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1.	Charlesworth, Deborah, et al. (författare) Trans-specificity at Loci Near the Self-Incompatibility Loci in Arabidopsis 2006 Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 172:4, s. 2699-2704 Tidskriftsartikel (refereegranskat)abstract We compared allele sequences of two loci near the Arabidopsis lyrata self-incompatibility (S) loci with sequences of A. thaliana orthologs and found high numbers of shared polymorphisms, even excluding singletons and sites likely to be highly mutable. This suggests maintenance of entire S-haplotypes for long evolutionary times and extreme recombination suppression in the region.
2.	Forsberg, Nils, 1981-, et al. (författare) Population structure in landrace barley (Hordeum vulgare L.) during the late 19th century crop failures in Fennoscandia 2019 Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 123:6, s. 733-745 Tidskriftsartikel (refereegranskat)abstract Agricultural disasters and the subsequent need for supply of relief seed can be expected to influence the genetic composition of crop plant populations. The consequences of disasters and seed relief have, however, rarely been studied since specimens sampled before the events are seldomly available. A series of crop failures struck northern Fennoscandia (Norway, Sweden and Finland) during the second half of the 19th century. In order to assess population genetic dynamics of landrace barley (Hordeum vulgare), and consequences of crop failure and possible seed relief during this time period, we genotyped seeds from 16 historical accessions originating from two time periods spanning the period of repeated crop failure. Reliable identification of genetic structuring is highly dependent on sampling regimes and detecting fine-scale geographic or temporal differentiation requires large sample sizes. The robustness of the results under different sampling regimes was evaluated by analyzing subsets of the data and an artificially pooled dataset. The results led to the conclusion that six individuals per accession were insufficient for reliable detection of the observed genetic structure. We found that population structure among the data was best explained by collection year of accessions, rather than geographic origin. The correlation with collection year indicated a change in genetic composition of landrace barley in the area after repeated crop failures, likely a consequence of introgression of relief seed in local populations. Identical genotypes were found to be shared among some accessions, suggesting founder effects and local seed exchange along known routes for trade and cultural exchange.
3.	Hagenblad, Jenny, Associate Professor, 1974-, et al. (författare) Chevalier barley : The influence of a world-leading malting variety 2022 Ingår i: Crop science. - : Wiley. - 0011-183X .- 1435-0653. ; 62:1, s. 235-246 Tidskriftsartikel (refereegranskat)abstract During the 19th century, ‘Chevalier’, said to have been developed from a single plant found in 1820, was the world-leading malting barley (Hordeum vulgare). The superior malting quality of Chevalier lead to its world-wide spread at the time of the development of the malting industry. In this study, we investigate how this cultivar was spread and adopted to Nordic seed systems of the time. Single nucleotide polymorphism genotyping of up to 155-yr-old museum specimens of historical grains labelled “Chevalier” and of Chevalier accessions preserved in genebanks, in total 282 individuals representing 47 accessions, allowed us to divide the accessions into four categories: True Chevalier, seed mixtures, crosses, and non-Chevaliers. Comparisons with previously genotyped Nordic landraces showed how, in the 19th century, Chevalier seed was mixed with locally produced landrace seed and cultivated together. We suggest that spontaneous outbreeding events gave rise to hybrids which were subsequently selected and propagated when resulting in superior genetic combinations. Such farmer-driven breeding activities would have preceded modern plant breeding but resembled the breeding principles that were later used, even though the scientific understanding of inheritance was not yet known.
