Mot en funktion för ett Arabidopsis-protein involverat i sackarosdynamik

System based models of plants rely on descriptions and assigned functions of genes, and currently 50% of the genes in Arabidopsis thaliana has either no assigned function or a function based on homology only. Mitogen activated protein kinases (MAPK's) are key players in cell signalling and are conserved among eukaryotes, though their targets are highly diverse. A recent study has described a small Arabidopsis protein (80), without homology to any described protein, as a phosphorylation target of the MAPK's MPK3/6. Further work established α-glucan phosphorylase (PHS) as interacting with 80 and described a delayed senescence phenotype for 80 knock-out plants. This work has examined the effect of flagellin and sucrose on the stability of the 80 protein in seedling culture. In whole plants the effect of 80 on glucose, sucrose and the glucose residue content of the soluble heteroglycan (SHG) pool, as well as 80's stability during senescence has been investigated. 80 was found to be degraded under induced leaf senescence, in a way similar to that of induced darkness in whole plant systems. At day-time leaves from 80knock-out plants exhibited an increase in sucrose and no changes in glucose content. At night-time 80knock-out plants exhibited an increased sucrose:glucose ratio. 80knock-out leaves did not exhibit significant changes in sucrose and glucose content during senescence. In seedlings, 80 was found to be stabilised by sucrose and flagellin, though the sucrose dependent stabilisation was partly inhibited by flagellin.Systembaserade modeller för växter baseras på dokumenterade beskrivningar av olika geners funktioner, och 50 % av generna i Arabidopsis thaliana har antingen ingen känd funktion eller enbart en presumtiv funktion baserad på homologi baserade med kända proteiner. Mitogen aktiverade protein kinaser (MAPK's) är viktiga delar av ellsignalleringen och ser väldigt lika ut mellan eukaryoter. De proteiner som fosforyleras av MAP kinaserna är däremot väldigt skiftande. Nyligen beskrevs a litet protein utan homologi till något känt protein, 80, som ett MPK3/6 fosforyleringsmål. Vidare studier har identifierat ett protein som interagerar med 80, ett α-glukan fosforylas (PHS). En försenad senescens och har också hittats hos blad av 80knock-outplantor som saknar en fungerande 80 gen (80 knockout). Det här arbetet har studerat hur 80 regleras av flagellin och sackaros i sterilkultur. I hela plantor har 80's effekt på glukos, sackaros och den lösliga heteroglukan (SHG) bundna glukospoolen studerats, liksom dess stabilitet under senescens. 80 degraderades vid inducerad senescens på samma sätt som under inducerat mörker i hela plantor. Under dagen hade blad från 80knockout plantor högre sackaros innehåll men oförändrade glukos nivåer, jämfört med vildtyps plantor. Under natten hade 80knockout en signifikant högre sackaros:glukos ratio. 80 hade ingen signifikant inverkan på sockerhalten under senescens. I sterilkultur stabiliserades 80 av sackaros och flagellin, men den sackaros beroende stabiliseringen delvis motverkades av flagellin

Släktforskning bland svenska äppelsorter – ny teknik avslöjar gamla släktband

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

Parametric mapping of QTL for resistance to European canker in apple in 'Aroma' x 'Discovery'

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

Transformation and gene-disruption in the apple-pathogen, Neonectria ditissima

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

Genetic diversity in gooseberry (Ribes uva-crispa), as estimated with SSR markers

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 'Hinnonma & BULL;en Keltainen' and 'Hinnonma & BULL;en 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 re-sources, while also illustrating the importance of a well-curated and phenotypically characterised set of reference cultivars for future studies

Apple genomics for the Swedish breeding programme

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

Parametric mapping of QTL for resistance to European canker in apple in ‘Aroma’ × ‘Discovery’

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’ × ‘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

Genetic Status of the Swedish Central collection of heirloom apple cultivars

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