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.
Highlights
Bos taurus is a well-studied model organism [1,2] and a species of great agricultural relevance, especially for Brazil, which is one of the world’s largest beef exporter [3] with a herd of estimated 209,541 million head [4]
We found 521 CNV regions (CNVRs) to occur in more than 1% of the population and denote them as ‘polymorphic CNVRs’ in the following
To exclude the possibility that polymorphic CNVRs with high frequency are technical artifacts of the mapping of indicus data onto the taurus assembly, we checked whether these CNVRs contained exclusively events of a particular copy number variation (CNV) state
Summary
Bos taurus is a well-studied model organism [1,2] and a species of great agricultural relevance, especially for Brazil, which is one of the world’s largest beef exporter [3] with a herd of estimated 209,541 million head [4]. Nelore (Bos taurus indicus) is the main cattle breed in Brazil. Genome-Wide Association of Meat-Relevant Cattle CNVs. National Counsel of Technological and Scientific Development (CNPq) fellowships.
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