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Browsing by department "Avdelningen för lantbruksvetenskaper"

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  • Eusuf, Saad Bin (2020)
    Stress response in plants is influenced by several external and internal factors and is executed in a modular way. Environmental stimuli or stress is sensed by cellular receptors and the signal is transduced inside cell via the phospho-activation of highly conserved intracellular signaling cascades like mitogen activated protein kinase (MAPK) cascades. The signal then activates biosynthesis pathways of major stress response hormones like Salicylic acid (SA). In Arabidopsis about 90% SA is synthesized via isochorismate pathway and Isochorismate synthase 1 (ICS1) is a rate limiting enzyme in this pathway. In this study, goal was to select transgenic ICS1 (homozygous) candidate lines from parent ICS1-CFP by selective regeneration. Then, by molecular and physiological characterization of transgenic ICS1-CFP plants, the function of ICS1 phosphorylation, more specifically, impact of different photoperiods (Long day; LD and Short day; SD) and stress conditions on ICS1 activity would have resolved. However, there were no homozygous candidate line from any parent ICS1-CFP plants after several screening. Nevertheless, ozone treated stress sensitivity test was performed with heterozygous ICS1-CFP candidate plants (T2 generation). Ozone treated stress depends on stomata factor because ozone enters into plants through stomata. Therefore, stomata index analysis was performed with sid2 and WT (Col-0) phenotypes and grown in LD and SD conditions. Since, stomata number was different between LD and SD plants of both sid2 and WT phenotypes, a different method named Xanthine-Xanthine oxidase (X/XO) treatment was applied that induce oxidative stress regardless of stomata. Although, WT and sid2 had shown sensitivity to the treatment, the overall cell death percentage was very low. Lastly, our aim was to observe the impact of different photoperiods on the activation of two particular MAPKs i.e MPK3 and MPK6 under stress conditions. The phosphorylated (P-MPK3 and P-MPK6) are found abundantly in ozone treated plants as an early response. In this experiment, plants were grown in both LD and SD, stressed with both ozone and X/XO treatments, the activation of P-MPK3 and P-MPK6 was observed by protein level analysis (western blotting) in detailed time course. Although, the activation was visualized in both LD and SD plants, qualitatively the pattern was similar between day type samples and activation signal was very weak in both stress methods. In addition, anti-ICS1 antibody provided by Agrsera TM was tested for its efficiency to detect endogenous ICS1 protein in plants in two experimental set-up. Although the antibody could detect overexpressed ICS1-CFP protein in samples, it was not that efficient to detect endogenous ICS1 in any of the experiments.
  • Lahtinen, Sonja (2020)
    The purpose of the study was to determine the possibilities of utilizing the by-product streams of fish processing industry in the production of fish oil and silage. In this thesis the effect of different antioxidants on the preservation of salmon scraps was studied and the utilisation of the dregs from which the oil was extracted as feed was considered. The scarps preserved in this study were from farmed salmon and consisted of internal organs and roe. The study had two experiments. The first one lasted for 65 days and in it formic acid was added to the scraps for a final acid content of 3 %. The scraps with only the formic acid acted as the control and the four different antioxidants studied were butylated hydroxyanisole (BHA), tert-butylhydroquinone (TBHQ), ethoxyquin mixture (Helmlox) and butylated hydroxytoluene (Ionol). The amount of Ionol was 100 ppm and for BHA, TBHQ and Helmlox there were two different amounts, 50 and 100 ppm. The second experiment lasted for 29 days and the formic acid content was 1 %. BHA and Helmlox antioxidants were used with an amount of 10 ppm. The oil and sediment parts from the experiments were analyzed separately. Based on the analyses the antioxidants or their amounts did not have an effect on the values extracted from the sediment. In the first experiment the analyses from the oil gave mostly highly significant (p<0,001) differences between the control and the antioxidants. There were also clear differences between the antioxidants but the different amounts did not have an effect on the AV-, PV- and TOTOX-values. In the second experiment the analyses from the oil gave only minor differences between the control and the antioxidants, the differences between different antioxidants being larger. The peroxide value of BHA was clearly larger than that of the control and Helmlox and therefore also the TOTOX-value was larger, which contradicts the results of the first experiment. In the second experiment also the measured amino acid contents diminished when the antioxidants were added which contradicts previous research. TBHQ worked best as an antioxidant, then BHA, Ionol and Helmlox in order. The usage of the dregs from the scraps as feed for pigs and chicken is limited by its high fish oil content. However for fur animals salmon scraps are suitable as feed products if the amino acid deficiencies are compensated with other feed products.
