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
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/130556

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network_name_str SEDICI (UNLP)
spelling 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
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dc.identifier.none.fl_str_mv http://sedici.unlp.edu.ar/handle/10915/130556
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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)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
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1387-1397
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instname:Universidad Nacional de La Plata
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