ArticlePloS one2009
Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 328 papers, 5 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
328 citing papers in PubMed, 5 syntheses or guidelines pooled it, 798 citations in OpenAlex.
- Genome-wide association studies and meta-analysis uncovers new candidate genes for growth and carcass traits in pigs.PloS one · 2018Pooled it
- Meta-analysis of genome-wide association from genomic prediction models.Animal genetics · 2016Pooled it
- Genetic architecture of fatty acid composition in the longissimus dorsi muscle revealed by genome-wide association studies on diverse pig populations.Genetics, selection, evolution : GSE · 2016Pooled it
- A meta analysis of genome-wide association studies for limb bone lengths in four pig populations.BMC genetics · 2015Pooled it
- Genome-wide association analyses for meat quality traits in Chinese Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) commercial population.Genetics, selection, evolution : GSE · 2015Pooled it
- A causal SNP in the promoter ofZoological research · 2026Article
- Development and Characterization of a Single Nucleotide Polymorphism Genotyping Panel for Duck Populations.Animals : an open access journal from MDPI · 2026Article
- An increased number of heterozygous calls in the AxiomTM Equine Genotyping Array.G3 (Bethesda, Md.) · 2026Article
- Revisiting Genetic Relationships of the Endangered Austrian Turopolje With Balkan and Commercial Pig Breeds Using Genome-Wide SNP Data.Animal genetics · 2026Article
- Widespread DNA off-targeting confounds RNA chromatin occupancy studies.Nature biotechnology · 2026Article
- Development and validation of a dual-purpose 60K single nucleotide polymorphism chip for simultaneous genotyping of chicken and duck.Animal bioscience · 2026Article
- Restructuring breeding programs 1: Integration of diversity.Genetics, selection, evolution : GSE · 2026Article
- Development and validation of high-density SNP array for genomic studies in Indian yak populations.BMC genomic data · 2026Article
- Genome-wide association analyses for growth, carcass composition, and meat quality traits of Iberian pigs fattened in free open air.Journal of animal science · 2026Article
- Genetic Insights Into Human-Driven Hybridization, Cultural Shifts, and Ecological Consequences of Feral Pigs (Ecology and evolution · 2026Article
- Characterization of genomic diversity and population structure of worldwide Duroc subpopulations and other pig breeds.Genetics, selection, evolution : GSE · 2025Article
- Genomic characterization and insights into the belted coat pattern of a local, reconstituted pig population.Animal biotechnology · 2025Article
- High-quality chromosome-scale genome assembly and annotation of Taohongling Sika deer (Cervus nippon kopschi).Scientific data · 2025Article
- Conservation of Native Livestock Breeds in Russia: Current State and Promising Prospects.Animals : an open access journal from MDPI · 2025Review
- Development and validation of a high-density 'Amahysnp' genotyping array in grain amaranth (Amaranthus hypochondriacus).BMC plant biology · 2025Article
268 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
27 authors at 15 institutions in 5 countries.
Funding
Abstract
backgroundThe dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay. METHODOLOGY/PRINCIPAL
findingsA total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274. CONCLUSIONS/SIGNIFICANCE: Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.