome browser http://signal.salk.edu/cgi-bin/AtSFP.
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