SNP arrays evaluation as tools in genetic improvement in Corriedale sheep in Uruguay
Evaluación de paneles de SNP como herramientas en la mejora genética de ovinos Corriedale en Uruguay
Avaliação de painéis de SNP como ferramentas em melhoramento genético de ovinos Corriedale no Uruguai
Editor(es): Carriquiry, Mariana
Resumen:
One control strategy for gastrointestinal nematodes (GIN) is genetic selection. This study´s objective was to compare eggs per gram of feces (FEC) and fiber diameter (FD) estimated breeding values (EBV) and genomic EBV (GEBV) in Corriedale breed. Analysis included 19547 lambs with data, and 454, 711 and 383 genotypes from 170, 507 and 50K SNP chips, respectively. A univariate animal model was used for EBV and GEBV estimation, which included contemporary group, type of birth and dam age as fixed effects, and age at recording as covariate. Differential weights (α) were considered in the genomic relationship matrix (G), and the best fit models were identified using Akaike´s Information Criterion (AIC), which were later used for GEBV and accuracies estimation. The use of α only impacted on low density SNP chips. No differences were observed in mean accuracies for the whole population. However, in the genotyped subgroup accuracies increased by 2% with the 170 SNP chip (α=0.25), and by 5% (α=0.5) and 14% (α=0.75) with the 507 SNP chip. No differences were observed in FD EBV and GEBV mean accuracies. These results show that it is possible to increase GEBV accuracies despite the use of low-density chips.
Una alternativa para el control de los nematodos gastrointestinales (NGI) es la selección genética. El objetivo de este trabajo fue comparar las precisiones de los valores de cría (EBV) y los EBV genómicos (GEBV) del recuento de huevos por gramo en heces (HPG) y diámetro de fibra (DF) en la raza Corriedale. El análisis incluyó 19547 corderos con datos fenotípicos y 454, 711 y 383 genotipados con paneles o chips de 170, 507 y 50K SNP, respectivamente. Los EBV y GEBV se estimaron con un modelo animal univariado que incluyó los efectos fijos: grupo contemporáneo, tipo de nacimiento y edad de la madre, y edad al registro como covariable. Se consideraron pesos diferenciales (α) en la matriz de relaciones genómicas, identificándose los modelos con mejor ajuste con el criterio de información de Akaike (AIC), que fueron utilizados para la estimación de los GEBV y sus precisiones. El uso de α solo impactó en el ajuste con paneles de baja densidad. No se encontraron diferencias en las precisiones promedio de la población total. En cambio, en el subgrupo de animales genotipados las precisiones aumentaron 2% con 170 SNP (α=0.25), y con 507 SNP 5% (α=0.5) y 14% (α=0.75). No hubo diferencias en precisiones de los EBV y los GEBV de DF. Los resultados muestran que es posible aumentar las precisiones de los GEBV aun con paneles de baja densidad.
Uma alternativa para o controle de nematóides gastrointestinais (NGI) é a seleção genética. O objetivo deste trabalho foi comparar as precisões dos valores genéticos estimados (EBV) e dos EBVs genômicos (GEBV) da contagem de ovos por grama de fezes (OPG) e diâmetro de fibra (DF) na raça Corriedale. A análise incluiu 19547 cordeiros com dados e 454, 711 e 383 genotipados de 170, 507 e 50K SNPs, respectivamente. Foram estimados os EBV e GEBV com um modelo animal univariado que incluiu efeitos fixos de grupo contemporâneo, tipo de nascimento e idade da mãe e idade no registro (covariável). Pesos diferenciais (α) foram considerados na matriz de relações genômicas, identificando os modelos com melhor ajuste via critério de informação de Akaike (AIC), os quais foram utilizados para estimar o GEBV e suas precisões. O uso de α somente impactou no ajuste com painéis de baixa densidade. Não foram encontradas diferenças na precisão média da população total. Em contraste, no subgrupo de animais genotipados as precisões aumentaram 2% com 170 SNPs (α = 0.25), e com 507 SNPs 5% (α = 0.5) e 14% (α = 0.75). Não houve diferenças na precisão de EBV e GEBV de DF. Os resultados mostram que é possível aumentar a precisão de GEBVs mesmo que se utilizem painéis de baixa densidade.
