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Genetic variation within a population is shaped by the life history traits of the species and the properties of the surrounding ecosystem. It is an important factor in the preservation of populations. According to the emerging field of community genetics, genetic variation within a population of one species may also influence the dynamics and diversity of associated species, extending the conservational relevance of intraspecific genetic diversity. Finnish populations of pedunculate oak (Quercus robur) offer an interesting study system for population genetics. Q. robur grows in south-western Finland at the northern limit of its natural range. Here, its distribution has been shaped by long-term climatic and geological changes as well as by human disturbance, and the current populations are small and strongly fragmented. As Q. robur supports a high diversity of associated species, it is considered to have great ecological and conservational importance. In this thesis, I studied the amount and distribution of genetic diversity within and among three Q. robur populations in south-western Finland using population genetic parameters. I also described the spatial and temporal sub-population structure of one population, on the island of Wattkast. The genetic data was based on 15 nuclear microsatellite loci. Additionally, I examined the effect of the genetic diversity and genotypic identity of the oaks within Wattkast on associated herbivore communities. In the analysis, I used observational data from two years. As predicted for widespread, long-lived tree species, the microsatellite loci showed high levels of diversity within the populations, but also significant differentiation among them. This may be due to fragmentation and to the marginality of the populations. Within the population on Wattkast, I observed patterns of spatial and temporal sub-population differentiation. The characteristics of the site, including the ongoing shift to less extensive land use, suggest that the population is in genetic disequilibrium. As both the genetic distance and the community dissimilarity between pairs of trees increased with increasing geographic distance, I could not conclude the genotypic identity of the host trees to have an effect on the herbivore community structure. However, higher heterozygosity was associated with higher richness and abundance of species. This result supports the notion that intraspecific genetic variation may increase associated species richness. Based on the results of my study, both the life history traits of the species and the historic habitat changes may be observed in the genetic structure of Q. robur populations in Finland. The results also suggest that preservation of genetic variation within the remaining stands may be a factor not only in the preservation of these populations, but also in the conservation of associated species diversity.

Five wild sea buckthorn populations in Finland were studied using 8 SSR markers to reveal genetic diversity within and among populations. Population samples were collected from four different locations on mainland and one from the Åland Islands. Allelic data obtained from SSR markers were subjected to statistical analysis and AMOVA, and rarefaction was used to correct effects of uneven population sample sizes on some population diversity indices. Results showed moderate to high genetic diversity levels, as mean HE of all populations was 0.55 and HO 0.50. Most populations showed larger observed heterozygosity levels than expected, one showed equal amounts and one population showed lower heterozygosity levels than expected. Most genetic variation of populations was found within individuals across populations (84%) and only some among populations (16%). A weighted neighbor-joining phylogenetic tree showed only some clustering based on populations. The results of this study show, that there is mentionable diversity in Finnish wild sea buckthorn populations, and that populations are only moderately differentiated. This information can be beneficial particularly in sea buckthorn breeding efforts, but also from a possible genetic resources’ and conservation standpoint.

Drought is one of the most important abiotic stresses that causes significant reductions in crop yield, and thus hinders the food security of the growing world population. In consequence, it is urgent to select crops able to resist drought, maintain high yield and have a good nutritive content. The purpose of this project was to evaluate the responses of different accessions of Andean lupin to drought stress, and identify if there are significant differences in their physiological responses. To identify germplasm for further investigation, thirty accessions of Lupinus mutabilis Sweet. and one accession of L. albococcineus Hort. were screened in two sets, A of 15 and B of 16 accessions. From these sets, four lines were chosen on the basis of extreme values in the measurements, and this set of four was investigated in depth (set C). In all experiments, ten seeds of each chosen accession were sown in pots and grown in a glasshouse with 22°C, 18 h days and 18°C, 6 h nights, and were well watered until day 50 after planting. The pots were arranged in a randomized complete block design. The eight most uniform plants were chosen, and four were exposed to water stress while watering of the other four was continued. Water stress consisted of controlled water loss from the soil, 20% water holding capacity at 2% per day over 9 days, so the soil reached 2% moisture content and was held at this level for 2 days more. In all experiments, leaf temperature, stomatal conductance, relative water content, water potential, ion membrane leakage, and shoot dry weight were measured and transpiration efficiency was calculated. In set C, carbon isotope discrimination, root length, root dry matter, proline content and soluble sugar content were also determined. The analysis of set A and B revealed significant differences between treatments for all the parameters measured, except for relative water content, and there were also differences amongst accessions in certain parameters. PI 457972 and PI 457981 were selected for further investigation because of their low stomatal conductance under water stress conditions and low water use, and PI 510572 was selected as sensitive to drought stress due to its high water use, ion membrane leakage and water potential under water stress conditions. In addition AC 2792 (L. albococcineus) was selected due to its low stomatal conductance and water use, and high leaf temperature under water stress conditions. In the final experiment, PI 457981 and PI 457972 appeared to avoid drought through appropriate stomatal characteristics. PI 457981 showed low stomatal conductance, high leaf temperature and also high root length, similarly, accession PI 457972 showed low water potential, low stomatal conductance, low carbon isotope discrimination and accumulation of soluble sugars. Accession PI 510572 contrasted for these stomatal traits, but interestingly it showed low membrane ion leakage, high proline content and soluble sugars content, suggesting that it was capable of drought tolerance by osmotic adjustment. Finally, accession AC2792 showed low water use, low water potential and low carbon isotope discrimination. This survey thus identified accessions of Andean lupin that were able to avoid drought stress through stomatal traits and root traits, and other that were able to tolerate drought through the accumulation of osmotically active substances. Thus, there are good prospects for breeding of Andean lupin to improve its drought resistance.

