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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF DAIRY CATTLE THROUGH GENOME SELECTION AND ANALYSIS Title: High-Throughput Phylogenomics: from Ancient DNA to Signatures of Human Animal Husbandry

item Decker, Jared -
item Pires, J -
item Conant, Gavin -
item Mckay, Stephanie -
item Vilkki, Johanna -
item Seabury, Christopher -
item Caetano, Alexandre -
item Johnson, Gary -
item Brenneman, Rick -
item Hanotte, Olivier -
item Eggert, Lori -
item Wiener, Pamela -
item Kim, Jong-Joo -
item Kim, Kwan -
item Neibergs, Holly -
item Chen, Kefei -
item Cooper, Alan -
item Mcewan, John -
item Brauning, Rudiger -
item Coutinho, Luiz -
item Babar, Masroor -
item Wilson, Gregory -
item Mcclure, Matthew -
item Rolf, Megan -
item Kim, Jaewoo -
item Schnabel, Robert -
item Taylor, Jeremy -

Submitted to: Cold Spring Harbor Meeting
Publication Type: Abstract Only
Publication Acceptance Date: April 25, 2009
Publication Date: May 7, 2009
Citation: Decker, J.E., Pires, J.C., Conant, G.C., Mckay, S.D., Heaton, M.P., Vilkki, J., Seabury, C.M., Caetano, A.R., Johnson, G.S., Brenneman, R.A., Hanotte, O., Eggert, L.S., Wiener, P., Kim, J., Kim, K.S., Sonstegard, T.S., Van Tassell, C.P., Neibergs, H.L., Chen, K., Cooper, A., Mcewan, J.C., Brauning, R., Coutinho, L.L., Babar, M.E., Wilson, G.A., Mcclure, M.C., Rolf, M.M., Kim, J., Schnabel, R.D., Taylor, J.F. 2009. HIGH-THROUGHPUT PHYLOGENOMICS: FROM ANCIENT DNA TO SIGNATURES OF HUMAN ANIMAL HUSBANDRY. Cold Spring Harbor Meeting.

Technical Abstract: We utilized the Illumina BovineSNP50 BeadChip with 54,693 single nucleotide polymorphism loci developed for Bos taurus taurus to rapidly genotype 677 individuals representing 61 Pecoran (horned ruminant) species diverged by up to 29 million years. We produced a completely bifurcating tree, the first phylogeny with this level of resolution for this rapidly radiated infraorder based upon 40,843 genome-wide SNP. The phylogeny proposes 17 new relationships and increases the support for 16 other nodes within the infraorder. We also successfully genotyped an ancient Bison priscus DNA sample amplified from 20,000 year old remains collected from Siberia and integrated this extinct species into the Bovini phylogeny. To accurately describe relationships between 48 cattle breeds and facilitate inferences concerning the history of domestication and breed formation we constructed a phylogenomic network that provides strong support for the hypothesis of two independent sites for cattle domestication in the Fertile Crescent and the Indus Valley, while also strongly suggesting that if it occurred, any third large-scale domestication event was more likely in Africa than East Asia. Finally, we genotyped 110 modern Bison bison representing 5 populations and demonstrated that hybridization with cattle ~150 years ago can be detected as introgressed haplotypes which comprise 1-3% of the haploid genome. These haplotypes are not randomly distributed within the genome and strongly suggest selection for cow-specific alleles within several regions of the genome.

Last Modified: 4/22/2015
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