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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
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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 La Estanzuela. |
Fecha actual : |
28/05/2019 |
Actualizado : |
05/09/2022 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
Circulación / Nivel : |
Internacional - -- |
Autor : |
KASPARY, T. E.; CUTTI, L.; BELLÉ, C.; CASAROTTO, G.; GROTH, M.Z; DA SILVA, G.B.P.; DE AGUIAR, A.C.M. |
Afiliación : |
TIAGO EDU KASPARY, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; LUAN CUTTI, Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Fitotecnia, 91540-000 Porto Alegre, Rio Grande do Sul, Brazil.; CRISTIANO BELLÉ, Universidade Federal de Santa Maria, Centro de Ciências Rurais, Departamento de Solos, 97105-900, Santa Maria, Rio Grande do Sul, Brazil.; GABRIELE CASAROTTO, Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Fitotecnia, 91540-000 Porto Alegre, Rio Grande do Sul, Brazil.; MÁRTIN ZANCHETT GROTH, Universidade Federal de Pelotas, Pós-Graduação em Ciência e Tecnologia de Sementes, Campus Capão do Leão s/n, Pelotas, Rio Grande do Sul, 96001-970, Brazil.; GERARDA BEATRIZ PINTO DA SILVA, Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Fitotecnia, Porto Alegre, Rio Grande do Sul, 91540-000, Brazil; ADALIN CEZAR MORAES DE AGUIAR, Universidade Federal de Viçosa, Programa de Pós-Graduação em Fitotecnia, Campus Universitário, Viçosa, Minas Gerais, 36570 900, Brazil. |
Título : |
Non-destructive analysis of photosynthetic pigments in Avena strigosa and Avena sative. |
Fecha de publicación : |
2019 |
Fuente / Imprenta : |
Australian Journal of Crop Science, 1 March 2019. volume 13, Issue 3, , Pages 354-359 [Open Access]. |
ISSN : |
1835-2707 |
DOI : |
10.21475/ajcs.19.13.03.p1149 |
Idioma : |
Inglés |
Contenido : |
Abstract:
Chlorophylls and carotenoids are the main photosynthetic pigments in plants. The photosynthetic potential of crop plants is used to determine the correct rate of nitrogen fertilization. To date, no studies have been conducted to understand the relationship between different methods of measurement of photosynthetic pigments in oats. The objective of this study was to quantify and compare the levels of photosynthetic pigments in Avena strigosa and A. sativa using two different methods, the extraction method and portable chlorophyll meter, and to determine whether the results of these two methods showed a significant correlation. Photosynthetic pigments were measured using both methods in a greenhouse and the laboratory at four developmental stages: tillering [28 days after sowing (DAS)], vegetative stage I (55 DAS), vegetative stage II (75 DAS), and reproductive stage (120 DAS). The same leaves were used to measure the relative chlorophyll content using a portable chlorophyll meter and extractable chlorophyll using the laboratory extraction method. The readings of the chlorophyll index differed for each developmental stage of both A. sativa and A. strigosa. The contents of chlorophyll a, chlorophyll b, and carotenoids determined using the extraction method showed high coefficients of correlation with the total chlorophyll index determined using the portable chlorophyll meter. Thus, the measurement of chlorophyll using the portable chlorophyll meter can be used for the accurate evaluation of the photosynthetic potential of oats, thus saving time and reagents. MenosAbstract:
Chlorophylls and carotenoids are the main photosynthetic pigments in plants. The photosynthetic potential of crop plants is used to determine the correct rate of nitrogen fertilization. To date, no studies have been conducted to understand the relationship between different methods of measurement of photosynthetic pigments in oats. The objective of this study was to quantify and compare the levels of photosynthetic pigments in Avena strigosa and A. sativa using two different methods, the extraction method and portable chlorophyll meter, and to determine whether the results of these two methods showed a significant correlation. Photosynthetic pigments were measured using both methods in a greenhouse and the laboratory at four developmental stages: tillering [28 days after sowing (DAS)], vegetative stage I (55 DAS), vegetative stage II (75 DAS), and reproductive stage (120 DAS). The same leaves were used to measure the relative chlorophyll content using a portable chlorophyll meter and extractable chlorophyll using the laboratory extraction method. The readings of the chlorophyll index differed for each developmental stage of both A. sativa and A. strigosa. The contents of chlorophyll a, chlorophyll b, and carotenoids determined using the extraction method showed high coefficients of correlation with the total chlorophyll index determined using the portable chlorophyll meter. Thus, the measurement of chlorophyll using the portable chlorophyll meter can be used for th... Presentar Todo |
Palabras claves : |
AVENA STRIGOSA SCHREB; CAROTENOIDS; CHLOROPHYLL; PORTABLE CHLOROPHYLL. |
Thesagro : |
AVENA SATIVA. |
Asunto categoría : |
L73 Enfermedades de los animales |
URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/12712/1/Kaspary-TE.-2019.-Australian-Jr.-Crop-Science.-Non-destructiveanalysisofphotosyntheticpigmentsinAvenastrigosaandAvenasativa.pdf
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Marc : |
LEADER 02441naa a2200277 a 4500 001 1059785 005 2022-09-05 008 2019 bl uuuu u00u1 u #d 022 $a1835-2707 024 7 $a10.21475/ajcs.19.13.03.p1149$2DOI 100 1 $aKASPARY, T. E. 245 $aNon-destructive analysis of photosynthetic pigments in Avena strigosa and Avena sative.$h[electronic resource] 260 $c2019 520 $aAbstract: Chlorophylls and carotenoids are the main photosynthetic pigments in plants. The photosynthetic potential of crop plants is used to determine the correct rate of nitrogen fertilization. To date, no studies have been conducted to understand the relationship between different methods of measurement of photosynthetic pigments in oats. The objective of this study was to quantify and compare the levels of photosynthetic pigments in Avena strigosa and A. sativa using two different methods, the extraction method and portable chlorophyll meter, and to determine whether the results of these two methods showed a significant correlation. Photosynthetic pigments were measured using both methods in a greenhouse and the laboratory at four developmental stages: tillering [28 days after sowing (DAS)], vegetative stage I (55 DAS), vegetative stage II (75 DAS), and reproductive stage (120 DAS). The same leaves were used to measure the relative chlorophyll content using a portable chlorophyll meter and extractable chlorophyll using the laboratory extraction method. The readings of the chlorophyll index differed for each developmental stage of both A. sativa and A. strigosa. The contents of chlorophyll a, chlorophyll b, and carotenoids determined using the extraction method showed high coefficients of correlation with the total chlorophyll index determined using the portable chlorophyll meter. Thus, the measurement of chlorophyll using the portable chlorophyll meter can be used for the accurate evaluation of the photosynthetic potential of oats, thus saving time and reagents. 650 $aAVENA SATIVA 653 $aAVENA STRIGOSA SCHREB 653 $aCAROTENOIDS 653 $aCHLOROPHYLL 653 $aPORTABLE CHLOROPHYLL 700 1 $aCUTTI, L. 700 1 $aBELLÉ, C. 700 1 $aCASAROTTO, G. 700 1 $aGROTH, M.Z 700 1 $aDA SILVA, G.B.P. 700 1 $aDE AGUIAR, A.C.M. 773 $tAustralian Journal of Crop Science, 1 March 2019. volume 13, Issue 3, , Pages 354-359 [Open Access].
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