4.	Hagenblad, Jenny, Associate Professor, 1974-, et al. (författare) Data from: Farmer fidelity in the Canary Islands revealed by ancient DNA from prehistoric seeds 2017 Annan publikationabstract The Canary Islands were settled in the first millennium AD by colonizers likely originating from North Africa. The settlers developed a farming economy with barley as the main crop. Archaeological evidence suggests the islands then remained isolated until European sea-travellers discovered and colonized them during the 14th and 15th centuries. Here we report a population study of ancient DNA from twenty-one archaeobotanical barley grains from Gran Canaria dating from 1050 to 1440 cal AD. The material showed exceptional DNA preservation and genotyping was carried out for 99 single nucleotide markers. In addition 101 extant landrace accessions from the Canary Islands and the western Mediterranean were genotyped. The archaeological material showed high genetic similarity to extant landraces from the Canary Islands. In contrast, accessions from the Canary Islands were highly differentiated from both Iberian and North African mainland barley. Within the Canary Islands, landraces from the easternmost islands were genetically differentiated from landraces from the western islands, corroborating the presence of pre-Hispanic barley cultivation on Lanzarote. The results demonstrate the potential of population genetic analyses of ancient DNA. They support the hypothesis of an original colonization, possibly from present day Morocco, and subsequent isolation of the islands and reveal a farmer fidelity to the local barley that has lasted for centuries.
5.	Hagenblad, Jenny, Associate Professor, 1974-, et al. (författare) Data from: Farmers without borders - genetic structuring in century old barley (Hordeum vulgare) 2014 Annan publikationabstract 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.
6.	Hagenblad, Jenny, Associate Professor, 1974-, et al. (författare) Data from: Morphological and genetic characterization of barley (Hordeum vulgare L.) landraces in the Canary Islands 2018 Annan publikationabstract Barley has been continuously cultivated in the Canary archipelago for millennia, and to this day landrace barley is the preferred choice for cultivation. We have morphologically and genetically characterized 57 landraces collected during the 21st century and conserved in genebanks. The majority of accessions were of the six-row type. Although landraces from the same island tended to be similar, the results showed morphological and genetic diversity both within and in the case of genetic data among islands. Accessions from the easternmost islands were genetically distinct from those from the central and western islands. Accessions from the western islands often had a mixed genetical composition, suggesting more recent exchange of plant material with the central islands. The geographic distribution of diversity suggests that conservation of barley genetic resources needs to consider all islands in the archipelago. Landrace barley from the Canary archipelago was found to be morphologically distinct from continental landrace barley. We suggest the uniqueness of Canarian barley, in terms of morphology and genetic diversity, can be used for marketing purposes providing added market value to the crop.
7.	Hagenblad, Jenny, Associate Professor, 1974-, et al. (författare) Data from: Twentieth-century changes in the genetic composition of Swedish field pea metapopulations 2012 Annan publikationabstract 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 nineteenth century or as extant gene bank accessions assembled in the late twentieth 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 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 harbor 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 twentieth century, although as genetically isolated populations.
8.	Hagenblad, Jenny, 1974-, et al. (författare) Haplotype Structure and Phenotypic Associations in the Chromosomal Regions Surrounding Two Arabidopsis thaliana Flowering Time Loci 2004 Ingår i: Genetics. - : Genetics Society of America. - 0016-6731 .- 1943-2631. ; 168:3, s. 1627-1638 Tidskriftsartikel (refereegranskat)abstract The feasibility of using linkage disequilbrium (LD) to fine-map loci underlying natural variation in Arabidopsis thaliana was investigated by looking for associations between flowering time and marker polymorphism in the genomic regions containing two candidate genes, FRI and FLC, both of which are known to contribute to natural variation in flowering. A sample of 196 accessions was used, and polymorphism was assessed by sequencing a total of 17 roughly 500-bp fragments. Using a novel Bayesian algorithm based on haplotype similarity, we demonstrate that LD could have been used to fine-map the FRI gene to a roughly 30-kb region and to identify two common loss-of-function alleles. Interestingly, because of genetic heterogeneity, simple single-marker associations would not have been able to map FRI with nearly the same precision. No clear evidence for previously unknown alleles at either locus was found, but the effect of population structure in causing false positives was evident.
