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Wang Z, Doekes H, Bijma P. Towards genetic improvement of social behaviours in livestock using large-scale sensor data: data simulation and genetic analysis. Genet Sel Evol 2023; 55:67. [PMID: 37770844 PMCID: PMC10537099 DOI: 10.1186/s12711-023-00840-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/11/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Harmful social behaviours, such as injurious feather pecking in poultry and tail biting in swine, reduce animal welfare and production efficiency. While these behaviours are heritable, selective breeding is still limited due to a lack of individual phenotyping methods for large groups and proper genetic models. In the near future, large-scale longitudinal data on social behaviours will become available, e.g. through computer vision techniques, and appropriate genetic models will be needed to analyse such data. In this paper, we investigated prospects for genetic improvement of social traits recorded in large groups by (1) developing models to simulate and analyse large-scale longitudinal data on social behaviours, and (2) investigating required sample sizes to obtain reasonable accuracies of estimated genetic parameters and breeding values (EBV). RESULTS Latent traits were defined as representing tendencies of individuals to be engaged in social interactions by distinguishing between performer and recipient effects. Animal movement was assumed random and without genetic variation, and performer and recipient interaction effects were assumed constant over time. Based on the literature, observed-scale heritabilities ([Formula: see text]) of performer and recipient effects were both set to 0.05, 0.1, or 0.2, and the genetic correlation ([Formula: see text]) between those effects was set to - 0.5, 0, or 0.5. Using agent-based modelling, we simulated ~ 200,000 interactions for 2000 animals (~ 1000 interactions per animal) with a half-sib family structure. Variance components and breeding values were estimated with a general linear mixed model. The estimated genetic parameters did not differ significantly from the true values. When all individuals and interactions were included in the analysis, the accuracy of EBV was 0.61, 0.70, and 0.76 for [Formula: see text] = 0.05, 0.1, and 0.2, respectively (for [Formula: see text]= 0). Including 2000 individuals each with only ~ 100 interactions, already yielded promising accuracies of 0.47, 0.60, and 0.71 for [Formula: see text] = 0.05, 0.1, and 0.2, respectively (with [Formula: see text] = 0). Similar results were found with [Formula: see text] of - 0.5 or 0.5. CONCLUSIONS We developed models to simulate and genetically analyse social behaviours for animals that are kept in large groups, anticipating the availability of large-scale longitudinal data in the near future. We obtained promising accuracies of EBV with ~ 100 interactions per individual, which would correspond to a few weeks of recording. Therefore, we conclude that animal breeding can be a promising strategy to improve social behaviours in livestock.
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Affiliation(s)
- Zhuoshi Wang
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands
| | - Harmen Doekes
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands
| | - Piter Bijma
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands
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Bonnefous C, Collin A, Guilloteau LA, Guesdon V, Filliat C, Réhault-Godbert S, Rodenburg TB, Tuyttens FAM, Warin L, Steenfeldt S, Baldinger L, Re M, Ponzio R, Zuliani A, Venezia P, Väre M, Parrott P, Walley K, Niemi JK, Leterrier C. Welfare issues and potential solutions for laying hens in free range and organic production systems: A review based on literature and interviews. Front Vet Sci 2022; 9:952922. [PMID: 35990274 PMCID: PMC9390482 DOI: 10.3389/fvets.2022.952922] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
In free-range and organic production systems, hens can make choices according to their needs and desires, which is in accordance with welfare definitions. Nonetheless, health and behavioral problems are also encountered in these systems. The aim of this article was to identify welfare challenges observed in these production systems in the EU and the most promising solutions to overcome these challenges. It is based on a review of published literature and research projects complemented by interviews with experts. We selected EU specific information for welfare problems, however, the selected literature regarding solutions is global. Free range use may increase the risk of infection by some bacteria, viruses and parasites. Preventive methods include avoiding contamination thanks to biosecurity measures and strengthening animals' natural defenses against these diseases which can be based on nutritional means with new diet components such as insect-derived products, probiotics and prebiotics. Phytotherapy and aromatherapy can be used as preventive and curative medicine and vaccines as alternatives to antibiotics and pesticides. Bone quality in pullets and hens prevents keel deviations and is favored by exercise in the outdoor range. Free range use also lead to higher exposure to variable weather conditions and predators, therefore shadow, fences and guard animals can be used to prevent heat stress and predation respectively. Granting a free range provides opportunities for the expression of many behaviors and yet many hens usually stay close to the house. Providing the birds with trees, shelters or attractive plants can increase range use. Small flock sizes, early experiences of enrichment and personality traits have also been found to enhance range use. Severe feather pecking can occur in free range production systems, although flocks using the outdoor area have better plumage than indoors. While many prevention strategies are facilitated in free range systems, the influence of genetics, prenatal and nutritional factors in free range hens still need to be investigated. This review provides information about practices that have been tested or still need to be explored and this information can be used by stakeholders and researchers to help them evaluate the applicability of these solutions for welfare improvement.
