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Fariello MI, Boitard S, Mercier S, Robelin D, Faraut T, Arnould C, Recoquillay J, Bouchez O, Salin G, Dehais P, Gourichon D, Leroux S, Pitel F, Leterrier C, SanCristobal M. Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: The local score approach. Mol Ecol 2017; 26:3700-3714. [DOI: 10.1111/mec.14141] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/28/2017] [Accepted: 03/30/2017] [Indexed: 01/19/2023]
Affiliation(s)
- María Inés Fariello
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
- Facultad de Ingeniería; Universidad de la República; Montevideo Uruguay
- Institut Pasteur; Unidad de Bioinformática; Montevideo Uruguay
| | - Simon Boitard
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
| | - Sabine Mercier
- Département Mathématique-Informatique, UFR SES; Université de Toulouse II; Toulouse Cedex 09 France
- UMR5219, Institut de Mathématiques; Université de Toulouse; Toulouse France
| | - David Robelin
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
| | - Thomas Faraut
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
| | - Cécile Arnould
- Unité de Physiologie de la Reproduction et des Comportements, UMR INRA - CNRS; Université de Tours; Tours France
| | - Julien Recoquillay
- UR83 Recherches Avicoles; INRA; Tours Nouzilly France
- Hubbard; Châteaubourg; France
| | - Olivier Bouchez
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
- GeT-PlaGe Genotoul; INRA; Castanet-Tolosan France
| | - Gérald Salin
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
- GeT-PlaGe Genotoul; INRA; Castanet-Tolosan France
| | | | - David Gourichon
- UE1295 Pôle d'Expérimentation Avicole de Tours; Tours Nouzilly France
| | - Sophie Leroux
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
| | - Frédérique Pitel
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
| | - Christine Leterrier
- Unité de Physiologie de la Reproduction et des Comportements, UMR INRA - CNRS; Université de Tours; Tours France
| | - Magali SanCristobal
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
- UMR5219, Institut de Mathématiques; Université de Toulouse; Toulouse France
- Département de Génie Mathématiques; INSA; Toulouse Cedex 4 France
- UMR 1201 Dynafor; INRA - INP Toulouse; Castanet-Tolosan France
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Recoquillay J, Pitel F, Arnould C, Leroux S, Dehais P, Moréno C, Calandreau L, Bertin A, Gourichon D, Bouchez O, Vignal A, Fariello MI, Minvielle F, Beaumont C, Leterrier C, Le Bihan-Duval E. A medium density genetic map and QTL for behavioral and production traits in Japanese quail. BMC Genomics 2015; 16:10. [PMID: 25609057 PMCID: PMC4307178 DOI: 10.1186/s12864-014-1210-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 12/30/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Behavioral traits such as sociability, emotional reactivity and aggressiveness are major factors in animal adaptation to breeding conditions. In order to investigate the genetic control of these traits as well as their relationships with production traits, a study was undertaken on a large second generation cross (F2) between two lines of Japanese Quail divergently selected on their social reinstatement behavior. All the birds were measured for several social behaviors (social reinstatement, response to social isolation, sexual motivation, aggression), behaviors measuring the emotional reactivity of the birds (reaction to an unknown object, tonic immobility reaction), and production traits (body weight and egg production). RESULTS We report the results of the first genome-wide QTL detection based on a medium density SNP panel obtained from whole genome sequencing of a pool of individuals from each divergent line. A genetic map was constructed using 2145 markers among which 1479 could be positioned on 28 different linkage groups. The sex-averaged linkage map spanned a total of 3057 cM with an average marker spacing of 2.1 cM. With the exception of a few regions, the marker order was the same in Japanese Quail and the chicken, which confirmed a well conserved synteny between the two species. The linkage analyses performed using QTLMAP software revealed a total of 45 QTLs related either to behavioral (23) or production (22) traits. The most numerous QTLs (15) concerned social motivation traits. Interestingly, our results pinpointed putative pleiotropic regions which controlled emotional reactivity and body-weight of birds (on CJA5 and CJA8) or their social motivation and the onset of egg laying (on CJA19). CONCLUSION This study identified several QTL regions for social and emotional behaviors in the Quail. Further research will be needed to refine the QTL and confirm or refute the role of candidate genes, which were suggested by bioinformatics analysis. It can be hoped that the identification of genes and polymorphisms related to behavioral traits in the quail will have further applications for other poultry species (especially the chicken) and will contribute to solving animal welfare issues in poultry production.
