Doctoral theses

The agricultural sector is one of the biggest contributors to climate change. To maintain high production, current agricultural practices rely heavily on fertilisers and chemical pesticides to protect against pests and pathogens. Unsustainable use of chemical pesticides can pollute soil and water and harm non-target organisms such as plants, animals, insects and microorganisms.

To reduce reliance on pesticides, a holistic approach combining various agronomic, mechanical and biological practices is recommended within the integrated pest management (IPM) framework. Within the European Union, Directive 2009/128/EC even mandates all plant production professionals to comply with IPM principles. Biological control, i.e. exploiting beneficial organisms to manage pests and pathogens, is a sustainable alternative to chemical pesticides, and the European Commission also recommends its use for sustainable plant protection.

Many biological control agents (BCAs) are microorganisms, and they can vary in performance and efficacy due to various biological and environmental factors. One of the factors that can influence BCA efficacy is their interaction with plants. Plant-microbe interactions involve complex molecular mechanisms, which aid plants in recognising pathogens and other microorganisms, while microbes utilise their molecular strategies to overcome or suppress plant defences. It has been established that plants exhibit genetic variation, which makes some individuals (genotypes) more or less susceptible to pathogens than others; however, how plant genetic variation can influence BCA efficacy is still not well understood.

This thesis aimed to better understand the influence of plant genetic variation on BCA efficacy using approximately 200 winter wheat genotypes. Two commercially important fungal pathogens, Zymoseptoria tritici, causing septoria tritici blotch (STB) and Fusarium graminearum, causing fusarium foot rot (FFR), were used. Disease management of these two pathogens contributes towards a large proportion of overall fungicide use globally. Clonostachys rosea was used as a BCA, which is reported to successfully control more than 30 pathogens, including Z. tritici and F. graminearum. Wheat genetic variation was explored by subjecting plants directly to the pathogen inoculation and on plants initially treated with C. rosea, which allowed disease susceptibility to be differentiated from biocontrol efficacy.

The degree to which a particular genotype benefitted from C. rosea application in disease reduction was used as a measure for biocontrol efficacy. Disease susceptibility and biocontrol efficacy were estimated at the phenotypic level by visually assessing the disease, and underlying genetic regions associated with the phenotypic variation were identified using genetic markers in the genome-wide association studies.

The results showed differences among winter wheat genotypes in susceptibility to both pathogens and genetic regions associated with disease resistance were identified. In addition, C. rosea biocontrol efficacy also varied among winter wheat genotypes, and genetic regions associated with biocontrol efficacy were distinct from disease susceptibility. Biocontrol efficacy by C. rosea showed better control of FFR compared to STB. Disease susceptibility and biocontrol efficacy also showed a positive correlation, indicating that susceptible plants benefitted more from C. rosea application.

Furthermore, changes in gene expression of underlying molecular mechanisms in wheat genotypes varying for biocontrol efficacy were investigated in direct interactions with Z. tritici and C. rosea exclusively and during their co-inoculation. The results show that C. rosea can induce distinct sets of defence-related genes directly and in the presence of Z. tritici, which can vary between genotypes with high and low biocontrol efficacy.

In summary, these findings demonstrate that winter wheat germplasm exhibits genetic variation for disease susceptibility caused by pathogens Z. tritici and F. graminearum and for C. rosea biocontrol efficacy of these diseases. Plant breeders consistently exploit plant genetic diversity for disease resistance to develop resistant cultivars. Similarly, genetic variation can potentially be utilised to optimise the biocontrol efficacy of C. rosea.

Using molecular markers, the selection of genotypes with lower susceptibility and higher biocontrol efficacy may be possible, making the simultaneous selection of traits feasible in future breeding programs. However, further research is recommended to expand these findings in other systems using diverse pathogens, BCAs and plant populations to better understand the breeding potential of biocontrol efficacy. The insights gained in this thesis contribute towards optimising biological control applications and offer knowledge that will support future disease management strategies and plant breeding initiatives, with the ultimate aim of minimising reliance on chemical pesticides.

Read more in the thesis: Plant genotype-dependent biocontrol of wheat diseases

Faba bean (Vicia faba L.) is an ancient crop with remarkable potential for increased cultivation in modern agriculture - especially in Nordic regions with shorter growing seasons. Like other legumes, faba bean naturally improves soil fertility by capturing nitrogen from the air, reducing the need for artificial fertilizers. Its seeds are also exceptionally rich in protein, making it a valuable food source in the transition towards greater consumption of plant-based proteins. Increasing faba bean cultivation could help reduce reliance on imported soy, lower fertilizer use, and enhance biodiversity in agricultural systems.

Despite these benefits, faba bean has received considerably less breeding attention than crops like wheat and soybean, which have undergone extensive genetic improvements for yield and seed quality. To support the expansion of faba bean cultivation and its use as a food source, a better understanding is needed of the genetic mechanisms that regulate key traits such as productivity, seed composition, and climate adaptation. This knowledge can be applied to develop genomic tools that make plant breeding more efficient, contributing to a more resilient and sustainable food system while enhancing regional self-sufficiency.

