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Genetic Structure of the European Charolais and Limousin Cattle Metapopulations Using Pedigree Analyses Alban Bouquet, Eric Venot, Denis Laloë, F

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Genetic Structure of the European Charolais and Limousin Cattle Metapopulations Using Pedigree Analyses Alban Bouquet, Eric Venot, Denis Laloë, F Genetic structure of the European Charolais and Limousin cattle metapopulations using pedigree analyses Alban Bouquet, Eric Venot, Denis Laloë, F. Forabosco, A. Fogh, T. Pabiou, K. Moore, Gilles Renand, Florence Phocas To cite this version: Alban Bouquet, Eric Venot, Denis Laloë, F. Forabosco, A. Fogh, et al.. Genetic structure of the European Charolais and Limousin cattle metapopulations using pedigree analyses. Journal of Animal Science, American Society of Animal Science, 2011, 89 (6), pp.1719-1730. 10.2527/jas.2010-3469. hal-01000450 HAL Id: hal-01000450 https://hal.archives-ouvertes.fr/hal-01000450 Submitted on 29 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Genetic structure of the European Charolais and Limousin cattle metapopulations using pedigree analyses A. Bouquet, E. Venot, D. Laloë, F. Forabosco, A. Fogh, T. Pabiou, K. Moore, J.-Å. Eriksson, G. Renand and F. Phocas J ANIM SCI 2011, 89:1719-1730. doi: 10.2527/jas.2010-3469 The online version of this article, along with updated information and services, is located on the World Wide Web at: http://www.journalofanimalscience.org/content/89/6/1719 www.asas.org Downloaded from www.journalofanimalscience.org at INRA Institut National de la Recherche Agronomique on September 30, 2013 References This article cites 31 articles, 6 of which you can access for free at: http://www.journalofanimalscience.org/content/89/6/1719#BIBL Citations This article has been cited by 1 HighWire-hosted articles: http://www.journalofanimalscience.org/content/89/6/1719#otherarticles Downloaded from www.journalofanimalscience.org at INRA Institut National de la Recherche Agronomique on September 30, 2013 Genetic structure of the European Charolais and Limousin cattle metapopulations using pedigree analyses 1 A. Bouquet,*† E. Venot,* D. Laloë,* F. Forabosco,‡ A. Fogh,§ T. Pabiou,# K. Moore,‖ J.-Å. Eriksson,¶ G. Renand,* and F. Phocas* *INRA, Animal Genetics and Integrative Biology, UMR 1313, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; †AgroParisTech, 16, rue Claude Bernard, F-75231 Paris Cedex 5, France; ‡Interbull Centre, Department of Animal Breeding and Genetics, SLU, Box 7023, 750007 Uppsala, Sweden; §Danish Agricultural Advisory Service, National Centre, Aarhus, Denmark; #Irish Cattle Breeding Federation, Highfield House, Bandon, Co. Cork, Ireland; ‖Scottish Agricultural College, Pentland Building, Bush Estate, Penicuik EH26 0PH, Edinburgh, United Kingdom; and ¶Swedish Dairy Association, Box 10, 101 24 Stockholm, Sweden ABSTRACT: Pedigree collected by the Interbeef ser- subpopulations (<1.3% in both breeds), or probability vice allowed genetic diversity to be assessed by using of gene origins. However, in each subpopulation, it was pedigree analyses for the European Charolais (CHA) shown that founders and also ancestors had unbalanced and Limousin (LIM) cattle populations registered in genetic contributions, leading to a moderate but con- national herdbooks in Denmark (DNK), France (FRA), tinuous reduction in genetic diversity. Analyses between Ireland (IRL), Sweden (SWE), and, solely for the LIM populations suggested that all European CHA and LIM breed, the United Kingdom (UK). The CHA data set populations were differentiated very little. The Swedish included 2,563,189 calves with weaning performance, CHA population was assessed as genetically more dis- of which 96.1% were recorded in FRA, 3.0% in SWE, tant from the other CHA populations because of fewer 0.5% in IRL, and 0.4% in DNK. The LIM data set in- gene flows from other countries and because of the use cluded 1,652,734 calves with weaning performance, of of North American sires to introgress the polled phe- which 91.9% were recorded in FRA, 4.9% in UK, 1.8% notype. In each European subpopulation, most of the in DNK, 0.9% SWE, and 0.5% in IRL. Pedigree files main ancestors, which explained 50% of gene origin, included 3,191,132 CHA and 2,409,659 LIM animals. were born in FRA. However, those main ancestors were Gene flows were rather limited between populations, different between countries. Moreover, in both breeds, except from FRA toward other countries. Pedigree the main ancestors, which explained 50% of the gene completeness was good in all subpopulations for both origin in DNK, IRL, SWE, and UK for the LIM breed, breeds and allowed the pedigree to be traced back to were found to