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| Acceso al texto completo restringido a Biblioteca INIA Las Brujas. Por información adicional contacte bibliolb@inia.org.uy. |
Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
Fecha : |
18/12/2017 |
Actualizado : |
15/10/2019 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
Autor : |
LOURENCO, D.A.L.; FRAGOMENI, B.O.; BRADFORD, H.L.; MENEZES I.R.; FERRAZ, J.B.S.; AGUILAR, I.; MISZTAL, I. |
Afiliación : |
D.A.L. LOURENCO, Universidad de Georgia (UG); B.O. FRAGOMENI, Universidad de Georgia (UG); H.L. BRADFORD, Universidad de Georgia (UG); I.R. MENEZES, FZEA, University of Sao Paulo.; J.B.S. FERRAZ, FZEA, University of Sao Paulo.; IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; I. MISZTAL, Universidad de Georgia (UG). |
Título : |
Implications of SNP weighting on single-step genomic predictions for different reference population sizes. |
Fecha de publicación : |
2017 |
Fuente / Imprenta : |
Journal of Animal Breeding and Genetics, 2017, v. 134 (6), p. 463-471. |
DOI : |
10.1111/jbg.12288 |
Idioma : |
Inglés |
Notas : |
Article history: Received: 28 February 2017 / Accepted: 19 July 2017.
This study was partially funded by the American Angus Association (St. Joseph, MO), Zoetis (Kalamazoo, MI) and by Agriculture and Food Research Initiative Competitive Grants no. 2015-67015-22936 from the US Department of Agriculture's National Institute of Food and Agriculture. We gratefully acknowledge the very helpful comments by the two anonymous reviewers, and we thank Andra H. Nelson for assisting with data analysis. |
Contenido : |
ABSTRACT.
We investigated the importance of SNP weighting in populations with 2,000 to 25,000 genotyped animals. Populations were simulated with two effective sizes (20 or 100) and three numbers of QTL (10, 50 or 500). Pedigree information was available for six generations; phenotypes were recorded for the four middle generations. Animals from the last three generations were genotyped for 45,000 SNP. Single-step genomic BLUP (ssGBLUP) and weighted ssGBLUP (WssGBLUP) were used to estimate genomic EBV using a genomic relationship matrix (G). The WssGBLUP performed better in small genotyped populations; however, any advantage for WssGBLUP was reduced or eliminated when more animals were genotyped. WssGBLUP had greater resolution for genome-wide association (GWA) as did increasing the number of genotyped animals. For few QTL, accuracy was greater for WssGBLUP than ssGBLUP; however, for many QTL, accuracy was the same for both methods. The largest genotyped set was used to assess the dimensionality of genomic information (number of effective SNP). The number of effective SNP was considerably less in weighted G than in unweighted G. Once the number of independent SNP is well represented in the genotyped population, the impact of SNP weighting becomes less important.
© 2017 Blackwell Verlag GmbH |
Palabras claves : |
ACCURAY; BAYES B; SNP WEIGHTING; VARIABLE SELECTION; WEIGTED SSGBLUP. |
Asunto categoría : |
-- |
Marc : |
LEADER 02612naa a2200277 a 4500 001 1057902 005 2019-10-15 008 2017 bl uuuu u00u1 u #d 024 7 $a10.1111/jbg.12288$2DOI 100 1 $aLOURENCO, D.A.L. 245 $aImplications of SNP weighting on single-step genomic predictions for different reference population sizes.$h[electronic resource] 260 $c2017 500 $aArticle history: Received: 28 February 2017 / Accepted: 19 July 2017. This study was partially funded by the American Angus Association (St. Joseph, MO), Zoetis (Kalamazoo, MI) and by Agriculture and Food Research Initiative Competitive Grants no. 2015-67015-22936 from the US Department of Agriculture's National Institute of Food and Agriculture. We gratefully acknowledge the very helpful comments by the two anonymous reviewers, and we thank Andra H. Nelson for assisting with data analysis. 520 $aABSTRACT. We investigated the importance of SNP weighting in populations with 2,000 to 25,000 genotyped animals. Populations were simulated with two effective sizes (20 or 100) and three numbers of QTL (10, 50 or 500). Pedigree information was available for six generations; phenotypes were recorded for the four middle generations. Animals from the last three generations were genotyped for 45,000 SNP. Single-step genomic BLUP (ssGBLUP) and weighted ssGBLUP (WssGBLUP) were used to estimate genomic EBV using a genomic relationship matrix (G). The WssGBLUP performed better in small genotyped populations; however, any advantage for WssGBLUP was reduced or eliminated when more animals were genotyped. WssGBLUP had greater resolution for genome-wide association (GWA) as did increasing the number of genotyped animals. For few QTL, accuracy was greater for WssGBLUP than ssGBLUP; however, for many QTL, accuracy was the same for both methods. The largest genotyped set was used to assess the dimensionality of genomic information (number of effective SNP). The number of effective SNP was considerably less in weighted G than in unweighted G. Once the number of independent SNP is well represented in the genotyped population, the impact of SNP weighting becomes less important. © 2017 Blackwell Verlag GmbH 653 $aACCURAY 653 $aBAYES B 653 $aSNP WEIGHTING 653 $aVARIABLE SELECTION 653 $aWEIGTED SSGBLUP 700 1 $aFRAGOMENI, B.O. 700 1 $aBRADFORD, H.L. 700 1 $aMENEZES I.R. 700 1 $aFERRAZ, J.B.S. 700 1 $aAGUILAR, I. 700 1 $aMISZTAL, I. 773 $tJournal of Animal Breeding and Genetics, 2017$gv. 134 (6), p. 463-471.
