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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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 | Acceso al texto completo restringido a Biblioteca INIA Las Brujas. Por información adicional contacte bibliolb@inia.org.uy. |
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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha actual : |
17/10/2014 |
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Actualizado : |
06/02/2020 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Circulación / Nivel : |
A - 2 |
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Autor : |
BLUMETTO, O.; OLIVAS, I.; TORRES, A.G.; VILLAGRA, A. |
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Afiliación : |
OSCAR RICARDO BLUMETTO VELAZCO, Instituto Nacional de Investigación Agropecuaria (INIA), Uruguay. |
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Título : |
Use of straw and wood shavings as nest material in primiparous does. |
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Fecha de publicación : |
2010 |
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Fuente / Imprenta : |
World Rabbit Science, 2010, v.18, No.4, p.237-242. |
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ISSN : |
1257-5011 |
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DOI : |
10.4995/wrs.2010.776 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received January 2010 / Accepted July 2010. |
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Contenido : |
ABSTRACT.
In rabbit production, several materials such as hay, straw, wood shavings or waste wool and cotton are used as nesting materials during parturition. In this work, straw and wood shavings were studied as potential materials for nest boxes, and a choice test was designed for this purpose. Two replicates of 30 primiparous does each were carried out. Does were housed 10 d before parturition in a double commercial cage, so each doe had access to 2 different nest boxes. One of the nests was filled with 8 cm of barley straw and the other with 8 cm of wood shavings, so the doe could choose which of them she prepared and gave birth in. During the 24 h prior to parturition, the state of the nest was assessed, according to the mixing of the material and the doe's hair and the preservation of the original material, as well as the chosen nest box. When the does gave birth, the number of live and dead newborn was recorded. In the first replicate, 87% of the does chose the straw nest box, while in the second replicate 93% of the does did so. The number of live kits at birth did not differ statistically for straw and wood shavings nests (8.36±1.74 vs. 6.85±3.44), but litters reared in straw reacted a higher size at weaning (7.98±1.73 vs. 6.29±3 35; P<0.05). Finally, all the nests achieved a good level of mixing between the original material and the hair of the doe and only 5% of the does removed the original material (regardless of whether it was straw or wood shavings) and made the nest only with their hair. In conclusion, our results suggest that does might have a strong preference for straw rather than wood shavings as nest material.
© WRSA UPV 2003. MenosABSTRACT.
In rabbit production, several materials such as hay, straw, wood shavings or waste wool and cotton are used as nesting materials during parturition. In this work, straw and wood shavings were studied as potential materials for nest boxes, and a choice test was designed for this purpose. Two replicates of 30 primiparous does each were carried out. Does were housed 10 d before parturition in a double commercial cage, so each doe had access to 2 different nest boxes. One of the nests was filled with 8 cm of barley straw and the other with 8 cm of wood shavings, so the doe could choose which of them she prepared and gave birth in. During the 24 h prior to parturition, the state of the nest was assessed, according to the mixing of the material and the doe's hair and the preservation of the original material, as well as the chosen nest box. When the does gave birth, the number of live and dead newborn was recorded. In the first replicate, 87% of the does chose the straw nest box, while in the second replicate 93% of the does did so. The number of live kits at birth did not differ statistically for straw and wood shavings nests (8.36±1.74 vs. 6.85±3.44), but litters reared in straw reacted a higher size at weaning (7.98±1.73 vs. 6.29±3 35; P<0.05). Finally, all the nests achieved a good level of mixing between the original material and the hair of the doe and only 5% of the does removed the original material (regardless of whether it was straw or wood shavings) and made ... Presentar Todo |
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Palabras claves : |
Behaviour; Nest material; Preference; Rabbit husbandry. |
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Thesagro : |
CONEJO; CONEJOS (ORYCTOLAGUS). |
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Asunto categoría : |
L01 Ganadería |
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Marc : |
LEADER 02453naa a2200265 a 4500
001 1051176
005 2020-02-06
008 2010 bl uuuu u00u1 u #d
022 $a1257-5011
024 7 $a10.4995/wrs.2010.776$2DOI
100 1 $aBLUMETTO, O.
245 $aUse of straw and wood shavings as nest material in primiparous does.$h[electronic resource]
260 $c2010
500 $aArticle history: Received January 2010 / Accepted July 2010.
520 $aABSTRACT. In rabbit production, several materials such as hay, straw, wood shavings or waste wool and cotton are used as nesting materials during parturition. In this work, straw and wood shavings were studied as potential materials for nest boxes, and a choice test was designed for this purpose. Two replicates of 30 primiparous does each were carried out. Does were housed 10 d before parturition in a double commercial cage, so each doe had access to 2 different nest boxes. One of the nests was filled with 8 cm of barley straw and the other with 8 cm of wood shavings, so the doe could choose which of them she prepared and gave birth in. During the 24 h prior to parturition, the state of the nest was assessed, according to the mixing of the material and the doe's hair and the preservation of the original material, as well as the chosen nest box. When the does gave birth, the number of live and dead newborn was recorded. In the first replicate, 87% of the does chose the straw nest box, while in the second replicate 93% of the does did so. The number of live kits at birth did not differ statistically for straw and wood shavings nests (8.36±1.74 vs. 6.85±3.44), but litters reared in straw reacted a higher size at weaning (7.98±1.73 vs. 6.29±3 35; P<0.05). Finally, all the nests achieved a good level of mixing between the original material and the hair of the doe and only 5% of the does removed the original material (regardless of whether it was straw or wood shavings) and made the nest only with their hair. In conclusion, our results suggest that does might have a strong preference for straw rather than wood shavings as nest material. © WRSA UPV 2003.
650 $aCONEJO
650 $aCONEJOS (ORYCTOLAGUS)
653 $aBehaviour
653 $aNest material
653 $aPreference
653 $aRabbit husbandry
700 1 $aOLIVAS, I.
700 1 $aTORRES, A.G.
700 1 $aVILLAGRA, A.
773 $tWorld Rabbit Science, 2010$gv.18, No.4, p.237-242.
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