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Biblioteca (s) : |
INIA La Estanzuela. |
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Fecha : |
21/02/2014 |
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Actualizado : |
05/12/2018 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
BRANDARIZ , S.; GONZÁLEZ RAYMÚNDEZ, A.; LADO, B.; MALOSETTI, M.; FRANCO GARCIA, A.; QUINCKE, M.; VON ZITZEWITZ, J.; CASTRO, M.; MATUS,I.; DEL POZO, A.; CASTRO, A.J.; GUTIÉRREZ, L. |
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Afiliación : |
SOFÍA P. BRANDARIZ, Universidad de la República (UdelaR); Facultad de Agronomía, Uruguay.; AGUSTÍN GONZÁLEZ REYMÚNDEZ; BETTINA LADO; MARCOS MALOSETTI; ANTONIO AUGUSTO FRANCO GARCIA; MARTIN CONRADO QUINCKE WALDEN, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; JARISLAV RAMON VON ZITZEWITZ VON SALVIATI, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; MARINA CASTRO DERENYI, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; IVÁN MATUS; ALEJANDRO DEL POZO; ARIEL J. CASTRO; LUCÍA GUTIÉRREZ. |
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Título : |
Ascertainment bias from imputation methods evaluation in wheat. |
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Fecha de publicación : |
2016 |
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Fuente / Imprenta : |
BMC Genomics, 2016, v. 17, p.773. |
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DOI : |
10.1186/s12864-016-3120-5 |
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Idioma : |
Inglés |
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Notas : |
OPEN ACCESS. Article history: Received 2016 Feb 24 // Accepted 2016 Sep 23. |
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Contenido : |
Abstract
BACKGROUND:
Whole-genome genotyping techniques like Genotyping-by-sequencing (GBS) are being used for genetic studies such as Genome-Wide Association (GWAS) and Genomewide Selection (GS), where different strategies for imputation have been developed. Nevertheless, imputation error may lead to poor performance (i.e. smaller power or higher false positive rate) when complete data is not required as it is for GWAS, and each marker is taken at a time. The aim of this study was to compare the performance of GWAS analysis for Quantitative Trait Loci (QTL) of major and minor effect using different imputation methods when no reference panel is available in a wheat GBS panel.
RESULTS:
In this study, we compared the power and false positive rate of dissecting quantitative traits for imputed and not-imputed marker score matrices in: (1) a complete molecular marker barley panel array, and (2) a GBS wheat panel with missing data. We found that there is an ascertainment bias in imputation method comparisons. Simulating over a complete matrix and creating missing data at random proved that imputation methods have a poorer performance. Furthermore, we found that when QTL were simulated with imputed data, the imputation methods performed better than the not-imputed ones. On the other hand, when QTL were simulated with not-imputed data, the not-imputed method and one of the imputation methods performed better for dissecting quantitative traits. Moreover, larger differences between imputation methods were detected for QTL of major effect than QTL of minor effect. We also compared the different marker score matrices for GWAS analysis in a real wheat phenotype dataset, and we found minimal differences indicating that imputation did not improve the GWAS performance when a reference panel was not available.
CONCLUSIONS:
Poorer performance was found in GWAS analysis when an imputed marker score matrix was used, no reference panel is available, in a wheat GBS panel. MenosAbstract
BACKGROUND:
Whole-genome genotyping techniques like Genotyping-by-sequencing (GBS) are being used for genetic studies such as Genome-Wide Association (GWAS) and Genomewide Selection (GS), where different strategies for imputation have been developed. Nevertheless, imputation error may lead to poor performance (i.e. smaller power or higher false positive rate) when complete data is not required as it is for GWAS, and each marker is taken at a time. The aim of this study was to compare the performance of GWAS analysis for Quantitative Trait Loci (QTL) of major and minor effect using different imputation methods when no reference panel is available in a wheat GBS panel.