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Affiliation(s)
| | - Anne Collin
- INRAE, Université de Tours, BOA, Nouzilly, France
| | | | - Vanessa Guesdon
- JUNIA, Comportement Animal et Systèmes d'Elevage, Lille, France
| | | | | | - T. Bas Rodenburg
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Frank A. M. Tuyttens
- ILVO, Instituut voor Landbouw-, Visserij- en Voedingsonderzoek, Melle, Belgium
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | | | - Sanna Steenfeldt
- Department of Animal Science, Aarhus University, Aarhus, Denmark
| | | | - Martina Re
- AIAB, Associazone Italiana per l'Agricultura Biologica, Rome, Italy
| | | | - Anna Zuliani
- Veterinari Senza Frontiere Italia, Sede c/o Istituto Zooprofilattico Sperimentale delle Venezie viale dell'Università, Padova, Italy
| | - Pietro Venezia
- Veterinari Senza Frontiere Italia, Sede c/o Istituto Zooprofilattico Sperimentale delle Venezie viale dell'Università, Padova, Italy
| | - Minna Väre
- Natural Resources Institute Finland (Luke), Bioeconomy and Environment, Helsinki, Finland
| | | | - Keith Walley
- Harper Adams University, Newport, United Kingdom
| | - Jarkko K. Niemi
- Natural Resources Institute Finland (Luke), Bioeconomy and Environment, Seinäjoki, Finland
| | - Christine Leterrier
- CNRS, IFCE, INRAE, Université de Tours, PRC, Nouzilly, France
- *Correspondence: Christine Leterrier
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3
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Zhang Z, Yang W, Zhu T, Wang L, Zhao X, Zhao G, Qu L, Jia Y. Genetic Parameter Estimation and Whole Sequencing Analysis of the Genetic Architecture of Chicken Keel Bending. Front Genet 2022; 13:833132. [PMID: 35401685 PMCID: PMC8984200 DOI: 10.3389/fgene.2022.833132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/24/2022] [Indexed: 11/18/2022] Open
Abstract
Bone health is particularly important for high-yielding commercial layer chickens. The keel of poultry is an extension of the abdomen side of the sternum along the sagittal plane and is one of the most important bones. In this study, the keel phenotype of White Leghorns laying hen flocks showed significant individual differences. To clarify its genetic mechanism, we first estimated the heritability of keel bend (KB) in White Leghorn, recorded the production performance of the chicken flock, examined the blood biochemical indexes and bone quality in KB and keel normal (KN) chickens, and performed whole-genome pooled sequencing in KB and KN chickens. We then performed selection elimination analysis to determine the genomic regions that may affect the keel phenotypes. The results show that KB is a medium heritability trait. We found that cage height had a significant effect on the KB (p < 0.01). At 48 weeks, there were significant differences in the number of eggs, the number of normal eggs, and eggshell strength (p < 0.05). The content of parathyroid hormone was lower (p < 0.01) and that of calcitonin was higher (p < 0.01) in KB chickens than in KN chickens. The differences in bone mineral density, bone strength, and bone cortical thickness of the humerus and femur were extremely significant (p < 0.01), with all being lower in KB chickens than in KN chickens. In addition, the bones of KB chickens contained more fat organization. A total of 128 genes were identified in selective sweep regions. We identified 10 important candidate genes: ACP5, WNT1, NFIX, CNN1, CALR, FKBP11, TRAPPC5, MAP2K7, RELA, and ENSGALG00000047166. Among the significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways found, we identifed two bone-related pathways, one involving “osteoclast differentiation” and the other the “MAPK signaling pathway.” These results may help us better understand the molecular mechanism of bone traits in chickens and other birds and provide new insights for the genetic breeding of chickens.
