Submitted to: PLoS One
Publication Type: Peer reviewed journal
Publication Acceptance Date: 5/1/2013
Publication Date: 6/1/2013
Publication URL: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0065942
Citation: Zhang, L., Mousel, M.R., Wu, X., Michal, J.J., Zhou, X., Ding, B., Lewis, G.S., Jiang, Z. 2013. Genome-wide genetic diversity and differentially selected regions among Suffolk, Rambouillet, Columbia, Polypay and Targhee sheep. PLoS One. 8(6):e65942. Interpretive Summary: Modern genetic technologies can be used to enhance the inherent abilities of lambs to convert livestock feed into human foods. Enhancing these inherent abilities would allow producers to conserve feed and natural resources, improve the value of their market lambs, and increase the efficiency of producing human foods. Thus, genetics studies are underway at the USDA, Agricultural Research Service, U.S. Sheep Experiment Station in collaboration with Washington State University to characterize the effects of breed, which is composed of animals with common ancestors and certain distinguishable characteristics, including genetic makeup, on various aspects of wool, growth, and relatedness. Recent results from these studies indicate that 5 common U.S. breeds have different genetics likely due to long term selection. Sheep producers can use this information to select breeds to make significant improvements in the efficiency of producing human foods
Technical Abstract: Sheep are among the major economically important livestock species worldwide because the animals produce milk, wool, skin, and meat. In the present study, the Illumina OvineSNP50 BeadChip was used to investigate genetic diversity and genome selection among Suffolk, Rambouillet, Columbia, Polypay and Targhee sheep breeds from the United States. After quality-control filtering of SNPs (single nucleotide polymorphisms), we used 48,026 SNPs, including 46,850 SNPs on autosomes that were in Hardy-Weinberg equilibrium and 1,176 SNPs on chromosome X for analysis. Genetic diversity analysis showed that the gene diversity, heterozygosity, and polymorphism information content among five sheep breeds were 0.3291-0.3576, 0.3496-0.3722 and 0.2619-0.2837, respectively. Phylogenetic analysis based on all 46,850 SNPs clearly separated Suffolk from Rambouillet, Columbia, Polypay, and Targhee, which was not surprising as Rambouillet contributed to the synthesis of the later three breeds. A scan of the genome revealed 42 and 41 differentially selected regions between Suffolk and Rambouillet and among Rambouillet-related breed populations, respectively. Ovine genome v3.1 assembly was used as reference to link functionally known homologous genes to economically important traits covered by these differentially selected regions. In brief, our present study provides a comprehensive genome-wide view on within- and between-breed genetic differentiation, biodiversity, and evolution among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds. These results may provide new guidance for the synthesis of new breeds with different breeding objectives.