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  • 1.
    Alvarez-Rodriguez, Manuel
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Atikuzzaman, Mohammad
    Linköping University, Department of Clinical and Experimental Medicine. Linköping University, Faculty of Medicine and Health Sciences. Department of Surgery and Theriogenology, Faculty of Veterinary Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet, Bangladesh.
    Venhoranta, Heli
    Linköping University, Department of Clinical and Experimental Medicine. Linköping University, Faculty of Medicine and Health Sciences. University of Helsinki, Department of Production Animal Medicine, Faculty of Veterinary Medicine, Saari, Finland.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Rodriguez-Martinez, Heriberto
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Expression of Immune Regulatory Genes in the Porcine Internal Genital Tract Is Differentially Triggered by Spermatozoa and Seminal Plasma2019In: International Journal of Molecular Sciences, ISSN 1422-0067, E-ISSN 1422-0067, Vol. 20, no 3, article id 513Article in journal (Refereed)
    Abstract [en]

    Mating or cervical deposition of spermatozoa or seminal plasma (SP) modifies the expression of genes affecting local immune defense processes at the oviductal sperm reservoir in animals with internal fertilization, frequently by down-regulation. Such responses may occur alongside sperm transport to or even beyond the reservoir. Here, immune-related gene expression was explored with cDNA microarrays on porcine cervix-to-infundibulum tissues, pre-/peri-ovulation. Samples were collected 24 h post-mating or cervical deposition of sperm-peak spermatozoa or SP (from the sperm-peak fraction or the whole ejaculate). All treatments of this interventional study affected gene expression. The concerted action of spermatozoa and SP down-regulated chemokine and cytokine (P00031), interferon-gamma signaling (P00035), and JAK/STAT (P00038) pathways in segments up to the sperm reservoir (utero-tubal junction (UTJ)/isthmus). Spermatozoa in the vanguard sperm-peak fraction (P1-AI), uniquely displayed an up-regulatory effect on these pathways in the ampulla and infundibulum. Sperm-free SP, on the other hand, did not lead to major effects on gene expression, despite the clinical notion that SP mitigates reactivity by the female immune system after mating or artificial insemination.

  • 2.
    Atikuzzaman, Mohammad
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Alvarez-Rodriguez, Manuel
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Carrillo, Alejandro Vicente
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Rodriguez-Martinez, Heriberto
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Conserved gene expression in sperm reservoirs between birds and mammals in response to mating.2017In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 18, no 1Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Spermatozoa are stored in the oviductal functional sperm reservoir in animals with internal fertilization, including zoologically distant classes such as pigs or poultry. They are held fertile in the reservoir for times ranging from a couple of days (in pigs), to several weeks (in chickens), before they are gradually released to fertilize the newly ovulated eggs. It is currently unknown whether females from these species share conserved mechanisms to tolerate such a lengthy presence of immunologically-foreign spermatozoa. Therefore, global gene expression was assessed using cDNA microarrays on tissue collected from the avian utero-vaginal junction (UVJ), and the porcine utero-tubal junction (UTJ) to determine expression changes after mating (entire semen deposition) or in vivo cloacal/cervical infusion of sperm-free seminal fluid (SF)/seminal plasma (SP).

    RESULTS: In chickens, mating changed the expression of 303 genes and SF-infusion changed the expression of 931 genes, as compared to controls, with 68 genes being common to both treatments. In pigs, mating or SP-infusion changed the expressions of 1,722 and 1,148 genes, respectively, as compared to controls, while 592 genes were common to both treatments. The differentially expressed genes were significantly enriched for GO categories related to immune system functions (35.72-fold enrichment). The top 200 differentially expressed genes of each treatment in each animal class were analysed for gene ontology. In both pig and chicken, an excess of genes affecting local immune defence were activated, though frequently these were down-regulated. Similar genes were found in both the chicken and pig, either involved in pH-regulation (SLC16A2, SLC4A9, SLC13A1, SLC35F1, ATP8B3, ATP13A3) or immune-modulation (IFIT5, IFI16, MMP27, ADAMTS3, MMP3, MMP12).

    CONCLUSION: Despite being phylogenetically distant, chicken and pig appear to share some gene functions for the preservation of viable spermatozoa in the female reservoirs.

  • 3.
    Atikuzzaman, Mohammad
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Alvarez-Rodriguez, Manuel
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Vicente Carrillo, Alejandro
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Rodriguez-Martinez, Heriberto
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Correction: Conserved gene expression in sperm reservoirs between birds and mammals in response to mating (vol 18, 98, 2017)2017In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 18, article id 563Article in journal (Other academic)
    Abstract [en]

    n/a

  • 4.
    Atikuzzaman, Mohammad
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Bhai Mehta, Ratnesh
    Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science.
    Fogelholm, Jesper
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Rodriguez-Martinez, Heriberto
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Mating induces the expression of immune- and pH-regulatory genes in the utero-vaginal junction containing mucosal sperm-storage tubuli of hens2015In: Reproduction, Vol. 150, no 6, p. 473-483Article in journal (Refereed)
    Abstract [en]

    The female chicken, as with other species with internal fertilization, can tolerate the presence of spermatozoa within specialized sperm-storage tubuli (SST) located in the mucosa of the utero-vaginal junction (UVJ) for days or weeks, without eliciting an immune response. To determine if the oviduct alters its gene expression in response to sperm entry, segments from the oviduct (UVJ, uterus, isthmus, magnum and infundibulum) of mated and unmated (control) hens, derived from an advanced inter-cross line between Red Junglefowl and White Leghorn, were explored 24 h after mating using cDNA microarray analysis. Mating shifted the expression of fifteen genes in the UVJ (53.33% immune-modulatory and 20.00% pH-regulatory) and seven genes in the uterus, none of the genes in the latter segment overlapping the former (with the differentially expressed genes themselves being less related to immune-modulatory function). The other oviductal segments did not show any significant changes. These findings suggest sperm deposition causes a shift in expression in the UVJ (containing mucosal SST) and the uterus for genes involved in immune-modulatory and pH-regulatory functions, both relevant for sperm survival in the hen's oviduct.

  • 5.
    Atikuzzaman, Mohammad
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Sanz, Libia
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Pla, Davinia
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Alvarez-Rodriguez, Manuel
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Rubér, Marie
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Calvete, Juan J.
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Rodriguez-Martinez, Heriberto
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Selection for higher fertility reflects in the seminal fluid proteome of modern domestic chicken2017In: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics, ISSN 1744-117X, E-ISSN 1878-0407, Vol. 21, p. 27-40Article in journal (Refereed)
    Abstract [en]

    The high egg-laying capacity of the modern domestic chicken (i.e. White Leghorn, WL) has arisen from the low egg-laying ancestor Red Junglefowl (RJF) via continuous trait selection and breeding. To investigate whether this long-term selection impacted the seminal fluid (SF)-proteome, 2DE electrophoresis-based proteomic analyses and immunoassays were conducted to map SF-proteins/cytokines in RJF, WL and a 9th generation Advanced Intercross Line (AIL) of RJF/WL-L13, including individual SF (n = 4, from each RJF, WL and AIL groups) and pools of the SF from 15 males of each group, analyzed by 2DE to determine their degree of intra-group (AIL, WL, and RJF) variability using Principal Component Analysis (PCA); respectively an inter-breed comparative analysis of intergroup fold change of specific SF protein spots intensity between breeds. The PCA clearly highlighted a clear intra-group similarity among individual roosters as well as a clear inter-group variability (e.g. between RJF, WL and AIL) validating the use of pools to minimize confounding individual variation. Protein expression varied considerably for processes related to sperm motility, nutrition, transport and survival in the female, including signaling towards immunomodulation. The major conserved SF-proteins were serum albumin and ovotransferrin. Aspartate aminotransferase, annexin A5, arginosuccinate synthase, glutathione S-transferase 2 and l-lactate dehydrogenase-A were RJF-specific. Glyceraldehyde-3-phosphate dehydrogenase appeared specific to the WL-SF while angiotensin-converting enzyme, γ-enolase, coagulation factor IX, fibrinogen α-chain, hemoglobin subunit α-D, lysozyme C, phosphoglycerate kinase, Src-substrate protein p85, tubulins and thioredoxin were AIL-specific. The RJF-SF contained fewer immune system process proteins and lower amounts of the anti-inflammatory/immunomodulatory TGF-β2 compared to WL and AIL, which had low levels- or lacked pro-inflammatory CXCL10 compared to RJF. The seminal fluid proteome differs between ancestor and modern chicken, with a clear enrichment of proteins and peptides related to immune-modulation for sperm survival in the female and fertility.

