ArticlePloS one2011
Tracing cattle breeds with principal components analysis ancestry informative SNPs.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Genomic solutions to metadata challenges: a case study on the 1000 Bull Genomes Project.Genetics, selection, evolution : GSE · 2026Article
- RASEL: An Ensemble Model for Selection of Core SNPs and Its Application for Identification and Classification of Cattle Breeds.Biochemical genetics · 2026Article
- A deep learning strategy for accurate identification of purebred and hybrid pigs across SNP chips.Journal of animal science and biotechnology · 2025Article
- Global and Local Ancestry and its Importance: A Review.Current genomics · 2024Review
- A Novel Insight into the Identification of Potential SNP Markers for the Genomic Characterization of Buffalo Breeds in Pakistan.Animals : an open access journal from MDPI · 2023Article
- Detecting SNP markers discriminating horse breeds by deep learning.Scientific reports · 2023Article
- Evaluating the use of statistical and machine learning methods for estimating breed composition of purebred and crossbred animals in thirteen cattle breeds using genomic information.Frontiers in genetics · 2023Article
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- Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data.Scientific reports · 2022Article
- Exploring genetic diversity and population structure of Punjab goat breeds using Illumina 50 K SNP bead chip.Tropical animal health and production · 2021Article
- Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPs.BMC genomics · 2021Article
- Insight into the Current Genetic Diversity and Population Structure of Domestic Reindeer (Animals : an open access journal from MDPI · 2020Article
- Identification of Ancestry Informative Marker (AIM) Panels to Assess Hybridisation between Feral and Domestic Sheep.Animals : an open access journal from MDPI · 2020Article
- Genetic structure of six cattle populations revealed by transcriptome-wide SNPs and gene expression.Genes & genomics · 2018Article
- Article
- Genetic differentiation of Mexican Holstein cattle and its relationship with Canadian and U.S. Holsteins.Frontiers in genetics · 2015Article
- Revisiting demographic processes in cattle with genome-wide population genetic analysis.Frontiers in genetics · 2015Article
- A comparison of principal component regression and genomic REML for genomic prediction across populations.Genetics, selection, evolution : GSE · 2014Article
- Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel.Molecular biology reports · 2014Article
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The recent release of the Bovine HapMap dataset represents the most detailed survey of bovine genetic diversity to date, providing an important resource for the design and development of livestock production. We studied this dataset, comprising more than 30,000 Single Nucleotide Polymorphisms (SNPs) for 19 breeds (13 taurine, three zebu, and three hybrid breeds), seeking to identify small panels of genetic markers that can be used to trace the breed of unknown cattle samples. Taking advantage of the power of Principal Components Analysis and algorithms that we have recently described for the selection of Ancestry Informative Markers from genomewide datasets, we present a decision-tree which can be used to accurately infer the origin of individual cattle. In doing so, we present a thorough examination of population genetic structure in modern bovine breeds. Performing extensive cross-validation experiments, we demonstrate that 250-500 carefully selected SNPs suffice in order to achieve close to 100% prediction accuracy of individual ancestry, when this particular set of 19 breeds is considered. Our methods, coupled with the dense genotypic data that is becoming increasingly available, have the potential to become a valuable tool and have considerable impact in worldwide livestock production. They can be used to inform the design of studies of the genetic basis of economically important traits in cattle, as well as breeding programs and efforts to conserve biodiversity. Furthermore, the SNPs that we have identified can provide a reliable solution for the traceability of breed-specific branded products.
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