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.
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.
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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