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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha : |
16/08/2022 |
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Actualizado : |
27/04/2023 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
MCWHORTER, T.M.; BERMANN, M.; GARCIA, A.L.S.; LEGARRA, A.; AGUILAR, I.; MISZTAL, I.; LOURENCO, D. |
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Afiliación : |
TAYLOR M. MCWHORTER, Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA; MATIAS BERMANN, Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA; ANDRE L. S. GARCIA, Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA; ANDRÉS LEGARRA, UMR GenPhySE, Institut National de la Recherche Agronomique, Castanet- Tolosan, France; IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; IGNACY MISZTAL, Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA; DANIELA LOURENCO, Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA. |
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Título : |
Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP. |
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Fecha de publicación : |
2023 |
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Fuente / Imprenta : |
Journal of Animal Breeding and Genetics, 2023, volume 140, issue 1, pp. 60-78. OPEN ACCESS. doi: https://doi.org/10.1111/jbg.12734 |
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ISSN : |
0931-2668; eISSN: 1439-0388 |
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DOI : |
10.1111/jbg.12734 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received 18 March 2019; Revised 15 July 2019; Accepted: 29 July 2019; First published 10 August 2022.
Correspondence: McWhorter, T.M.; Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States; email:taylor.mcwhorter@uga.edu --
This study was partially funded by Agriculture and Food Research Initiative Competitive Grant no. 2020?67015?31030 from the U.S. Department of Agriculture, Australian Government's National Institute of Food and Agriculture (Washington, DC). -- This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. License Creative Commons: https://creativecommons.org/licenses/by-nc-nd/4.0/ |
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Contenido : |
ABSTRACT.- Single-step genomic BLUP (ssGBLUP) relies on the combination of the genomic ((Formula presented.)) and pedigree relationship matrices for all ((Formula presented.)) and genotyped ((Formula presented.)) animals. The procedure ensures (Formula presented.) and (Formula presented.) are compatible so that both matrices refer to the same genetic base (?tuning?). Then (Formula presented.) is combined with a proportion of (Formula presented.) (?blending?) to avoid singularity problems and to account for the polygenic component not accounted for by markers. This computational procedure has been implemented in the reverse order (blending before tuning) following the sequential research developments. However, blending before tuning may result in less optimal tuning because the blended matrix already contains a proportion of (Formula presented.). In this study, the impact of ?tuning before blending? was compared with ?blending before tuning? on genomic estimated breeding values (GEBV), single nucleotide polymorphism (SNP) effects and indirect predictions (IP) from ssGBLUP using American Angus Association and Holstein Association USA, Inc. data. Two slightly different tuning methods were used; one that adjusts the mean diagonals and off-diagonals of (Formula presented.) to be similar to those in (Formula presented.) and another one that adjusts based on the average difference between all elements of (Formula presented.) and (Formula presented.). Over 6 million Angus growth records and 5.9 million Holstein udder depth records were available. Genomic information was available on 51,478 Angus and 105,116 Holstein animals. Average realized relationship estimates among groups of animals were similar across scenarios. Scatterplots show that GEBV, SNP effects and IP did not noticeably change for all animals in the evaluation regardless of the order of computations and when using blending parameter of 0.05. Formulas were derived to determine the blending parameter that maximizes changes in the genomic relationship matrix and GEBV when changing the order of blending and tuning. Algebraically, the change is maximized when the blending parameter is equal to 0.5. Overall, tuning (Formula presented.) before blending, regardless of blending parameter used, had a negligible impact on genomic predictions and SNP effects in this study. © 2022 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd. MenosABSTRACT.- Single-step genomic BLUP (ssGBLUP) relies on the combination of the genomic ((Formula presented.)) and pedigree relationship matrices for all ((Formula presented.)) and genotyped ((Formula presented.)) animals. The procedure ensures (Formula presented.) and (Formula presented.) are compatible so that both matrices refer to the same genetic base (?tuning?). Then (Formula presented.) is combined with a proportion of (Formula presented.) (?blending?) to avoid singularity problems and to account for the polygenic component not accounted for by markers. This computational procedure has been implemented in the reverse order (blending before tuning) following the sequential research developments. However, blending before tuning may result in less optimal tuning because the blended matrix already contains a proportion of (Formula presented.). In this study, the impact of ?tuning before blending? was compared with ?blending before tuning? on genomic estimated breeding values (GEBV), single nucleotide polymorphism (SNP) effects and indirect predictions (IP) from ssGBLUP using American Angus Association and Holstein Association USA, Inc. data. Two slightly different tuning methods were used; one that adjusts the mean diagonals and off-diagonals of (Formula presented.) to be similar to those in (Formula presented.) and another one that adjusts based on the average difference between all elements of (Formula presented.) and (Formula presented.). Over 6 million Angus growth rec... Presentar Todo |
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Palabras claves : |
Genetic base; Indirect predictions; Residual polygenic effect; Scaling of genomic matrices; Single-step genomic best linear unbiased prediction. |
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Asunto categoría : |
L10 Genética y mejoramiento animal |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/16748/1/J-Animal-Breeding-Genetics-2022-McWhorter-Implication-of-the-order-of-blending-and-tuning-when-computing-the-genomic.pdf
https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/jbg.12734?download=true
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Marc : |
LEADER 04321naa a2200289 a 4500
001 1063528
005 2023-04-27
008 2023 bl uuuu u00u1 u #d
022 $a0931-2668; eISSN: 1439-0388
024 7 $a10.1111/jbg.12734$2DOI
100 1 $aMCWHORTER, T.M.
