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  • 1.
    Atikuzzaman, Mohammad
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för kliniska vetenskaper. Linköpings universitet, Medicinska fakulteten.
    Bhai Mehta, Ratnesh
    Linköpings universitet, Medicinska fakulteten. Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för neuro- och inflammationsvetenskap.
    Fogelholm, Jesper
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Wright, Dominic
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Rodriguez-Martinez, Heriberto
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för kliniska vetenskaper. Linköpings universitet, Medicinska fakulteten.
    Mating induces the expression of immune- and pH-regulatory genes in the utero-vaginal junction containing mucosal sperm-storage tubuli of hens2015Inngår i: Reproduction, Vol. 150, nr 6, s. 473-483Artikkel i tidsskrift (Fagfellevurdert)
    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.

    Fulltekst (pdf)
    fulltext
  • 2. Bestill onlineKjøp publikasjonen >>
    Fogelholm, Jesper
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Genomics and Transcriptomics of Behaviour and Plumage Colouration2020Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The aim throughout this thesis has been to investigate the underlying genetics of behaviours and feather colour and plumage patterns by using chickens as a model organism. Chickens are extremely important as a food source, both in terms of egg, as well as meat production. As such there is a large research interest for them, and they provide an excellent model to study the effects of domestication and evolution, since the ancestor to our domestic breeds the Red Junglefowl can still be found living freely in the wild. This allows us to set up long term crossing experiments where we can harness the power of recombination events and genome wide sequencing to perform genome wide mapping studies. I also want to take the opportunity to integrate the results from all of my work and consider it in perspective of the domestication syndrome.

    In Paper I we investigated the Social Reinstatement behaviour which combines aspects of sociality and anxiousness. We detected several QTL and some overlap with Open Field behaviour from previous work within the group. By combining genomic and transcriptomic methods three strong candidate genes were found: TTRAP, ACOT9 and PRDX4.

    In Paper II Tonic Immobility, another classic behaviour was examined. Once more there was some overlap with the QTL regions discovered in earlier work, and it turns out that two of the most well supported candidate genes for Tonic Immobility is ACOT9 and PRDX4. These two genes had also been implicated with a pH dependent meat quality trait. Therefore, we conducted experiments in an additional smaller scale test cohort to investigate any potential link between the two traits. Following statistical multiple testing corrections, no significant association was found.

    The remaining papers in the thesis investigated different types of feather patterning and colour. In Paper III we determined that the underlying genetic mechanism behind the striped appearance of the sex-linked barring feathers is likely caused by cyclic depletion and renewal of the pigment producing melanocyte cells during feather growth, which is a consequence of specific mutations in the gene CDKN2A.

    Paper IV took a quantitative approach to colour by measuring and quantifying the pheomelanic colour ranging from dark red to yellow. We identified five main candidate genes for the intensity of red colouration, CREBBP, WDR24, ARL8A, PHLDA3 and LAD1. They are all regulated by a trans-acting eQTL located within the QTL region previously associated with behaviours in Paper I and Paper II.

    Finally, in Paper V we turned our attention from pigment-based colour traits to an iridescent structural colour. Here we followed up the QTL mapping performed in our F8 lab intercross with a Genome Wide Association Study in two feral populations from the islands of Kauai and Bermuda. RNA-sequencing was then performed in selected individuals from both feral populations in addition to individuals from the F3 generation of our domestic x wild intercross. The main region of interest is located between 17.4 -17.5Mb on chromosome Z, with the main candidate genes being MAP3K1, Zinc finger RNA binding protein 2, and Zinc finger protein. After integrating and viewing the results from the work conducted as a part of this thesis from the perspective of the Domestication Syndrome, I have found that there are a lot of potential connections between the traits that I have studied. For instance, the same QTL region on chromosome 10 is detected in association with the behaviour traits in Paper I and Paper II and the quantitative colour trait in Paper IV. I believe that the domestication syndrome is caused by the underlying functional arrangement of the genome, which causes correlated responses in nearby genes and their associated traits, when selective forces such as domestication are applied on the primary trait.