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Affiliation(s)
- Zhihao Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Science, Beijing, China
| | - Weifang Yang
- Beijing General Station of Animal Husbandry, Beijing, China
| | - Tao Zhu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Liang Wang
- Beijing General Station of Animal Husbandry, Beijing, China
| | - Xiaoyu Zhao
- Hebei Dawu Poultry Breeding Co., Ltd., Hebei, China
| | | | - Lujiang Qu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Lujiang Qu, ; Yaxiong Jia,
| | - Yaxiong Jia
- Institute of Animal Sciences, Chinese Academy of Agricultural Science, Beijing, China
- *Correspondence: Lujiang Qu, ; Yaxiong Jia,
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Determining the variation in premaxillary and dentary bone morphology that may underlie beak shape between two pure layer lines. Poult Sci 2021; 100:101500. [PMID: 34700097 PMCID: PMC8554249 DOI: 10.1016/j.psj.2021.101500] [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: 06/10/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/22/2022] Open
Abstract
Beak treatment is an effective method of reducing the damage inflicted by severe feather pecking (SFP) but there is significant pressure to eliminate these treatments and rely solely on alternative strategies. Substantial variation in beak shape exists within non-beak treated layer flocks and beak shape appears to be heritable. There is the potential to use this pre-existing variation and genetically select for hens whose beak shapes are less apt to cause damage during SFP. To do this, we must first understand the range of phenotypes that exist for both the external beak shape and the bones that provide its structure. The objective of this study was to determine the variation in premaxillary (within the top beak) and dentary (within the bottom beak) bone morphology that exists in 2 non-beak treated pure White Leghorn layer lines using geometric morphometrics to analyze radiographs. Lateral head radiographs were taken of 825 hens and the premaxillary and dentary bones were landmarked. Landmark coordinates were standardized by Procrustes superimposition and the covariation was analyzed by principal components analysis and multivariate regression using Geomorph (an R package). Three principal components (PCs) explained 85% of total premaxillary bone shape variation and showed that the shape ranged from long and narrow with pointed bone tips to short and wide with more curved tips. Two PCs explained 81% of total dentary bone shape variation. PC1 described the dentary bone length and width and PC2 explained the angle between the bone tip and its articular process. For both bones, shape was significantly associated with bone size and differed significantly between the two lines. Bone size accounted for 42% of the total shape variation for both bones. Together, the results showed a range of phenotypic variation in premaxillary and dentary bone shape, which in turn may influence beak shape. These bone phenotypes will guide further quantitative genetic and behavioral analyses that will help identify which beaks shapes cause the least damage when birds engage in SFP.
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Zhu T, Zhao X, Jia Y, Chen Y, Wang L, Lv X, Yang W, Qu L. Genetic parameter estimation for feather damage in laying hens. JOURNAL OF APPLIED ANIMAL RESEARCH 2021. [DOI: 10.1080/09712119.2021.1921780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Tao Zhu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People’s Republic of China
| | - Xiaoyu Zhao
- Hebei Dawu Poultry Breeding Co., Ltd, Hebei, People’s Republic of China
| | - Yaxiong Jia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Yu Chen
- Beijing Animal Husbandry and Veterinary Station, Beijing, People’s Republic of China
| | - Liang Wang
- Beijing Animal Husbandry and Veterinary Station, Beijing, People’s Republic of China
| | - Xueze Lv
- Beijing Animal Husbandry and Veterinary Station, Beijing, People’s Republic of China
| | - Weifang Yang
- Beijing Animal Husbandry and Veterinary Station, Beijing, People’s Republic of China
| | - Lujiang Qu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People’s Republic of China
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Comparison of Changes in the Plumage and Body Condition, Egg Production, and Mortality of Different Non-Beak-Trimmed Pure Line Laying Hens during the Egg-Laying Period. Animals (Basel) 2021; 11:ani11020500. [PMID: 33671858 PMCID: PMC7918532 DOI: 10.3390/ani11020500] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 11/20/2022] Open
Abstract
Simple Summary The spread of both alternative and non-cage laying hen housing systems and the more forceful European refusal of beak trimming generate new problems in commercial egg production. The hybrid layers, which have been genetically selected under cage housing conditions for more decades, have lively temperament, are more susceptible for feather pecking and, in more cases, they are expressly aggressive, which led to permanent conflict situations in the large group keeping systems. Therefore, the omission of beak trimming could lead to an increased risk for feather pecking and consequently to a risk for increased mortality in the hen house by using the current commercial layers. Therefore, changes in the live weight, plumage and body condition, egg production, and mortality of different TETRA pure line non-beak-trimmed laying hens were compared during the egg-production period in our study, where the plumage condition was considered as an indicator trait for feather pecking. Our results confirm the findings of former studies that the genetic background of the hens is an important factor impacting feather pecking and suggest that breeding for an improved plumage condition might be a potential way to improve animal welfare in non-beak-trimmed layer flocks. Abstract The experiment was carried out with altogether 1740 non-beak-trimmed laying hens, which originated from Bábolna TETRA Ltd., representing two different types (Rhode Island Red (RIR) and Rhode Island White (RIW)) and four different lines (Lines 1–2: RIR, Lines 3–4: RIW). The plumage and body condition of randomly selected 120 hens (30 hens/line) was examined at 20, 46, and 62 weeks of age. The egg production and the mortality of the sampled hens were recorded daily. Based on the results, it was established that the lines differ clearly in most of the examined traits. It was also pointed out that injurious pecking of the hens resulted not only in damages in the plumage but also in the body condition. The results obviously demonstrated that the highest egg production and the lowest mortality rate were reached by those hens, which had the best plumage and body condition. Because the occurrence of injurious pecking seems to depend on the genetic background, selection of the hens (lines, families, individuals) for calm temperament will be very important in the future in order to maintain the high production level in non-beak-trimmed layer flocks.
