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  • 1.
    Hagenblad, Jenny
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Leino, Matti W.
    The Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Hernàndez Afonso, Guacimara
    Center for the Conservation of Agricultural Biodiversity of Tenerife (CCBAT), Canary Islands, Spain.
    Afonso Morales, Desirée
    Agricultural Biodiversity of Tenerife (CCBAT), Canary Islands, Spain.
    Morphological and genetic characterization of barley (Hordeum vulgare L.) landraces in the Canary Islands2019In: Genetic Resources and Crop Evolution, ISSN 0925-9864, E-ISSN 1573-5109, Vol. 66, no 2, p. 465-480Article in journal (Refereed)
    Abstract [en]

    Barley has been continuously cultivated in the Canary archipelago for millennia, and to this day landrace barley is the preferred choice for cultivation. We have morphologically and genetically characterized 57 landraces collected during the twenty-first century and conserved in genebanks. The majority of accessions were of the six-row type. Although landraces from the same island tended to be similar, the results showed morphological and genetic diversity both within and in the case of genetic data among islands. Accessions from the easternmost islands were genetically distinct from those from the central and western islands. Accessions from the western islands often had a mixed genetical composition, suggesting more recent exchange of plant material with the central islands. The geographic distribution of diversity suggests that conservation of barley genetic resources needs to consider all islands in the archipelago. Landrace barley from the Canary archipelago was found to be morphologically distinct from continental landrace barley. We suggest the uniqueness of Canarian barley, in terms of morphology and genetic diversity, can be used for marketing purposes providing added market value to the crop.

  • 2.
    Helsen, Kenny
    et al.
    Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway; Plant Conservation and Population Biology, Biology Department, University of Leuven, Heverlee, Belgium.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Acharya, Kamal P
    Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
    Brunet, Jörg
    Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Cousins, Sara AO
    Department of Physical Geography, Stockholm University, Stockholm, Sweden.
    Decocq, Guillaume
    Edysan (FRE 3498 CNRS), Centre National de la Recherche Scientifique, Université de Picardie Jules Verne, Amiens Cedex, France.
    De Frenne, Pieter
    Forest & Nature Lab, Ghent University, Gontrode-Melle, Belgium.
    Kimberley, Adam
    Department of Physical Geography, Stockholm University, Stockholm, Sweden.
    Kolb, Annette
    Vegetation Ecology and Conservation Biology, Faculty of Biology/Chemistry (FB 02), Institute of Ecology, University of Bremen, Bremen, Germany.
    Michaelis, Jana
    Vegetation Ecology and Conservation Biology, Faculty of Biology/Chemistry (FB 02), Institute of Ecology, University of Bremen, Bremen, Germany.
    Plue, Jan
    Department of Physical Geography, Stockholm University, Stockholm, Sweden.
    Verheyen, Kris
    Forest & Nature Lab, Ghent University, Gontrode-Melle, Belgium.
    Speed, James DM
    Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway.
    Graae, Bente J
    Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
    No genetic erosion after five generations for Impatiens glandulifera populationsacross the invaded range in Europe2019In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 20, article id 20Article in journal (Refereed)
    Abstract [en]

    Background: The observation that many alien species become invasive despite low genetic diversity has long been considered the ‘genetic paradox’ in invasion biology. This paradox is often resolved through the temporal buildup genetic diversity through multiple introduction events. These temporal dynamics in genetic diversity are especially important for annual invasive plants that lack a persistent seed bank, for which population persistence is strongly dependent on consecutive seed ‘re-establishment’ in each growing season. Theory predicts that the number of seeds during re-establishment, and the levels of among-population gene flow can strongly affect recolonization dynamics, resulting in either an erosion or build-up of population genetic diversity through time. This study focuses on temporal changes in the population genetic structure of the annual invasive plant Impatiens glandulifera across Europe. We resampled 13 populations in 6 regions along a 1600 km long latitudinal gradient from northern France to central Norway after 5 years, and assessed population genetic diversity with 9 microsatellite markers.

    Results: Our study suggests sufficiently high numbers of genetically diverse founders during population re- establishment, which prevent the erosion of local genetic diversity. We furthermore observe that I. glanduliferaexperiences significant among-population gene flow, gradually resulting in higher genetic diversity and lower overall genetic differentiation through time. Nonetheless, moderate founder effects concerning population genetic composition (allele frequencies) were evident, especially for smaller populations.

    Despite the initially low genetic diversity, this species seems to be successful at persisting across its invaded range, and will likely continue to build up higher genetic diversity at the local scale.

  • 3. Palmé, Anna
    et al.
    Fitzgerald, Heli
    Botany, Finnish Museum of Natural History, University of Helsinki, Finland.
    Weibull, Jens
    Swedish University of Agricultural Sciences.
    Bjureke, Kristina
    Natural History Museum, Norway.
    Eisto, Kaija
    Endresen, Dag
    Geo-Ecology Research Group, Natural History Museum, Oslo, Norway.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Hyvärinen, Marko
    Botany, University of Helsinki, Finland.
    Kiviharju, Elina
    Natural Resources Institute Finland (Luke), Helsinki, Finland.
    Lund, Birgitte
    Rasmussen, Morten
    Þorbjörnsson, Hjörtur
    Reykjavík Botanic Garden, Reykjavik, Iceland.
    Nordic Crop Wild Relative conservation: A report from two collaborative projects 2015–20192019Report (Other academic)
    Abstract [en]

    The report summarizes results from a cooperation among all the Nordic countries during the period 2015 – 2019 (two projects). The work has focused on the conservation of Crop Wild Relatives (CWR), i.e. wild plant species closely related to crops. They are of special importance to humanity since traits of potential value for food security and climate change adaptation can be transferred from CWR into crops. The projects represent the first joint action on the Nordic level regarding in situ conservation of CWR. Substantial progress has been made regarding CWR conservation planning, including development of a Nordic CWR checklist and identification of suitable sites for CWR conservation. A set of recommended future actions was developed, with the most important one being initiation of active in situ conservation of CWR in all Nordic countries.

  • 4.
    Larsson, Per
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. The Cultural History Association of Southern Sweden, Lund, Sweden ; Swedish Museum of Agriculture, Nordic Museum, Stockholm, Sweden.
    Oliveira, H. R.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, Faculdade das Ciências Humanas e Sociais, Universidade do Algarve, Faro, Portugal.
    Lundström, Maria
    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.
    Lageras, P.
    The Archaeologists, National Historical Museums, Lund, Sweden.
    Leino, M. W.
    The Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Population genetic structure in Fennoscandian landrace rye (Secale cereale L.) spanning 350 years2019In: Genetic Resources and Crop Evolution, ISSN 0925-9864, E-ISSN 1573-5109, Vol. 66, no 5, p. 1059-1071Article in journal (Refereed)
    Abstract [en]

    Rye (Secale cereale L.) was for centuries the economically most important crop in Fennoscandia (Denmark, Finland, Norway and Sweden). Historical records tell of a range of different types adapted to climate and varying cultivation practices. Genetic analyses of genebank maintained landrace rye have yet failed, with a few exceptions, to detect differentiation between rye types. Concerns have been raised that genebank material does not truly reflect the historical variation in landrace rye. In this study, we have therefore genotyped old and historical samples of rye as well as extant material. Two historical seventeenth century samples were obtained from a grave and a museum archive respectively, and 35 old samples were taken from 100 to 140-year-old seed collections and museum artefacts made of straw. We could confirm the results of previous studies suggesting Fennoscandian landrace rye to be one major meta-population, genetically different from other European rye landraces, but with no support for slash-and-burn types of rye being genetically different from other rye landraces. Only small differences in genetic diversity and allele distribution was found between old landrace rye from museum collections and extant genebank accessions, arguing against a substantial change in the genetic diversity during twentieth century cultivation and several regenerations during genebank maintenance. The genotypes of the old and historical samples suggest that the genetic structure of Fennoscandian landrace rye has been relatively stable for 350years. In contrast, we find that the younger samples and early improved cultivars belong to a different genetic group, more related to landraces from Central Europe.