    Delarbeid
    1. Genetics and Genomics of Social Behavior in a Chicken Model
    Åpne denne publikasjonen i ny fane eller vindu >>Genetics and Genomics of Social Behavior in a Chicken Model
    Vise andre…
    2018 (engelsk)Inngår i: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 209, nr 1, s. 209-221Artikkel i tidsskrift (Fagfellevurdert) Published
    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.

    sted, utgiver, år, opplag, sider
    GENETICS SOCIETY AMERICA, 2018
    Emneord
    behavior; eQTL; QTL; sociality
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-148106 (URN)10.1534/genetics.118.300810 (DOI)000432188600016 ()29531010 (PubMedID)
    Merknad

    Funding Agencies|Carl Tryggers Stiftelse, Swedish Research Council (VR); Swedish Research Council for Environment; Agricultural Sciences and Spatial Planning (FORMAS); European Research Council [GENEWELL 322206]

    Tilgjengelig fra: 2018-05-30 Laget: 2018-05-30 Sist oppdatert: 2020-04-20
    2. Genetical Genomics of Tonic Immobility in the Chicken
    Åpne denne publikasjonen i ny fane eller vindu >>Genetical Genomics of Tonic Immobility in the Chicken
    Vise andre…
    2019 (engelsk)Inngår i: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, nr 5, artikkel-id 341Artikkel i tidsskrift (Fagfellevurdert) Published
    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.

    sted, utgiver, år, opplag, sider
    MDPI, 2019
    Emneord
    QTL; eQTL; tonic immobility; behaviour; domestication; muscle pH
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-158576 (URN)10.3390/genes10050341 (DOI)000470964100020 ()31067744 (PubMedID)
    Merknad

    Funding Agencies|Swedish Research Council (VR) [621-2011-4802]; Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS) [221-2012-667]; European Research Council [GENEWELL 322206, FERALGEN 772874]

    Tilgjengelig fra: 2019-07-03 Laget: 2019-07-03 Sist oppdatert: 2020-04-20
    3. The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes in CDKN2A
    Åpne denne publikasjonen i ny fane eller vindu >>The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes in CDKN2A
    Vise andre…
    2017 (engelsk)Inngår i: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 13, nr 4, artikkel-id e1006665Artikkel i tidsskrift (Fagfellevurdert) Published
    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.

    sted, utgiver, år, opplag, sider
    PUBLIC LIBRARY SCIENCE, 2017
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-138926 (URN)10.1371/journal.pgen.1006665 (DOI)000402549200008 ()28388616 (PubMedID)
    Merknad

    Funding Agencies|Swedish Research Council; Knut and Alice Wallenberg Foundation; Erasmus-Mundus fellowship; Swedish Research Council of the European Graduate School in Animal Breeding and Genetics

    Tilgjengelig fra: 2017-06-27 Laget: 2017-06-27 Sist oppdatert: 2020-04-20
    4. CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken
    Åpne denne publikasjonen i ny fane eller vindu >>CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken
    Vise andre…
    2020 (engelsk)Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 10, nr 1, artikkel-id 1161Artikkel i tidsskrift (Fagfellevurdert) 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.

    sted, utgiver, år, opplag, sider
    Nature Publishing Group, 2020
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-165248 (URN)10.1038/s41598-020-57710-7 (DOI)31980681 (PubMedID)2-s2.0-85078253816 (Scopus ID)
    Tilgjengelig fra: 2020-04-20 Laget: 2020-04-20 Sist oppdatert: 2020-04-27bibliografisk kontrollert
    Fulltekst (pdf)
    fulltext
    Download (png)
    presentationsbild
  • 3.
    Fogelholm, Jesper
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Henriksen, Rie
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Höglund, Andrey
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Huq, N.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Johnsson, M.
    The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, United Kingdom, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Lenz, Reiner
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Jensen, Per
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Wright, Dominic
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken2020Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 10, nr 1, artikkel-id 1161Artikkel i tidsskrift (Fagfellevurdert)
    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.

