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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., 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
Leino, M. W., Solberg, S. O., Tunset, H. M., Fogelholm, J., Karlsson Strese, E.-M. & Hagenblad, J. (2018). Patterns of Exchange of Multiplying Onion (Allium cepa L. Aggregatum-Group) in Fennoscandian Home Gardens. Economic Botany, 72(3), 346-356
Open this publication in new window or tab >>Patterns of Exchange of Multiplying Onion (Allium cepa L. Aggregatum-Group) in Fennoscandian Home Gardens
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2018 (English)In: Economic Botany, ISSN 0013-0001, E-ISSN 1874-9364, Vol. 72, no 3, p. 346-356Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Springer, 2018
Keywords
Aggregating onion; shallot; potato onion; on-farm conservation; SSRs
National Category
Botany
Identifiers
urn:nbn:se:liu:diva-153392 (URN)10.1007/s12231-018-9426-2 (DOI)000451303600007 ()
Note

Funding Agencies|Swedish Board of Agriculture

Available from: 2018-12-17 Created: 2018-12-17 Last updated: 2019-08-02
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
Hagenblad, J., Oliveira, H. R., Forsberg, N. E. G. & Leino, M. W. (2016). Geographical distribution of genetic diversity in Secale landrace and wild accessions. BMC Plant Biology, 16(23)
Open this publication in new window or tab >>Geographical distribution of genetic diversity in Secale landrace and wild accessions
2016 (English)In: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 16, no 23Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
BioMed Central, 2016
Keywords
Rye, Population structure, SNP, Ascertainment bias, Genetic variation, Phylogeography
National Category
Genetics
Identifiers
urn:nbn:se:liu:diva-124223 (URN)10.1186/s12870-016-0710-y (DOI)000368417000005 ()26786820 (PubMedID)
Note

Funding agencies: Lagersberg foundation; Sven och Lilly Lawskis Fond for Naturvetenskaplig Forskning; "Genomics and Evolutionary Biology" project - North Portugal Regional Operational Programme, under the National Strategic Reference Framework (NSRF), the European Regional

Available from: 2016-01-22 Created: 2016-01-22 Last updated: 2017-11-30Bibliographically approved
Solberg, S. Ø., Kolodinska Brantestam, A., Olsson, K., Leino, M., Weibull, J. & Yndgaard, F. (2015). Diversity in local cultivars of Pisum sativum collected from home gardens in Sweden. Biochemical Systematics and Ecology, 62, 194-203
Open this publication in new window or tab >>Diversity in local cultivars of Pisum sativum collected from home gardens in Sweden
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2015 (English)In: Biochemical Systematics and Ecology, ISSN 0305-1978, E-ISSN 1873-2925, Vol. 62, p. 194-203Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Pergamon Press, 2015
Keywords
Classification Conservation Garden pea iPBS Morphology PGene SSRs
National Category
Other Agricultural Sciences not elsewhere specified
Identifiers
urn:nbn:se:liu:diva-121569 (URN)10.1016/j.bse.2015.09.004 (DOI)000364265300028 ()
Note

Funding agencies: Nordic Council of Ministers; Swedish Board of Agriculture

Available from: 2015-09-25 Created: 2015-09-25 Last updated: 2018-01-11Bibliographically approved
Forsberg, N., Russell, J., Macaulay, M., Leino, M. & Hagenblad, J. (2015). Farmers without borders-genetic structuring in century old barley (Hordeum vulgare). Heredity, 114(2), 195-206
Open this publication in new window or tab >>Farmers without borders-genetic structuring in century old barley (Hordeum vulgare)
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2015 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 114, no 2, p. 195-206Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Nature Publishing Group, 2015
National Category
Biological Sciences
Identifiers
urn:nbn:se:liu:diva-110675 (URN)10.1038/hdy.2014.83 (DOI)000348071600008 ()25227257 (PubMedID)
Available from: 2014-09-18 Created: 2014-09-18 Last updated: 2017-12-05
Selçuk, A., Forsberg, N., Hagenblad, J. & Leino, M. W. (2015). Molecular Genotyping of HistoricalBarley Landraces Reveals Novel CandidateRegions for Local Adaption. Crop science, 55(6), 2766-2776
Open this publication in new window or tab >>Molecular Genotyping of HistoricalBarley Landraces Reveals Novel CandidateRegions for Local Adaption
2015 (English)In: Crop science, ISSN 0011-183X, E-ISSN 1435-0653, Vol. 55, no 6, p. 2766-2776Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Crop Science Society of America, 2015
Keywords
aged DNA, flowering time, historical samples, Hordeum vulgare, landraces, SNP
National Category
Botany Agricultural Sciences
Identifiers
urn:nbn:se:liu:diva-122553 (URN)10.2135/cropsci2015.02.0119 (DOI)000368265600035 ()
Note

Funding agencies: Lagersberg foundation; Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS)

Available from: 2015-11-09 Created: 2015-11-09 Last updated: 2017-12-01
Börjeson, A., Strese, E.-M. & Leino, M. W. (2014). Från Sammet till Pansar - svenska åkrar i nya kläder. Sveriges utsädesförenings tidskrift (1), 7-22
Open this publication in new window or tab >>Från Sammet till Pansar - svenska åkrar i nya kläder
2014 (Swedish)In: Sveriges utsädesförenings tidskrift, ISSN 0039-6990, no 1, p. 7-22Article in journal (Other (popular science, discussion, etc.)) Published
Place, publisher, year, edition, pages
Sveriges utsädseförening, 2014
National Category
Natural Sciences
Identifiers
urn:nbn:se:liu:diva-109349 (URN)
Available from: 2014-08-14 Created: 2014-08-14 Last updated: 2017-12-05
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-4654-5722

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