The Finnish dairy cattle population has been subjected to systematic quantitative studies over decades. The Western Finncattle (WFC) has evolved over the last century with a production level comparable to other remaining local breeds in Europe. The heritability is used in designing the data collection and in predicting the changes expected from the selection and the variation parameters are used in constructing the economic selection indices genetic improvement scheme and in computing the bulls’ and cows’ breeding values. WFC has no recent studies on the genetic variation in milk production traits. The thesis research was set to estimate the heritability of milk, fat and protein yield, fat%, protein%, protein-fat ratio and somatic cell count (SCC) and the genetic correlation amongst them. Records from Western Finncattle primiparous cows calving in the period 2002–2016 were used for the genetic analyses. The raw data consisted of 5455 cows distributed across 2512 herds. The variance components were estimated with single and multi-trait animal model using a Bayesian approach and R studio package MCMCglmm. With requiring at least 5 cows in each herd-year subclass in the estimation, the data size was reduced to 1763 cows in 233 herds. The heritability of milk, protein and fat yield, protein%, fat% and SCC was in single (and in brackets for multi) trait analysis 0.36 (0.37), 027(0.30), 0.32 (0.30), 0.61(0.43), 0.52 (0.49) and 0.06 (0.15), respectively. Amongst yield traits and also between the content traits the genetic correlation was high, 0.73–0.94 and 0.43–0.59, respectively. The content traits (with milk yield in the denominator) had a negative genetic correlation with milk yield while no correlation with the protein and fat yield. There was an environmental correlation between content and yield traits for protein and fat. No correlations exist between SCC and other traits except an environmental correlation with milk yield and protein content. Despite the small population size of the WFC population, the effective population size is satisfactory and therefore no reduction in genetic variation is expected. Overall, the analysis on production traits and pedigree data shows that the Western Finncattle have much potential for genetic improvement.

Antibiotic resistance is a worldwide problem and it threatens the prevention and treatment of infections caused by different pathogens. All living organisms produce natural products including ribosomal peptides with great variety. They are widely distributed in nature and they are playing more significant role in the search of new antimicrobial compounds used as therapeutical agents. Bacteria are a prolific source of peptides many of which are antimicrobial and microbial genomes are widely believed to encode new antimicrobial peptides. Genome mining has expanded the number of families of ribosomally synthesized natural products in recent years. These In silico approaches together with molecular biology and chemical analysis aim to identify novel compounds. In this study an unknown cyanobactin-like gene cluster was discovered by genome mining from genomes of cyanobacteria and also other bacteria. The aim of this work was to study the occurrence of the gene clusters in various bacterial genomes and the structures of novel peptides. The active biosynthesis of these peptides was tested by LCMS- and Q-TOF -analyses based on bioinformatic predictions. The production of the predicted peptides was also tested with stable sulphur isotope labelling. The aim was also to clone the genes needed for peptide biosynthesis into E. coli and to study antimicrobial activities of these peptides. Bioinformatic analyses suggested that the gene clusters encoded 1–8 precursor peptides together with protease. The precursor peptides had conserved leader sequence (LPxQxxPVxR) and a highly variable core sequences, often encoding an even number of cysteines. The mature peptide is eventually formed from core sequence through post-translational changes in the precursor peptide. The gene cluster was present in 38 bacterial genomes representing a diverse selection of bacterial phyla including cyanobacteria, proteobacteria, actinobacteria, bacteroidetes, firmicutes and planctomycetes. Analyses of the precursor peptide core regions suggested that the products are 8–131 amino acids in length. These peptides could be divided into two groups based on their structures: They form a selection of disulphide-bridge stabilized peptides with 2–5 disulphide-bridges as well as short cationic peptides with an ?-helical structure. Surprisingly, these types of peptides are common in eukaryotes and part of the innate immune system displaying potent antimicrobial properties but very rarely reported for bacteria. The peptides predicted from bioinformatic analysis were detected from Pseudanabaena sp. PCC 6802 using a combination of molecular biology and structural chemistry. Heterologous expression of the gene cluster from Pseudanabaena sp. PCC 6802 in E. coli confirmed that the gene cluster is active. A set of short cationic synthetic peptides with ?-helical structure predicted from Oscillatoria sp. PCC 10802, Dickeya zeae Ech1591, Vibrio nigripulchritudo SOn1, Agarivorans albus MKT 106, Roseibium sp. TrichSKD4 and Yersinia frederiksenii ATCC 33641 were shown to have potent antimicrobial activity between 0.8–100 ?g/ml. These findings prove that predicted cysteine containing peptides are produced by bacteria and some peptides from this novel family have antimicrobial activity, which might pave the way for new possible drugs derived from natural products.

