title: Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle.
abstract: Brazil is one of the largest beef producers and exporters in the world with the Nelore breed representing the vast majority of Brazilian cattle (Bos taurus indicus). Despite the great adaptability of the Nelore breed to tropical climate, meat tenderness (MT) remains to be improved. Several factors including genetic composition can influence MT. In this article, we report a genome-wide analysis of copy number variation (CNV) inferred from Illumina® High Density SNP-chip data for a Nelore population of 723 males. We detected >2,600 CNV regions (CNVRs) representing ≈6.5% of the genome. Comparing our results with previous studies revealed an overlap in ≈1400 CNVRs (>50%). A total of 1,155 CNVRs (43.6%) overlapped 2,750 genes. They were enriched for processes involving guanosine triphosphate (GTP), previously reported to influence skeletal muscle physiology and morphology. Nelore CNVRs also overlapped QTLs for MT reported in other breeds (8.9%, 236 CNVRs) and from a previous study with this population (4.1%, 109 CNVRs). Two CNVRs were also proximal to glutathione metabolism genes that were previously associated with MT. Genome-wide association study of CN state with estimated breeding values derived from meat shear force identified 6 regions, including a region on BTA3 that contains genes of the cAMP and cGMP pathway. Ten CNVRs that overlapped regions associated with MT were successfully validated by qPCR. Our results represent the first comprehensive CNV study in Bos taurus indicus cattle and identify regions in which copy number changes are potentially of importance for the MT phenotype.
authors.affiliation: Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
authors.forename: Vinicius Henrique da
authors.initials: VH
authors.lastname: Silva
authors.affiliation: Embrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil.
authors.forename: Luciana Correia de Almeida
authors.initials: LC
authors.lastname: Regitano
authors.affiliation: Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München (LMU), Amalienstrasse 17, 80333, München, Germany.
authors.forename: Ludwig
authors.initials: L
authors.lastname: Geistlinger
authors.affiliation: Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
authors.forename: Fábio
authors.initials: F
authors.lastname: Pértille
authors.affiliation: Embrapa Informática Agropecuaria, Campinas, São Paulo, Brazil.
authors.forename: Poliana Fernanda
authors.identifier: http://orcid.org/0000-0002-9991-6566
authors.initials: PF
authors.lastname: Giachetto
authors.affiliation: Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
authors.forename: Ricardo Augusto
authors.identifier: http://orcid.org/0000-0002-3880-1263
authors.initials: RA
authors.lastname: Brassaloti
authors.affiliation: Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
authors.forename: Natália Silva
authors.initials: NS
authors.lastname: Morosini
authors.affiliation: Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München (LMU), Amalienstrasse 17, 80333, München, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Zimmer
authors.affiliation: Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
authors.forename: Luiz Lehmann
authors.initials: LL
authors.lastname: Coutinho
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D056915:DNA Copy Number Variations; D055106:Genome-Wide Association Study; D008460:Meat / Q000592:standards*; D018482:Muscle, Skeletal / Q000378:metabolism; D040641:Quantitative Trait Loci