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Registro completo
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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 : |
14/11/2015 |
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Actualizado : |
07/04/2017 |
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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 : |
LADO, J.; PASCUAL, M.; ZACARÍAS, L.; RODRIGO, M.J. |
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Afiliación : |
JOANNA LADO LINDNER, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
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Título : |
Efecto de la temperatura de conservación en el contenido de carotenoides y vitamina C en frutos de pomelo rojo. (Effect of Storage Temperature on Carotenoid and Vitamin C Content in Red Grapefruit.) |
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Fecha de publicación : |
2015 |
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Fuente / Imprenta : |
Agrociencia Uruguay, 2015, v.19, no.1, p. 48-56. |
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Idioma : |
Español |
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Contenido : |
RESUMEN.
Los carotenoides y la vitamina C son componentes importantes de la calidad nutricional y organoléptica en los frutos cítricos. Los frutos de pomelo rojo deben su coloración a la presencia de licopeno, un caroteno lineal de color rojo, tanto en la piel como en la pulpa, una característica muy inusual en los frutos cítricos. Esta propiedad le confiere a los frutos un interés especial dada la gran actividad antioxidante de este compuesto y sus posibles beneficios para la salud. La conservación refrigerada es una práctica habitual durante la postcosecha de los frutos cítricos. El objetivo de este estudio fue evaluar el efecto de la temperatura de conservación en el contenido de carotenoides y vitamina C en la piel y la pulpa de frutos de pomelo rojo Star Ruby (SR). Los resultados indican que los frutos almacenados hasta ocho semanas a 12 ºC alcanzan concentraciones de carotenoides
totales en la piel tres a cuatro veces superiores a las de los frutos mantenidos a 2 ºC. La mayor temperatura de almacenamiento (12 ºC) potenció la acumulación de los carotenos lineales (fitoeno, fitoflueno y licopeno) y se observó una disminución de los carotenoides derivados del licopeno (β-caroteno y xantofilas). De forma similar, el contenido en vitamina C se incrementó ligeramente en la piel de los frutos conservados a 12 ºC. Sin embargo, en la pulpa no hubo cambios significativos en el contenido de carotenoides ni de vitamina C en función de la temperatura de almacenamiento.
SUMMARY.
Carotenoids and vitamin C are important attributes that contribute to the organoleptic and nutritional quality in citrus fruits. The fruits of red grapefruit owe their colouration to the presence of lycopene, a red linear carotene, both in the peel and the pulp, a very unusual feature in citrus fruits. This property confers relevant nutritional interest due to its powerful antioxidant activity and possible health benefits of the fruit. Postharvest refrigerated storage is a common practice in citrus fruits. In this study, we evaluated the effect of storage temperature on carotenoids and vitamin C content in the pulp and the peel of red Star Ruby (SR) grapefruit. Results indicate that the fruit stored up to eight weeks at 12 °C reach concentrations of total carotenoids in the peel three to four times higher than fruits kept at 2 °C. The higher storage temperature (12 ºC) favored the accumulation of linear
carotenes (phytoene, phytofluene and lycopene) while decreased the level of carotenoids derived from lycopene (β-carotene and xanthophylls). Similarly, vitamin C content slightly increased in the peel of fruits stored at 12 ºC. However, no changes in carotenoid and vitamin C contents occurred in the pulp due to postharvest temperature. MenosRESUMEN.
Los carotenoides y la vitamina C son componentes importantes de la calidad nutricional y organoléptica en los frutos cítricos. Los frutos de pomelo rojo deben su coloración a la presencia de licopeno, un caroteno lineal de color rojo, tanto en la piel como en la pulpa, una característica muy inusual en los frutos cítricos. Esta propiedad le confiere a los frutos un interés especial dada la gran actividad antioxidante de este compuesto y sus posibles beneficios para la salud. La conservación refrigerada es una práctica habitual durante la postcosecha de los frutos cítricos. El objetivo de este estudio fue evaluar el efecto de la temperatura de conservación en el contenido de carotenoides y vitamina C en la piel y la pulpa de frutos de pomelo rojo Star Ruby (SR). Los resultados indican que los frutos almacenados hasta ocho semanas a 12 ºC alcanzan concentraciones de carotenoides
totales en la piel tres a cuatro veces superiores a las de los frutos mantenidos a 2 ºC. La mayor temperatura de almacenamiento (12 ºC) potenció la acumulación de los carotenos lineales (fitoeno, fitoflueno y licopeno) y se observó una disminución de los carotenoides derivados del licopeno (β-caroteno y xantofilas). De forma similar, el contenido en vitamina C se incrementó ligeramente en la piel de los frutos conservados a 12 ºC. Sin embargo, en la pulpa no hubo cambios significativos en el contenido de carotenoides ni de vitamina C en función de la temperatura de almacenamiento.
