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Title: Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

item PORTO-NETO, LAERCIO - University Of Queensland
item Sonstegard, Tad
item Liu, Ge - George
item Bickhart, Derek
item GONDRO, CEDRIC - University Of New England
item SILVA, MARCOS - Embrapa
item MACHADO, MARCO - Embrapa
item UTSUNOMIYA, YURI - Universidade Estadual Paulista (UNESP)
item GARCIA, JOSE - Universidade Estadual Paulista (UNESP)
item Van Tassell, Curtis - Curt

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/20/2012
Publication Date: 12/13/2013
Citation: Porto-Neto, L.R., Sonstegard, T.S., Liu, G., Bickhart, D.M., Gondro, C., Silva, M., Machado, M., Utsunomiya, Y.T., Garcia, J.F., Van Tassell, C.P. 2013. Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping. Biomed Central (BMC) Genomics. DOI:10.1186/1471-2164-14-876.

Interpretive Summary: This report is to identify genome regions or genes affecting meat and milk production that have been selected during the natural and artificial processes of sub-species and breed formation, respectively. Ultimately, this information will be used to accelerate genetic improvement for production in existing breeds or development of new improved breeds. Our comparison study used influential animals from more than 19 breeds and included two sub-species to represent separate domestication events; one for temperate regions and the other for tropical production. Advanced DNA tools using about 700,000 single nucleotide polymorphism markers provided the information on genetic content of each breed for implementing comparison methodology. The main regions found in this study confirm previous results about the role of genes affecting stature in growth selection and reproduction.

Technical Abstract: Natural selection has molded the evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos primigenius taurus more adapted to temperate climates and the tropically adapted Bos primigenius indicus. After domestication, human selection exponentially intensified these differences, especially after the introduction of the concept of breed type in the 19th century. To better understand the genetic differences between these subspecies and detect genomic regions potentially under divergent selection, animals from the International Bovine HapMap Experiment were genotyped for over 750,000 SNP across the genome and compared using smoothed FST. The taurine sample was represented by ten breeds and the contrasting zebu cohort by three breeds. Each cattle group evidenced similar numbers of polymorphic markers well distributed across the genome. Principal component analyses and unsupervised hierarchical clustering confirmed the well characterized main division between these subspecies of domestic cattle. The top 1% smoothed FST, associated to positive selection contained 48 genomic regions across 17 chromosomes. Amongst the strongest signals were the BTA7:~50Mb and BTA14:~25Mb; both regions harboring candidate genes and very different patterns of linkage disequilibrium that potentially represent intrinsic differences between cattle types. Nearly half of the top FST signals (n=22) were previously detected using a lower density SNP assay. The bottom 1% of the smoothed FST values included 24 regions across 13 chromosomes, which are potentially associated to balancing selection. These regions often overlap with copy number variants, including the highly variable region at BTA23:~24Mb that harbors a large number of MHC genes. Under these regions, 318 unique Ensembl genes are annotated; many of which are linked to immune response resulting in a significant overrepresentation of immune related pathways. Genomic regions that are potentially linked to purifying or balancing selection processes in domestic cattle were identified. These regions are of particular interest to understand the natural and human selective pressures to which these subspecies were exposed to and how the genetic background of these populations evolved in response to environmental challenges and human manipulation.