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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha : |
23/05/2016 |
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Actualizado : |
11/12/2018 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
MASUDA, Y.; MISZTAL, I.; TSURUTA, S.; LEGARRA, A.; AGUILAR, I.; LOURENCO, D.A.L.; FRAGOMENI, B.O.; LAWLOR, T.J. |
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Afiliación : |
Department of Animal and Dairy Science, University of Georgia; Department of Animal and Dairy Science, University of Georgia; Department of Animal and Dairy Science, University of Georgia; INRA (Institut National de la Recherche Agronomique); IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; Department of Animal and Dairy Science, University of Georgia; Department of Animal and Dairy Science, University of Georgia; Holstein Association USA Inc. |
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Título : |
Implementation of genomic recursions in single-step genomic best linear unbiased predictor for US Holsteins with a large number of genotyped animals. |
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Fecha de publicación : |
2016 |
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Fuente / Imprenta : |
Journal of Dairy Science, 2016, v.99, no.3, p.1968-1974. OPEN ACCESS |
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DOI : |
10.3168/jds.2015-10540 |
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Idioma : |
Inglés |
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Notas : |
OPEN ACCESS. Received 19 October 2015, Accepted 1 December 2015, Available online 21 January 2016 |
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Contenido : |
ABSTRACT.
The objectives of this study were to develop and evaluate an efficient implementation in the computation of the inverse of genomic relationship matrix with the recursion algorithm, called the algorithm for proven and young (APY), in single-step genomic BLUP. We validated genomic predictions for young bulls with more than 500,000 genotyped animals in final score for US Holsteins. Phenotypic data included 11,626,576 final scores on 7,093,380 US Holstein cows, and genotypes were available for 569,404 animals. Daughter deviations for young bulls with no classified daughters in 2009, but at least 30 classified daughters in 2014 were computed using all the phenotypic data. Genomic predictions for the same bulls were calculated with single-step genomic BLUP using phenotypes up to 2009. We calculated the inverse of the genomic relationship matrix View the MathML source based on a direct inversion of genomic relationship matrix on a small subset of genotyped animals (core animals) and extended that information to noncore animals by recursion. We tested several sets of core animals including 9,406 bulls with at least 1 classified daughter, 9,406 bulls and 1,052 classified dams of bulls, 9,406 bulls and 7,422 classified cows, and random samples of 5,000 to 30,000 animals. Validation reliability was assessed by the coefficient of determination from regression of daughter deviation on genomic predictions for the predicted young bulls. The reliabilities were 0.39 with 5,000 randomly chosen core animals, 0.45 with the 9,406 bulls, and 7,422 cows as core animals, and 0.44 with the remaining sets. With phenotypes truncated in 2009 and the preconditioned conjugate gradient to solve mixed model equations, the number of rounds to convergence for core animals defined by bulls was 1,343; defined by bulls and cows, 2,066; and defined by 10,000 random animals, at most 1,629. With complete phenotype data, the number of rounds decreased to 858, 1,299, and at most 1,092, respectively. Setting up View the MathML source for 569,404 genotyped animals with 10,000 core animals took 1.3 h and 57 GB of memory. The validation reliability with APY reaches a plateau when the number of core animals is at least 10,000. Predictions with APY have little differences in reliability among definitions of core animals. Single-step genomic BLUP with APY is applicable to millions of genotyped animals.
© 2016, THE AUTHORS. Published by FASS and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/). MenosABSTRACT.
