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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha : |
21/02/2014 |
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Actualizado : |
18/12/2018 |
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Tipo de producción científica : |
Artículos Indexados |
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Autor : |
MISZTAL, I.; FRAGOMENI, B.; LOURENÇO, D. A. L.; TSURUTA, S.; MASUDA, Y.; AGUILAR, I.; LEGARRA, A.; LAWLOR, T. J. |
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Afiliación : |
IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
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Título : |
Efficient inversion of genomic relationship matrix by the Algorithm for Proven and Young (APY). |
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Fecha de publicación : |
2015 |
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Fuente / Imprenta : |
Interbull Bulletin, 2015, v. 49, p. 111-116. |
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Idioma : |
Inglés |
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Contenido : |
ABSTRACT.
The purpose of this study was to evaluate properties of the inverse of the genomic relationship matrix derived with the algorithm for proven and young (APY) and the accuracy of genomic selection in single-step genomic best linear unbiased prediction (ssGBLUP). The APY implements genomic recursions on a subset of genotyped animals. When that subset is small, the cost of APY is approximately linear in memory and computations, effectively removing restrictions on the number of genotypes. Tests involved 10 102 702 final scores from 6 930 618 Holstein cows. A total of 100 000 animals with genotypes were used in the analyses and included 23 174 sires, 27 215 cows and 49 611 young animals. Genomic estimated breeding values (GEBVs) were calculated using ssGBLUP with a regular inverse of the genomic relationship matrix (G) and with G inverse from APY. Many subsets were tested including only sires, only cows and random samples from 2 000 to 20 000 animals. When the number of animals in the subset was ≥15,000, the correlations between GEBV with APY and
GEBV with the regular inverse were ≥0.99. Best convergence rate was achieved with random samples. A theory on APY was derived and is based on the fact that additive effects of animals in the subset are linear functions of the effects of independent chromosome segments (ICSs); the number of segments is a function of the effective population size. Accuracy of GEBV with APY can be slightly superior to that of a regular inverse. The inverse with APY is computed from G, which in turn is derived from single nucleotide polymorphism (SNP) BLUP and indirectly from BayesB or other SNP-based prediction methods. Strategies like SNP selection, SNP weighting, and use of causative SNPs from sequence analysis can be incorporated in APY without additional cost. The APY removes size limitations from ssGBLUP and facilitates a model with a complex genetic architecture. MenosABSTRACT.
The purpose of this study was to evaluate properties of the inverse of the genomic relationship matrix derived with the algorithm for proven and young (APY) and the accuracy of genomic selection in single-step genomic best linear unbiased prediction (ssGBLUP). The APY implements genomic recursions on a subset of genotyped animals. When that subset is small, the cost of APY is approximately linear in memory and computations, effectively removing restrictions on the number of genotypes. Tests involved 10 102 702 final scores from 6 930 618 Holstein cows. A total of 100 000 animals with genotypes were used in the analyses and included 23 174 sires, 27 215 cows and 49 611 young animals. Genomic estimated breeding values (GEBVs) were calculated using ssGBLUP with a regular inverse of the genomic relationship matrix (G) and with G inverse from APY. Many subsets were tested including only sires, only cows and random samples from 2 000 to 20 000 animals. When the number of animals in the subset was ≥15,000, the correlations between GEBV with APY and
GEBV with the regular inverse were ≥0.99. Best convergence rate was achieved with random samples. A theory on APY was derived and is based on the fact that additive effects of animals in the subset are linear functions of the effects of independent chromosome segments (ICSs); the number of segments is a function of the effective population size. Accuracy of GEBV with APY can be slightly superior to that of a regular... Presentar Todo |
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Palabras claves : |
BIG POPULATION; GENOMIC RECURSION; INVERSION; SINGLE-STEP METHOD. |
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Asunto categoría : |
-- |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/12204/1/1387-2387-1-PB.pdf
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Marc : |
LEADER 02658naa a2200253 a 4500
001 1012458
005 2018-12-18
008 2015 bl uuuu u00u1 u #d
100 1 $aMISZTAL, I.