9.	Hagenblad, Jenny, 1974-, et al. (författare) Linkage Disequilibrium Between Incompatibility Locus Region Genes 2006 Ingår i: Genetics. - Baltimore, MD, USA : The Genetics Society. - 0016-6731 .- 1943-2631. ; 173, s. 1057-1073 Tidskriftsartikel (refereegranskat)abstract We have studied diversity in Arabidopsis lyrata of sequencesorthologous to the ARK3 gene of A. thaliana. Our main goal wasto test for recombination in the S-locus region. In A. thaliana,the single-copy ARK3 gene is closely linked to the non-functionalcopies of the self-incompatibility loci, and the ortholog inA. lyrata (a self-incompatible species) is in the homologousgenome region and is known as Aly8. It is thus of interest totest whether Aly8 sequence diversity is elevated due to closelinkage to the highly polymorphic incompatibility locus, asis theoretically predicted. However, Aly8 is not a single-copygene, and the presence of paralogs could also lead to the appearanceof elevated diversity. We established a typing approach basedon different lengths of Aly8 PCR products and show that mostA. lyrata haplotypes have a single copy, but some have two genecopies, both closely linked to the incompatibility locus, onebeing a pseudogene. We determined the phase of multiple haplotypesin families of plants from Icelandic and other populations.Different Aly8 sequence types are associated with differentSRK alleles, while haplotypes with the same SRK sequences tendto have the same Aly8 sequence. There is evidence of some exchangeof sequences between different Aly8 sequences, making it difficultto determine which ones are allelic or to estimate the diversity.However, the homogeneity of the Aly8 sequences of each S-haplotypesuggests that recombination between the loci has been very infrequentover the evolutionary history of these populations. Overall,the results suggest that recombination rarely occurs in theinterval between the S-loci and Aly8 and that linkage to theS-loci can probably account for the observed high Aly8 diversity.
10.	Hagenblad, Jenny, Associate Professor, 1974-, et al. (författare) Morphological and genetic characterization of barley (Hordeum vulgare L.) landraces in the Canary Islands 2019 Ingår i: Genetic Resources and Crop Evolution. - : Springer Netherlands. - 0925-9864 .- 1573-5109. ; 66:2, s. 465-480 Tidskriftsartikel (refereegranskat)abstract Barley has been continuously cultivated in the Canary archipelago for millennia, and to this day landrace barley is the preferred choice for cultivation. We have morphologically and genetically characterized 57 landraces collected during the twenty-first century and conserved in genebanks. The majority of accessions were of the six-row type. Although landraces from the same island tended to be similar, the results showed morphological and genetic diversity both within and in the case of genetic data among islands. Accessions from the easternmost islands were genetically distinct from those from the central and western islands. Accessions from the western islands often had a mixed genetical composition, suggesting more recent exchange of plant material with the central islands. The geographic distribution of diversity suggests that conservation of barley genetic resources needs to consider all islands in the archipelago. Landrace barley from the Canary archipelago was found to be morphologically distinct from continental landrace barley. We suggest the uniqueness of Canarian barley, in terms of morphology and genetic diversity, can be used for marketing purposes providing added market value to the crop.
11.	Hagenblad, Jenny, Associate Professor, 1974-, et al. (författare) Population structure in landrace barley (Hordeum vulgare L.) during the late 19th century crop failures in Fennoscandia 2019 Annan publikationabstract Agricultural disasters and the subsequent need for supply of relief seed can be expected to influence the genetic composition of crop plant populations. The consequences of disasters and seed relief have, however, rarely been studied since specimens sampled before the events are seldomly available. A series of crop failures struck northern Fennoscandia (Norway, Sweden and Finland) during the second half of the 19th century. In order to assess population genetic dynamics of landrace barley (Hordeum vulgare), and consequences of crop failure and possible seed relief during this time period, we genotyped seeds from 16 historical accessions originating from two time periods spanning the period of repeated crop failure. Reliable identification of genetic structuring is highly dependent on sampling regimes and detecting fine-scale geographic or temporal differentiation requires large sample sizes. The robustness of the results under different sampling regimes was evaluated by analyzing subsets of the data and an artificially pooled dataset. The results led to the conclusion that six individuals per accession were insufficient for reliable detection of the observed genetic structure. We found that population structure among the data was best explained by collection year of accessions, rather than geographic origin. The correlation with collection year indicated a change in genetic composition of landrace barley in the area after repeated crop failures, likely a consequence of introgression of relief seed in local populations. Identical genotypes were found to be shared among some accessions, suggesting founder effects and local seed exchange along known routes for trade and cultural exchange. MethodsIndividual 19th century seeds were genotyped using an Illumina Golden Gate assay for the C-384 barley SNP set detailed by Moragues et al. (2010). Quality control based on CG10 scores led to the exclusion of 26 low performance samples, including all nine negative controls. Samples with more than 25 % missing data (39 samples), markers with more than 20 % missing data (92 SNPs) and monomorphic SNPs (140 SNPs) were also excluded, in that order. Usage notesHeterozygous loci and missing values are given in the data set as -9. Genotypes in the dataset are homozygous genotypes.