This thesis characterized hundreds of faba bean varieties from around the world, evaluating their traits under Swedish field conditions to assess how well they adapt and perform in a Nordic climate. Through advanced genetic analysis, sections of the species' DNA were identified that influence critical traits such as plant height, flowering time, seed size, and seed yield. These genetic insights offer valuable guidance for future breeding efforts, enabling the development of faba bean varieties that are both more productive and better suited to northern growing conditions.

The research also explored, in detail, how faba bean seeds develop and store key nutrients such as protein, starch, and oil - essential components for both human food and animal feed. By understanding how these nutrients accumulate during seed development and identifying the genes that regulate their formation, improvements can be made to enhance the crop’s nutritional value and its processing qualities for food production. Another important finding concerns flowering, a key factor in the crop’s adaptation to short growing seasons. The study identified a specific family of genes that regulate when and how faba bean plants flower.

By generating new genetic tools and insights for improving faba bean, this research supports the development of a more sustainable agricultural system with greater crop diversity and enhanced plant-based protein sources for the future.

Read more in the thesis: Genetic insights into seed development, flowering and diversity in faba bean - Pre-breeding for sustainable agriculture

Rapeseed is mostly grown for its oil, but the leftover seed meal (RSM) is a valuable source of protein that could be used in animal feed. However, RSM contains antinutritional compounds - glucosinolates, sinapine, and phytic acid - that make it less nutritious, less palatable, and harder for animals to digest. Traditional breeding has struggled to reduce these compounds, and genetic modification faces strict regulations.

In this research, we used a modern genetic technique called CRISPR-Cas gene editing to tackle this problem. CRISPR is commonly known as being similar to genetic scissors, because of its ability to make cuts in genes. The cuts caused effectively switch off genes, making it possible to alter the genetics of an organism, without introducing foreign DNA, as is done when genetic modification is used.

In order to implement CRISPR in rapeseed, we first needed to develop a method to regenerate rapeseed plants from individual cells. Then, we were able to precisely cut the genes responsible for producing the unwanted compounds using CRISPR. The cells with the edited genes were then grown to full plants again. Doing this we created plants with significantly lower levels of antinutritional compounds. For example, we reduced glucosinolate content by up to 64%, while modifying sinapine-related genes cut levels by up to 73%. We also reduced phytic acid in the seed by 62%.

This research opens the door for healthier, more sustainable animal feed while demonstrating a promising way to improve crops using gene editing without the need for traditional genetic modification.

Read more in the thesis: Enhancing rapeseed seedcake quality for feed and food using CRISPR-Cas RNP gene editing

While the sufficient supply of nitrogen ensures healthy growth in all plants, the excess of nitrogen fertilizers in agriculture to support high yields often causes environmental contamination. Improving crop nitrogen use efficiency, especially in staple crops such as wheat, will effectively contribute to the maintenance of high yields, a more sustainable food production, and a decrease of environmental contamination caused by current agricultural practices.

When we were kids, we were often told to eat all our food to grow strong and healthy; notably fruits and vegetables, which are rich in nutrients and minerals that are essential for our development. The same principle applies to plants: nutrients are vital for their growth and survival. Among these, one nutrient stands out as the most important and often most growth-limiting nutrient in a plant's life: nitrogen (N).

Nitrogen is crucial for plant growth, playing a critical role in their entire life cycle. For crops that are a staple in the human diet, such as wheat, N is particularly important. However, in a Nordic context, the use of N fertilizers to ensure high yields has increased eutrophication in the Baltic Sea. Therefore, increasing crop N use efficiency has become a high priority in modern agriculture.

The present research focused on N use efficiency in spring wheat, a promising crop for Nordic climates, by using a methodology to separate crop N accumulation efficiency into three components: N uptake efficiency, N utilization efficiency, and grain N content. The thesis examined key traits and breeding targets in spring wheat to gain a better understanding and improve the N use efficiency of the crop when grown under different environmental conditions. A central aspect of the thesis was the development of a simplified, less-destructive method to assess the key traits for improved N use efficiency in breeding populations. The final part of the thesis focused on the analysis of genetic data and the identification of specific regions of the wheat genome that are linked to the crop’s N use.

The results highlight the strong associations between, firstly, the two key breeding goals for spring wheat, i.e., high grain yield and protein content; and, secondly, the three different wheat types in the Nordic region, i.e., high yield, intermediate, and high protein content wheats. While high N utilization efficiency and high grain N content were associated with high-yield and high-protein wheat types, respectively, the N uptake efficiency was not associated with any wheat type or breeding target. Root traits are important for N uptake but were predominantly influenced by variety and environment (including their interaction) rather than wheat type in the investigated plant material. Together with the identification of various genomic regions associated with key traits for improved N use efficiency, the successful 
development of a more efficient methodology to phenotype these traits will subsequently pave the way for more efficient breeding of spring wheat with improved N use efficiency.

