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Bakovic, V., Höglund, A., Martin Cerezo, M. L., Henriksen, R. & Wright, D. (2022). Genomic and gene expression associations to morphology of a sexual ornament in the chicken. G3: Genes, Genomes, Genetics, 12(9), Article ID jkac174.
Open this publication in new window or tab >>Genomic and gene expression associations to morphology of a sexual ornament in the chicken
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2022 (English)In: G3: Genes, Genomes, Genetics, E-ISSN 2160-1836, Vol. 12, no 9, article id jkac174Article in journal (Refereed) Published
Abstract [en]

How sexual selection affects the genome ultimately relies on the strength and type of selection, and the genetic architecture of the involved traits. While associating genotype with phenotype often utilizes standard trait morphology, trait representations in morphospace using geometric morphometric approaches receive less focus in this regard. Here, we identify genetic associations to a sexual ornament, the comb, in the chicken system (Gallus gallus). Our approach combined genome-wide genotype and gene expression data (>30k genes) with different aspects of comb morphology in an advanced intercross line (F8) generated by crossing a wild-type Red Junglefowl with a domestic breed of chicken (White Leghorn). In total, 10 quantitative trait loci were found associated to various aspects of comb shape and size, while 1,184 expression QTL were found associated to gene expression patterns, among which 98 had overlapping confidence intervals with those of quantitative trait loci. Our results highlight both known genomic regions confirming previous records of a large effect quantitative trait loci associated to comb size, and novel quantitative trait loci associated to comb shape. Genes were considered candidates affecting comb morphology if they were found within both confidence intervals of the underlying quantitative trait loci and eQTL. Overlaps between quantitative trait loci and genome-wide selective sweeps identified in a previous study revealed that only loci associated to comb size may be experiencing on-going selection under domestication.

Place, publisher, year, edition, pages
Oxford University Press, 2022
Keywords
QTL; eQTL; chicken comb; domestication
National Category
Genetics
Identifiers
urn:nbn:se:liu:diva-187414 (URN)10.1093/g3journal/jkac174 (DOI)000828783500001 ()35801935 (PubMedID)
Note

Funding Agencies|Ministry of Education, Youth and Sports of the Czech Republic [CZ LM2018140]; National Genomics Infrastructure in Genomics Production Stockholm - Science for Life Laboratory; SNIC/Uppsala Multidisciplinary Centre for Advanced Computational Science

Available from: 2022-08-23 Created: 2022-08-23 Last updated: 2024-01-17Bibliographically approved
Katajamaa, R., Wright, D., Henriksen, R. & Jensen, P. (2021). Cerebellum size is related to fear memory and domestication of chickens.. Biology Letters, 17(2), Article ID 20200790.
Open this publication in new window or tab >>Cerebellum size is related to fear memory and domestication of chickens.
2021 (English)In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 17, no 2, article id 20200790Article in journal (Refereed) Published
Abstract [en]

Red Junglefowl (Gallus gallus) were selected for divergent levels of fear of humans during eight generations, causing the selection lines to differ in fear levels as well as in the proportional brain and cerebellum masses. Birds from the two lines were then crossed to obtain an F3 intercross in order to study the correlations between brain mass and fear learning. We exposed 105 F3-animals individually to a fear habituation and memory test at 8 days of age, where the reactions to repeated light flashes were assessed on 2 consecutive days. After culling, the absolute and relative sizes of each of four brain regions were measured. Stepwise regression was used to analyse the effects of the size of each brain region on habituation and memory. There were no effects of any brain region on the habituation on day one. However, birds with a larger absolute size of cerebellum had significantly reduced reactions to the fearful stimuli on day two, indicating a better memory of the stimuli. No other regions had significant effects. We conclude that increased cerebellum size may have been important in facilitating chicken domestication, allowing them to adapt to a life with humans.

