Discovering ancestors and connecting relatives in large genomic databases
- Autores
- Nani, Juan Pablo; Bacheller, Lillian R.; Cole, John B.; VanRaden, Paul M.
- Año de publicación
- 2020
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Genomic evaluation has improved both plant and animal breeding by allowing more accurate estimation of an individual's genetic potential. Because often only a small proportion of the population to be evaluated has been genotyped, genomic estimations rely heavily on complete pedigree information. Confirmation, discovery, and correction of parentage and connected relatives allow the creation of more complete pedigrees, which in turn increase the number of usable phenotypic records and prediction accuracy. Previous methods accounted for parent-progeny conflicts using SNP. More recently haplotype methods allowed discovery of distant relationships such as maternal grandsire (MGS) and maternal great-grandsire (MGGS) with improved accuracy. However, discovered MGS and MGGS often were not used, because no dam information was available to link them to the calf. An automated procedure to discover and fill missing maternal identification information was developed, allowing discovered MGS and MGGS to be used in imputation as well as in calculating breeding values for animals in the US dairy cattle database. An MGS was discovered for 295,136 animals with unknown dam, and the MGGS was discovered for 153,909 of these animals. A virtual maternal identification was added for animals with missing information. The effect of pedigree completion on progeny inbreeding, breeding values, and reliabilities was examined. Mean inbreeding of animals with missing maternal pedigree information was 6.69% before and 6.87% after pedigree assignment; expected future inbreeding was 7.24% before and 7.20% after assignment. Reliabilities for traditional breeding values increased from 26.6 to 32.6% for milk yield, 25.9 to 32.0% for fat yield, and 26.9 to 32.9% for protein yield; genomic reliabilities also increased slightly from 76.2 to 77.1% for milk, 76.0 to 76.9% for fat, and 76.3 to 77.3% for protein. The procedure developed for pedigree completion is a useful tool for improving accuracy of national and international evaluations and aiding producers in making better mating decisions.
EEA Rafaela
Fil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina. Agricultural Research Service. Animal Genomics and Improvement Laboratory; Estados Unidos
Fil: Bacheller, Lillian R. Council on Dairy Cattle Breeding; Estados Unidos
Fil: Cole, John B. Agricultural Research Service. Animal Genomics and Improvement Laboratory; Estados Unidos
Fil: VanRaden, Paul M. Agricultural Research Service. Animal Genomics and Improvement Laboratory; Estados Unidos - Fuente
- Journal of dairy science 103 (2) : 1729 - 1734. (February 2020)
- Materia
-
Ancestry
Genetic Inheritance
Pedigree Livestock
Genomics
Genotypes
Ascendencia
Herencia Genética
Pedigrí
Genómica
Genotipos - Nivel de accesibilidad
- acceso restringido
- Condiciones de uso
- Repositorio
- Institución
- Instituto Nacional de Tecnología Agropecuaria
- OAI Identificador
- oai:localhost:20.500.12123/7030
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Discovering ancestors and connecting relatives in large genomic databasesNani, Juan PabloBacheller, Lillian R.Cole, John B.VanRaden, Paul M.AncestryGenetic InheritancePedigree LivestockGenomicsGenotypesAscendenciaHerencia GenéticaPedigríGenómicaGenotiposGenomic evaluation has improved both plant and animal breeding by allowing more accurate estimation of an individual's genetic potential. Because often only a small proportion of the population to be evaluated has been genotyped, genomic estimations rely heavily on complete pedigree information. Confirmation, discovery, and correction of parentage and connected relatives allow the creation of more complete pedigrees, which in turn increase the number of usable phenotypic records and prediction accuracy. Previous methods accounted for parent-progeny conflicts using SNP. More recently haplotype methods allowed discovery of distant relationships such as maternal grandsire (MGS) and maternal great-grandsire (MGGS) with improved accuracy. However, discovered MGS and MGGS often were not used, because no dam information was available to link them to the calf. An automated procedure to discover and fill missing maternal identification information was developed, allowing discovered MGS and MGGS to be used in imputation as well as in calculating breeding values for animals in the US dairy cattle database. An MGS was discovered for 295,136 animals with unknown dam, and the MGGS was discovered for 153,909 