This research suggests the utilization of practical tools and proposes N use efficiency to be used as a regular target for the breeding of spring wheat varieties that are both productive and support environmental sustainability. These advancements can help to reduce the agricultural sector’s environmental footprint while simultaneously supporting food sustainability in Nordic regions.

Read more in the thesis: Towards sustainable spring wheat cultivation: enhancing nitrogen use efficiency through strategic breeding

Sugar is an inevitable part of day-to-day life be it for making home-made as well as processed goods, alcoholic beverages, soft drinks and dairy products or it could be part of bioplastics, cosmetics, biofuels and medicines. Commercially, it plays an important role in food-processing industries.

Globally, sugar is produced mainly from sugar cane and sugar beet. Sugar beet is the main source of sugar especially in countries with a temperate climate. Around 20% of the sugar produced in the world comes from sugar beet, where the sucrose content in different cultivars ranges from 13-22%. However, the sugar production and productivity are often affected by a plethora of environmental stress factors as well as by pests and diseases.

Among the diseases affecting the crop, there are several diseases caused by viral pathogens, which are transmitted by different vectors (e.g., protozoa, leafhoppers or aphids). Virus yellows (VY) disease of sugar beet is transmitted mainly by the green peach aphid and the black bean aphid, and the disease may result in a yield loss of up to 30%. This disease is associated with multiple viruses and hence very complex. In Europe, these viruses are beet mild yellowing virus (BMYV), beet chlorosis virus (BChV), beet yellows virus (BYV) and beet mosaic virus (BtMV).

Recently, turnip yellows virus (TuYV) is also seen to infect sugar beet even though it before was not considered as a host. Neonicotinoid chemicals were previously used for managing the aphid vectors transmitting these viruses. Currently, the use of these chemicals is restricted in EU and alternate ways to manage VY need to be explored. One of the best ways to do that is to develop cultivars with durable virus resistance. In this project, our focus was on BMYV as it is the most common among the viruses in the VY-complex in Europe as well as in Sweden.

To develop resistant or tolerant cultivars, insights into the virus-sugar beet interactions need to be gained through studies. We performed experiments using a resistant genotype of wild beet and a susceptible genotype of sugar beet, looking at the responses to BMYV infection using different molecular techniques. Virus quantifications were done at different time points after inoculation with BMYV.

The results showed that the virus content in the resistant plants was always lower than in the susceptible plants. The lack of symptom expression and lower virus titre revealed that the wild beet genotype was partially resistant against BMYV. Fourteen potential candidate genes were identified for resistance against BMYV. These genes are known from other studies to have a role in defence responses to viruses 
in plants and may be involved in the response that protects the plant from the stress caused by the virus infection. Therefore, they are of high interest for future studies. We also identified genome regions linked to susceptibility and resistance to BMYV.

Collectively our studies enabled identification of the most common poleroviruses (BMYV, BChV and TuYV) causing VY in Sweden as well as candidate genes for defence responses and genome regions for BMYV resistance in the wild beet genotype. This would lay a foundation for breeding programs to develop resistant cultivars of sugar beet that could be used by farmers in sugar beet cultivation and limit the usage of chemical insecticides.

Read more in the thesis: Virus yellows of sugar beet – exploring pathogen diversity and host resistance - Groundwork for resistance breeding

To combat the effect of climate change, it is often said that it is necessary for humanity to replace part of their meat consumption with plant-based alternatives. This idea of a “protein shift” has led to several novel food products, such as textured pea-proteins. It has also increased interest in fringe protein crops, such as faba bean. Another interesting avenue is found where the field of plant based food overlaps with industrial waste products. While “Industrial waste” might not be the first thing we think of when talking about food. There are examples, such as sausage manufacturing, where side streams are already effectively utilized for food production.

In the case of plants, there has been research conducted on harvest waste, such as broccoli leafs and stem, and on side streams from industry, such as the seedcake left after rapeseed is pressed for oil. The potato starch industry has its own side stream of interest, the potato fruit juice. The potato fruit juice is comprised mainly of water, proteins and glycoalkaloids. Glycoalkaloids are toxic compounds, and thus the protein must be purified before it can be consumed by humans. One of the most abundant proteins in potato are the patatins. Being both highly nutritious, and a good foaming agent the patatins are often compared to eggs, a product that has been especially challenging to replace in plant based foods. Patatin is also largely flavourless, something that has been a challenge for products based on both beans and peas. Unfortunately, the patatins have proven prone to coagulation during processing, making them impossible to extract at high enough quality.

While breeding crops for processing traits is common practice in some crops, generation of new potato varieties through crosses is impractical. There are however good biotechnology applications available which can be used to achieve the desired traits. With the development of new CRISPR/Cas methods, researchers have gained the ability to make more precise edits than ever before.

This thesis explores the idea of using precision editing methods based on the CRISPR/Cas system to enhance protein properties in potato tubers. We studied two potential targets, the patatins that were mentioned above, and another protein found in potato tubers called Pho1a, which is thought to be involved in starch granule formation. The analysis of patatin showed that modification is possible, and several patatins can be modified at once. The patatins are a large group of proteins that all come from different genes. It was also discovered that these genes are not equally represented on the protein level, but rather a few genes were responsible for producing a majority of the protein. These high efficiency genes would be a great starting point for future modifications.