  • 5.
    Lempiäinen-Avci, Mia
    et al.
    Department of Biology, University of Turku, Turku, Finland; Herbarium, Biodiversity Unit, University of Turku, Turku, Finland; Archaeological Museum, University of Stavanger, Stavanger, Norge.
    Lundström, Maria
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Huttunen, Sanna
    Herbarium, Biodiversity Unit, University of Turku, Turku, Finland.
    Leino, Matti W.
    Nordiska Museet, Swedish Museum of Cultural History, Stockholm, Sweden; The Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Archaeological and Historical Materials as a Means to Explore Finnish Crop History2018In: Environmental Archaeology, ISSN 1461-4103, E-ISSN 1749-6314Article in journal (Refereed)
    Abstract [en]

    In Northern Europe, barley (Hordeum vulgare L.) has been cultivated for almost 6000 years. Thus far, 150-year-old grains from historical collections have been used to investigate the distribution of barley diversity and how the species has spread across the region. Genetic studies of archaeobotanical material from agrarian sites could potentially clarify earlier migration patterns and cast further light on the origin of barley landraces. In this study, we aimed to evaluate different archaeological and historical materials with respect to DNA content, and to explore connections between Late Iron Age and medieval barley populations and historical samples of barley landraces in north-west Europe. The material analysed consisted of archaeological samples of charred barley grains from four sites in southern Finland, and historical material, with 33 samples obtained from two herbaria and the seed collections of the Swedish museum of cultural history.

    The DNA concentrations obtained from charred archaeological barley remains were too low for successful KASP genotyping confirming previously reported difficulties in obtaining aDNA from charred remains. Historical samples from herbaria and seed collection confirmed previously shown strong genetic differentiation between two-row and six-row barley. Six-row barley accessions from northern and southern Finland tended to cluster apart, while no geographical structuring was observed among two-row barley. Genotyping of functional markers revealed that the majority of barley cultivated in Finland in the late nineteenth and early twentieth century was late-flowering under increasing day-length, supporting previous findings from northern European barley.

    The full text will be freely available from 2019-12-11 11:48
  • 6.
    Lundström, Maria
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Forsberg, Nils
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Heimdahl, Jens
    The Archaeologists, National Historical Museums, Hägersten, Sweden.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Leino, Matti W.
    Nordiska museet, Swedish Museum of Cultural History, Stockholm, Sweden; The Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Genetic analyses of Scandinavian desiccated, charred and waterlogged remains of barley (Hordeum vulgare L.)2018In: Journal of Archaeological Science: Reports, ISSN 2352-409X, Vol. 22, p. 11-20Article in journal (Refereed)
    Abstract [en]

    Barley, Hordeum vulgare L., has been cultivated in Fennoscandia (Denmark, Norway, Sweden, Finland) since the start of the Neolithic around 4000 years BCE. Genetic studies of extant and 19th century barley landraces from the area have previously shown that distinct genetic groups exist with geographic structure according to latitude, suggesting strong local adaptation of cultivated crops. It is, however, not known what time depth these patterns reflect. Here we evaluate different archaeobotanical specimens of barley, extending several centuries in time, for their potential to answer this question by analysis of aDNA. Forty-six charred grains, nineteen waterlogged specimens and nine desiccated grains were evaluated by PCR and KASP genotyping. The charred samples did not contain any detectable endogenous DNA. Some waterlogged samples permitted amplification of endogenous DNA, however not sufficient for subsequent analysis. Desiccated plant materials provided the highest genotyping success rates of the materials analysed here in agreement with previous studies. Five desiccated grains from a grave from 1679 in southern Sweden were genotyped with 100 SNP markers and data compared to genotypes of 19th century landraces from Fennoscandia. The results showed that the genetic composition of barley grown in southern Sweden changed very little from late 17th to late 19th century and farmers stayed true to locally adapted crops in spite of societal and agricultural development.

  • 7.
    Leino, Matti W.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. 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
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Karlsson Strese, Else-Marie
    Nord Museum, Sweden.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Norwegian Univ Sci and Technol, Norway.
    Patterns of Exchange of Multiplying Onion (Allium cepa L. Aggregatum-Group) in Fennoscandian Home Gardens2018In: Economic Botany, ISSN 0013-0001, E-ISSN 1874-9364, Vol. 72, no 3, p. 346-356Article in journal (Refereed)
    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.
    De Frenne, Pieter
    et al.
    Forest & Nature Lab, Ghent University, Geraardsbergsesteenweg 267, BE-9090 Gontrode-Melle, Belgium;.
    Brunet, Jörg
    Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Box 49, SE-230 53 Alnarp, Sweden.
    Decocq, Guillaume
    EDYSAN (FRE 3498 CNRS-UPJV), Universite de Picardie Jules Verne, 1 rue des Louvels, FR-80037 Amiens Cedex, France.
    J. Graae, Bente
    Department of Biology, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Hermy, Martin
    Forest, Nature & Landscape, K.U. Leuven Celestijnenlaan 200E, BE-3001, Leuven, Belgium.
    Kolb, Annette
    Vegetation Ecology & Conservation Biology, FB2, University of Bremen, Leobener Str., DE-28359 Bremen, Germany.
    H. Lemke, Isgard
    Vegetation Ecology & Conservation Biology, FB2, University of Bremen, Leobener Str., DE-28359 Bremen, Germany.
    Ma, Shiyu
    Forest & Nature Lab, Ghent University, Geraardsbergsesteenweg 267, BE-9090 Gontrode-Melle, Belgium.
    Orczewska, Anna
    Department of Ecology, Faculty of Biology & Environmental Protection, University of Silesia, ul. Bankowa 9, PL-40-007 Katowice, Poland.
    Plue, Jan
    Department of Physical Geography Stockholm University, SE-106 91 Stockholm, Sweden.
    Vranckx, Guy
    Plant Conservation & Population Biology, K.U. Leuven, Kasteelpark Arenberg 31, Box 2435, BE-3001 Leuven, Belgium.
    Wulf, Monika
    Institute of Land Use Systems, Leibniz-ZALF, Eberswalder Strasse 84, DE-15374 M€uncheberg, Germany.
    Verheyen, Kris
    Forest & Nature Lab, Ghent University, Geraardsbergsesteenweg 267, BE-9090 Gontrode-Melle, Belgium.
    Biological Flora of the British Isles: Milium effusum2017In: Journal of Ecology, ISSN 0022-0477, E-ISSN 1365-2745, Vol. 105, no 3, p. 839-858Article in journal (Refereed)
    Abstract [en]

    1. This account presents information on all aspects of the biology of Milium effusum L. (Wood Millet)

    that are relevant to understanding its ecological characteristics and behaviour. The main topics

    are presented within the standard framework of the Biological Flora of the British Isles: distribution,

    habitat, communities, responses to biotic factors, responses to environment, structure and physiology,

    phenology, floral and seed characters, herbivores and disease, history, and conservation.

    2. The grass Milium effusum is a common species of mature woodland in central and southern England,

    but is less common in the wetter parts of northern England, Wales, Scotland and Ireland. Worldwide,

    the species is native to many temperate, boreal, subarctic and subalpine parts of the northern

    hemisphere: from eastern North America across most of Europe (excluding Mediterranean climates) to

    the Ural Mountains and Black Sea, extending eastwards to the Himalaya, Korea and Japan.

    3. Wood Millet is a shade-tolerant, relatively tall grass (up to 18 m) producing up to 700 caryopses

    per individual. It is characteristic of temperate deciduous woodland, but can also occur in other

    woodland and forest types and even in scrub, alpine meadows, along railways and roads, and on

    rocks. In woods, it is one of the most conspicuous plants of the herb layer in the early summer after

    the disappearance of spring flowering species. While the species is generally considered an ancient

    woodland indicator in England and western Europe, it is also known to colonize secondary, postagricultural

    forests relatively rapidly in other areas such as Denmark, southern Sweden and Poland.