Place, publisher, year, edition, pages
The Royal Society, 2021
Keywords
brain, chicken, domestication
National Category
Behavioral Sciences Biology
Identifiers
urn:nbn:se:liu:diva-176021 (URN)10.1098/rsbl.2020.0790 (DOI)33529547 (PubMedID)
Available from: 2021-06-01 Created: 2021-06-01 Last updated: 2023-12-28
Fogelholm, J., Henriksen, R., Höglund, A., Huq, N., Johnsson, M., Lenz, R., . . . Wright, D. (2020). CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken. Scientific Reports, 10(1), Article ID 1161.
Open this publication in new window or tab >>CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken
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2020 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 10, no 1, article id 1161Article in journal (Refereed) Published
Abstract [en]

Plumage colouration in birds is important for a plethora of reasons, ranging from camouflage, sexual signalling, and species recognition. The genes underlying colour variation have been vital in understanding how genes can affect a phenotype. Multiple genes have been identified that affect plumage variation, but research has principally focused on major-effect genes (such as those causing albinism, barring, and the like), rather than the smaller effect modifier loci that more subtly influence colour. By utilising a domestic × wild advanced intercross with a combination of classical QTL mapping of red colouration as a quantitative trait and a targeted genetical genomics approach, we have identified five separate candidate genes (CREBBP, WDR24, ARL8A, PHLDA3, LAD1) that putatively influence quantitative variation in red-brown colouration in chickens. By treating colour as a quantitative rather than qualitative trait, we have identified both QTL and genes of small effect. Such small effect loci are potentially far more prevalent in wild populations, and can therefore potentially be highly relevant to colour evolution.

Place, publisher, year, edition, pages
Nature Publishing Group, 2020
National Category
Genetics
Identifiers
urn:nbn:se:liu:diva-165248 (URN)10.1038/s41598-020-57710-7 (DOI)000546559900001 ()31980681 (PubMedID)2-s2.0-85078253816 (Scopus ID)
Note

Funding agencies:  Carl Tryggers Stiftelse; Swedish Research CouncilSwedish Research Council; Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS)Swedish Research Council Formas; European Research CouncilEuropean Research Council (ER

Available from: 2020-04-20 Created: 2020-04-20 Last updated: 2023-12-28Bibliographically approved
Ruiz-Conca, M., Gardela, J., Martínez, C. A., Wright, D., López-Bejar, M., Rodriguez-Martinez, H. & Alvarez-Rodriguez, M. (2020). Natural Mating Differentially Triggers Expression of Glucocorticoid Receptor (NR3C1)-Related Genes in the Preovulatory Porcine Female Reproductive Tract. International Journal of Molecular Sciences, 21(12), Article ID E4437.
Open this publication in new window or tab >>Natural Mating Differentially Triggers Expression of Glucocorticoid Receptor (NR3C1)-Related Genes in the Preovulatory Porcine Female Reproductive Tract
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2020 (English)In: International Journal of Molecular Sciences, ISSN 1661-6596, E-ISSN 1422-0067, Vol. 21, no 12, article id E4437Article in journal (Refereed) Published
Abstract [en]

Mating initiates dynamic modifications of gene transcription in the female reproductive tract, preparing the female for fertilization and pregnancy. Glucocorticoid signaling is essential for the homeostasis of mammalian physiological functions. This complex glucocorticoid regulation is mediated through the glucocorticoid receptor, also known as nuclear receptor subfamily 3 group C member 1 (NR3C1/GR) and related genes, like 11β-hydroxysteroid dehydrogenases (HSD11Bs) and the FK506-binding immunophilins, FKBP5 and FKBP4. This study tested the transcriptome changes in NR3C1/GR regulation in response to natural mating and/or cervical deposition of the sperm-peak ejaculate fraction collected using the gloved-hand method (semen or only its seminal plasma), in the preovulatory pig reproductive tract (cervix to infundibulum, 24 h after mating/insemination/infusion treatments). Porcine cDNA microarrays revealed 22 NR3C1-related transcripts, and changes in gene expression were triggered by all treatments, with natural mating showing the largest differences, including NR3C1, FKBP5, FKBP4, hydroxysteroid 11-beta dehydrogenase 1 and 2 (HSD11B1, HSD11B2), and the signal transducer and activator of transcription 5A (STAT5A). Our data suggest that natural mating induces expression changes that might promote a reduction of the cortisol action in the oviductal sperm reservoir. Together with the STAT-mediated downregulation of cytokine immune actions, this reduction may prevent harmful effects by promoting tolerance towards the spermatozoa stored in the oviduct and perhaps elicit spermatozoa activation and detachment after ovulation.