The second target investigated was Pho1a. When working with genes, it is often easier to remove something than to add it. This is why we started by producing Pho1a deficient potatoes. These produced small malformed starch granules, suggesting that elimination of the protein is not desirable, and that this could be a good target for the harder to achieve enhancing modifications.

Read more in the thesis: Gene editing for tuber protein utilization in potato (Solanum tuberosum)

Timothy is one of the most important forage crops in Sweden and in other countries in Northern Europe. It is grown in mixtures with other plant species, such as red clover, for grazing or as feed for livestock. Timothy has been cultivated in Sweden since the beginning of the 18th century. It is tolerant to cold winters and can grow productively for some years without having to be re-seeded, as it is a perennial crop. Therefore, in addition to its importance as a forage crop, it can also benefit the environment by reducing soil erosion and improving soil quality through less tillage. 
However, the production of timothy in Sweden and other Nordic countries is limited by short growing seasons and unpredictable changes in weather due to climate changes.

To cope with the adverse conditions and to enable the production of sufficient and high-quality timothy fodder, we need to develop new cultivars that are adapted to the changing climate. An important step towards the development of new cultivars is to evaluate the diversity in traits affecting yield and quality such as plant development, tiller formation, and growth within timothy and related species. Wild populations of timothy are native to Sweden and Northern Europe and are adapted to different habitats and climates. They may harbour diversity and different combinations of traits not seen in cultivars and may be used as donors and genetic resources of favourable traits and genes for improvement of timothy cultivars.

In this thesis a diverse collection of 246 accessions of timothy and its two related species turf timothy (Phleum nodosum) and alpine timothy (Phleum alpinum) have been studied. These species have different geographical distributions. In Sweden, timothy grows at low altitudes throughout the country, while turf timothy has a southern distribution and alpine timothy is restricted to high altitudes in northern Sweden. The studied accessions are from different habitats and locations in Northern Europe and include wild accessions from natural populations, semi-wild accessions collected nearby cultivated fields, landraces (local farmers' varieties), and breeding lines and cultivars from breeding programs.

An accession can be described as a collection of seeds from a specific site. Plants of all accessions have been individually evaluated for biomass production, lengths of different developmental stages (from emergence to heading) and production of 
different tiller types (vegetative, reproductive and non-flowering elongated tillers) under greenhouse and field conditions.

The greenhouse and field studies showed that these three species differed in their development, tiller formation and growth, and large variation was found within each species. Interestingly, in timothy the group of cultivars and the group of wild accessions did not differ in biomass production. However, they differed in development, where the cultivars showed a faster development and reached stem elongation and flowering earlier than the wild accessions. This suggests that the breeding of timothy has favoured fast growing plants. The cultivars also formed a larger portion of reproductive tillers, while the wild accessions had more vegetative tillers, which increased by latitude. In turf timothy, cultivars formed the highest proportion of non-flowering elongated tillers among all accessions and species, while no such tillers were produced by alpine timothy. Leaves have higher digestibility than stems by cows, and if the non-flowering elongated tillers has a higher fraction of leaves compared to other plant parts, it is possible that this tiller 
type can contribute with a more digestible feed. Some wild accessions and  landraces showed interesting combinations of development and tiller type formation and should be further investigated as potential genetic resources.

In addition, turf timothy accessions with favourable traits may be crossed with timothy or further domesticated for development of a new forage grass. Thirty-tree of the accessions from the three species were further studied by whole genome resequencing to investigate how the domestication process and breeding have affected the genomes of the species. A different pattern of genetic diversity was found in timothy and turf timothy compared to alpine timothy, showing higher genetic similarity in alpine timothy. This suggests that alpine timothy has a different mating system with higher degree of self-pollination.

Moreover, no clear genetic differentiation was found between cultivated and wild accessions in both timothy and turf timothy. However, some genomic regions were highly differentiated, which indicates that these regions have been under selection during domestication and breeding. These genomic regions are associated with different biological processes such as synthesis of lignin. Lignin production increases in stems and leaves of grasses during growth and decreases forage digestibility and quality. In addition, other genomic regions were found to be associated with metabolism, signalling and the response to abiotic stresses which are likely to influence the adaptation of these species. The identified phenotypic and genetic diversity, as well as accessions with different combinations of traits are important resources for further studies in greenhouse and in field, and for developing genomic-based methods in timothy breeding.

Read more in the thesis: Phenotypic and genetic diversity in wild and domesticated timothy and related Phleum species

Plant breeding is under increasing pressure to improve crops' performance due to factors, such as climate change, a growing population and financial demands. Forages are a widely cultivated crop in Northern Europe and are vital for the ruminant industry and ecological farming. Forage is a mixture of grasses and legumes that grows over multiple years and can be harvested up to three times per season. Red clover is one of the key forage legumes and as a legume red clover had a high protein content attributed to its symbiosis with bacteria that binds atmospheric nitrogen.