  • 6.
    Bélteky, Johan
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Agnvall, Beatrix
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Domestication and tameness: brain geneexpression in red junglefowl selected for less fear of humans suggests effects on reproduction and immunology2016In: Royal Society Open Science, E-ISSN 2054-5703, no 3, article id 160033Article in journal (Refereed)
    Abstract [en]

    The domestication of animals has generated a set of phenotypicmodifications, affecting behaviour, appearance, physiologyand reproduction, which are consistent across a range ofspecies. We hypothesized that some of these phenotypes couldhave evolved because of genetic correlation to tameness,an essential trait for successful domestication. Starting froman outbred population of red junglefowl, ancestor of alldomestic chickens, we selected birds for either high or lowfear of humans for five generations. Birds from the fifthselected generation (S5) showed a divergent pattern of growthand reproduction, where low fear chickens grew larger andproduced larger offspring. To examine underlying geneticmechanisms, we used microarrays to study gene expressionin thalamus/hypothalamus, a brain region involved in fearand stress, in both the parental generation and the S5. Whileparents of the selection lines did not show any differentiallyexpressed genes, there were a total of 33 genes with adjustedp-values below 0.1 in S5. These were mainly related to spermfunction,immunological functions, with only a few known tobe relevant to behaviour. Hence, five generations of divergentselection for fear of humans produced changes in hypothalamicgene expression profiles related to pathways associated withmale reproduction and to immunology. This may be linked to the effects seen on growth and size of offspring. These results support the hypothesis thatdomesticated phenotypes may evolve because of correlated effects related to reduced fear of humans.

  • 7.
    Fallahshahroudi, Amir
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    de Kock, Neil
    Department of Chemistry, BMC, Analytical Chemistry and Neurochemistry, University of.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Bektic, Lejla
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Ubhayasekera, S J Kumari A
    Department of Chemistry, BMC, Analytical Chemistry and Neurochemistry, University of.
    Bergquist, Jonas
    Department of Chemistry, BMC, Analytical Chemistry and Neurochemistry, University of.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication.2017In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 7, no 2Article in journal (Refereed)
    Abstract [en]

    The stress response has been largely modified in all domesticated animals, offering a strong tool for genetic mapping. In chickens, ancestral Red Junglefowl react stronger both in terms of physiology and behavior to a brief restraint stress than domesticated White Leghorn, demonstrating modified functions of the hypothalamic-pituitary-adrenal (HPA) axis. We mapped quantitative trait loci (QTL) underlying variations in stress-induced hormone levels using 232 birds from the 12th generation of an advanced intercross between White Leghorn and Red Junglefowl, genotyped for 739 genetic markers. Plasma levels of corticosterone, dehydroepiandrosterone (DHEA), and pregnenolone (PREG) were measured using LC-MS/MS in all genotyped birds. Transcription levels of the candidate genes were measured in the adrenal glands or hypothalamus of 88 out of the 232 birds used for hormone assessment. Genes were targeted for expression analysis when they were located in a hormone QTL region and were differentially expressed in the pure breed birds. One genome-wide significant QTL on chromosome 5 and two suggestive QTL together explained 20% of the variance in corticosterone response. Two significant QTL for aldosterone on chromosome 2 and 5 (explaining 19% of the variance), and one QTL for DHEA on chromosome 4 (explaining 5% of the variance), were detected. Orthologous DNA regions to the significant corticosterone QTL have been previously associated with the physiological stress response in other species but, to our knowledge, the underlying gene(s) have not been identified. SERPINA10 had an expression QTL (eQTL) colocalized with the corticosterone QTL on chromosome 5 and PDE1C had an eQTL colocalized with the aldosterone QTL on chromosome 2. Furthermore, in both cases, the expression levels of the genes were correlated with the plasma levels of the hormones. Hence, both these genes are strong putative candidates for the domestication-induced modifications of the stress response in chickens. Improved understanding of the genes associated with HPA-axis reactivity can provide insights into the pathways and mechanisms causing stress-related pathologies.

  • 8.
    Fallahshahroudi, Amir
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    de Kock, Nick
    Department of Chemistry - Biomedical Center, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Sweden.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Ubhayasekera, S.J. Kumari A.
    Department of Chemistry - Biomedical Center, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Sweden.
    Bergqvist, Jonas
    Department of Chemistry - Biomedical Center, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Sweden.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Domestication Effects on Stress Induced Steroid Secretion and Adrenal Gene Expression in Chickens2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, p. 1-10, article id 15345Article in journal (Refereed)
    Abstract [en]

    Understanding the genetic basis of phenotypic diversity is a challenge in contemporary biology. Domestication provides a model for unravelling aspects of the genetic basis of stress sensitivity. The ancestral Red Junglefowl (RJF) exhibits greater fear-related behaviour and a more pronounced HPA-axis reactivity than its domesticated counterpart, the White Leghorn (WL). By comparing hormones (plasmatic) and adrenal global gene transcription profiles between WL and RJF in response to an acute stress event, we investigated the molecular basis for the altered physiological stress responsiveness in domesticated chickens. Basal levels of pregnenolone and dehydroepiandrosterone as well as corticosterone response were lower in WL. Microarray analysis of gene expression in adrenal glands showed a significant breed effect in a large number of transcripts with over-representation of genes in the channel activity pathway. The expression of the best-known steroidogenesis genes were similar across the breeds used. Transcription levels of acute stress response genes such as StAR, CH25 and POMC were upregulated in response to acute stress. Dampened HPA reactivity in domesticated chickens was associated with changes in the expression of several genes that presents potentially minor regulatory effects rather than by means of change in expression of critical steroidogenic genes in the adrenal.

  • 9.
    Fallahsharoudi, Amir
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    de Kock, Neil
    Department of Chemistry e Biomedical Center, Analytical Chemistry and Neurochemistry - BMC, 75124 Uppsala, Sweden.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Bektic, Lejla
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Ubhayasekera, S J Kumari A
    Department of Chemistry e Biomedical Center, Analytical Chemistry and Neurochemistry - BMC, 75124 Uppsala, Sweden.
    Bergquist, Jonas
    Department of Chemistry e Biomedical Center, Analytical Chemistry and Neurochemistry - BMC, 75124 Uppsala, Sweden.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    QTL mapping of stress related gene expression in a cross between domesticated chickens and ancestral red junglefowl.2017In: Molecular and Cellular Endocrinology, ISSN 0303-7207, E-ISSN 1872-8057, Vol. 446, p. 52-58, article id S0303-7207(17)30090-4Article in journal (Refereed)
    Abstract [en]

    Domestication of animals is associated with numerous alterations in physiology, morphology, and behavior. Lower reactivity of the hypothalamic-pituitary-adrenal (HPA) axis and reduced fearfulness is seen in most studied domesticates, including chickens. Previously we have shown that the physiological stress response as well as expression levels of hundreds of genes in the hypothalamus and adrenal glands are different between domesticated White Leghorn and the progenitor of modern chickens, the Red Junglefowl. To map genetic loci associated with the transcription levels of genes involved in the physiological stress response, we conducted an eQTL analysis in the F12 generation of an inter-cross between White Leghorn and Red Junglefowl. We selected genes for further studies based on their known function in the regulation of the HPA axis or sympathoadrenal (SA) system, and measured their expression levels in the hypothalamus and the adrenal glands after a brief stress exposure (physical restraint). The expression values were treated as quantitative traits for the eQTL mapping. The plasma levels of corticosterone were also assessed. We analyzed the correlation between gene expression and corticosterone levels and mapped eQTL and their potential effects on corticosterone levels. The effects on gene transcription of a previously found QTL for corticosterone response were also investigated. The expression levels of the glucocorticoid receptor (GR) in the hypothalamus and several genes in the adrenal glands were correlated with the post-stress levels of corticosterone in plasma. We found several cis- and trans-acting eQTL for stress-related genes in both hypothalamus and adrenal. In the hypothalamus, one eQTL for c-FOS and one QTL for expression of GR were found. In the adrenal tissue, we identified eQTL for the genes NR0B1, RGS4, DBH, MAOA, GRIN1, GABRB2, GABRB3, and HSF1. None of the found eQTL were significant predictors of corticosterone levels. The previously found QTL for corticosterone was associated with GR expression in hypothalamus. Our data suggests that domestication related modification in the stress response is driven by changes in the transcription levels of several modulators of the HPA and SA systems in hypothalamus and adrenal glands and not by changes in the expression of the steroidogenic genes. The presence of eQTL for GR in hypothalamus combined with the negative correlation between GR expression and corticosterone response suggests GR as a candidate for further functional studies regarding modification of stress response during chicken domestication.