    4. The species has a wide amplitude in terms of soil acidity and nutrient availability, but predominantly

    grows on soils of intermediate soil fertility and soil pH and with high organic matter concentration.

    However, M. effusum can tolerate large quantities of tree-leaf litter on the forest floor and is

    able to grow on very acidic soils.

    5. Changes in land use, climate, densities of large herbivores and atmospheric deposition of nitrogen

    are having effects on populations of Wood Millet. Significant responses of the life-history traits and

    population characteristics have been detected in response to environmental variation and to experimental

    treatments of temperature, nutrients, light and acidity. In many of its habitats across its range,

    M. effusum is currently becoming more frequent. During the last century, its mean elevation of

    occurrence in upland areas of Europe has also increased by several hundreds of metres. Typically,

    management actions are directed towards the conservation of its main habitat type (e.g. ancient

    woodlands of the Milio-Fagetum association) rather than to the species specifically.

  • 9.
    Lundström, Maria
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    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; 3The Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Evolutionary history of the NAM-B1 gene in wild and domesticated tetraploid wheat2017In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 18, article id 118Article in journal (Refereed)
    Abstract [en]

    Background

    The NAM-B1 gene in wheat has for almost three decades been extensively studied and utilized in breeding programs because of its significant impact on grain protein and mineral content and pleiotropic effects on senescence rate and grain size. First detected in wild emmer wheat, the wild-type allele of the gene has been introgressed into durum and bread wheat. Later studies have, however, also found the presence of the wild-type allele in some domesticated subspecies. In this study we trace the evolutionary history of the NAM-B1 in tetraploid wheat species and evaluate it as a putative domestication gene.

    Results

    Genotyping of wild and landrace tetraploid accessions showed presence of only null alleles in durum. Domesticated emmer wheats contained both null alleles and the wild-type allele while wild emmers, with one exception, only carried the wild-type allele. One of the null alleles consists of a deletion that covers several 100 kb. The other null-allele, a one-basepair frame-shift insertion, likely arose among wild emmer. This allele was the target of a selective sweep, extending over several 100 kb.

    Conclusions

    The NAM-B1 gene fulfils some criteria for being a domestication gene by encoding a trait of domestication relevance (seed size) and is here shown to have been under positive selection. The presence of both wild-type and null alleles in domesticated emmer does, however, suggest the gene to be a diversification gene in this species. Further studies of genotype-environment interactions are needed to find out under what conditions selection on different NAM-B1 alleles have been beneficial.

  • 10.
    Hagenblad, Jenny
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Morales, Jacob
    University of Las Palmas de Gran Canaria, Research Group Tarha, Department of Historical Sciences, Las Palmas, Spain.
    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; The Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Rodríguez-Rodríguez, Amelia C.
    University of Las Palmas de Gran Canaria, Research Group Tarha, Department of Historical Sciences, , Las Palmas, Spain.
    Farmer fidelity in the Canary Islands revealed by ancient DNA from prehistoric seeds2017In: Journal of Archaeological Science, ISSN 0305-4403, E-ISSN 1095-9238, Vol. 78, p. 10p. 78-87Article in journal (Refereed)
    Abstract [en]

    The Canary Islands were settled in the first millennium AD by colonizers likely originating from North Africa. The settlers developed a farming economy with barley as the main crop. Archaeological evidence suggests the islands then remained isolated until European sea-travellers discovered and colonized them during the 14th and 15th centuries. Here we report a population study of ancient DNA from twenty-one archaeobotanical barley grains from Gran Canaria dating from 1050 to 1440 cal AD. The material showed exceptional DNA preservation and genotyping was carried out for 99 single nucleotide markers. In addition 101 extant landrace accessions from the Canary Islands and the western Mediterranean were genotyped. The archaeological material showed high genetic similarity to extant landraces from the Canary Islands. In contrast, accessions from the Canary Islands were highly differentiated from both Iberian and North African mainland barley. Within the Canary Islands, landraces from the easternmost islands were genetically differentiated from landraces from the western islands, corroborating the presence of pre-Hispanic barley cultivation on Lanzarote. The results demonstrate the potential of population genetic analyses of ancient DNA. They support the hypothesis of an original colonization, possibly from present day Morocco, and subsequent isolation of the islands and reveal a farmer fidelity to the local barley that has lasted for centuries.

    The full text will be freely available from 2019-12-18 15:17
  • 11.
    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.

  • 12.
    Vanhala, Tytti
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Normann, Kjersti R.
    Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
    Lundström, Maria
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Weller, James L.
    School of Biological Sciences, University of Tasmania, Hobart, TAS 7001, Australia..
    Leino, Matti
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Nordiska museet - Swedish Museum of Cultural History, SE-643 98, Julita, Sweden.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Norwegian University of Science and Technology, Trondheim, Norway.
    Flowering time adaption in Swedish landrace pea (Pisum sativum L.)2016In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 17, no 1, p. 117-Article in journal (Refereed)
    Abstract [en]

    Background: Cultivated crops have repeatedly faced new climatic conditions while spreading from their site oforigin. In Sweden, at the northernmost fringe of Europe, extreme conditions with temperature-limited growthseasons and long days require specific adaptation. Pea (Pisum sativum L.) has been cultivated in Sweden formillennia, allowing for adaptation to the local environmental conditions to develop. To study such adaptation, 15Swedish pea landraces were chosen alongside nine European landraces, seven cultivars and three wild accessions.Number of days to flowering (DTF) and other traits were measured and the diversity of the flowering time genesHIGH RESPONSE TO PHOTOPERIOD (HR), LATE FLOWERING (LF) and STERILE NODES (SN) was assessed. Furthermore, theexpression profiles of LF and SN were obtained.Results: DTF was positively correlated with the length of growing season at the site of origin (GSO) of the Swedishlandraces. Alleles at the HR locus were significantly associated with DTF with an average difference of 15.43 daysbetween the two detected haplotypes. LF expression was found to have a significant effect on DTF when analysedon its own, but not when HR haplotype was added to the model. HR haplotype and GSO together explained themost of the detected variation in DTF (49.6 %).Conclusions: We show local adaptation of DTF, primarily in the northernmost accessions, and links betweengenetic diversity and diversity in DTF. The links between GSO and genetic diversity of the genes are less clear-cutand flowering time adaptation seems to have a complex genetic background.

  • 13.
    Hagenblad, Jenny
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Oliveira, Hugo R
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. CIBIO-Research Centre in Biodiversity and Genetic Resources, Campus Agrário de Vairão. R. Padre Armando Quintas, Vairão, Portugal; Nordiska Museet, Swedish Museum of Cultural History; Stockholm, Sweden.
    Forsberg, Nils E. G.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    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.
    Geographical distribution of genetic diversity in Secale landrace and wild accessions2016In: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 16, no 23Article in journal (Refereed)
    Abstract [en]

    Background: Rye, Secale cereale L., has historically been a crop of major importance and is still a key cereal in manyparts of Europe. Single populations of cultivated rye have been shown to capture a large proportion of the geneticdiversity present in the species, but the distribution of genetic diversity in subspecies and across geographical areasis largely unknown. Here we explore the structure of genetic diversity in landrace rye and relate it to that of wildand feral relatives.Results: A total of 567 SNPs were analysed in 434 individuals from 76 accessions of wild, feral and cultivated rye. Geneticdiversity was highest in cultivated rye, slightly lower in feral rye taxa and significantly lower in the wild S. strictum Presl.and S. africanum Stapf. Evaluation of effects from ascertainment bias suggests underestimation of diversity primarily inS. strictum and S. africanum. Levels of ascertainment bias, STRUCTURE and principal component analyses all supportedthe proposed classification of S. africanum and S. strictum as a separate species from S. cereale. S. afghanicum (Vav.)Roshev, S. ancestrale Zhuk., S. dighoricum(Vav.) Roshev, S. segetale (Zhuk.) Roshev and S. vavilovii Grossh. seemed, incontrast, to share the same gene pool as S. cereale and their genetic clustering was more dependent on geographicalorigin than taxonomic classification. S. vavilovii was found to be the most likely wild ancestor of cultivated rye. Amongcultivated rye landraces from Europe, Asia and North Africa five geographically discrete genetic clusters were identified.These had only limited overlap with major agro-climatic zones. Slash-and-burn rye from the Finnmark area in Scandinaviaformed a distinct cluster with little similarity to other landrace ryes. Regional studies of Northern and South-West Europedemonstrate different genetic distribution patterns as a result of varying cultivation intensity.Conclusions: With the exception of S. strictum and S. africanum different rye taxa share the majority of the geneticvariation. Due to the vast sharing of genetic diversity within the S. cereale clade, ascertainment bias seems to be a lesserproblem in rye than in predominantly selfing species. By exploiting within accession diversity geographic structure can beshown on a much finer scale than previously reported.