Improving red clover yields and forage quality faces multiple challenges, due to factors such as changes in growing conditions. One key approach to meeting the demands of red clover is to increase genetic gain by improving plant breeding efficiency. Genetic gain is the improvement of a trait over generations attributed to the change in the plants genetics. Plant breeding aims to increase genetic gain by influencing three components, genetic variance, accuracy, intensity and time. Genetic variation is the genetic resources available in the breeding population. Accuracy and intensity is how well a breeder select parents based on their genetic attributer rather than environmental effects, and how many parents are chosen. The time refers to the time required for each breeding cycle. This thesis focused on studying genetic variation in the northern European red clover and investigated various statistical models in order to implement selection based on genetics (genomic selection) for increased efficiency of red clover breeding.

The red clover genetic resources studied in this thesis include wild populations, landraces (farmer’s varieties), old cultivars, and red clover used in current breeding programs. These include both diploid and tetraploid red clover. The analysis of genetic variation in red clover in current breeding programs may be insufficient for efficient improvement. However, potentially interesting genetic materials for breeding were identified, and their inclusion in the crop’s breeding programs can aid in increasing genetic gain.

Field trials were conducted for diploids of two maturity classes (late and middle-late) and tetraploids at different locations in Sweden, and forage yield and forage quality data were collected. Their corresponding genomic data were obtained by DNA sequencing of specific DNA markers. Phenotypic and genomic data were used for genomic prediction and marker-trait association analysis. Genomic prediction models that target a single trait at a time were compared to models targeting single traits across multiple time points or multiple traits at one time point. The aim was to use the information across multiple traits or time points to better describe the underlying genetics of the target traits.

The results showed that even though single-trait models had higher predictive ability; i.e. higher accuracy of estimates, than multi-trait models, they showed potential bias. This bias could over or underestimate the performance of red clover populations and could be due to the model’s failure to capture important genetic effects. The bias could be due to genetic effects where the effect of a gene is non-linear to the response on the trait. These effects are often due to the presence of dominant alleles or epistasis effects between multiple genes. However, by introducing multiple traits and using the correlation between them these effects could be captured.

Thus, this thesis highlights key aspects of red clover in terms of exploiting its available genetic resources for increased genetic gain through genomics-driven breeding. Additionally, pitfalls in utilizing various prediction models for increased accuracy and speed were highlighted. This research contributes to red clover breeding efficiency so that new varieties can be developed faster and meet current and future demands.

Read more in the thesis: Advancing red clover breeding through genomic selection methods

Timothy (Phleum pratense) is an important forage grass cultivated for grazing, silage and hay. Farmers grow timothy in mixed stands with legumes, including clover and alfalfa. With global warming, climate patterns are changing worldwide, resulting in intense rainfall and longer periods of drought that affect agricultural productivity and cause significant economic losses to farmers. Therefore, it is essential to understand how timothy responds to environmental factors such as drought and waterlogging (flooding).

For this study, we selected a total of 244 wild and domesticated accessions of timothy and two closely related species, turf timothy (P. nodosum) and alpine timothy (P. alpinum) from different European countries. The growth of these accessions was evaluated in the field and greenhouse. The results showed that wild accessions and cultivars of timothy and turf timothy did not differ in biomass, but they did differ in flowering time. Based on these results, we selected 19 wild accessions and cultivars of the three Phleum species that represented the diversity of our collection. Plants of the selected accessions were exposed to waterlogging by submerging them in a bucket full of water, and to drought by not watering them. We then studied their phenotypic (observable characteristics) response to the stress. Based on these results, we narrowed down and selected eight accessions to study their physiological response and changes in gene expression to abiotic stress in leaves and roots.

Plants are unable to move from stress due to their sessile nature. Therefore, they employ various physiological and genetic mechanisms to adapt to stress. Waterlogging leads to a lack of oxygen, causing hypoxia within roots. Interestingly, we found that the three Phleum species exposed to waterlogging had similar dry weights than their respective control plants. Belowground, due to the accumulation of ethylene (plant hormone), plants responded to waterlogging by developing adventitious roots that grow from the crown, and also developed air-filled cavities in the roots called aerenchyma.

Adventitious roots and aerenchyma facilitate the diffusion of oxygen into roots, and carbon dioxide, and toxic volatiles out of the roots. Most of the accessions showed a smaller root system in waterlogging conditions. However, some accessions were able to maintain root growth, indicating that they might be more tolerant. A large root system is crucial for achieving high yields. Aerenchyma and a large root system could be used as selection criteria for waterlogging-tolerant accessions.

Drought can limit the uptake of water and nutrients, which negatively impacts plant growth. In response to drought, Phleum species increased the size of their root systems while reducing shoot growth. This larger root system allows the plant to explore the soil more effectively in search of water and nutrients. The production and accumulation of metabolites, amino acids, hormones and other compounds was also triggered by drought. For example, two timothy accessions and one turf timothy produce proline, an amino acid that helps protect plants against osmotic drought and oxidative damage. On the other hand, alpine timothy seems to produce two polyamines, putrescine and spermidine, which are involved in drought tolerance, rather than proline.