245 $aImplication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP.$h[electronic resource]
260 $c2023
500 $aArticle history: Received 18 March 2019; Revised 15 July 2019; Accepted: 29 July 2019; First published 10 August 2022. Correspondence: McWhorter, T.M.; Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States; email:taylor.mcwhorter@uga.edu -- This study was partially funded by Agriculture and Food Research Initiative Competitive Grant no. 2020?67015?31030 from the U.S. Department of Agriculture, Australian Government's National Institute of Food and Agriculture (Washington, DC). -- This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. License Creative Commons: https://creativecommons.org/licenses/by-nc-nd/4.0/
520 $aABSTRACT.- Single-step genomic BLUP (ssGBLUP) relies on the combination of the genomic ((Formula presented.)) and pedigree relationship matrices for all ((Formula presented.)) and genotyped ((Formula presented.)) animals. The procedure ensures (Formula presented.) and (Formula presented.) are compatible so that both matrices refer to the same genetic base (?tuning?). Then (Formula presented.) is combined with a proportion of (Formula presented.) (?blending?) to avoid singularity problems and to account for the polygenic component not accounted for by markers. This computational procedure has been implemented in the reverse order (blending before tuning) following the sequential research developments. However, blending before tuning may result in less optimal tuning because the blended matrix already contains a proportion of (Formula presented.). In this study, the impact of ?tuning before blending? was compared with ?blending before tuning? on genomic estimated breeding values (GEBV), single nucleotide polymorphism (SNP) effects and indirect predictions (IP) from ssGBLUP using American Angus Association and Holstein Association USA, Inc. data. Two slightly different tuning methods were used; one that adjusts the mean diagonals and off-diagonals of (Formula presented.) to be similar to those in (Formula presented.) and another one that adjusts based on the average difference between all elements of (Formula presented.) and (Formula presented.). Over 6 million Angus growth records and 5.9 million Holstein udder depth records were available. Genomic information was available on 51,478 Angus and 105,116 Holstein animals. Average realized relationship estimates among groups of animals were similar across scenarios. Scatterplots show that GEBV, SNP effects and IP did not noticeably change for all animals in the evaluation regardless of the order of computations and when using blending parameter of 0.05. Formulas were derived to determine the blending parameter that maximizes changes in the genomic relationship matrix and GEBV when changing the order of blending and tuning. Algebraically, the change is maximized when the blending parameter is equal to 0.5. Overall, tuning (Formula presented.) before blending, regardless of blending parameter used, had a negligible impact on genomic predictions and SNP effects in this study. © 2022 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd.
653 $aGenetic base
653 $aIndirect predictions
653 $aResidual polygenic effect
653 $aScaling of genomic matrices
653 $aSingle-step genomic best linear unbiased prediction
700 1 $aBERMANN, M.
700 1 $aGARCIA, A.L.S.
700 1 $aLEGARRA, A.
700 1 $aAGUILAR, I.
700 1 $aMISZTAL, I.
700 1 $aLOURENCO, D.