  • Afrane, Yaw (2020)
    The world population is growing and is expected to reach over 9 billion in about 30 years. Climate change is also widely expected to worsen famines in certain regions of the world. This will drastically increase global food demand. Food security efforts should be therefore be geared towards promoting food crops that can thrive in these regions and can withstand the condition likely to be brought about by changing climate. Cassava is a typical example of such a crop. This study investigated the use of digital images to estimate growth parameters of young cassava plants. Cassava was cultivated in pots at the University of Helsinki greenhouse at Viikki. The plants were given different water level (100%, 60% and 30% saturation) and potassium (0.1, 1.0, 4.0, 16.0 and 32.0mM) treatments. Digital red-green-blue (RGB) and multispectral images were taken every other week for 5 consecutive times. The images were processed to obtain leaf area, Normalized Difference Vegetation Index (NDVI), and Crop Senescence Index (CSI) and correlated with directly measured growth parameters of the young cassava crops. It was observed that leaf area that was computed from images, and NDVI which was computed from the multispectral images have significant positive correlations with the growth parameters, ie, actual leaf area, chlorophyll content, and plant biomass. CSI however showed weak a correlation between the growth parameters of the young cassava plants. Images leaf area and NDVI were then used to identify the changes in the effects of the water and potassium treatments.
  • Wickström, Annika (2020)
    'Candidatus Liberibacter solanacearum' (CLso) is a frequent bacterium in carrot in southern and western Finland but is also occurring in South Savonia. The bacterium is unculturable, lives as a parasite and multiplies in the phloem vessels and is transmitted by the carrot psyllid Trioza apicalis. In Spain, France and Finland the bacterium has also been found in parsnip. The aim of this thesis was to study the occurrence and genetic variation of this bacterium in carrot and parsnip in Satakunda, Southwest Finland and South Savonia from such parsnip and carrot fields where psyllids and discolouration symptoms in foliage have been detected. All the samples were collected based on foliar discolouration symptoms. Four wild plants from the family Polygonaceae were collected from one carrot field and one parsnip field in Satakunda. These plants showed similar foliar discolouration as the carrots. Other criteria for collecting the carrot samples was based on occurrence of psyllids and leaf curling. Samples of parsnips were collected from vegetable farms, where parsnips were grown nearby the carrot fields and where psyllids had been detected. The samples were analysed by real-time PCR with primer combination specific to CLso. Those samples that had high amounts of bacteria were chosen for sequencing and detection of haplotype. CLso was detected in 62,9 % of the carrot samples, in 90,8 % of the parsnip foliage samples and in 76,9 % of the parsnip root samples and in all the samples of symptomatic wild plants. Based on the ftsZ gene sequence, a new haplotype of CLso, named haplotype H, was identified in three of the parsnip samples from Satakunda and in two samples of pale persicaria (Persicaria lapathifolia (L.) Gray). This is the ninth haplotype of CLso identified.