After the drought period, the plants were re-watered to observe their response to rehydration. Both timothy and turf timothy are sensitive to drought, but they responded to re-watering by producing more tillers and leaves. For breeding purposes, traits such as increased rooting volume, ability to maintain turgor and growth rate, and fast recovery could be used to select material. The several wild accessions and the old and new cultivars used in these studies showed that there is a large diversity in adaptation to waterlogging and drought. The diversity in how they grow, and in their transcriptomes and metabolites show that they have traits that makes them interesting for further use.

This is possibly one of the first reports of transcriptional responses to drought and waterlogging in Phleum species. These findings provide valuable information for breeding timothy. Additionally, this study represents a pioneering effort to elucidate the transcriptional responses of alpine timothy and turf timothy to stress, making a significant contribution to our understanding of Phleum species' adaptive mechanisms.

Read more in the thesis: Responses to waterlogging and drought of timothy and related Phleum species: phenotype and transcriptome diversity

Aphanomyces root rot (ARR) in pea is caused by the oomycete pathogen Aphanomyces euteiches Drechs. Oomycetes, also known as water molds, resemble fungi in their growth and appearance but are more closely related to algae. The first report of A. euteiches as a threat to pea production goes back to 1925 but the pathogen has since become a major constraint in all pea growing regions with temperate climate. Infected plants display typical root rot symptoms, such as brown and water-soaked lesions and a general reduction of the root volume. Mitigation methods against the pathogen are scarce, as many commercial fungicides have no effect on suppressing the oomycete and additionally, A. euteiches produces thick-walled survival structures (oospores) that can remain in the soil for long periods. Crop rotation and avoidance of fields with high occurrence of A. euteiches in the soil are therefore the most efficient available measures against the disease.

The deployment of resistant cultivars would be the economically and environmentally most beneficial way to reduce yield losses caused by ARR. Currently, there is no commercial pea cultivar available that carries full resistance to ARR but several genetic individuals (genotypes) carry partial resistance and are used in breeding programs. It is known that resistance to ARR is linked with unfavourable breeding traits. An example for a pea genotype with resistance to ARR is the old German landrace PI180693. It carries partial resistance to A. euteiches but also undesirable breeding traits such as long stems, a dark seed coat and smooth seeds that are associated with a starchy flavour. The line is currently used in Swedish pea breeding programs and crossed with the commercial pea cultivar Linnea. Linnea is a cultivar that carries all the desirable breeding traits such as wrinkly seeds, a sweet flavour, a normal growth length but is also highly susceptible to ARR. Classical breeding programs focus on crosses between the two genotypes and could benefit from available genetic markers which allow for screening for desirable genes at an early growth stage. The goal of this thesis was to identify genes that are associated with ARR resistance and thereby gaining new insights into the genetic diversity of A. euteiches and its degree to cause infection (virulence) in pea.

In this thesis, I confirmed the potential of PI180693 partial resistance in growth chamber, greenhouse and field trials and found how crosses with the commercial cultivar Linnea displayed higher levels of resistance to ARR than their susceptible parental line. Controlled infections of Linnea and PI180693 with A. euteiches, followed by analyses on the differential regulation of genes revealed a very distinct immune reaction of the two pea genotypes. The immune reaction was both host- and time-dependent. We cross-referenced differentially regulated genes with genes situated in genomic regions associated with resistance to ARR and identified a set of 39 candidate disease resistance genes that can be used for the development of genetic markers in future breeding programs.

To further support ARR resistance breeding, more detailed knowledge about the pathogen diversity and population structure across pea growing regions is essential. The thesis work includes genetic analyses on a collection of European A. euteiches strains from six different countries, spanning from north to south. Three genetically differentiated groups were identified: a central European, a  northeastern, and a genetically very distinct group in the south. We found signs of genetic recombination in the mostly clonally reproducing pathogen, as well as evidence for genetic movement of A. euteiches between countries. The southern group of strains shared no common ancestry with the other groups and differed in oospore size and virulence on pea – all of them possible indicationsto view the southern group as a separate Aphanomyces species.

The thesis results contribute to future resistance breeding programs with a better understanding of the genetics underlying ARR resistance in pea, and new insights into genetic diversity, population structure and virulence of European A. euteiches strains.

Läs mer i avhandlingen: Aphanomyces root rot in pea - Genomic insights into pathogen diversity and disease resistance

Have you ever wondered if those sprouted potatoes in your kitchen are safe to eat? It seems that this might not be the case. Sprouted potatoes can accumulate glycoalkaloids, natural toxins found in the Solanaceae family, i.e. the potato and tomato. Consuming too much glycoalkaloids can lead to unpleasant symptoms, ranging from stomach upset to more severe issues like headaches and confusion.

