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Larsson, P., Oliveira, H. R., Lundström, M., Hagenblad, J., Lageras, P. & Leino, M. W. (2019). Population genetic structure in Fennoscandian landrace rye (Secale cereale L.) spanning 350 years. Genetic Resources and Crop Evolution, 66(5), 1059-1071
Open this publication in new window or tab >>Population genetic structure in Fennoscandian landrace rye (Secale cereale L.) spanning 350 years
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2019 (English)In: Genetic Resources and Crop Evolution, ISSN 0925-9864, E-ISSN 1573-5109, Vol. 66, no 5, p. 1059-1071Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
SPRINGER, 2019
Keywords
Ancient DNA; Genebank conservation; Kompetitive allele specific PCR (KASP); Slash-and-burn agriculture; Straw artefacts; Museum collection
National Category
Ecology
Identifiers
urn:nbn:se:liu:diva-158323 (URN)10.1007/s10722-019-00770-0 (DOI)000467910500006 ()2-s2.0-85064277688 (Scopus ID)
Note

Funding Agencies|Lagersberg foundation; Royal Academy of Science; Helge Ax:son Johnson Foundation; Crafoord Foundation; Sven and Lilly Lawski Foundation; Swedish Research Council; Berit Wallenberg Foundation

Available from: 2019-07-02 Created: 2019-07-02 Last updated: 2019-11-06
Lempiäinen-Avci, M., Lundström, M., Huttunen, S., Leino, M. W. & Hagenblad, J. (2018). Archaeological and Historical Materials as a Means to Explore Finnish Crop History. Environmental Archaeology
Open this publication in new window or tab >>Archaeological and Historical Materials as a Means to Explore Finnish Crop History
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2018 (English)In: Environmental Archaeology, ISSN 1461-4103, E-ISSN 1749-6314Article in journal (Refereed) Epub ahead of print
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.

Place, publisher, year, edition, pages
Routledge, 2018
Keywords
aDNA, archaeobotany, barley, genetic diversity, Hordeum vulgare, KASP, landraces
National Category
Genetics
Identifiers
urn:nbn:se:liu:diva-151277 (URN)10.1080/14614103.2018.1482598 (DOI)2-s2.0-85048366875 (Scopus ID)
Available from: 2018-09-14 Created: 2018-09-14 Last updated: 2018-12-11Bibliographically approved
Lundström, M. (2018). Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials. (Doctoral dissertation). Linköping: Linköping University Electronic Press
Open this publication in new window or tab >>Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Crop plants have undergone a multitude of genetic changes during and following their domestication. The spread of agriculture brought the crops to new geographic regions exposing them to new environments and selection pressures along the way. This gave rise to many local variants with traits favoured both by agricultural practices and the environment.

Agriculture was introduced in Fennoscandia (Norway, Sweden, Finland and Denmark) around 4000 BC. The composition of the archaeobotanical record gives some clues as to which species were cultivated, but macroscale analyses rarely reach beyond that. Therefore, methods like genetic analysis are necessary to expand our knowledge about the history of crop cultivation. Under optimal conditions, DNA can survive in biological samples for several hundred thousand years. The preservation of plant specimens in the Fennoscandian climate has, however, rarely been explored. This thesis therefore attempts to dive deeper into the Fennoscandian cultivation history through genetic analyses of aged plant materials from both museum collections and archaeological sources. Cereal grains from a range of preservation conditions were evaluated to find which ones might be of interest for genetic investigations. Desiccated materials gave the highest success rates, in agreement with previous studies. Waterlogged materials appeared to contain small amounts of endogenous DNA, whereas genetic analysis of charred cereals failed completely in all samples.

Population structure was investigated in 17-19th century materials of both barley and rye from Sweden and Finland. Northern and southern populations of Finnish six-row barley were distinct from one another. In southern Sweden, genetic analysis suggested conserved population structure extending over 200 years. The genetic composition of rye also seemed mostly conserved, but rye did not show geographic population structure across the investigated region in Sweden and Finland.