The objectives of this study were to develop and evaluate an efficient implementation in the computation of the inverse of genomic relationship matrix with the recursion algorithm, called the algorithm for proven and young (APY), in single-step genomic BLUP. We validated genomic predictions for young bulls with more than 500,000 genotyped animals in final score for US Holsteins. Phenotypic data included 11,626,576 final scores on 7,093,380 US Holstein cows, and genotypes were available for 569,404 animals. Daughter deviations for young bulls with no classified daughters in 2009, but at least 30 classified daughters in 2014 were computed using all the phenotypic data. Genomic predictions for the same bulls were calculated with single-step genomic BLUP using phenotypes up to 2009. We calculated the inverse of the genomic relationship matrix View the MathML source based on a direct inversion of genomic relationship matrix on a small subset of genotyped animals (core animals) and extended that information to noncore animals by recursion. We tested several sets of core animals including 9,406 bulls with at least 1 classified daughter, 9,406 bulls and 1,052 classified dams of bulls, 9,406 bulls and 7,422 classified cows, and random samples of 5,000 to 30,000 animals. Validation reliability was assessed by the coefficient of determination from regression of daughter deviation on genomic predictions for the predicted young bulls. The reliabilities were 0.39 with 5,000 rand... Presentar Todo |
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Palabras claves : |
FINAL SCORE; GENOMIC EVALUATION; GENOMIC RELATIONSHIP MATRIX. |
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Thesagro : |
SsGBLUP; TORO. |
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Asunto categoría : |
-- |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/12160/1/1-s2.0-S0022030216000825-main.pdf
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Marc : |
LEADER 03610naa a2200289 a 4500
001 1054839
005 2018-12-11
008 2016 bl uuuu u00u1 u #d
024 7 $a10.3168/jds.2015-10540$2DOI
100 1 $aMASUDA, Y.
245 $aImplementation of genomic recursions in single-step genomic best linear unbiased predictor for US Holsteins with a large number of genotyped animals.$h[electronic resource]
260 $c2016
500 $aOPEN ACCESS. Received 19 October 2015, Accepted 1 December 2015, Available online 21 January 2016
520 $aABSTRACT. The objectives of this study were to develop and evaluate an efficient implementation in the computation of the inverse of genomic relationship matrix with the recursion algorithm, called the algorithm for proven and young (APY), in single-step genomic BLUP. We validated genomic predictions for young bulls with more than 500,000 genotyped animals in final score for US Holsteins. Phenotypic data included 11,626,576 final scores on 7,093,380 US Holstein cows, and genotypes were available for 569,404 animals. Daughter deviations for young bulls with no classified daughters in 2009, but at least 30 classified daughters in 2014 were computed using all the phenotypic data. Genomic predictions for the same bulls were calculated with single-step genomic BLUP using phenotypes up to 2009. We calculated the inverse of the genomic relationship matrix View the MathML source based on a direct inversion of genomic relationship matrix on a small subset of genotyped animals (core animals) and extended that information to noncore animals by recursion. We tested several sets of core animals including 9,406 bulls with at least 1 classified daughter, 9,406 bulls and 1,052 classified dams of bulls, 9,406 bulls and 7,422 classified cows, and random samples of 5,000 to 30,000 animals. Validation reliability was assessed by the coefficient of determination from regression of daughter deviation on genomic predictions for the predicted young bulls. The reliabilities were 0.39 with 5,000 randomly chosen core animals, 0.45 with the 9,406 bulls, and 7,422 cows as core animals, and 0.44 with the remaining sets. With phenotypes truncated in 2009 and the preconditioned conjugate gradient to solve mixed model equations, the number of rounds to convergence for core animals defined by bulls was 1,343; defined by bulls and cows, 2,066; and defined by 10,000 random animals, at most 1,629. With complete phenotype data, the number of rounds decreased to 858, 1,299, and at most 1,092, respectively. Setting up View the MathML source for 569,404 genotyped animals with 10,000 core animals took 1.3 h and 57 GB of memory. The validation reliability with APY reaches a plateau when the number of core animals is at least 10,000. Predictions with APY have little differences in reliability among definitions of core animals. Single-step genomic BLUP with APY is applicable to millions of genotyped animals. © 2016, THE AUTHORS. Published by FASS and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).
650 $aSsGBLUP
650 $aTORO
653 $aFINAL SCORE
653 $aGENOMIC EVALUATION
653 $aGENOMIC RELATIONSHIP MATRIX
700 1 $aMISZTAL, I.
700 1 $aTSURUTA, S.
700 1 $aLEGARRA, A.