While glycoalkaloid content in table potato cultivars has received high attention due to the consideration of food safety, glycoalkaloids in starch potato cultivars have received less investigation. The total production of starch potatoes is estimated at 336, 200 tonnes in the year 2020 in Sweden, showing an increasing trend of total production over the last five years. However, the processing of starch potatoes generates substantial by-products, such as potato fruit juice and pulp, often relegated to low-value animal feed or waste. The challenge of turning the by-products into economically valuable compounds, e.g. food-grade proteins and fibre, is in removing the accumulated glycoalkaloids in the by-products while extracting proteins and fibre, which is complex and costly.

In this thesis, we investigated the differencesin glycoalkaloid metabolism in starch potato cultivars compared to table potato cultivars, which are commonly used cultivars in Sweden. We also obtained glycoalkaloid-free starch potatoes, using the modern breeding tool CRISPR/Cas9. These glycoalkaloid-free starch potatoes offer a novel approach for the production of food-grade potato protein and fibre products from industrial by-products. Beyond ensuring a safer potato consumption experience, this innovation transforms waste into valuable resources, aligning with the global shift towards sustainability and environmentally conscious practices.

Read more in the thesis

In Europe, including Sweden, wheat is a major crop, and most of Sweden's wheat is grown during winter. But there's a problem – fungal diseases can damage wheat and cause big losses in its production. Compared to other crops, it takes a long time to breed winter wheat because it requires long period to grow in low temperature in order to flower. To save time and money for the breeders, we created new methods for selection of plants resistant to diseases. These methods incorporate disease selection into rapid growth conditions and early stage of wheat plants in combination with modern genetic tools.

We focused on two diseases that largely damage wheat production: Fusarium head blight (FHB) and Septoria tritici blotch (STB). FHB reduces the productivity of wheat, lowers the quality of the grains, and creates toxins that can be dangerous for human and animal consumption. STB on the other hand is the second most damaging disease to wheat production in Europe. For this reason, farmers spend large sums of money on fungicides to control STB using chemicals, which can be an environmental problem.

To tackle these challenges, we made a special breeding plan called Speed breeding (SB) for winter wheat which we tested on hundreds of winter wheat breeding lines. With SB, wheat grew 30-50% faster in greenhouses compared to the traditional ways, and the plants remained healthy. This time-saving let us study three generations of wheat for FHB resistance in just one year. We also developed genetic markers for FHB resistance. These markers show that SB works well for breeding for FHB resistance. To make it easier to check for FHB, we developed new techniques to see how severe the disease is on infected seeds. For that we used an RGB camera and a technique that can read and capture the qualities of the infected seeds with FHB.

Unlike FHB, which needs the plant to be fully grown to be studied, we studied STB resistance when wheat was much younger at seedling stage. This way we can speed up the breeding process and find out which genes make it resist the disease. We discovered new genetic markers that help wheat resist STB at seedling stage and confirmed other markers that can have effect throughout its life. Also, we checked if a microorganism agent could help wheat seedlings resist STB disease. Although we only studied the interaction of the microorganism and wheat under controlled conditions, if it works in field conditions, it will prove to be an environmentally safe alternative strategy for STB control.

We took all these ideas and put them to use in the breeding industry. Breeders can now use our new breeding methods and make wheat varieties with improved resistance against diseases. This will help farmers keep wheat growing sustainably, ensures we have enough food, and avoid problems when diseases strike.

Read more in the thesis: Novel methods for disease resistance breeding in winter wheat

Phenotyping, the process of measuring plants’ physical and biochemical traits, has become increasingly important in plant breeding and agricultural research. Traditional phenotyping methods involve expensive and time-consuming procedures. However, recent advances in digital imaging technology have made it possible to perform cost-effective phenotyping using RGB (red, green, and blue) imaging.

RGB imaging uses a standard camera to capture images of plants and extract data on traits such as leaf area, shape, and color. The images are then analyzed using computer vision algorithms to obtain quantitative measurements that can be used to identify desirable traits and select plant varieties tolerant of abiotic and biotic stresses. One advantage of RGB imaging is its affordability compared to other phenotyping methods: it requires only a standard camera and basic image analysis software, making it accessible to researchers with limited resources.

The work in this thesis started by developing an affordable imaging system to collect imaging data with imaging sensors such as RGB, thermal, MSI, and HSI cameras to provide a comprehensive understanding of plant health and performance. Paper I presents a blueprint of this system and a pipeline for analyzing the RGB and thermal images. This may help researchers interested in cost-efficiently monitoring plant growth and complex traits such as drought tolerance, disease resistance, and nutrient use efficiency. Paper III shows that affordable phenotyping based on RGB imaging could also help improve crop yield and quality because it was successfully used in conjunction with analysis of gluten parameters to identify wheat genotypes that maintain stable gluten production when exposed to abiotic stresses such as heat and drought. Finally, imaging-based evaluation of morphological parameters was successfully used to predict FHB in kernels and measure quality parameters in tubers (Papers II and VI).

The resulting morphological data was used to build a training model to estimate CS disease symptoms in potato tubers (Paper IV). This model is valuable because it enables evaluation of disease symptoms without subjectivity or the need for deep expertise. The methods here presented could thus revolutionize plant breeding and 
agricultural research by providing fast, accurate, and cost-effective data on plant traits.

