Association of copy number variation at Intron 3 of HMGA2 with navel length in Bos indicus
Navel injuries caused by friction against the pasture can promote infection, reproductive problems and costly treatments in beef cattle raised in extensive systems. A haplotype-based genome-wide association study (GWAS) was performed for visual scores of navel length at yearling in Nellore cattle (B...
| Autores principales: | , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media
2018
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/98960 |
| _version_ | 1855513549252591616 |
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| author | Aguiar, T.S. Torrecilha, R.B.P. Milanesi, M. Utsunomiya, A.T.H. Trigo, B.B. Tijjani, A. Musa, H.H. Lopes, F.L. Ajmone-Marsan, P. Carvalheiro, R. Neves, H.H.R. Carmo, A.S. do Hanotte, Olivier H. Sonstegard, T.S. García, J.F. Utsunomiya, Yuri Tani |
| author_browse | Aguiar, T.S. Ajmone-Marsan, P. Carmo, A.S. do Carvalheiro, R. García, J.F. Hanotte, Olivier H. Lopes, F.L. Milanesi, M. Musa, H.H. Neves, H.H.R. Sonstegard, T.S. Tijjani, A. Torrecilha, R.B.P. Trigo, B.B. Utsunomiya, A.T.H. Utsunomiya, Yuri Tani |
| author_facet | Aguiar, T.S. Torrecilha, R.B.P. Milanesi, M. Utsunomiya, A.T.H. Trigo, B.B. Tijjani, A. Musa, H.H. Lopes, F.L. Ajmone-Marsan, P. Carvalheiro, R. Neves, H.H.R. Carmo, A.S. do Hanotte, Olivier H. Sonstegard, T.S. García, J.F. Utsunomiya, Yuri Tani |
| author_sort | Aguiar, T.S. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Navel injuries caused by friction against the pasture can promote infection, reproductive problems and costly treatments in beef cattle raised in extensive systems. A haplotype-based genome-wide association study (GWAS) was performed for visual scores of navel length at yearling in Nellore cattle (Bos indicus) using data from 2,016 animals and 503,088 single nucleotide polymorphism (SNP) markers. The strongest signal (p = 1.01 × 10-9) was found on chromosome 5 spanning positions 47.9-48.2 Mbp. This region contains introns 3 and 4 and exons 4 and 5 of the high mobility group AT-hook 2 gene (HMGA2). Further inspection of the region with whole genome sequence data of 21 Nellore bulls revealed correlations between counts of the significant haplotype and copy number gains of a ∼6.2 kbp segment of intron 3 of HMGA2. Analysis of genome sequences from five African B. indicus and four European Bos taurus breeds revealed that the copy number variant (CNV) is indicine-specific. This intronic CNV was then validated through quantitative polymerase chain reaction (qPCR) using Angus animals as copy neutral controls. Importantly, the CNV was not detectable by means of conventional SNP-based GWAS or SNP probe intensity analyses. Given that HMGA2 affects the expression of the insulin-like growth factor 2 gene (IGF2) together with the pleomorphic adenoma gene 1 (PLAG1), and that the latter has been repeatedly shown to be associated with quantitative traits of economic importance in cattle, these findings highlight the emerging role of variants impacting the insulin-like growth factor pathway to cattle breeding. |
| format | Journal Article |
| id | CGSpace98960 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace989602025-01-27T15:00:52Z Association of copy number variation at Intron 3 of HMGA2 with navel length in Bos indicus Aguiar, T.S. Torrecilha, R.B.P. Milanesi, M. Utsunomiya, A.T.H. Trigo, B.B. Tijjani, A. Musa, H.H. Lopes, F.L. Ajmone-Marsan, P. Carvalheiro, R. Neves, H.H.R. Carmo, A.S. do Hanotte, Olivier H. Sonstegard, T.S. García, J.F. Utsunomiya, Yuri Tani animal breeding cattle genetics Navel injuries caused by friction against the pasture can promote infection, reproductive problems and costly treatments in beef cattle raised in extensive systems. A haplotype-based genome-wide association study (GWAS) was performed for visual scores of navel length at yearling in Nellore cattle (Bos indicus) using data from 2,016 animals and 503,088 single nucleotide polymorphism (SNP) markers. The strongest signal (p = 1.01 × 10-9) was found on chromosome 5 spanning positions 47.9-48.2 Mbp. This region contains introns 3 and 4 and exons 4 and 5 of the high mobility group AT-hook 2 gene (HMGA2). Further inspection of the region with whole genome sequence data of 21 Nellore bulls revealed correlations between counts of the significant haplotype and copy number gains of a ∼6.2 kbp segment of intron 3 of HMGA2. Analysis of genome sequences from five African B. indicus and four European Bos taurus breeds revealed that the copy number variant (CNV) is indicine-specific. This intronic CNV was then validated through quantitative polymerase chain reaction (qPCR) using Angus animals as copy neutral controls. Importantly, the CNV was not detectable by means of conventional SNP-based GWAS or SNP probe intensity analyses. Given that HMGA2 affects the expression of the insulin-like growth factor 2 gene (IGF2) together with the pleomorphic adenoma gene 1 (PLAG1), and that the latter has been repeatedly shown to be associated with quantitative traits of economic importance in cattle, these findings highlight the emerging role of variants impacting the insulin-like growth factor pathway to cattle breeding. 2018-12-07 2019-01-08T09:40:59Z 2019-01-08T09:40:59Z Journal Article https://hdl.handle.net/10568/98960 en Open Access Frontiers Media Aguiar, T.S., Torrecilha, R.B.P., Milanesi, M., Utsunomiya, A.T.H., Trigo, B.B., Tijjani, A., Musa, H.H., Lopes, F.L., Ajmone-Marsan, P., Carvalheiro, R., Neves, H.H.R., do Carmo, A.S., Hanotte, O., Sonstegard, T.S., Garcia, J.F. and Utsunomiya, Y.T. 2018. Association of copy number variation at Intron 3 of HMGA2 with navel length in Bos indicus. Frontiers in Genetics |
| spellingShingle | animal breeding cattle genetics Aguiar, T.S. Torrecilha, R.B.P. Milanesi, M. Utsunomiya, A.T.H. Trigo, B.B. Tijjani, A. Musa, H.H. Lopes, F.L. Ajmone-Marsan, P. Carvalheiro, R. Neves, H.H.R. Carmo, A.S. do Hanotte, Olivier H. Sonstegard, T.S. García, J.F. Utsunomiya, Yuri Tani Association of copy number variation at Intron 3 of HMGA2 with navel length in Bos indicus |
| title | Association of copy number variation at Intron 3 of HMGA2 with navel length in Bos indicus |
| title_full | Association of copy number variation at Intron 3 of HMGA2 with navel length in Bos indicus |
| title_fullStr | Association of copy number variation at Intron 3 of HMGA2 with navel length in Bos indicus |
| title_full_unstemmed | Association of copy number variation at Intron 3 of HMGA2 with navel length in Bos indicus |
| title_short | Association of copy number variation at Intron 3 of HMGA2 with navel length in Bos indicus |
| title_sort | association of copy number variation at intron 3 of hmga2 with navel length in bos indicus |
| topic | animal breeding cattle genetics |
| url | https://hdl.handle.net/10568/98960 |
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