12.	Hagenblad, Jenny, Associate Professor, 1974-, et al. (författare) Studentaktiverande gruppdiskussioner för fördjupat lärande 2022 Ingår i: Använd rummet. - Lund : Studentlitteratur AB. - 9789144157795 ; , s. 275-281 Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract I det här kapitlet betonar vi gruppdiskussioners betydelse för att aktivera studenter och gynna deras lärande. Undervisningen på kursen "Evolution" bedrevs omväxlande i traditionell undervisningssal och i ALC. Tyngdpunkten på kursen ligger på studenternas gruppdiskussioner. Fokus i kapitlet ligger på de aktiviteter som studenterna genomför i ALC.
13.	Helsen, Kenny, et al. (författare) No genetic erosion after five generations for Impatiens glandulifera populationsacross the invaded range in Europe 2019 Ingår i: BMC Genetics. - : BioMed Central. - 1471-2156. ; 20 Tidskriftsartikel (refereegranskat)abstract Background: The observation that many alien species become invasive despite low genetic diversity has long been considered the ‘genetic paradox’ in invasion biology. This paradox is often resolved through the temporal buildup genetic diversity through multiple introduction events. These temporal dynamics in genetic diversity are especially important for annual invasive plants that lack a persistent seed bank, for which population persistence is strongly dependent on consecutive seed ‘re-establishment’ in each growing season. Theory predicts that the number of seeds during re-establishment, and the levels of among-population gene flow can strongly affect recolonization dynamics, resulting in either an erosion or build-up of population genetic diversity through time. This study focuses on temporal changes in the population genetic structure of the annual invasive plant Impatiens glandulifera across Europe. We resampled 13 populations in 6 regions along a 1600 km long latitudinal gradient from northern France to central Norway after 5 years, and assessed population genetic diversity with 9 microsatellite markers.Results: Our study suggests sufficiently high numbers of genetically diverse founders during population re- establishment, which prevent the erosion of local genetic diversity. We furthermore observe that I. glanduliferaexperiences significant among-population gene flow, gradually resulting in higher genetic diversity and lower overall genetic differentiation through time. Nonetheless, moderate founder effects concerning population genetic composition (allele frequencies) were evident, especially for smaller populations.Despite the initially low genetic diversity, this species seems to be successful at persisting across its invaded range, and will likely continue to build up higher genetic diversity at the local scale.
14.	Jakobsson, Mattias, et al. (författare) A unique recent origin of the allotetraploid species Arabidopsis suecica: Evidence from nuclear DNA markers 2006 Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 23:6, s. 1217-1231 Tidskriftsartikel (refereegranskat)abstract A coalescent-based method was used to investigate the origins of the allotetraploid Arabidopsis suecica, using 52 nuclear microsatellite loci typed in eight individuals of A. suecica and 14 individuals of its maternal parent Arabidopsis thaliana, and four short fragments of genomic DNA sequenced in a sample of four individuals of A. suecica and in both its parental species A. thaliana and Arabidopsis arenosa. All loci were variable in A. thaliana but only 24 of the 52 microsatellite loci and none of the four sequence fragments were variable in A. suecica. We explore a number of possible evolutionary scenarios for A. suecica and conclude that it is likely that A. suecica has a recent, unique origin between 12,000 and 300,000 years ago. The time estimates depend strongly on what is assumed about population growth and rates of mutation. When combined with what is known about the history of glaciations, our results suggest that A. suecica originated south of its present distribution in Sweden and Finland and then migrated north, perhaps in the wake of the retreating ice.
