Page Banner

United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF DAIRY CATTLE THROUGH GENOME SELECTION AND ANALYSIS Title: Bovine Genetic Diversity Revealed By mtDNA Sequence Variation

Authors
item Sonstegard, Tad
item Van Tassell, Curtis
item McClure, Matthew
item Chung, Hoyoung -

Submitted to: BARC Poster Day
Publication Type: Abstract Only
Publication Acceptance Date: March 16, 2011
Publication Date: April 18, 2011
Citation: Sonstegard, T.S., Van Tassell, C.P., Mcclure, M.C., Chung, H. 2011. Bovine Genetic Diversity Revealed By mtDNA Sequence Variation [abstrac]. BARC Poster Day. No. 15.

Technical Abstract: Mitochondrial DNA single nucleotide polymorphism (SNP) data were used to determine genetic distance, nucleotide diversity, construction of haplotypes, estimation of information contents, and phylogenic relationships in bovine HapMap breeds. The Bovine International HapMap panel consists of 720 animals from 27 cattle breeds including water buffalo (Bubalus bubalis) as an out-group population. Of the 364 mtDNA SNP present on the Illumina BovineHD BeadChip, 128 SNP (35%) were segregating across the 27 breeds analyzed (0.978 average major allele frequency), and 26 SNP (7.21%) were segregating within almost every breed, with the other 102 SNP having breed or subspecies-specific segregation. Nucleotide diversity was greater in Bos indicus than Bos taurus breeds (0.1538 vs. 0.0242, respectively), whereas sequence identities were greatest in B. taurus. Guernsey and Brahman had the greatest (0.9892) and least (0.7721) within breed sequence identities, respectively. Phylogenetic analysis revealed a distinct segregation pattern between B. taurus and B. indicus populations, showing a clear pattern of departure from the out-group. Interestingly, Romagnola (B. taurus), was phylogenetically between the taurus and indicus groups. These results may be caused by population-specific SNP, for instance, SNP at positions 2,558 bp (A/G) and 14,434 bp (A/G) appear to be the subspecies-specific indels as they segregate in the B. indicus breeds but neither allele is detectable in the majority of the B. taurus breeds. The SNP at nucleotide positions 9,978, 12,750, 16,042, and 16,113 bp have the largest individual effects on the determination of genetic distance between breeds and subspecies. However, the 16,113 bp SNP has no significant effects on genetic distances when only taurine breeds are analyzed. The sequence files containing the distinguishing genetic variants are highly effective on the determination of genetic events, and can be considered as a standard for characterization of individuals and breeds, as well as other species.

Last Modified: 10/30/2014