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Affiliation(s)
| | - Frédérique Pitel
- UMR INRA/Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENSAT / Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENVT Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
| | - Cécile Arnould
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380, Nouzilly, France.
- CNRS, UMR7247, F-37380, Nouzilly, France.
- Université François Rabelais de Tours, F-37000, Tours, France.
- IFCE, F-37380, Nouzilly, France.
| | - Sophie Leroux
- UMR INRA/Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENSAT / Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENVT Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
| | - Patrice Dehais
- UMR INRA/Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENSAT / Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENVT Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INRA, Sigenae UR875 Biométrie et Intelligence Artificielle, F-31326, Castanet-Tolosan, France.
| | - Carole Moréno
- UMR INRA/Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENSAT / Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENVT Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
| | - Ludovic Calandreau
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380, Nouzilly, France.
- CNRS, UMR7247, F-37380, Nouzilly, France.
- Université François Rabelais de Tours, F-37000, Tours, France.
- IFCE, F-37380, Nouzilly, France.
| | - Aline Bertin
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380, Nouzilly, France.
- CNRS, UMR7247, F-37380, Nouzilly, France.
- Université François Rabelais de Tours, F-37000, Tours, France.
- IFCE, F-37380, Nouzilly, France.
| | - David Gourichon
- UE1295 Pôle d'Expérimentation Avicole de Tours, F-37380, Nouzilly, France.
| | - Olivier Bouchez
- UMR INRA/Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENSAT / Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENVT Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INRA, GeT-PlaGe Genotoul, F-31326, Castanet-Tolosan, France.
| | - Alain Vignal
- UMR INRA/Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENSAT / Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENVT Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
| | - Maria Ines Fariello
- UMR INRA/Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENSAT / Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENVT Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- Institut Pasteur, Montevideo, Uruguay.
| | - Francis Minvielle
- INRA, UMR1313 GABI Génétique Animale et Biologie Intégrative, F-78530, Jouy-en-Josas, France.
| | | | - Christine Leterrier
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380, Nouzilly, France.
- CNRS, UMR7247, F-37380, Nouzilly, France.
- Université François Rabelais de Tours, F-37000, Tours, France.
- IFCE, F-37380, Nouzilly, France.
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Recoquillay J, Leterrier C, Calandreau L, Bertin A, Pitel F, Gourichon D, Vignal A, Beaumont C, Le Bihan-Duval E, Arnould C. Evidence of phenotypic and genetic relationships between sociality, emotional reactivity and production traits in Japanese quail. PLoS One 2013; 8:e82157. [PMID: 24324761 PMCID: PMC3852745 DOI: 10.1371/journal.pone.0082157] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/22/2013] [Indexed: 11/23/2022] Open
Abstract
The social behavior of animals, which is partially controlled by genetics, is one of the factors involved in their adaptation to large breeding groups. To understand better the relationships between different social behaviors, fear behaviors and production traits, we analyzed the phenotypic and genetic correlations of these traits in Japanese quail by a second generation crossing of two lines divergently selected for their social reinstatement behavior. Analyses of results for 900 individuals showed that the phenotypic correlations between behavioral traits were low with the exception of significant correlations between sexual behavior and aggressive pecks both at phenotypic (0.51) and genetic (0.90) levels. Significant positive genetic correlations were observed between emotional reactivity toward a novel object and sexual (0.89) or aggressive (0.63) behaviors. The other genetic correlations were observed mainly between behavioral and production traits. Thus, the level of emotional reactivity, estimated by the duration of tonic immobility, was positively correlated with weight at 17 and 65 days of age (0.76 and 0.79, respectively) and with delayed egg laying onset (0.74). In contrast, a higher level of social reinstatement behavior was associated with an earlier egg laying onset (-0.71). In addition, a strong sexual motivation was correlated with an earlier laying onset (-0.68) and a higher number of eggs laid (0.82). A low level of emotional reactivity toward a novel object and also a higher aggressive behavior were genetically correlated with a higher number of eggs laid (0.61 and 0.58, respectively). These results bring new insights into the complex determinism of social and emotional reactivity behaviors in birds and their relationships with production traits. Furthermore, they highlight the need to combine animal welfare and production traits in selection programs by taking into account traits of sociability and emotional reactivity.