Strawberry breeding in Finland began 60 years ago and has largely relied on traditional breeding methods. The geography of Finland, as well as local consumer preferences for darker-coloured strawberries, have been the main focus of selection in all implemented Finnish breeding programs. With several successful and popular cultivars have been released, the current focus is on increasing yield and disease resistance while maintaining the excellent fruit quality of breeders' selections. A panel of 175 garden strawberry accessions was created and trialled at the Natural Resources Institute Finland (Luke) as part of a Nordic-Baltic pre-breeding collaboration between the institute and the Norwegian breeding company Graminor AS. A medium-density, genome-wide scan for 50K SNPs has been performed on each individual of the panel. This panel represents the genetic diversity present and typical for cultivated strawberry in the Nordic-Baltic region, and it is expected to provide Nordic breeders with markers tailored to their plant material diversity, supporting their future selection decisions and accelerating their breeding cycles. In this study, symptom severities of two strawberry leaf diseases (leaf spot caused by Mycosphaerella fragariae and leaf scorch caused by Diplocarpon earlianum) and seven fruit quality traits (berry weight, skin colour, flesh colour, evenness of flesh colour, basket appearance, predominant berry shape and tip type) were scored in the panel. GAPIT and statgenGWAS statistical packages in R were used to run five different GWAS models: Significant SNP-trait associations were found using single-locus (GLM and MLM) and multi-locus (FarmCPU and BLINK) association mapping analyses. The study had shed a light on the importance of considering several statistical models and parameters for a maximum benefit of association mapping studies. Among significant SNP-trait associations for fruit weight, fruit skin colour and fruit flesh colour, four were partially characterized by inspecting their allelic effects. On chromosome Fvb6-1, appearance of consensus, significant signals from the flesh colour trait of secondary-position berries is discussed. Nine significant SNP-marker associations were detected for berry weight.

Fusarium Head Blight (FHB) is an important cereal disease worldwide and has become an essential breeding target in wheat. FHB generates considerable losses in terms of grain yield and quality of the seeds in cereal crops. The mycotoxins produced by some Fusarium species, such as deoxynivalenol (DON), directly impact the farmers. In fact, DON accumulation results in unmarketable harvest due to the associated health hazards (vomiting, diarrhea, fever etc). Facing DON risks, the European Commission had to establish a maximum concentration of the mycotoxin in unprocessed cereals. Avoidance mechanisms of the plants against disease infections were identified in diverse studies and are known as the passive resistance. These mechanisms related to phenotypic traits such as variations in plant height (PH), heading date (HD) or the presence of awns could possibly reduce the FHB infection of the wheat. On another hand, the active resistance is determined by genetic factors so called quantitative trait loci (QTL). QTL identification via population mapping was established to be a useful tool to find loci regions associated with FHB resistance. Therefore, in this study we aimed to find phenotypic and genotypic correlations with Fusarium Head Blight resistance among 108 winter bread wheat genotypes. By estimating the heritability of the agronomic traits, we wanted to determine if it would be efficient to breed for those traits. Furthermore, we had the objective to detect FHB resistance QTL from our winter bread wheat genotypes and finally, to observe the overlapping QTL’s regions between FHB resistance and the QTL of the HD or of the PH. It was found that the HD had strong negative phenotypic and genotypic coefficients of correlation with FHB severity and DON concentration. The HD had also an important heritability and direct effect on FHB severity. By performing a GWAS analysis, QTL associated to FHB resistance were found on the chromosomes 1B, 2B, 3A, 3B, 5A, 5B, 5D, 6A, 6B ,7B among the studied genotypes. Overlapping QTL were observed between FHB resistance and HD on the chromosomes 1B, 2B, 3B, 5A, 5B, 6B but also between FHB resistance and PH on the chromosomes 2B, 3A, 3B, 5A, 6A. In conclusion, the HD was considered as an escape mechanism against FHB. It seems to be feasible to select chromosomes fragments with favorable QTL for FHB genetic resistance. Those traits could be involved in marker assisted or genomic selection programmes after the approval of the observed QTL detected to develop FHB resistant cultivars.

