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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha : |
26/04/2023 |
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Actualizado : |
19/06/2023 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
REBOLLO, I.; SCHEFFEL, S.; BLANCO, P.H.; MOLINA, F.; MARTÍNEZ, S.; CARRACELAS, G.; AGUILAR, I.; PÉREZ DE VIDA, F.; ROSAS, J.E. |
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Afiliación : |
MARÍA INÉS REBOLLO PANUNCIO, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; Department of Statistics, College of Agriculture, Universidad de la República, Montevideo, Uruguay; SHEILA SCHEFFEL, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; Department of Statistics, College of Agriculture, Universidad de la República, Montevideo, Uruguay; PEDRO HORACIO BLANCO BARRAL, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; FEDERICO MOLINA CASELLA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; SEBASTIÁN MARTÍNEZ KOPP, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; JULIO GONZALO CARRACELAS GARRIDO, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; FERNANDO BLAS PEREZ DE VIDA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; JUAN EDUARDO ROSAS CAISSIOLS, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; Department of Statistics, College of Agriculture, Universidad de la República, Montevideo, Uruguay. |
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Título : |
Consolidating twenty-three years of historical data from an irrigated subtropical rice breeding program in Uruguay. |
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Fecha de publicación : |
2023 |
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Fuente / Imprenta : |
Crop Science, 2023. https://doi.org/10.1002/csc2.20955 - [Article in Press]. |
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ISSN : |
1435-0653 |
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DOI : |
10.1002/csc2.20955 |
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Idioma : |
Inglés |
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Notas : |
Article history: First published 15 March 2023. -- Corresponding author: jrosas@inia.org.uy -- |
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Contenido : |
Breeding programs generate vast amount of data which are often scattered in separate files. This hinders the application of modern breeding tools such as multi-environment analyses and genomic selection. This research work describes the process of consolidating 23 years of phenotypic, pedigree, and genomic records from the Uruguayan national rice (Oryza sativa L.) breeding program, and the features and structure of the resulting database. Using a custom-made R code, we gathered all the available data from 1997 to 2020 corresponding to field trials, blast disease evaluation nurseries, laboratory analyses of milling and cooking quality, pedigree information, and genomic information for selected advanced breeding lines, and organized it into a relational database. Records of 996 trials in 12 locations over a span of 23 years, 91,636 field plots with information on 14 phenotypic variables, pedigree for 19,447 genotypes, and genomic information regarding 61,260 single nucleotide polymorphism (SNP) markers for 965 genotypes were recovered. The dataset is structured in trials, phenotypes, lines, genomic information, and SNP tables in an easy-to-access relational database, which will be a valuable resource for rice breeding. © 2023 American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America |
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Palabras claves : |
Breeding program; Breeding trials; Phenotypic data. |
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Thesagro : |
ORYZA SATIVA L. |
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Asunto categoría : |
F30 Genética vegetal y fitomejoramiento |
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Marc : |
LEADER 02322naa a2200301 a 4500
001 1064059
005 2023-06-19
008 2023 bl uuuu u00u1 u #d
022 $a1435-0653
024 7 $a10.1002/csc2.20955$2DOI
100 1 $aREBOLLO, I.
245 $aConsolidating twenty-three years of historical data from an irrigated subtropical rice breeding program in Uruguay.$h[electronic resource]
260 $c2023
500 $aArticle history: First published 15 March 2023. -- Corresponding author: jrosas@inia.org.uy --
520 $aBreeding programs generate vast amount of data which are often scattered in separate files. This hinders the application of modern breeding tools such as multi-environment analyses and genomic selection. This research work describes the process of consolidating 23 years of phenotypic, pedigree, and genomic records from the Uruguayan national rice (Oryza sativa L.) breeding program, and the features and structure of the resulting database. Using a custom-made R code, we gathered all the available data from 1997 to 2020 corresponding to field trials, blast disease evaluation nurseries, laboratory analyses of milling and cooking quality, pedigree information, and genomic information for selected advanced breeding lines, and organized it into a relational database. Records of 996 trials in 12 locations over a span of 23 years, 91,636 field plots with information on 14 phenotypic variables, pedigree for 19,447 genotypes, and genomic information regarding 61,260 single nucleotide polymorphism (SNP) markers for 965 genotypes were recovered. The dataset is structured in trials, phenotypes, lines, genomic information, and SNP tables in an easy-to-access relational database, which will be a valuable resource for rice breeding. © 2023 American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America
650 $aORYZA SATIVA L
653 $aBreeding program
653 $aBreeding trials
653 $aPhenotypic data
700 1 $aSCHEFFEL, S.
700 1 $aBLANCO, P.H.
700 1 $aMOLINA, F.
700 1 $aMARTÍNEZ, S.
700 1 $aCARRACELAS, G.
700 1 $aAGUILAR, I.
700 1 $aPÉREZ DE VIDA, F.
700 1 $aROSAS, J.E.
773 $tCrop Science, 2023. https://doi.org/10.1002/csc2.20955 - [Article in Press].