245 $aEfficient inversion of genomic relationship matrix by the Algorithm for Proven and Young (APY).$h[electronic resource]
260 $c2015
520 $aABSTRACT. The purpose of this study was to evaluate properties of the inverse of the genomic relationship matrix derived with the algorithm for proven and young (APY) and the accuracy of genomic selection in single-step genomic best linear unbiased prediction (ssGBLUP). The APY implements genomic recursions on a subset of genotyped animals. When that subset is small, the cost of APY is approximately linear in memory and computations, effectively removing restrictions on the number of genotypes. Tests involved 10 102 702 final scores from 6 930 618 Holstein cows. A total of 100 000 animals with genotypes were used in the analyses and included 23 174 sires, 27 215 cows and 49 611 young animals. Genomic estimated breeding values (GEBVs) were calculated using ssGBLUP with a regular inverse of the genomic relationship matrix (G) and with G inverse from APY. Many subsets were tested including only sires, only cows and random samples from 2 000 to 20 000 animals. When the number of animals in the subset was ≥15,000, the correlations between GEBV with APY and GEBV with the regular inverse were ≥0.99. Best convergence rate was achieved with random samples. A theory on APY was derived and is based on the fact that additive effects of animals in the subset are linear functions of the effects of independent chromosome segments (ICSs); the number of segments is a function of the effective population size. Accuracy of GEBV with APY can be slightly superior to that of a regular inverse. The inverse with APY is computed from G, which in turn is derived from single nucleotide polymorphism (SNP) BLUP and indirectly from BayesB or other SNP-based prediction methods. Strategies like SNP selection, SNP weighting, and use of causative SNPs from sequence analysis can be incorporated in APY without additional cost. The APY removes size limitations from ssGBLUP and facilitates a model with a complex genetic architecture.
653 $aBIG POPULATION
653 $aGENOMIC RECURSION
653 $aINVERSION
653 $aSINGLE-STEP METHOD
700 1 $aFRAGOMENI, B.
700 1 $aLOURENÇO, D. A. L.
700 1 $aTSURUTA, S.
700 1 $aMASUDA, Y.
700 1 $aAGUILAR, I.
700 1 $aLEGARRA, A.
700 1 $aLAWLOR, T. J.
773 $tInterbull Bulletin, 2015$gv. 49, p. 111-116.
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Registro original : |
INIA Las Brujas (LB) |
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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha actual : |
20/02/2024 |
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Actualizado : |
20/02/2024 |
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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 : |
MACHADO, M.; MARTÍNEZ, R.; ANDRES, S.; SUMARAH, M.W.; RENAUD, J.B.; ARMIÉN, A.G.; BARROS, C.S.L.; RIET-CORREA, F.; MENCHACA, A.; SCHILD, C. |
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Afiliación : |
MIZAEL MACHADO DA COSTA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; RAFAEL MARTÍNEZ, acuarembó, 45000, Uruguay, Tacuarembó, 45000, Uruguay; SOL ANDRES, CENUR Noreste, Universidad de la República, Tacuarembó, 45000, Uruguay; MARK W. SUMARAH, London Research and Development Centre, Agriculture & Agri-Food Canada, London, N5V 4T3, ON, Canada; JUSTIN B. RENAUD, London Research and Development Centre, Agriculture & Agri-Food Canada, London, N5V 4T3, ON, Canada; ANÍBAL G. ARMIÉN, California Animal Health & Food Safety Laboratory System (CAHFS), School of Veterinary Medicine, University of California, Davis, 95616, CA, United States; CLAUDIO S. L. BARROS, Faculdade de Medicina Veterinária e Zootecnia (FMZV), Universidade Federal de Mato Grosso do Sul (, UFMS, Campo Grande 79070-900, Mato Grosso do Sul, Brazil; FRANKLIN RIET-CORREA AMARAL, Programa de Pós-Graduação em Ciência Animal nos Trópicos, Universidade Federal da Bahia (UFBA, Salvador, Bahia, 49170-110, Brazil; JOSE ALEJO MENCHACA BARBEITO, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; CARLOS SCHILD, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; California Animal Health and Food Safety Laboratory System-San Bernardino Branch, University of California, San Bernardino, 92408, CA, United States. |
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Título : |
Poisoning by Baccharis coridifolia in early-weaned beef calves: pathological study and new macrocyclic trichothecene identification. |
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Fecha de publicación : |
2023 |
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Fuente / Imprenta : |
Toxins. 2023; 15(12):681. https://doi.org/10.3390/toxins15120681 -- OPEN ACCESS. |
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ISSN : |
eISSN 2072-6651 |
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DOI : |
10.3390/toxins15120681 |
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Idioma : |
Inglés |
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Notas : |
Article history: Submission received: 19 October 2023; Revised: 20 November 2023; Accepted: 27 November 2023; Published: 1 December 2023. -- Supplementary Materials: The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/toxins15120681/s1 -- This article belongs to the Special Issue Toxins: 15th Anniversary (https://www.mdpi.com/journal/toxins/special_issues/U270856NY7 ). --
