SNPchiMp: a database to disentangle the SNPchip jungle in bovine livestock

Nicolazzi, Ezequiel Luís; Picciolini, Matteo; Strozzi, Francesco; Schnabel, Robert D.; Lawley, Cindy; Pirani, Ali; Brew, Fiona; Stella, Alessandra

doi:10.1186/1471-2164-15-123

Cited by 53 publications

(48 citation statements)

References 10 publications

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“…To determine which SNPs from the Illumina BovineSNP50 v1 array data map to the FTO gene, the SNPchiMp v.3 database was used (Nicolazzi et al . ). The DNA samples were extracted from frozen semen of 31 SS sires and muscle tissue samples of 160 progeny‐tested half‐sibs using the DNeasy Blood & Tissue Kit (Qiagen).…”

Section: Results Of the Association Analysis Between The Fto Snps And mentioning

confidence: 97%

FTO gene variants are associated with growth and carcass traits in cattle

et al. 2015

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An important aim in animal breeding is the improvement of growth and meat quality traits. Previous studies have demonstrated that genetic variants in the fat mass and obesity associated (FTO) gene have a relatively large effect on human obesity as well as on body composition in rodents and, more recently, in livestock. Here, we examined the effects of the FTO gene variants on growth and carcass traits in the Slovenian population of Simmental (SS) and Brown (SB) cattle. To validate and identify new polymorphisms, we used sequencing, PCR-RFLP analysis and TaqMan assays in the SS breed and FTO gene variants data from the Illumina BovineSNP50 v1 array for the SB breed. Sequencing of the eight samples of progeny-tested SS sires detected 108 single nucleotide polymorphisms (SNPs) in the bovine FTO gene. Statistical analyses between growth and carcass traits and 34 FTO polymorphisms revealed significant association of FTO variants with lean meat percentage in both breeds. Additionally, FTO SNPs analyzed in SS cattle were associated with fat percentage, bone weight and live weight at slaughter. The FTO gene can thus be regarded as a candidate gene for the marker-assisted selection programs in our and possibly other populations of cattle. Future studies in cattle might reveal novel roles for the FTO gene in shaping carcass traits in livestock species as well as body composition control in other mammals.

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Section: Results Of the Association Analysis Between The Fto Snps And mentioning

confidence: 97%

FTO gene variants are associated with growth and carcass traits in cattle

et al. 2015

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“…The map files were created by downloading OARv.4.0 SNP positions from the SNPchiMp database (Nicolazzi et al . ). Only markers located on autosomes were considered for further analyses.…”

Section: Methodsmentioning

confidence: 97%

Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds

Signer-Hasler

Burren

Ammann³

et al. 2019

Animal Genetics

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A dataset consisting of 787 animals with high-density SNP chip genotypes (346 774 SNPs) and 939 animals with medium-density SNP chip genotypes (33 828 SNPs) from eight indigenous Swiss sheep breeds was analyzed to characterize population structure, quantify genomic inbreeding based on runs of homozygosity and identify selection signatures. In concordance with the recent known history of these breeds, the highest genetic diversity was observed in Engadine Red sheep and the lowest in Valais Blacknose sheep. Correlation between F PED and F ROH was around 0.50 and thereby lower than that found in similar studies in cattle. Mean F ROH estimates from medium-density data and HD data were highly correlated (0.95). Signatures of selection and candidate gene analysis revealed that the most prominent signatures of selection were found in the proximity of genes associated with body size (NCAPG, LCORL, LAP3, SPP1, PLAG1, ALOX12, TP53), litter size (SPP1), milk production (ABCG2, SPP1), coat color (KIT, ASIP, TBX3) and horn status (RXFP2). For the Valais Blacknose sheep, the private signatures in proximity of genes/QTL influencing body size, coat color and fatty acid composition were confirmed based on runs of homozygosity analysis. These private signatures underline the genetic uniqueness of the Valais Blacknose sheep breed. In conclusion, we identified differences in the genetic make-up of Swiss sheep breeds, and we present relevant candidate genes responsible for breed differentiation in locally adapted breeds.

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“…Other formats are accepted, but are recoded to AB format before loading. Recoding is based on allele coding information from SNPchiMP (Nicolazzi et al, 2015, Nicolazzi et al, 2014. Overall if a QC step fails then the animal's genotype is invalidated from the ICBF system.…”

Section: Genotype Qc Pipelinementioning

confidence: 99%

SNP Data Quality Control in a National Beef and Dairy Cattle System and Highly Accurate SNP Based Parentage Verification and Identification

McClure¹,

McCarthy²,

Flynn³

et al. 2017

Preprint

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A major use of genetic data is parentage verification and identification as inaccurate pedigrees negatively affect genetic gain. Since 2012 the international standard for single nucleotide polymorphism (SNP) based verification in Bos taurus cattle has been the ISAG 100 and 200 SNP panels. While these SNP sets have provided an increased level of parentage accuracy over microsatellite markers (MS), they can validate the wrong parent for an animal at <1% misconcordance rate levels, indicating that more SNP are needed if a more accurate pedigree is required. With rapidly increasing numbers of cattle being genotyped in Ireland that represent 61 Bos taurus breeds from a wide range of farm types: beef/dairy, AI/pedigree/commercial, purebred/crossbred, and large to small herd size the Irish Cattle Breeding Federation (ICBF) analysed different SNP densities to determine that at a minimum >500 SNP are needed to consistently predict only one set of parents at a <1% misconcordance rate. For parentage validation and prediction ICBF uses 800 SNP selected based on SNP clustering quality, ISAG200 inclusion, call rate (CR), and minor allele frequency (MAF) in the Irish cattle population. Large datasets require sample and SNP quality control (QC). Most publications only deal with SNP QC via CR, MAF, parent-progeny conflicts, and Hardy-Weinberg deviation, but not sample QC. We report here a genomic sample QC pipeline to deal with the unique challenges of >1,000,000 genotypes from a national herd such as SNP genotype errors from mis-tagging of animals, lab errors, farm errors, and multiple other issues that can arise.

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SNPchiMp: a database to disentangle the SNPchip jungle in bovine livestock

Cited by 53 publications

References 10 publications

FTO gene variants are associated with growth and carcass traits in cattle

FTO gene variants are associated with growth and carcass traits in cattle

Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds

SNP Data Quality Control in a National Beef and Dairy Cattle System and Highly Accurate SNP Based Parentage Verification and Identification

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