15.	Kawabe, Akira, et al. (författare) Centromere Locations and Associated Chromosome Rearrangements in Arabidopsis lyrata and A. thaliana 2006 Ingår i: Genetics. - Baltimore, MD, USA : The Genetics Society. - 0016-6731 .- 1943-2631. ; 173:3, s. 1613-1619 Tidskriftsartikel (refereegranskat)abstract We analyzed linkage and chromosomal positions of genes in A. lyrata ssp. petraea that are located near the centromere (CEN) regions of A. thaliana, using at least two genes from the short and long arms of each chromosome. In our map, genes from all 10 A. thaliana chromosome arms are also tightly linked in A. lyrata. Genes from the regions on the two sides of CEN5 have distant map localizations in A. lyrata (genes on the A. thaliana short-arm genes are on linkage group AL6, and long-arm genes are on AL7), but genes from the other four A. thaliana centromere regions remain closely linked in A. lyrata. The observation of complete linkage between short- and long-arm centromere genes, but not between genes in other genome regions that are separated by similar physical distances, suggests that crossing-over frequencies near the A. lyrata ssp. petraea centromere regions are low, as in A. thaliana. Thus, the centromere positions appear to be conserved between A. thaliana and A. lyrata, even though three centromeres have been lost in A. thaliana, and the core satellite sequences in the two species are very different. We can now definitively identify the three centromeres that were eliminated in the fusions that formed the A. thaliana chromosomes. However, we cannot tell whether genes were lost along with these centromeres, because such genes are absent from the A. thaliana genome, which is the sole source of markers for our mapping.
16.	Kawabe, Akira, et al. (författare) Comparative gene mapping in Arabidopsis lyrata chromosomes 6 and 7 and A. thaliana chromosome IV : Evolutionary history, rearrangements and local recombination rates 2006 Ingår i: Genetical Research. - 0016-6723 .- 1469-5073. ; 88:1, s. 45-56 Tidskriftsartikel (refereegranskat)abstract We have increased the density of genetic markers on the Arabidopsis lyrata chromosomes AL6 and AL7 corresponding to the A. thaliana chromosome IV, in order to determine chromosome rearrangements between these two species, and to compare recombination fractions across the same intervals. We confirm the two rearrangements previously inferred (a reciprocal translocation and a large inversion, which we infer to be pericentric). By including markers around the centromere regions of A. thaliana chromosomes IV and V, we localize the AL6 centromere, and can localize the breakpoints of these chromosome rearrangements more precisely than previously. One translocation breakpoint was close to the centromere, and the other coincided with one end of the inversion, suggesting that a single event caused both rearrangements. At the resolution of our mapping, apart from these rearrangements, all other markers are in the same order in A. lyrata and A. thaliana. We could thus compare recombination rates in the two species. We found slightly higher values in A. thaliana, and a minimum estimate for regions not close to a centromere in A. lyrata is 4-5 centimorgans per megabase. The mapped region of AL7 includes the self-incompatibility loci (S-loci), and this region has been predicted to have lower recombination than elsewhere in the genome. We mapped 17 markers in a region of 1·23 Mb surrounding these loci, and compared the approximately 600 kb closest to the S-loci with the surrounding region of approximately the same size. There were significantly fewer recombination events in the closer than the more distant region, supporting the above prediction, but showing that the low recombination region is very limited in size. © 2006 Cambridge University Press.
17.	Larsson, Per, et al. (författare) Population genetic structure in Fennoscandian landrace rye (Secale cereale L.) spanning 350years 2019 Ingår i: Genetic Resources and Crop Evolution. - : Springer Science and Business Media LLC. - 0925-9864 .- 1573-5109. ; 66:5, s. 1059-1071 Tidskriftsartikel (refereegranskat)abstract 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.