Place, publisher, year, edition, pages
MDPI, 2020
Keywords
FKBP4, FKBP5, NR3C1, female reproductive tract, glucocorticoid, mating, microarrays, pig, spermatozoa, transcriptomics
National Category
Veterinary Science
Identifiers
urn:nbn:se:liu:diva-167532 (URN)10.3390/ijms21124437 (DOI)000554607300001 ()32580389 (PubMedID)2-s2.0-85087100063 (Scopus ID)
Note

Funding agencies: Research Council FORMAS, Stockholm [2017-00946, 2019-00288]; Swedish Research Council (Vetenskapsradet, VR)Swedish Research Council [2015-05919]; Government of Spain-Ministry of Education, Culture and Sports [FPU15/06029]; Seneca Foundation Murcia (Spain)

Available from: 2020-07-24 Created: 2020-07-24 Last updated: 2023-12-28Bibliographically approved
Höglund, A., Henriksen, R., Fogelholm, J., Churcher, A. M., Guerrero-Bosagna, C. M., Martinez-Barrio, A., . . . Wright, D. (2020). The methylation landscape and its role in domestication and gene regulation in the chicken. Nature Ecology & Evolution, 4, 1713-1724
Open this publication in new window or tab >>The methylation landscape and its role in domestication and gene regulation in the chicken
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2020 (English)In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 4, p. 1713-1724Article in journal (Refereed) Published
Abstract [en]

Domestication is one of the strongest examples of artificial selection and has produced some of the most extreme within-species phenotypic variation known. In the case of the chicken, it has been hypothesized that DNA methylation may play a mechanistic role in the domestication response. By inter-crossing wild-derived red junglefowl with domestic chickens, we mapped quantitative trait loci for hypothalamic methylation (methQTL), gene expression (eQTL) and behaviour. We find large, stable methylation differences, with 6,179 cis and 2,973 trans methQTL identified. Over 46% of the trans effects were genotypically controlled by five loci, mainly associated with increased methylation in the junglefowl genotype. In a third of eQTL, we find that there is a correlation between gene expression and methylation, while statistical causality analysis reveals multiple instances where methylation is driving gene expression, as well as the reverse. We also show that methylation is correlated with some aspects of behavioural variation in the inter-cross. In conclusion, our data suggest a role for methylation in the regulation of gene expression underlying the domesticated phenotype of the chicken.

Place, publisher, year, edition, pages
Springer Nature, 2020
National Category
Genetics
Identifiers
urn:nbn:se:liu:diva-170139 (URN)10.1038/s41559-020-01310-1 (DOI)000571690300001 ()32958860 (PubMedID)2-s2.0-85091215995 (Scopus ID)
Note

Funding agencies:  European Research CouncilEuropean Research Council (ERC) [772874]; Swedish Research Council (VR)Swedish Research Council; Carl Tryggers Stiftelse; Linkoping University Neuro-network

Available from: 2020-09-30 Created: 2020-09-30 Last updated: 2023-12-28Bibliographically approved
Álvarez-Rodríguez, M., Martinez, C., Wright, D. & Rodríguez-Martinez, H. (2020). The role of semen and seminal plasma in inducing large-scale genomic changes in the female porcine peri-ovulatory tract. Scientific Reports, 10(1), Article ID 5061.
Open this publication in new window or tab >>The role of semen and seminal plasma in inducing large-scale genomic changes in the female porcine peri-ovulatory tract
2020 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 10, no 1, article id 5061Article in journal (Refereed) Published
Abstract [en]

