Association Mapping With Single-Feature Polymorphisms

Kim, Sung Hoon; Zhao, Keyan; Jiang, Rong; Molitor, John; Borevitz, Justin O.; Nordborg, Magnus; Marjoram, Paul

doi:10.1534/genetics.105.052720

Cited by 32 publications

(28 citation statements)

References 48 publications

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“…The polymorphism detection and genotyping power are stronger when averaged across 50-kb intervals containing Ϸ100 (86-126 inner-quartile range) 25-bp features. The added resolution more than makes up for the lower per-site accuracy (23,25) compared with dideoxy sequencing of a single Ϸ500-bp fragment every 100 kb (6). Features within Ϯ25 kb of the central probe in a gene were used to estimate diversity.…”

Section: Methodsmentioning

confidence: 99%

“…Population studies based on SNPs generally benefit from high-quality data but typically sparse genome coverage, whereas SFPs tend to be of lower quality yet exceptionally abundant. A power analysis evaluating decay of linkage disequilibrium across various simulated study design parameters indicated that the abundance of lower-quality SFPs compensates for a lack of SNP density (25). In addition, the probability of detecting potential causative polymorphism is considerably greater (17).…”

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confidence: 99%

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Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana

Borevitz

Hazen

Michael

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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154

148

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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 frequencydependent 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. evolutionary genomics ͉ gene array ͉ nucleotide diversity

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana

Borevitz

Hazen

Michael

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

154

148

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“…Technologies have also been developed, which make use of tag arrays for detection of the products of genotyping reactions. These novel array-or chip-based markers are useful for a variety of purposes including genome-wide association studies, population studies, bulk segregant analysis, quantitative trait loci (QTL) interval mapping, whole genome profiling and background screening and so on (Steinmetz et al, 2002;Winzeler et al, 2003;Wenzl et al, 2004Wenzl et al, , 2007aHazen et al, 2005;Kim et al, 2006). A brief account of the development and use of these highthroughput array-based molecular markers in plants is presented in this study.…”

Section: Introductionmentioning

confidence: 99%

Array-based high-throughput DNA markers for crop improvement

2008

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The last two decades have witnessed a remarkable activity in the development and use of molecular markers both in animal and plant systems. This activity started with lowthroughput restriction fragment length polymorphisms and culminated in recent years with single nucleotide polymorphisms (SNPs), which are abundant and uniformly distributed. Although the latter became the markers of choice for many, their discovery needed previous sequence information. However, with the availability of microarrays, SNP platforms have been developed, which allow genotyping of thousands of markers in parallel. Besides SNPs, some other novel marker systems, including single feature polymorphisms, diversity array technology and restriction site-associated DNA markers, have also been developed, where arraybased assays have been utilized to provide for the desired ultra-high throughput and low cost. These microarray-based markers are the markers of choice for the future and are already being used for construction of high-density maps, quantitative trait loci (QTL) mapping (including expression QTLs) and genetic diversity analysis with a limited expense in terms of time and money. In this study, we briefly describe the characteristics of these array-based marker systems and review the work that has already been done involving development and use of these markers, not only in simple eukaryotes like yeast, but also in a variety of seed plants with simple or complex genomes.

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“…T ECHNOLOGICAL advances in DNA sequencing have facilitated direct analyses of nucleotide diversity and large-scale single nucleotide polymorphism (SNP) discovery in diverse eukaryotes, as well as the development of highly parallel SNP genotyping methods and high-resolution linkage disequilibrium (LD)-based association mapping approaches for identifying functionally important nucleotide polymorphisms ( Jorde 1995( Jorde , 2000Lindblad-Toh et al 2000;Risch 2000;Syvanen 2001Syvanen , 2005Buckler and Thornsberry 2002;Nordborg and Tavare 2002;Flint-Garcia et al 2003;Weigel and Nordborg 2005;Kim et al 2006). Very high DNA marker densities are needed for identifying DNA polymorphisms linked to phenotypic and quantitative trait loci through whole-genome association mapping approaches and can only be achieved using SNPs, the most abundant class of DNA polymorphisms (Collins et al 1998;Aquadro et al 2001;Wiltshire et al 2003).…”

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confidence: 99%

Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

Kolkman

Berry²,

Leόn³

et al. 2007

Genetics

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Genetic diversity in modern sunflower (Helianthus annuus L.) cultivars (elite oilseed inbred lines) has been shaped by domestication and breeding bottlenecks and wild and exotic allele introgression -the former narrowing and the latter broadening genetic diversity. To assess single nucleotide polymorphism (SNP) frequencies, nucleotide diversity, and linkage disequilibrium (LD) in modern cultivars, alleles were resequenced from 81 genic loci distributed throughout the sunflower genome. DNA polymorphisms were abundant; 1078 SNPs (1/45.7 bp) and 178 insertions-deletions (INDELs) (1/277.0 bp) were identified in 49.4 kbp of DNA/genotype. SNPs were twofold more frequent in noncoding (1/32.1 bp) than coding (1/ 62.8 bp) sequences. Nucleotide diversity was only slightly lower in inbred lines (u ¼ 0.0094) than wild populations (u ¼ 0.0128). Mean haplotype diversity was 0.74. When extraploted across the genome ($3500 Mbp), sunflower was predicted to harbor at least 76.4 million common SNPs among modern cultivar alleles. LD decayed more slowly in inbred lines than wild populations (mean LD declined to 0.32 by 5.5 kbp in the former, the maximum physical distance surveyed), a difference attributed to domestication and breeding bottlenecks. SNP frequencies and LD decay are sufficient in modern sunflower cultivars for very high-density genetic mapping and high-resolution association mapping.

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Association Mapping With Single-Feature Polymorphisms

Cited by 32 publications

References 48 publications

Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana

Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana

Array-based high-throughput DNA markers for crop improvement

Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

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