be infrequently used in FRA. Those re- the French population. A relatively high level of genetic sults were consistent with the low relationship coef- diversity was assessed in each CHA and LIM subpopu- ficients estimated between subpopulations (<0.6% in lation by estimating either effective population sizes both the CHA and LIM breeds). Therefore, in both (Ne >244 and Ne >345 in the CHA and LIM subpopu- breeds, each subpopulation may constitute a reservoir lations, respectively), relationship coefficients within of genetic diversity for the other ones. Key words: beef cattle, founder, genetic distance, genetic diversity, pedigree analysis, subdivided population ©2011 American Society of Animal Science. All rights reserved. J. Anim. Sci. 2011. 89:1719–1730 doi:10.2527/jas.2010-3469 INTRODUCTION 1960s, French breeding animals have been steadily ex- ported abroad to establish local purebred populations The Charolais (CHA) and Limousin (LIM) popula- able to provide bulls to commercial herds (Bougler et tions are the 2 main beef cattle breeds in France (FRA). al., 1973; Blackburn and Gollin, 2009). The different Owing to their high growth and muscularity perfor- national CHA and LIM subpopulations are bred ac- mance, those breeds have been used worldwide for beef cording to different selection practices or objectives and production in pure or cross-breeding systems. Since the are connected by limited gene flows. They therefore constitute metapopulations. As a result of genetic drift 1 Corresponding author: [email protected] or different selection, such subpopulations become ge- Received August 29, 2010. netically differentiated over time. This differentiation Accepted January 6, 2011. is nevertheless counterbalanced by gene flows between 1719 1720 Bouquet et al. populations (Wang and Caballero, 1999). To date, 2 Federation, personal communication) in DNK, FRA, pedigree analyses of CHA and LIM populations have and IRL, respectively, for the CHA population and 8% been carried out at the national level to assess within- (A. Fogh, personal communication), 14% (Bouquet et population diversity in Ireland (IRL; Mc Parland et al., 2009), 20% (R. Evans, Irish Cattle Breeding Fed- al., 2007) and FRA (Bouquet et al., 2009). Both studies eration, personal communication), and 5% (K. Moore, revealed a moderate decline in genetic diversity within personal communication) in DNK, FRA, IRL, and UK, national populations. However, it is possible that the respectively, for the LIM population. This informa- subdivision could help to maintain genetic diversity in tion was not available in SWE (J.-Å. Eriksson, per- the global population. sonal communication). Performance data sets included In 2007, the Interbeef project was launched to devel- 2,563,189 CHA and 1,652,734 LIM age-adjusted wean- op international genetic evaluations of CHA and LIM ing weights of purebred calves born between 1989 and cattle. For the European countries taking part in this 2008. The numbers of weaning weights recorded per project, the aim was to enlarge the choice of breeding birth country are presented in Table 1 for both breeds. animals to other foreign populations based on a com- Available information in the performance file also in- mon genetic evaluation (Venot et al., 2007). Pedigree cluded herd and birth year of calves. Animal identifi- and performance were therefore collected for CHA and cation numbers were standardized according to rules LIM purebred animals from 4 different countries—Den- described by Pabiou et al. (2007) so that each animal mark (DNK), FRA, IRL, and Sweden (SWE)—and had a unique identification number. Pedigrees from all from the United Kingdom (UK) for the LIM breed. countries were then pooled together into a single file, The aim of this article was to assess, for both breeds, eliminating redundant genealogies. After editing, the the within- and between-population genetic diversity pedigree file included 3,191,132 CHA and 2,409,659 by taking advantage of the whole pedigree information LIM animals, whose distribution per birth country is collected among countries. presented in Table 1 for both breeds. A detailed de- scription of the data structure was given by Venot et al. (2009). Only important facts are mentioned here MATERIALS AND METHODS to facilitate the understanding of subsequent analyses. Animal Care At first, the numbers of recorded animals in total and per herd differed markedly between countries, although Animal care and use committee approval was not their evolution was similar for both breeds within a necessary for this study because data were obtained country. In IRL, the CHA and LIM populations had from preexisting databases. a particular data
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