A long-standing question in Fennoscandian crop history has been the interpretation of historical written records mentioning Brassica (cole crops, turnips and mustards), as well as the species identity of archaeobotanical finds of Brassica seeds. Thus, Next Generation Sequencing (NGS) was applied to identify which Brassica types that were cultivated in 17th century Kalmar, Sweden. The analysis corroborated morphological species classification in two of the investigated subfossil seeds, whereas no conclusions could be drawn from the remaining samples. The genome coverages were too low to allow subspecies identification.

Wheat has been cultivated in Fennoscandia since the introduction of agriculture but has increased dramatically in importance over the last century. The functional allele of the wheat nutrition gene NAM-B1 was found to be particularly prominent in Fennoscandian wheats, likely associated with its effect on grain maturation time. Here the evolutionary history of NAM-B1 was investigated to see if it could truly be considered a domestication gene as suggested in a previous study. By studying extant landrace materials of Mediterranean tetraploid wheat, it was found that the non-functional allele showed signs indicative of a selective sweep. This selection did not, however, appear to have occurred during domestication.

In conclusion, aged plant specimens from both museum and archaeological contexts could contribute greatly to our knowledge about historical cultivation, extending the investigated period into the mid 17th century. Subfossil and waterlogged archaeobotanical materials do contain endogenous DNA, suggesting that they are better suited for genetic analysis than charred ones, at least as far as cereals are concerned. There is potential for classifying archaeological Brassica remains using NGS, even though further optimisation of sample and library preparation may be necessary. And finally, despite NAM-B1 showing signs of selection it should not be considered a domestication gene in tetraploid wheat.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2018. p. 52
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1959
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:liu:diva-152569 (URN)10.3384/diss.diva-152569 (DOI)9789176851944 (ISBN)
Public defence
2018-12-19, Planck, Fysikhuset, Campus Valla, Linköping, 09:15 (English)
Opponent
Supervisors
Available from: 2018-11-07 Created: 2018-11-07 Last updated: 2019-09-30Bibliographically approved
Lundström, M., Forsberg, N., Heimdahl, J., Hagenblad, J. & Leino, M. W. (2018). Genetic analyses of Scandinavian desiccated, charred and waterlogged remains of barley (Hordeum vulgare L.). Journal of Archaeological Science: Reports, 22, 11-20
Open this publication in new window or tab >>Genetic analyses of Scandinavian desiccated, charred and waterlogged remains of barley (Hordeum vulgare L.)
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2018 (English)In: Journal of Archaeological Science: Reports, ISSN 2352-409X, Vol. 22, p. 11-20Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
Ancient DNA, Barley, Population structure, 17th century, Landraces
National Category
Genetics
Identifiers
urn:nbn:se:liu:diva-151282 (URN)10.1016/j.jasrep.2018.09.006 (DOI)
Available from: 2018-09-14 Created: 2018-09-14 Last updated: 2019-08-02Bibliographically approved
Lundström, M., Leino, M. W. & Hagenblad, J. (2017). Evolutionary history of the NAM-B1 gene in wild and domesticated tetraploid wheat. BMC Genetics, 18, Article ID 118.
Open this publication in new window or tab >>Evolutionary history of the NAM-B1 gene in wild and domesticated tetraploid wheat
2017 (English)In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 18, article id 118Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
BioMed Central, 2017
Keywords
Selective sweep, Grain protein content (GPC), Emmer, Durum, Domestication gene
National Category
Genetics Evolutionary Biology
Identifiers
urn:nbn:se:liu:diva-144103 (URN)10.1186/s12863-017-0566-7 (DOI)000418687000001 ()
Available from: 2018-01-05 Created: 2018-01-05 Last updated: 2019-08-02Bibliographically approved
Vanhala, T., Normann, K. R., Lundström, M., Weller, J. L., Leino, M. & Hagenblad, J. (2016). Flowering time adaption in Swedish landrace pea (Pisum sativum L.). BMC Genetics, 17(1), 117
Open this publication in new window or tab >>Flowering time adaption in Swedish landrace pea (Pisum sativum L.)
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2016 (English)In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 17, no 1, p. 117-Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
BioMed Central, 2016
Keywords
Crop evolution, HIGH RESPONSE TO PHOTOPERIOD (HR), LATE FLOWERING (LF), Legumes, Local adaptation, STERILE NODES (SN
National Category
Genetics
Identifiers
urn:nbn:se:liu:diva-130546 (URN)10.1186/s12863-016-0424-z (DOI)000381569600001 ()27521156 (PubMedID)
Note

