ArticlePloS one2014
Design and characterization of a 52K SNP chip for goats.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 114 papers.
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Who cites it
114 citing papers in PubMed, 272 citations in OpenAlex.
- Inference of Genetic Structure and the Process of Population Formation in Nepalese Native Goats Using Uniparental and Genome-Wide Markers.Animals : an open access journal from MDPI · 2026Article
- Genome-Wide Diversity of Goats From Indonesia and the Philippines Reveals Local Ancestry With Different Levels of Cosmopolitan Admixture.Genome biology and evolution · 2026Article
- An increased number of heterozygous calls in the AxiomTM Equine Genotyping Array.G3 (Bethesda, Md.) · 2026Article
- Decoding Complex Traits in Goats Through Genome-Wide Association Studies: Progress, Challenges, and Perspectives.International journal of molecular sciences · 2026Review
- Evolution and Comparative Analysis of Sheep Reference Genomes: From Fragmented Assemblies to Telomere-to-Telomere Genomics.Biology · 2026Review
- Progress on genome-wide association studies and selection signature analysis for agronomic traits in Chinese sheep and goats: review.Animal bioscience · 2026Article
- Signature of Selection Analysis Reveals Candidate Genes Related to Climate Adaptation and Production Traits in Lao Native Goats.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2026Article
- Development and application of SNP chips in goat breeding: a mini review.Frontiers in veterinary science · 2026Review
- Normalized cumulative gain as an alternative evaluation measure for genomic selection models.Genetics, selection, evolution : GSE · 2025Article
- Conservation of Native Livestock Breeds in Russia: Current State and Promising Prospects.Animals : an open access journal from MDPI · 2025Review
- Genome landscape and genetic architecture of recombination in domestic goats (Capra hircus).Genetics, selection, evolution : GSE · 2025Article
- 'Highly-Informative' Genetic Markers Can Bias Conclusions: Examples and General Solutions.Molecular ecology resources · 2025Article
- IMAGE001: A new livestock multispecies SNP array to characterize genomic variation in European livestock gene bank collections.Animal genetics · 2025Article
- Development of a 5K Liquid-Phase Genome-Wide Breeding Chip for Xinglong Buffalo.Animals : an open access journal from MDPI · 2025Article
- Genomic advancements in goat breeding: enhancing productivity, disease resistance, and sustainability in India's rural economy.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Review
- Candidate Genes, Markers, Signatures of Selection, and Quantitative Trait Loci (QTLs) and Their Association with Economic Traits in Livestock: Genomic Insights and Selection.International journal of molecular sciences · 2025Review
- Article
- Design and verification of a 25 K multiple-SNP liquid-capture chip by target sequencing for dairy goat.BMC genomics · 2025Article
- Article
- Genomic Tools for Medicinal Properties of Goat Milk for Cosmetic and Health Benefits: A Narrative Review.International journal of molecular sciences · 2025Review
54 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
28 authors at 16 institutions in 7 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50-60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.
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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.