Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana

By Richard M. Clark, Gabriele Beate Schweikert, C. Toomajian, Stephan Ossowski, Georg Zeller, Paul Shinn, Norman Warthmann, T. Hu, G. Fu, David A. Hinds and 8 more. Science, 2007

756 citations recorded by the source corpus.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/01ad565d517fbe90852996cb7cb45ff9616a8ca5

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In Plant Science

1. M. Thomson
2. G. Eizenga
3. Jianming Yu
4. Edward S. Buckler
5. Bin Han
6. Michael A. Gore
7. Xuehui Huang
8. D. Mackill

Citations in the corpus

• Status and Prospects of Association Mapping in Plants (2008, methodology): “, on average one SNP every 166 bp) (Clark et al., 2007), a rate about 11-fold higher than that of human populations (Hinds et al.”
• Evolution of Gene Duplication in Plants1[OPEN] (2016, background): “Nonetheless, R genes belong to one of the most highly variable gene families (Clark et al., 2007) and tend to have an excess of pseudogenes (Zou et al., 2009a).”
• Natural variations and genome-wide association studies in crop plants. (2014, methodology): “This method, known as microarray-based genotyping, enables direct scanning of allelic variation across the genome, covering hundreds to thousands of SNPs in a short time (17, 102, 121).”
• Fast and flexible simulation of DNA sequence data. (2008, methodology): “…utilized existing data to make inferences about additional unobserved data (either additional SNPs or genotypes from additional individuals), including “hide the SNP” studies, bootstrap resampling studies, and more sophisticated methods (Durrant et al. 2004; Stram 2004; Scheet and Stephens 2006).”
• A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana (2009, background): “5, with many rare alleles [22], so the QTL discovery rate is not as efficient.”
• Metabolomics for functional genomics, systems biology, and biotechnology. (2010, methodology): “Further advancements in gene sequencing techniques will allow us to determine variations in genome sequences between two parents of experimental lines prior to QTL analysis (28, 116).”
• A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety (2007, background): “This type of molecular variation seems to be common in allogamous plants [86] and could also be a characteristic of autogamous species [33].”
• The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates (2011, background): “The peak at ∼25 Mb on A. thaliana chromosome 1 corresponds to a region of high intraspecific polymorphism (Clark et al. 2007). correspondence between divergence and polymorphism suggests that mutation rates vary among chromosomal regions and contributes to correlations between KA and KS. Yang &…”
• 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana (2016, background): “This was followed by a Cell 166, 481–491, This is an open access article und whole-genome map of deletions and SNPs in 20 global accessions (Clark et al., 2007), which in turn was the basis of a 250k SNP array with multiple markers in each haplotype block (Kim et al., 2007).”