Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle.
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 i...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2016-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4922624?pdf=render |
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| author | Vinicius Henrique da Silva Luciana Correia de Almeida Regitano Ludwig Geistlinger Fábio Pértille Poliana Fernanda Giachetto Ricardo Augusto Brassaloti Natália Silva Morosini Ralf Zimmer Luiz Lehmann Coutinho |
| author_facet | Vinicius Henrique da Silva Luciana Correia de Almeida Regitano Ludwig Geistlinger Fábio Pértille Poliana Fernanda Giachetto Ricardo Augusto Brassaloti Natália Silva Morosini Ralf Zimmer Luiz Lehmann Coutinho |
| author_sort | Vinicius Henrique da Silva |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-10T18:08:33Z |
| format | Article |
| id | doaj.art-9e4eb8576f8444be8ed75aa93dac9777 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T18:08:33Z |
| publishDate | 2016-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-9e4eb8576f8444be8ed75aa93dac97772022-12-22T01:38:34ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-01116e015771110.1371/journal.pone.0157711Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle.Vinicius Henrique da SilvaLuciana Correia de Almeida RegitanoLudwig GeistlingerFábio PértillePoliana Fernanda GiachettoRicardo Augusto BrassalotiNatália Silva MorosiniRalf ZimmerLuiz Lehmann CoutinhoBrazil 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.http://europepmc.org/articles/PMC4922624?pdf=render |
| spellingShingle | Vinicius Henrique da Silva Luciana Correia de Almeida Regitano Ludwig Geistlinger Fábio Pértille Poliana Fernanda Giachetto Ricardo Augusto Brassaloti Natália Silva Morosini Ralf Zimmer Luiz Lehmann Coutinho Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle. PLoS ONE |
| title | Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle. |
| title_full | Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle. |
| title_fullStr | Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle. |
| title_full_unstemmed | Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle. |
| title_short | Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle. |
| title_sort | genome wide detection of cnvs and their association with meat tenderness in nelore cattle |
| url | http://europepmc.org/articles/PMC4922624?pdf=render |
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