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Sokołowicz Z, Dykiel M, Topczewska J, Krawczyk J, Augustyńska-Prejsnar A. The Effect of the Type of Non-Caged Housing System, Genotype and Age on the Behaviour of Laying Hens. Animals (Basel) 2020; 10:E2450. [PMID: 33371385 PMCID: PMC7767380 DOI: 10.3390/ani10122450] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 11/17/2022] Open
Abstract
This study investigated the welfare of laying hens in different non-caged housing systems, namely a deep-litter barn system (BS), a free-range system (FRS) and an organic system (OS). The study was conducted on 270 hens of a native breed Green-legged Partridge (Z-11) and 270 Hy-Line Brown hybrids. Visual scans were performed to record behaviour of hens. Hens were housed in groups of 30 and observed over the course of one day at 20, 36 and 56 weeks of age. Dustbathing, scratching, wing stretching, wing flapping and preening were recorded as comfort behaviours. Pecking, fighting, threatening and chasing were recorded as agonistic behaviours. The percentage of run use was higher in native hens than in commercial hens (p < 0.05). The proportion of hens exhibiting comfort behaviours housed in the FRS and OS was similar but over twice as high as in the BS (p < 0.05). In the FRS and OS, the percentage of hens displaying comfort behaviours increased with age (p < 0.05). In all the production systems, the percentage of birds displaying comfort behaviours was higher in native breed hens than in commercial breeds (p < 0.05). In the BS, the higher proportion of hens displaying an agonistic behaviour was seen more in commercial breed than in the native breed hens (p < 0.05). The percentage of birds displaying an agonistic behaviour declined with hen age, both in commercial and native breed hens.
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Affiliation(s)
- Zofia Sokołowicz
- Department of Animal Production and Poultry Products Evaluation, University of Rzeszów, Zelwerowicza Street 4, 35-601 Rzeszów, Poland; (Z.S.); (A.A.-P.)
| | - Magdalena Dykiel
- Department of Food Production and Safety, Carpathion State College in Krosno, Rynek 1, 38-400 Krosno, Poland;
| | - Jadwiga Topczewska
- Department of Animal Production and Poultry Products Evaluation, University of Rzeszów, Zelwerowicza Street 4, 35-601 Rzeszów, Poland; (Z.S.); (A.A.-P.)
| | - Józefa Krawczyk
- Department of Poultry Breeding, National Research Institute of Animal Production, Krakowska Street 1, 32-083 Balice n. Kraków, Poland;
| | - Anna Augustyńska-Prejsnar
- Department of Animal Production and Poultry Products Evaluation, University of Rzeszów, Zelwerowicza Street 4, 35-601 Rzeszów, Poland; (Z.S.); (A.A.-P.)
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Angelovičová M, Angelovič M, Zeleňáková L. Research of selected physical indicators of table eggs in the small-scale breedings from the aspect of health safety. POTRAVINARSTVO 2020. [DOI: 10.5219/1357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this study was to investigate selected indicators of the table eggs in small-scale breedings, focusing mainly on the eggshell and its contamination and damage. Our object of study was eggs, shell, damage, and contamination of table eggs. Four small-scale breedings were randomly selected in Slovakia. These breeds were alternatively with an outdoor free-range. Laying hens Dominant was bred under conditions small-scale breeds No.1, No. 2 and No. 3 in the 1st laying cycle, and No. 4 in the 2nd laying cycle. Egg weight was balanced in three small-scale breedings. Egg weight was significantly higher in the fourth small-scale breeding, statistically significant (p <0.05) compared to egg weight in the studied 3 small-scale breedings. Shell weight and shell thickness in the equatorial plane of the egg were balanced in three small-scale breedings and in the fourth small-scale breedings were significantly higher, statistically significant (p <0.05). The higher egg weight per breeding is related to the higher laying hens age that was in the 2nd laying cycle compared to laying hens 3 small-scale breedings in the 1st laying cycle. Higher eggshell weight in three farms may be related to improved conditions in breeding hygiene, as confirmed by the results of investigations into contamination and damage to table eggs. These differences may also be related to nutrition.
