Journal of Applied Genetics

, Volume 59, Issue 2, pp 203–223 | Cite as

Association study between copy number variation and beef fatty acid profile of Nellore cattle

  • Marcos Vinicius Antunes de Lemos
  • Elisa Peripolli
  • Mariana Piatto Berton
  • Fabiele Loise Braga Feitosa
  • Bianca Ferreira Olivieri
  • Nedenia Bonvino Stafuzza
  • Rafael Lara Tonussi
  • Sabrina Kluska
  • Hermenegildo Lucas Justino Chiaia
  • Lenise Mueller
  • Adrielli Mathias Ferrinho
  • Angelica Simone Cravo Prereira
  • Henrique Nunes de Oliveira
  • Lucia Galvão de Albuquerque
  • Fernando Baldi
Animal Genetics • Original Paper

Abstract

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.

Keywords

Nellore Genomic selection Copy number variation Fatty acids Structural variation Bos indicus 

Abbreviations

MUFA

Sum of monounsaturated fatty acids

FA

Fatty acid

CNV

Copy number variation

CNVR

Copy number variation regions

GWAS

Genome-wide association study

QTL

Quantitative trait loci

PUFA

Sum of polyunsaturated fatty acids

CLA

Conjugated linoleic acid

GO

Gene ontology

MAF

Minor allele frequency

SFA

Sum of saturated fatty acids

ω3

Sum of omega 3 acids

ω6

Sum of omega 6 acids

BAF

Allele B frequency

IMF

Intramuscular fat

LDL

Low-density lipoprotein

BTA

Bos Taurus chromosome

LRR

Log R ratio

SNP

Single nucleotide polymorphism

Notes

Authors’ contributions

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.

Compliance with ethical standards

Ethics approval

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

Not applicable.

Conflict of interest

The authors declare that they have no competing interests.

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Copyright information

© Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2018

Authors and Affiliations

  • Marcos Vinicius Antunes de Lemos
    • 1
  • Elisa Peripolli
    • 1
  • Mariana Piatto Berton
    • 1
  • Fabiele Loise Braga Feitosa
    • 1
  • Bianca Ferreira Olivieri
    • 1
  • Nedenia Bonvino Stafuzza
    • 1
  • Rafael Lara Tonussi
    • 1
  • Sabrina Kluska
    • 1
  • Hermenegildo Lucas Justino Chiaia
    • 1
  • Lenise Mueller
    • 2
  • Adrielli Mathias Ferrinho
    • 2
  • Angelica Simone Cravo Prereira
    • 2
  • Henrique Nunes de Oliveira
    • 1
  • Lucia Galvão de Albuquerque
    • 1
  • Fernando Baldi
    • 1
  1. 1.Faculdade de Ciências Agrárias e VeterináriasUNESPJaboticabalBrazil
  2. 2.Faculdade de Medicina Veterinária e ZootecniaUSPPirassunungaBrazil

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