| 1. |
- Fundová, Irena
(författare)
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Quantitative genetics of wood quality traits in Scots pine
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Wood quality of commercial tree species is important for many wood processingindustries and thus should be considered for inclusion in forest tree improvementprograms. This thesis evaluated the suitability of various proxy methods for rapid andnon-destructive assessment of wood quality traits on standing trees of Scots pine and thepotential for genetic improvement of different wood quality traits through recurrentselective breeding.Penetrometer Pilodyn and micro-drill Resistograph were tested for non-destructiveassessment of wood density (DENPIL and DENRES, respectively), using SilviScan density(DENSILV) as a benchmark. A strong additive genetic correlation was observed betweenDENSILV and DENRES (rA = 0.96), whilst the correlation with DENPIL was substantiallylower (rA = 0.74). Furthermore, SilviScan stiffness (MOESILV) was used as a benchmarkfor evaluation of several approaches of calculating the dynamic modulus of elasticity(MOE) from standing-tree acoustic velocity (VELTREE). The combination of VELTREEand adjusted DENRES provided the most accurate estimate of MOETREE (rA = 0.91).Additionally, non-destructive acoustic sensing tools were tested at different stages ofwood processing (on standing trees, felled logs and sawn boards) using destructivelymeasured sawn-board stiffness (static modulus of elasticity, MOES) and strength(modulus of rupture, MOR) as benchmarks. They proved to be capable of accuratelypredicting MOES (rA ≈ 0.8) while VELTREE, adjusted DENRES and MOETREE wellreflected MOR (rA ≈ 0.9). Genetic variation of shape stability of sawn boards (bow, crookand twist) was also investigated. Under-bark grain angle (GRA) was found to be a goodpredictor of sawn-board twisting and crooking (rA = 0.84 and 0.62, respectively). Thechemical composition of juvenile wood (proportion of cellulose, hemicelluloses, ligninand extractives) was predicted from Fourier transform infrared (FTIR) spectra usingpartial least squares regression (PLSR) modeling. Individual-tree narrow-senseheritabilities (ℎi2) for all of the studied wood quality traits varied from low to moderate.Genetic improvement of sawn-board DEN, MOES and MOR as the target traits couldbe achieved through selective breeding for MOETREE, DENRES, stem straightness (STR)or GRA. Selection focusing on GRA would also result in lower bow, crook and twist.Despite the negative genetic correlations between growth and wood quality traits, apossibility of their simultaneous improvement was identified. An index combining stemdiameter (DBH) and MOETREE provided the best compromise.
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| 2. |
- Hu, Jia
(författare)
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Climate-friendly rice - characterisation of rice varieties associated with low-methane emissions and improved bioenergy properties
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Paddy rice cultivation contributes to global warming by emitting methane into the atmosphere. The aims of the work presented in this thesis were to breed climatefriendly rice varieties, to increase rice straw utilisation to reduce the impact of rice cultivation on the environment. The results showed that fumarate and ethanol were the two major exudate compounds from SUSIBA2-rice roots regulating methane emissions from SUSIBA2-rice paddies. A naturally occurring low-methane rice variety was identified and field testing demonstrated that it could be successfully grown in Uppsala, Sweden, opening up possibilities for expanding rice cultivation into high-latitude countries. Key candidate genes important in adaptation of rice to Scandinavian light and climate conditions were identified. By crossing a naturally occurring low-methane rice variety with four high-yielding elite varieties, four independent lines of low-methane rice with high yield potential were developed. Field trials demonstrated that methane emissions from the selected lines were reduced by 70%. Analysis of carbon allocation and molecular analyses of gene activities revealed that sugar transporters such as SUT and SWEET participated in allocation of carbon to aboveground tissues, contributing to the high yield and lowmethane properties. The results also indicated that increasing the lipid content in rice straw could increase its value in bioenergy production. Overall, this thesis shows that plant breeding can successfully address several pressing issues affecting sustainability in rice production by reducing greenhouse gas emissions, increasing crop productivity and diversity, and improving bioenergy production from straw.
