ArticleInternational journal of biological sciences2010
A global view of 54,001 single nucleotide polymorphisms (SNPs) on the Illumina BovineSNP50 BeadChip and their transferability to water buffalo.
Article in International journal of biological sciences, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 42 citations in OpenAlex.
- Exploring Genomic Variability in the Mediterranean Buffalo Breed: A Step Towards Custom SNP Array.Animals : an open access journal from MDPI · 2026Article
- Molecular Diversity of the Casein Gene Cluster in Bovidae: Insights from SNP Microarray Analysis.Animals : an open access journal from MDPI · 2024Article
- SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP-array.Evolutionary applications · 2023Article
- Article
- Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other TwoFrontiers in genetics · 2021Article
- Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species.G3 (Bethesda, Md.) · 2020Article
- Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.Nature communications · 2020Article
- Identification of additional loci associated with antibody response to Mycobacterium avium ssp. Paratuberculosis in cattle by GSEA-SNP analysis.Mammalian genome : official journal of the International Mammalian Genome Society · 2017Article
- Genome wide screening of candidate genes for improving piglet birth weight using high and low estimated breeding value populations.International journal of biological sciences · 2014Article
- Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle.BMC genetics · 2013Article
- Whole-genome sequencing of Theileria parva strains provides insight into parasite migration and diversification in the African continent.DNA research : an international journal for rapid publication of reports on genes and genomes · 2013Article
- Investigation of transferability of BovineSNP50 BeadChip from cattle to water buffalo for genome wide association study.Molecular biology reports · 2013Article
- Genome-wide genetic diversity and differentially selected regions among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep.PloS one · 2013Article
- Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle.PloS one · 2013Article
- Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks.BMC evolutionary biology · 2012Article
- Sequencing technologies and genome sequencing.Journal of applied genetics · 2011Review
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Illumina BovineSNP50 BeadChip features 54,001 informative single nucleotide polymorphisms (SNPs) that uniformly span the entire bovine genome. Among them, 52,255 SNPs have locations assigned in the current genome assembly (Btau_4.0), including 19,294 (37%) intragenic SNPs (i.e., located within genes) and 32,961 (63%) intergenic SNPs (i.e., located between genes). While the SNPs represented on the Illumina Bovine50K BeadChip are evenly distributed along each bovine chromosome, there are over 14,000 genes that have no SNPs placed on the current BeadChip. Kernel density estimation, a non-parametric method, was used in the present study to identify SNP-poor and SNP-rich regions on each bovine chromosome. With bandwidth = 0.05 Mb, we observed that most regions have SNP densities within 2 standard deviations of the chromosome SNP density mean. The SNP density on chromosome X was the most dynamic, with more than 30 SNP-rich regions and at least 20 regions with no SNPs. Genotyping ten water buffalo using the Illumina BovineSNP50 BeadChip revealed that 41,870 of the 54,001 SNPs are fully scored on all ten water buffalo, but 6,771 SNPs are partially scored on one to nine animals. Both fully scored and partially/no scored SNPs are clearly clustered with various sizes on each chromosome. However, among 43,687 bovine SNPs that were successfully genotyped on nine and ten water buffalo, only 1,159 were polymorphic in the species. These results indicate that the SNPs sites, but not the polymorphisms, are conserved between two species. Overall, our present study provides a solid foundation to further characterize the SNP evolutionary process, thus improving understanding of within- and between-species biodiversity, phylogenetics and adaption to environmental changes.
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