RESULTS:
In this study, we compared the power and false positive rate of dissecting quantitative traits for imputed and not-imputed marker score matrices in: (1) a complete molecular marker barley panel array, and (2) a GBS wheat panel with missing data. We found that there is an ascertainment bias in imputation method comparisons. Simulating over a complete matrix and creating missing data at random proved that imputation methods have a poorer performance. Furthermore, we found that when QTL were simulated with imputed data, the imputation methods performed better than the not-imputed ones. On the other hand, when QTL were simulated with not-imputed data, the not-imputed method and one of the imputation methods performed better for dissecting quantitative traits. Moreover, larger differences between ... Presentar Todo |
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Palabras claves : |
FALSE POSITIVE; FALSO POSITIVO; GBS; GWAS; POWER; QTLs. |
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Thesagro : |
MEJORAMIENTO DE TRIGO. |
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Asunto categoría : |
F30 Genética vegetal y fitomejoramiento |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/12122/1/s12864-016-3120-5.pdf
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3120-5
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Marc : |
LEADER 02972nam a2200349 a 4500
001 1047336
005 2018-12-05
008 2016 bl uuuu u0uu1 u #d
024 7 $a10.1186/s12864-016-3120-5$2DOI
100 1 $aBRANDARIZ , S.
245 $aAscertainment bias from imputation methods evaluation in wheat.$h[electronic resource]
260 $aBMC Genomics, 2016, v. 17, p.773.$c2016
500 $aOPEN ACCESS. Article history: Received 2016 Feb 24 // Accepted 2016 Sep 23.
520 $aAbstract BACKGROUND: Whole-genome genotyping techniques like Genotyping-by-sequencing (GBS) are being used for genetic studies such as Genome-Wide Association (GWAS) and Genomewide Selection (GS), where different strategies for imputation have been developed. Nevertheless, imputation error may lead to poor performance (i.e. smaller power or higher false positive rate) when complete data is not required as it is for GWAS, and each marker is taken at a time. The aim of this study was to compare the performance of GWAS analysis for Quantitative Trait Loci (QTL) of major and minor effect using different imputation methods when no reference panel is available in a wheat GBS panel. RESULTS: In this study, we compared the power and false positive rate of dissecting quantitative traits for imputed and not-imputed marker score matrices in: (1) a complete molecular marker barley panel array, and (2) a GBS wheat panel with missing data. We found that there is an ascertainment bias in imputation method comparisons. Simulating over a complete matrix and creating missing data at random proved that imputation methods have a poorer performance. Furthermore, we found that when QTL were simulated with imputed data, the imputation methods performed better than the not-imputed ones. On the other hand, when QTL were simulated with not-imputed data, the not-imputed method and one of the imputation methods performed better for dissecting quantitative traits. Moreover, larger differences between imputation methods were detected for QTL of major effect than QTL of minor effect. We also compared the different marker score matrices for GWAS analysis in a real wheat phenotype dataset, and we found minimal differences indicating that imputation did not improve the GWAS performance when a reference panel was not available. CONCLUSIONS: Poorer performance was found in GWAS analysis when an imputed marker score matrix was used, no reference panel is available, in a wheat GBS panel.
650 $aMEJORAMIENTO DE TRIGO
653 $aFALSE POSITIVE
653 $aFALSO POSITIVO
653 $aGBS
653 $aGWAS
653 $aPOWER
653 $aQTLs
700 1 $aGONZÁLEZ RAYMÚNDEZ, A.
700 1 $aLADO, B.
700 1 $aMALOSETTI, M.
700 1 $aFRANCO GARCIA, A.
700 1 $aQUINCKE, M.
700 1 $aVON ZITZEWITZ, J.
700 1 $aCASTRO, M.
700 1 $aMATUS,I.
700 1 $aDEL POZO, A.
700 1 $aCASTRO, A.J.
700 1 $aGUTIÉRREZ, L.
