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Salim B, Nakao R, Chatanga E, Marcuzzi O, Eissawi MA, Almathen F, Hanotte O, Giovambattista G. Exploring genetic diversity and variation of Ovar-DRB1 gene in Sudan Desert Sheep using targeted next-generation sequencing. BMC Genomics 2024; 25:160. [PMID: 38331741 PMCID: PMC10851530 DOI: 10.1186/s12864-024-10053-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/25/2024] [Indexed: 02/10/2024] Open
Abstract
INTRODUCTION The Ovar-DRB1 gene, a crucial element of the Major Histocompatibility Complex (MHC) Class II region, initiates adaptive immunity by presenting antigens to T-cells. Genetic diversity in sheep, particularly in MHC Class II genes like Ovar-DRB1, directly influences the specturm of presented antigens impacting immune responses and disease susceptability. Understanding the allelic diversity of Ovar-DRB1 gene in Sudan Desert Sheep (SDS) is essential for uncovering the genetic basis of immune responses and disease resistance, given the the breeds significance in Sudan's unique environment. METHODS Utilizing Targeted Next-Generation Sequencing (NGS) we explore allelic diversity in Ovar-DRB1 gene within SDS. Successfully ampliying and and sequencing the second exon of this gene in 288 SDS samples representing six breeds provided a comprehensive allelic profile, enabling a detalied examination of the gene's genetic makeup. RESULTS We identifed forty-six alleles, including four previously unreported, enrichness the genetic diversity of SDS breeds. These alleles exhibiting non-uniform distribution, varying frequencies across breeds, indicating a breed-specific genetic landscape. Certain alleles, known and novel, show higher frequencies in specific populations, suggesting potential associations with adaptive immune responses. Identifying these alleles sets the stage for investigating their functional roles and implications for disease resistance. Genetic differentiation among SDS breeds, as indicated by FST values and clustering analyses, highlights a unique genetic makeup shaped by geographic and historical factors. These differentiation patterns among SDS breeds have broader implications for breed conservation and targeted breeding to enhance disease resistance in specific populations. CONCLUSION This study unveils Ovar-DRB1 gene allelic diversity in SDS breeds through targeted NGS and genetic analyses, revealing new alleles that underscore the breeds' unique genetic profile. Insights into the genetic factors governing immune responses and disease resistance emerge, promising for optimization of breeding strategies for enhanced livestock health in Sudan's unique environment.
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Affiliation(s)
- Bashir Salim
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, Khartoum-North, Sudan.
- Camel Research Center, King Faisal University, Al-Hasa, Saudi Arabia.
| | - Ryo Nakao
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Elisha Chatanga
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Olivia Marcuzzi
- Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), La Plata, Argentina
| | | | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
- International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Guillermo Giovambattista
- Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), La Plata, Argentina
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Genomic heterozygosity is associated with parasite abundance, but the effects are not mediated by host condition. Evol Ecol 2023; 37:75-96. [PMID: 36568713 PMCID: PMC9666582 DOI: 10.1007/s10682-022-10175-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/17/2022] [Indexed: 12/27/2022]
Abstract
Whether, when, and how genetic diversity buffers individuals and populations against infectious disease risk is a critical and open question for understanding wildlife disease and zoonotic disease risk. Several, but not all, studies have found negative relationships between infection and heterozygosity in wildlife. Since they can host multiple zoonotic infections, we sampled a population of wild deer mice (Peromyscus maniculatus), sequenced their genomes, and examined their fecal samples for coccidia and nematode eggs. We analyzed coccidia infection status, abundance, and coinfection status in relation to per-locus and per-individual measures of heterozygosity, as well as identified SNPs associated with infection status. Since heterozygosity might affect host condition, and condition is known to affect immunity, it was included as a co-variate in the per-individual analyses and as response variable in relation to heterozygosity. Not only did coccidia-infected individuals have lower levels of genome-wide per-locus diversity across all metrics, but we found an inverse relationship between genomic diversity and severity of coccidia infection. We also found weaker evidence that coinfected individuals had lower levels of private allelic variation than all other groups. In the per-individual analyses, relationships between heterozygosity and infection were marginal but followed the same negative trends. Condition was negatively correlated with infection, but was not associated with heterozygosity, suggesting that effects of heterozygosity on infection were not mediated by host condition in this system. Association tests identified multiple loci involved in the inflammatory response, with a particular role for NF-κB signaling, supporting previous work on the genetic basis of coccidia resistance. Taken together, we find that increased genome-wide neutral diversity, the presence of specific genetic variants, and improved condition positively impact infection status. Our results underscore the importance of considering host genomic variation as a buffer against infection, especially in systems that can harbor zoonotic diseases. Supplementary Information The online version contains supplementary material available at 10.1007/s10682-022-10175-8.
