title: Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus.
abstract: Apart from single nucleotide polymorphism (SNP), copy number variation (CNV) is another important type of genetic variation, which may affect growth traits and play key roles for the production of beef cattle. To date, no genome-wide association study (GWAS) for CNV and body traits in beef cattle has been reported, so the present study aimed to investigate this type of association in one of the most important cattle subspecies: Bos indicus (Nellore breed).
  
  
  
  We have used intensity data from over 700,000 SNP probes across the bovine genome to detect common CNVs in a sample of 2230 Nellore cattle, and performed GWAS between the detected CNVs and nine growth traits. After filtering for frequency and length, a total of 231 CNVs ranging from 894 bp to 4,855,088 bp were kept and tested as predictors for each growth trait using linear regression analysis with principal components correction. There were 49 significant associations identified among 17 CNVs and seven body traits after false discovery rate correction (P < 0.05). Among the 17 CNVs, three were significant or marginally significant for all the traits. We have compared the locations of associated CNVs with quantitative trait locus and the RefGene database, and found two sets of 9 CNVs overlapping with either known QTLs or genes, respectively. The gene overlapping with CNV100, KCNJ12, is a functional candidate for muscle development and plays critical roles in muscling traits.
  
  
  
  This study presents the first CNV-based GWAS of growth traits using high density SNP microarray data in cattle. We detected 17 CNVs significantly associated with seven growth traits and one of them (CNV100) may be involved in growth traits through KCNJ12.
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.|College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi, 712100, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil.
authors.forename: Yuri T
authors.initials: YT
authors.lastname: Utsunomiya
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.|Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China.
authors.forename: Lingyang
authors.initials: L
authors.lastname: Xu
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.
authors.forename: El Hamidi Abdel
authors.initials: el HA
authors.lastname: Hay
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.
authors.forename: Derek M
authors.initials: DM
authors.lastname: Bickhart
authors.affiliation: Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635, Brazil.
authors.forename: Pamela Almeida
authors.initials: PA
authors.lastname: Alexandre
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.
authors.forename: Benjamin D
authors.initials: BD
authors.lastname: Rosen
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.
authors.forename: Steven G
authors.initials: SG
authors.lastname: Schroeder
authors.affiliation: Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil.
authors.forename: Roberto
authors.initials: R
authors.lastname: Carvalheiro
authors.affiliation: Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil.
authors.forename: Haroldo Henrique
authors.initials: HH
authors.lastname: de Rezende Neves
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.|Present address: Recombinetics, Inc., St Paul, MN, 55104, USA.
authors.forename: Tad S
authors.initials: TS
authors.lastname: Sonstegard
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.
authors.forename: Curtis P
authors.initials: CP
authors.lastname: Van Tassell
authors.affiliation: Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635, Brazil.
authors.forename: José Bento Sterman
authors.initials: JB
authors.lastname: Ferraz
authors.affiliation: Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635, Brazil.
authors.forename: Heidge
authors.initials: H
authors.lastname: Fukumasu
authors.affiliation: Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil. jfgarcia@fmva.unesp.br.|Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, 16050-680, Brazil. jfgarcia@fmva.unesp.br.|International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil. jfgarcia@fmva.unesp.br.
authors.forename: Jose Fernando
authors.initials: JF
authors.lastname: Garcia
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA. george.liu@ars.usda.gov.
authors.forename: George E
authors.initials: GE
authors.lastname: Liu
mesh_terms: D000818:Animals; D049628:Body Size; D001947:Breeding; D002417:Cattle; D056915:DNA Copy Number Variations; D056726:Genetic Association Studies; D055106:Genome-Wide Association Study; D005838:Genotype; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable
keywords: Association; Body size; Bos indicus; Copy number variation (CNV); EBV