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Registro completo
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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 Treinta y Tres. Por información adicional contacte bibliott@inia.org.uy. |
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Registro completo
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Biblioteca (s) : |
INIA Treinta y Tres. |
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Fecha actual : |
03/06/2015 |
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Actualizado : |
11/10/2019 |
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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 : |
GEALY, D.R.; SALDAIN, N.; TALBERT, R.E. |
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Afiliación : |
NESTOR ELIO SALDAIN CROCCE, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
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Título : |
Emergence of red rice (Oryza sativa) ecotypes under dry-seeded rice (Oriza sativa) culture. |
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Fecha de publicación : |
2000 |
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Fuente / Imprenta : |
Weed Technology, 2000, v. 14, |
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Páginas : |
p. 406-412. |
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ISSN : |
0011-183X |
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DOI : |
10.1614/0890-037X(2000)014[0406:EORROS]2.0.CO;2 |
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Idioma : |
Inglés |
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Notas : |
Article history: received for publication August 31, 1998; revised form February 25, 2000. |
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Contenido : |
Abstract:
The effect of seeding depth on emergence of red rice (Oryza sativa) ecotypes from Arkansas (AR), Louisiana (LA), and Mississippi (MS) was determined under dry-seeded rice production in clay and silt loam soils in Arkansas. By 21 d after planting (DAP), all red rice ecotypes had emerged from planting depths of 1.3, 2.5, 5.0, and 7.5 cm in both clay and silt loam soils. In silt loam soil, seedling emergence from 2.5 cm 7 DAP tended to be greater than from 1.3 cm in an early (normal temperature) planting. Also in this situation, the LA ecotype emerged more vigorously than the other ecotypes at all seeding depths and emerged from 7.5 cm at levels 1.5 times those of the other ecotypes at the same depth. In the clay soil, seedling emergence from 7.5 cm at 21 DAP was greater for the LA and MS ecotypes than for the AR ecotype in an early planting, but these differences were not observed for a late (elevated temperature) planting. Seedling emergence was earlier and
greater in silt loam than in clay. The LA ecotype generally produced the greatest aboveground dry matter, especially at the early planting. The MS ecotype averaged 30% less dry matter production than the AR ecotype for the late planting in both soils. The ability of the LA and MS ecotypes to emerge from greater depths than the AR ecotype under certain soil and temperature conditions suggests that they could be more difficult to control with cultural practices used in dry-seeded rice culture. |
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Palabras claves : |
GERMINATION; ORYZA SATIVA L; RED RICE; RED RICE EMERGENCE DEPTH; SOIL TEXTURE. |
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Thesagro : |
ARROZ; ARROZ ROJO; EMERGENCIA; GERMINACION; TEXTURA DEL SUELO. |
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Asunto categoría : |
H60 Malezas y escardas |
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Marc : |
LEADER 02398naa a2200313 a 4500
001 1052699
005 2019-10-11
008 2000 bl uuuu u00u1 u #d
022 $a0011-183X
024 7 $a10.1614/0890-037X(2000)014[0406:EORROS]2.0.CO;2$2DOI
100 1 $aGEALY, D.R.
245 $aEmergence of red rice (Oryza sativa) ecotypes under dry-seeded rice (Oriza sativa) culture.
260 $c2000
300 $ap. 406-412.
500 $aArticle history: received for publication August 31, 1998; revised form February 25, 2000.
520 $aAbstract: The effect of seeding depth on emergence of red rice (Oryza sativa) ecotypes from Arkansas (AR), Louisiana (LA), and Mississippi (MS) was determined under dry-seeded rice production in clay and silt loam soils in Arkansas. By 21 d after planting (DAP), all red rice ecotypes had emerged from planting depths of 1.3, 2.5, 5.0, and 7.5 cm in both clay and silt loam soils. In silt loam soil, seedling emergence from 2.5 cm 7 DAP tended to be greater than from 1.3 cm in an early (normal temperature) planting. Also in this situation, the LA ecotype emerged more vigorously than the other ecotypes at all seeding depths and emerged from 7.5 cm at levels 1.5 times those of the other ecotypes at the same depth. In the clay soil, seedling emergence from 7.5 cm at 21 DAP was greater for the LA and MS ecotypes than for the AR ecotype in an early planting, but these differences were not observed for a late (elevated temperature) planting. Seedling emergence was earlier and greater in silt loam than in clay. The LA ecotype generally produced the greatest aboveground dry matter, especially at the early planting. The MS ecotype averaged 30% less dry matter production than the AR ecotype for the late planting in both soils. The ability of the LA and MS ecotypes to emerge from greater depths than the AR ecotype under certain soil and temperature conditions suggests that they could be more difficult to control with cultural practices used in dry-seeded rice culture.
650 $aARROZ
650 $aARROZ ROJO
650 $aEMERGENCIA
650 $aGERMINACION
650 $aTEXTURA DEL SUELO
653 $aGERMINATION
653 $aORYZA SATIVA L
653 $aRED RICE
653 $aRED RICE EMERGENCE DEPTH
653 $aSOIL TEXTURE
700 1 $aSALDAIN, N.
700 1 $aTALBERT, R.E.
773 $tWeed Technology, 2000$gv. 14
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