2022 | |
Accuracy Corriedale FEC GEBV HPG OPG Precisão Precisión |
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Inglés | |
Universidad de la República | |
COLIBRI | |
https://hdl.handle.net/20.500.12008/36472 | |
Acceso abierto | |
Licencia Creative Commons Atribución (CC - By 4.0) |
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---|---|
author | Carracelas, Beatriz |
author2 | Navajas, Elly Ana Vera, Brenda Ciappesoni, Gabriel |
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author_facet | Carracelas, Beatriz Navajas, Elly Ana Vera, Brenda Ciappesoni, Gabriel |
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dc.contributor.filiacion.none.fl_str_mv | Carracelas Beatriz, Instituto Nacional de Investigación Agropecuaria (INIA), Unidad de Biotecnología, Las Brujas, Uruguay https://orcid.org/0000-0003-1340-367X Navajas Elly Ana, Instituto Nacional de Investigación Agropecuaria (INIA), Unidad de Biotecnología, Las Brujas, Uruguay https://orcid.org/0000-0002-9018-4741 Vera Brenda, Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción de Carne y Lana, Las Brujas, Uruguay https://orcid.org/0000-0002-5706-4721 Ciappesoni Gabriel, Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción de Carne y Lana, Las Brujas, Uruguay https://orcid.org/0000-0002-0091-3956 |
dc.creator.editor.none.fl_str_mv | Carriquiry, Mariana |
dc.creator.none.fl_str_mv | Carracelas, Beatriz Navajas, Elly Ana Vera, Brenda Ciappesoni, Gabriel |
dc.date.accessioned.none.fl_str_mv | 2023-03-22T18:00:39Z |
dc.date.available.none.fl_str_mv | 2023-03-22T18:00:39Z |
dc.date.issued.none.fl_str_mv | 2022 |
dc.description.abstract.none.fl_txt_mv | One control strategy for gastrointestinal nematodes (GIN) is genetic selection. This study´s objective was to compare eggs per gram of feces (FEC) and fiber diameter (FD) estimated breeding values (EBV) and genomic EBV (GEBV) in Corriedale breed. Analysis included 19547 lambs with data, and 454, 711 and 383 genotypes from 170, 507 and 50K SNP chips, respectively. A univariate animal model was used for EBV and GEBV estimation, which included contemporary group, type of birth and dam age as fixed effects, and age at recording as covariate. Differential weights (α) were considered in the genomic relationship matrix (G), and the best fit models were identified using Akaike´s Information Criterion (AIC), which were later used for GEBV and accuracies estimation. The use of α only impacted on low density SNP chips. No differences were observed in mean accuracies for the whole population. However, in the genotyped subgroup accuracies increased by 2% with the 170 SNP chip (α=0.25), and by 5% (α=0.5) and 14% (α=0.75) with the 507 SNP chip. No differences were observed in FD EBV and GEBV mean accuracies. These results show that it is possible to increase GEBV accuracies despite the use of low-density chips. Una alternativa para el control de los nematodos gastrointestinales (NGI) es la selección genética. El objetivo de este trabajo fue comparar las precisiones de los valores de cría (EBV) y los EBV genómicos (GEBV) del recuento de huevos por gramo en heces (HPG) y diámetro de fibra (DF) en la raza Corriedale. El análisis incluyó 19547 corderos con datos fenotípicos y 454, 711 y 383 genotipados con paneles o chips de 170, 507 y 50K SNP, respectivamente. Los EBV y GEBV se estimaron con un modelo animal univariado que incluyó los efectos fijos: grupo contemporáneo, tipo de nacimiento y edad de la madre, y edad al registro como covariable. Se consideraron pesos diferenciales (α) en la matriz de relaciones genómicas, identificándose los modelos con mejor ajuste con el criterio de información de Akaike (AIC), que fueron utilizados para la estimación de los GEBV y sus precisiones. El uso de α solo impactó en el ajuste con paneles de baja densidad. No se encontraron diferencias en las precisiones promedio de la población total. En cambio, en el subgrupo de animales genotipados las precisiones aumentaron 2% con 170 SNP (α=0.25), y con 507 SNP 5% (α=0.5) y 14% (α=0.75). No hubo diferencias en precisiones de los EBV y los GEBV de DF. Los resultados muestran que es posible aumentar las precisiones de los GEBV aun con paneles de baja densidad. Uma alternativa para o controle de nematóides gastrointestinais (NGI) é a seleção