700 1 $aAGUILAR, I.
700 1 $aLOURENCO, D.A.L.
700 1 $aFRAGOMENI, B.O.
700 1 $aLAWLOR, T.J.
773 $tJournal of Dairy Science, 2016$gv.99, no.3, p.1968-1974. OPEN ACCESS
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INIA Las Brujas (LB) |
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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 : |
29/01/2020 |
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Actualizado : |
23/03/2020 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Circulación / Nivel : |
Internacional - -- |
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Autor : |
KOLMER, J.A.; HERMAN, A.; ORDOÑEZ, M.E.; GERMAN, S.; MORGOUNOV, A.; PRETORIUS, Z.; VISSER, B.; ANISKSTER, Y.; ACEVEDO, M. |
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Afiliación : |
J. A. KOLMER, United States Department of Agriculture - Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, United States; A. HERMAN, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, United States; M. E. ORDOÑEZ, Pontificia Universidad Católica del Ecuador, Quito, Ecuador; SILVIA ELISA GERMAN FAEDO, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; A. MORGOUNOV, International Wheat and Maize Improvement Center, Ankara, Turkey; Z. PRETORIUS, University of the Free State, Faculty of Natural and Agricultural Sciences, Bloemfontein, South Africa; B. VISSER, University of the Free State, Faculty of Natural and Agricultural Sciences, Bloemfontein, South Africa; Y. ANIKSTER, Institute for Cereal Crop Improvement, Tel Aviv University, Tel Aviv, Israel; M. ACEVEDO, International Programs-CALS, Cornell University, Ithaca, NY, United States. |
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Título : |
Endemic and panglobal genetic groups, and divergence of host-associated forms in worldwide collections of the wheat leaf rust fungus Puccinia triticina as determined by genotyping by sequencing. |
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Fecha de publicación : |
2020 |
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Fuente / Imprenta : |
Heredity, 1 March 2020, Volume 124, Issue 3, Pages 397-409. Doi: https://doi.org/10.1038/s41437-019-0288-x |
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ISSN : |
0018-067X |
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DOI : |
10.1038/s41437-019-0288-x |
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Idioma : |
Inglés |
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Notas : |
Article history: Received: 5 September 2019 / Revised: 3 December 2019 / Accepted: 3 December 2019 / Published online: 20 December 2019.
Supplementary information The online version of this article (https://doi.org/10.1038/s41437-019-0288-x) contains supplementary material, which is available to authorized users. |
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Contenido : |
ABSTRACT.
The wheat leaf rust fungus, Puccinia triticina, is found in the major wheat growing regions of the world and is a leading cause of yield loss in wheat. Populations of P. triticina are highly variable for virulence to resistance genes in wheat and adapt quickly to resistance genes in wheat cultivars. The objectives of this study were to determine the genetic relatedness of worldwide collections of P. triticina using restriction site associated genotyping by sequencing. A total of 558 isolates of P. triticina from wheat producing regions in North America, South America, Europe, the Middle East, Ethiopia, Russia, Pakistan, Central Asia, China, New Zealand, and South Africa were characterized at 6745 single nucleotide loci. Isolates were also tested for virulence to 20 near-isogenic lines that differ for leaf rust resistance genes. Populations that were geographically proximal were also more closely related for genotypes. In addition, groups of isolates within regions that varied for genotype were similar to groups from other regions, which indicated past and recent migration across regions. Isolates from tetraploid durum wheat in five different regions were highly related with distinct genotypes compared to isolates from hexaploid common wheat. Based on a molecular clock, isolates from durum wheat found only in Ethiopia were the first to diverge from a common ancestor form of P. triticina that is found on the wild wheat relative Aegilops speltoides, followed by the divergence of isolates found worldwide that are virulent to durum wheat, and then by isolates found on common wheat.
© 2019, The Author(s), under exclusive licence to The Genetics Society. MenosABSTRACT.
