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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle

Authors
item Decker, Jared -
item Mckay, Stephanie -
item Rolf, Megan -
item Kim, Jaewoo -
item Alcala, Antonio Molina -
item Sonstegard, Tad
item Hanotte, Olivier -
item Gotherstrom, Anders -
item Seabury, Chrostopher -
item Praharani, Lisa -
item Babar, Masroor Ellahi -
item Regitano, Luciana Correia -
item Yildiz, Mehmet Ali -
item Heaton, Michael
item Lui, Wansheng -
item Lei, Chu-Zhao -
item Reecy, James -
item Saif-Ur-Rehman, Muhammad -
item Schnabel, Robert -
item Taylor, Jeremy -

Submitted to: PLoS Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 4, 2014
Publication Date: March 27, 2014
Citation: Decker, J.E., Mckay, S.D., Rolf, M.M., Kim, J., Alcala, A., Sonstegard, T.S., Hanotte, O., Gotherstrom, A., Seabury, C.M., Praharani, L., Babar, M., Regitano, L. ., Yildiz, M., Heaton, M.P., Lui, W., Lei, C., Reecy, J.M., Saif-Ur-Rehman, M., Schnabel, R.D., Taylor, J.F. 2014. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genetics. 10(3):e1004254.

Interpretive Summary: The DNA of domesticated plants and animals contains information about how species were domesticated, exported, and bred by early farmers. Modern breeds were developed by lengthy and complex processes; however, our use of 134 breeds and new analytical models has enabled us to elucidate some of the processes and events that created modern cattle diversity. In Asia, Africa, North and South America, humpless (Bos t. taurus or taurine) and humped (Bos t. indicus or indicine) cattle were crossbred to produce hybrids adapted to the environment and endemic production systems. We argue that understanding the various migrations, exportation and admixture of different cattle ecotypes in the formation of breeds have been important forces in shaping modern bovine genomic variation. Understanding the origin of cattle populations provides an important knowledge tool that facilitates identification of adaptive variants in the bovine genome that can be used to improve cattle production efficiency in the face of changing climate and growing human populations.

Technical Abstract: The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle are shown to be of Iberian, and not African, decent. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that exportation and admixture have been important forces in shaping modern bovine genomic variation.

Last Modified: 12/18/2014
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