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Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials
Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
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: urn:nbn:se:liu:diva-152569DOI: 10.3384/diss.diva-152569ISBN: 9789176851944 (print)OAI: oai:DiVA.org:liu-152569DiVA, id: diva2:1261340
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: 2018-12-11Bibliographically approved
List of papers
1. Genetic analyses of Scandinavian desiccated, charred and waterlogged remains of barley (Hordeum vulgare L.)
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: 2018-12-11Bibliographically approved
2. Archaeological and Historical Materials as a Means to Explore Finnish Crop History
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
3. Evolutionary history of the NAM-B1 gene in wild and domesticated tetraploid wheat
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: 2018-12-11Bibliographically approved

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