Water Buffalo Genome Science Comes of Age

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

Whole genome single nucleotide polymorphism (SNP) transfer from cattle to water buffalo

Single nucleotide polymorphisms (SNPs) represent the most abundant form of genetic variation serving as valuable tools for linking genes to normal physiological changes, diseases, and responses to pathogens, chemicals, drugs, vaccines and adaption to environmental changes. In recent years, the cattle research community has discovered a large number of SNPs in the genome of the species. These publicly available SNPs have led to the development of a high-density SNP genotyping microarray with 54,001 bovine SNPs, most of which have been mapped to the current bovine genome assembly Btau_4.0; we annotated the SNPs on a whole genome level. We classified these SNPs into intergenic (between-gene) and intragenic (within-gene) categories and found that most genes do not have an intragenic SNP. In contrast, all intergenic regions have at least 1 SNP and there are many more intergenic SNPs than intragenic SNPs. Kernel density plots also identified SNP-poor and SNP-rich regions on each bovine chromosome. In contrast to cattle, SNP resources in water buffalo are decidedly lacking; the community has however, started to work on genome sequencing, mapping and phylogenetic investigation of the species. Due to the similarities between cattle and water buffalo, we investigated the cross-species transferability of the 52,255 SNPs on the BovineSNP50 Genotyping BeadChip placed in Btau_4.0. Among them, only ~10% had no calls and of the called SNPs, only 3,067 remained polymorphic in water buffalo. Of the transferable SNPs, 37.2% were intragenic and 62.8% intergenic. We also targeted 20 genes associated with muscle growth and development and found that 15 genes had a total of 69 SNPs on the BovineSNP50 BeadChip; among them, 56 were genotyped on ≥9 water buffalo samples. Overall, our present annotation and characterization of the BovineSNP50 BeadChip will help users design their experiments and explain their results. Our work may also provide some useful suggestions on updating the bovine SNP array in the near future. Furthermore, the results of this research make it possible to identify potential economically important genes in water buffalo, set groundwork for future water buffalo research, and develop genomic technologies for advancing water buffalo genome science and applications

A Global View of 54,001 Single Nucleotide Polymorphisms (SNPs) on the Illumina BovineSNP50 BeadChip and Their Transferability to Water Buffalo

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

Water Buffalo Genome Science Comes of Age

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.</p