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  • 1.
    Fallahsharoudi, Amir
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Løtvedt, Pia
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Beltéky, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Altimiras, Jordi
    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.
    Changes in pituitary gene expression may underlie multiple domesticated traits in chickens.2019In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 122, no 2, p. 195-204Article in journal (Refereed)
    Abstract [en]

    Domesticated animals share a unique set of morphological and behavioral traits, jointly referred to as the domesticated phenotype. Striking similarities amongst a range of unrelated domesticated species suggest that similar regulatory mechanisms may underlie the domesticated phenotype. These include color pattern, growth, reproduction, development and stress response. Although previous studies have focused on the brain to find mechanisms underlying domestication, the potential role of the pituitary gland as a target of domestication is highly overlooked. Here, we study gene expression in the pituitary gland of the domesticated White Leghorn chicken and its wild ancestor, the Red Junglefowl. By overlapping differentially expressed genes with a previously published list of functionally important genes in the pituitary gland, we narrowed down to 34 genes. Amongst them, expression levels of genes with inhibitory function on pigmentation (ASIP), main stimulators of metabolism and sexual maturity (TSHB and DIO2), and a potential inhibitor of broodiness (PRLR), were higher in the domesticated breed. Additionally, expression of 2 key inhibitors of the stress response (NR3C1, CRHR2) was higher in the domesticated breed. We suggest that changes in the transcription of important modulatory genes in the pituitary gland can account not only for domestication of the stress response in domestic chickens, but also for changes in pigmentation, development, and reproduction. Given the pivotal role of the pituitary gland in the regulation of multiple shared domesticated traits, we suggest that similar changes in pituitary transcriptome may contribute to the domesticated phenotype in other species as well.

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  • 2.
    Forsberg, Nils
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Norwegian University of Science and Technology, Trondheim, Norway.
    Leino, Matti W.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Nordiska museet, Swedish Museum of Cultural History, Stockholm, Sweden; Stockholm University, Stockholm, Sweden.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Population structure in landrace barley (Hordeum vulgare L.) during the late 19th century crop failures in Fennoscandia2019In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 123, p. 733-745Article in journal (Refereed)
    Abstract [en]

    Agricultural disasters and the subsequent need for supply of relief seed can be expected to influence the genetic composition of crop plant populations. The consequences of disasters and seed relief have, however, rarely been studied since specimens sampled before the events are seldomly available. A series of crop failures struck northern Fennoscandia (Norway, Sweden and Finland) during the second half of the 19th century. In order to assess population genetic dynamics of landrace barley (Hordeum vulgare), and consequences of crop failure and possible seed relief during this time period, we genotyped seeds from 16 historical accessions originating from two time periods spanning the period of repeated crop failure. Reliable identification of genetic structuring is highly dependent on sampling regimes and detecting fine-scale geographic or temporal differentiation requires large sample sizes. The robustness of the results under different sampling regimes was evaluated by analyzing subsets of the data and an artificially pooled dataset. The results led to the conclusion that six individuals per accession were insufficient for reliable detection of the observed genetic structure. We found that population structure among the data was best explained by collection year of accessions, rather than geographic origin. The correlation with collection year indicated a change in genetic composition of landrace barley in the area after repeated crop failures, likely a consequence of introgression of relief seed in local populations. Identical genotypes were found to be shared among some accessions, suggesting founder effects and local seed exchange along known routes for trade and cultural exchange.

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  • 3.
    Forsberg, Nils
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. Norwegian University of Science and Technology, Trondheim, Norway.
    Russell, J.
    The James Hutton Institute, Invergowire, Dundee, Scotland, UK..
    Macaulay, M.
    The James Hutton Institute, Invergowire, Dundee, Scotland, UK..
    Leino, Matti
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. Swedish Museum of Cultural History, Julita, Sweden.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Farmers without borders-genetic structuring in century old barley (Hordeum vulgare)2015In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 114, no 2, p. 195-206Article in journal (Refereed)
    Abstract [en]

