Association study between copy number variation and beef fatty acid profile of Nellore cattle
The aim of this study was to analyze the association between the copy number variation regions (CNVRs) and fatty acid profile phenotypes for saturated (SFA), monosaturated (MUFA), polyunsaturated (PUFA), ω6 and ω3 fatty acids, PUFA/SFA and ω6/ω3 ratios, as well as for their sums, in Nellore cattle (Bos primigenius indicus). A total of 963 males were finished in feedlot and slaughtered with approximately 2 years of age. Animals were genotyped with the BovineHD BeadChip (Illumina Inc., San Diego, CA, USA). The copy number variation (CNV) detection was performed using the PennCNV algorithm. Log R ratio (LRR) and allele B frequency (BAF) were used to estimate the CNVs. The association analyses were done using the CNVRuler software and applying a logistic regression model. The phenotype was adjusted using a linear model considering the fixed effects of contemporary group and the animal age at slaughter. The fatty acid profile was analyzed on samples of longissimus thoracis muscle using gas chromatography with a 100-m capillary column. For the association analysis, the adjusted phenotypic values were considered for the traits, while the data was adjusted for the effects of the farm and year of birth, management groups at birth, weaning, and superannuation. A total of 186 CNVRs were significant for SFA (43), MUFA (42), PUFA (66), and omega fatty acid (35) groups, totaling 278 known genes. On the basis of the results, several genes were associated with several fatty acids of different saturations. Olfactory receptor genes were associated with C12:0, C14:0, and C18:0 fatty acids. The SAMD8 and BSCL2 genes, both related to lipid metabolic process, were associated with C12:0. The RAPGEF6 gene was found to be associated with C18:2 cis-9 cis-12 n-6, and its function is related to regulation of GTPase activity. Among the results, we highlighted the olfactory receptor activity (GO:0004984), G-protein-coupled receptor activity (GO:0004930), potassium:proton antiporter activity (GO:0015386), sodium:proton antiporter activity (GO:0015385), and odorant-binding (GO:0005549) molecular functions. A large number of genes associated with fatty acid profile within the CNVRs were identified in this study. These findings must contribute to better elucidate the genetic mechanism underlying the fatty acid profile of intramuscular fat in Nellore cattle.
KeywordsNellore Genomic selection Copy number variation Fatty acids Structural variation Bos indicus
Sum of monounsaturated fatty acids
Copy number variation
Copy number variation regions
Genome-wide association study
Quantitative trait loci
Sum of polyunsaturated fatty acids
Conjugated linoleic acid
Minor allele frequency
Sum of saturated fatty acids
Sum of omega 3 acids
Sum of omega 6 acids
Allele B frequency
Bos Taurus chromosome
Log R ratio
Single nucleotide polymorphism
MVAL, FLBF, MPB, ASCP, and FB conceived and designed the experiment; MVAL, MPB, HLJC, FLBF, EP, SK, BFO, NBS, AMF, LFM, RLT, LGA, and HN performed the experiments; MVAL, HN, ASCP, NBS, and FB did analysis and interpretation of results; MVAL, ACSP, and FB drafted the manuscript. All authors read and approved the final manuscript.
This work was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) with grant numbers (#2013/11853-4, #2011/2141-0, and #2009/16118-5). MVA Lemos, FLB Feitosa, and E Peripolli received support from FAPESP, Fundação de Amparo à Pesquisa do Estado de São Paulo. HLJ Chiaia, MP Berton, S Kluska, and BF Olivieri received scholarships from the Coordination Office for Advancement of University-level Personnel (CAPES; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) in conjunction with the Postgraduate Program on Genetics and Animal Breeding, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (FCAV, UNESP). F Baldi received support from FAPESP, Fundação de Amparo à Pesquisa do Estado de São Paulo grant #2011/21241-0 and Lucia G. Albuquerque from FAPESP, Fundação de Amparo à Pesquisa do Estado de São Paulo grant #2009/16118-5.
Compliance with ethical standards
This study was approved by the ethics committee of the Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal-SP, Brazil.
Consent for publication
Conflict of interest
The authors declare that they have no competing interests.
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