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Zhu T, Zhang TY, Wen J, Zhao X, Chen Y, Jia Y, Wang L, Lv X, Yang W, Guan Z, Ning Z, Qu L. The Genetic Architecture of the Chickens Dropping Moisture by Genetic Parameter Estimation and Genome-Wide Association. Front Genet 2020; 11:806. [PMID: 32849807 PMCID: PMC7403505 DOI: 10.3389/fgene.2020.00806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/06/2020] [Indexed: 11/16/2022] Open
Abstract
Dropping moisture (DM) refers to the water content of feces. High DM in chickens could be disadvantageous to pathogen control and fecal treatment in chicken farms. DM can be affected by environment, nutrition, disease, and genetics. In the present study, significant individual differences were presented in the DM of Rhode Island Red (RIR) chicken population, indicating that genetics could contribute to DM in the chickens. Subsequently, we estimated the genetic parameters of DM and conducted a genome-wide association study (GWAS) to find the potential genomic regions related to DM. The results showed that the heritability of DM ranged from 0.25 to 0.32. Furthermore, 11 significant loci on chromosome 7 were found to be associated with DM levels by the GWAS. The SNP rs15833816 within the COL6A3 gene was the most significant SNP related to DM. Hens carrying the G allele including GA and GG produced higher DM (P < 0.01) levels than those carrying the other genotype AA. Our results showed that DM is a medium-inheritable trait and that COL6A3 could be a potential candidate gene that regulates DM level in chickens.
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Affiliation(s)
- Tao Zhu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Tong-Yu Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Junhui Wen
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaoyu Zhao
- Hebei Dawu Poultry Breeding Co., Ltd., Hebei, China
| | - Yu Chen
- Beijing Animal Husbandry and Veterinary Station, Beijing, China
| | - Yaxiong Jia
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liang Wang
- Beijing Animal Husbandry and Veterinary Station, Beijing, China
| | - Xueze Lv
- Beijing Animal Husbandry and Veterinary Station, Beijing, China
| | - Weifang Yang
- Beijing Animal Husbandry and Veterinary Station, Beijing, China
| | - Zi Guan
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhonghua Ning
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lujiang Qu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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10
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Ellen ED, van der Sluis M, Siegford J, Guzhva O, Toscano MJ, Bennewitz J, van der Zande LE, van der Eijk JAJ, de Haas EN, Norton T, Piette D, Tetens J, de Klerk B, Visser B, Rodenburg TB. Review of Sensor Technologies in Animal Breeding: Phenotyping Behaviors of Laying Hens to Select Against Feather Pecking. Animals (Basel) 2019; 9:ani9030108. [PMID: 30909407 PMCID: PMC6466287 DOI: 10.3390/ani9030108] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 11/23/2022] Open
Abstract
Simple Summary The European Cooperation in Science and Technology (COST) Action GroupHouseNet aims to provide synergy among scientists to prevent damaging behavior in group-housed pigs and laying hens. One goal of this network is to determine how genetic and genomic tools can be used to breed animals that are less likely to perform damaging behavior on their pen-mates. In this review, the focus is on feather-pecking behavior in laying hens. Reducing feather pecking in large groups of hens is a challenge, because it is difficult to identify and monitor individual birds. However, current developments in sensor technologies and animal breeding have the potential to identify individual animals, monitor individual behavior, and link this information back to the underlying genotype. We describe a combination of sensor technologies and “-omics” approaches that could be used to select against feather-pecking behavior in laying hens. Abstract Damaging behaviors, like feather pecking (FP), have large economic and welfare consequences in the commercial laying hen industry. Selective breeding can be used to obtain animals that are less likely to perform damaging behavior on their pen-mates. However, with the growing tendency to keep birds in large groups, identifying specific birds that are performing or receiving FP is difficult. With current developments in sensor technologies, it may now be possible to identify laying hens in large groups that show less FP behavior and select them for breeding. We propose using a combination of sensor technology and genomic methods to identify feather peckers and victims in groups. In this review, we will describe the use of “-omics” approaches to understand FP and give an overview of sensor technologies that can be used for animal monitoring, such as ultra-wideband, radio frequency identification, and computer vision. We will then discuss the identification of indicator traits from both sensor technologies and genomics approaches that can be used to select animals for breeding against damaging behavior.
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Affiliation(s)
- Esther D Ellen
- Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands.
| | - Malou van der Sluis
- Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands.
- Department of Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, 3508 TD Utrecht, The Netherlands.
| | - Janice Siegford
- Animal Behavior and Welfare Group, Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA.
| | - Oleksiy Guzhva
- Department Biosystems and Technology, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden.
| | - Michael J Toscano
- Center for Proper Housing: Poultry and Rabbits University of Bern, CH 3052 Zollikofen, Switzerland.
| | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany.
| | - Lisette E van der Zande
- Adaptation Physiology Group, Wageningen University & Research, 6700 AH Wageningen, The Netherlands.
| | - Jerine A J van der Eijk
- Adaptation Physiology Group, Wageningen University & Research, 6700 AH Wageningen, The Netherlands.