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| Acceso al texto completo restringido a Biblioteca INIA La Estanzuela. Por información adicional contacte bib_le@inia.org.uy. |
Registro completo
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Biblioteca (s) : |
INIA La Estanzuela. |
Fecha actual : |
06/09/2021 |
Actualizado : |
25/04/2022 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
Circulación / Nivel : |
Internacional - -- |
Autor : |
CLAVIJO, F.; CURLAND, R.D.; CROCE, V.; LAPAZ, M.I.; DILL-MACKY, R.; PEREYRA, S.; SIRI, M.I. |
Afiliación : |
FELIPE CLAVIJO,, Universidad de la República Facultad de Química, 201894, Área Microbiología, Departamento de Biociencias, Montevideo, Montevideo, Uruguay.; REBECCA D. CURLAND,, University of Minnesota System, 311816, Plant Pathology, Minneapolis, Minnesota, United States.; VALENTINA CROCE, Universidad de la República Facultad de Química, 201894, Área Microbiología, Departamento de Biociencias, Montevideo, Montevideo, Uruguay.; MARÍA INÉS LAPAZ, Universidad de la República Facultad de Química, 201894, Área Microbiología, Departamento de Biociencias, Montevideo, Montevideo, Uruguay.; RUTH DILL-MACKY, University of Minnesota System, 311816, Plant Pathology, Minneapolis, Minnesota, United States.; SILVIA ANTONIA PEREYRA CORREA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; MARÍA INÉS INÉS SIRI, Universidad de la República Facultad de Química, 201894, Área Microbiología, Departamento de Biociencias, Montevideo, Montevideo, Uruguay. |
Título : |
Genetic and phenotypic characterization of Xanthomonas species pathogenic of wheat in Uruguay. |
Fecha de publicación : |
2022 |
Fuente / Imprenta : |
Phytopathology, March 2022, vol. 112 (3): 511-520. Doi: https://doi.org/10.1094/PHYTO-06-21-0231-R |
ISSN : |
e-ISSN:1943-7684 |
DOI : |
10.1094/PHYTO-06-21-0231-R |
Idioma : |
Inglés |
Notas : |
Article history: Accepted for publication/ Posted online on 12 Aug 2021, First Look. |
Contenido : |
Abstract: Bacterial diseases affecting wheat production in Uruguay are an issue of growing concern yet remain largely uninvestigated in the region. Surveys of 61 wheat fields carried out from 2017 to 2019 yielded a regional collection of 63 strains identified by 16S rRNA gene analysis as Xanthomonas spp. A real-time PCR protocol using species-specific primers previously reported allowed the identification of 44 strains as X. translucens, the causal agent of bacterial leaf streak (BLS) in wheat and other cereal crops. Multilocus sequence analysis (MLSA) of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD) revealed that these strains were most closely related to X. translucens pv. undulosa, the pathovar that is most commonly associated with BLS of wheat. Multilocus sequence typing (MLST) was applied to examine the genetic diversity among X. translucens strains. Strains were assigned to four different sequence types, three of which have been previously reported globally. Additionally, 17 Xanthomonas strains not belonging to X. translucens were obtained from diseased wheat leaves. Phylogenetic analysis showed that these strains are closely related to Xanthomonas prunicola, and clustered together with previously uncharacterized Xanthomonas strains isolated from wheat in Minnesota, US. In planta pathogenicity assays carried out on a BLS susceptible wheat cultivar showed that X. translucens pv. undulosa strains caused brown necrosis symptoms typical of BLS, while non-translucens Xanthomonas sp. strains elicited an atypical symptom of dry necrosis. These findings suggest that local wheat fields are affected by X. translucens pv. undulosa, and by a new wheat pathogen within the Xanthomonas genus. MenosAbstract: Bacterial diseases affecting wheat production in Uruguay are an issue of growing concern yet remain largely uninvestigated in the region. Surveys of 61 wheat fields carried out from 2017 to 2019 yielded a regional collection of 63 strains identified by 16S rRNA gene analysis as Xanthomonas spp. A real-time PCR protocol using species-specific primers