Funding agencies: Swedish Board of Agriculture; Erik Philip-Sorensen Foundation; Royal Swedish Academy of Forestry and Agriculture (CF Lundstrom foundation); Royal Swedish Academy of Forestry and Agriculture (Adolf Dahl foundation)

Available from: 2016-08-15 Created: 2016-08-15 Last updated: 2019-08-02
Karlsson Strese, E.-M., Lundström, M., Hagenblad, J. & Leino, M. W. (2014). Genetic Diversity in Remnant Swedish Hop (Humulus lupulus L.) Yards from the 15th to 18th Century. Economic Botany, 68(3), 231-245
Open this publication in new window or tab >>Genetic Diversity in Remnant Swedish Hop (Humulus lupulus L.) Yards from the 15th to 18th Century
2014 (English)In: Economic Botany, ISSN 0013-0001, E-ISSN 1874-9364, Vol. 68, no 3, p. 231-245Article in journal (Refereed) Published
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.

Abstract [sv]

Humle (Humulus lupulus L.) är en flerårig växt som odlas för användning i ölproduktion. Växten är tvåbyggare och honplantorna producerar kottar som innehåller ämnen som förbättrar ölets smak och hållbarhet. Öl var länge en viktig del av livsmedelsförsörjningen i norra Europa, varför humle varit en mycket betydelsefull gröda under de senaste 1000 åren. I Sverige var humleodling enligt lag obligatorisk för jordbrukare från år 1414 till 1860. I dag är den svenska odlingen av humle försumbar men förvildade humleplantor från historiska odlingar kan fortfarande hittas. Med hjälp av historiska kartor och dokument har vi återfunnit humlebestånd från tio historiska humleodlingar från 1400- till 1700-talet. Prov togs från ett femtontal plantor av varje population och genotypades med tio SSR markörer och en markör diagnostisk för kön. Dessutom genotypades 25 kloner av gamla lantsorter och sorter från Europa bevarade i genbanker. Resultaten visar på hög grad av klonalitet och låg frekvens av sexuell reproduktion inom populationerna. Två populationer hade markant högre genetisk diversitet och ett större antal haplotyper, i dessa populationer förekom också en blandning av han- och honplantor. Populationerna var alla tydligt differentierade från varandra och inga haplotyper förkom i mer än en population, vilket påvisar lågt utbyte av genetiskt material. Dessa resultat tyder på att naturlig spridning och genetisk rekombination är ovanligt eller sker långsamt i Sverige. Analysen av de europeiska klonerna från genbanker visade att flera kloner hade identiska genotyper och totalt sett begränsad genetisk diversitet. De svenska populationerna var i de flesta fall genetiskt klart särskiljbara från genbanksklonerna. Detta resultat kontrasterar mot informationen i historiska dokument som beskriver massiv introduktion av humlekloner från kontinentala Europa under 1800-talet och visar att denna import inte ersatte den humle som tidigare odlats. En möjlig bättre klimatanpassning av de ursprungliga svenska humlesorterna och en eventuell primitiv historisk förädling diskuteras.

Place, publisher, year, edition, pages
Springer, 2014
Keywords
Brewing, crop migration, dioecious plants, historic maps, microsatellites, plant longevity, ethnobotany
National Category
Biological Sciences
Identifiers
urn:nbn:se:liu:diva-109296 (URN)10.1007/s12231-014-9273-8 (DOI)000343160800001 ()
Available from: 2014-08-11 Created: 2014-08-11 Last updated: 2019-08-02
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-2017-4177

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