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| 3. |
- Högberg, Niclas
(författare)
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Sensing the worms : automated behaviour monitoring for detection of parasitism in grazing livestock
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Gastrointestinal nematodes (GIN) are common in grazing livestock and is a major cause of impaired health and productivity. Current control practices of GIN infections depend largely on the use of anthelmintic drugs. However, misuse of anthelmintic drugs has led to a widespread development of anthelmintic resistance. Behavioural monitoring has been suggested as a novel method to detect parasite infection in grazing livestock, enabling targeted (selective) treatment, where only infected groups or individual animals within a group are treated. The aim of this thesis was to investigate how multispecies GIN parasite infections affect behavioural patterns in grazing livestock on a group level using different on-animal sensors. The effect of subclinical GIN infection on activity and rumination patterns in first season grazing steers were investigated in contrasting groups during two grazing seasons, using different commercial sensors. The results indicate that untreated steers exposed to a higher GIN level had an increased lying time, lower activity level and affected rumination patterns over time, compared with dewormed steers. To enable the assessment of behavioural responses in lambs, the validity of two sensors for cattle for use in lambs were first evaluated. The effect of subclinical GIN infection on activity in lambs around weaning was then investigated in a replicated grazing trial with treated and untreated groups. The results indicate untreated lambs had a shorter daily lying time over time as well as a lower activity level, compared with dewormed lambs. In conclusion, this thesis supports that behavioural patterns are affected by subclinical GIN infections and the results demonstrate the potential use of automated behavioural observations as a diagnostic tool.
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| 4. |
- Nickel, David, 1990
(författare)
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Process development for platform chemical production from agricultural and forestry residues
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- As part of a bio-based economy, biorefineries are envisaged to sustainably produce platform chemicals via biochemical conversion of agricultural and forestry residues. However, supply risks, the recalcitrance of lignocellulosic biomass, and inhibitor formation during pretreatment impair the economic feasibility of such biorefineries. In this thesis, process design and assessment were developed with the aim of addressing these hurdles and improving the cost-effectiveness of lignocellulose-derived platform chemicals. To expand the feedstock base and reduce operational costs, logging residues served as underutilised and inexpensive raw material. The major impediment in converting logging residues was their high recalcitrance and low cellulose content, which resulted in low attainable ethanol titres during simultaneous saccharification and co-fermentation (SSCF). Pretreatment optimisation reduced inhibitor formation and recalcitrance, and led to enzymatic hydrolysis yields at par with those obtained for stem wood, despite the less favourable chemical composition. Upgrading logging residues with carbohydrate-rich oat hulls increased ethanol titres to >50 g/L using batch SSCF at 20% WIS loadings, demonstrating the potential to further decrease downstream processing costs. To alleviate the toxicity of inhibitors generated during pretreatment, preadaptation was applied to Saccharomyces cerevisiae . Exposure to the inhibitors in the pretreated liquid fraction improved ethanol production during subsequent fermentation. Transferring the concept of preadaptation to lactic acid production by Bacillus coagulans cut the process times by half and more than doubled the average specific lactic acid productivity, showcasing how preadaptation could decrease operational costs. To assess the performance and robustness of process designs against process input variations, a multi-scale variability analysis framework was developed. The framework included models for bioprocess, flowsheet, techno-economic, and life cycle assessment. In a case study, multi-feed processes, in which solids and cells are fed to the process using model-based predictions, were more robust against variable cellulolytic activities than batch SSCFs in a wheat straw-based ethanol biorefinery. The developed framework can be used to identify robust biorefinery process designs, which simultaneously meet technological, economic, and environmental goals.
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| 5. |
- Aboshady, Hadeer Moursy
(författare)
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Genomic variation and molecular mechanisms of the host response to gastrointestinal nematodes in small ruminants
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Gastrointestinal nematode (GIN) infections are one of the major constrains for sheep and goat production worldwide. One of the promising control strategies is the genetic selection for resistant animals as there are no issues due to anthelmintic resistance and it aligns to demands for chemical-free food. Exploring possible phenotypic and genomic markers that could be used in breeding scheme besides understanding the mechanisms responsible for resistance were the main goals of this thesis. Thesis consists of General introduction, a brief description of GIN biology and methods to control GIN with focus on phenotypic and genomic markers, four papers and General discussion. In paper Ⅰ, a systematic review and meta-analysis were conducted to re-analyse and summarize the findings on immunoglobulins response to GIN in the literature and discuss the potential to use immunoglobulins as biomarkers of the host resistance. A conceptual model summarizing the role of immunoglobulins in resistance to GIN is proposed. In paper Ⅱ, transcriptome profiling of the abomasal mucosa and lymph node tissues were compared between non-infected, resistant and susceptible Creole goats experimentally infected with Haemonchus contortus. Results indicated that the maintenance of the integrity of the mucosa has probably the priority for the host at late infection stage. In paper Ⅲ, the dynamics of the response of the abomasal mucosa of resistant and susceptible Creole goats experimentally infected with H. contortus were compared. The immune response was activated through many relevant pathways including the Th1 immune response at different time post-infection. Interestingly, the results showed a simultaneous time series activation of Th2 related genes in resistant compared to susceptible kids. In paper Ⅳ, the genomic variants of Creole goats resistant and susceptible to H. contortus were discovered from RNAsequencing data at four different times post-infection. Single nucleotide polymorphisms, insertions and deletions that distinguish the resistant and the susceptible groups were identified and characterized through functional analysis. The T cell receptor signalling pathway was one of the top significant pathways that distinguish the resistant from the susceptible group with genomic variants in 78% of genes in this pathway.