  • 14.
    Videvall, Elin
    et al.
    Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden.
    Sletvold, Nina
    Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University.
    Ågren, Jon
    Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
    Hansson, Bengt
    Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden.
    Strong Maternal Effects on Gene Expression inArabidopsis lyrata Hybrids2016In: Molecular Biology and Evolution, ISSN 0737-4038, Vol. 33, no 4, p. 984-994Article in journal (Refereed)
    Abstract [en]

    Hybridization between populations or species can have pronounced fitness consequences. Yet little is known about howhybridization affects gene regulation. Three main models have been put forward to explain gene expression patterns inhybrids: additive, dominance, or parental effects. Here, we use high throughput RNA-sequencing to examine the extent towhich hybrid gene expression follows predictions by each of the three models. We performed a reciprocal crossingexperiment between two differentiated populations of the perennial herb Arabidopsis lyrata and sequenced RNA inrosette leaves of 12-week-old plants grown in greenhouse conditions. The two parental populations had highly differentiatedgene expression patterns. In hybrids, a majority of genes showed intermediate expression relative to that of theirparental populations (i.e., additive effects), but expression was frequently more similar to the maternal than to theirpaternal population (i.e., maternal effects). Allele-specific expression analyses showed that in the vast majority of cases,genes with pronounced maternal effect expressed both the maternal and the paternal allele. Maternal effects on hybridgene expression have rarely been documented previously and our study suggests it could be more common thanpreviously assumed. Whether the maternal effect on gene expression persists to later life-stages, and whether thevariation in gene expression is manifested in other aspects of the phenotype, remain to be elucidated. Our findingsare relevant for understanding the consequences of outbreeding and hybridization and open up several questions forfuture studies.

  • 15.
    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.

  • 16.
    Hagenblad, Jenny
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Hülskötter, Jennifer
    Norwegian University of Science and Technology, Department of Biology, NO-7491 Trondheim, Norway, 3University of Applied Sciences Bremen, DE-28199 Bremen, Germany.
    Acharya, Kamal Prasad
    Norwegian University of Science and Technology, Department of Biology, NO-7491 Trondheim, Norway.
    Brunet, Jörg
    Swedish University of Agricultural Sciences, Southern Swedish Forest Research Centre, SE-230 53 Alnarp, Sweden.
    Chabrerie, Olivier
    Plant Biodiversity Lab, FRE 3498 CNRS, Université de Picardie Jules Verne, FR-80037 Amiens, Cedex, France..
    Cousins, Sara A. O.
    Department of Physical Geography and Quaternary Geology, Stockholm University, SE-106 91 Stockholm, Sweden.
    Dar, Pervaiz A
    Department of Botany, University of Kashmir, Srinagar – 190006, Jammu & Kashmir, India..
    Diekmann, Martin
    Vegetation Ecology and Conservation Biology, Institute of Ecology, University of Bremen, DE-28359 Bremen, Germany.
    De Frenne, Pieter
    Forest & Nature Lab,Ghent University, BE-9090 Melle Gontrode, Belgium..
    Hermy, Martin
    Division Forest, Nature and Landscape, University of Leuven, BE-3001 Leuven, Belgium.
    Jamoneau, Aurélien
    Plant Biodiversity Lab, FRE 3498 CNRS, Université de Picardie Jules Verne, FR-80037 Amiens, Cedex, France..
    Kolb, Annette
    Vegetation Ecology and Conservation Biology, Institute of Ecology, University of Bremen, DE-28359 Bremen, Germany.
    Lemke, Isgard
    Vegetation Ecology and Conservation Biology, Institute of Ecology, University of Bremen, DE-28359 Bremen, Germany.
    Plue, Jan
    Department of Physical Geography and Quaternary Geology, Stockholm University, SE-106 91 Stockholm, Sweden.
    Reshi, Zafar A.
    Department of Botany, University of Kashmir, Srinagar – 190006, Jammu & Kashmir, India..
    Jessen Graae, Bente
    Norwegian University of Science and Technology, Department of Biology, NO-7491 Trondheim, Norway..
    Low genetic diversity despite multipleintroductions of the invasive plant species Impatiens glandulifera in Europe2015In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 16, no 103Article in journal (Refereed)
    Abstract [en]

    Background: Invasive species can be a major threat to native biodiversity and the number of invasive plant speciesis increasing across the globe. Population genetic studies of invasive species can provide key insights into theirinvasion history and ensuing evolution, but also for their control. Here we genetically characterise populations ofImpatiens glandulifera, an invasive plant in Europe that can have a major impact on native plant communities. Wecompared populations from the species’ native range in Kashmir, India, to those in its invaded range, along alatitudinal gradient in Europe. For comparison, the results from 39 other studies of genetic diversity in invasivespecies were collated.

    Results: Our results suggest that I. glandulifera was established in the wild in Europe at least twice, from an areaoutside of our Kashmir study area. Our results further revealed that the genetic diversity in invasive populations ofI. glandulifera is unusually low compared to native populations, in particular when compared to other invasivespecies. Genetic drift rather than mutation seems to have played a role in differentiating populations in Europe. Wefind evidence of limitations to local gene flow after introduction to Europe, but somewhat less restrictions in thenative range. I. glandulifera populations with significant inbreeding were only found in the species’ native rangeand invasive species in general showed no increase in inbreeding upon leaving their native ranges. In Europe wedetect cases of migration between distantly located populations. Human activities therefore seem to, at leastpartially, have facilitated not only introductions, but also further spread of I. glandulifera across Europe.

    Conclusions: Although multiple introductions will facilitate the retention of genetic diversity in invasive ranges,widespread invasive species can remain genetically relatively invariant also after multiple introductions. Phenotypicplasticity may therefore be an important component of the successful spread of Impatiens glandulifera across Europe.

  • 17.
    Selçuk, Aslan
    et al.
    Uppsala, Sweden.
    Forsberg, Nils
    Trondheim, Norway.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Leino, Matti W.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Julita, Sweden.
    Molecular Genotyping of HistoricalBarley Landraces Reveals Novel CandidateRegions for Local Adaption2015In: Crop science, ISSN 0011-183X, E-ISSN 1435-0653, Vol. 55, no 6, p. 2766-2776Article in journal (Refereed)
    Abstract [en]

    Barley landraces from Northern Europe formgenetically distinct latitudinal groups, suggestingthat adaption plays an important role inthe geographical distribution of genetic diversity.Here, we investigate how Northern Europeanbarley landraces relate to landraces fromother parts of Europe and whether candidategenes for climate adaption can be identified.For this purpose, 27 barley landraces, availableas century-old seed specimens, were genotypedwith a 384 single nucleotide polymorphism(SNP) assay. Landraces from the Nordiccountries formed a genetically distinct grouprelative to landraces from Central and SouthernEurope. Polymorphic positions in the floweringtime genes HvCO1, HvFT1, Ppd-H1, and VRN1-H1 were genotyped. The previously known alleledistribution of Ppd-H1 with the responsive allelepresent in the South and the nonresponsiveallele in the North was confirmed. The otherthree genes were more variable in Central andSouthern Europe compared to the North andneither of the flowering time genes showedany geographically correlated variation withinthe Nordic countries. Allelic frequencies fromthe 384 SNP set were correlated with climaticvariables. This allowed us to identify five SNPsputatively associated with length of growth season,and two SNPs putatively associated withprecipitation. The results show how historicalcrop specimens can be used to study howgenetic variation has been geographically distributedand the genetics of adaption.