Semen modifies the expression of genes related to immune function along the porcine female internal genital tract. Whether other pathways are induced by the deposition of spermatozoa and/or seminal plasma (SP), is yet undocumented. Here, to determine their relative impact on the uterine and tubal transcriptomes, microarray analyses were performed on the endocervix, endometrium and endosalpinx collected from pre-ovulatory sows 24 h after either mating or artificial insemination (AI) with specific ejaculate fractions containing spermatozoa or sperm-free SP. After enrichment analysis, we found an overrepresentation of genes and pathways associated with sperm transport and binding, oxidative stress and cell-to-cell recognition, such as PI3K-Akt, FoxO signaling, glycosaminoglycan biosynthesis and cAMP-related transcripts, among others. Although semen (either after mating or AI) seemed to have the highest impact along the entire genital tract, our results demonstrate that the SP itself also modifies the transcriptome. The detected modifications of the molecular profiles of the pre/peri-ovulatory endometrium and endosalpinx suggest an interplay for the survival, transport and binding of spermatozoa through, for instance the up-regulation of the Estrogen signaling pathway associated with attachment and release from the oviductal reservoir.

Place, publisher, year, edition, pages
Nature Publishing Group, 2020
National Category
Animal and Dairy Science
Identifiers
urn:nbn:se:liu:diva-165212 (URN)10.1038/s41598-020-60810-z (DOI)000560807000001 ()32193402 (PubMedID)2-s2.0-85082042350 (Scopus ID)
Note

Funding agency: Linköping University

Available from: 2020-04-20 Created: 2020-04-20 Last updated: 2023-12-28Bibliographically approved
Alvarez-Rodriguez, M., Atikuzzaman, M., Venhoranta, H., Wright, D. & Rodriguez-Martinez, H. (2019). Expression of Immune Regulatory Genes in the Porcine Internal Genital Tract Is Differentially Triggered by Spermatozoa and Seminal Plasma. International Journal of Molecular Sciences, 20(3), Article ID 513.
Open this publication in new window or tab >>Expression of Immune Regulatory Genes in the Porcine Internal Genital Tract Is Differentially Triggered by Spermatozoa and Seminal Plasma
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2019 (English)In: International Journal of Molecular Sciences, ISSN 1661-6596, E-ISSN 1422-0067, Vol. 20, no 3, article id 513Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
MDPI, 2019
Keywords
transcriptomics; microarray; bioinformatics; spermatozoa; seminal plasma; immune-regulation; female internal genitalia; pig
National Category
Medical Genetics
Identifiers
urn:nbn:se:liu:diva-156214 (URN)10.3390/ijms20030513 (DOI)000462412500057 ()30691059 (PubMedID)2-s2.0-85060587196 (Scopus ID)
Note

Funding Agencies|Research Council FORMAS, Stockholm [2017-00946]; Swedish Research Council (Vetenskapsradet, VR) [2015-05919]

Available from: 2019-04-09 Created: 2019-04-09 Last updated: 2022-02-10Bibliographically approved
Henriksen, R., Gering, E. & Wright, D. (2018). Feralisation: The Understudied Counterpoint to Domestication. In: Pierre Pontarotti (Ed.), Origin and Evolution of Biodiversity: (pp. 183-195). Cham: Springer
Open this publication in new window or tab >>Feralisation: The Understudied Counterpoint to Domestication
2018 (English)In: Origin and Evolution of Biodiversity / [ed] Pierre Pontarotti, Cham: Springer, 2018, p. 183-195Chapter in book (Refereed)
Abstract [en]

