ArticlePloS one2017
Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis).
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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44 citing papers in PubMed, 115 citations in OpenAlex.
- Integration of Morphological and Genome-Wide SNP Data Reveals Regional Diversity in Thai Swamp Buffalo.Animals : an open access journal from MDPI · 2026Article
- TheMicroorganisms · 2026Review
- Exploring Genomic Variability in the Mediterranean Buffalo Breed: A Step Towards Custom SNP Array.Animals : an open access journal from MDPI · 2026Article
- Machine learning-based discovery of informative SNPs for population assignment through whole genome sequencing.BMC genomics · 2025Article
- Comparative Single-Cell Transcriptomic Landscape Reveals the Regulatory Mechanisms of Lactation during Selective Breeding in Asian Water Buffalo.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Development of a 5K Liquid-Phase Genome-Wide Breeding Chip for Xinglong Buffalo.Animals : an open access journal from MDPI · 2025Article
- Development and Application of a 40 K Liquid Capture Chip for Beef Cattle.Animals : an open access journal from MDPI · 2025Article
- Genomic selection, gene editing, and reproductive biotechnology: a triad for the improvement of native buffalo breeds in a developing country perspective like Pakistan.Tropical animal health and production · 2025Review
- Whole-genome sequencing reveals genetic structure and adaptive genes in Nepalese buffalo breeds.BMC genomics · 2024Article
- Molecular Diversity of the Casein Gene Cluster in Bovidae: Insights from SNP Microarray Analysis.Animals : an open access journal from MDPI · 2024Article
- Development and validation of a 5K low-density SNP chip for Hainan cattle.BMC genomics · 2024Article
- Article
- A genotyping array for the globally invasive vector mosquito, Aedes albopictus.Parasites & vectors · 2024Article
- Transcriptome-Wide Association Study Reveals Potentially Candidate Genes Responsible for Milk Production Traits in Buffalo.International journal of molecular sciences · 2024Article
- Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project.GigaScience · 2024Article
- Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data.Animal biotechnology · 2023Article
- Article
- Whole-Genome-Based Web Genomic Resource for Water Buffalo (Frontiers in genetics · 2022Article
- Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN).BMC genomics · 2021Article
- A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes.BMC genomics · 2021Article
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Authors and funding
25 authors at 10 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here.
methodsThe genomes of 73 buffaloes of 4 different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of 22 million of sequence variants among the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome, inferred from the bovine genome sequence, 90,000 putative single nucleotide polymorphisms were selected to create an Axiom® Buffalo Genotyping Array 90K.
resultsThis 90K "SNP-Chip" was tested in several river buffalo populations and found to have ∼70% high quality and polymorphic SNPs. Of the 90K SNPs about 24K were also found to be polymorphic in swamp buffalo. The SNP chip was used to investigate the structure of buffalo populations, and could distinguish buffalo from different farms. A Genome Wide Association Study identified genomic regions on 5 chromosomes putatively involved in milk production.
conclusionThe 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes. This SNP Chip could also be used to analyse swamp buffalo, but many loci are not informative and creation of a revised SNP set specific for swamp buffalo would be advised.
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