The wheat leaf rust fungus, Puccinia triticina, is found in the major wheat growing regions of the world and is a leading cause of yield loss in wheat. Populations of P. triticina are highly variable for virulence to resistance genes in wheat and adapt quickly to resistance genes in wheat cultivars. The objectives of this study were to determine the genetic relatedness of worldwide collections of P. triticina using restriction site associated genotyping by sequencing. A total of 558 isolates of P. triticina from wheat producing regions in North America, South America, Europe, the Middle East, Ethiopia, Russia, Pakistan, Central Asia, China, New Zealand, and South Africa were characterized at 6745 single nucleotide loci. Isolates were also tested for virulence to 20 near-isogenic lines that differ for leaf rust resistance genes. Populations that were geographically proximal were also more closely related for genotypes. In addition, groups of isolates within regions that varied for genotype were similar to groups from other regions, which indicated past and recent migration across regions. Isolates from tetraploid durum wheat in five different regions were highly related with distinct genotypes compared to isolates from hexaploid common wheat. Based on a molecular clock, isolates from durum wheat found only in Ethiopia were the first to diverge from a common ancestor form of P. triticina that is found on the wild wheat relative Aegilops speltoides, followed by the di... Presentar Todo |
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Palabras claves : |
TRITICUM; WHEAT. |
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Thesagro : |
TRIGO. |
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Asunto categoría : |
F01 Cultivo |
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Marc : |
LEADER 02936naa a2200289 a 4500
001 1060708
005 2020-03-23
008 2020 bl uuuu u00u1 u #d
022 $a0018-067X
024 7 $a10.1038/s41437-019-0288-x$2DOI
100 1 $aKOLMER, J.A.
245 $aEndemic and panglobal genetic groups, and divergence of host-associated forms in worldwide collections of the wheat leaf rust fungus Puccinia triticina as determined by genotyping by sequencing.$h[electronic resource]
260 $c2020
500 $aArticle history: Received: 5 September 2019 / Revised: 3 December 2019 / Accepted: 3 December 2019 / Published online: 20 December 2019. Supplementary information The online version of this article (https://doi.org/10.1038/s41437-019-0288-x) contains supplementary material, which is available to authorized users.
520 $aABSTRACT. The wheat leaf rust fungus, Puccinia triticina, is found in the major wheat growing regions of the world and is a leading cause of yield loss in wheat. Populations of P. triticina are highly variable for virulence to resistance genes in wheat and adapt quickly to resistance genes in wheat cultivars. The objectives of this study were to determine the genetic relatedness of worldwide collections of P. triticina using restriction site associated genotyping by sequencing. A total of 558 isolates of P. triticina from wheat producing regions in North America, South America, Europe, the Middle East, Ethiopia, Russia, Pakistan, Central Asia, China, New Zealand, and South Africa were characterized at 6745 single nucleotide loci. Isolates were also tested for virulence to 20 near-isogenic lines that differ for leaf rust resistance genes. Populations that were geographically proximal were also more closely related for genotypes. In addition, groups of isolates within regions that varied for genotype were similar to groups from other regions, which indicated past and recent migration across regions. Isolates from tetraploid durum wheat in five different regions were highly related with distinct genotypes compared to isolates from hexaploid common wheat. Based on a molecular clock, isolates from durum wheat found only in Ethiopia were the first to diverge from a common ancestor form of P. triticina that is found on the wild wheat relative Aegilops speltoides, followed by the divergence of isolates found worldwide that are virulent to durum wheat, and then by isolates found on common wheat. © 2019, The Author(s), under exclusive licence to The Genetics Society.
650 $aTRIGO
653 $aTRITICUM
653 $aWHEAT
700 1 $aHERMAN, A.
700 1 $aORDOÑEZ, M.E.
700 1 $aGERMAN, S.
700 1 $aMORGOUNOV, A.
700 1 $aPRETORIUS, Z.
700 1 $aVISSER, B.
700 1 $aANISKSTER, Y.
700 1 $aACEVEDO, M.
773 $tHeredity, 1 March 2020, Volume 124, Issue 3, Pages 397-409. Doi: https://doi.org/10.1038/s41437-019-0288-x
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