title: Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle.
abstract: The use of genome-wide association results combined with other genomic approaches may uncover genes and metabolic pathways related to complex traits. In this study, the phenotypic and genotypic data of 1475 Nellore (Bos indicus) cattle and 941,033 single nucleotide polymorphisms (SNPs) were used for genome-wide association study (GWAS) and copy number variations (CNVs) analysis in order to identify candidate genes and putative pathways involved with the feed conversion ratio (FCR). The GWAS was based on the Bayes B approach analyzing genomic windows with multiple regression models to estimate the proportion of genetic variance explained by each window. The CNVs were detected with PennCNV software using the log R ratio and B allele frequency data. CNV regions (CNVRs) were identified with CNVRuler and a linear regression was used to associate CNVRs and the FCR. Functional annotation of associated genomic regions was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) and the metabolic pathways were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We showed five genomic windows distributed over chromosomes 4, 6, 7, 8, and 24 that explain 12 % of the total genetic variance for FCR, and detected 12 CNVRs (chromosomes 1, 5, 7, 10, and 12) significantly associated [false discovery rate (FDR) < 0.05] with the FCR. Significant genomic regions (GWAS and CNV) harbor candidate genes involved in pathways related to energetic, lipid, and protein metabolism. The metabolic pathways found in this study are related to processes directly connected to feed efficiency in beef cattle. It was observed that, even though different genomic regions and genes were found between the two approaches (GWAS and CNV), the metabolic processes covered were related to each other. Therefore, a combination of the approaches complement each other and lead to a better understanding of the FCR.
authors.affiliation: Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870, Frederiksberg, Denmark.|Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil.
authors.forename: Miguel Henrique
authors.initials: MH
authors.lastname: de Almeida Santana
authors.affiliation: Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
authors.forename: Gerson Antônio Oliveira
authors.initials: GA
authors.lastname: Junior
authors.affiliation: Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
authors.forename: Aline Silva Mello
authors.initials: AS
authors.lastname: Cesar
authors.affiliation: Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil.
authors.forename: Mateus Castelani
authors.initials: MC
authors.lastname: Freua
authors.affiliation: Empresa Brasileira de Pesquisa Agropecuária, CNPGC/EMBRAPA, BR 262 km 4, 79002-970, Campo Grande, Brazil.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: da Costa Gomes
authors.affiliation: Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil.
authors.forename: Saulo
authors.initials: S
authors.lastname: da Luz E Silva
authors.affiliation: Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil.
authors.forename: Paulo Roberto
authors.initials: PR
authors.lastname: Leme
authors.affiliation: Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil.
authors.forename: Heidge
authors.initials: H
authors.lastname: Fukumasu
authors.affiliation: Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil.
authors.forename: Minos Esperândio
authors.initials: ME
authors.lastname: Carvalho
authors.affiliation: Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil.|University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
authors.forename: Ricardo Vieira
authors.initials: RV
authors.lastname: Ventura
authors.affiliation: Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo, 13418-900, Piracicaba, Brazil.
authors.forename: Luiz Lehmann
authors.initials: LL
authors.lastname: Coutinho
authors.affiliation: Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870, Frederiksberg, Denmark.
authors.forename: Haja N
authors.initials: HN
authors.lastname: Kadarmideen
authors.affiliation: Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil.
authors.forename: José Bento Sterman
authors.initials: JB
authors.lastname: Ferraz
mesh_terms: D000821:Animal Feed; D000822:Animal Husbandry; D000818:Animals; D001499:Bayes Theorem; D001835:Body Weight; D002417:Cattle / Q000235:genetics* / Q000254:growth & development; D056915:DNA Copy Number Variations; D056726:Genetic Association Studies; D005838:Genotype; D008297:Male; D053858:Metabolic Networks and Pathways; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D000069466:Red Meat
keywords: CNV; Feed efficiency; GWAS; Genomics; Nellore cattle; SNPs