Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits.

Joaquim Manoel Da Silva,Samuel Rezende Paiva,Alexandre Rodrigues Caetano,Michel Eduardo Beleza Yamagishi,Poliana Fernanda Giachetto,Luiz Otávio Da Silva,Leandro Carrijo Cintra

doi:10.1186/s12864-016-2752-9

Abstract

BackgroundCopy 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.ResultsGenome-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.ConclusionsObtained 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2752-9) contains supplementary material, which is available to authorized users.

Highlights

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
CNV length varied from 20.01 Kb to 7.75 Mbp (320 ± 413 Kbp)
Obtained results allowed for direct comparisons of CNV detection results with two distinct platforms (HD single nucleotide polymorphism (SNP) genotyping and NG sequencing), and with previous reports from independent studies

Summary

Introduction

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. Copy number variations (CNVs) have been shown to account for substantial portions of genomic variation in humans. NGS protocols randomly generate reads and close to the entire genome can be sampled with high coverage and resolution, promoting higher accuracy in CNV detection and greater precision when estimating breakpoints [24, 25]

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