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Registro original : |
INIA La Estanzuela (LE) |
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha actual : |
24/07/2023 |
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Actualizado : |
24/07/2023 |
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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 : |
FERNÁNDEZ-TURREN, G.; CAJARVILLE, C.; PÉREZ-RUCHEL, A.; HIRIGOYEN, D.; CONSTANTÍN, M.; GONZÁLEZ, V.; MADERA, J.; EIRALDI, F.; KOZLOSKI, G.V.; REPETTO, J.L. |
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Afiliación : |
GONZALO FERNÁNDEZ-TURREN, Departamento de Bovinos, Facultad de Veterinaria - Instituto de Producción Animal-UdelaR, Ruta 1 km 42,500, CP 80100, San José, Uruguay.; CECILIA CAJARVILLE, Departamento de Nutrición Animal, Facultad de Veterinaria - Instituto de Producción Animal-UdelaR.; ANALÍA PÉREZ-RUCHEL, Departamento de Nutrición Animal, Facultad de Veterinaria - Instituto de Producción Animal-UdelaR.; DARÍO JAVIER HIRIGOYEN TREVIN, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; MARINA CONSTANTÍN, Laboratorio de nutrición Cooperativa COLAVECO, Uruguay.; VÍCTOR GONZÁLEZ, Laboratorio de nutrición Cooperativa COLAVECO, Uruguay; JENNIFER MADERA, Laboratorio de nutrición Cooperativa COLAVECO, Uruguay.; FULVIO EIRALDI, Veterinario de ejercicio liberal.; GILBERTO V. KOZLOSKI, Laboratorio de Nutrición de Rumiantes, Universidad Federal de Santa María, Brasil.; JOSÉ L. REPETTO, Departamento de Bovinos, Facultad de Veterinaria - Instituto de Producción Animal-UdelaR, Ruta 1 km 42,500, CP 80100, San José, Uruguay. |
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Título : |
Evaluación nutritiva de harinas y expeller de soja presentes en Uruguay en la alimentación de vacas lecheras. [Nutritional evaluation of soybean meal and expellers present in Uruguay in the dairy cattle feeding.] |
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Complemento del título : |
Sección: Artículos originales. |
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Fecha de publicación : |
2018 |
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Fuente / Imprenta : |
Veterinaria (Montevideo), 2018, v. 54, no. 209, p. 31-38. -- OPEN ACCESS. |
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ISSN : |
0376-4362 (impresa); 1688-4809 (en línea). |
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DOI : |
10.29155/VET.54.209.5 |
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Idioma : |
Español |
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Notas : |
Article history: Recibido 11 Noviembre 2017; Aceptado 19 Abril 2018; Publicado 1 Mayo 2018. -- Autor para correspondencia: G. Fernández-Turren, email to: gonzalofernandezt@gmail.com -- Publicación de la Sociedad de Medicina Veterinaria del Uruguay (SMVU). |
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Contenido : |
RESUMEN.- La composición química y degradabilidad ruminal de los subproductos derivados de la soja pueden verse afectadas según su proceso industrial de obtención. El objetivo de este estudio fue determinar el valor proteico en vacas lecheras de harinas y expeller de soja presentes en Uruguay. Se obtuvieron muestras de estos subproductos en distribuidores de alimentos para vacunos de la cuenca lechera uruguaya. Se analizó la composición química, degradabilidad ruminal in situ (determinando: fracción soluble, tasa de degradación y degradabilidad efectiva) y su fermentescibilidad in vitro. Se comparó la composición química y degradabilidad ruminal in situ de las muestras con la base de datos del programa NRC (NRC, 2001). Todos los resultados fueron comparados a través de un análisis de varianza. Las harinas presentaron menor contenido de extracto etéreo, materia orgánica y mayor contenido proteico (P<0,05), mayor tasa de degradación y degradabilidad efectiva in situ, además de una mayor tasa de producción de gas in vitro en comparación con los expeller (P<0,01). La degradabilidad ruminal in vitro no varió entre subproductos (P=0,432). La comparación de datos con la base del NRC (NRC, 2001) indicó una menor producción de leche (L/d) debido a una mayor degradabilidad ruminal de las harinas y expeller evaluados. En base a las diferencias encontradas entre la composición química y degradabilidad ruminal de los subproductos analizados y los datos incorporados en el programa (NRC, 2001) sería recomendable emplear datos nacionales a la hora de formular dietas. ------------------- SUMMARY.