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  • 1. Asplund, Linnea
    et al.
    Bergqvist, Göran
    Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Leino, Matti
    Swedish Museum of Cultural History, Julita, Sweden.
    Westerbergh, Anna
    Department of Plant Biology and Forest Genetics, BioCenter, Swedish University of Agricultural Sciences, Uppsala.
    Weih, Martin
    Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Swedish Spring Wheat Varieties with the Rare High Grain Protein Allele of NAM-B1 Differ in Leaf Senescence and Grain Mineral Content2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 3, p. e59704-Article in journal (Refereed)
    Abstract [en]

    Some Swedish spring wheat varieties have recently been shown to carry a rare wildtype (wt) allele of the gene NAM-B1,known to affect leaf senescence and nutrient retranslocation to the grain. The wt allele is believed to increase grain proteinconcentration and has attracted interest from breeders since it could contribute to higher grain quality and more nitrogenefficientvarieties. This study investigated whether Swedish varieties with the wt allele differ from varieties with one of themore common, non-functional alleles in order to examine the effect of the gene in a wide genetic background, and possiblyexplain why the allele has been retained in Swedish varieties. Forty varieties of spring wheat differing in NAM-B1 allele typewere cultivated under controlled conditions. Senescence was monitored and grains were harvested and analyzed formineral nutrient concentration. Varieties with the wt allele reached anthesis earlier and completed senescence faster thanvarieties with the non-functional allele. The wt varieties also had more ears, lighter grains and higher yields of P and K.Contrary to previous information on effects of the wt allele, our wt varieties did not have increased grain N concentration orgrain N yield. In addition, temporal studies showed that straw length has decreased but grain N yield has remainedunaffected over a century of Swedish spring wheat breeding. The faster development of wt varieties supports thehypothesis of NAM-B1 being preserved in Fennoscandia, with its short growing season, because of accelerateddevelopment conferred by the NAM-B1 wt allele. Although the possible effects of other gene actions were impossible todistinguish, the genetic resource of Fennoscandian spring wheats with the wt NAM-B1 allele is interesting to investigatefurther for breeding purposes.

  • 2.
    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.

  • 3. Börjeson, Agneta
    et al.
    Strese, Else-Marie
    Nordiska Museet.
    Leino, Matti W.
    Linköping University, Department of Physics, Chemistry and Biology, Molecular genetics.
    Från Sammet till Pansar - svenska åkrar i nya kläder2014In: Sveriges utsädesförenings tidskrift, ISSN 0039-6990, no 1, p. 7-22Article in journal (Other (popular science, discussion, etc.))
  • 4.
    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.

  • 5.
    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.

  • 6.
    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.

  • 7.
    Hagenblad, Jenny
    et al.
    Uppsala University.
    Zie, Jenny
    Stockholm University.
    Leino, Matti W.
    Linköping University, Department of Physics, Chemistry and Biology, Molecular genetics. Linköping University, The Institute of Technology.
    Exploring the population genetics of genebank and historical landrace varierties2012In: Genetic Resources and Crop Evolution, ISSN 0925-9864, E-ISSN 1573-5109, Vol. 59, no 6, p. 1185-1199Article in journal (Refereed)
    Abstract [en]

    Landrace accessions have long been recognized as an important source of genetic diversity for crop species, and landraces are stored in genebanks across the world as genetic resources for future crop development. Landraces are also an important part of the human cultural heritage and as such they have been used for genetic studies to make inferences about historical agriculture. However, surprisingly little is known about the within-accession diversity of landrace crops of different species. In order to evaluate the diversity of Swedish landraces we used microsatellite markers to genotype accessions of four species (barley, pea, oats and rye), both extant genebank material and 114-year-old seed samples of similar geographic origin and type. We found consistently high levels of within-population genetic diversity in the historical material, but varying and often lower diversity levels in the genebank accessions. We also make tentative conclusions about how representative the genebank material is to what was originally cultivated in its reported area of origin and suggest that the true identity of the genebank accessions is unclear and that historical seed collections should be a more appropriate material for the study of historical agriculture.

  • 8.
    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.

  • 9.
    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.

  • 10.
    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)
  • 11.
    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.

  • 12.
    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.

  • 13.
    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
  • 14.
    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.

  • 15.
    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.

  • 16.
    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.

  • 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.
    Solberg, Svein Øivind
    et al.
    Nordic Genetic Resource Center, Alnarp, Sweden.
    Kolodinska Brantestam, Agnese
    University of Latvia, Institute of Biology, Salaspils LV-2169, Latvia.
    Olsson, Kestin
    Nordic Genetic Resource Center, Alnarp, Sweden.
    Leino, Matti
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. National Museum of Cultural History (Nordiska Museet), Julita, Sweden.
    Weibull, Jens
    Swedish Board of Agriculture, Plant and Environment Department, Plant Regulations Division, Jönköping, Sweden.
    Yndgaard, Flemming
    Nordic Genetic Resource Center, Alnarp, Sweden.
    Diversity in local cultivars of Pisum sativum collected from home gardens in Sweden2015In: Biochemical Systematics and Ecology, ISSN 0305-1978, E-ISSN 1873-2925, Vol. 62, p. 194-203Article in journal (Refereed)
    Abstract [en]

    Although one would assume that finding any local cultivars in home gardens in a modern society such as Sweden is unlikely, such cultivars were in fact found. More than 170 seed accessions of vegetables, pulses and other seed-propagated garden crops maintained in home gardens and dating back at least to the 1950s have been assembled following the nationwide ‘Seed Call’. Of these, 32 garden pea accessions were taxonomically characterized and compared with 43 accessions already present in the gene bank. In addition tomorphological descriptors, SSR and retrotransposon-based iPBS markers were applied. Based on five SSR markers, potential duplicates could be located within nine pair/groups, or 25% of the accessions. Through combining this analysis with iPBS markers, the potential duplicates were reduced to five pair/groups. Combination of markers and the morphological descriptors further reduced the number to two groups; one group including four wrinkle-seeded accessions and one including two other wrinkle-seeded accessions. Acombination of genotypic and phenotypic markers proved a good method to identify trueand false duplicates. The results showed that the ‘Seed Call’ complements the NordGen collection and broadens the collection's genetic diversity. No clustering according to region of origin could be found, suggesting that the collected material predominantly represents old cultivars.

  • 19.
    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.

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