18.	Leino, Matti W., 1976-, et al. (författare) Patterns of Exchange of Multiplying Onion (Allium cepa L. Aggregatum-Group) in Fennoscandian Home Gardens 2018 Ingår i: Economic Botany. - : Springer Science and Business Media LLC. - 0013-0001 .- 1874-9364. ; 72:3, s. 346-356 Tidskriftsartikel (refereegranskat)abstract 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.
19.	Lempiäinen-Avci, Mia, et al. (författare) Archaeological and Historical Materials as a Means to Explore Finnish Crop History 2020 Ingår i: Environmental Archaeology. - : Routledge. - 1461-4103 .- 1749-6314. ; 25:1, s. 37-52 Tidskriftsartikel (refereegranskat)abstract 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.
20.	Lundström, Maria, 1986-, et al. (författare) Evolutionary history of the NAM-B1 gene in wild and domesticated tetraploid wheat 2017 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 18 Tidskriftsartikel (refereegranskat)abstract 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.
21.	Lundström, Maria, 1986- (författare) Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials 2018 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract 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.
22.	Lundström, Maria, 1986-, et al. (författare) Genetic analyses of Scandinavian desiccated, charred and waterlogged remains of barley (Hordeum vulgare L.) 2018 Ingår i: Journal of Archaeological Science. - : Elsevier BV. - 2352-409X .- 2352-4103. ; 22, s. 11-20 Tidskriftsartikel (refereegranskat)abstract 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.
23.	Palmé, Amma E, et al. (författare) SNP Markers and Evaluation of Duplicate Holdings of Brassica oleracea in Two European Genebanks 2020 Ingår i: PLANTS. - : MDPI AG. - 2223-7747. ; 9 Tidskriftsartikel (refereegranskat)abstract Around the world, there are more than 1500 genebanks storing plant genetic resources tobe used in breeding and research. Such resources are essential for future food security, but many genebanks experience backlogs in their conservation work, often combined with limited budgets. Therefore, avoiding duplicate holdings is on the agenda. A process of coordination has started, aiming at sharing the responsibility of maintaining the unique accessions while allowing access according to the international treaty for plant genetic resources. Identifying duplicate holdings based on passport data has been one component of this. In the past, and especially in vegetables, different selections within the same varieties were common and the naming practices of cultivars/selections were flexible. Here, we examined 10 accession pairs/groups of cabbage (Brassica oleracea var. capitata) with similar names maintained in the Russian and Nordic genebanks. The accessions were analyzed for 11 morphological traits and with a SNP (Single Nucleotide Polymorphism) array developed for B. napus. Both proved to be useful tools for understanding the genetic structure among the accessions and for identifying duplicates, and a subset of 500 SNP markers are suggested for futureBrassica oleracea genetic characterization. Within five out of 10 pairs/groups, we detected clear genetic differences among the accessions, and three of these were confirmed by significant differences in one or several morphological traits. In one case, a white cabbage and a red cabbage had similar accession names. The study highlights the necessity to be careful when identifying duplicate accessions based solely on the name, especially in older cross-pollinated species such as cabbage.
24.	Palmé, Anna, et al. (författare) Nordic Crop Wild Relative conservation : A report from two collaborative projects 2015–2019 2019 Rapport (övrigt vetenskapligt/konstnärligt)abstract The report summarizes results from a cooperation among all the Nordic countries during the period 2015 – 2019 (two projects). The work has focused on the conservation of Crop Wild Relatives (CWR), i.e. wild plant species closely related to crops. They are of special importance to humanity since traits of potential value for food security and climate change adaptation can be transferred from CWR into crops. The projects represent the first joint action on the Nordic level regarding in situ conservation of CWR. Substantial progress has been made regarding CWR conservation planning, including development of a Nordic CWR checklist and identification of suitable sites for CWR conservation. A set of recommended future actions was developed, with the most important one being initiation of active in situ conservation of CWR in all Nordic countries.

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