ArticleBMC genetics2008
SNP discovery in swine by reduced representation and high throughput pyrosequencing.
Article in BMC genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
40 citing papers in PubMed, 111 citations in OpenAlex.
- Wheat Water-Soluble Carbohydrate Remobilisation under Water Deficit byCurrent issues in molecular biology · 2023Article
- Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- Harnessing the power of RADseq for ecological and evolutionary genomics.Nature reviews. Genetics · 2016Review
- Reduced Representation Libraries from DNA Pools Analysed with Next Generation Semiconductor Based-Sequencing to Identify SNPs in Extreme and Divergent Pigs for Back Fat Thickness.International journal of genomics · 2015Article
- Recent trends and perspectives of molecular markers against fungal diseases in wheat.Frontiers in microbiology · 2015Review
- Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array.Plant biotechnology journal · 2014Article
- All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing.BMC genomics · 2014Article
- Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms.BMC genomics · 2014Article
- Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
- Article
- Patterns of transcriptome divergence in the male accessory gland of two closely related species of field crickets.Genetics · 2013Article
- Genome-wide SNP and STR discovery in the Japanese crested ibis and genetic diversity among founders of the Japanese population.PloS one · 2013Article
- Article
- Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol.PLoS genetics · 2013Article
- Development and mapping of SNP assays in allotetraploid cotton.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2012Article
- Comprehensive evaluation of SNP identification with the Restriction Enzyme-based Reduced Representation Library (RRL) method.BMC genomics · 2012Article
- Article
- Article
- Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape.Molecular ecology · 2011Article
- Sequencing technologies and genome sequencing.Journal of applied genetics · 2011Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRelatively little information is available for sequence variation in the pig. We previously used a combination of short read (25 base pair) high-throughput sequencing and reduced genomic representation to discover > 60,000 single nucleotide polymorphisms (SNP) in cattle, but the current lack of complete genome sequence limits this approach in swine. Longer-read pyrosequencing-based technologies have the potential to overcome this limitation by providing sufficient flanking sequence information for assay design. Swine SNP were discovered in the present study using a reduced representation of 450 base pair (bp) porcine genomic fragments (approximately 4% of the swine genome) prepared from a pool of 26 animals relevant to current pork production, and a GS-FLX instrument producing 240 bp reads.
resultsApproximately 5 million sequence reads were collected and assembled into contigs having an overall observed depth of 7.65-fold coverage. The approximate minor allele frequency was estimated from the number of observations of the alternate alleles. The average coverage at the SNPs was 12.6-fold. This approach identified 115,572 SNPs in 47,830 contigs. Comparison to partial swine genome draft sequence indicated 49,879 SNP (43%) and 22,045 contigs (46%) mapped to a position on a sequenced pig chromosome and the distribution was essentially random. A sample of 176 putative SNPs was examined and 168 (95.5%) were confirmed to have segregating alleles; the correlation of the observed minor allele frequency (MAF) to that predicted from the sequence data was 0.58.
conclusionThe process was an efficient means to identify a large number of porcine SNP having high validation rate to be used in an ongoing international collaboration to produce a highly parallel genotyping assay for swine. By using a conservative approach, a robust group of SNPs were detected with greater confidence and relatively high MAF that should be suitable for genotyping in a wide variety of commercial populations.
Indexed as
Identifiers
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.