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Affiliation(s)
| | - Christine Leterrier
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, Nouzilly, France
- CNRS, UMR7247, Nouzilly, France
- Université François Rabelais de Tours, Tours, France
- IFCE, Nouzilly, France
| | - Ludovic Calandreau
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, Nouzilly, France
- CNRS, UMR7247, Nouzilly, France
- Université François Rabelais de Tours, Tours, France
- IFCE, Nouzilly, France
| | - Aline Bertin
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, Nouzilly, France
- CNRS, UMR7247, Nouzilly, France
- Université François Rabelais de Tours, Tours, France
- IFCE, Nouzilly, France
| | - Frédérique Pitel
- INRA-ENVT, UMR444 Génétique Cellulaire, Castanet-Tolosan, France
| | - David Gourichon
- UE1295 Pôle d’Expérimentation Avicole de Tours, Nouzilly, France
| | - Alain Vignal
- INRA-ENVT, UMR444 Génétique Cellulaire, Castanet-Tolosan, France
| | | | | | - Cécile Arnould
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, Nouzilly, France
- CNRS, UMR7247, Nouzilly, France
- Université François Rabelais de Tours, Tours, France
- IFCE, Nouzilly, France
- * E-mail:
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Gabaldón T, Martin T, Marcet-Houben M, Durrens P, Bolotin-Fukuhara M, Lespinet O, Arnaise S, Boisnard S, Aguileta G, Atanasova R, Bouchier C, Couloux A, Creno S, Almeida Cruz J, Devillers H, Enache-Angoulvant A, Guitard J, Jaouen L, Ma L, Marck C, Neuvéglise C, Pelletier E, Pinard A, Poulain J, Recoquillay J, Westhof E, Wincker P, Dujon B, Hennequin C, Fairhead C. Comparative genomics of emerging pathogens in the Candida glabrata clade. BMC Genomics 2013; 14:623. [PMID: 24034898 PMCID: PMC3847288 DOI: 10.1186/1471-2164-14-623] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/31/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Candida glabrata follows C. albicans as the second or third most prevalent cause of candidemia worldwide. These two pathogenic yeasts are distantly related, C. glabrata being part of the Nakaseomyces, a group more closely related to Saccharomyces cerevisiae. Although C. glabrata was thought to be the only pathogenic Nakaseomyces, two new pathogens have recently been described within this group: C. nivariensis and C. bracarensis. To gain insight into the genomic changes underlying the emergence of virulence, we sequenced the genomes of these two, and three other non-pathogenic Nakaseomyces, and compared them to other sequenced yeasts. RESULTS Our results indicate that the two new pathogens are more closely related to the non-pathogenic N. delphensis than to C. glabrata. We uncover duplications and accelerated evolution that specifically affected genes in the lineage preceding the group containing N. delphensis and the three pathogens, which may provide clues to the higher propensity of this group to infect humans. Finally, the number of Epa-like adhesins is specifically enriched in the pathogens, particularly in C. glabrata. CONCLUSIONS Remarkably, some features thought to be the result of adaptation of C. glabrata to a pathogenic lifestyle, are present throughout the Nakaseomyces, indicating these are rather ancient adaptations to other environments. Phylogeny suggests that human pathogenesis evolved several times, independently within the clade. The expansion of the EPA gene family in pathogens establishes an evolutionary link between adhesion and virulence phenotypes. Our analyses thus shed light onto the relationships between virulence and the recent genomic changes that occurred within the Nakaseomyces. SEQUENCE ACCESSION NUMBERS Nakaseomyces delphensis: CAPT01000001 to CAPT01000179Candida bracarensis: CAPU01000001 to CAPU01000251Candida nivariensis: CAPV01000001 to CAPV01000123Candida castellii: CAPW01000001 to CAPW01000101Nakaseomyces bacillisporus: CAPX01000001 to CAPX01000186.
