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

Vanessa Nichole Michelizzi

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.

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

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