genética. O objetivo deste trabalho foi comparar as precisões dos valores genéticos estimados (EBV) e dos EBVs genômicos (GEBV) da contagem de ovos por grama de fezes (OPG) e diâmetro de fibra (DF) na raça Corriedale. A análise incluiu 19547 cordeiros com dados e 454, 711 e 383 genotipados de 170, 507 e 50K SNPs, respectivamente. Foram estimados os EBV e GEBV com um modelo animal univariado que incluiu efeitos fixos de grupo contemporâneo, tipo de nascimento e idade da mãe e idade no registro (covariável). Pesos diferenciais (α) foram considerados na matriz de relações genômicas, identificando os modelos com melhor ajuste via critério de informação de Akaike (AIC), os quais foram utilizados para estimar o GEBV e suas precisões. O uso de α somente impactou no ajuste com painéis de baixa densidade. Não foram encontradas diferenças na precisão média da população total. Em contraste, no subgrupo de animais genotipados as precisões aumentaram 2% com 170 SNPs (α = 0.25), e com 507 SNPs 5% (α = 0.5) e 14% (α = 0.75). Não houve diferenças na precisão de EBV e GEBV de DF. Os resultados mostram que é possível aumentar a precisão de GEBVs mesmo que se utilizem painéis de baixa densidade. |
dc.format.extent.es.fl_str_mv | e998 |
dc.format.mimetype.es.fl_str_mv | application/pdf |
dc.identifier.citation.es.fl_str_mv | Carracelas B, Navajas EA, Vera B, Ciappesoni G. "SNP arrays evaluation as tools in genetic improvement in Corriedale sheep in Uruguay". Agrociencia Uruguay. [en línea] 2022, 26(2):e998. Doi: 10.31285/AGRO.26.998. |
dc.identifier.doi.none.fl_str_mv | 10.31285/AGRO.26.998 |
dc.identifier.issn.none.fl_str_mv | 2730-5066 |
dc.identifier.uri.none.fl_str_mv | https://hdl.handle.net/20.500.12008/36472 |
dc.language.iso.none.fl_str_mv | en eng |
dc.publisher.es.fl_str_mv | Facultad de Agronomía, Universidad de la República - INIA |
dc.relation.ispartof.es.fl_str_mv | Agrociencia Uruguay, 2022 26(2):e998 |
dc.rights.license.none.fl_str_mv | Licencia Creative Commons Atribución (CC - By 4.0) |
dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess |
dc.source.none.fl_str_mv | reponame:COLIBRI instname:Universidad de la República instacron:Universidad de la República |
dc.subject.es.fl_str_mv | Accuracy Corriedale FEC GEBV HPG OPG Precisão Precisión |
dc.title.none.fl_str_mv | SNP arrays evaluation as tools in genetic improvement in Corriedale sheep in Uruguay Evaluación de paneles de SNP como herramientas en la mejora genética de ovinos Corriedale en Uruguay Avaliação de painéis de SNP como ferramentas em melhoramento genético de ovinos Corriedale no Uruguai |
dc.type.es.fl_str_mv | Artículo |
dc.type.none.fl_str_mv | info:eu-repo/semantics/article |
dc.type.version.none.fl_str_mv | info:eu-repo/semantics/publishedVersion |
description | One control strategy for gastrointestinal nematodes (GIN) is genetic selection. This study´s objective was to compare eggs per gram of feces (FEC) and fiber diameter (FD) estimated breeding values (EBV) and genomic EBV (GEBV) in Corriedale breed. Analysis included 19547 lambs with data, and 454, 711 and 383 genotypes from 170, 507 and 50K SNP chips, respectively. A univariate animal model was used for EBV and GEBV estimation, which included contemporary group, type of birth and dam age as fixed effects, and age at recording as covariate. Differential weights (α) were considered in the genomic relationship matrix (G), and the best fit models were identified using Akaike´s Information Criterion (AIC), which were later used for GEBV and accuracies estimation. The use of α only impacted on low density SNP chips. No differences were observed in mean accuracies for the whole population. However, in the genotyped subgroup accuracies increased by 2% with the 170 SNP chip (α=0.25), and by 5% (α=0.5) and 14% (α=0.75) with the 507 SNP chip. No differences were observed in FD EBV and GEBV mean accuracies. These results show that it is possible to increase GEBV accuracies despite the use of low-density chips. |
eu_rights_str_mv | openAccess |
format | article |
id | COLIBRI_6d29c7640b8b74b3faa60a841bbfea04 |
identifier_str_mv | Carracelas B, Navajas EA, Vera B, Ciappesoni G. "SNP arrays evaluation as tools in genetic improvement in Corriedale sheep in Uruguay". Agrociencia Uruguay. [en línea] 2022, 26(2):e998. Doi: 10.31285/AGRO.26.998. 2730-5066 10.31285/AGRO.26.998 |