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Affiliation(s)
- Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, Barcelona, 08003, Spain
- Comparative Genomics Group, CRG-Centre for Genomic Regulation, Doctor Aiguader, 88, Barcelona, 08003, Spain
| | - Tiphaine Martin
- Université de Bordeaux 1, LaBRI, INRIA Bordeaux Sud-Ouest (MAGNOME), Talence, F-33405, France
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, Barcelona, 08003, Spain
| | - Pascal Durrens
- Université de Bordeaux 1, LaBRI, INRIA Bordeaux Sud-Ouest (MAGNOME), Talence, F-33405, France
| | - Monique Bolotin-Fukuhara
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Olivier Lespinet
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Sylvie Arnaise
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Stéphanie Boisnard
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Gabriela Aguileta
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, Barcelona, 08003, Spain
| | - Ralitsa Atanasova
- APHP, Hôpital St Antoine, Service de Parasitologie-Mycologie, and UMR S945, Inserm, Université P. M. Curie, Paris, France
| | - Christiane Bouchier
- Département Génomes et Génétique, Institut Pasteur, Plate-forme Génomique, rue du Dr. Roux, Paris, F-75015, France
| | - Arnaud Couloux
- CEA, IG, DSV, Genoscope, 2 rue Gaston Crémieux, Evry Cedex, 91057, France
| | - Sophie Creno
- Département Génomes et Génétique, Institut Pasteur, Plate-forme Génomique, rue du Dr. Roux, Paris, F-75015, France
| | - Jose Almeida Cruz
- Architecture et Réactivité de l‘ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg Cedex, F-67084, France
- Present adress: Champalimaud Foundation, Av. Brasília, Lisboa, 1400-038, Portugal
| | - Hugo Devillers
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Adela Enache-Angoulvant
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
- APHP, Hôpital Bicêtre, Service de Microbiologie, Paris, France
| | - Juliette Guitard
- APHP, Hôpital St Antoine, Service de Parasitologie-Mycologie, and UMR S945, Inserm, Université P. M. Curie, Paris, France
| | - Laure Jaouen
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Laurence Ma
- Département Génomes et Génétique, Institut Pasteur, Plate-forme Génomique, rue du Dr. Roux, Paris, F-75015, France
| | - Christian Marck
- Institut de biologie et technologies de Saclay (iBiTec-S), Gif-sur-Yvette cedex, 91191, France
| | | | - Eric Pelletier
- CEA, IG, DSV, Genoscope, 2 rue Gaston Crémieux, Evry Cedex, 91057, France
| | - Amélie Pinard
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Julie Poulain
- CEA, IG, DSV, Genoscope, 2 rue Gaston Crémieux, Evry Cedex, 91057, France
| | - Julien Recoquillay
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
| | - Eric Westhof
- Architecture et Réactivité de l‘ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg Cedex, F-67084, France
| | - Patrick Wincker
- CEA, IG, DSV, Genoscope, 2 rue Gaston Crémieux, Evry Cedex, 91057, France
| | - Bernard Dujon
- Institut Pasteur, Unité de Génétique moléculaires des levures, UMR3525 CNRS, UFR927, Université P. M. Curie, 25 rue du Docteur Roux, Paris Cedex15, F75724, France
| | - Christophe Hennequin
- APHP, Hôpital St Antoine, Service de Parasitologie-Mycologie, and UMR S945, Inserm, Université P. M. Curie, Paris, France
| | - Cécile Fairhead
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France
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