Refining genomewide association for growth and fat deposition traits in an F₂ pig population
- Autores
- Gualdrón Duarte, J. L.; Cantet, Rodolfo Juan Carlos; Bernal Rubio, Y. L.; Bates, Ronald O.; Ernst, Catherine W.; Raney, Nancy E.; Rogberg Muñoz, Andrés; Steibel, Juan P.
- Año de publicación
- 2016
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- The identification of genomic regions that affect additive genetic variation and contain genes involved in controlling growth and fat deposition has enormous impact in the farm animal industry (e.g., carcass merit and meat quality). Therefore, a genomewide association study was implemented in an F₂ pig population using a 60,000 SNP marker panel for traits related to growth and fat deposition. Estimated genomic EBV were linearly transformed to calculate SNP effects and to identify genomic positions possibly associated with the genetic variability of each trait. Genomic segments were then defined considering the markers included in a region 1 Mb up- and downstream from the SNP with the smallest -value and a false discovery rate < 0.05 for each trait. The significance for each 2-Mb segment was tested using the Bonferroni correction. Significant SNP were detected on SSC2, SSC3, SSC5, and SSC6, but 2-Mb segment significant effects were observed on SSC3 for weight at birth (wt_birth) and on SSC6 for 10th-rib backfat and last-rib backfat measured by ultrasound at different ages. Furthermore, a 6-Mb segment on SSC6 was also considered because the 2-Mb segments for 10 different fat deposition traits were overlapped. Although the segment effects for each trait remain significant, the proportion of additive variance explained by this larger segment was slightly smaller in some traits. In general, the results confirm the presence of genetic variability for wt_birth on SSC3 (18.0-20.2 Mb) and for fat deposition traits on SSC6 (133.8-136.0 Mb). Within these regions, fibrosin (FBRS) and myosin light chain, phosphorylatable, fast skeletal muscle (MYLPF) genes could be considered as candidates for the wt_birth signal on SSC3, and the SERPINE1 mRNAbinding protein 1 gene (SERBP1) may be a candidate for the fat deposition trait signals on SSC6.
Facultad de Ciencias Veterinarias
Instituto de Genética Veterinaria - Materia
-
Veterinaria
fat
genome association
growth
pig
single nucleotide polymorphism - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- http://creativecommons.org/licenses/by-nc-sa/4.0/
- Repositorio
- Institución
- Universidad Nacional de La Plata
- OAI Identificador
- oai:sedici.unlp.edu.ar:10915/130556
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Refining genomewide association for growth and fat deposition traits in an F₂ pig populationGualdrón Duarte, J. L.Cantet, Rodolfo Juan CarlosBernal Rubio, Y. L.Bates, Ronald O.Ernst, Catherine W.Raney, Nancy E.Rogberg Muñoz, AndrésSteibel, Juan P.Veterinariafatgenome associationgrowthpigsingle nucleotide polymorphismThe identification of genomic regions that affect additive genetic variation and contain genes involved in controlling growth and fat deposition has enormous impact in the farm animal industry (e.g., carcass merit and meat quality). Therefore, a genomewide association study was implemented in an F₂ pig population using a 60,000 SNP marker panel for traits related to growth and fat deposition. Estimated genomic EBV were linearly transformed to calculate SNP effects and to identify genomic positions possibly associated with the genetic variability of each trait. Genomic segments were then defined considering the markers included in a region 1 Mb up- and downstream from the SNP with the smallest -value and a false discovery rate < 0.05 for each trait. The significance for each 2-Mb segment was tested using the Bonferroni correction. Significant SNP were detected on SSC2, SSC3, SSC5, and SSC6, but 2-Mb segment significant effects were observed on SSC3 for weight at birth (wt_birth) and on SSC6 for 10th-rib backfat and last-rib backfat measured by ultrasound at different ages. Furthermore, a 6-Mb segment on SSC6 was also considered because the 2-Mb segments for 10 different fat deposition traits were overlapped. Although the segment effects for each trait remain significant, the proportion of additive variance explained by this larger segment was slightly smaller in some traits. In general, the results confirm the presence of genetic variability for wt_birth on SSC3 (18.0-20.2 Mb) and for fat deposition traits on SSC6 (133.8-136.0 Mb). Within these regions, fibrosin (FBRS) and myosin light chain, phosphorylatable, fast skeletal muscle (MYLPF) genes could be considered as candidates for the wt_birth signal on SSC3, and the SERPINE1 mRNAbinding protein 1 gene (SERBP1) may be a candidate for the fat deposition trait signals on SSC6.Facultad de Ciencias VeterinariasInstituto de Genética Veterinaria2016-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArticulohttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdf1387-1397http://sedici.unlp.edu.ar/handle/10915/130556enginfo:eu-repo/semantics/altIdentifier/issn/1525-3163info:eu-repo/semantics/altIdentifier/issn/0021-8812info:eu-repo/semantics/altIdentifier/doi/10.2527/jas.2015-0182info:eu-repo/semantics/altIdentifier/pmid/27135998info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-09-29T11:32:37Zoai:sedici.unlp.edu.ar:10915/130556Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-09-29 11:32:38.031SEDICI (UNLP) - Universidad Nacional de La Platafalse |
dc.title.none.fl_str_mv |
Refining genomewide association for growth and fat deposition traits in an F₂ pig population |
title |
Refining genomewide association for growth and fat deposition traits in an F₂ pig population |
spellingShingle |
Refining genomewide association for growth and fat deposition traits in an F₂ pig population Gualdrón Duarte, J. L. Veterinaria fat genome association growth pig single nucleotide polymorphism |
title_short |
Refining genomewide association for growth and fat deposition traits in an F₂ pig population |
title_full |
