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Gjøen J, Jean-Joseph H, Kotrschal K, Jensen P. Domestication and social environment modulate fear responses in young chickens. Behav Processes 2023:104906. [PMID: 37311492 DOI: 10.1016/j.beproc.2023.104906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 06/15/2023]
Abstract
Domesticated species differ from their wild ancestors in a mosaic of traits. Classical domestication theories agree that reactivity to fear and stress is one of the main traits affected. Domesticated species are expected to be less fear and stress prone to than their wild counterparts. To test this hypothesis, we compared the behavioural responses of White Leghorn (WL) chicks to their wild counterparts, Red Junglefowl (RJF) chicks in risk-taking situations. In order to obtain food, the chicks faced an unknown and potentially harmful object at the presence or absence of a social partner. We found that according to our predictions, RJF were more stressed and fearful of the object than the WL. Still, RJF were more explorative than WL. Additionally, the presence of a social partner reduced the fear response in both, but had a stronger effect on RJF. Finally, WL were more food orientated than the RJF. Our results confirmed classical domestication hypotheses of downregulation of the stress system and importance of the social partner in domesticated farm chicken.
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Affiliation(s)
- Johanna Gjøen
- AVIAN Behavior Genetics and Physiology Group, IFM Biology, Linköping University, Sweden
| | - Hillary Jean-Joseph
- Department of Behavioural and Cognitive Biology, University of Vienna, Austria; Wolf Science Center, University of Veterinary Medicine, Vienna, Medical University of Vienna, University of Vienna, Austria; Domestication Lab, University of Veterinary Medicine, Vienna, Medical University of Vienna, University of Vienna, Austria.
| | - Kurt Kotrschal
- Department of Behavioural and Cognitive Biology, University of Vienna, Austria
| | - Per Jensen
- AVIAN Behavior Genetics and Physiology Group, IFM Biology, Linköping University, Sweden.
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Lobo D, Linheiro R, Godinho R, Archer JP. On taming the effect of transcript level intra-condition count variation during differential expression analysis: A story of dogs, foxes and wolves. PLoS One 2022; 17:e0274591. [PMID: 36136981 PMCID: PMC9498955 DOI: 10.1371/journal.pone.0274591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 08/31/2022] [Indexed: 11/22/2022] Open
Abstract
The evolution of RNA-seq technologies has yielded datasets of scientific value that are often generated as condition associated biological replicates within expression studies. With expanding data archives opportunity arises to augment replicate numbers when conditions of interest overlap. Despite correction procedures for estimating transcript abundance, a source of ambiguity is transcript level intra-condition count variation; as indicated by disjointed results between analysis tools. We present TVscript, a tool that removes reference-based transcripts associated with intra-condition count variation above specified thresholds and we explore the effects of such variation on differential expression analysis. Initially iterative differential expression analysis involving simulated counts, where levels of intra-condition variation and sets of over represented transcripts are explicitly specified, was performed. Then counts derived from inter- and intra-study data representing brain samples of dogs, wolves and foxes (wolves vs. dogs and aggressive vs. tame foxes) were used. For simulations, the sensitivity in detecting differentially expressed transcripts increased after removing hyper-variable transcripts, although at levels of intra-condition variation above 5% detection became unreliable. For real data, prior to applying TVscript, ≈20% of the transcripts identified as being differentially expressed were associated with high levels of intra-condition variation, an over representation relative to the reference set. As transcripts harbouring such variation were removed pre-analysis, a discordance from 26 to 40% in the lists of differentially expressed transcripts is observed when compared to those obtained using the non-filtered reference. The removal of transcripts possessing intra-condition variation values within (and above) the 97th and 95th percentiles, for wolves vs. dogs and aggressive vs. tame foxes, maximized the sensitivity in detecting differentially expressed transcripts as a result of alterations within gene-wise dispersion estimates. Through analysis of our real data the support for seven genes with potential for being involved with selection for tameness is provided. TVscript is available at: https://sourceforge.net/projects/tvscript/.