  • 10.
    Fogelholm, Jesper
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Inkabi, Samuel
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Höglund, Andrey
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Abbey-Lee, Robin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Johnsson, Martin
    Univ Edinburgh, Scotland; Swedish Univ Agr Sci, Sweden.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Henriksen, Rie
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Genetical Genomics of Tonic Immobility in the Chicken2019In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, no 5, article id 341Article in journal (Refereed)
    Abstract [en]

    Identifying the molecular mechanisms of animal behaviour is an enduring goal for researchers. Gaining insight into these mechanisms enables us to gain a greater understanding of behaviour and their genetic control. In this paper, we perform Quantitative Trait Loci (QTL) mapping of tonic immobility behaviour in an advanced intercross line between wild and domestic chickens. Genes located within the QTL interval were further investigated using global expression QTL (eQTL) mapping from hypothalamus tissue, as well as causality analysis. This identified five candidate genes, with the genes PRDX4 and ACOT9 emerging as the best supported candidates. In addition, we also investigated the connection between tonic immobility, meat pH and struggling behaviour, as the two candidate genes PRDX4 and ACOT9 have previously been implicated in controlling muscle pH at slaughter. We did not find any phenotypic correlations between tonic immobility, struggling behaviour and muscle pH in a smaller additional cohort, despite these behaviours being repeatable within-test.

  • 11.
    Foyer, Pernilla
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. Swedish National Defence College, Stockholm, Sweden.
    Wilsson, Erik
    Swedish Armed Forces Dog Instruction Centre, Märsta, Sweden.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Early experiences modulate stress coping in a population of German shepherd dogs2013In: Applied Animal Behaviour Science, ISSN 0168-1591, E-ISSN 1872-9045, Vol. 146, no 1-4, p. 79-87Article in journal (Refereed)
    Abstract [en]

    Early experiences may alter later behavioural expressions in animals and these differences can be consistent through adulthood. In dogs, this may have a profound impact on welfare and working ability and, it is therefore interesting to evaluate how experiences during the first weeks of life contribute to shaping the long-term behaviour. We analysed data from 503 dogs from 105 litters, bred at the Swedish Armed Forces Dog Kennel. For each dog, the data comprised information on dam and sire, sex, litter size, sex ratio of litter, date of birth, and weight at birth, and at 10 days of age. Between the ages of 377 and 593 days, the dogs were tested in a temperament test, assessing their suitability as working dogs. The behaviour test comprised 12 different sub-tests, and was scored on a behavioural rating scale. A principal component analysis showed that the test performance could largely be attributed to four principal components (explaining 55.7% of variation), labelled Confidence, Physical Engagement, Social Engagement and Aggression. We analysed the effects of the different early life variables and sex on the principal component scores (PC scores) using linear modelling. PC scores on Confidence were affected by parity, sex and litter size, and Physical Engagement was affected by parity, growth rate, litter size and season of birth. Social Engagement was affected by growth rate and sex, and Aggression was affected by sex. Some of these effects disappeared when they were combined into a single linear model, but most of them remained significant also when controlling for collinearity. The results suggest that the early environment of dogs have long-lasting effects on their behaviour and coping styles in a stressful test situation and this knowledge can be used in the work with breeding of future military or police working dogs.

  • 12.
    Gering, E.
    et al.
    Kellogg Biological Station, Michigan State Universiry, 3700 East Gull Lake Road, Hickory Corners, MI 49060, USA.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Willis, P.
    Department of Biology, University of Victoria, Cunningham 202, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada.
    Getty, T.
    Kellogg Biological Station, Michigan State Universiry, 3700 East Gull Lake Road, Hickory Corners, MI 49060, USA.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Mixed ancestry and admixture in Kauai's feral chickens: invasion of domestic genes into ancient Red Junglefowl reserviors2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 9, p. 2112-2124Article in journal (Refereed)
    Abstract [en]

    A major goal of invasion genetics is to determine how establishment histories shape non-native organisms' genotypes and phenotypes. While domesticated species commonly escape cultivation to invade feral habitats, few studies have examined how this process shapes feral gene pools and traits. We collected genomic and phenotypic data from feral chickens (Gallus gallus) on the Hawaiian island of Kauai to (i) ascertain their origins and (ii) measure standing variation in feral genomes, morphology and behaviour. Mitochondrial phylogenies (D-loop & whole Mt genome) revealed two divergent clades within our samples. The rare clade also contains sequences from Red Junglefowl (the domestic chicken's progenitor) and ancient DNA sequences from Kauai that predate European contact. This lineage appears to have been dispersed into the east Pacific by ancient Polynesian colonists. The more prevalent MtDNA clade occurs worldwide and includes domesticated breeds developed recently in Europe that are farmed within Hawaii. We hypothesize this lineage originates from recently feralized livestock and found supporting evidence for increased G. gallus density on Kauai within the last few decades. SNPs obtained from whole-genome sequencing were consistent with historic admixture between Kauai's divergent (G. gallus) lineages. Additionally, analyses of plumage, skin colour and vocalizations revealed that Kauai birds' behaviours and morphologies overlap with those of domestic chickens and Red Junglefowl, suggesting hybrid origins. Together, our data support the hypotheses that (i) Kauai's feral G. gallus descend from recent invasion(s) of domestic chickens into an ancient Red Junglefowl reservoir and (ii) feral chickens exhibit greater phenotypic diversity than candidate source populations. These findings complicate management objectives for Pacific feral chickens, while highlighting the potential of this and other feral systems for evolutionary studies of invasions.

  • 13.
    Gering, Eben
    et al.
    Michigan State Univ, MI 48824 USA.
    Incorvaia, Darren
    Michigan State Univ, MI 48824 USA.
    Henriksen, Rie
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Getty, Thomas
    Michigan State Univ, MI 48824 USA.
    Maladaptation in feral and domesticated animals2019In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 12, no 7, p. 1274-1286Article, review/survey (Refereed)
    Abstract [en]

    Selection regimes and population structures can be powerfully changed by domestication and feralization, and these changes can modulate animal fitness in both captive and natural environments. In this review, we synthesize recent studies of these two processes and consider their impacts on organismal and population fitness. Domestication and feralization offer multiple windows into the forms and mechanisms of maladaptation. Firstly, domestic and feral organisms that exhibit suboptimal traits or fitness allow us to identify their underlying causes within tractable research systems. This has facilitated significant progress in our general understandings of genotype-phenotype relationships, fitness trade-offs, and the roles of population structure and artificial selection in shaping domestic and formerly domestic organisms. Additionally, feralization of artificially selected gene variants and organisms can reveal or produce maladaptation in other inhabitants of an invaded biotic community. In these instances, feral animals often show similar fitness advantages to other invasive species, but they are also unique in their capacities to modify natural ecosystems through introductions of artificially selected traits. We conclude with a brief consideration of how emerging technologies such as genome editing could change the tempos, trajectories, and ecological consequences of both domestication and feralization. In addition to providing basic evolutionary insights, our growing understanding of mechanisms through which artificial selection can modulate fitness has diverse and important applications-from enhancing the welfare, sustainability, and efficiency of agroindustry, to mitigating biotic invasions.

  • 14.
    Henriksen, Rie
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Andersson, L
    Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    The domesticated brain: genetics of brain mass and brain structure in an avian species.2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6Article in journal (Refereed)
    Abstract [en]

    As brain size usually increases with body size it has been assumed that the two are tightly constrained and evolutionary studies have therefore often been based on relative brain size (i.e. brain size proportional to body size) rather than absolute brain size. The process of domestication offers an excellent opportunity to disentangle the linkage between body and brain mass due to the extreme selection for increased body mass that has occurred. By breeding an intercross between domestic chicken and their wild progenitor, we address this relationship by simultaneously mapping the genes that control inter-population variation in brain mass and body mass. Loci controlling variation in brain mass and body mass have separate genetic architectures and are therefore not directly constrained. Genetic mapping of brain regions indicates that domestication has led to a larger body mass and to a lesser extent a larger absolute brain mass in chickens, mainly due to enlargement of the cerebellum. Domestication has traditionally been linked to brain mass regression, based on measurements of relative brain mass, which confounds the large body mass augmentation due to domestication. Our results refute this concept in the chicken.

  • 15.
    Jensen, Per
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Persson, Mia E
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Sundman, Ann-Sofie
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Roth, Lina S. V.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    The Genetics of How Dogs Became Our Social Allies2016In: Current directions in psychological science (Print), ISSN 0963-7214, E-ISSN 1467-8721, Vol. 25, no 5, p. 334-338Article in journal (Refereed)
    Abstract [en]

    Dogs were domesticated from wolves about 15,000 years ago, and an important selection pressure (intentional orunintentional) has been their ability to communicate and cooperate with people. They show extensive human-directedsociability, which varies within as well as between breeds and is not shared by ancestral wolves. Hence, dogs arepotentially ideal models for studying the genetics of social behavior. Here, we review some recent research carried outby us and others on this subject. We present results showing that recent selection of different breed types can be usedas a model system for investigating the genetic architecture of personalities. Furthermore, we review data showingthat human-directed social behavior is significantly related to a small number of genes that have known connectionsto human social disorders such as autism and schizophrenia. We suggest that dogs are excellent study subjects foranalyzing the evolution and genetics of social behavior and can serve as probes for human health and welfare.