    The geographic distribution of genetic diversity can reveal the evolutionary history of a species. For crop plants, phylogeographic patterns also indicate how seed has been exchanged and spread in agrarian communities. Such patterns are, however, easily blurred by the intense seed trade, plant improvement and even genebank conservation during the twentieth century, and discerning fine-scale phylogeographic patterns is thus particularly challenging. Using historical crop specimens, these problems are circumvented and we show here how high-throughput genotyping of historical nineteenth century crop specimens can reveal detailed geographic population structure. Thirty-one historical and nine extant accessions of North European landrace barley (Hordeum vulgare L.), in total 231 individuals, were genotyped on a 384 single nucleotide polymorphism assay. The historical material shows constant high levels of within-accession diversity, whereas the extant accessions show more varying levels of diversity and a higher degree of total genotype sharing. Structure, discriminant analysis of principal components and principal component analysis cluster the accessions in latitudinal groups across country borders in Finland, Norway and Sweden. FST statistics indicate strong differentiation between accessions from southern Fennoscandia and accessions from central or northern Fennoscandia, and less differentiation between central and northern accessions. These findings are discussed in the context of contrasting historical records on intense within-country south to north seed movement. Our results suggest that although seeds were traded long distances, long-term cultivation has instead been of locally available, possibly better adapted, genotypes.

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  • 4.
    Leino, Matti W.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Molecular genetics. Linköping University, The Institute of Technology.
    Boström, E.
    Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Twentieth-century changes in the genetic composition of Swedish field pea metapopulations2013In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 110, no 4, p. 338-346Article in journal (Refereed)
    Abstract [en]

    Landrace crops are formed by local adaptation, genetic drift and gene flow through seed exchange. In reverse, the study of genetic structure between landrace populations can reveal the effects of these forces over time. We present here the analysis of genetic diversity in 40 Swedish field pea (Pisum sativum L.) populations, either available as historical seed samples from the late 19th century or as extant gene bank accessions assembled in the late 20th century. The historical material shows constant high levels of within-population diversity, whereas the extant accessions show varying, and overall lower, levels of within-population diversity. Structure and principal component analysis (PCA) cluster most accessions, both extant and historical, in groups after geographical origin. County-wise analyses of the accessions show that the genetic diversity of the historical accessions is largely overlapping. In contrast, most extant accessions show signs of genetic drift. They harbour a subset of the alleles found in the historical accessions and are more differentiated from each other. These results reflect how historically, present metapopulations have been preserved during the 20th century, although as genetically isolated populations.

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  • 5.
    Martin Cerezo, Maria Luisa
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Lopez, Saioa
    Wellcome Trust Res Labs, England; UCL, England.
    van Dorp, Lucy
    UCL, England.
    Hellenthal, Garrett
    UCL, England.
    Johnsson, Martin
    Swedish Univ Agr Sci, Sweden.
    Gering, Eben
    Michigan State Univ, MI 48824 USA; Michigan State Univ, MI 48824 USA; Nova Southeastern Univ, FL 33314 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.
    Population structure and hybridisation in a population of Hawaiian feral chickens2023In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 130, no 3, p. 154-162Article in journal (Refereed)
    Abstract [en]

    Chickens are believed to have inhabited the Hawaiian island of Kauai since the first human migrations around 1200AD, but numbers have peaked since the tropical storms Iniki and Iwa in the 1980s and 1990s that destroyed almost all the chicken coops on the island and released large numbers of domestic chickens into the wild. Previous studies have shown these now feral chickens are an admixed population between Red Junglefowl (RJF) and domestic chickens. Here, using genetic haplotypic data, we estimate the time of the admixture event between the feral population on the island and the RJF to 1981 (1976-1995), coinciding with the timings of storm Iwa and Iniki. Analysis of genetic structure reveals a greater similarity between individuals inhabiting the northern and western part of the island to RJF than individuals from the eastern part of the island. These results point to the possibility of introgression events between feral chickens and the wild chickens in areas surrounding the Kokee State Park and the Alakai plateau, posited as two of the major RJF reservoirs in the island. Furthermore, we have inferred haplotype blocks from pooled data to determine the most plausible source of the feral population. We identify a clear contribution from RJF and layer chickens of the White Leghorn (WL) breed. This work provides independent confirmation of the traditional hypothesis surrounding the origin of the feral populations and draws attention to the possibility of introgression of domestic alleles into the wild reservoir.

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