| 1. |
- Charlesworth, Deborah, et al.
(författare)
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Trans-specificity at Loci Near the Self-Incompatibility Loci in Arabidopsis
- 2006
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 172:4, s. 2699-2704
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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.
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| 2. |
- Forsberg, Nils, 1981-, et al.
(författare)
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Population structure in landrace barley (Hordeum vulgare L.) during the late 19th century crop failures in Fennoscandia
- 2019
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 123:6, s. 733-745
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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.
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| 3. |
- Hagenblad, Jenny, Associate Professor, 1974-, et al.
(författare)
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Chevalier barley : The influence of a world-leading malting variety
- 2022
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Ingår i: Crop science. - : Wiley. - 0011-183X .- 1435-0653. ; 62:1, s. 235-246
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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.
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| 4. |
- Hagenblad, Jenny, Associate Professor, 1974-, et al.
(författare)
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Data from: Farmer fidelity in the Canary Islands revealed by ancient DNA from prehistoric seeds
- 2017
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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.
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| 5. |
- Hagenblad, Jenny, Associate Professor, 1974-, et al.
(författare)
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Data from: Farmers without borders - genetic structuring in century old barley (Hordeum vulgare)
- 2014
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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.
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| 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
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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.
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| 7. |
- Hagenblad, Jenny, Associate Professor, 1974-, et al.
(författare)
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Data from: Twentieth-century changes in the genetic composition of Swedish field pea metapopulations
- 2012
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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.
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| 8. |
- Hagenblad, Jenny, 1974-, et al.
(författare)
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Haplotype Structure and Phenotypic Associations in the Chromosomal Regions Surrounding Two Arabidopsis thaliana Flowering Time Loci
- 2004
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Ingår i: Genetics. - : Genetics Society of America. - 0016-6731 .- 1943-2631. ; 168:3, s. 1627-1638
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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.
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| 9. |
- Hagenblad, Jenny, 1974-, et al.
(författare)
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Linkage Disequilibrium Between Incompatibility Locus Region Genes
- 2006
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Ingår i: Genetics. - Baltimore, MD, USA : The Genetics Society. - 0016-6731 .- 1943-2631. ; 173, s. 1057-1073
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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.
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| 10. |
- Hagenblad, Jenny, Associate Professor, 1974-, et al.
(författare)
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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
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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.
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