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  • 1.
    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.

  • 2.
    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.

  • 3.
    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.

  • 4.
    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.

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