previously reported allowed the identification of 44 strains as X. translucens, the causal agent of bacterial leaf streak (BLS) in wheat and other cereal crops. Multilocus sequence analysis (MLSA) of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD) revealed that these strains were most closely related to X. translucens pv. undulosa, the pathovar that is most commonly associated with BLS of wheat. Multilocus sequence typing (MLST) was applied to examine the genetic diversity among X. translucens strains. Strains were assigned to four different sequence types, three of which have been previously reported globally. Additionally, 17 Xanthomonas strains not belonging to X. translucens were obtained from diseased wheat leaves. Phylogenetic analysis showed that these strains are closely related to Xanthomonas prunicola, and clustered together with previously uncharacterized Xanthomonas strains isolated from wheat in Minnesota, US. In planta pathogenicity assays carried out on a BLS susceptible wheat cultivar showed that X. translucens pv. undulosa strains caused brown necrosis symptoms typical of BLS, while non-translucens... Presentar Todo |
Palabras claves : |
Bacterial leaf streak; Bacterial Pathogens; Multilocus sequence analysis and typing; POPULATION BIOLOGY; WHEAT; Xanthomonas. |
Thesagro : |
FITOPATOLOGIA; TRIGO; TRITICUM AESTIVUM; URUGUAY. |
Asunto categoría : |
H20 Enfermedades de las plantas |
Marc : |
LEADER 02834naa a2200349 a 4500 001 1062388 005 2022-04-25 008 2022 bl uuuu u00u1 u #d 022 $ae-ISSN:1943-7684 024 7 $a10.1094/PHYTO-06-21-0231-R$2DOI 100 1 $aCLAVIJO, F. 245 $aGenetic and phenotypic characterization of Xanthomonas species pathogenic of wheat in Uruguay.$h[electronic resource] 260 $c2022 500 $aArticle history: Accepted for publication/ Posted online on 12 Aug 2021, First Look. 520 $aAbstract: Bacterial diseases affecting wheat production in Uruguay are an issue of growing concern yet remain largely uninvestigated in the region. Surveys of 61 wheat fields carried out from 2017 to 2019 yielded a regional collection of 63 strains identified by 16S rRNA gene analysis as Xanthomonas spp. A real-time PCR protocol using species-specific primers previously reported allowed the identification of 44 strains as X. translucens, the causal agent of bacterial leaf streak (BLS) in wheat and other cereal crops. Multilocus sequence analysis (MLSA) of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD) revealed that these strains were most closely related to X. translucens pv. undulosa, the pathovar that is most commonly associated with BLS of wheat. Multilocus sequence typing (MLST) was applied to examine the genetic diversity among X. translucens strains. Strains were assigned to four different sequence types, three of which have been previously reported globally. Additionally, 17 Xanthomonas strains not belonging to X. translucens were obtained from diseased wheat leaves. Phylogenetic analysis showed that these strains are closely related to Xanthomonas prunicola, and clustered together with previously uncharacterized Xanthomonas strains isolated from wheat in Minnesota, US. In planta pathogenicity assays carried out on a BLS susceptible wheat cultivar showed that X. translucens pv. undulosa strains caused brown necrosis symptoms typical of BLS, while non-translucens Xanthomonas sp. strains elicited an atypical symptom of dry necrosis. These findings suggest that local wheat fields are affected by X. translucens pv. undulosa, and by a new wheat pathogen within the Xanthomonas genus. 650 $aFITOPATOLOGIA 650 $aTRIGO 650 $aTRITICUM AESTIVUM 650 $aURUGUAY 653 $aBacterial leaf streak 653 $aBacterial Pathogens 653 $aMultilocus sequence analysis and typing 653 $aPOPULATION BIOLOGY 653 $aWHEAT 653 $aXanthomonas 700 1 $aCURLAND, R.D. 700 1 $aCROCE, V. 700 1 $aLAPAZ, M.I. 700 1 $aDILL-MACKY, R. 700 1 $aPEREYRA, S. 700 1 $aSIRI, M.I. 773 $tPhytopathology, March 2022, vol. 112 (3): 511-520. Doi: https://doi.org/10.1094/PHYTO-06-21-0231-R
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