  • 16.
    Johnsson, Martin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Gering, Eben
    Department of Zoology, Michigan University, Michigan, USA.
    Willis, Pamela
    Department of Biology, University of Victoria, Victoria, British Columbia, Canada.
    Lopez, Saioa
    UCL Genetics Institute, University College London, London, UK.
    Van Dorp, Lucy
    UCL Genetics Institute, University College London, London, UK.
    Hellenthal, Garrett
    UCL Genetics Institute, University College London, London, UK.
    Henriksen, Rie
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Friberg, Urban
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Feralisation targets different genomic loci to domestication in the chicken.2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 12950Article in journal (Refereed)
    Abstract [en]

    Feralisation occurs when a domestic population recolonizes the wild, escaping its previous restricted environment, and has been considered as the reverse of domestication. We have previously shown that Kauai Island's feral chickens are a highly variable and admixed population. Here we map selective sweeps in feral Kauai chickens using whole-genome sequencing. The detected sweeps were mostly unique to feralisation and distinct to those selected for during domestication. To ascribe potential phenotypic functions to these genes we utilize a laboratory-controlled equivalent to the Kauai population-an advanced intercross between Red Junglefowl and domestic layer birds that has been used previously for both QTL and expression QTL studies. Certain sweep genes exhibit significant correlations with comb mass, maternal brooding behaviour and fecundity. Our analyses indicate that adaptations to feral and domestic environments involve different genomic regions and feral chickens show some evidence of adaptation at genes associated with sexual selection and reproduction.

  • 17.
    Johnsson, Martin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Gustafsson, Ida
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Rubin, Carl-Johan
    Department of Medical Biochemistry and Michrobiology, BMC, Uppsala University, Uppsala, Sweden.
    Sahlqvist, Anna-Stina
    Department of Medical Sciences, Uppsala University, Uppsalam, Sweden.
    Jonnson, Kenneth B.
    Department of Surgical Sciences, Orthopeadics, Akademiska sjukhuset, Uppsala university, Uppsala, Sweden.
    Kjere, Susanne
    Department of Medical Sciences, Uppsala University,.
    Ekwall, Olov
    Departmet of Rheumatology and Inflammation Research, Institute of Medicine, The Sahlgrenska Academy, Gothenburg, Sweden.
    Kämpe, Olle
    Department of Medical Sciences, Uppsala University, Uppsalam, Sweden.
    Andersson, Leif
    Department of Medical Biochemistry and Michrobiology, BMC, Uppsala University, Uppsala, Sweden.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    A Sexual Ornament in Chickens Is Affected bu Pleiotropic Alleles at HAO1 and BMP2, Selected during Domestication2012In: PLOS Genetics, ISSN 1553-7390, Vol. 8, no 8, p. e10002914-Article in journal (Refereed)
    Abstract [en]

    Domestication is one of the strongest forms of short-term, directional selection. Although selection is typically only exerted on one or a few target traits, domestication can lead to numerous changes in many seemingly unrelated phenotypes. It is unknown whether such correlated responses are due to pleiotropy or linkage between separate genetic architectures. Using three separate intercrosses between wild and domestic chickens, a locus affecting comb mass (a sexual ornament in the chicken) and several fitness traits (primarily medullary bone allocation and fecundity) was identified. This locus contains two tightly-linked genes, BMP2 and HAO1, which together produce the range of pleiotropic effects seen. This study demonstrates the importance of pleiotropy (or extremely close linkage) in domestication. The nature of this pleiotropy also provides insights into how this sexual ornament could be maintained in wild populations.

  • 18.
    Johnsson, Martin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Univ Edinburgh, Scotland; Swedish Univ Agr Sci, Sweden.
    Henriksen, Rie
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Fogelholm, Jesper
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Höglund, Andrey
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Genetics and Genomics of Social Behavior in a Chicken Model2018In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 209, no 1, p. 209-221Article in journal (Refereed)
    Abstract [en]

    The identification of genes affecting sociality can give insights into the maintenance and development of sociality and personality. In this study, we used the combination of an advanced intercross between wild and domestic chickens with a combined QTL and eQTL genetical genomics approach to identify genes for social reinstatement, a social and anxiety-related behavior. A total of 24 social reinstatement QTL were identified and overlaid with over 600 eQTL obtained from the same birds using hypothalamic tissue. Correlations between overlapping QTL and eQTL indicated five strong candidate genes, with the gene TTRAP being strongly significantly correlated with multiple aspects of social reinstatement behavior, as well as possessing a highly significant eQTL.

  • 19.
    Johnsson, Martin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Univ Edinburgh, England; Swedish Univ Agr Sci, Sweden.
    Henriksen, Rie
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Swedish Univ Agr Sci, Sweden.
    Höglund, Andrey
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Swedish Univ Agr Sci, Sweden.
    Fogelholm, Jesper
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Swedish Univ Agr Sci, Sweden.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Swedish Univ Agr Sci, Sweden.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Swedish Univ Agr Sci, Sweden.
    Genetical genomics of growth in a chicken model2018In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 19, article id 72Article in journal (Refereed)
    Abstract [en]

    Background: The genetics underlying body mass and growth are key to understanding a wide range of topics in biology, both evolutionary and developmental. Body mass and growth traits are affected by many genetic variants of small effect. This complicates genetic mapping of growth and body mass. Experimental intercrosses between individuals from divergent populations allows us to map naturally occurring genetic variants for selected traits, such as body mass by linkage mapping. By simultaneously measuring traits and intermediary molecular phenotypes, such as gene expression, one can use integrative genomics to search for potential causative genes. Results: In this study, we use linkage mapping approach to map growth traits (N = 471) and liver gene expression (N = 130) in an advanced intercross of wild Red Junglefowl and domestic White Leghorn layer chickens. We find 16 loci for growth traits, and 1463 loci for liver gene expression, as measured by microarrays. Of these, the genes TRAK1, OSBPL8, YEATS4, CEP55, and PIP4K2B are identified as strong candidates for growth loci in the chicken. We also show a high degree of sex-specific gene-regulation, with almost every gene expression locus exhibiting sex-interactions. Finally, several trans-regulatory hotspots were found, one of which coincides with a major growth locus. Conclusions: These findings not only serve to identify several strong candidates affecting growth, but also show how sex-specificity and local gene-regulation affect growth regulation in the chicken.

  • 20.
    Johnsson, Martin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jonsson, Kenneth B
    Uppsala Univ, Akad Sjukhuset, Dept Surg Sci, Orthopaed, Uppsala, Sweden.
    Andersson, Leif
    Uppsala Univ, Dept Med Biochem & Microbiol, BMC, Uppsala, Sweden.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Genetic Regulation of Bone Metabolism in the Chicken: Similarities and Differences to Mammalian Systems2015In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 11, no 5, article id e1005250Article in journal (Refereed)
    Abstract [en]

    Birds have a unique bone physiology, due to the demands placed on them through egg production. In particular their medullary bone serves as a source of calcium for eggshell production during lay and undergoes continuous and rapid remodelling. We take advantage of the fact that bone traits have diverged massively during chicken domestication to map the genetic basis of bone metabolism in the chicken. We performed a quantitative trait locus (QTL) and expression QTL (eQTL) mapping study in an advanced intercross based on Red Junglefowl (the wild progenitor of the modern domestic chicken) and White Leghorn chickens. We measured femoral bone traits in 456 chickens by peripheral computerised tomography and femoral gene expression in a subset of 125 females from the cross with microarrays. This resulted in 25 loci for female bone traits, 26 loci for male bone traits and 6318 local eQTL loci. We then overlapped bone and gene expression loci, before checking for an association between gene expression and trait values to identify candidate quantitative trait genes for bone traits. A handful of our candidates have been previously associated with bone traits in mice, but our results also implicate unexpected and largely unknown genes in bone metabolism. In summary, by utilising the unique bone metabolism of an avian species, we have identified a number of candidate genes affecting bone allocation and metabolism. These findings can have ramifications not only for the understanding of bone metabolism genetics in general, but could also be used as a potential model for osteoporosis as well as revealing new aspects of vertebrate bone regulation or features that distinguish avian and mammalian bone.

  • 21.
    Johnsson, Martin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jonsson, Kenneth B
    Department of Surgical Sciences, Orthopaedics, Akademiska Sjukhuset, Uppsala University, Uppasla, Sweden.
    Andersson, Leif
    Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Quantitative trait locus and genetical genomics analysis identifies putatively causal genes for fecundity and brooding in the chicken2016In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 2, p. 311-319Article in journal (Refereed)
    Abstract [en]

    Life history traits such as fecundity are important to evolution because they make up components of lifetime fitness. Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding. We found 12 loci for different aspects of egg fecundity. We then combined the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. Overlaps between egg loci and expression loci, and trait–gene expression correlations identify 29 candidates from bone and five from hypothalamus. The candidate quantitative trait genes include fibroblast growth factor 1, and mitochondrial ribosomal proteins L42 and L32. In summary, we found putative quantitative trait genes for egg traits in the chicken that may have been affected by regulatory variants under chicken domestication. These represent, to the best of our knowledge, some of the first candidate genes identified by genome-wide mapping for life history traits in an avian species.