Read more in the thesis: Developing affordable high-throughput plant phenotyping methods for breeding of cereals and tuber crops

Wheat is a staple food for 2.5 billion people in 89 countries around the world. In Sweden, food made from wheat is a part of our daily diet. A day without food from wheat is impossible to imagine. Recent extreme weather events, such as the severe heat and drought in 2018, have affected wheat yield and protein quality negatively in Sweden and worldwide. The future climate will be more extreme and will affect wheat yield and quality severely. To keep a continuing supply of wheat, we need wheat varieties that are able to provide good yields and quality in varying and extreme growing conditions. To develop new wheat varieties, we need to understand how climate change affects wheat yield and quality. We also have a substantial need for rapid and cost-effective wheat yield and quality screening methods to develop new wheat varieties.

We studied the yield, flour, dough mixing and bread-making quality of spring wheat grown in different stress environments, both in the field and in the greenhouse. We used different techniques, such as RGB imaging, to analyze plant biomass and evaluate yield. To analyze protein quality, we used size exclusion high performance liquid chromatography (SE-HPLC), mass spectroscopy (LC-MS/MS), near infrared spectroscopy, swelling index of glutenins (SIG) and solvent retention capacity (SRC). We used a mixograph to study dough mixing quality. Additionally, we baked the bread and measured bread volumes from wheat grown in different environments.

We found a lower yield and biomass in the wheat grown under severe heat and drought. We also found that severe heat and drought increased the gluten strength but reduced the protein concentration in the flour made from wheat grown in field. For the wheat grown in the greenhouse, we found higher gluten strength and protein concentration in wheat grown under the heat and drought conditions. The optimum time for dough mixing was one of the traits that was not affected by the varying climatic conditions. We recommend using dough mixing time, together with gluten strength and protein concentration, to help with the selection of varities in the breeding projects.

SE-HPLC, SIG and SRC tests used in our study required very small amounts of flour (16 mg to 1 g); in comparison to the industrial flour and dough mixing tests, such as farinograph and extensograph tests, which require a large amount of flour. Thus, SE-HPLC, SIG and SRC could be used as alternative tests to the farinograph and extensograph tests for wheat quality evaluation by both breeding and milling companies. The phenotyping results indicated that RGB cameras and image analysis could be useful tools to evaluate the yield resistance of the wheat genotypes.

In the thesis, the new information we have provided on climate change effects on wheat, as well as the information on the combination of different techniques for measuring yield and quality of wheat, could help breeders to develop new cultivars and millers to evaluate wheat quality at a reduced financial and time cost.

Read more in the thesis: Wheat quality under a climate spell - A focus on protein, physico-chemical and growth characteristics evaluated using innovatively combined approaches

Most people probably have their own ideas about the most tasty types of apple. Some can even identify a few apple cultivars by name and have personal favourites among the different cultivars available. The question then is whether we need plant breeding to develop new cultivars, if we already have access to so many different tasty apples?

While there are indeed vast numbers of apple cultivars available, few can be grown commercially at a profit. Commercial apple producers struggle every day with the challenges of running an orchard and, as the global climate and cultivation practices change, new problems are emerging. The purpose of plant breeding is to develop new cultivars that are better adapted to current or future conditions, thereby easing the burden on growers and helping to improve the profitability of apple production. Advances achieved by breeding may include improved resistance to pests and diseases, to reduce the need for chemical treatments if such are available and better adaptation to the current and future climate (considering ongoing global warming).

Sweden’s geographical location in the Scandinavian Peninsula in northern Europe presents special challenges to local apple growers, for example by a short growing season. In addition, the cool humid climate favours a serious disease known as European canker, which causes severe losses to growers by strangling branches or entire trees. Furthermore, with future global warming bud break and flowering is expected to occur earlier, which might lead to an increased risk of late spring frosts occurring during flowering, which is already an important problem that could ruin the yield of entire orchards.

Recognising the special challenges faced by Nordic apple growers, Sweden has had a dedicated domestic apple breeding programme running since the 1940s, with the goal of delivering new cultivars that can help farmers meet these special challenges. The aim of this thesis was to establish the infrastructure needed to make use of technological advances in plant breeding achieved in the past decade, so that the Swedish apple programme can continue doing its important work, but with increased efficiency.

The work in the thesis started by investigating the genetic resources currently vailable (Paper I) and making a contribution to the available toolbox (Paper II). The information obtained was used to identify regions of the apple genome conferring resistance to European canker (Papers III & IV). The effect under Nordic conditions of some previously identified regions of the apple genome regulating date of flowering and fruit harvest was then assessed (Paper V). Date of 50% canopy autumn senescence was found to be associated with how far north a cultivar can be grown, which is an important first step in gaining better knowledge about the genetic basis of adaptation to central and northern Sweden (Paper VI). Lastly, use of the knowledge generated in the thesis was exemplified by a discussion on possible crosses for further breeding in relation to the key traits studied.

Read more in the thesis: Apple genomics for the Swedish breeding programme