773 $tJournal of Animal Breeding and Genetics, 2023, volume 140, issue 1, pp. 60-78. OPEN ACCESS. doi: https://doi.org/10.1111/jbg.12734
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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 : |
22/05/2023 |
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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 : |
VIGLIECCA, M.; GONZÁLEZ, P.; MACHÍN, A.; VICENTE, E.; SILVERA, E. |
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Afiliación : |
MICAELA VIGLIECCA, Universidad de la República, Facultad de Agronomía, Departamento de Protección Vegetal, Montevideo, Uruguay; PABLO GONZÁLEZ, Universidad de la República, Facultad de Agronomía, Departamento de Protección Vegetal, Montevideo, Uruguay; ALEX MACHÍN, Universidad de la República, Facultad de Agronomía Departamento de Protección Vegetal, Salto, Uruguay; CARLOS ESTEBAN VICENTE CASTRO, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ELISA SILVERA, Universidad de la República, Facultad de Agronomía Departamento de Protección Vegetal, Salto, Uruguay. |
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Título : |
First report of root and crown rot caused by Dactylonectria novozelandica on strawberry in Uruguay. [Primer reporte de Dactylonectria novozelandica causando necrosis de raíz y corona en frutilla en Uruguay]. [Primeiro relato de Dactylonectria novozelandica causando necrose de raiz e coroa em morangos no Uruguay]. |
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Complemento del título : |
Plant protection |
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Fecha de publicación : |
2022 |
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Fuente / Imprenta : |
Agrociencia Uruguay, 2022, Vol.26, number 2, e962. https://doi.org/10.31285/AGRO.26.962 -- OPEN ACCESS. |
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ISSN : |
2730-5066 |
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DOI : |
10.31285/AGRO.26.962 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received 26 Aug 2021; Accepted 1 Aug 2022; Published 12 Aug 2022. -- Correspondence: Elisa Silvera-Pérez, esilvera@fagro.edu.uy -- Editor:
Leonardo De La Fuente, Auburn University, Department of Entomology & Plant Pathology, Auburn (AL), United States. -- License: This work is licensed under a Creative Commons Attribution 4.0 International License. (https://creativecommons.org/licenses/by/4.0/ ) |
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Contenido : |
ABSTRACT.- Since 2015, a high mortality rate of strawberry plants has been observed in the north of Uruguay related to crown and root diseases caused by a pathogens complex. In 2016, associated with the death of plants, Cylindrocarpon spp. was isolated with a frequency of 42.4 %, ranking third, preceded by Neopestalotiopsis sp. and Fusarium spp. Aiming to increase the knowledge of the pathogens that integrate the complex, three isolates of Cylindrocarpon spp. were characterized by molecular, morphological and pathogenicity analyses in strawberry plants. Dactylonectria novozelandica was identified as causal agent of crown and root necrosis of strawberry in Salto, Uruguay. .-.-.-.-.-.-.-.-.-.-..-RESUMEN.- Desde 2015, se observó una alta mortandad de plantas de frutilla en el norte de Uruguay relacionada con enfermedades de corona y raíz causadas por un complejo de patógenos. En 2016, asociado con la muerte de plantas, Cylindrocarpon spp. se aisló con una frecuencia de 42,4 %, ocupando el tercer lugar, precedido por Neopestalotiopsis sp. y Fusarium spp. Con el objetivo de incrementar el conocimiento de los patógenos que integran el complejo, se caracterizaron tres aislados de Cylindrocarpon spp. mediante análisis moleculares, morfológicos y de patogenicidad en plantas de frutilla. Se identificó Dactylonectria novozelandica como agente causal de necrosis de corona y raíz de frutilla en Salto, Uruguay. .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.RESUMO.- A partir do ano 2015 um número significativo de mortes se observou em plantas de morango no norte do Uruguai devido a doenças da coroa e raiz causadas por um complexo de patógenos. Associado à morte, Cylindrocarpon spp foi isolado com uma frequência de 42,4% no 2016, ocupando o terceiro lugar de incidência depois de Neopestalotiopsis sp. e Fusarium spp. O objetivo do trabalho foi caracterizar três isolados de Cylindrocarpon spp por meio de análises moleculares, morfológicas e patogênicas em morangueiro. Dactylonectria novozelandica causou necorsis de cora e raiz em uma plantas de morango em Salto, Uruguai. Copyright (c) 2022 Agrociencia Uruguay MenosABSTRACT.- Since 2015, a high mortality rate of strawberry plants has been observed in the north of Uruguay related to crown and root diseases caused by a pathogens complex. In 2016, associated with the death of plants, Cylindrocarpon spp. was isolated with a frequency of 42.4 %, ranking third, preceded by Neopestalotiopsis sp. and Fusarium spp. Aiming to increase the knowledge of the pathogens that integrate the complex, three isolates of Cylindrocarpon spp. were characterized by molecular, morphological and pathogenicity analyses in strawberry plants. Dactylonectria novozelandica was identified as causal agent of crown and root necrosis of strawberry in Salto, Uruguay. .-.-.-.-.-.-.-.-.-.-..-RESUMEN.- Desde 2015, se observó una alta mortandad de plantas de frutilla en el norte de Uruguay relacionada con enfermedades de corona y raíz causadas por un complejo de patógenos. En 2016, asociado con la muerte de plantas, Cylindrocarpon spp. se aisló con una frecuencia de 42,4 %, ocupando el tercer lugar, precedido por Neopestalotiopsis sp. y Fusarium spp. Con el objetivo de incrementar el conocimiento de los patógenos que integran el complejo, se caracterizaron tres aislados de Cylindrocarpon spp. mediante análisis moleculares, morfológicos y de patogenicidad en plantas de frutilla. Se identificó Dactylonectria novozelandica como agente causal de necrosis de corona y raíz de frutilla en Salto, Uruguay. .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.RESUMO.- A partir do ano 2015 um número signif... Presentar Todo |
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Palabras claves : |
Cylindrocarpon spp; Histona; Histone; Pathogenicity test; Prueba de patogenicidad; Teste patogênico. |
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Asunto categoría : |
H20 Enfermedades de las plantas |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/17164/1/2730-5066-962.pdf
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Marc : |
LEADER 03605naa a2200277 a 4500
001 1064152
005 2023-05-22
008 2022 bl uuuu u00u1 u #d
022 $a2730-5066
024 7 $a10.31285/AGRO.26.962$2DOI
100 1 $aVIGLIECCA, M.