SUMMA... Presentar Todo |
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Palabras claves : |
ASCORBIC ACID; CAROTENOIDS; CITRUS FRUITS; POSTHARVEST. |
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Thesagro : |
ACIDO ASCORBICO; CAROTENOIDES; CITRUS; FRUTOS CITRICOS; STAR RUBY; TECNOLOGIA POSCOSECHA. |
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Asunto categoría : |
F01 Cultivo |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/5191/1/Lado-J.-2015.-Agrociencia-v.191-p.48-56.pdf
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Marc : |
LEADER 03638naa a2200277 a 4500
001 1053882
005 2017-04-07
008 2015 bl uuuu u00u1 u #d
100 1 $aLADO, J.
245 $aEfecto de la temperatura de conservación en el contenido de carotenoides y vitamina C en frutos de pomelo rojo. (Effect of Storage Temperature on Carotenoid and Vitamin C Content in Red Grapefruit.)
260 $c2015
520 $aRESUMEN. Los carotenoides y la vitamina C son componentes importantes de la calidad nutricional y organoléptica en los frutos cítricos. Los frutos de pomelo rojo deben su coloración a la presencia de licopeno, un caroteno lineal de color rojo, tanto en la piel como en la pulpa, una característica muy inusual en los frutos cítricos. Esta propiedad le confiere a los frutos un interés especial dada la gran actividad antioxidante de este compuesto y sus posibles beneficios para la salud. La conservación refrigerada es una práctica habitual durante la postcosecha de los frutos cítricos. El objetivo de este estudio fue evaluar el efecto de la temperatura de conservación en el contenido de carotenoides y vitamina C en la piel y la pulpa de frutos de pomelo rojo Star Ruby (SR). Los resultados indican que los frutos almacenados hasta ocho semanas a 12 ºC alcanzan concentraciones de carotenoides totales en la piel tres a cuatro veces superiores a las de los frutos mantenidos a 2 ºC. La mayor temperatura de almacenamiento (12 ºC) potenció la acumulación de los carotenos lineales (fitoeno, fitoflueno y licopeno) y se observó una disminución de los carotenoides derivados del licopeno (β-caroteno y xantofilas). De forma similar, el contenido en vitamina C se incrementó ligeramente en la piel de los frutos conservados a 12 ºC. Sin embargo, en la pulpa no hubo cambios significativos en el contenido de carotenoides ni de vitamina C en función de la temperatura de almacenamiento. SUMMARY. Carotenoids and vitamin C are important attributes that contribute to the organoleptic and nutritional quality in citrus fruits. The fruits of red grapefruit owe their colouration to the presence of lycopene, a red linear carotene, both in the peel and the pulp, a very unusual feature in citrus fruits. This property confers relevant nutritional interest due to its powerful antioxidant activity and possible health benefits of the fruit. Postharvest refrigerated storage is a common practice in citrus fruits. In this study, we evaluated the effect of storage temperature on carotenoids and vitamin C content in the pulp and the peel of red Star Ruby (SR) grapefruit. Results indicate that the fruit stored up to eight weeks at 12 °C reach concentrations of total carotenoids in the peel three to four times higher than fruits kept at 2 °C. The higher storage temperature (12 ºC) favored the accumulation of linear carotenes (phytoene, phytofluene and lycopene) while decreased the level of carotenoids derived from lycopene (β-carotene and xanthophylls). Similarly, vitamin C content slightly increased in the peel of fruits stored at 12 ºC. However, no changes in carotenoid and vitamin C contents occurred in the pulp due to postharvest temperature.
650 $aACIDO ASCORBICO
650 $aCAROTENOIDES
650 $aCITRUS
650 $aFRUTOS CITRICOS
650 $aSTAR RUBY
650 $aTECNOLOGIA POSCOSECHA
653 $aASCORBIC ACID
653 $aCAROTENOIDS
653 $aCITRUS FRUITS
653 $aPOSTHARVEST
700 1 $aPASCUAL, M.
700 1 $aZACARÍAS, L.
700 1 $aRODRIGO, M.J.
773 $tAgrociencia Uruguay, 2015$gv.19, no.1, p. 48-56.
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