| |
|
|
|
Registro completo
|
|
Biblioteca (s) : |
INIA La Estanzuela. |
|
Fecha : |
21/02/2014 |
|
Actualizado : |
05/12/2018 |
|
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
|
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. |
|
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. |
|
Título : |
Ascertainment bias from imputation methods evaluation in wheat. |
|
Fecha de publicación : |
2016 |
|
Fuente / Imprenta : |
BMC Genomics, 2016, v. 17, p.773. |
|
DOI : |
10.1186/s12864-016-3120-5 |
|
Idioma : |
Inglés |
|
Notas : |
OPEN ACCESS. Article history: Received 2016 Feb 24 // Accepted 2016 Sep 23. |
|
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 |
|
Palabras claves : |
FALSE POSITIVE; FALSO POSITIVO; GBS; GWAS; POWER; QTLs. |
|
Thesagro : |
MEJORAMIENTO DE TRIGO. |
|
Asunto categoría : |
F30 Genética vegetal y fitomejoramiento |
|
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
|
|
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.
Descargar
Esconder MarcPresentar Marc Completo |
|
Registro original : |
INIA La Estanzuela (LE) |
|
|
Biblioteca
|
Identificación
|
Origen
|
Tipo / Formato
|
Clasificación
|
Cutter
|
Registro
|
Volumen
|
Estado
|
Volver
|
|
|
 | Acceso al texto completo restringido a Biblioteca INIA Treinta y Tres. Por información adicional contacte bibliott@inia.org.uy. |
|
Registro completo
|
|
Biblioteca (s) : |
INIA Treinta y Tres. |
|
Fecha actual : |
29/04/2019 |
|
Actualizado : |
11/10/2019 |
|
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
|
Circulación / Nivel : |
-- - -- |
|
Autor : |
MARESCA, S.; LÓPEZ VALIENTE, S.; RODRÍGUEZ A.M.; TESTA, L.M.; LONG, N. M.; QUINTANS, G.; PAVAN, E. |
|
Afiliación : |
SEBASTIÁN MARESCA, Instituto Nacional de Tecnología Agropecuaria, Cuenca del Salado Experimental Station. Argentina.; SEBASTIÁN LÓPEZ VALIENTE, Instituto Nacional de Tecnología Agropecuaria, Cuenca del Salado Experimental Station. Argentina.; ALEJANDRO M. RODRÍGUEZ, Instituto Nacional de Tecnología Agropecuaria, Cuenca del Salado Experimental Station. Argentina.; LAURA M. TESTA, Instituto Nacional de Tecnología Agropecuaria, Balcarse Experimental Station. Argentina.; NATHAN M. LONG, Department of Animal Veterinary Science, Clemson University, USA.; GRACIELA QUINTANS ILARIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ENRIQUE PAVAN, Instituto Nacional de Tecnología Agropecuaria, Balcarse Experimental Station. Argentina. |
|
Título : |
The influence of protein restriction during mid- to late gestation on beef offspring growth, carcass characteristic and meat quality. |
|
Fecha de publicación : |
2019 |
|
Fuente / Imprenta : |
Meat Science, 2019. v.153, p. 103-108. |
|
DOI : |
10.1016/j.meatsci.2019.03.014 |
|
Idioma : |
Inglés |
|
Notas : |
Article history :Received 22 May 2018; Received in revised form 20 February 2019; Accepted 20 March 2019. Available online 21 March 2019. |
|
Contenido : |
Abstract:
The objective of this study was to determine whether crude protein intake during the last three months of gestation affects growth performance, carcass characteristics and meat quality of steer progeny. At 134 ± 14 d of gestation, 68 multiparous Angus cows were blocked by BW and expected calving date and randomly assigned to diets that contained either low or high dietary crude protein concentrations and were allotted in 12 pens per treatment. After calving, cows were managed together on improved pastures during lactation. After weaning at 219 ± 13 d of age, steers calves were stockered on natural pastures until 687 ± 13 d of age then placed into a feedlot for 83d before slaughter. Maternal dietary protein concentration had no influence on offspring body weight and growth rate during rearing or finishing phases (P > .10). Rib fat thickness of steers was not affected (P = .38) by maternal nutrition treatments, however, LM area was greater in HP steers than LP steers at entrance into the feedlot (P = .01) and end of finishing phase (P = .04). Hot carcass weight was similar between treatments (P = .69), however dressing percentage was increased in HP relative to LP steers (P = .01). Tenderness of Longissimus muscle was increased in HP compared to LP steers after 3 and 14d
(P < .001) of aging. No treatment differences in troponin-t degradation (P = .77) and collagen content (P = .58) were observed. Muscle fiber diameter was similar in LP and HP steers (P = .20), suggesting that increase of LM area in HP steers could be due to muscle hyperplasia. These data indicated that level of protein during mid to late gestation does not affect offspring growth but has impacts on carcass composition and meat quality of steer progeny. MenosAbstract:
The objective of this study was to determine whether crude protein intake during the last three months of gestation affects growth performance, carcass characteristics and meat quality of steer progeny. At 134 ± 14 d of gestation, 68 multiparous Angus cows were blocked by BW and expected calving date and randomly assigned to diets that contained either low or high dietary crude protein concentrations and were allotted in 12 pens per treatment. After calving, cows were managed together on improved pastures during lactation. After weaning at 219 ± 13 d of age, steers calves were stockered on natural pastures until 687 ± 13 d of age then placed into a feedlot for 83d before slaughter. Maternal dietary protein concentration had no influence on offspring body weight and growth rate during rearing or finishing phases (P > .10). Rib fat thickness of steers was not affected (P = .38) by maternal nutrition treatments, however, LM area was greater in HP steers than LP steers at entrance into the feedlot (P = .01) and end of finishing phase (P = .04). Hot carcass weight was similar between treatments (P = .69), however dressing percentage was increased in HP relative to LP steers (P = .01). Tenderness of Longissimus muscle was increased in HP compared to LP steers after 3 and 14d
(P < .001) of aging. No treatment differences in troponin-t degradation (P = .77) and collagen content (P = .58) were observed. Muscle fiber diameter was similar in LP and HP steers (P = .20), sugges... Presentar Todo |
|
Palabras claves : |
RESTRICCIÓN NUTRICIONAL; RESTRICCIÓN PROTEICA; RESTRICCIONES EN GESTACIÓN. |
|
Thesagro : |
BOVINOS DE CARNE; GESTACION. |
|
Asunto categoría : |
L02 Alimentación animal |
|
Marc : |
LEADER 02742naa a2200277 a 4500
001 1059746
005 2019-10-11
008 2019 bl uuuu u00u1 u #d
024 7 $a10.1016/j.meatsci.2019.03.014$2DOI
100 1 $aMARESCA, S.
245 $aThe influence of protein restriction during mid- to late gestation on beef offspring growth, carcass characteristic and meat quality.$h[electronic resource]
260 $c2019
500 $aArticle history :Received 22 May 2018; Received in revised form 20 February 2019; Accepted 20 March 2019. Available online 21 March 2019.
520 $aAbstract: The objective of this study was to determine whether crude protein intake during the last three months of gestation affects growth performance, carcass characteristics and meat quality of steer progeny. At 134 ± 14 d of gestation, 68 multiparous Angus cows were blocked by BW and expected calving date and randomly assigned to diets that contained either low or high dietary crude protein concentrations and were allotted in 12 pens per treatment. After calving, cows were managed together on improved pastures during lactation. After weaning at 219 ± 13 d of age, steers calves were stockered on natural pastures until 687 ± 13 d of age then placed into a feedlot for 83d before slaughter. Maternal dietary protein concentration had no influence on offspring body weight and growth rate during rearing or finishing phases (P > .10). Rib fat thickness of steers was not affected (P = .38) by maternal nutrition treatments, however, LM area was greater in HP steers than LP steers at entrance into the feedlot (P = .01) and end of finishing phase (P = .04). Hot carcass weight was similar between treatments (P = .69), however dressing percentage was increased in HP relative to LP steers (P = .01). Tenderness of Longissimus muscle was increased in HP compared to LP steers after 3 and 14d (P < .001) of aging. No treatment differences in troponin-t degradation (P = .77) and collagen content (P = .58) were observed. Muscle fiber diameter was similar in LP and HP steers (P = .20), suggesting that increase of LM area in HP steers could be due to muscle hyperplasia. These data indicated that level of protein during mid to late gestation does not affect offspring growth but has impacts on carcass composition and meat quality of steer progeny.
650 $aBOVINOS DE CARNE
650 $aGESTACION
653 $aRESTRICCIÓN NUTRICIONAL
653 $aRESTRICCIÓN PROTEICA
653 $aRESTRICCIONES EN GESTACIÓN
700 1 $aLÓPEZ VALIENTE, S.
700 1 $aRODRÍGUEZ A.M.
700 1 $aTESTA, L.M.
700 1 $aLONG, N. M.
700 1 $aQUINTANS, G.
700 1 $aPAVAN, E.
773 $tMeat Science, 2019.$gv.153, p. 103-108.
Descargar
Esconder MarcPresentar Marc Completo |
|
Registro original : |
INIA Treinta y Tres (TT) |
|
|
Biblioteca
|
Identificación
|
Origen
|
Tipo / Formato
|
Clasificación
|
Cutter
|
Registro
|
Volumen
|
Estado
|
Volver
|
| Expresión de búsqueda válido. Check! |
|
|
