Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits.
Copy number variations (CNVs) have been shown to account for substantial portions of observed genomic variation and have been associated with qualitative and quantitative traits and the onset of disease in a number of species. Information from high-resolution studies to detect, characterize and estimate population-specific variant frequencies will facilitate the incorporation of CNVs in genomic studies to identify genes affecting traits of importance.



Genome-wide CNVs were detected in high-density single nucleotide polymorphism (SNP) genotyping data from 1,717 Nelore (Bos indicus) cattle, and in NGS data from eight key ancestral bulls. A total of 68,007 and 12,786 distinct CNVs were observed, respectively. Cross-comparisons of results obtained for the eight resequenced animals revealed that 92 % of the CNVs were observed in both datasets, while 62 % of all detected CNVs were observed to overlap with previously validated cattle copy number variant regions (CNVRs). Observed CNVs were used for obtaining breed-specific CNV frequencies and identification of CNVRs, which were subsequently used for gene annotation. A total of 688 of the detected CNVRs were observed to overlap with 286 non-redundant QTLs associated with important production traits in cattle. All of 34 CNVs previously reported to be associated with milk production traits in Holsteins were also observed in Nelore cattle. Comparisons of estimated frequencies of these CNVs in the two breeds revealed 14, 13, 6 and 14 regions in high (>20 %), low (<20 %) and divergent (NEL > HOL, NEL < HOL) frequencies, respectively.



Obtained results significantly enriched the bovine CNV map and enabled the identification of variants that are potentially associated with traits under selection in Nelore cattle, particularly in genome regions harboring QTLs affecting production traits.
Faculdade de Ciências Agrárias, Biológicas e Sociais Aplicadas, Universidade do Estado de Mato Grosso (UNEMAT), Av. Prof Dr. Renato Figueiro Varella, CEP 78.690-000, Nova Xavantina, Mato Grosso, Brazil.|Programa de Pós-Graduação em Genética e Biologia Molecular-Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil.
Joaquim Manoel
JM
da Silva
Embrapa Informática Agropecuária - Laboratório Multiusuário de Bioinformática (LMB), Campinas, São Paulo, Brazil.
Poliana Fernanda
PF
Giachetto
Embrapa Gado de Corte, Campo Grande, Mato Grosso do Sul, Brazil.
Luiz Otávio
LO
da Silva
Embrapa Informática Agropecuária - Laboratório Multiusuário de Bioinformática (LMB), Campinas, São Paulo, Brazil.
Leandro Carrijo
LC
Cintra
Embrapa - Secretaria de Relações Internacionais, Brasília, Distrito Federal, Brazil.|Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil.|CNPq Fellow, ᅟ, ᅟ
Samuel Rezende
SR
Paiva
Embrapa Informática Agropecuária - Laboratório Multiusuário de Bioinformática (LMB), Campinas, São Paulo, Brazil.
Michel Eduardo Beleza
ME
Yamagishi
Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. alexandre.caetano@embrapa.br.|CNPq Fellow, ᅟ, ᅟ. alexandre.caetano@embrapa.br.
Alexandre Rodrigues
AR
Caetano
D000818:Animals; D002417:Cattle; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D056915:DNA Copy Number Variations; D016678:Genome; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D015203:Reproducibility of Results
Beef cattle; Copy number variants; High-throughput nucleotide sequencing; SNP genotyping