- Behavioural Ecology Group, Wageningen University & Research, 6700 AH Wageningen, The Netherlands.
| | - Elske N de Haas
- Department of Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, 3508 TD Utrecht, The Netherlands.
- Institute for Agricultural and Fisheries Research (ILVO), Animal Sciences Unit, 9090 Melle, Belgium.
| | - Tomas Norton
- M3-BIORES, Division Animal and Human Health Engineering, Department of Biosystems, KU Leuven, B-3001 Heverlee, Belgium.
| | - Deborah Piette
- M3-BIORES, Division Animal and Human Health Engineering, Department of Biosystems, KU Leuven, B-3001 Heverlee, Belgium.
| | - Jens Tetens
- Functional Breeding Group, Department of Animal Sciences, Georg-August University, 37077 Göttingen, Germany.
| | | | - Bram Visser
- Hendrix Genetics Research, Technology & Services B.V., 5830 AC Boxmeer, The Netherlands.
| | - T Bas Rodenburg
- Department of Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, 3508 TD Utrecht, The Netherlands.
- Adaptation Physiology Group, Wageningen University & Research, 6700 AH Wageningen, The Netherlands.
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11
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Brinker T, Bijma P, Vereijken A, Ellen ED. The genetic architecture of socially-affected traits: a GWAS for direct and indirect genetic effects on survival time in laying hens showing cannibalism. Genet Sel Evol 2018; 50:38. [PMID: 30037326 PMCID: PMC6057005 DOI: 10.1186/s12711-018-0409-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/06/2018] [Indexed: 12/01/2022] Open
Abstract
Background Cannibalism is an important welfare problem in the layer industry. Cannibalism is a social behavior where individual survival is affected by direct genetic effects (DGE) and indirect genetic effects (IGE). Previous studies analysed repeated binomial survival, instead of survival time, which improved accuracies of breeding value predictions. Our study aimed at identifying SNPs associated with DGE and IGE for survival time, and comparing results from models that analyse survival time and repeated binomial survival. Methods Survival data of three layer crosses (W1 * WA, W1 * WB, and W1 * WC) were used. Each individual had one survival time record and 13 monthly survival (0/1) records. Approximately 30,000 single nucleotide polymorphisms (SNPs) were included in the genome-wide association study (GWAS), using a linear mixed model for survival time, a linear mixed model and a generalized linear mixed model for repeated binomial survival (0/1). Backwards elimination was used to determine phenotypic and genetic variance explained by SNPs. Results The same quantitative trait loci were identified with all models. A SNP associated with DGE was found in cross W1 * WA, with an allele substitution effect of 22 days. This SNP explained 3% of the phenotypic variance, and 36% of the total genetic variance. Four SNPs associated with DGE were found in cross W1 * WB, with effects ranging from 16 to 35 days. These SNPs explained 1 to 6% of the phenotypic variance and 9 to 44% of the total genetic variance. Our results suggest a link of DGE and IGE for survival time in layers with the gamma-aminobutyric acid (GABA) system, since a SNP located near a gene for a GABA receptor was associated with DGE and with IGE (not significant). Conclusions This is one of the first large studies investigating the genetic architecture of a socially-affected trait. The power to detect SNP associations was relatively low and thus we expect that many effects on DGE and IGE remained undetected. Yet, GWAS results revealed SNPs with large DGE and a link of DGE and IGE for survival time in layers with the GABAergic system, which supports existing evidence for the involvement of GABA in the development of abnormal behaviors. Electronic supplementary material The online version of this article (10.1186/s12711-018-0409-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tessa Brinker
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Piter Bijma
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Addie Vereijken
- Research and Technology Centre, Hendrix Genetics, P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Esther D Ellen
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.
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12
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13
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Signor SA, Abbasi M, Marjoram P, Nuzhdin SV. Conservation of social effects (Ψ ) between two species of Drosophila despite reversal of sexual dimorphism. Ecol Evol 2017; 7:10031-10041. [PMID: 29238534 PMCID: PMC5723616 DOI: 10.1002/ece3.3523] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 12/15/2022] Open
Abstract
Indirect genetic effects (IGEs) describe the effect of the genes of social partners on the phenotype of a focal individual. Here, we measure indirect genetic effects using the “coefficient of interaction” (Ψ) to test whether Ψ evolved between Drosophila melanogaster and D. simulans. We compare Ψ for locomotion between ethanol and nonethanol environments in both species, but only D. melanogaster utilizes ethanol ecologically. We find that while sexual dimorphism for locomotion has been reversed in D. simulans, there has been no evolution of social effects between these two species. What did evolve was the interaction between genotype‐specific Ψ and the environment, as D. melanogaster varies unpredictably between environments and D. simulans does not. In this system, this suggests evolutionary lability of sexual dimorphism but a conservation of social effects, which brings forth interesting questions about the role of the social environment in sexual selection.