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P SS, Chennuru S, Krovvidi S, Chitichoti J. Status of tick-borne haemoprotozoan infection in south Indian sheep in association with variation in Ovar-DRB1 gene. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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New insights into the past and recent evolutionary history of the Corsican mouflon (Ovis gmelini musimon) to inform its conservation. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01399-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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LaCava MEF, Malmberg JL, Edwards WH, Johnson LNL, Allen SE, Ernest HB. Spatio-temporal analyses reveal infectious disease-driven selection in a free-ranging ungulate. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210802. [PMID: 34430048 PMCID: PMC8355672 DOI: 10.1098/rsos.210802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/06/2021] [Indexed: 05/07/2023]
Abstract
Infectious diseases play an important role in wildlife population dynamics by altering individual fitness, but detecting disease-driven natural selection in free-ranging populations is difficult due to complex disease-host relationships. Chronic wasting disease (CWD) is a fatal infectious prion disease in cervids for which mutations in a single gene have been mechanistically linked to disease outcomes, providing a rare opportunity to study disease-driven selection in wildlife. In Wyoming, USA, CWD has gradually spread across mule deer (Odocoileus hemionus) populations, producing natural variation in disease history to evaluate selection pressure. We used spatial variation and a novel temporal comparison to investigate the relationship between CWD and a mutation at codon 225 of the mule deer prion protein gene that slows disease progression. We found that individuals with the 'slow' 225F allele were less likely to test positive for CWD, and the 225F allele was more common in herds exposed to CWD longer. We also found that in the past 2 decades, the 225F allele frequency increased more in herds with higher CWD prevalence. This study expanded on previous research by analysing spatio-temporal patterns of individual and herd-based disease data to present multiple lines of evidence for disease-driven selection in free-ranging wildlife.
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Affiliation(s)
- Melanie E. F. LaCava
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, Program in Ecology, University of Wyoming, Laramie, WY 82071, USA
| | - Jennifer L. Malmberg
- Department of Veterinary Sciences, Wyoming State Veterinary Laboratory, University of Wyoming, Laramie, WY 82070, USA
| | - William H. Edwards
- Wyoming Game and Fish Department, Wildlife Health Laboratory, Laramie, WY 82070, USA
| | - Laura N. L. Johnson
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY 82071, USA
| | - Samantha E. Allen
- Wyoming Game and Fish Department, Department of Veterinary Sciences, University of Wyoming, Laramie, WY 82070, USA
| | - Holly B. Ernest
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, Program in Ecology, University of Wyoming, Laramie, WY 82071, USA
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Bourgoin G, Portanier E, Poirel MT, Itty C, Duhayer J, Benabed S, Cockenpot A, Callait-Cardinal MP, Garel M. Reproductive females and young mouflon ( Ovis gmelini musimon × Ovis sp.) in poor body condition are the main spreaders of gastrointestinal parasites. Parasitology 2021; 148:809-818. [PMID: 33593470 PMCID: PMC11010168 DOI: 10.1017/s0031182021000329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 02/11/2021] [Accepted: 02/13/2021] [Indexed: 11/07/2022]
Abstract
Several individual, environmental and parasitic factors can influence the impacts of parasites on host's fitness and on host's ability to transmit these parasites to new hosts. Identifying these factors and the individuals who play a greater role in parasite transmission is of main concern for the development of parasite control strategies. In the present study, we aimed to describe the diversity of gastrointestinal parasites and to identify the individual factors influencing the faecal spreading of parasites in a free-ranging population of Mediterranean mouflon. From the analysis of 433 faecal samples, we found Eimeria spp. and gastrointestinal strongyles (GIS) were the most common parasites (>94%). The faecal oocyst counts of Eimeria spp. were the highest during the first years of life. It was 1.6 times higher in females than in males and 2.5 times higher in individuals in poor than in good body condition. Similarly, the faecal egg count of GIS was higher in females and decreased with age, but only in males. Finally, reproductive females had GIS faecal egg count values 2.6 times higher than non-reproductive females. Management strategies of parasites should thus primarily focus on reproductive females and young individuals in poor body condition as they represent the main contamination source of the environment.
