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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 : |
18/12/2017 |
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Actualizado : |
15/10/2019 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
LOURENCO, D.A.L.; FRAGOMENI, B.O.; BRADFORD, H.L.; MENEZES I.R.; FERRAZ, J.B.S.; AGUILAR, I.; MISZTAL, I. |
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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). |
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Título : |
Implications of SNP weighting on single-step genomic predictions for different reference population sizes. |
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Fecha de publicación : |
2017 |
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Fuente / Imprenta : |
Journal of Animal Breeding and Genetics, 2017, v. 134 (6), p. 463-471. |
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DOI : |
10.1111/jbg.12288 |
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Idioma : |
Inglés |
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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. |
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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 |
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Palabras claves : |
ACCURAY; BAYES B; SNP WEIGHTING; VARIABLE SELECTION; WEIGTED SSGBLUP. |
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Asunto categoría : |
-- |
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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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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 : |
14/02/2022 |
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Actualizado : |
14/02/2022 |
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Tipo de producción científica : |
Capítulo en Libro Técnico-Científico |
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Autor : |
GARCÍA-PRÉCHAC, F.; SALVO, L.; ERNST, O.; SIRI-PRIETO, G.; QUINCKE, A.; TERRA, J.A. |
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Afiliación : |
FERNANDO GARCÍA-PRÉCHAC, Facultad de Agronomía, Universidad de La República, Uruguay; LUCÍA SALVO, Facultad de Agronomía, Universidad de La República, Uruguay; OSWALDO ERNST, Facultad de Agronomía, Universidad de La República, Uruguay; GUILLERMO SIRI-PRIETO, Facultad de Agronomía, Universidad de La República, Uruguay; JUAN ANDRES QUINCKE WALDEN, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; JOSÉ ALFREDO TERRA FERNÁNDEZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
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Título : |
Long-term effects of different agricultural soil use and management systems on soil degradation in Uruguay. |
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Fecha de publicación : |
2022 |
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Fuente / Imprenta : |
In: Li R., Napier T.L., El-Swaify S.A., Sabir M., Rienzi E. (eds). Global Degradation of Soil and Water Resources. Springer, Singapore, 2022. https://doi.org/10.1007/978-981-16-7916-2_7 |
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Páginas : |
p.77-92. |
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ISBN : |
978-981-16-7915-5 (print); 978-981-16-7916-2 (eBook) |
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DOI : |
10.1007/978-981-16-7916-2_7 |
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Idioma : |
Inglés |
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Notas : |
Chapter history: First Online 01 January 2022. |
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Contenido : |
The objective of the present paper is to review and update the experimental results and the model predictions about soil erosion and SOC content changes in Argiudolls of Uruguay. |
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Palabras claves : |
Cropping system; Ecosystem; SOILS. |
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Asunto categoría : |
P30 Ciencia del suelo y manejo del suelo |
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Marc : |
LEADER 01081naa a2200253 a 4500
001 1062740
005 2022-02-14
008 2022 bl uuuu u00u1 u #d
024 7 $a10.1007/978-981-16-7916-2_7$2DOI
100 1 $aGARCÍA-PRÉCHAC, F.
245 $aLong-term effects of different agricultural soil use and management systems on soil degradation in Uruguay.$h[electronic resource]
260 $c2022
300 $ap.77-92.
500 $aChapter history: First Online 01 January 2022.
520 $aThe objective of the present paper is to review and update the experimental results and the model predictions about soil erosion and SOC content changes in Argiudolls of Uruguay.
653 $aCropping system
653 $aEcosystem
653 $aSOILS
700 1 $aSALVO, L.
700 1 $aERNST, O.
700 1 $aSIRI-PRIETO, G.
700 1 $aQUINCKE, A.
700 1 $aTERRA, J.A.
773 $tIn: Li R., Napier T.L., El-Swaify S.A., Sabir M., Rienzi E. (eds). Global Degradation of Soil and Water Resources. Springer, Singapore, 2022. https://doi.org/10.1007/978-981-16-7916-2_7
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