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| 2. |
- Nordlander, Josefine, et al.
(författare)
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Genetic diversity in gooseberry (Ribes uva-crispa), as estimated with SSR markers
- 2022
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Ingår i: Scientia Horticulturae. - : Elsevier BV. - 0304-4238 .- 1879-1018. ; 306
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Tidskriftsartikel (refereegranskat)abstract
- European gooseberry (Ribes uva-crispa L.) is a popular berry crop in many European countries, including Sweden, Denmark and Ukraine. There is no active gooseberry breeding programme in either Sweden or Denmark, but a successful programme is operating in Ukraine. In Sweden and Denmark, research on gooseberries is primarily focused on collection and phenotypic evaluation of genetic resources. As part of these activities, a large number of inventory finds have been collected but have not yet been characterised morphologically or molecularly. The goal of this study was thus to characterise gooseberry germplasm with 15 simple sequence repeat (SSR) markers. From 242 accessions analysed, 153 unique genotypes were identified. Cultivars that have been in widespread cultivation in Sweden, such as the Finnish cultivars ‘Hinnonmäen Keltainen’ and ‘Hinnonmäen Punainen’, had relatively large numbers of synonymous samples. While many inventory finds were identifiable as synonyms of known cultivars, several were found to constitute unique genotypes within the germplasm studied. The studied genotypes clustered relatively well in three posterior groups, consisting of cultivars originating before and after the American gooseberry mildew (Sphaerotheca mors-uvae) outbreak around 1900 and cultivars originating from the territory of the former Soviet Union. A fourth genetic cluster consisting mainly of inventory finds from central and northern Sweden was also identified. In addition, it was possible to verify recorded and stipulated parentages for some of the cultivars studied and to identify three likely parent-parent-child trios. Thus, inventories of local gooseberry germplasm and a subsequent genotyping proved successful in finding unique local genotypes, with potential local adaptation. The data obtained provide a foundation for future studies of gooseberry genetic resources, while also illustrating the importance of a well-curated and phenotypically characterised set of reference cultivars for future studies.
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| 4. |
- Skytte Af Sätra, Jonas
(författare)
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Apple genomics for the Swedish breeding programme
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Swedish apple (Malus domestica Borkh.) cultivation is a niche market setting specific requirements on new apple cultivars. Notably, the growing season is short, especially in central and northern Sweden, and there are relatively few pesticides available, making resistance to diseases important. The past decade has seen major developments in tools for genomics-led breeding in apple and targeted application of these tools could facilitate a major increase in efficiency. The aim of this thesis has been to lay the foundations for genomics-led breeding in the Swedish apple breeding programme. In a first step, the status of available genetic resources was investigated and curated (Paper I). A robust high-resolution virtual linkage map (Paper II) was then developed by analysis of two whole genome sequences and use of a high-density linkage map. Identification of pedigree relationships and use of a reliable map for marker ordering enabled production of highly curated and phase-resolved marker data. Apple germplasm was screened for resistance to European canker (Neonectria ditissima) and quantitative trait loci (QTL) in segregating offspring of ‘Aroma’ x ‘Discovery’ were mapped (Paper III). The metabolomic profiles of the parents during early stages of infection provided insight on the potential roles of two of the mapped QTL, and indicated that ‘Santana’ might provide a complementary source of resistance (Paper IV). The effect of previously published genomic regions and QTL intervals for date of flowering and harvest date under Nordic conditions were investigated in germplasm relevant for Nordic apple breeding (Paper V). A study on the genetic basis for adaptation to northern Sweden was initiated, with the timing of canopy senescence identified as a correlating trait (Paper VI). The applicability of the novel data obtained was illustrated by discussing future crosses that could be relevant for breeding to improve resistance to N. ditissima and adaptation to central and northern Sweden.
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| 5. |
- Skytte af Sätra, Jonas, et al.