  • 22.
    Johnsson, Martin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Rubin, Carl-Johan
    Department of Medical Biochemistry and Michrobiology, BMC, Uppsala University, Sweden.
    Höglund, Andrey
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Sahlqvist, A-S,
    Research group of Autoimmunity, Akademiska sjukhuset, Uppsala University, Sweden.
    Jonsson, K.B.
    Department of Surgical Sciences, Orthopaedics, Akademiska sjukhuset, Uppsala university, Sweden.
    Kerje, S.
    Research group of Autoimmunity, Akademiska sjukhuset, Uppsala University, Sweden.
    Ekwall, O.
    Research group of Autoimmunity, Akademiska sjukhuset, Uppsala University, Sweden.
    Kämpe, O.
    Research group of Autoimmunity, Akademiska sjukhuset, Uppsala University, Sweden.
    Andersson, L.
    Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    The role of pleiotropy and linkage in genes affecting a sexual ornament and bone allocation in the chicken2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 9, p. 2275-2286Article in journal (Refereed)
    Abstract [en]

    Sexual selection and the ornaments that inform such choices have been extensively studied, particularly from a phenotypic perspective. Although more is being revealed about the genetic architecture of sexual ornaments, much still remains to be discovered. The comb of the chicken is one of the most widely recognized sexual ornaments, which has been shown to be correlated with both fecundity and bone allocation. In this study, we use a combination of multiple intercrosses between White Leghorn populations and wild-derived Red Junglefowl to, first, map quantitative trait loci (QTL) for bone allocation and, second, to identify expression QTL that correlate and colocalize with comb mass. These candidate quantitative genes were then assessed for potential pleiotropic effects on bone tissue and fecundity traits. We identify genes that correlate with both relative comb mass and bone traits suggesting a combination of both pleiotropy and linkage mediates gene regulatory variation in these traits.

  • 23.
    Johnsson, Martin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Williams, Michael J
    Institutionen för neurovetenskap, Uppsala universitet.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Genetical Genomics of Behavior: A novel chicken genomic model for anxiety behavior2016In: Genetics, ISSN 0016-6731, Vol. 202, no 1, p. 327+-Article in journal (Refereed)
    Abstract [en]

    The identification of genetic variants responsible for behavioral variation is an enduring goal in biology, with wide-scale ramifications, ranging from medical research to evolutionary theory on personality syndromes. Here, we use for the first time a large-scale genetical genomics analysis in the brain of the chicken to identify genes affecting anxiety as measured by an open field test. We combine quantitative trait locus (QTL) analysis in 572 individuals and expression QTL (eQTL) analysis in 129 individuals from an advanced intercross between domestic chickens and Red Junglefowl. We identify ten putative quantitative trait genes affecting anxiety behavior. These genes were tested for an association in the mouse Heterogenous Stock anxiety (open field) dataset and human GWAS datasets for bipolar disorder, major depressive disorder and schizophrenia. Although comparisons between species are complex, associations were observed for four of the candidate genes in mouse, and three of the candidate genes in humans. Using a multi-model approach we have therefore identified a number of putative quantitative trait genes affecting anxiety behavior, principally in the chicken but also with some potentially translational effects as well. This study demonstrates that the chicken is an excellent model organism for the genetic dissection of behavior.

  • 24.
    Karlsson, Anna-Carin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Fallahshahroudi, Amir
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Johnsen, Hanna
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Andersson, Leif
    Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    The effect of a domestication related mutation in the thyroid stimulating hormone receptor (TSHR) on photoperiodic response and reproduction in chickenManuscript (preprint) (Other academic)
    Abstract [en]

    The thyroid stimulating hormone receptor (TSHR) has been suggested to be a “domestication locus” in the chicken. A strong selective sweep over the gene in domestic breeds of chicken, but not in the ancestral Red Junglefowl, and significant effects of a mutation in TSHR on domestication related traits in chicken, indicate that the gene has been important for the chicken domestication. The TSHR play a key role in the signal transduction of seasonal reproduction, which is characteristically less strict in domestic animals. We investigated the effect of the mutation on reproductive traits as well as TSHB, TSHR, DIO2 and DIO3 gene expression during altered day length (photoperiod) in females and males intercross chickens homozygous for the mutation (d/d) or wild type homozygotes (w/w). This allowed an assessment of the effect of genotype at this locus against a random mix of RJF and WL genotypes throughout the rest of the genome. The TSHR gene expression was significantly lower in both d/d females and males, in comparison to w/w individuals, indicating a strong effect of the “domestic” mutation on gene expression. The d/d females showed a faster increase in the onset of laying than w/w females, and d/d males showed a reduced response to altered day length in testicular size and significant lower levels of TSHB and DIO3 expression, in comparison to w/w males. Additionally, pure White Leghorn females kept under natural day length in Sweden during December showed active ovaries and significant lower levels of TSHR and DIO3 expression in comparison to Red Junglefowl females kept under similar conditions. Our study suggest that the TSHR mutation affects photoperiodic response in chicken in the direction of being less dependent on seasonal reproduction, a typical domestication feature, and may therefore have been important for the chicken domestication.

  • 25.
    Karlsson, Anna-Carin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Fallahsharoudi, Amir
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Johnsen, Hanna
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Andersson, Leif
    Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    A domestication related mutation in the thyroid stimulating hormonereceptor gene (TSHR) modulates photoperiodic response andreproduction in chickens2016In: General and Comparative Endocrinology, ISSN 0016-6480, E-ISSN 1095-6840, Vol. 228, p. 69-78Article in journal (Refereed)
    Abstract [en]

    The thyroid stimulating hormone receptor gene (TSHR) has been suggested to be a ‘‘domestication locus”in the chicken. A strong selective sweep over TSHR in domestic breeds together with significant effects ofa mutation in the gene on several domestication related traits, indicate that the gene has been importantfor chicken domestication. TSHR plays a key role in the signal transduction of seasonal reproduction,which is characteristically less strict in domestic animals. We used birds from an advanced intercross linebetween ancestral Red Junglefowl (RJF) and domesticated White Leghorn (WL) to investigate effects ofthe mutation on reproductive traits as well as on TSHB, TSHR, DIO2 and DIO3 gene expression duringaltered day length (photoperiod). We bred chickens homozygous for either the mutation (d/d) or wildtype allele (w/w), allowing assessment of the effect of genotype at this locus while also controlling forbackground variation in the rest of the genome. TSHR gene expression in brain was significantly lowerin both d/d females and males and d/d females showed a faster onset of egg laying at sexual maturity thanw/w. Furthermore, d/d males showed a reduced testicular size response to decreased day length, andlower levels of TSHB and DIO3 expression. Additionally, purebred White Leghorn females kept under naturalshort day length in Sweden during December had active ovaries and lower levels of TSHR and DIO3expression compared to Red Junglefowl females kept under similar conditions. Our study indicates thatthe TSHR mutation affects photoperiodic response in chicken by reducing dependence of seasonal reproduction,a typical domestication feature, and may therefore have been important for chickendomestication.

  • 26.
    Nätt, Daniel
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Rubin, Carl-Johan
    Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Beltéky, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Andersson, Leif
    Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens2012In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 13, no 59Article in journal (Refereed)
    Abstract [en]

    Variations in gene expression, mediated by epigenetic mechanisms, may cause broad phenotypic effects in animals. However, it has been debated to what extent expression variation and epigenetic modifications, such as patterns of DNA methylation, are transferred across generations, and therefore it is uncertain what role epigenetic variation may play in adaptation. Here, we show that in Red Junglefowl, ancestor of domestic chickens, gene expression and methylation profiles in thalamus/hypothalamus differ substantially from that of a domesticated egg laying breed. Expression as well as methylation differences are largely maintained in the offspring, demonstrating reliable inheritance of epigenetic variation. Some of the inherited methylation differences are tissue-specific, and the differential methylation at specific loci are little changed after eight generations of intercrossing between Red Junglefowl and domesticated laying hens. There was an over-representation of differentially expressed and methylated genes in selective sweep regions associated with chicken domestication. Hence, our results show that epigenetic variation is inherited in chickens, and we suggest that selection of favourable epigenomes, either by selection of genotypes affecting epigenetic states, or by selection of methylation states which are inherited independently of sequence differences, may have been an important aspect of chicken domestication.

  • 27.
    Per, Jensen
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Dominic, Wright
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Behavioral Genetics and Animal Science2013In: Genetics and the Behavior of Domestic Animals / [ed] Temple Grandin, Mark J. Deesing, Amsterdam, Netherlands: Academic Press, 2013, 2, p. 41-80Chapter in book (Other academic)
    Abstract [en]

    Behavior is shaped by both genetics and experience--nature and nurture. This book synthesizes research from behavioral genetics and animal and veterinary science, bridging the gap between these fields. The objective is to show that principles of behavioral genetics have practical applications to agricultural and companion animals.