instacron_str | Universidad de la República |
institution | Universidad de la República |
instname_str | Universidad de la República |
language | eng |
language_invalid_str_mv | en |
network_acronym_str | COLIBRI |
network_name_str | COLIBRI |
oai_identifier_str | oai:colibri.udelar.edu.uy:20.500.12008/36472 |
publishDate | 2022 |
reponame_str | COLIBRI |
repository.mail.fl_str_mv | mabel.seroubian@seciu.edu.uy |
repository.name.fl_str_mv | COLIBRI - Universidad de la República |
repository_id_str | 4771 |
rights_invalid_str_mv | Licencia Creative Commons Atribución (CC - By 4.0) |
spelling | Carracelas Beatriz, Instituto Nacional de Investigación Agropecuaria (INIA), Unidad de Biotecnología, Las Brujas, Uruguay https://orcid.org/0000-0003-1340-367XNavajas Elly Ana, Instituto Nacional de Investigación Agropecuaria (INIA), Unidad de Biotecnología, Las Brujas, Uruguay https://orcid.org/0000-0002-9018-4741Vera Brenda, Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción de Carne y Lana, Las Brujas, Uruguay https://orcid.org/0000-0002-5706-4721Ciappesoni Gabriel, Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción de Carne y Lana, Las Brujas, Uruguay https://orcid.org/0000-0002-0091-39562023-03-22T18:00:39Z2023-03-22T18:00:39Z2022Carracelas B, Navajas EA, Vera B, Ciappesoni G. "SNP arrays evaluation as tools in genetic improvement in Corriedale sheep in Uruguay". Agrociencia Uruguay. [en línea] 2022, 26(2):e998. Doi: 10.31285/AGRO.26.998.2730-5066https://hdl.handle.net/20.500.12008/3647210.31285/AGRO.26.998One control strategy for gastrointestinal nematodes (GIN) is genetic selection. This study´s objective was to compare eggs per gram of feces (FEC) and fiber diameter (FD) estimated breeding values (EBV) and genomic EBV (GEBV) in Corriedale breed. Analysis included 19547 lambs with data, and 454, 711 and 383 genotypes from 170, 507 and 50K SNP chips, respectively. A univariate animal model was used for EBV and GEBV estimation, which included contemporary group, type of birth and dam age as fixed effects, and age at recording as covariate. Differential weights (α) were considered in the genomic relationship matrix (G), and the best fit models were identified using Akaike´s Information Criterion (AIC), which were later used for GEBV and accuracies estimation. The use of α only impacted on low density SNP chips. No differences were observed in mean accuracies for the whole population. However, in the genotyped subgroup accuracies increased by 2% with the 170 SNP chip (α=0.25), and by 5% (α=0.5) and 14% (α=0.75) with the 507 SNP chip. No differences were observed in FD EBV and GEBV mean accuracies. These results show that it is possible to increase GEBV accuracies despite the use of low-density chips.Una alternativa para el control de los nematodos gastrointestinales (NGI) es la selección genética. El objetivo de este trabajo fue comparar las precisiones de los valores de cría (EBV) y los EBV genómicos (GEBV) del recuento de huevos por gramo en heces (HPG) y diámetro de fibra (DF) en la raza Corriedale. El análisis incluyó 19547 corderos con datos fenotípicos y 454, 711 y 383 genotipados con paneles o chips de 170, 507 y 50K SNP, respectivamente. Los EBV y GEBV se estimaron con un modelo animal univariado que incluyó los efectos fijos: grupo contemporáneo, tipo de nacimiento y edad de la madre, y edad al registro como covariable. Se consideraron pesos diferenciales (α) en la matriz de relaciones genómicas, identificándose los modelos con mejor ajuste con el criterio de información de Akaike (AIC), que fueron utilizados para la estimación de los GEBV y sus precisiones. El uso de α solo impactó en el ajuste con paneles de baja densidad. No se encontraron diferencias en las precisiones promedio de la población total. En cambio, en el subgrupo de animales genotipados las precisiones aumentaron 2% con 170 SNP (α=0.25), y con 507 SNP 5% (α=0.5) y 14% (α=0.75). No hubo diferencias en precisiones de los EBV y los GEBV de DF. Los resultados muestran que es posible aumentar las precisiones de los GEBV aun con paneles de baja densidad.Uma alternativa para o controle de nematóides gastrointestinais (NGI) é a seleção genética. O objetivo deste trabalho foi comparar as