ArticleBMC genomics2009
Mining for single nucleotide polymorphisms in pig genome sequence data.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 29 citations in OpenAlex.
- A causal SNP in the promoter ofZoological research · 2026Article
- Assessing Population Structure and Signatures of Selection in Wanbei Pigs Using Whole Genome Resequencing Data.Animals : an open access journal from MDPI · 2022Article
- Genetic architecture and selection of Anhui autochthonous pig population revealed by whole genome resequencing.Frontiers in genetics · 2022Article
- Genetic Diversity and Ancestral Study for Korean Native Pigs Using 60K SNP Chip.Animals : an open access journal from MDPI · 2020Article
- Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig.Frontiers in genetics · 2020Article
- An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs.BMC genetics · 2016Article
- Genome sequencing and analysis of Mangalica, a fatty local pig of Hungary.BMC genomics · 2014Article
- Analysis of muscle and ovary transcriptome of Sus scrofa: assembly, annotation and marker discovery.DNA research : an international journal for rapid publication of reports on genes and genomes · 2011Article
- Genomic Diversity in Pig (Sus scrofa) and its Comparison with Human and other Livestock.Current genomics · 2011Article
- New SNP of the porcine perilipin 2 (PLIN2) gene, association with carcass traits and expression analysis in skeletal muscle.Molecular biology reports · 2011Article
- Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome.BMC genomics · 2009Article
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSingle nucleotide polymorphisms (SNPs) are ideal genetic markers due to their high abundance and the highly automated way in which SNPs are detected and SNP assays are performed. The number of SNPs identified in the pig thus far is still limited.
resultsA total of 4.8 million whole genome shotgun sequences obtained from the NCBI trace-repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project" were analysed for the presence of SNPs. Available BAC and BAC-end sequences and their naming and mapping information, all obtained from SangerInstitute FTP site, served as a rough assembly of a reference genome. In 1.2 Gb of pig genome sequence, we identified 98,151 SNPs in which one of the sequences in the alignment represented the polymorphism and 6,374 SNPs in which two sequences represent an identical polymorphism. To benchmark the SNP identification method, 163 SNPs, in which the polymorphism was represented twice in the sequence alignment, were selected and tested on a panel of three purebred boar lines and wild boar. Of these 163 in silico identified SNPs, 134 were shown to be polymorphic in our animal panel.
conclusionThis SNP identification method, which mines for SNPs in publicly available porcine shotgun sequences repositories, provides thousands of high quality SNPs. Benchmarking in an animal panel showed that more than 80% of the predicted SNPs represented true genetic variation.
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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.