    The continuing domestication of animals is a complex process whose myriad impacts on animal behavior are commonly under-appreciated. Genetic factors play a significant role in both species-specific behaviors and behavioral differences exhibited by individuals in the same species. Leading authorities explore the impact of increased intensities of selection on domestic animal behavior. Rodents, cattle, pigs, sheep, horses, herding and guard dogs, and poultry are all included in these discussions of genetics and behavior, making this book useful to veterinarians, livestock producers, laboratory animal researchers and technicians, animal trainers and breeders, and any researcher interested in animal behavior.

    • Includes four new chapters on dog and fox behavior, pig behavior, the effects of domestication and horse behavior
    • Synthesizes research from behavioral genetics, animal science, and veterinary literature
    • Broaches fields of behavior genetics and behavioral research
    • Includes practical applications of principles discovered by behavioral genetics researchers
    • Covers many species ranging from pigs, dogs, foxes, rodents, cattle, horses, and cats
  • 28.
    Persson, Mia
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Roth, Lina
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Human-directed social behaviour in dogs shows significant heritability2015In: Genes, Brain and Behavior, ISSN 1601-1848, E-ISSN 1601-183X, Vol. 14, no 4, p. 337-344Article in journal (Refereed)
    Abstract [en]

    Through domestication and co-evolution with humans, dogs have developed abilities to attract human attention, e.g. in a manner of seeking assistance when faced with a problem solving task. The aims of this study were to investigate within breed variation in human-directed contact seeking in dogs and to estimate its genetic basis. To do this, 498 research beagles, bred and kept under standardized conditions, were tested in an unsolvable problem task. Contact seeking behaviours recorded included both eye contact and physical interactions. Behavioural data was summarized through a principal component analysis, resulting in four components: test interactions, social interactions, eye contact and physical contact. Females scored significantly higher on social interactions and physical contact and age had an effect on eye contact scores. Narrow sense heritabilities (h2) of the two largest components were estimated at 0.32 and 0.23 but were not significant for the last two components. These results show that within the studied dog population, behavioural variation in human-directed social behaviours was sex dependent and that the utilization of eye contact seeking increased with age and experience. Hence, heritability estimates indicate a significant genetic contribution to the variation found in human-directed social interactions, suggesting that social skills in dogs have a genetic basis, but can also be shaped and enhanced through individual experiences. This research gives the opportunity to further investigate the genetics behind dogs’ social skills, which could also play a significant part into research on human social disorders such as autism.

  • 29.
    Persson, Mia
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Roth, Lina
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Batakis, Petros
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Genomic Regions Associated With Interspecies Communication in Dogs Contain Genes Related to Human Social Disorders2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 33439Article in journal (Refereed)
    Abstract [en]

    Unlike their wolf ancestors, dogs have unique social skills for communicating and cooperating with humans. Previously, significant heritabilities for human-directed social behaviors have been found in laboratory beagles. Here, a Genome-Wide Association Study identified two genomic regions associated with dog's human-directed social behaviors. We recorded the propensity of laboratory beagles, bred, kept and handled under standardized conditions, to initiate physical interactions with a human during an unsolvable problem-task, and 190 individuals were genotyped with an HD Canine SNP-chip. One genetic marker on chromosome 26 within the SEZ6L gene was significantly associated with time spent close to, and in physical contact with, the human. Two suggestive markers on chromosome 26, located within the ARVCF gene, were also associated with human contact seeking. Strikingly, four additional genes present in the same linkage blocks affect social abilities in humans, e.g., SEZ6L has been associated with autism and COMT affects aggression in adolescents with ADHD. This is, to our knowledge, the first genome-wide study presenting candidate genomic regions for dog sociability and inter-species communication. These results advance our understanding of dog domestication and raise the use of the dog as a novel model system for human social disorders.

  • 30.
    Pértille, Fábio
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Univ Sao Paulo, Brazil.
    Da Silva, Vinicius H.
    Wageningen Univ and Res, Netherlands; Netherlands Inst Ecol NIOO KNAW, Netherlands; Swedish Univ Agr Sci, Sweden.
    Johansson, Anna M.
    Swedish Univ Agr Sci, Sweden.
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Coutinho, Luiz L.
    Univ Sao Paulo, Brazil.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Guerrero Bosagna, Carlos
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification2019In: Epigenetics, ISSN 1559-2294, E-ISSN 1559-2308Article in journal (Refereed)
    Abstract [en]

    DNA methylation in CpGs dinucleotides is associated with high mutability and disappearance of CpG sites during evolution. Although the high mutability of CpGs is thought to be relevant for vertebrate evolution, very little is known on the role of CpG-related mutations in the genomic diversification of vertebrates. Our study analysed genetic differences in chickens, between Red Junglefowl (RJF; the living closest relative to the ancestor of domesticated chickens) and domesticated breeds, to identify genomic dynamics that have occurred during the process of their domestication, focusing particularly on CpG-related mutations. Single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) between RJF and these domesticated breeds were assessed in a reduced fraction of their genome. Additionally, DNA methylation in the same fraction of the genome was measured in the sperm of RJF individuals to identify possible correlations with the mutations found between RJF and the domesticated breeds. Our study shows that although the vast majority of CpG-related mutations found relate to CNVs, CpGs disproportionally associate to SNPs in comparison to CNVs, where they are indeed substantially under-represented. Moreover, CpGs seem to be hotspots of mutations related to speciation. We suggest that, on the one hand, CpG-related mutations in CNV regions would promote genomic flexibility in evolution, i.e., the ability of the genome to expand its functional possibilities; on the other hand, CpG-related mutations in SNPs would relate to genomic specificity in evolution, thus, representing mutations that would associate with phenotypic traits relevant for speciation.

  • 31.
    Schwochow Thalmann, Doreen
    et al.
    Swedish University of Agriculture Science, Sweden; University of Paris Saclay, France.
    Ring, Henrik
    Uppsala University, Sweden.
    Sundstrom, Elisabeth
    Uppsala University, Sweden.
    Cao, Xiaofang
    Uppsala University, Sweden.
    Larsson, Marten
    Uppsala University, Sweden.
    Kerje, Susanne
    Uppsala University, Sweden.
    Höglund, Andrey
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Fogelholm, Jesper
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jemth, Per
    Uppsala University, Sweden.
    Hallbook, Finn
    Uppsala University, Sweden.
    BedHom, Bertrand
    University of Paris Saclay, France.
    Dorshorst, Ben
    Virginia Tech, VA USA.
    Tixier-Boichard, Michele
    University of Paris Saclay, France.
    Andersson, Leif
    Swedish University of Agriculture Science, Sweden; Uppsala University, Sweden; Texas AandM University, TX 77843 USA.
    The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes in CDKN2A2017In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 13, no 4, article id e1006665Article in journal (Refereed)
    Abstract [en]

    Sex-linked barring is a fascinating plumage pattern in chickens recently shown to be associated with two non-coding and two missense mutations affecting the ARF transcript at the CDKN2A tumor suppressor locus. It however remained a mystery whether all four mutations are indeed causative and how they contribute to the barring phenotype. Here, we show that Sex-linked barring is genetically heterogeneous, and that the mutations form three functionally different variant alleles. The B0 allele carries only the two non-coding changes and is associated with the most dilute barring pattern, whereas the B1 and B2 alleles carry both the two non-coding changes and one each of the two missense mutations causing the Sex-linked barring and Sex-linked dilution phenotypes, respectively. The data are consistent with evolution of alleles where the non-coding changes occurred first followed by the two missense mutations that resulted in a phenotype more appealing to humans. We show that one or both of the non-coding changes are cis-regulatory mutations causing a higher CDKN2A expression, whereas the missense mutations reduce the ability of ARF to interact with MDM2. Caspase assays for all genotypes revealed no apoptotic events and our results are consistent with a recent study indicating that the loss of melanocyte progenitors in Sex-linked barring in chicken is caused by premature differentiation and not apoptosis. Our results show that CDKN2A is a major locus driving the differentiation of avian melanocytes in a temporal and spatial manner.

  • 32.
    Sundman, Ann-Sofie
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Similar recent selection criteria associated with different behavioural effects in two dog breeds2016In: Genes, Brain and Behavior, ISSN 1601-1848, E-ISSN 1601-183X, Vol. 15, no 8, p. 750-756Article in journal (Refereed)
    Abstract [en]

    Selection during the last decades has split some established dog breeds into morphologically and behaviourally divergent types. These breed splits are interesting models for behaviour genetics since selection has often been for few and well-defined behavioural traits. The aim of this study was to explore behavioural differences between selection lines in golden and Labrador retriever, in both of which a split between a common type (pet and conformation) and a field type (hunting) has occurred. We hypothesized that the behavioural profiles of the types would be similar in both breeds. Pedigree data and results from a standardized behavioural test from 902 goldens (698 common and 204 field) and 1672 Labradors (1023 and 649) were analysed. Principal component analysis revealed six behavioural components: curiosity, play interest, chase proneness, social curiosity, social greeting and threat display. Breed and type affected all components, but interestingly there was an interaction between breed and type for most components. For example, in Labradors the common type had higher curiosity than the field type (F1,1668 = 18.359; P < 0.001), while the opposite was found in goldens (F1,897 = 65.201; P < 0.001). Heritability estimates showed considerable genetic contributions to the behavioural variations in both breeds, but different heritabilities between the types within breeds was also found, suggesting different selection pressures. In conclusion, in spite of similar genetic origin and similar recent selection criteria, types behave differently in the breeds. This suggests that the genetic architecture related to behaviour differs between the breeds.

