The water buffalo is vital to the lives of small farmers and to the economy of many countries worldwide. Not only are they draught animals, but they are also a source of meat, horns, skin and particularly the rich and precious milk that may be converted to creams, butter, yogurt and many cheeses. Genome analysis of water buffalo has advanced significantly in recent years. This review focuses on currently available genome resources in water buffalo in terms of cytogenetic characterization, whole genome mapping and next generation sequencing. No doubt, these resources indicate that genome science comes of age in the species and will provide knowledge and technologies to help optimize production potential, reproduction efficiency, product quality, nutritional value and resistance to diseases. As water buffalo and domestic cattle, both members of the Bovidae family, are closely related, the vast amount of cattle genetic/genomic resources might serve as shortcuts for the buffalo community to further advance genome science and biotechnologies in the species.

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.