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| 6. |
- Anglart, Dorota
(författare)
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Indicators of mastitis and milk quality in dairy cows : data, modeling, and prediction in automatic milking systems
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Methods for generating predictions of important and generally accepted indicators of udder inflammation and poor milk quality, such as somatic cell count (SCC) or changes in milk homogeneity, are few. The aim of this thesis was to investigate methods to identify indicators of mastitis and poor milk quality in dairy cows using data generated by automatic milking systems (AMS).The first part of the project investigated the relationship between SCC and data regularly recorded by the AMS using models that could capture nonlinear associations between the explanatory variables and the outcome. This information could be used in modeling the SCC. Furthermore, three statistical methods, generalized additive model, random forest and multilayer perceptron, were compared for their ability to predict SCC using data generated by the AMS. The results showed that equally low prediction error was obtained using generalized additive model or multilayer perceptron for prediction of SCC based on AMS data.The second part explored the dynamics of changes in milk homogeneity in cows milked in AMS using descriptive statistics for clots collected by inline filters, scored for density. Clots were found among certain cows and cow periods and appeared in new quarters over time. Models were fitted for detecting and predicting clots in single cow milkings as well as for detecting clots in milkings over a longer period. The models successfully distinguished periods of milking free of changes in milk homogeneity, although the detection and prediction performance was poor. The prediction target and severity grade of each density category is discussed.
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| 7. |
- Bella David, Aneth
(författare)
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Revisiting push-pull technology: Below and aboveground mechanisms for ecosystem services
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Push-pull technology is an effective and ecological solution to suppressing major Lepidopteran pests of cereals, in particular stem-borers (Busseola fusca, Chilo partellus), the fall armyworm (Spodoptera frugiperda) and the parasitic weed Striga. The technology exploits plant-insect interactions in intercropping practices to manage the pests, increasing productivity while maintaining ecosystem resilience. In this study, we show that long-term (14 – 18 years) push-pull farming cause shifts in soil microbial communities, increasing the diversity of fungal taxa than bacteria. Further, the shift in the structure of soil microbial populations seems to require time to establish as observed by the weak impact of Desmodium species cultivated for just two years on soil microbial structure. However, even under the short-term cultivation period, individual taxa enrichment associated to the Desmodium were observed. On the other hand, whole soil microorganisms as well as rhizobia appeared to have little impact on the constitutive release of volatile emissions by Desmodium. Whether the plants grew on live or autoclaved soil, Desmodium did not release volatiles implicated in repelling lepidopteran pests, which is in stark contrast to previous reports. Upon herbivory of Desmodium by Spodoptera frugiperda larvae, a marginal increase in volatile emissions was observed. In line with this observation and contrary to expectation, intact Desmodium spp. did not deter oviposition by gravid S. frugiperda. In feeding bioassays, neonate S. frugiperda larvae strongly preferred Desmodium spp. to maize diet, but did not grow well nor did they survive on it. Older larvae were frequently immobilised on the stems, often dying in position after a few days. Deeper investigation showed that stems and leaves of Desmodium were covered with a dense web of straight and hooked silicon-rich trichomes of varying lengths that prevented larval movement, piercing their cuticle in the struggle. In this light, we propose that in a push-pull setting, Desmodium acts as a mechanical barrier and trap crop instead of a volatiles-dependent “push” crop as previously purported. In addition, intercropping practices have been shown to reduce insect pest populations through diverse mechanisms such as barrier effect and resource concentration. Push-pull technology shows that ecological approaches to pest management and increasing productivity can be effective. A clear understanding of the mechanisms of action of such approaches is critical for further improvements as well as translation into other agro-ecological practices.