Reaxys Chemistry database information. Substances: Trichothecene, Roridin A. -- Funding: This research received no external funding. --
Acknowledgments: We thank Alejandra Custodio from Plataforma de Investigación en Salud Animal (PSA) of Instituto Nacional de Investigación Agropecuaria (INIA) for technical assistance with the histologic techniques, Ana Laura Vildoza for support with postmortem examination, Christina Heard (CAHFS) for the electron microscopy preparations, and Megan Kelman (AAFC) for technical support. Mizael Machado and Alejo Menchaca are researchers of the "Sistema Nacional de Investigadores" (SNI, ANII) of Uruguay. -- Document type: Article Gold Open Access, Article Green Open Access. -- Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
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Contenido : |
ABSTRACT.- This study investigated two outbreaks of spontaneous poisoning by Baccharis coridifolia (Asteraceae) in early-weaned beef calves in Tacuarembó, Uruguay. A total of 34 affected calves showed signs of salivation, anorexia, apathy, marked dehydration, and diarrhea. Deaths occurred 36-72 h after consumption and mortality varied from 37.5% to 43.3% for outbreak 1 and outbreak 2, respectively. The main pathological findings include diffuse severe necrosis of the prestomachs and lymphoid tissues. Ultrastructurally, epithelial cells of the rumen showed swelling, lysis of the organelles, degradation of intercellular attachments, and degradation of the nuclear chromatin. Using LC-MS with diagnostic fragmentation filtering, 56 macrocyclic trichothecenes including glycosyl and malonyl conjugates were identified. The total concentration of macrocyclic trichothecenes, including conjugates, was estimated to be 1.2 ± 0.1 mg/g plant material. This is the first report of these malonyl-glucose conjugates from Baccharis coridifolia. © 2023 by the authors. |
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Palabras claves : |
Baccharis; Mio-mio; PLATAFORMA DE INVESTIGACIÓN EN SALUD ANIMAL - INIA; Poisonous plants; Ruminants; Toxicity; Uruguay. |
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Asunto categoría : |
L01 Ganadería |
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URL : |
https://www.mdpi.com/2072-6651/15/12/681/pdf
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Marc : |
LEADER 03462naa a2200349 a 4500
001 1064468
005 2024-02-20
008 2023 bl uuuu u00u1 u #d
022 $aeISSN 2072-6651
024 7 $a10.3390/toxins15120681$2DOI
100 1 $aMACHADO, M.
245 $aPoisoning by Baccharis coridifolia in early-weaned beef calves$bpathological study and new macrocyclic trichothecene identification.$h[electronic resource]
260 $c2023
500 $aArticle history: Submission received: 19 October 2023; Revised: 20 November 2023; Accepted: 27 November 2023; Published: 1 December 2023. -- Supplementary Materials: The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/toxins15120681/s1 -- This article belongs to the Special Issue Toxins: 15th Anniversary (https://www.mdpi.com/journal/toxins/special_issues/U270856NY7 ). -- Reaxys Chemistry database information. Substances: Trichothecene, Roridin A. -- Funding: This research received no external funding. -- Acknowledgments: We thank Alejandra Custodio from Plataforma de Investigación en Salud Animal (PSA) of Instituto Nacional de Investigación Agropecuaria (INIA) for technical assistance with the histologic techniques, Ana Laura Vildoza for support with postmortem examination, Christina Heard (CAHFS) for the electron microscopy preparations, and Megan Kelman (AAFC) for technical support. Mizael Machado and Alejo Menchaca are researchers of the "Sistema Nacional de Investigadores" (SNI, ANII) of Uruguay. -- Document type: Article Gold Open Access, Article Green Open Access. -- Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
520 $aABSTRACT.- This study investigated two outbreaks of spontaneous poisoning by Baccharis coridifolia (Asteraceae) in early-weaned beef calves in Tacuarembó, Uruguay. A total of 34 affected calves showed signs of salivation, anorexia, apathy, marked dehydration, and diarrhea. Deaths occurred 36-72 h after consumption and mortality varied from 37.5% to 43.3% for outbreak 1 and outbreak 2, respectively. The main pathological findings include diffuse severe necrosis of the prestomachs and lymphoid tissues. Ultrastructurally, epithelial cells of the rumen showed swelling, lysis of the organelles, degradation of intercellular attachments, and degradation of the nuclear chromatin. Using LC-MS with diagnostic fragmentation filtering, 56 macrocyclic trichothecenes including glycosyl and malonyl conjugates were identified. The total concentration of macrocyclic trichothecenes, including conjugates, was estimated to be 1.2 ± 0.1 mg/g plant material. This is the first report of these malonyl-glucose conjugates from Baccharis coridifolia. © 2023 by the authors.
653 $aBaccharis
653 $aMio-mio
653 $aPLATAFORMA DE INVESTIGACIÓN EN SALUD ANIMAL - INIA
653 $aPoisonous plants
653 $aRuminants
653 $aToxicity
653 $aUruguay
700 1 $aMARTÍNEZ, R.
700 1 $aANDRES, S.
700 1 $aSUMARAH, M.W.
700 1 $aRENAUD, J.B.
700 1 $aARMIÉN, A.G.
700 1 $aBARROS, C.S.L.
700 1 $aRIET-CORREA, F.
700 1 $aMENCHACA, A.
700 1 $aSCHILD, C.
773 $tToxins. 2023; 15(12):681. https://doi.org/10.3390/toxins15120681 -- OPEN ACCESS.
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