- The chemical composition and ruminal degradability of soybean by products can be affected by the industrial processes through which are obtained. The objective of this study was to determine the protein value for dairy cows of soybean meal and expeller present in Uruguay. Samples of soybean meal and expeller were taken from several Uruguayan suppliers. The chemical composition, in situ ruminal degradability (determining: soluble fraction, degradation rate and effective degradability) and its in vitro degradability of protein were analyzed. The chemical composition and in situ ruminal degradability of the samples were compared with the NRC (NRC, 2001) software database. All the results were compared through an analysis of variance. The soybean meal presented a lower content of ether extract and organic matter with a higher protein content (P<0.05), higher rate of degradation and effective degradability in situ, in addition
to a higher rate of in vitro gas production when compared with expeller (P<0,01). In vitro ruminal degradability did not vary between byproducts (P=0.432). The results of the simulation indicate that the production is lower than that of which is predicted by the NRC (NRC, 2001), because to a higher protein degradability of soybean meal and expeller evaluated. Based on the differences found between the chemical composition and
ruminal degradability of the byproducts analyzed and the data incorporated in the software (NRC, 2001), it would be advisable to use national data when formulating diets. MenosRESUMEN.- La composición química y degradabilidad ruminal de los subproductos derivados de la soja pueden verse afectadas según su proceso industrial de obtención. El objetivo de este estudio fue determinar el valor proteico en vacas lecheras de harinas y expeller de soja presentes en Uruguay. Se obtuvieron muestras de estos subproductos en distribuidores de alimentos para vacunos de la cuenca lechera uruguaya. Se analizó la composición química, degradabilidad ruminal in situ (determinando: fracción soluble, tasa de degradación y degradabilidad efectiva) y su fermentescibilidad in vitro. Se comparó la composición química y degradabilidad ruminal in situ de las muestras con la base de datos del programa NRC (NRC, 2001). Todos los resultados fueron comparados a través de un análisis de varianza. Las harinas presentaron menor contenido de extracto etéreo, materia orgánica y mayor contenido proteico (P<0,05), mayor tasa de degradación y degradabilidad efectiva in situ, además de una mayor tasa de producción de gas in vitro en comparación con los expeller (P<0,01). La degradabilidad ruminal in vitro no varió entre subproductos (P=0,432). La comparación de datos con la base del NRC (NRC, 2001) indicó una menor producción de leche (L/d) debido a una mayor degradabilidad ruminal de las harinas y expeller evaluados. En base a las diferencias encontradas entre la composición química y degradabilidad ruminal de los subproductos analizados y los datos incorporados en el programa (NRC, 2... Presentar Todo |
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Palabras claves : |
Expeller; Proteína degradable en rumen; Rumen-degraded protein; Soybean meal. |
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Thesagro : |
HARINA DE SOJA; PRODUCCION DE LECHE. |
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Asunto categoría : |
F01 Cultivo |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/17302/1/Fernandez-Turren-et-al.-2018-SMVU-v54-n209.pdf
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Marc : |
LEADER 04569naa a2200337 a 4500
001 1064267
005 2023-07-24
008 2018 bl uuuu u00u1 u #d
022 $a0376-4362 (impresa); 1688-4809 (en línea).
024 7 $a10.29155/VET.54.209.5$2DOI
100 1 $aFERNÁNDEZ-TURREN, G.