245 $aFirst report of root and crown rot caused by Dactylonectria novozelandica on strawberry in Uruguay. [Primer reporte de Dactylonectria novozelandica causando necrosis de raíz y corona en frutilla en Uruguay]. [Primeiro relato de Dactylonectria novozelandica causando necrose de raiz e coroa em morangos no Uruguay].$h[electronic resource]
260 $c2022
500 $aArticle history: Received 26 Aug 2021; Accepted 1 Aug 2022; Published 12 Aug 2022. -- Correspondence: Elisa Silvera-Pérez, esilvera@fagro.edu.uy -- Editor: Leonardo De La Fuente, Auburn University, Department of Entomology & Plant Pathology, Auburn (AL), United States. -- License: This work is licensed under a Creative Commons Attribution 4.0 International License. (https://creativecommons.org/licenses/by/4.0/ )
520 $aABSTRACT.- Since 2015, a high mortality rate of strawberry plants has been observed in the north of Uruguay related to crown and root diseases caused by a pathogens complex. In 2016, associated with the death of plants, Cylindrocarpon spp. was isolated with a frequency of 42.4 %, ranking third, preceded by Neopestalotiopsis sp. and Fusarium spp. Aiming to increase the knowledge of the pathogens that integrate the complex, three isolates of Cylindrocarpon spp. were characterized by molecular, morphological and pathogenicity analyses in strawberry plants. Dactylonectria novozelandica was identified as causal agent of crown and root necrosis of strawberry in Salto, Uruguay. .-.-.-.-.-.-.-.-.-.-..-RESUMEN.- Desde 2015, se observó una alta mortandad de plantas de frutilla en el norte de Uruguay relacionada con enfermedades de corona y raíz causadas por un complejo de patógenos. En 2016, asociado con la muerte de plantas, Cylindrocarpon spp. se aisló con una frecuencia de 42,4 %, ocupando el tercer lugar, precedido por Neopestalotiopsis sp. y Fusarium spp. Con el objetivo de incrementar el conocimiento de los patógenos que integran el complejo, se caracterizaron tres aislados de Cylindrocarpon spp. mediante análisis moleculares, morfológicos y de patogenicidad en plantas de frutilla. Se identificó Dactylonectria novozelandica como agente causal de necrosis de corona y raíz de frutilla en Salto, Uruguay. .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.RESUMO.- A partir do ano 2015 um número significativo de mortes se observou em plantas de morango no norte do Uruguai devido a doenças da coroa e raiz causadas por um complexo de patógenos. Associado à morte, Cylindrocarpon spp foi isolado com uma frequência de 42,4% no 2016, ocupando o terceiro lugar de incidência depois de Neopestalotiopsis sp. e Fusarium spp. O objetivo do trabalho foi caracterizar três isolados de Cylindrocarpon spp por meio de análises moleculares, morfológicas e patogênicas em morangueiro. Dactylonectria novozelandica causou necorsis de cora e raiz em uma plantas de morango em Salto, Uruguai. Copyright (c) 2022 Agrociencia Uruguay
653 $aCylindrocarpon spp
653 $aHistona
653 $aHistone
653 $aPathogenicity test
653 $aPrueba de patogenicidad
653 $aTeste patogênico
700 1 $aGONZÁLEZ, P.
700 1 $aMACHÍN, A.
700 1 $aVICENTE, E.
700 1 $aSILVERA, E.
773 $tAgrociencia Uruguay, 2022, Vol.26, number 2, e962. https://doi.org/10.31285/AGRO.26.962 -- OPEN ACCESS.
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