  • 18.
    Hagenblad, Jenny
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Bostrom, Erik
    Norwegian University of Science and Technology, Norway .
    Nygards, Lena
    Swedish University of Agriculture Science, Sweden .
    Leino, Matti
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Genetic diversity in local cultivars of garden pea (Pisum sativum L.) conserved on farm and in historical collections2014In: Genetic Resources and Crop Evolution, ISSN 0925-9864, E-ISSN 1573-5109, Vol. 61, no 2, p. 413-422Article in journal (Refereed)
    Abstract [en]

    During a national Swedish collection mission of vegetable varieties conserved on farm more than 70 pea accessions were obtained, many of which had been grown locally for more than 100 years. In spite of a likely origin in the multitude of obsolete commercial pea varieties available on the Swedish seed market in the nineteenth century, the rediscovered local cultivars have lost their original names and cultivar identity while being maintained on farm. To analyze genetic diversity in the repatriated material, 20 accessions were genotyped with twelve SSR markers and compared with 15 obsolete cultivars kept in genebanks and 13 cultivars preserved as non-viable seeds collected in 1877-1918. Most of the local cultivars were genetically distinct from each other, and in only a few cases could a possible origin in a tested obsolete cultivar be suggested. These results reflect the wide diversity of pea cultivars present in Sweden during the nineteenth century. Both between and within accession genetic diversity was larger among the historical samples of obsolete cultivars compared to local cultivars and cultivars preserved in genebanks, indicating genetic erosion over time both in genebanks and during conservation on farm. The constraints on identifying and verifying historical cultivars using genetic markers are discussed.

  • 19.
    Karlsson Strese, Else-Marie
    et al.
    Nordiska Museet–Swedish Museum of Cultural History, Julita, Sweden.
    Lundström, Maria
    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.
    Leino, Matti W.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. Nordiska Museet–Swedish Museum of Cultural History, Julita, Sweden.
    Genetic Diversity in Remnant Swedish Hop (Humulus lupulus L.) Yards from the 15th to 18th Century2014In: Economic Botany, ISSN 0013-0001, E-ISSN 1874-9364, Vol. 68, no 3, p. 231-245Article in journal (Refereed)
    Abstract [en]

    Hop (Humulus lupulus L.) is a perennial plant cultivated for its use in beer production. The plant is dioecious, and the female plants produce cones containing substances that enhance the taste and durability of beer. Beer was long an essential part of food supply in Northern Europe, and hop has thus been a very important crop during the last 1,000 years. In Sweden, hop cultivation was, by law, mandatory for farmers from 1414 till 1860. Today, Swedish hop cultivation is negligible, but historical remnant hop plants can still be found as feral populations. Using historical maps and documents, we have located ten historical hop yards from the 15th to 18th century where hop plants still persist as now feral populations. Some fifteen plants of each population were sampled and genotyped with ten SSR markers and one marker diagnostic for sex type. In addition, 25 genebank preserved clones of older landraces and cultivars from Europe were genotyped. Genotyping results show abundant clonality and low rates of sexual reproduction within the feral populations. Two of the populations had markedly higher genetic diversity and a higher number of haplotypes, and in these populations a mix of female and male plants was also found. The populations were all clearly differentiated, with no haplotypes shared between populations and little evidence of exchange of genetic material. These results indicate that natural spread and genetic recombination is uncommon or slow in Sweden, and that the feral plants could be remnants of the original historical cultivations. In the assembly of European genebank clones, several clones showed identical genotypes and overall limited genetic diversity. The Swedish populations were in most cases genetically clearly different from the genebank clones. This contrasts with historical records of massive introductions of hop clones from continental Europe during the 19th century and shows that these imports did not replace the original hops being cultivated. A possible better adaption of the Swedish hops and primitive historical breeding are discussed.

  • 20.
    Leino, Matti W.
    et al.
    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.
    Potato onion: The missing link to onion cultivation in the past2014In: Bulletin för trädgårdshistorisk forskning, ISSN 1652-2362, E-ISSN 2001-1261, no 27, p. 17-19Article in journal (Other academic)
  • 21.
    Oliveira, Hugo R.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. CIBIO-Research Centre in Biodiversity and Genetic Resources, Campus Agrário de Vairão. R. Padre Armando Quintas, Vairão 4485-661, Portugal .
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Leino, Matti
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Leigh, Fiona J.
    National Institute Agriculture Bot NIAB, England .
    Lister, Diane L.
    University of Cambridge, England .
    Pena-Chocarro, Leonor
    Escuela Espanola Hist and Arqueol Roma CSIC, Italy .
    Jones, Martin K.
    University of Cambridge, England .
    Wheat in the Mediterranean revisited - tetraploid wheat landraces assessed with elite bread wheat Single Nucleotide Polymorphism markers2014In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 15, no 54Article in journal (Refereed)
    Abstract [en]

    Background: Single Nucleotide Polymorphism (SNP) panels recently developed for the assessment of genetic diversity in wheat are primarily based on elite varieties, mostly those of bread wheat. The usefulness of such SNP panels for studying wheat evolution and domestication has not yet been fully explored and ascertainment bias issues can potentially affect their applicability when studying landraces and tetraploid ancestors of bread wheat. We here evaluate whether population structure and evolutionary history can be assessed in tetraploid landrace wheats using SNP markers previously developed for the analysis of elite cultivars of hexaploid wheat. Results: We genotyped more than 100 tetraploid wheat landraces and wild emmer wheat accessions, some of which had previously been screened with SSR markers, for an existing SNP panel and obtained publically available genotypes for the same SNPs for hexaploid wheat varieties and landraces. Results showed that quantification of genetic diversity can be affected by ascertainment bias but that the effects of ascertainment bias can at least partly be alleviated by merging SNPs to haplotypes. Analyses of population structure and genetic differentiation show strong subdivision between the tetraploid wheat subspecies, except for durum and rivet that are not separable. A more detailed population structure of durum landraces could be obtained than with SSR markers. The results also suggest an emmer, rather than durum, ancestry of bread wheat and with gene flow from wild emmer. Conclusions: SNP markers developed for elite cultivars show great potential for inferring population structure and can address evolutionary questions in landrace wheat. Issues of marker genome specificity and mapping need, however, to be addressed. Ascertainment bias does not seem to interfere with the ability of a SNP marker system developed for elite bread wheat accessions to detect population structure in other types of wheat.

  • 22.
    Sletvold, Nina
    et al.
    Evolutionary Biology Centre, Uppsala University, Sweden.
    Mousset, Mathilde
    Evolutionary Biology Centre, Uppsala University, Sweden.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Bengt, Hansson
    Lund University, Sweden.
    Ågren, Jon
    Evolutionary Biology Centre, Uppsala University, Sweden.
    Strong inbreeding depression in two Scandinavian populations of the self-incompatible perennial herb Arabidopsis Lyrata2013In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 67, no 10, p. 2876-2888Article in journal (Refereed)
    Abstract [en]

    Inbreeding depression is a key factor influencing mating system evolution in plants, but current understanding of its relationship with selfing rate is limited by a sampling bias with few estimates for self-incompatible species. We quantified inbreeding depression () over two growing seasons in two populations of the self-incompatible perennial herb Arabidopsis lyrata ssp. petraea in Scandinavia. Inbreeding depression was strong and of similar magnitude in both populations. Inbreeding depression for overall fitness across two seasons (the product of number of seeds, offspring viability, and offspring biomass) was 81% and 78% in the two populations. Chlorophyll deficiency accounted for 81% of seedling mortality in the selfing treatment, and was not observed among offspring resulting from outcrossing. The strong reduction in both early viability and late quantitative traits suggests that inbreeding depression is due to deleterious alleles of both large and small effect, and that both populations experience strong selection against the loss of self-incompatibility. A review of available estimates suggested that inbreeding depression tends to be stronger in self-incompatible than in self-compatible highly outcrossing species, implying that undersampling of self-incompatible taxa may bias estimates of the relationship between mating system and inbreeding depression.