of these animals. A virtual maternal identification was added for animals with missing information. The effect of pedigree completion on progeny inbreeding, breeding values, and reliabilities was examined. Mean inbreeding of animals with missing maternal pedigree information was 6.69% before and 6.87% after pedigree assignment; expected future inbreeding was 7.24% before and 7.20% after assignment. Reliabilities for traditional breeding values increased from 26.6 to 32.6% for milk yield, 25.9 to 32.0% for fat yield, and 26.9 to 32.9% for protein yield; genomic reliabilities also increased slightly from 76.2 to 77.1% for milk, 76.0 to 76.9% for fat, and 76.3 to 77.3% for protein. The procedure developed for pedigree completion is a useful tool for improving accuracy of national and international evaluations and aiding producers in making better mating decisions.EEA RafaelaFil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina. Agricultural Research Service. Animal Genomics and Improvement Laboratory; Estados UnidosFil: Bacheller, Lillian R. Council on Dairy Cattle Breeding; Estados UnidosFil: Cole, John B. Agricultural Research Service. Animal Genomics and Improvement Laboratory; Estados UnidosFil: VanRaden, Paul M. Agricultural Research Service. Animal Genomics and Improvement Laboratory; Estados UnidosElsevier; American Dairy Science Association2020-04-02T16:03:20Z2020-04-02T16:03:20Z2020-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/7030https://www.journalofdairyscience.org/article/S0022-0302(19)31091-4/fulltext0022-0302https://doi.org/10.3168/jds.2019-17580Journal of dairy science 103 (2) : 1729 - 1734. (February 2020)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccess2025-09-29T13:44:55Zoai:localhost:20.500.12123/7030instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-29 13:44:55.338INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse |
dc.title.none.fl_str_mv |
Discovering ancestors and connecting relatives in large genomic databases |
title |
Discovering ancestors and connecting relatives in large genomic databases |
spellingShingle |
Discovering ancestors and connecting relatives in large genomic databases Nani, Juan Pablo Ancestry Genetic Inheritance Pedigree Livestock Genomics Genotypes Ascendencia Herencia Genética Pedigrí Genómica Genotipos |
title_short |
Discovering ancestors and connecting relatives in large genomic databases |
title_full |
Discovering ancestors and connecting relatives in large genomic databases |
title_fullStr |
Discovering ancestors and connecting relatives in large genomic databases |
title_full_unstemmed |
Discovering ancestors and connecting relatives in large genomic databases |
title_sort |
Discovering ancestors and connecting relatives in large genomic databases |
dc.creator.none.fl_str_mv |
Nani, Juan Pablo Bacheller, Lillian R. Cole, John B. VanRaden, Paul M. |
author |
Nani, Juan Pablo |
author_facet |
Nani, Juan Pablo Bacheller, Lillian R. Cole, John B. VanRaden, Paul M. |
author_role |
author |
author2 |
Bacheller, Lillian R. Cole, John B. VanRaden, Paul M. |
author2_role |
author author author |
dc.subject.none.fl_str_mv |
Ancestry Genetic Inheritance Pedigree Livestock Genomics Genotypes Ascendencia Herencia Genética Pedigrí Genómica Genotipos |
topic |
Ancestry Genetic Inheritance Pedigree Livestock Genomics Genotypes Ascendencia Herencia Genética Pedigrí Genómica Genotipos |
dc.description.none.fl_txt_mv |
Genomic evaluation has improved both plant and animal breeding by allowing more accurate estimation of an individual's genetic potential. Because often only a small proportion of the population to be evaluated has been genotyped, genomic estimations rely heavily on complete pedigree information. Confirmation, discovery, and correction of parentage and connected relatives allow the creation of more complete pedigrees, which in turn increase the number of usable phenotypic records and prediction accuracy. Previous methods accounted for parent-progeny conflicts using SNP. More recently haplotype methods allowed discovery of distant relationships such as maternal grandsire (MGS) and maternal great-grandsire (MGGS) with improved accuracy. However, discovered MGS and MGGS often were not used, because no dam information was available to link them to the calf. An automated procedure to discover and fill missing maternal identification information was developed, allowing discovered MGS and MGGS to be used in imputation as well as in calculating breeding values for animals in the US dairy cattle database. An MGS was discovered for 295,136 animals with unknown dam, and the MGGS was discovered for 153,909 of these animals. A virtual maternal identification