  • 33.
    Wirén, Anders
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Domestication-related variation in social preferences in chickens is affected by genotype on a growth QTL2013In: Genes, Brain and Behavior, ISSN 1601-1848, E-ISSN 1601-183X, Vol. 12, no 3, p. 330-337Article in journal (Refereed)
    Abstract [en]

    A growth-related QTL on chicken chromosome 1 has previously been shown to influence domestication behaviour in chickens. In this study, we used Red Junglefowl (RJF) and White Leghorn (WL) as well as the intercross between them to investigate whether stress affects the way birds allocate their time between familiar and unfamiliar conspecifics in a social preference test (‘social support seeking’), and how this is related to genotype at specific loci within the growth QTL. Red Junglefowl males spent more time with unfamiliar chickens before the stressful event compared to the other birds, whereas all birds except WL males tended to spend less time with unfamiliar ones after stress. A significant QTL locus was found to influence both social preference under undisturbed circumstances and social support seeking. The WL allele at this QTL was associated not only with a preference for unfamiliar individuals but also with a shift towards familiar ones in response to stress (social support seeking). A second, suggestive QTL also affected social support seeking, but in the opposite direction; the WL allele was associated with increased time spent with unfamiliar individuals. The region contains several possible candidate genes, and gene expression analysis of a number of them showed differential expression between RJF and WL of AVPR2 (receptor for vasotocin), and possibly AVPR1a (another vasotocin receptor) and NRCAM (involved in neural development) in the lower frontal lobes of the brains of RJF and WL animals. These three genes continue to be interesting candidates for the observed behavioural effects.

  • 34.
    Wirén, Anders
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Effects of a Chicken Growth QTL on Behaviour are due to Linkage rather than PleiotropyManuscript (preprint) (Other academic)
    Abstract [en]

    earlier studies, we have found pleiotropic effects of a growth QTL in chickens on behavioural traits that have changed as a result of domestication. In this study we performed a) a refined analysis of the QTL in an advanced intercross line between Red Junglefowl (RJF) and White Leghorn layers (WL) to investigate if different behavioural and physiological traits are associated with different regions of the QTL, and b) brain gene expression analysis (using qRT-PCR) in RJF and WL, comparing the expression between breeds of a number of genes within the growth QTL that may be considered candidates for affecting behavioural traits. The refined QTL analysis was performed on 62 birds from a selected line corresponding to the F7 generation of an RJF×WL intercross (SAIL). The gene expression analysis was performed on 12 RJF and 10 WL birds. In addition to recording of weight data, the SAIL birds were exposed to a behavioural test measuring aspects of sociality and emotionality. The QTL analysis found a significant association between body weight at 8 days of age and a 1.7 MB region in the QTL, and a suggestive association between emotionality related behaviours and a different part, 7.5 MB large, of the QTL. The gene expression analysis showed differential expression of AVPR2 (receptor for vasotocin), possibly AVPR1a (another vasotocin receptor) and NRCAM (involved in neural development) in the lower frontal lobes of the brains of RJF and WL birds. It therefore seems that linkage of several different genes affecting different traits, rather than pleiotropy of one or a few, may explain the many effects of this QTL, and that AVPR2, AVPR1a and NRCAM cannot be discarded as candidate genes for the observed effects.

  • 35.
    Wirén, Anders
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Social preference and support seeking in chickens is related to genotype on a growth QTLManuscript (preprint) (Other academic)
    Abstract [en]

    A growth related QTL on chicken chromosome 1 has previously been shown to influence both emotionality and social behaviour in an intercross line between Red Junglefowl (RJF, ancestor of all domestic chicken breeds) and the domesticated White Leghorn layer (WL). Social support from a familiar animal has been shown to attenuate stress response in other species. In this study we therefore used the RJF×WL intercross line to investigate whether stress in the form of physical restraint affects the way birds allocate their time between familiar and unfamiliar conspecifics in a social preference test. A refined QTL study was performed, focussing on the region of the previously reported growth QTL to find possible loci affecting traits related to social preference and social support. A significant QTL was found to influence both social preference under undisturbed circumstances and social support seeking in response to stress. A WL allele at this QTL was associated with a preference for unfamiliar individuals but also with a shift towards familiar ones in response to stress. A second, suggestive, QTL also affected social support seeking, but in the opposite direction; a WL allele was associated with seeking social support from unfamiliar individuals. It is difficult to speculate on causative genes, but it is worth noting that AVPR1a (known for effects on social behaviour), AVPR2, NRCAM (related to autism) and GRIP1 (Glutamate Receptor Interacting Protein) are located this chromosomal area.

  • 36.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    QTL Mapping of Behaviour in the Zebrafish2011In: Zebrafish Models in Neurobehavioural Research / [ed] A.V. Kalueff and J.M. Chachat, New York, USA: Humana Press, 2011, 1, p. 101-141Chapter in book (Other academic)
    Abstract [en]

    The study of complex traits is one of the greatest current challenges in biology, and the exact mechanism whereby individual genes cause small quantitative variation in any given trait still remains largely unresolved. In the case of behavioural traits, with lower heritabilities and repeatabilities as compared to other character-types, this problem is exacerbated even further. One of the principal forms of genetic analysis for quantitative traits is via QTL (quantitative trait loci) mapping, with the power of this approach even greater in model organisms due to the array of genomic tools available. These tools give a genuine possibility of identifying the actual causative genes or nucleotides responsible for the variation (the quantitative trait nucleotide, or QTN). The zebrafish displays a range of behaviours that are both complex and bear a striking similarity to some of the behavioural measurements performed in other model organisms, notably affecting anxiety and social aggregation. The combination of the behavioural variation present in the zebrafish and the genetic and genomic advantages to QTL mapping available for this species paves the way for its use in generating a new model for the genetic dissection of such trait types. This chapter aims to first discuss the zebrafish as a behavioural model suitable for QTL mapping, focussing in particular on the behaviours of shoaling and predator inspection, before giving an overview of what is contained in a QTL study and the types of crossings, analysis and their relevance to behavioural QTL mapping. Finally two case studies are presented, one of anxiety behaviour in mice, one of shoaling and boldness behaviour in zebrafish.

  • 37.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    QTL Mapping Using Behavioral traits in the Adult Zebrafish2012In: Zebrafish Protocols for Neurobehavioral Research / [ed] Allan V. Kalueff and Adam Michael Stewart, Humana Press, 2012, p. 301-312Chapter in book (Refereed)
    Abstract [en]

       Zebrafish (Danio rerio) play an integral role in biomedical research, enabling researchers to examine physiological mechanisms and pathways relevant to human pathogenesis and its therapy. That, along with their low cost, easy manipulation, short reproductive cycles, and physiological homology to humans, has made zebrafish a vital model organism for neuroscience research. Zebrafish Protocols for Neurobehavioral Research addresses protocols for both larval and adult models, written by the leading experts in the field of zebrafish research.  Part I of this book takes advantage of the high-throughput nature of larval models to offer protocols for research requiring high output, easily manipulated screens. The second half of the book focuses on the robust and sophisticated behaviors of adult zebrafish, suitable for the neurophenotyping of complex traits and multi-domain disorders.  Importantly, these models complement each other, working together to provide researchers with valuable insights into neurobiology of normal and pathological behavior. Thorough and cutting-edge, this volume is a useful, authoritative reference guide that should hold a coveted spot in zebrafish laboratories across the globe

  • 38.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    The Genetic Architecture of Domestication in Animals2015In: Bioinformatics and Biology Insights, ISSN 1177-9322, E-ISSN 1177-9322, Vol. 9, no S4, p. 11-20Article in journal (Refereed)
    Abstract [en]

    Domestication has been essential to the progress of human civilization, and the process itself has fascinated biologists for hundreds of years. Domestication has led to a series of remarkable changes in a variety of plants and animals, in what is termed the "domestication phenotype." In domesticated animals, this general phenotype typically consists of similar changes in tameness, behavior, size/morphology, color, brain composition, and adrenal gland size. This domestication phenotype is seen in a range of different animals. However, the genetic basis of these associated changes is still puzzling. The genes for these different traits tend to be grouped together in clusters in the genome, though it is still not clear whether these clusters represent pleiotropic effects, or are in fact linked clusters. This review focuses on what is currently known about the genetic architecture of domesticated animal species, if genes of large effect (often referred to as major genes) are prevalent in driving the domestication phenotype, and whether pleiotropy can explain the loci underpinning these diverse traits being colocated.