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Affiliation(s)
- Sarah A Signor
- Program in Molecular and Computational Biology Dornsife College of Letters, Arts and Sciences University of Southern California Los Angeles CA USA
| | - Mohammad Abbasi
- Graduate Program in Computational Biology Dornsife College of Letters, Arts and Sciences University of Southern California Los Angeles CA USA
| | - Paul Marjoram
- Program in Molecular and Computational Biology Dornsife College of Letters, Arts and Sciences University of Southern California Los Angeles CA USA.,Department of Preventive Medicine Keck School of Medicine University of Southern California Los Angeles CA USA
| | - Sergey V Nuzhdin
- Program in Molecular and Computational Biology Dornsife College of Letters, Arts and Sciences University of Southern California Los Angeles CA USA
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14
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Bailey NW, Marie-Orleach L, Moore AJ. Indirect genetic effects in behavioral ecology: does behavior play a special role in evolution? Behav Ecol 2017. [DOI: 10.1093/beheco/arx127] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Nathan W Bailey
- School of Biology, University of St Andrews, St Andrews, Fife, UK
| | | | - Allen J Moore
- Department of Genetics, University of Georgia, Athens, GA USA
- Department of Entomology, University of Georgia, Athens, GA USA
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15
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Yao J, Wang X, Yan H, Cai X, Wang M, Tu Y, Yang C. Enhanced Expression of Serotonin Receptor 5-Hydroxytryptamine 2C is Associated with Increased Feather Damage in Dongxiang Blue-Shelled Layers. Behav Genet 2017; 47:369-374. [PMID: 28275879 DOI: 10.1007/s10519-017-9839-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 02/13/2017] [Indexed: 11/29/2022]
Abstract
The gene encoding the serotonin receptor 5-hydroxytraptamine 2C (HTR2C) has been implicated in behavioral phenotypes in a number of species. In previous studies, a mutation in the chicken HTR2C gene was found to be associated with feather condition, thereby suggesting a relationship between the gene and receiving feather pecking activity. The present study analyzed the chicken HTR2C gene at both the genomic make-up and expression level in Dongxiang blue-shelled layer. A significant association between the single nucleotide polymorphism (SNP) rs13640917 (C/T) and feather condition was confirmed in the Chinese local layer. Enhanced HTR2C gene expression (151.1-fold) that was associated with high feather damage indicated that the right cerebrum might be the critical region for HTR2C to participate in the regulation of receiving feather pecking behavior.
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Affiliation(s)
- Junfeng Yao
- Shanghai Academy of Agricultural Sciences, No. 2901 Beidi road, Minghang Qu, Shanghai, 201106, China.,National Poultry Engineer Research Center, Shanghai, China
| | - Xiaoliang Wang
- Shanghai Academy of Agricultural Sciences, No. 2901 Beidi road, Minghang Qu, Shanghai, 201106, China.,National Poultry Engineer Research Center, Shanghai, China
| | - Huangxiang Yan
- Shanghai Academy of Agricultural Sciences, No. 2901 Beidi road, Minghang Qu, Shanghai, 201106, China.,National Poultry Engineer Research Center, Shanghai, China
| | - Xia Cai
- Shanghai Academy of Agricultural Sciences, No. 2901 Beidi road, Minghang Qu, Shanghai, 201106, China.,National Poultry Engineer Research Center, Shanghai, China
| | - Min Wang
- National Poultry Engineer Research Center, Shanghai, China
| | - Yingying Tu
- National Poultry Engineer Research Center, Shanghai, China
| | - Changsuo Yang
- Shanghai Academy of Agricultural Sciences, No. 2901 Beidi road, Minghang Qu, Shanghai, 201106, China. .,National Poultry Engineer Research Center, Shanghai, China.
