|Xu, Lingyang - University Of Maryland|
|Schroeder, Steven - Steve|
|Song, Jiuzhou - University Of Maryland|
|Van Tassell, Curtis - Curt|
|Liu, Ge - George|
Submitted to: Molecular Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/18/2014
Publication Date: 11/26/2014
Citation: Xu, L., Bickhart, D.M., Cole, J.B., Schroeder, S.G., Song, J., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2014. Genomic signatures reveal geographic adaption and human selection in cattle. Molecular Biology and Evolution. 32(3):711-25. Interpretive Summary: Milk production is an economically important sector of global agriculture. Using multiple independent methods, we detected hundreds of candidate regions and genes under positive selection in the cattle genome. We specifically identified and validated the LAP3 and SAR1B genes, which were related to milk production traits. In addition, our results revealed two major evolutionary mechanisms that have affected cattle differentiation. Farmers, scientists, and policy planners who need to improve animal health and production based on genome-enable animal selection will benefit from this manuscript.
Technical Abstract: We investigated geographic adaptation and human selection using high-density SNP data of five diverse cattle breeds. Based on allele frequency differences, we detected hundreds of candidate regions under positive selection across Holstein, Angus, Charolais, Brahman, and N'Dama. In addition to well-known genes such as KIT, MC1R, ASIP, GHR, LCORL, NCAPG, WIF1 and ABCA12, we found evidence for a variety of novel and less-known genes under selection in cattle, such as LAP3, SAR1B, LRIG3, FGF5, and NUDCD3. A selective sweep near LAP3 was further validated by next generation sequencing. Genome wide association analysis involving 26,362 Holsteins confirmed that LAP3 and SAR1B were related to milk production traits, suggesting that our candidate regions were likely functional. In addition, haplotype network analyses revealed that genetic hitchhiking and recombination are two major evolutionary mechanisms. Our results provided a glimpse into geographic adaptation and human selection during cattle domestication, breed formation, and recent genetic improvement. These findings will facilitate genome-assisted breeding to improve animal production and health.