Bilberry is a soft fruit, growing wild in the forests of Europe, and especially Nordic and East European countries. Its demand is growing on the market, thanks to its heath beneficial components like anthocyanins, present in both skin and flesh of the berry. It however has a very short shelf-life. The goal of this study was to identify pectinase genes, with a focus on two subfamilies, polygalacturonase (PG) and pectate lyase (PL). The main interest was to study those that are expressed during bilberry’s ripening, to get a better understanding of this process. Bioinformatics were used to identify the annotated genes from the bilberry genome, and point out candidates, from which transcripts are found during ripening, with BLAST searches within a transcriptome of ripening bilberry fruit. The expression of the PL candidates was then studied with qPCR analysis. The study identified 70 PG-coding genes and 25 PL-coding genes, of which 35 and 12, respectively, were found in the ripening berry. The expression of five PL genes was increased during ripening, suggesting a role in the softening of the fruit. Two of those had a notably higher relative increase, making them prime candidates for further study.

Kasvit tuottavat ensisijaisen aineenvaihdunnan eli primaarimetabolian avulla tarvitsemansa amino-, nukleiini- ja rasvahapot. Näitä molekyylejä kasvit käyttävät kasvuun ja kehitykseen sekä elintoimintojensa turvaamiseen. Suuri osa primaarimetabolian geeneistä on hyvin konservoituneita eli ne ovat säilyneet lähes muuttumattomana kasvilajista toiseen miljoonien vuosien ajan. Sekundaarimetaboliitteja kasvit tuottavat vuorovaikuttaakseen ympäristönsä kanssa. Sekundaarimetaboliittien biosynteesin voi laukaista esimerkiksi kasvin kokema stressi, joka aiheutuu kasvinsyöjistä, taudinaiheuttajista, toisista kasveista tai jos kasvi altistuu liikaa ultraviolettisäteilylle. Ympäristötekijöillä, kuten pH:lla, veden saatavuudella, lämpötilalla ja maaperän suolapitoisuudella on myös suuri vaikutus sekundaarimetaboliittien biosynteesiin sekä vaihteluun saman kasvilajin sisällä. Suurin osa kasvien sekundaarimetaboliiteista syntetisoidaan sikimaatti-, isoprenoidi- ja polyketidireittiä pitkin. Polyketidit toimivat muun muassa pigmentteinä ja osana kasvin puolustusjärjestelmää. Gerberassa esiintyy harvinaista polyketidijohdannaista, 4-hydroksi-5-metyylikumariinia (HMC), jonka biosynteesistä 2-pyronisyntaasi G2PS2:n on päätelty vastaavan. Tässä tutkielmassa selvitettiin g2ps2:n osallisuutta HMC:n biosynteesiin käyttämällä Virus induced gene silencing (VIGS)- menetelmää sekä proteiinin ylituottoa gerberan kallussolukossa. VIGS- menetelmä ei toiminut tässä kokeessa g2ps2- geenin aikaisen ekspression takia. Kokeet gerberan Regina- lajikkeen kallussolukossa sen sijaan vaikuttivat lupaavilta ja kallus osoittautui hyödylliseksi menetelmäksi gerberan polyketidisyntaasien tutkimiseen.

Recent trends in urbanization have contributed to re-defining urban demand and rural supply across the global agricultural landscape. These dynamic interactions occur within both formal agricultural economies, as well as within informal networks of non-commodity exchange. This research identifies on-the-ground systems of non-commodity exchange practiced in urban agroecology, and explores the implications of these systems of exchange upon the demand for changes in the ways humans relate to food, and the governing structures determining their distribution. Framed by the exploration of urban agroecology as a science, practice and social movement, this research probes exchange pathways across two city-sponsored urban agriculture networks: The P-Patch Community Gardening Program in Seattle, United States and the Allotment Gardens of Helsinki, Finland. As both garden networks are embedded within each city’s respective development plan, these sites offer the distinct benefit of probing civic responsibility and active engagement within civic agriculture outside of the discourse of food production for self as a political act. I employ an interdisciplinary approach to this research methodology which draws from the disciplines of planning, human geography, sociology, and agroecology. Data was collected and analyzed utilizing qualitative methods including semi-structured interview and ethnographic photography. I argue that the identification of these non-commodity exchange systems, and the fragmented urban place-based knowledge pockets from which they emerged, can be utilized to derive principals useful in the design and management of sustainable urban agroecosystems.