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Affiliation(s)
- Gilles Bourgoin
- Laboratoire de parasitologie vétérinaire, Université de Lyon, VetAgro Sup – Campus Vétérinaire de Lyon, 1 avenue Bourgelat, BP 83, F-69280 Marcy l'Etoile, France
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, F-69622Villeurbanne, France
| | - Elodie Portanier
- Laboratoire de parasitologie vétérinaire, Université de Lyon, VetAgro Sup – Campus Vétérinaire de Lyon, 1 avenue Bourgelat, BP 83, F-69280 Marcy l'Etoile, France
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, F-69622Villeurbanne, France
| | - Marie-Thérèse Poirel
- Laboratoire de parasitologie vétérinaire, Université de Lyon, VetAgro Sup – Campus Vétérinaire de Lyon, 1 avenue Bourgelat, BP 83, F-69280 Marcy l'Etoile, France
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, F-69622Villeurbanne, France
| | - Christian Itty
- Office Français de la Biodiversité, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, F-38610Gières, France
| | - Jeanne Duhayer
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, F-69622Villeurbanne, France
| | - Slimania Benabed
- Laboratoire de parasitologie vétérinaire, Université de Lyon, VetAgro Sup – Campus Vétérinaire de Lyon, 1 avenue Bourgelat, BP 83, F-69280 Marcy l'Etoile, France
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, F-69622Villeurbanne, France
| | - Anne Cockenpot
- Laboratoire de parasitologie vétérinaire, Université de Lyon, VetAgro Sup – Campus Vétérinaire de Lyon, 1 avenue Bourgelat, BP 83, F-69280 Marcy l'Etoile, France
| | - Marie-Pierre Callait-Cardinal
- Laboratoire de parasitologie vétérinaire, Université de Lyon, VetAgro Sup – Campus Vétérinaire de Lyon, 1 avenue Bourgelat, BP 83, F-69280 Marcy l'Etoile, France
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, F-69622Villeurbanne, France
| | - Mathieu Garel
- Office Français de la Biodiversité, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, F-38610Gières, France
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Pérez-González J, Carranza J, Martínez R, Benítez-Medina JM. Host Genetic Diversity and Infectious Diseases. Focus on Wild Boar, Red Deer and Tuberculosis. Animals (Basel) 2021; 11:1630. [PMID: 34072907 PMCID: PMC8229303 DOI: 10.3390/ani11061630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/19/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
Host genetic diversity tends to limit disease spread in nature and buffers populations against epidemics. Genetic diversity in wildlife is expected to receive increasing attention in contexts related to disease transmission and human health. Ungulates such as wild boar (Sus scrofa) and red deer (Cervus elaphus) are important zoonotic hosts that can be precursors to disease emergence and spread in humans. Tuberculosis is a zoonotic disease with relevant consequences and can present high prevalence in wild boar and red deer populations. Here, we review studies on the genetic diversity of ungulates and determine to what extent these studies consider its importance on the spread of disease. This assessment also focused on wild boar, red deer, and tuberculosis. We found a disconnection between studies treating genetic diversity and those dealing with infectious diseases. Contrarily, genetic diversity studies in ungulates are mainly concerned with conservation. Despite the existing disconnection between studies on genetic diversity and studies on disease emergence and spread, the knowledge gathered in each discipline can be applied to the other. The bidirectional applications are illustrated in wild boar and red deer populations from Spain, where TB is an important threat for wildlife, livestock, and humans.
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Affiliation(s)
- Javier Pérez-González
- Biology and Ethology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain
| | - Juan Carranza
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Córdoba, Spain;
| | - Remigio Martínez
- Infectious Pathology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain; (R.M.); (J.M.B.-M.)
| | - José Manuel Benítez-Medina
- Infectious Pathology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain; (R.M.); (J.M.B.-M.)