(författare)
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Characterization of autumn senescence in the Swedish Central Collection of heritage apple cultivars
- 2023
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Ingår i: Acta Horticulturae. - 0567-7572 .- 2406-6168. ; 1384, s. 257-265
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Konferensbidrag (refereegranskat)abstract
- Starting in the late 1970s, the use of modern apple cultivars prompted an inventory and collection of old apple cultivars grown in Sweden. This initially led to the establishment of a series of local clonal archives, and later to the establishment of the Swedish Central collection between 2012 and 2016. The collection contains considerable phenotypic variation for traits that could be relevant to future breeding goals of Sweden’s national breeding program, such as climatic adaptation. Recommendations for cultivations of horticultural perennials are based on the classification of Sweden into 9 climatic zones, including the alpine region. The Swedish Central Collection has apple cultivars recommended for cultivation up to zone 6, stretching up to latitude 65 along the coastal regions. Currently, most of the production of dessert apples in Sweden is concentrated around latitude 55, though there are commercial orchards further north. Recently, commercial orchards aiming at cider production have been established as far north as latitude 63. Thus, Swedish commercial apple production is placed at the northern frontier, with special requirements for climatic adaptation. Currently, little is known about which key characters are underlying climatic adaptation but phenological properties are generally important for the adaptation of trees to northern climates. While certain phenological traits such as spring bud break and the onset of flowering have been relatively well studied in apple, autumn phenological traits such as senescence have received relatively little attention. Thus, we have assessed the Swedish Central Collection of apple heritage cultivars for autumn senescence over three years (2019-2021). The timing of onset of senescence and rate of senescence were analysed for year-to-year variation and the impact of temperature, and compared with historical data on hardiness and putative NAC18.1, Md-ACS1 and Md-ACO1 genotypes.
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| 6. |
- Skytte Af Sätra, Jonas, et al.
(författare)
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Genetic Status of the Swedish Central collection of heirloom apple cultivars
- 2020
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Ingår i: Scientia Horticulturae. - : Elsevier BV. - 0304-4238 .- 1879-1018. ; 272
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Tidskriftsartikel (refereegranskat)abstract
- Cultivated apple is one of the most widely grown fruit crops worldwide. With the introduction of modern apple cultivars, from foreign and national breeding programs, the use of local cultivars decreased during the 20th century. In order to minimize genetic erosion and avoid loss of special genotypes, a number of local clonal archives were established across Sweden, with the goal of retaining old and local cultivars. About 220 apple cultivars, appointed for preservation, obtained the status of mandate cultivars. Initially, they were identified based on pomological traits, but prior to the establishment of the Swedish Central Collection they were genotyped with simple sequence repeat (SSR) markers. SSR markers helped to evaluate the status of the preserved material, as well as to find the best possible true-to-type source for propagation, thus guiding the establishment of the Central Collection. Recently, 215 accessions from this collection were genotyped using the 20 K apple Infinium (R) single nucleotide polymorphism (SNP) array, in order to gain insight into its genetic structure. The initial SSR analysis confirmed the identity of multiple samples with the same cultivar name grown in different locations and identified several mislabeled samples. In the subsequent SNP analysis we identified 30 clonal relationships and a number of parent-offspring relationships, including 18 trios. We also identified five cultivar samples with inconsistent ploidy levels between the SNP and SSR data, in some cases indicating problematic samples preserved in either the Central Collection or some of the local clonal archives. These cultivars need further investigation to ensure their true-to-typeness. Furthermore, the Swedish Central Collection has continued to grow since the onset of this work and now contains additional cultivars, which should be included in future studies. The results indicate that a number of the preserved mandate cultivars holds high potential value for modern breeding programs.
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| 7. |
- Skytte Af Sätra, Jonas, et al.
(författare)
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Parametric mapping of QTL for resistance to European canker in apple in 'Aroma' x 'Discovery'
- 2023
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Ingår i: Tree Genetics and Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- Resistance to European canker (Neonectria ditissima) in apple is currently one of the most important breeding targets for commercial production in Sweden. Previous research has identified significant genetic variation in susceptibility to the disease, with the local Swedish cultivar 'Aroma' considered as one of the most resistant cultivars. Identification of genetic regions underlying the resistance of this cultivar would be a valuable tool for future breeding. Thus, we performed Bayesian quantitative trait loci (QTL) mapping for resistance to European canker in a full-sib family of 'Aroma' x 'Discovery'. Mapping was performed with the area under the disease progression curves (AUDPCs) from all seven (AUDPC_All7) and the first four assessments (AUDPC_First4), and three parameters of a sigmoid growth model for lesion length. As a scale for the effect of the different parameters, historic phenotypic data from screenings of a genetically diverse germplasm was compiled and re-analyzed. The parametrization of the data on lesion growth increased the number of QTL that could be identified with high statistical power, and provided some insight into their roles during different stages of disease development in the current experimental setup. Five QTL regions with strong or decisive evidence were identified on linkage groups 1, 8, 15, and 16. The QTL regions could be assigned to either of the parameters lesion length at the first assessment ('LL_A1'), the maximal lesion growth rate (lesion length doubling time, 't_gen'), and the lesion length at girdling ('LL_G'). Three of these QTL were traced along the pedigrees of some known relatives of the FS family, and discussed in relation to future crosses for breeding and genetic research.