precisões dos valores genéticos estimados (EBV) e dos EBVs genômicos (GEBV) da contagem de ovos por grama de fezes (OPG) e diâmetro de fibra (DF) na raça Corriedale. A análise incluiu 19547 cordeiros com dados e 454, 711 e 383 genotipados de 170, 507 e 50K SNPs, respectivamente. Foram estimados os EBV e GEBV com um modelo animal univariado que incluiu efeitos fixos de grupo contemporâneo, tipo de nascimento e idade da mãe e idade no registro (covariável). Pesos diferenciais (α) foram considerados na matriz de relações genômicas, identificando os modelos com melhor ajuste via critério de informação de Akaike (AIC), os quais foram utilizados para estimar o GEBV e suas precisões. O uso de α somente impactou no ajuste com painéis de baixa densidade. Não foram encontradas diferenças na precisão média da população total. Em contraste, no subgrupo de animais genotipados as precisões aumentaram 2% com 170 SNPs (α = 0.25), e com 507 SNPs 5% (α = 0.5) e 14% (α = 0.75). Não houve diferenças na precisão de EBV e GEBV de DF. Os resultados mostram que é possível aumentar a precisão de GEBVs mesmo que se utilizem painéis de baixa densidade.Submitted by Colombo Cabanas Stephanie (stephanie.colombo@fic.edu.uy) on 2023-03-14T11:59:19Z No. of bitstreams: 2 license_rdf: 19875 bytes, checksum: 9fdbed07f52437945402c4e70fa4773e (MD5) 2730-5066--998.pdf: 750909 bytes, checksum: e390053b4ca19c2093ffd22ab2026836 (MD5)Approved for entry into archive by Muniz Andrea (rosmeri8@hotmail.com) on 2023-03-22T17:00:03Z (GMT) No. of bitstreams: 2 license_rdf: 19875 bytes, checksum: 9fdbed07f52437945402c4e70fa4773e (MD5) 2730-5066--998.pdf: 750909 bytes, checksum: e390053b4ca19c2093ffd22ab2026836 (MD5)Made available in DSpace by Luna Fabiana (fabiana.luna@seciu.edu.uy) on 2023-03-22T18:00:39Z (GMT). No. of bitstreams: 2 license_rdf: 19875 bytes, checksum: 9fdbed07f52437945402c4e70fa4773e (MD5) 2730-5066--998.pdf: 750909 bytes, checksum: e390053b4ca19c2093ffd22ab2026836 (MD5) Previous issue date: 2022e998application/pdfenengFacultad de Agronomía, Universidad de la República - INIAAgrociencia Uruguay, 2022 26(2):e998Las obras depositadas en el Repositorio se rigen por la Ordenanza de los Derechos de la Propiedad Intelectual de la Universidad de la República.(Res. Nº 91 de C.D.C. de 8/III/1994 – D.O. 7/IV/1994) y por la Ordenanza del Repositorio Abierto de la Universidad de la República (Res. Nº 16 de C.D.C. de 07/10/2014)info:eu-repo/semantics/openAccessLicencia Creative Commons Atribución (CC - By 4.0)AccuracyCorriedaleFECGEBVHPGOPGPrecisãoPrecisiónSNP arrays evaluation as tools in genetic improvement in Corriedale sheep in UruguayEvaluación de paneles de SNP como herramientas en la mejora genética de ovinos Corriedale en UruguayAvaliação de painéis de SNP como ferramentas em melhoramento genético de ovinos Corriedale no UruguaiArtículoinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:COLIBRIinstname:Universidad de la Repúblicainstacron:Universidad de la RepúblicaCarracelas, BeatrizNavajas, Elly AnaVera, BrendaCiappesoni, GabrielCarriquiry, MarianaLICENSElicense.txtlicense.txttext/plain; charset=utf-84267http://localhost:8080/xmlui/bitstream/20.500.12008/36472/5/license.txt6429389a7df7277b72b7924fdc7d47a9MD55CC-LICENSElicense_urllicense_urltext/plain; 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- Universidad de la Repúblicafalse |
spellingShingle | SNP arrays evaluation as tools in genetic improvement in Corriedale sheep in Uruguay Carracelas, Beatriz Accuracy Corriedale FEC GEBV HPG OPG Precisão Precisión |
status_str | publishedVersion |
title | SNP arrays evaluation as tools in genetic improvement in Corriedale sheep in Uruguay |
title_full | SNP arrays evaluation as tools in genetic improvement in Corriedale sheep in Uruguay |
title_fullStr | SNP arrays evaluation as tools in genetic improvement in Corriedale sheep in Uruguay |
title_full_unstemmed | SNP arrays evaluation as tools in genetic improvement in Corriedale sheep in Uruguay |
title_short | SNP arrays evaluation as tools in genetic improvement in Corriedale sheep in Uruguay |
title_sort | SNP arrays evaluation as tools in genetic improvement in Corriedale sheep in Uruguay |
topic | Accuracy Corriedale FEC GEBV HPG OPG Precisão Precisión |
url | https://hdl.handle.net/20.500.12008/36472 |