  • 39.
    Wright, Dominic
    et al.
    Uppsala University.
    Boije, H.
    Uppsala University.
    Meadows, J.R.S.
    Uppsala University.
    Bedhom, B.
    INRA, AgroParisTech.
    Gourichon, D.
    INRA, AgroParisTech.
    Vieaud, A.
    INRA.
    Tixier-Boichard, M.
    INRA.
    Rubin, C.-J.
    Uppsala University Hospital.
    Imsland, F.
    Uppsala University.
    Hallbook, F.
    Uppsala University.
    Andersson, L.
    Uppsala University.
    Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens2009In: PLoS Genetics, ISSN 1553-7390, Vol. 5, no 6, p. e1000512-Article in journal (Refereed)
    Abstract [en]

    Pea-comb is a dominant mutation in chickens that drastically reduces the size of the comb and wattles. It is an adaptive trait in cold climates as it reduces heat loss and makes the chicken less susceptible to frost lesions. Here we report that Pea-comb is caused by a massive amplification of a duplicated sequence located near evolutionary conserved non-coding sequences in intron 1 of the gene encoding the SOX5 transcription factor. This must be the causative mutation since all other polymorphisms associated with the Pea-comb allele were excluded by genetic analysis. SOX5 controls cell fate and differentiation and is essential for skeletal development, chondrocyte differentiation, and extracellular matrix production. Immunostaining in early embryos demonstrated that Pea-comb is associated with ectopic expression of SOX5 in mesenchymal cells located just beneath the surface ectoderm where the comb and wattles will subsequently develop. The results imply that the duplication expansion interferes with the regulation of SOX5 expression during the differentiation of cells crucial for the development of comb and wattles. The study provides novel insight into the nature of mutations that contribute to phenotypic evolution and is the first description of a spontaneous and fully viable mutation in this developmentally important gene.

  • 40.
    Wright, Dominic
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, United Kingdom.
    Kerje, Susanne
    Department of Medical Biochemistry & Microbiology, BMC, Uppsala University, Uppsala, Sweden.
    Brändström, Helena
    Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden.
    Schütz, Karin
    Department of Animal Environment & Health, Section of Ethology, Swedish University of Agricultural Sciences, Skara, Sweden.
    Kindmark, Andreas
    Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden.
    Andersson, Leif
    Department of Medical Biochemistry & Microbiology, BMC, Uppsala University, Uppsala, Sweden.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Pizzari, Tommaso
    Edward Grey Institute, Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom.
    The genetic architecture of a female sexual ornament2008In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 62, no 1, p. 86-98Article in journal (Refereed)
    Abstract [en]

    Understanding the evolution of sexual ornaments, and particularly that of female sexual ornaments, is an enduring challenge in evolutionary biology. Key to this challenge are establishing the relationship between ornament expression and female reproductive investment, and determining the genetic basis underpinning such relationship. Advances in genomics provide unprecedented opportunities to study the genetic architecture of sexual ornaments in model species. Here, we present a quantitative trait locus (QTL) analysis of a female sexual ornament, the comb of the fowl, Gallus gallus, using a large-scale intercross between red junglefowl and a domestic line, selected for egg production. First, we demonstrate that female somatic investment in comb reflects female reproductive investment. Despite a trade-off between reproductive and skeletal investment mediated by the mobilization of skeletal minerals for egg production, females with proportionally large combs also had relatively high skeletal investment. Second, we identify a major QTL for bisexual expression of comb mass and several QTL specific to female comb mass. Importantly, QTL for comb mass were nonrandomly clustered with QTL for female reproductive and skeletal investment on chromosomes one and three. Together, these results shed light onto the physiological and genetic architecture of a female ornament. 

  • 41.
    Wright, Dominic
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Rubin, C
    Uppsala University.
    Schutz, K
    AgResearch Ltd.
    Kerje, S
    Uppsala University.
    Kindmark, A
    University of Uppsala Hospital.
    Brandstrom, H
    University of Uppsala Hospital.
    Andersson, L
    Uppsala University.
    Pizzari, T
    University of Oxford.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Onset of Sexual Maturity in Female Chickens is Genetically Linked to Loci Associated with Fecundity and a Sexual Ornament2012In: Reproduction in domestic animals, ISSN 0936-6768, E-ISSN 1439-0531, Vol. 47, no SI, p. 31-36Article in journal (Refereed)
    Abstract [en]

    Onset of sexual maturation is a trait of extreme importance both evolutionarily and economically. Unsurprisingly therefore, domestication has acted to reduce the time to sexual maturation in a variety of animals, including the chicken. In comparison with wild progenitor chickens [the Red Junglefowl (RJF)], domestic layer hens attain maturity approximately 20% earlier. In addition, domestic layers also possess larger combs (a sexual ornament), produce more eggs and have denser bones. A large quantitative trait loci (QTL) analysis (n = 377) was performed using an F2 intercross between a White Leghorn layer breed and a RJF population, with onset of sexual maturity measured and mapped to three separate loci. This cross has already been analysed for comb mass, egg production and bone allocation. Onset of sexual maturity significantly correlated with comb mass, whilst the genetic architecture for sexual maturity and comb mass overlapped at all three loci. For two of these loci, the QTL for sexual maturity and comb mass were statistically indistinguishable from pleiotropy, suggesting that the alleles that increase comb mass also decrease onset of sexual maturity.

  • 42.
    Wright, Dominic
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Zoology . Linköping University, The Institute of Technology.
    Rubin, C-J
    Dept. of Medical Biochemistry and Microbiology, BMC, Uppsala University.
    Martinez Barrio, A
    Dept. of Medical Sciences, Uppsala University Hospital.
    Schütz, K
    Linnaeus Centre for Bioinformatics, Uppsala University.
    Kerje, S
    Dept. of Medical Biochemistry and Microbiology, BMC, Uppsala University.
    Brändström, H
    Dept. of Medical Biochemistry and Microbiology, BMC, Uppsala University.
    Kindmark, A
    Dept. of Medical Biochemistry and Microbiology, BMC, Uppsala University.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Zoology . Linköping University, The Institute of Technology.
    Andersson, L
    Linköping University, Department of Physics, Chemistry and Biology, Zoology . Linköping University, The Institute of Technology.
    The genetic architecture of domestication in the chicken: effects of pleiotropy and linkage2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, p. 5140-5156Article in journal (Refereed)
    Abstract [en]

    The extent of pleiotropy and epistasis in quantitative traits remains equivocal. In the caseof pleiotropy, multiple quantitative trait loci are often taken to be pleiotropic if theirconfidence intervals overlap, without formal statistical tests being used to ascertain ifthese overlapping loci are statistically significantly pleiotropic. Additionally, the degreeto which the genetic correlations between phenotypic traits are reflected in thesepleiotropic quantitative trait loci is often variable, especially in the case of antagonisticpleiotropy. Similarly, the extent of epistasis in various morphological, behavioural andlife-history traits is also debated, with a general problem being the sample sizes requiredto detect such effects. Domestication involves a large number of trade-offs, which arereflected in numerous behavioural, morphological and life-history traits which haveevolved as a consequence of adaptation to selective pressures exerted by humans andcaptivity. The comparison between wild and domestic animals allows the geneticanalysis of the traits that differ between these population types, as well as being ageneral model of evolution. Using a large F2 intercross between wild and domesticatedchickens, in combination with a dense SNP and microsatellite marker map, bothpleiotropy and epistasis were analysed. The majority of traits were found to segregate in11 tight ‘blocks’ and reflected the trade-offs associated with domestication. These blockswere shown to have a pleiotropic ‘core’ surrounded by more loosely linked loci. Incontrast, epistatic interactions were almost entirely absent, with only six pairs identifiedover all traits analysed. These results give insights both into the extent of such blocks inevolution and the development of domestication itself.

  • 43.
    Wright, Dominic
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology.
    Ward, A.J.W.
    Department of Biology, University of Leicester, Leicester, United Kingdom.
    Croft, D.P.
    Institute for Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.
    Krause, J.
    Institute for Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.
    Social organization, grouping, and domestication in fish2006In: Zebrafish, ISSN 1545-8547, Vol. 3, no 2, p. 141-155Article, review/survey (Refereed)
    Abstract [en]

    The zebrafish (Danio rerio) is now established as one of the pre-eminent model vertebrate study animals in biology, providing an excellent opportunity to integrate the fields of genetics and behavioral ecology. Considerable attention has been paid to the social organization of animals and the study of zebrafish in this context allows behavioral geneticists to gain an insight into this fundamentally important field. This paper reviews the literature on the social organization of fish, with special reference to the zebrafish. The mechanisms and functions of social behavior in fish and the current understanding of the behavioral genetics of these are discussed. Finally, the impact of domestication on the expression of wild-type behavior patterns in laboratory fish is considered. © Mary Ann Liebert, Inc.

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