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| 8. |
- Skytte Af Sätra, Jonas, et al.
(författare)
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Släktforskning bland svenska äppelsorter – ny teknik avslöjar gamla släktband
- 2020
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Annan publikation (populärvet., debatt m.m.)abstract
- Äppelodling har en lång historia i Sverige. Genom århundradena har det uppstått en rik flora av sorter runt om i landet, vissa mer framgångsrika än andra. I början av 1900-talet påbörjades försöksverksamhet med frukt i Alnarp, ett arbete som även resulterade i några nya sorter. Senare följde ett renodlat växtförädlingsprogram på Balsgård, som släppte sin första sort ’Alice’ 1963. Men det är först nu som vi med tillgång till moderna genetiska markörer på allvar har kunnat påbörja släktforskningen bland gamla såväl som moderna äppelsorter.
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| 9. |
- Skytte af Sätra, Jonas, et al.
(författare)
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Why we thrive beneath a northern sky - genomic signals of selection in apple for adaptation to northern Sweden
- 2024
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Ingår i: Heredity. - 0018-067X .- 1365-2540.
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Tidskriftsartikel (refereegranskat)abstract
- Good understanding of the genomic regions underlying adaptation of apple to boreal climates is needed to facilitate efficient breeding of locally adapted apple cultivars. Proper infrastructure for phenotyping and evaluation is essential for identification of traits responsible for adaptation, and dissection of their genetic composition. However, such infrastructure is costly and currently not available for the boreal zone of northern Sweden. Therefore, we used historical pomological data on climate adaptation of 59 apple cultivars and whole genome sequencing to identify genomic regions that have undergone historical selection among apple cultivars recommended for cultivation in northern Sweden. We found the apple collection to be composed of two ancestral groups that are largely concordant with the grouping into 'hardy' and 'not hardy' cultivars based on the pomological literature. Using a number of genome-wide scans for signals of selection, we obtained strong evidence of positive selection at a genomic region around 29 MbHFTH1 of chromosome 1 among apple cultivars in the 'hardy' group. Using phased genotypic data from the 20 K apple Infinium (R) SNP array, we identified haplotypes associated with the two cultivar groups and traced transmission of these haplotypes through the pedigrees of some apple cultivars. This demonstrates that historical data from pomological literature can be analyzed by population genomic approaches as a step towards revealing the genomic control of a key property for a horticultural niche market. Such knowledge is needed to facilitate efficient breeding strategies for development of locally adapted apple cultivars in the future. The current study illustrates the response to a very strong selective pressure imposed on tree crops by climatic factors, and the importance of genetic research on this topic and feasibility of breeding efforts in the light of the ongoing climate change.
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| 10. |
- Vélëz, Heriberto, et al.
(författare)
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Transformation and gene-disruption in the apple-pathogen, Neonectria ditissima
- 2022
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Ingår i: HEREDITAS. - : Springer Science and Business Media LLC. - 1601-5223. ; 159
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Tidskriftsartikel (refereegranskat)abstract
- Background Apple production in Sweden and elsewhere is being threatened by the fungus, Neonectria ditissima, which causes a disease known as European canker. The disease can cause extensive damage and the removal of diseased wood and heavily infected trees can be laborious and expensive. Currently, there is no way to eradicate the fungus from infected trees and our knowledge of the infection process is limited. Thus, to target and modify genes efficiently, the genetic transformation technique developed for N. ditissima back in 2003 was modified. Results The original protocol from 2003 was upgraded to use enzymes currently available in the market for making protoplasts. The protoplasts were viable, able to uptake foreign DNA, and able to regenerate back into a mycelial colony, either as targeted gene-disruption mutants or as ectopic mutants expressing the green fluorescent protein (GFP). Conclusions A new genetic transformation protocol has been established and the inclusion of hydroxyurea in the buffer during the protoplast-generation step greatly increased the creation of knockout mutants via homologous recombination. Pathogenicity assays using the GFP-mutants showed that the mutants were able to infect the host and cause disease.
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