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16
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Baud A, Mulligan MK, Casale FP, Ingels JF, Bohl CJ, Callebert J, Launay JM, Krohn J, Legarra A, Williams RW, Stegle O. Genetic Variation in the Social Environment Contributes to Health and Disease. PLoS Genet 2017; 13:e1006498. [PMID: 28121987 PMCID: PMC5266220 DOI: 10.1371/journal.pgen.1006498] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 11/21/2016] [Indexed: 11/29/2022] Open
Abstract
Assessing the impact of the social environment on health and disease is challenging. As social effects are in part determined by the genetic makeup of social partners, they can be studied from associations between genotypes of one individual and phenotype of another (social genetic effects, SGE, also called indirect genetic effects). For the first time we quantified the contribution of SGE to more than 100 organismal phenotypes and genome-wide gene expression measured in laboratory mice. We find that genetic variation in cage mates (i.e. SGE) contributes to variation in organismal and molecular measures related to anxiety, wound healing, immune function, and body weight. Social genetic effects explained up to 29% of phenotypic variance, and for several traits their contribution exceeded that of direct genetic effects (effects of an individual's genotypes on its own phenotype). Importantly, we show that ignoring SGE can severely bias estimates of direct genetic effects (heritability). Thus SGE may be an important source of "missing heritability" in studies of complex traits in human populations. In summary, our study uncovers an important contribution of the social environment to phenotypic variation, sets the basis for using SGE to dissect social effects, and identifies an opportunity to improve studies of direct genetic effects.
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Affiliation(s)
- Amelie Baud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Megan K. Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Jesse F. Ingels
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Casey J. Bohl
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Jacques Callebert
- AP-HP, Hôpital Lariboisière, Department of Biochemistry, INSERM U942, Paris, France
| | - Jean-Marie Launay
- AP-HP, Hôpital Lariboisière, Department of Biochemistry, INSERM U942, Paris, France
| | - Jon Krohn
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | | | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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17
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Grams V, Bögelein S, Grashorn MA, Bessei W, Bennewitz J. Quantitative Genetic Analysis of Traits Related to Fear and Feather Pecking in Laying Hens. Behav Genet 2014; 45:228-35. [DOI: 10.1007/s10519-014-9695-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 11/21/2014] [Indexed: 11/24/2022]
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18
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Ellen ED, Rodenburg TB, Albers GAA, Bolhuis JE, Camerlink I, Duijvesteijn N, Knol EF, Muir WM, Peeters K, Reimert I, Sell-Kubiak E, van Arendonk JAM, Visscher J, Bijma P. The prospects of selection for social genetic effects to improve welfare and productivity in livestock. Front Genet 2014; 5:377. [PMID: 25426136 PMCID: PMC4227523 DOI: 10.3389/fgene.2014.00377] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/13/2014] [Indexed: 11/24/2022] Open
Abstract
Social interactions between individuals living in a group can have both positive and negative effects on welfare, productivity, and health of these individuals. Negative effects of social interactions in livestock are easier to observe than positive effects. For example, laying hens may develop feather pecking, which can cause mortality due to cannibalism, and pigs may develop tail biting or excessive aggression. Several studies have shown that social interactions affect the genetic variation in a trait. Genetic improvement of socially-affected traits, however, has proven to be difficult until relatively recently. The use of classical selection methods, like individual selection, may result in selection responses opposite to expected, because these methods neglect the effect of an individual on its group mates (social genetic effects). It has become clear that improvement of socially-affected traits requires selection methods that take into account not only the direct effect of an individual on its own phenotype but also the social genetic effects, also known as indirect genetic effects, of an individual on the phenotypes of its group mates. Here, we review the theoretical and empirical work on social genetic effects, with a focus on livestock. First, we present the theory of social genetic effects. Subsequently, we evaluate the evidence for social genetic effects in livestock and other species, by reviewing estimates of genetic parameters for direct and social genetic effects. Then we describe the results of different selection experiments. Finally, we discuss issues concerning the implementation of social genetic effects in livestock breeding programs. This review demonstrates that selection for socially-affected traits, using methods that target both the direct and social genetic effects, is a promising, but sometimes difficult to use in practice, tool to simultaneously improve production and welfare in livestock.
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Affiliation(s)
- Esther D Ellen
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands
| | - T Bas Rodenburg
- Behavioural Ecology Group, Wageningen University Wageningen, Netherlands
| | - Gerard A A Albers
- Hendrix Genetics, Research and Technology Centre Boxmeer, Netherlands
| | | | - Irene Camerlink
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands ; Adaptation Physiology Group, Wageningen University Wageningen, Netherlands
| | - Naomi Duijvesteijn
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands ; TOPIGS Research Centre IPG Beuningen, Netherlands
| | | | - William M Muir
- Department of Animal Science, Purdue University West Lafayette, IN, USA
| | - Katrijn Peeters
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands ; Hendrix Genetics, Research and Technology Centre Boxmeer, Netherlands
| | - Inonge Reimert
- Adaptation Physiology Group, Wageningen University Wageningen, Netherlands
| | - Ewa Sell-Kubiak
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands
| | | | | | - Piter Bijma
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands
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