  • 23.
    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.

  • 24.
    Asplund, Linnéa
    et al.
    Department of Ecology and Evolution, Uppsala University and Department of Crop Production Ecology, Swedish University of Agricultural Sciences.
    Leino, Matti
    Linköping University, Department of Physics, Chemistry and Biology, Molecular genetics. Linköping University, The Institute of Technology.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Molecular genetics. Linköping University, The Institute of Technology.
    Allelic Variation at the Rht8 Locus in a 19th Century Wheat Collection2012In: The Scientific World Journal, ISSN 1537-744X, p. 385610-Article in journal (Refereed)
    Abstract [en]

    Wheat breeding during the 20th century has put large efforts into reducing straw length and increasing harvest index. In the 1920s an allele of Rht8 with dwarfing effects, found in the Japanese cultivar “Akakomugi,” was bred into European cultivars and subsequently spread over the world. Rht8 has not been cloned, but the microsatellite marker WMS261 has been shown to be closely linked to it and is commonly used for genotyping Rht8. The “Akakomugi” allele is strongly associated with WMS261-192bp. Numerous screens of wheat cultivars with different geographical origin have been performed to study the spread and influence of the WMS261-192bp during 20th century plant breeding. However, the allelic diversity of WMS261 in wheat cultivars before modern plant breeding and introduction of the Japanese dwarfing genes is largely unknown. Here, we report a study of WMS261 allelic diversity in a historical wheat collection from 1865 representing worldwide major wheats at the time. The majority carried the previously reported 164 bp or 174 bp allele, but with little geographical correlation. In a few lines, a rare 182 bp fragment was found. Although straw length was recognized as an important character already in the 19th century, Rht8 probably played a minor role for height variation. The use of WMS261 and other functional markers for analyses of historical specimens and characterization of historic crop traits is discussed.

  • 25.
    Karlsson Strese, Else-Marie
    et al.
    Nordiska museet, Julita - Sveriges lantbruksmuseum.
    Tollin, Clas
    Sveriges lantbruksuniversitet , Uppsala.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Den svenska humlens ursprung2012In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 106, no 3-4, p. 165-176Article in journal (Other academic)
  • 26.
    Hagenblad, Jenny
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Asplund, Linnea
    Swedish University of Agriculture Science, Sweden .
    Balfourier, Francois
    INRA, France .
    Ravel, Catherine
    INRA, France .
    Leino, Matti W
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Strong presence of the high grain protein content allele of NAM-B1 in Fennoscandian wheat2012In: Theoretical and Applied Genetics, ISSN 0040-5752, E-ISSN 1432-2242, Vol. 125, no 8, p. 1677-1686Article in journal (Refereed)
    Abstract [en]

    Grain protein content in wheat has been shown to be affected by the NAM-B1 gene where the wildtype allele confers high levels of protein and micronutrients but can reduce yield. Two known non-functional alleles instead increase yield but lead to lower levels of protein and micronutrients. The wildtype allele in hexaploid bread wheat is so far mainly known from historical specimens and a few lines with an emmer wheat introgression. Here we report a screening for the wildtype allele in wheats of different origin. First, a worldwide core collection of 367 bread wheats with worldwide origin was screened and five accessions carrying the wildtype NAM-B1 allele were found. Several of these could be traced to a Fennoscandian origin and the wildtype allele was more frequent in spring wheat. These findings, together with the late maturation of spring wheat, suggested that the faster maturation caused by the wildtype allele might have preserved it in areas with a short growing season. Thus a second set consisting of 138 spring wheats of a northern origin was screened and as many as 33 % of the accessions had the wildtype allele, all of a Fennoscandian origin. The presence of the wildtype allele in landraces and cultivars is in agreement with the use of landraces in Fennoscandian wheat breeding. Last, 22 spelt wheats, a wheat type previously suggested to carry the wildtype allele, were screened and five wildtype accessions found. The wildtype NAM-B1 accessions found could be a suitable material for plant breeding efforts directed towards increasing the nutrient content of bread wheat.

  • 27.
    W Leino, Matti W
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Ecology. Linköping University, The Institute of Technology.
    Hagenblad, Jenny
    Uppsala University.
    Nineteenth Century Seeds Reveal the Population Genetics of Landrace Barley (Hordeum vulgare)2010In: MOLECULAR BIOLOGY AND EVOLUTION, ISSN 0737-4038, Vol. 27, no 4, p. 964-973Article in journal (Refereed)
    Abstract [en]

    Barley (Hordeum vulgare) is a major crop, grown worldwide and in a wide range of climatic conditions. Despite its importance as a crop species, little is known about the population genetics of barley and the effects of bottlenecks, adaptation, and gene flow on genetic diversity within and between landrace populations. In areas with highly developed agriculture, such as Northern Europe, these types of genetic studies are hampered by lack of landraces preserved in situ or ex situ. Here, we report a genetic study of Swedish landrace barley using 113-year-old seed samples. The results demonstrate differing levels of variation with some latitudinal effect. We also detect clear population differentiation and population structure within Sweden into a southern and a northern cluster. These results possibly reflect different introduction routes of barley into Sweden. We thus show that the study of historic material can be an important alternative for regions where no or little extant landrace material is available.

  • 28.
    Asplund, Linnea
    et al.
    Uppsala University.
    Hagenblad, Jenny
    Uppsala University.
    Leino, Matti W
    Linköping University, Department of Physics, Chemistry and Biology, Molecular genetics. Linköping University, The Institute of Technology.
    Re-evaluating the history of the wheat domestication gene NAM-B1 using historical plant material2010In: JOURNAL OF ARCHAEOLOGICAL SCIENCE, ISSN 0305-4403, Vol. 37, no 9, p. 2303-2307Article in journal (Refereed)
    Abstract [en]

    The development of agriculture is closely associated with the domestication of wheat, one of the earliest crop species. During domestication key genes underlying traits important to Neolithic agriculture were targeted by selection. One gene believed to be such a domestication gene is NAM-B1, affecting both nutritional quality and yield but with opposite effects. A null mutation, first arisen in emmer wheat, decreases the nutritional quality but delays maturity and increases grain size; previously the ancestral allele was believed lost during the domestication of durum and bread wheat by indirect selection for larger grain. By genotyping 63 historical seed samples originating from the 1862 International Exhibition in London, we found that the ancestral allele was present in two spelt wheat and two bread wheat cultivars widely cultivated at the time. This suggests that fixation of the mutated allele of NAM-B1 in bread wheat, if at all, occurred during modern crop improvement rather than during domestication. We also discuss the value of using archaeological and historical plant material to further the understanding of the development of agriculture.