    Fulltekst (pdf)
    fulltext
  • 4.
    Fogelholm, Jesper
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Inkabi, Samuel
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Höglund, Andrey
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Abbey-Lee, Robin
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Johnsson, Martin
    Univ Edinburgh, Scotland; Swedish Univ Agr Sci, Sweden.
    Jensen, Per
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Henriksen, Rie
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Wright, Dominic
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Genetical Genomics of Tonic Immobility in the Chicken2019Inngår i: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, nr 5, artikkel-id 341Artikkel i tidsskrift (Fagfellevurdert)
    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.

    Fulltekst (pdf)
    fulltext
  • 5.
    Johnsson, Martin
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten. Univ Edinburgh, Scotland; Swedish Univ Agr Sci, Sweden.
    Henriksen, Rie
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Fogelholm, Jesper
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Höglund, Andrey
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Jensen, Per
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Wright, Dominic
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Genetics and Genomics of Social Behavior in a Chicken Model2018Inngår i: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 209, nr 1, s. 209-221Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 6.
    Johnsson, Martin
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten. Univ Edinburgh, England; Swedish Univ Agr Sci, Sweden.
    Henriksen, Rie
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten. Swedish Univ Agr Sci, Sweden.
    Höglund, Andrey
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten. Swedish Univ Agr Sci, Sweden.
    Fogelholm, Jesper
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten. Swedish Univ Agr Sci, Sweden.
    Jensen, Per
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten. Swedish Univ Agr Sci, Sweden.
    Wright, Dominic
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten. Swedish Univ Agr Sci, Sweden.
    Genetical genomics of growth in a chicken model2018Inngår i: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 19, artikkel-id 72Artikkel i tidsskrift (Fagfellevurdert)
    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.

    Fulltekst (pdf)
    fulltext
  • 7.
    Leino, Matti W.
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten. Stockholm Univ, Sweden; Nord Museum, Sweden.
    Solberg, Svein O.
    Nord Genet Resource Ctr, Sweden; Inland Norway Univ Appl Sci, Norway.
    Tunset, Hanna Maja
    Norwegian Univ Sci and Technol, Norway.
    Fogelholm, Jesper
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Karlsson Strese, Else-Marie
    Nord Museum, Sweden.
    Hagenblad, Jenny
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten. Norwegian Univ Sci and Technol, Norway.
    Patterns of Exchange of Multiplying Onion (Allium cepa L. Aggregatum-Group) in Fennoscandian Home Gardens2018Inngår i: Economic Botany, ISSN 0013-0001, E-ISSN 1874-9364, Vol. 72, nr 3, s. 346-356Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Multiplying onion (Allium cepa L. Aggregatum-Group), commonly known as shallot or potato onion, has a long tradition of cultivation in Fennoscandian home gardens. During the last decades, more than 80 accessions, maintained as vegetatively propagated clones, have been gathered from home gardens in all Fennoscandian countries. A genetic analysis showed regional patterns of accessions belonging to the same genetic group. However, accessions belonging to the same genetic group could originate in any of the countries. These results suggested both short- and long-distance exchange of set onions, which was confirmed by several survey responses. Some of the most common genetic groups also resembled different modern varieties. The morphological characterization illustrated that most characters were strongly influenced by environment and set onion properties. The only reliably scorable trait was bulb skin color. Neither our morphological nor genetic results support a division between potato onions and shallots. Instead, naming seems to follow linguistic traditions. An ethnobotanical survey tells of the Fennoscandian multiplying onions as being a crop with reliable harvest, excellent storage ability, and good taste. An increased cultivation of this material on both household and commercial scale should be possible.

  • 8.
    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
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Fogelholm, Jesper
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Wright, Dominic
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    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 CDKN2A2017Inngår i: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 13, nr 4, artikkel-id e1006665Artikkel i tidsskrift (Fagfellevurdert)
    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.

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