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16. Comparative Genome Organization of Vertebrates: The First International Workshop on Comparative Genome Organization

Author

Andersson, L., Archibald, A., Ashburner, M., Audun, S., Barendse, W., Bitgood, J., Bottema, C., Broad, T., Brown, S., Burt, D., Charlier, C., Copeland, N., Davis, S., Davisson, M., Edwards, J., Eggen, A., Elgar, G., Eppig, J. T., Franklin, I., Grewe, P., Gill, T., Graves, J. A. M., Hawken, R., Hetzel, J., Hilyard, A., Jacob, H., Jaswinska, L., Jenkins, N., Kunz, H., Levan, G., Lie, O., Lyons, L., Maccarone, P., Mellersh, C., Montgomery, G., Moore, S., Moran, C., Morizot, D., Neff, M., Nicholas, F., O’Brien, S., Parsons, Y., Peters, J., Postlethwait, J., Raymond, M., Rothschild, M., Schook, L., Sugimoto, Y., Szpirer, C., Tate, M., Taylor, J., VandeBerg, J., Wakefield, M., Wienberg, J., and Womack, J.

Published
1996
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27. Large-scale investigation of response to [i]Eimeria Maxima[/i] challenge in broilers

Author

HAMZIC, Edin, Bed'Hom, Bertrand, Juin, Herve, Hawken, R, Abrahamsen, M. S., Elsen, Jean Michel, Servin, Bertrand, Pinard - Van Der Laan, Marie-Helene, Demeure, Olivier, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Molecular Biology and Genetics (DMBG), Aarhus University [Aarhus]-Research Centre Flakkebjerg, Elevage Alternatif et Santé des Monogastriques (UE EASM), Institut National de la Recherche Agronomique (INRA), Cobb-Vantress Inc, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)

Subjects
broilers, disease indicators, [SDV]Life Sciences [q-bio], parasitic diseases, Eimeria maxima, coccidiosis, large-scale study
Abstract

Coccidiosis, a parasitic disease of the intestinal tract caused by members of the genera Eimeria and Isospora, is one of the most common and costly diseases in chicken. The aims of this study were to assess the effect of the challenge and level of variability of measured parameters in chickens during the challenge with Eimeria maxima. Furthermore, this study aimed to investigate which parameters are the most relevant indicators of the health status. Finally, the study also aimed to estimate accuracy of prediction for traits that cannot be measured on large scale (such as intestinal lesion score and fecal oocyst count) using parameters that can easily be measured on all animals. The study was performed in two parts: a pilot challenge on 240 animals, followed by a large-scale challenge on 2,024 animals. In both experiments, animals were challenged with 50,000 Eimeria maxima oocysts at 16 days of age. In the pilot challenge all animals were measured for BW gain, plasma coloration, hematocrit and rectal temperature and in addition a subset of 48 animals was measured for oocyst count and the intestinal lesion score. All animals from the second challenge were measured for BW gain, plasma coloration and hematocrit whereas a subset of 184 animals were measured for intestinal lesion scores, fecal oocyst count, blood parameters, plasma protein content and composition. Most of the parameters measured were significantly affected by the challenge. Lesion scores for duodenum and jejunum (P

Published
2015
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28. GWAS using ssGBLUP

Author

Misztal, Ignacy, Wang, Huiyu, Aguilar, Ignacio, Legarra, Andres, Tsuruta, Shogo, Lourenco, D. A. L., Fragomeni, Breno, Zhang, X, Muir, William, Cheng, H. H., Okimoto, R, Wing, T, Hawken, R, Zumbach, B., Fernando, Rohan, University of Georgia [USA], Genus Plc, Instituto Nacional de Investigación Agropecuaria (INIA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Purdue University, Cobb-Vantress Inc, and Iowa State University (ISU)

Subjects
[SDV]Life Sciences [q-bio], ssgblup, gwas, snp variance, [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014

31. Data compression can discriminate broilers by selection line, detect haplotypes, and estimate genetic potential for complex phenotypes.

Author

Hudson, N. J., Hawken, R. J., Okimoto, R., Sapp, R. L., and Reverter, A.

Subjects
*BROILER chickens, *HAPLOTYPES, *PHENOTYPES, *DATA analysis, *ANIMAL nutrition
Abstract

Accurately establishing the relationships among individuals lays the foundation for genetic analyses such as genome-wide association studies and identification of selection signatures. Of particular interest to the poultry industry are estimates of genetic merit based on molecular data. These estimates can be commercially exploited in marker-assisted breeding programs to accelerate genetic improvement. Here, we test the utility of a new method we have recently developed to estimate animal relatedness and applied it to genetic parameter estimation in commercial broilers. Our approach is based on the concept of data compression from information theory. Using the real-world compressor gzip to estimate normalized compression distance (NCD) we have built compression-based relationship matrices (CRM) for 988 chickens from 4 commercial broiler lines--2 male and 2 female lines. For all pairs of individuals, we found a strong negative relationship between the commonly used genomic relationship matrix (GRM) and NCD. This reflects the fact that "similarity" is the inverse of "distance." The CRM explained more genetic variation than the corresponding GRM in 2 of 3 phenotypes, with corresponding improvements in accuracy of genomic-enabled predictions of breeding value. A sliding-window version of the analysis highlighted haplotype regions of the genome apparently under selection in a line-specific manner. In the male lines, we retrieved high population-specific scores for IGF-1 and a cognate receptor, INSR. For the female lines, we detected an extreme score for a region containing a reproductive hormone receptor (GNRHR). We conclude that our compression-based method is a valid approach to established relationships and identify regions under selective pressure in commercial lines of broiler chickens. [ABSTRACT FROM AUTHOR]