  • 29.
    Leino, Matti W.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Molecular genetics. Linköping University, The Institute of Technology.
    Hagenblad, Jenny
    Uppsala University.
    Edqvist, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Molecular genetics. Linköping University, The Institute of Technology.
    Karlsson Strese, Else-Marie
    Swedish Museum of Cultural History.
    DNA preservation and utility of a historic seed collection2009In: Seed Science Research, ISSN 0960-2585, E-ISSN 1475-2735, Vol. 19, p. 125-135Article in journal (Refereed)
    Abstract [en]

    Historic collections of biological material are important genetic resources for taxonomic, evolutionary and historical research. In this paper we describe a seed collection dating from 1862 to 1918 maintained at the Swedish Museum of Cultural History. The collection contains over 3000 well-documented seed samples of various agricultural crops, mostly cereals. A subset of 100 samples divided over ten species frequently represented in the collection and a range of ages were tested for germinability and DNA preservation. None of these accessions were found to contain viable seeds. DNA extracted from the seeds was degraded, but the amount of degradation varied between species. DNA quality was evaluated by yield, fragment size and size of amplification product. Quality was highest for DNA extracted from Pisum sativum and Vicia sativa. DNA extracted from Brassica napus, Beta vulgaris and Trifolium pratense was more fragmented, and DNA extracted from Triticum aestivum, Secale sereale, Hordeum vulgare, Avena sativa and Phleum pratense was most degraded. Polymerase chain reaction (PCR) amplification of ribosomal DNA fragments of up to 700 bp was permitted for most samples in all species. To test whether single-copy nuclear genes could be amplified from the extracted DNA, microsatellite markers were used on the Pisum sativum and Hordeum vulgare samples. Polymorphisms of microsatellite markers were detected between samples for both species. The results show that the 19th-century seed collection can be utilized to infer genetic relationships among obsolete cultivars as well as for other types of genetic research based on sequence or marker analysis.

  • 30.
    Hagenblad, Jenny
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Olsson, Maria
    Uppsala University.
    Parker, Heidi G
    NHGRI.
    Ostrander, Elaine A
    NHGRI.
    Ellegren , Hans
    Uppsala University.
    Population genomics of the inbred Scandinavian wolf2009In: MOLECULAR ECOLOGY, ISSN 0962-1083 , Vol. 18, no 7, p. 1341-1351Article in journal (Refereed)
    Abstract [en]

    The Scandinavian wolf population represents one of the genetically most well-characterized examples of a severely bottlenecked natural population (with only two founders), and of how the addition of new genetic material (one immigrant) can at least temporarily provide a genetic rescue. However, inbreeding depression has been observed in this population and in the absence of additional immigrants, its long-term viability is questioned. To study the effects of inbreeding and selection on genomic diversity, we performed a genomic scan with approximately 250 microsatellite markers distributed across all autosomes and the X chromosome. We found linkage disequilibrium (LD) that extended up to distances of 50 Mb, exceeding that of most outbreeding species studied thus far. LD was particularly pronounced on the X chromosome. Overall levels of observed genomic heterozygosity did not deviate significantly from simulations based on known population history, giving no support for a general selection for heterozygotes. However, we found evidence supporting balancing selection at a number of loci and also evidence suggesting directional selection at other loci. For markers on chromosome 23, the signal of selection was particularly strong, indicating that purifying selection against deleterious alleles may have occurred even in this very small population. These data suggest that population genomics allows the exploration of the effects of neutral and non-neutral evolution on a finer scale than what has previously been possible.

  • 31.
    Jakobsson, Mattias
    et al.
    Department of Human Genetics University of Michigan.
    Hagenblad, Jenny
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Tavaré, Simon
    Molecular and Computational Biology University of Southern California.
    Säll, Torbjörn
    Department of Cell and Organism Biology, Genetics Lund University, Sweden.
    Halldén, Christer
    Department of Clinical Chemistry Malmö university, Sweden.
    Lind-Halldén, Christina
    Department of Mathematics and Natural Sciences Kristianstad University, Sweden.
    Nordborg, magnus
    Molecular and Computational Biology University of Southern California.
    A Unique Recent Origin of the Allotetraploid Species Arabidopsis suecica: Evidence from Nuclear DNA Markers2006In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 23, no 6, p. 1217-1231Article in journal (Refereed)
    Abstract [en]

    A coalescent-based method was used to investigate the origins of the allotetraploid Arabidopsis suecica, using 52 nuclear microsatellite loci typed in eight individuals of A. suecica and 14 individuals of its maternal parent Arabidopsis thaliana, and four short fragments of genomic DNA sequenced in a sample of four individuals of A. suecica and in both its parental species A. thaliana and Arabidopsis arenosa. All loci were variable in A. thaliana but only 24 of the 52 microsatellite loci and none of the four sequence fragments were variable in A. suecica. We explore a number of possible evolutionary scenarios for A. suecica and conclude that it is likely that A. suecica has a recent, unique origin between 12,000 and 300,000 years ago. The time estimates depend strongly on what is assumed about population growth and rates of mutation. When combined with what is known about the history of glaciations, our results suggest that A. suecica originated south of its present distribution in Sweden and Finland and then migrated north, perhaps in the wake of the retreating ice.

  • 32.
    Kawabe, Akira
    et al.
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.
    Hansson, Bengt
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.
    Hagenblad, Jenny
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.
    Forrest, Alan
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.
    Charlesworth, Deborah
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.
    Centromere Locations and Associated Chromosome Rearrangements in Arabidopsis lyrata and A. thaliana2006In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 173, no 3, p. 1613-1619Article in journal (Refereed)
    Abstract [en]

    We analyzed linkage and chromosomal positions of genes in A. lyrata ssp. petraea that are located near the centromere (CEN) regions of A. thaliana, using at least two genes from the short and long arms of each chromosome. In our map, genes from all 10 A. thaliana chromosome arms are also tightly linked in A. lyrata. Genes from the regions on the two sides of CEN5 have distant map localizations in A. lyrata (genes on the A. thaliana short-arm genes are on linkage group AL6, and long-arm genes are on AL7), but genes from the other four A. thaliana centromere regions remain closely linked in A. lyrata. The observation of complete linkage between short- and long-arm centromere genes, but not between genes in other genome regions that are separated by similar physical distances, suggests that crossing-over frequencies near the A. lyrata ssp. petraea centromere regions are low, as in A. thaliana. Thus, the centromere positions appear to be conserved between A. thaliana and A. lyrata, even though three centromeres have been lost in A. thaliana, and the core satellite sequences in the two species are very different. We can now definitively identify the three centromeres that were eliminated in the fusions that formed the A. thaliana chromosomes. However, we cannot tell whether genes were lost along with these centromeres, because such genes are absent from the A. thaliana genome, which is the sole source of markers for our mapping.

  • 33.
    Kawabe, Akira
    et al.
    Institute of Evolutionary Biology University of Edingburgh, UK.
    Hansson, Bengt
    Department of Animal Ecology Lund University, Sweden.
    Forrest, Alan
    Institute of Evolutionary Biology University of Edingburgh, UK.
    Hagenblad, Jenny
    University of Edinburgh.
    Charlesworth, Deborah
    Insitute of Evolutionary Biology University of Edingburgh, UK.
    Comparative gene mapping in Arabidopsis lyrata chromosomes 6 and 7 and A. thaliana chromosome IV: Evolutionary history, rearrangements and local recombination rates2006In: Genetical Research, ISSN 0016-6723, E-ISSN 1469-5073, Vol. 88, no 1, p. 45-56Article in journal (Refereed)
    Abstract [en]

    We have increased the density of genetic markers on the Arabidopsis lyrata chromosomes AL6 and AL7 corresponding to the A. thaliana chromosome IV, in order to determine chromosome rearrangements between these two species, and to compare recombination fractions across the same intervals. We confirm the two rearrangements previously inferred (a reciprocal translocation and a large inversion, which we infer to be pericentric). By including markers around the centromere regions of A. thaliana chromosomes IV and V, we localize the AL6 centromere, and can localize the breakpoints of these chromosome rearrangements more precisely than previously. One translocation breakpoint was close to the centromere, and the other coincided with one end of the inversion, suggesting that a single event caused both rearrangements. At the resolution of our mapping, apart from these rearrangements, all other markers are in the same order in A. lyrata and A. thaliana. We could thus compare recombination rates in the two species. We found slightly higher values in A. thaliana, and a minimum estimate for regions not close to a centromere in A. lyrata is 4-5 centimorgans per megabase. The mapped region of AL7 includes the self-incompatibility loci (S-loci), and this region has been predicted to have lower recombination than elsewhere in the genome. We mapped 17 markers in a region of 1·23 Mb surrounding these loci, and compared the approximately 600 kb closest to the S-loci with the surrounding region of approximately the same size. There were significantly fewer recombination events in the closer than the more distant region, supporting the above prediction, but showing that the low recombination region is very limited in size. © 2006 Cambridge University Press.