Feralisation is a complex process that occurs when a domestic population is returned to the wild. It impacts species invasion biology, speciation, conservation and hybridisation and can be thought of as the reverse of domestication. Domestication has been an area of intense interest and study ever since Darwin, and useful as a model for evolution and the effects of strong directional selection. Despite domestication being used to identify genes affecting a large number of traits that change with selection, little is known about the genomic changes associated with feralisation. Much of the current work on the genetics of feralisation has focused on the detection of early hybrids (F1 or F2) between wild and domestic populations. Feralisation can lead to large changes in morphology, behaviour and many other traits, with the process of feralisation involving the sudden return of both natural and sexual selection. Such evolutionary forces influence predatory, foraging and mate choice decisions and exert strong effects on once domesticated, now feral, individuals. As such, feralisation provides a unique opportunity to observe the genomic and phenotypic responses to selection from a known (domesticated) standpoint and identify the genes underlying these selective targets. In this review, we summarise what is known in particular regarding the genomics of feralisation, and also the changes that feralisation has induced on brain size and behaviour.

Place, publisher, year, edition, pages
Cham: Springer, 2018
Keywords
Domestic Population; Strong Directional Selection; Brain Composition; Comb Size; Feral Animals
National Category
Biological Sciences
Identifiers
urn:nbn:se:liu:diva-194421 (URN)10.1007/978-3-319-95954-2_11 (DOI)2-s2.0-85062706029 (Scopus ID)9783319959542 (ISBN)9783319959535 (ISBN)
Note

Funding: The research was carried out within the framework of the Linköping University Neuro-network. The project was supported by grants from the Swedish Research Council (VR), the European Research Council (advanced research grant GENEWELL 322206, consolidator grant FERALGEN 772874) and the National Science Foundation under Cooperative Agreement No. DBI-0939454. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Available from: 2023-06-07 Created: 2023-06-07 Last updated: 2023-08-24Bibliographically approved
Karlsson, A.-C., Fallahsharoudi, A., Johnsen, H., Hagenblad, J., Wright, D., Andersson, L. & Jensen, P. (2016). A domestication related mutation in the thyroid stimulating hormonereceptor gene (TSHR) modulates photoperiodic response andreproduction in chickens. General and Comparative Endocrinology, 228, 69-78
Open this publication in new window or tab >>A domestication related mutation in the thyroid stimulating hormonereceptor gene (TSHR) modulates photoperiodic response andreproduction in chickens
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2016 (English)In: General and Comparative Endocrinology, ISSN 0016-6480, E-ISSN 1095-6840, Vol. 228, p. 69-78Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Elsevier, 2016
Keywords
Domestication, DIO2, DIO3, TSHB Chicken, Gallus gallus
National Category
Zoology
Identifiers
urn:nbn:se:liu:diva-125283 (URN)10.1016/j.ygcen.2016.02.010 (DOI)000372681400010 ()26873630 (PubMedID)
Note

Funding agencies:  Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning, FORMAS (Formel Excel); Swedish Research Council, VR; European Research Council (ERC) [322206]

Available from: 2016-02-19 Created: 2016-02-19 Last updated: 2023-12-28
Bélteky, J., Agnvall, B., Johnsson, M., Wright, D. & Jensen, P. (2016). Domestication and tameness: brain geneexpression in red junglefowl selected for less fear of humans suggests effects on reproduction and immunology. Royal Society Open Science (3), Article ID 160033.
Open this publication in new window or tab >>Domestication and tameness: brain geneexpression in red junglefowl selected for less fear of humans suggests effects on reproduction and immunology
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2016 (English)In: Royal Society Open Science, E-ISSN 2054-5703, no 3, article id 160033Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Royal Society Publishing, 2016
Keywords
artificial selection, gene expression, microarray, chicken, fearfulness
National Category
Ecology
Identifiers
urn:nbn:se:liu:diva-130501 (URN)10.1098/rsos.160033 (DOI)000384411000002 ()
Note

Funding agencies:  Research council Formas; Vetenskapsradet; ERC [322206]

Available from: 2016-08-11 Created: 2016-08-11 Last updated: 2023-12-28
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ORCID iD: ORCID iD iconorcid.org/0000-0003-2329-2635

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