Published
2017
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37. Generation of a radiation hybrid map of porcine chromosome 13

Author

ALEXANDER, L.J., Hawken, R., MURTAUGH, J., Sun, J., FLICKINGER, G., BEATTIE, C.W., Robic, Annie, Milan, Denis, Yerle, Martine, Gellin, Joël, Schook, L.B., Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
1998

38. Characterization of a porcine radiation hybrid (RH) panel

Author

ALEXANDER, L.J., Hawken, R., MURTAUGH, J., FLICKINGER, G., BEATTIE, C.W., Robic, Annie, Milan, Denis, Yerle, Martine, Gellin, Joël, Schook, L.B., Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access; International audience

Published
1998

39. Construction of a whole genome radiation hybrid panel for high-resolution gene mapping in pigs

Author

Yerle, Martine, Pinton, Philippe, Robic, Annie, Delcros, Chantal, Hawken, R., ALEXANDER, L.J., BEATTIE, C.W., Schook, L.B., Milan, Denis, Gellin, Joël, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access; International audience

Published
1998

40. Evidence for pleiotropism and recent selection in thePLAG1region in Australian Beef cattle

Author

Fortes, M. R. S., primary, Kemper, K., additional, Sasazaki, S., additional, Reverter, A., additional, Pryce, J. E., additional, Barendse, W., additional, Bunch, R., additional, McCulloch, R., additional, Harrison, B., additional, Bolormaa, S., additional, Zhang, Y. D., additional, Hawken, R. J., additional, Goddard, M. E., additional, and Lehnert, S. A., additional

Published
2013
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41. From Conflicts to wise practice agreement and national strategy: cooperative learning and coastal stewardship in estuarine floodplain management, Tweed River, eastern Australia

Author

White, Ian, Melville, Michael D, MacDonald, Bennett, Quirk, R, Hawken, R, Tunks, Mark, Buckley, D, Beattie, R N, Williams, John, Heath, Lance, White, Ian, Melville, Michael D, MacDonald, Bennett, Quirk, R, Hawken, R, Tunks, Mark, Buckley, D, Beattie, R N, Williams, John, and Heath, Lance

Abstract

Appropriate information, participatory processes and wise practice agreements are key elements in reducing conflicts over the use and management of coastal resources. In this work we describe the evolution of a cooperative learning approach to coastal floodplain management, incorporating these elements. Government-encouraged drainage of coastal floodplains in eastern Australia caused accelerated oxidation of acid sulfate soils and export of diffuse acidic drainage into streams. Major impacts on infrastructure, ecology, fisheries and aquaculture resulted. In the Tweed River estuary, in 1987, all gilled organisms were killed by acid discharge from floodplain canelands. This generated major conflicts between fishers, environmentalists and sugarcane producers. The cooperative learning partnership that evolved, involving cane farmers, local government, and researchers, has produced better strategies for managing sulfidic estuarine areas and mitigating impacts on downstream ecosystems. These underpinned mandatory best practice management guidelines for the NSW sugar industry. Increases in productivity and decreases in acid discharge have resulted. Fish kills on the Tweed and elsewhere also generated broader, parallel whole-of-government approaches that led to Australia's national strategy for managing coastal acid sulfate soils and the rapid adoption of information and strategies across Australia.

Published
2007

42. From Conflict to Industry- Regulated Best Practice Guidelines: a Case Study of Estuarine Flood Plain Management of the Tweed River Eastern Australia

Author

Hoanh, C. T., Tuong, T. P., Gowing, J. W., Hardy, B., White, Ian, Melville, Michael D., MacDonald, Bennett, Quirk, R., Hawken, R., Tunks, Mark, Buckley, D., Beattie, R. N., Heath, Lance, Williams, J., Hoanh, C. T., Tuong, T. P., Gowing, J. W., Hardy, B., White, Ian, Melville, Michael D., MacDonald, Bennett, Quirk, R., Hawken, R., Tunks, Mark, Buckley, D., Beattie, R. N., Heath, Lance, and Williams, J.

Abstract

Different sectors of society claim rights to use valuable coastal ecosystem resources. Conflicts over their use are therefore inevitable. In eastern Australia, government-encouraged development and drainage of coastal flood plains, principally for agricul

Published
2006

43. Gene network analyses of first service conception in Brangus heifers: Use of genome and trait associations, hypothalamic-transcriptome information, and transcription factors1

Author

Fortes, M. R. S., primary, Snelling, W. M., additional, Reverter, A., additional, Nagaraj, S. H., additional, Lehnert, S. A., additional, Hawken, R. J., additional, DeAtley, K. L., additional, Peters, S. O., additional, Silver, G. A., additional, Rincon, G., additional, Medrano, J. F., additional, Islas-Trejo, A., additional, and Thomas, M. G., additional

Published
2012
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44. Genome-wide association studies of female reproduction in tropically adapted beef cattle1

Author

Hawken, R. J., primary, Zhang, Y. D., additional, Fortes, M. R. S., additional, Collis, E., additional, Barris, W. C., additional, Corbet, N. J., additional, Williams, P. J., additional, Fordyce, G., additional, Holroyd, R. G., additional, Walkley, J. R. W., additional, Barendse, W., additional, Johnston, D. J., additional, Prayaga, K. C., additional, Tier, B., additional, Reverter, A., additional, and Lehnert, S. A., additional

Published
2012
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