Refining genomewide association for growth and fat deposition traits in an F₂ pig population |
title_fullStr |
Refining genomewide association for growth and fat deposition traits in an F₂ pig population |
title_full_unstemmed |
Refining genomewide association for growth and fat deposition traits in an F₂ pig population |
title_sort |
Refining genomewide association for growth and fat deposition traits in an F₂ pig population |
dc.creator.none.fl_str_mv |
Gualdrón Duarte, J. L. Cantet, Rodolfo Juan Carlos Bernal Rubio, Y. L. Bates, Ronald O. Ernst, Catherine W. Raney, Nancy E. Rogberg Muñoz, Andrés Steibel, Juan P. |
author |
Gualdrón Duarte, J. L. |
author_facet |
Gualdrón Duarte, J. L. Cantet, Rodolfo Juan Carlos Bernal Rubio, Y. L. Bates, Ronald O. Ernst, Catherine W. Raney, Nancy E. Rogberg Muñoz, Andrés Steibel, Juan P. |
author_role |
author |
author2 |
Cantet, Rodolfo Juan Carlos Bernal Rubio, Y. L. Bates, Ronald O. Ernst, Catherine W. Raney, Nancy E. Rogberg Muñoz, Andrés Steibel, Juan P. |
author2_role |
author author author author author author author |
dc.subject.none.fl_str_mv |
Veterinaria fat genome association growth pig single nucleotide polymorphism |
topic |
Veterinaria fat genome association growth pig single nucleotide polymorphism |
dc.description.none.fl_txt_mv |
The identification of genomic regions that affect additive genetic variation and contain genes involved in controlling growth and fat deposition has enormous impact in the farm animal industry (e.g., carcass merit and meat quality). Therefore, a genomewide association study was implemented in an F₂ pig population using a 60,000 SNP marker panel for traits related to growth and fat deposition. Estimated genomic EBV were linearly transformed to calculate SNP effects and to identify genomic positions possibly associated with the genetic variability of each trait. Genomic segments were then defined considering the markers included in a region 1 Mb up- and downstream from the SNP with the smallest -value and a false discovery rate < 0.05 for each trait. The significance for each 2-Mb segment was tested using the Bonferroni correction. Significant SNP were detected on SSC2, SSC3, SSC5, and SSC6, but 2-Mb segment significant effects were observed on SSC3 for weight at birth (wt_birth) and on SSC6 for 10th-rib backfat and last-rib backfat measured by ultrasound at different ages. Furthermore, a 6-Mb segment on SSC6 was also considered because the 2-Mb segments for 10 different fat deposition traits were overlapped. Although the segment effects for each trait remain significant, the proportion of additive variance explained by this larger segment was slightly smaller in some traits. In general, the results confirm the presence of genetic variability for wt_birth on SSC3 (18.0-20.2 Mb) and for fat deposition traits on SSC6 (133.8-136.0 Mb). Within these regions, fibrosin (FBRS) and myosin light chain, phosphorylatable, fast skeletal muscle (MYLPF) genes could be considered as candidates for the wt_birth signal on SSC3, and the SERPINE1 mRNAbinding protein 1 gene (SERBP1) may be a candidate for the fat deposition trait signals on SSC6. Facultad de Ciencias Veterinarias Instituto de Genética Veterinaria |
description |
The identification of genomic regions that affect additive genetic variation and contain genes involved in controlling growth and fat deposition has enormous impact in the farm animal industry (e.g., carcass merit and meat quality). Therefore, a genomewide association study was implemented in an F₂ pig population using a 60,000 SNP marker panel for traits related to growth and fat deposition. Estimated genomic EBV were linearly transformed to calculate SNP effects and to identify genomic positions possibly associated with the genetic variability of each trait. Genomic segments were then defined considering the markers included in a region 1 Mb up- and downstream from the SNP with the smallest -value and a false discovery rate < 0.05 for each trait. The significance for each 2-Mb segment was tested using the Bonferroni correction. Significant SNP were detected on SSC2, SSC3, SSC5, and SSC6, but 2-Mb segment significant effects were observed on SSC3 for weight at birth (wt_birth) and on SSC6 for 10th-rib backfat and last-rib backfat measured by ultrasound at different ages. Furthermore, a 6-Mb segment on SSC6 was also considered because the 2-Mb segments for 10 different fat deposition traits were overlapped. Although the segment effects for each trait remain significant, the proportion of additive variance explained by this larger segment was slightly smaller in some traits. In general, the results confirm the presence of genetic variability for wt_birth on SSC3 (18.0-20.2 Mb) and for fat deposition traits on SSC6 (133.8-136.0 Mb). Within these regions, fibrosin (FBRS) and myosin light chain, phosphorylatable, fast skeletal muscle (MYLPF) genes could be considered as candidates for the wt_birth signal on SSC3, and the SERPINE1 mRNAbinding protein 1 gene (SERBP1) may be a candidate for the fat deposition trait signals on SSC6. |
publishDate |
2016 |
dc.date.none.fl_str_mv |
2016-04 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Articulo http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
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article |
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http://sedici.unlp.edu.ar/handle/10915/130556 |
url |
http://sedici.unlp.edu.ar/handle/10915/130556 |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/issn/1525-3163 info:eu-repo/semantics/altIdentifier/issn/0021-8812 info:eu-repo/semantics/altIdentifier/doi/10.2527/jas.2015-0182 info:eu-repo/semantics/altIdentifier/pmid/27135998 |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) |
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openAccess |
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http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) |
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application/pdf 1387-1397 |
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