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
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/7030

id INTADig_3c1554b28b2eb50530e12d4704ef5744
oai_identifier_str oai:localhost:20.500.12123/7030
network_acronym_str INTADig
repository_id_str l
network_name_str INTA Digital (INTA)
spelling 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
_version_ 1844619143200899072
score 12.559606