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Gagnon M, Yannic G, Boyer F, Côté SD. Adult survival in migratory caribou is negatively associated with MHC functional diversity. Heredity (Edinb) 2020; 125:290-303. [PMID: 32728043 DOI: 10.1038/s41437-020-0347-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 07/04/2020] [Accepted: 07/16/2020] [Indexed: 11/09/2022] Open
Abstract
Genes of the major histocompatibility complex (MHC) are involved in acquired immunity in vertebrates. Only a few studies have investigated the fitness consequences of MHC gene diversity in wild populations. Here, we looked at the association between annual survival and body mass and MHC-DRB exon 2 (MHC-DRB) genetic diversity, obtained from high-throughput sequencing, in two declining migratory caribou (Rangifer tarandus) herds. To disentangle the potential direct and general effects of MHC-DRB genetic diversity, we compared different indices of diversity that were either based on DNA-sequence variation or on physicochemical divergence of the translated peptides, thereby covering a gradient of allelic-to-functional diversity. We found that (1) body mass was not related to MHC-DRB diversity or genotype, and (2) adult survival probability was negatively associated with point accepted mutation distance, a corrected distance that considers the likelihood of each amino acid substitution to be accepted by natural selection. In addition, we found no evidence of fluctuating selection over time on MHC-DRB diversity. We concluded that direct effects were involved in the negative relationship between MHC functional diversity and survival, although the mechanism underlying this result remains unclear. A possible explanation could be that individuals with higher MHC diversity suffer higher costs of immunity (immunopathology). Our results suggest that genetic diversity is not always beneficial even in genes that are likely to be strongly shaped by balancing selection.
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Affiliation(s)
- Marianne Gagnon
- Département de Biologie, Caribou Ungava and Centre d'Études Nordiques, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
| | - Glenn Yannic
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France.
| | - Frédéric Boyer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Steeve D Côté
- Département de Biologie, Caribou Ungava and Centre d'Études Nordiques, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
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Portanier E, Garel M, Devillard S, Duhayer J, Poirel MT, Henri H, Régis C, Maillard D, Redman E, Itty C, Michel P, Bourgoin G. Does host socio-spatial behavior lead to a fine-scale spatial genetic structure in its associated parasites? ACTA ACUST UNITED AC 2019; 26:64. [PMID: 31697232 PMCID: PMC6836744 DOI: 10.1051/parasite/2019062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/16/2019] [Indexed: 11/15/2022]
Abstract
Gastro-intestinal nematodes, especially Haemonchus contortus, are widespread pathogenic parasites of small ruminants. Studying their spatial genetic structure is as important as studying host genetic structure to fully understand host-parasite interactions and transmission patterns. For parasites having a simple life cycle (e.g., monoxenous parasites), gene flow and spatial genetic structure are expected to strongly rely on the socio-spatial behavior of their hosts. Based on five microsatellite loci, we tested this hypothesis for H. contortus sampled in a wild Mediterranean mouflon population (Ovis gmelini musimon × Ovis sp.) in which species- and environment-related characteristics have been found to generate socio-spatial units. We nevertheless found that their parasites had no spatial genetic structure, suggesting that mouflon behavior was not enough to limit parasite dispersal in this study area and/or that other ecological and biological factors were involved in this process, for example other hosts, the parasite life cycle, or the study area history.
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Affiliation(s)
- Elodie Portanier
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France
| | - Mathieu Garel
- Office National de la Chasse et de la Faune Sauvage, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France
| | - Sébastien Devillard
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France
| | - Jeanne Duhayer
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France - Office National de la Chasse et de la Faune Sauvage, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France - Université de Lyon, VetAgro Sup, Campus Vétérinaire de Lyon, 1 Avenue Bourgelat, BP 83, 69280 Marcy l'Etoile, France
| | - Marie-Thérèse Poirel
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France - Université de Lyon, VetAgro Sup, Campus Vétérinaire de Lyon, 1 Avenue Bourgelat, BP 83, 69280 Marcy l'Etoile, France
| | - Hélène Henri
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France
| | - Corinne Régis
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France
| | - Daniel Maillard
- Office National de la Chasse et de la Faune Sauvage, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France
| | - Elizabeth Redman
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Faculty of Veterinary Medicine, CA-T3B 2C3 Calgary, Canada
| | - Christian Itty
- Office National de la Chasse et de la Faune Sauvage, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France
| | - Patricia Michel
- GIEC du Caroux-Espinouse, Fagairolles, 34610 Castanet-Le-Haut, France
| | - Gilles Bourgoin
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France - Université de Lyon, VetAgro Sup, Campus Vétérinaire de Lyon, 1 Avenue Bourgelat, BP 83, 69280 Marcy l'Etoile, France
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