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Affiliation(s)
- Diana Lobo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- * E-mail: (DL); (JPA)
| | - Raquel Linheiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - John Patrick Archer
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- * E-mail: (DL); (JPA)
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Maekawa F, Nagino K, Yang J, Htike NTT, Tsukahara S, Ubuka T, Tsutsui K, Kawashima T. Strain differences in intermale aggression and possible factors regulating increased aggression in Japanese quail. Gen Comp Endocrinol 2018; 256:63-70. [PMID: 28765073 DOI: 10.1016/j.ygcen.2017.07.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/21/2017] [Accepted: 07/25/2017] [Indexed: 10/19/2022]
Abstract
The National Institute for Environmental Studies (NIES) of Japan established a strain of Japanese quail (Coturnix japonica) known as NIES-L by rotation breeding in a closed colony for over 35years; accordingly, the strain has highly inbred-like characteristics. Another strain called NIES-Brn has been maintained by randomized breeding in a closed colony to produce outbred-like characteristics. The current study aimed to characterize intermale aggressive behaviors in both strains and to identify possible factors regulating higher aggression in the hypothalamus, such as sex hormone and neuropeptide expression. Both strains displayed a common set of intermale aggressive behaviors that included pecking, grabbing, mounting, and cloacal contact behavior, although NIES-Brn quail showed significantly more grabbing, mounting, and cloacal contact behavior than did NIES-L quail. We examined sex hormone levels in the blood and diencephalon in both strains. Testosterone concentrations were significantly higher in the blood and diencephalon of NIES-Brn quail compared to NIES-L quail. We next examined gene expression in the hypothalamus of both strains using an Agilent gene expression microarray and real-time RT-PCR and found that gene expression of mesotocin (an oxytocin homologue) was significantly higher in the hypothalamus of NIES-Brn quail compared to NIES-L quail. Immunohistochemistry of the hypothalamus revealed that numbers of large cells (cell area>500μm2) expressing mesotocin were significantly higher in the NIES-Brn strain compared to the NIES-L strain. Taken together, our findings suggest that higher testosterone and mesotocin levels in the hypothalamus may be responsible for higher aggression in the NIES-Brn quail strain.
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Affiliation(s)
- Fumihiko Maekawa
- National Institute for Environmental Studies, Tsukuba, Japan; Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan.
| | - Koki Nagino
- National Institute for Environmental Studies, Tsukuba, Japan; Laboratory of Integrative Brain Sciences, Department of Biology and Center for Medical Life Science, Waseda University, Tokyo, Japan
| | - Jiaxin Yang
- National Institute for Environmental Studies, Tsukuba, Japan
| | - Nang T T Htike
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Shinji Tsukahara
- National Institute for Environmental Studies, Tsukuba, Japan; Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Takayoshi Ubuka
- Laboratory of Integrative Brain Sciences, Department of Biology and Center for Medical Life Science, Waseda University, Tokyo, Japan; Jeffrey Cheah School of Medicine and Health Sciences, Brain Research Institute Monash Sunway, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Kazuyoshi Tsutsui
- Laboratory of Integrative Brain Sciences, Department of Biology and Center for Medical Life Science, Waseda University, Tokyo, Japan
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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] [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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Jensen P. Adding ‘epi-’ to behaviour genetics: implications for animal domestication. J Exp Biol 2015; 218:32-40. [DOI: 10.1242/jeb.106799] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In this review, it is argued that greatly improved understanding of domestication may be gained from extending the field of behaviour genetics to also include epigenetics. Domestication offers an interesting framework of rapid evolutionary changes caused by well-defined selection pressures. Behaviour is an important phenotype in this context, as it represents the primary means of response to environmental challenges. An overview is provided of the evidence for genetic involvement in behavioural control and the presently used methods for finding so-called behaviour genes. This shows that evolutionary changes in behaviour are to a large extent correlated to changes in patterns of gene expression, which brings epigenetics into the focus. This area is concerned with the mechanisms controlling the timing and extent of gene expression, and a lot of focus has been placed on methylation of cytosine in promoter regions, usually associated with genetic downregulation. The review considers the available evidence that environmental input, for example stress, can modify methylation and other epigenetic marks and subsequently affect behaviour. Furthermore, several studies are reviewed, demonstrating that acquired epigenetic modifications can be inherited and cause trans-generational behaviour changes. In conclusion, epigenetics may signify a new paradigm in this respect, as it shows that genomic modifications can be caused by environmental signals, and random mutations in DNA sequence are therefore not the only sources of heritable genetic variation.
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Affiliation(s)
- Per Jensen
- Linköping University, IFM Biology, AVIAN Behaviour Genomics and Physiology Group, 58183 Linköping, Sweden
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