title: Genomic signatures reveal new evidences for selection of important traits in domestic cattle.
abstract: We investigated diverse genomic selections using high-density single nucleotide polymorphism data of five distinct 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. Selective sweeps near LAP3 were then 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 further revealed distinct selective pressures and evolution patterns across these five cattle breeds. Our results provided a glimpse into diverse genomic selection during cattle domestication, breed formation, and recent genetic improvement. These findings will facilitate genome-assisted breeding to improve animal production and health.
authors.affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA.
authors.forename: Lingyang
authors.initials: L
authors.lastname: Xu
authors.affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
authors.forename: Derek M
authors.initials: DM
authors.lastname: Bickhart
authors.affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
authors.forename: John B
authors.initials: JB
authors.lastname: Cole
authors.affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
authors.forename: Steven G
authors.initials: SG
authors.lastname: Schroeder
authors.affiliation: Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA.
authors.forename: Jiuzhou
authors.initials: J
authors.lastname: Song
authors.affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
authors.forename: Curtis P Van
authors.initials: CP
authors.lastname: Tassell
authors.affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
authors.forename: Tad S
authors.initials: TS
authors.lastname: Sonstegard
authors.affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA George.Liu@ars.usda.gov.
authors.forename: George E
authors.initials: GE
authors.lastname: Liu
mesh_terms: D000818:Animals; D002417:Cattle / Q000145:classification* / Q000235:genetics*; D003612:Dairying; D005260:Female; D005787:Gene Frequency; D005828:Genetics, Population; D016678:Genome / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics*; D008892:Milk; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012641:Selection, Genetic / Q000235:genetics*
keywords: cattle genome; haplotype network; population structure; positive selection