245 $aEvaluación nutritiva de harinas y expeller de soja presentes en Uruguay en la alimentación de vacas lecheras. [Nutritional evaluation of soybean meal and expellers present in Uruguay in the dairy cattle feeding.]$h[electronic resource]
260 $c2018
500 $aArticle history: Recibido 11 Noviembre 2017; Aceptado 19 Abril 2018; Publicado 1 Mayo 2018. -- Autor para correspondencia: G. Fernández-Turren, email to: gonzalofernandezt@gmail.com -- Publicación de la Sociedad de Medicina Veterinaria del Uruguay (SMVU).
520 $aRESUMEN.- La composición química y degradabilidad ruminal de los subproductos derivados de la soja pueden verse afectadas según su proceso industrial de obtención. El objetivo de este estudio fue determinar el valor proteico en vacas lecheras de harinas y expeller de soja presentes en Uruguay. Se obtuvieron muestras de estos subproductos en distribuidores de alimentos para vacunos de la cuenca lechera uruguaya. Se analizó la composición química, degradabilidad ruminal in situ (determinando: fracción soluble, tasa de degradación y degradabilidad efectiva) y su fermentescibilidad in vitro. Se comparó la composición química y degradabilidad ruminal in situ de las muestras con la base de datos del programa NRC (NRC, 2001). Todos los resultados fueron comparados a través de un análisis de varianza. Las harinas presentaron menor contenido de extracto etéreo, materia orgánica y mayor contenido proteico (P<0,05), mayor tasa de degradación y degradabilidad efectiva in situ, además de una mayor tasa de producción de gas in vitro en comparación con los expeller (P<0,01). La degradabilidad ruminal in vitro no varió entre subproductos (P=0,432). La comparación de datos con la base del NRC (NRC, 2001) indicó una menor producción de leche (L/d) debido a una mayor degradabilidad ruminal de las harinas y expeller evaluados. En base a las diferencias encontradas entre la composición química y degradabilidad ruminal de los subproductos analizados y los datos incorporados en el programa (NRC, 2001) sería recomendable emplear datos nacionales a la hora de formular dietas. ------------------- SUMMARY.- The chemical composition and ruminal degradability of soybean by products can be affected by the industrial processes through which are obtained. The objective of this study was to determine the protein value for dairy cows of soybean meal and expeller present in Uruguay. Samples of soybean meal and expeller were taken from several Uruguayan suppliers. The chemical composition, in situ ruminal degradability (determining: soluble fraction, degradation rate and effective degradability) and its in vitro degradability of protein were analyzed. The chemical composition and in situ ruminal degradability of the samples were compared with the NRC (NRC, 2001) software database. All the results were compared through an analysis of variance. The soybean meal presented a lower content of ether extract and organic matter with a higher protein content (P<0.05), higher rate of degradation and effective degradability in situ, in addition to a higher rate of in vitro gas production when compared with expeller (P<0,01). In vitro ruminal degradability did not vary between byproducts (P=0.432). The results of the simulation indicate that the production is lower than that of which is predicted by the NRC (NRC, 2001), because to a higher protein degradability of soybean meal and expeller evaluated. Based on the differences found between the chemical composition and ruminal degradability of the byproducts analyzed and the data incorporated in the software (NRC, 2001), it would be advisable to use national data when formulating diets.
650 $aHARINA DE SOJA
650 $aPRODUCCION DE LECHE
653 $aExpeller
653 $aProteína degradable en rumen
653 $aRumen-degraded protein
653 $aSoybean meal
700 1 $aCAJARVILLE, C.
700 1 $aPÉREZ-RUCHEL, A.
700 1 $aHIRIGOYEN, D.
700 1 $aCONSTANTÍN, M.
700 1 $aGONZÁLEZ, V.
700 1 $aMADERA, J.
700 1 $aEIRALDI, F.
700 1 $aKOZLOSKI, G.V.
700 1 $aREPETTO, J.L.
773 $tVeterinaria (Montevideo), 2018$gv. 54, no. 209, p. 31-38. -- OPEN ACCESS.
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