was added for animals with missing information. The effect of pedigree completion on progeny inbreeding, breeding values, and reliabilities was examined. Mean inbreeding of animals with missing maternal pedigree information was 6.69% before and 6.87% after pedigree assignment; expected future inbreeding was 7.24% before and 7.20% after assignment. Reliabilities for traditional breeding values increased from 26.6 to 32.6% for milk yield, 25.9 to 32.0% for fat yield, and 26.9 to 32.9% for protein yield; genomic reliabilities also increased slightly from 76.2 to 77.1% for milk, 76.0 to 76.9% for fat, and 76.3 to 77.3% for protein. The procedure developed for pedigree completion is a useful tool for improving accuracy of national and international evaluations and aiding producers in making better mating decisions. EEA Rafaela Fil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina. Agricultural Research Service. Animal Genomics and Improvement Laboratory; Estados Unidos Fil: Bacheller, Lillian R. Council on Dairy Cattle Breeding; Estados Unidos Fil: Cole, John B. Agricultural Research Service. Animal Genomics and Improvement Laboratory; Estados Unidos Fil: VanRaden, Paul M. Agricultural Research Service. Animal Genomics and Improvement Laboratory; Estados Unidos |
description |
Genomic evaluation has improved both plant and animal breeding by allowing more accurate estimation of an individual's genetic potential. Because often only a small proportion of the population to be evaluated has been genotyped, genomic estimations rely heavily on complete pedigree information. Confirmation, discovery, and correction of parentage and connected relatives allow the creation of more complete pedigrees, which in turn increase the number of usable phenotypic records and prediction accuracy. Previous methods accounted for parent-progeny conflicts using SNP. More recently haplotype methods allowed discovery of distant relationships such as maternal grandsire (MGS) and maternal great-grandsire (MGGS) with improved accuracy. However, discovered MGS and MGGS often were not used, because no dam information was available to link them to the calf. An automated procedure to discover and fill missing maternal identification information was developed, allowing discovered MGS and MGGS to be used in imputation as well as in calculating breeding values for animals in the US dairy cattle database. An MGS was discovered for 295,136 animals with unknown dam, and the MGGS was discovered for 153,909 of these animals. A virtual maternal identification was added for animals with missing information. The effect of pedigree completion on progeny inbreeding, breeding values, and reliabilities was examined. Mean inbreeding of animals with missing maternal pedigree information was 6.69% before and 6.87% after pedigree assignment; expected future inbreeding was 7.24% before and 7.20% after assignment. Reliabilities for traditional breeding values increased from 26.6 to 32.6% for milk yield, 25.9 to 32.0% for fat yield, and 26.9 to 32.9% for protein yield; genomic reliabilities also increased slightly from 76.2 to 77.1% for milk, 76.0 to 76.9% for fat, and 76.3 to 77.3% for protein. The procedure developed for pedigree completion is a useful tool for improving accuracy of national and international evaluations and aiding producers in making better mating decisions. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-04-02T16:03:20Z 2020-04-02T16:03:20Z 2020-02 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/20.500.12123/7030 https://www.journalofdairyscience.org/article/S0022-0302(19)31091-4/fulltext 0022-0302 https://doi.org/10.3168/jds.2019-17580 |
url |
http://hdl.handle.net/20.500.12123/7030 https://www.journalofdairyscience.org/article/S0022-0302(19)31091-4/fulltext https://doi.org/10.3168/jds.2019-17580 |
identifier_str_mv |
0022-0302 |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/restrictedAccess |
eu_rights_str_mv |
restrictedAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Elsevier; American Dairy Science Association |
publisher.none.fl_str_mv |
Elsevier; American Dairy Science Association |
dc.source.none.fl_str_mv |
Journal of dairy science 103 (2) : 1729 - 1734. (February 2020) reponame:INTA Digital (INTA) instname:Instituto Nacional de Tecnología Agropecuaria |
reponame_str |
INTA Digital (INTA) |
collection |
INTA Digital (INTA) |
instname_str |
Instituto Nacional de Tecnología Agropecuaria |
repository.name.fl_str_mv |
INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria |
repository.mail.fl_str_mv |
tripaldi.nicolas@inta.gob.ar |
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1844619143200899072 |
score |
12.559606 |