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INIA Las Brujas (LB) |
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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha actual : |
23/08/2022 |
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Actualizado : |
22/05/2023 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Nacionales |
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Circulación / Nivel : |
Nacional - -- |
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Autor : |
CARRACELAS, B.; NAVAJAS, E.; VERA, B.; CIAPPESONI, G. |
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Afiliación : |
EMERITA BEATRIZ CARRACELAS MARQUEZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ELLY ANA NAVAJAS VALENTINI, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; BRENDA VERA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; CARLOS GABRIEL CIAPPESONI SCARONE, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
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Título : |
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]. |
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Complemento del título : |
Animal production and pastures. |
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Fecha de publicación : |
2022 |
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Fuente / Imprenta : |
Agrociencia Uruguay, 2022, vol. 26, number 2, article e998. doi: https://doi.org/10.31285/AGRO.26.998 |
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ISSN : |
2730-5066 |
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DOI : |
10.31285/AGRO.26.998 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received 09 Feb 2022; Accepted 30 May 2022; Published 19 Aug 2022. Editor: Mariana Carriquiry, Universidad de la República, Facultad de Agronomía, Montevideo, Uruguay. Correspondence: Beatriz Carracelas, bcarracelas@inia.org.uy -- License: This work is licensed under a Creative Commons Attribution 4.0 International License. (CC BY 4.0). |
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Contenido : |
ABSTRACT.- One control strategy for gastrointestinal nematodes (GIN) is genetic selection. This studys 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 (?) were considered in the genomic relationship matrix (G), and the best fit models were identified using Akaikes Information Criterion (AIC), which were later used for GEBV and accuracies estimation. The use of 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 (?=0.25), and by 5% (?=0.5) and 14% (?=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 -.-.-.-.-.-.-.-.-.-.-.-..-RESUMEN.- Una alternativa para el control de losnematodos 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 (?) en la matriz de relaciones genómicas, identificándose los modelos con mejor ajuste con el criterio de información de Akaike (AIC), que fueron utili-zados para la estimación de los GEBV y sus precisiones. El uso de ?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 (?=0.25), y con 507 SNP 5% (?=0.5) y 14% (?=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. -.-.-.-.-.-.-.-.-.-.-.-..-RESUMO.- Uma alternativa para o controle de nematóidesgastrointestinais (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. Aanálise 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 (?) 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 ?=0.75 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 (?=0.25), e com 507 SNPs 5% (?=0.5) e 14% (?=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. MenosABSTRACT.- One control strategy for gastrointestinal nematodes (GIN) is genetic selection. This studys 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 (?) were considered in the genomic relationship matrix (G), and the best fit models were identified using Akaikes Information Criterion (AIC), which were later used for GEBV and accuracies estimation. The use of 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 (?=0.25), and by 5% (?=0.5) and 14% (?=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 -.-.-.-.-.-.-.-.-.-.-.-..-RESUMEN.- Una alternativa para el control de losnematodos 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... Presentar Todo |
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Palabras claves : |
Accuracy; FEC; GEBV; HPG; OPG; Precisão; Precisión. |
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Thesagro : |
CORRIEDALE. |
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Asunto categoría : |
L10 Genética y mejoramiento animal |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/16637/1/998-Article-Text-6221-1-10-20220819.pdf
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Marc : |
LEADER 05383naa a2200289 a 4500
001 1063543
005 2023-05-22
008 2022 bl uuuu u00u1 u #d
022 $a2730-5066
024 7 $a10.31285/AGRO.26.998$2DOI
100 1 $aCARRACELAS, B.
245 $aSNP arrays evaluation as tools in genetic improvement in Corriedale sheep in Uruguay. [Evaluación de paneles de SNP como herramientas en la mejora genética de ovinos Corriedale en Uruguay]. [Avaliação de painéis de SNP como ferramentas em melhoramento genético de ovinos Corriedale no Uruguai].$h[electronic resource]
260 $c2022
500 $aArticle history: Received 09 Feb 2022; Accepted 30 May 2022; Published 19 Aug 2022. Editor: Mariana Carriquiry, Universidad de la República, Facultad de Agronomía, Montevideo, Uruguay. Correspondence: Beatriz Carracelas, bcarracelas@inia.org.uy -- License: This work is licensed under a Creative Commons Attribution 4.0 International License. (CC BY 4.0).
520 $aABSTRACT.- One control strategy for gastrointestinal nematodes (GIN) is genetic selection. This studys 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 (?) were considered in the genomic relationship matrix (G), and the best fit models were identified using Akaikes Information Criterion (AIC), which were later used for GEBV and accuracies estimation. The use of 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 (?=0.25), and by 5% (?=0.5) and 14% (?=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 -.-.-.-.-.-.-.-.-.-.-.-..-RESUMEN.- Una alternativa para el control de losnematodos 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 (?) en la matriz de relaciones genómicas, identificándose los modelos con mejor ajuste con el criterio de información de Akaike (AIC), que fueron utili-zados para la estimación de los GEBV y sus precisiones. El uso de ?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 (?=0.25), y con 507 SNP 5% (?=0.5) y 14% (?=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. -.-.-.-.-.-.-.-.-.-.-.-..-RESUMO.- Uma alternativa para o controle de nematóidesgastrointestinais (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. Aanálise 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 (?) 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 ?=0.75 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 (?=0.25), e com 507 SNPs 5% (?=0.5) e 14% (?=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.
650 $aCORRIEDALE
653 $aAccuracy
653 $aFEC
653 $aGEBV
653 $aHPG
653 $aOPG
653 $aPrecisão
653 $aPrecisión
700 1 $aNAVAJAS, E.
700 1 $aVERA, B.
700 1 $aCIAPPESONI, G.
773 $tAgrociencia Uruguay, 2022, vol. 26, number 2, article e998. doi: https://doi.org/10.31285/AGRO.26.998
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