  • 34.
    Hagenblad, Jenny
    et al.
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
    Bechsgaard, Jesper
    Bioinformatics Research Center (BiRC), Department of Ecology and Genetics, University of Aarhus, Aarhus C, Denmark.
    Charlesworth, Deborah
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
    Linkage Disequilibrium Between Incompatibility Locus Region Genes2006In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 173, p. 1057-1073Article in journal (Refereed)
    Abstract [en]

    We have studied diversity in Arabidopsis lyrata of sequencesorthologous to the ARK3 gene of A. thaliana. Our main goal wasto test for recombination in the S-locus region. In A. thaliana,the single-copy ARK3 gene is closely linked to the non-functionalcopies of the self-incompatibility loci, and the ortholog inA. lyrata (a self-incompatible species) is in the homologousgenome region and is known as Aly8. It is thus of interest totest whether Aly8 sequence diversity is elevated due to closelinkage to the highly polymorphic incompatibility locus, asis theoretically predicted. However, Aly8 is not a single-copygene, and the presence of paralogs could also lead to the appearanceof elevated diversity. We established a typing approach basedon different lengths of Aly8 PCR products and show that mostA. lyrata haplotypes have a single copy, but some have two genecopies, both closely linked to the incompatibility locus, onebeing a pseudogene. We determined the phase of multiple haplotypesin families of plants from Icelandic and other populations.Different Aly8 sequence types are associated with differentSRK alleles, while haplotypes with the same SRK sequences tendto have the same Aly8 sequence. There is evidence of some exchangeof sequences between different Aly8 sequences, making it difficultto determine which ones are allelic or to estimate the diversity.However, the homogeneity of the Aly8 sequences of each S-haplotypesuggests that recombination between the loci has been very infrequentover the evolutionary history of these populations. Overall,the results suggest that recombination rarely occurs in theinterval between the S-loci and Aly8 and that linkage to theS-loci can probably account for the observed high Aly8 diversity.

  • 35.
    Charlesworth, Deborah
    et al.
    University of Edinburgh, UK.
    Kamau, Esther
    University of Edinburgh, UK.
    Hagenblad, Jenny
    University of Edinburgh.
    Tang, Chunlao
    University of Edinburgh.
    Trans-specificity at Loci Near the Self-Incompatibility Loci in Arabidopsis2006In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 172, no 4, p. 2699-2704Article in journal (Refereed)
    Abstract [en]

      We compared allele sequences of two loci near the Arabidopsis lyrata self-incompatibility (S) loci with sequences of A. thaliana orthologs and found high numbers of shared polymorphisms, even excluding singletons and sites likely to be highly mutable. This suggests maintenance of entire S-haplotypes for long evolutionary times and extreme recombination suppression in the region.

  • 36.
    Hagenblad, Jenny
    et al.
    University of Southern California, Los Angeles, USA.
    Tang, Chunlao
    University of Southern California, Los Angeles, USA.
    Molitor, John
    University of Southern California, Los Angeles, USA.
    Werner, Jonathan
    Salk Institute for Biological Studies, La Jolla, California, USA.
    Zhao, Keyan
    University of Southern California, Los Angeles, USA.
    Zheng, Honggang
    University of Southern California, Los Angeles, USA.
    Marjoram, Paul
    University of Southern California, Los Angeles, USA.
    Weigel, Detlef
    Salk Institute for Biological Studies, La Jolla, California, USA.
    Nordborg, Magnus
    University of Southern California, Los Angeles, USA.
    Haplotype Structure and Phenotypic Associations in the Chromosomal Regions Surrounding Two Arabidopsis thaliana Flowering Time Loci2004In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 168, no 3, p. 1627-1638Article in journal (Refereed)
    Abstract [en]

    The feasibility of using linkage disequilbrium (LD) to fine-map loci underlying natural variation in Arabidopsis thaliana was investigated by looking for associations between flowering time and marker polymorphism in the genomic regions containing two candidate genes, FRI and FLC, both of which are known to contribute to natural variation in flowering. A sample of 196 accessions was used, and polymorphism was assessed by sequencing a total of 17 roughly 500-bp fragments. Using a novel Bayesian algorithm based on haplotype similarity, we demonstrate that LD could have been used to fine-map the FRI gene to a roughly 30-kb region and to identify two common loss-of-function alleles. Interestingly, because of genetic heterogeneity, simple single-marker associations would not have been able to map FRI with nearly the same precision. No clear evidence for previously unknown alleles at either locus was found, but the effect of population structure in causing false positives was evident.

  • 37.
    Hagenblad, Jenny
    et al.
    Lund University, Sweden.
    Nordborg, Magnus
    Lund University, Sweden.
    Sequence Variation and Haplotype Structure Surrounding the Flowering Time Locus FRI in Arabidopsis thaliana2002In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 161, no 1, p. 289-298Article in journal (Refereed)
    Abstract [en]

    Linkage disequilibrium in highly selfing organisms is expected to extend well beyond the scale of individual genes. The pattern of polymorphism in such species must thus be studied over a larger scale. We sequenced 14 short (0.5-1 kb) fragments from a 400-kb region surrounding the flowering time locus FRI in a sample of 20 accessions of Arabidopsis thaliana. The distribution of allele frequencies, as quantified by Tajima’s D, varies considerably over the region and is incompatible with a standard neutral model. The region is characterized by extensive haplotype structure, with linkage disequilibrium decaying over 250 kb. In particular, recombination is evident within 35 kb of FRI in a haplotype associated with a functionally important allele. This suggests that A. thaliana may be highly suitable for linkage disequilibrium mapping.

  • 38.
    Nordborg, Magnus
    et al.
    University of Southern California, Los Angeles, USA.
    Borevitz, Justin O.
    Salk Institute for Biological Studies, La Jolla, California, USA.
    Bergelson, Joy
    University of Chicago, Illinois, USA.
    Berry, Charles C.
    University of California, San Diego, La Jolla, USA.
    Chory, Joanne
    Salk Institute for Biological Studies, La Jolla, California, USA.
    Hagenblad, Jenny
    Lund University, Sweden.
    Kreitman, Martin
    University of Chicago, Illinois, USA.
    Maloo, Julin N
    Salk Institute for Biological Studies, La Jolla, California, USA.
    Noyes, Tina
    Stanford University School of Medicine, California, USA.
    Oefner, Peter J.
    Stanford University School of Medicine, California, USA.
    Stahl, Eli A.
    University of Chicago, Illinois, USA.
    Weigel, Detlef
    Salk Institute for Biological Studies, La Jolla, California, USA.
    The extent of linkage disequilibrium in Arabidopsis thaliana2002In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 30, no 2, p. 190-193Article in journal (Other academic)
    Abstract [en]

    Linkage disequilibrium (LD), the nonrandom occurrence of alleles in haplotypes, has long been of interest to population geneticists. Recently, the rapidly increasing availability of genomic polymorphism data has fueled interest in LD as a tool for fine-scale mapping, in particular for human disease loci(1). The chromosomal extent of LD is crucial in this context, because it determines how dense a map must be for associations to be detected and, conversely, limits how finely loci may be mapped(2). Arabidopsis thaliana is expected to harbor unusually extensive LD because of its high degree of selfing(3). Several polymorphism studies have found very strong LD within individual loci, but also evidence of some recombination(4-6). Here we investigate the pattern of LD on a genomic scale and show that in global samples, LD decays within approximately 1 cM, or 250 kb. We also show that LD in local populations may be much stronger than that of global populations, presumably as a result of founder events. The combination of a relatively high level of polymorphism and extensive haplotype structure bodes well for developing a genome-wide LD map in A. thaliana.

  • 39.
    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.

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