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| 8. |
- Bottani, Gabriela
(författare)
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Bolivian creole cattle: population structure, genetic diversity and management practices
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Characterization studies of local livestock breeds are important to identify their potential and value for the Global Animal Genetic Resources. Important traits have been attributed to local breeds including adaptability and resilience to harsh environments and other traits with potential use in breeding schemes oriented towards the challenges of climate change. The aim of this thesis was to generate baseline information for the development of future conservation and breeding programs for the Creole cattle in Bolivia. For this purpose, three Creole cattle populations were included in this study: the Chaqueño (CHA), the Saavedreño (CEASIP) and a population from Pasorapa (PASO).In the first part of this thesis, the main characteristics of the production and management system in Pasorapa were described. Further, the identification and evaluation of elements affecting the sustainability of the production system and the development of breeding and conservation programs was done. Open-ended and closedended questionnaires and interviews with 81 smallholders from 11 communities from Pasorapa were performed. Poor infrastructure and deficient health management practices were found. The rearing system based on two stages with animals released in the mountains for about 7 months of the year and feeding mainly of native plant species, showed a strong interaction between the cattle and the environment. Farmer perceptions about diseases, mortality causes and selection criteria were described, showing that additionally to body conformation, farmers considered coat color for selection of breeding and replacement animals. Productivity, income and ecosystem services were identified as the main factors affecting the sustainability of the system.In the second part of this study, the population structure, genetic diversity, linkage disequilibrium (LD) and ROH based inbreeding levels of the three cattle populations were assessed using a 50K SNP array. Pairwise FST values indicated low to moderate differentiation between populations. Admixture analysis showed clear signs of admixture among and within populations. CEASIP had the highest proportion of ROHs for the length classes 4-8 Mb, 8-16 Mb and >16 Mb. FROH coefficient values were higher for CHA and CEASIP populations for the >4 Mb and >16 Mb length classes indicating past and recent inbreeding. PASO had the lowest inbreeding coefficients for all ROH length classes. LD and effective population size of PASO might have been influenced by recurrent bottleneck episodes. LD pattern in CEASIP indicated that a 50K SNP array could be applied for association studies in this population.
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| 9. |
- Bösch, Yvonne
(författare)
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Ecology of fungal denitrifiers in terrestrial ecosystems : global patterns and effects of management in agricultural soils
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Denitrification is the dominant source of nitrous oxide (N2O) from terrestrial ecosystems, a potent greenhouse gas and stratospheric ozone-depleting agent. Fungi can perform denitrification and terminate the process with N2O, making them a potentially important source of N2O. This thesis aimed to broaden the understanding of the ecology of this understudied group in the nitrogen cycle by assessing their global abundance and distribution in terrestrial ecosystems and evaluating the effects of soil management practices on their abundance, community composition, and contribution to N2O production in agricultural soils.Fungi carrying the denitrification marker gene nirK were rare and cosmopolitan and compared to prokaryotic denitrifiers, they were most abundant in forests and croplands, although prokaryotes dominated in all biomes. Agricultural management practices affected the abundance and community composition of fungal denitrifiers through changes in the availability of carbon and nitrogen. Long-term fertilization increased their abundance, irrespective of soil type or climate, but did not affect fungal contributions to potential N2O production. Instead, the genetic potential of bacterial denitrifiers was more important. In unfertilized soils, biotic and abiotic controls of N2O production rates were important, but in fertilized soils only abiotic soil properties were involved. Inversion tillage, compared with other types of tillage, led to a reduction of the genetic potential for fungal denitrification relative to that of bacterial denitrifiers and selected for fungi with opportunistic lifestyles. These results highlight that fungal denitrifiers are found across all terrestrial ecosystems, are significantly influenced by soil management but contribute less to N2O emissions than their prokaryotic counterparts.
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| 10. |
- Castro, David
(författare)
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Who comes first? Implications of the plant-microbiome-soil continuum feedback on plant performance
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Plants are sessile organisms that rely on their ability to explore the soil to access the nutrients and water they need to survive. Plants have co-evolved with certain groups of bacteria and fungi that provide nutrients and water and enhance tolerance to abiotic and biotic stressors in exchange for Carbon (C). This symbiotic interaction is central to plant establishment and survival in harsh environments, where edaphic properties exert selective pressures on plant growth and modulate the composition of the soil microbiome community, with potential detrimental effects on ecosystem composition. Globally, more than 50% of the biodiversity hotspots are in soils with particular characteristics, thus, edaphic properties are considered as second in importance after climatic variables. In this thesis, the aim was to study the impact of the soil properties on plant establishment and performance and how this affects the ability of the plant to recruit a microbial community to their roots, with a focus on the ectomycorrhizal fungi (EcM). The results presented in this thesis suggest that both edaphic properties and soil microbiome modulates plant establishment and growth. In addition, changing edaphic properties induce changes in plant metabolism that have direct impact on the root-associated community. These changes redefine plants’ C economy toward less demanding symbionts, having direct impact on the soil organic matter (SOM) dynamics. My results provide new insights on how anthropogenic-induced changes in the soil can have a strong impact on the soil ecology, which can in consequence, have a major impact in the forest biodiversity.
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