  • Zhao, Chuanhui (2020)
    The research of this thesis was focused on anaerobic digestion of cow manure mixed with different types of biowaste, especially those material that are available in Finland. The research was conducted by search, collection, and analysis of different data in literature. Topic of the thesis was predetermined by the Co-Creation Lab project of Helsinki Institute of Sustainability Science (HELSUS), which was seeking solution to achieve carbon neutral cow milk production. The solution was co-approached by three participants conducting thesis from technological, economical, and legislative points of view, in which I was responsible for writing mainly the technological part, and general findings in economic efficiency and legislative terms by the other two co-creators were also included in this thesis. The research was mainly related with the whole cycle of biogas production, including basics about anaerobic digestion (AD), applications of the biogas and digestate as a product and by-product of AD. Substrates for AD were researched with a focus to find the best combination of cow manure (CM) and biowaste in regard with methane yield outcome, especially a mixture of CM and silage waste that suits the cow farming situation in Finland. Methane yields for mono-digestion of various types of biowaste and co-digestion of CM with different biomass were collected and analyzed. Premises for biogas plant establishment were researched briefly, including facility composition, and consideration of feasibility and raw material availability. CM with grass containing 75% timothy and 25% meadow fescue grass at 70%:30% mixing ratio could be the best combination of CM: grass co-digestion, followed by 0.5:0.5 mixed CM and perennial ryegrass. Furthermore, CM mixed with food waste at 52:48% ratio could be the best combination among co-digestion of CM with biowaste other than grass, followed by CM and food waste mixed with 68%:32% ratio, and CM with oat straw mixed at 1:2 ratio could be a considerable combination of CM and crop waste.
  • Bergholm, Jenna (2020)
    Food chains have lengthened on account of globalization during the last decades which has led to multiple sustainability concerns related to transport emissions, food security, externalization of environmental costs, consumers’ alienation from agriculture and the origin of food and the economic situation of farmers. Organic and local food, farmers’ markets and community supported agriculture are seen as some ways to enhance the sustainability of the food system. Globally, there is in abundance research about farmers’ markets and their customers. However, there is still relatively little research from Finland about farmers’ markets. In this master’s thesis, the socio-economic and demographic markers of rural event visitors were analyzed to determine their relation to purchasing and event visiting habits. The empirical data were collected through use of a survey administered at a recurrent market event. The results showed that 75.4% of the respondents were female, and that the average age among respondents was 51.8 years. In addition, 63% were living in Hyvinkää, where the event was organized. Domestic origin, price, and healthiness were the most commonly mentioned factors that affected the buying decisions. It was discovered that age had an influence on buying organic, for example, respondents in the age groups 20–29 and 30–39 were buying more organic food compared to other groups, and respondents in age group 70+ less compared to other groups (p=0.003). Income, education, or individual family composition did not affect the tendency to buy organic.
  • Soleimanbeigi, Shirin (2020)
    Selective degeneration and dysregulation of specific neuronal populations is a common hallmark shared by neurodegenerative diseases affecting the aging population. Parkinson’s disease (PD) is one of the most prevalent neurodegenerative diseases with debilitating clinical manifestations that follow a chronic and progressive course. Pathological hallmarks of PD involve gradual and specific loss of DA (DA) neurons and widespread presence of Lewy body (LB) inclusions that consist of aggregated presynaptic protein, α-Synuclein (αSyn). Treatment of PD remains to be at symptomatic management as the underlying mechanisms that trigger neurodegeneration are still not fully elucidated. Over the past two decades, microRNAs (miRNAs) have become a major area of interest within biomedical fields and gained increasing momentum in the context of neurodegenerative diseases. In recent developments, changes in mature miRNA profiles have been reported in aging tissue and many age-related diseases, including PD. More recently, a number of studies have found that the most essential enzyme in the miRNA biogenesis pathway, Dicer, exhibits reduced expression with aging. To these ends, a genetic mouse model based on heterozygous knockout of Dicer (DicerHET) was introduced to simulate Dicer downregulation. Initial investigations identified the DicerHET model as a promising tool for studying the relationship between disrupted miRNA biogenesis and neurodegeneration associated with PD. To facilitate future investigations and speed up screening of potential therapeutic compounds using this genetic model, in the current work, we aimed to produce a DicerHET in vitro model with a practical and convenient genetic engineering approach. The main focus of this work was to validate the model and establish a standardized reproducible approach suitable for research that addresses the role of miRNA biogenesis in PD. The desired DicerHET genotype was generated in vitro by employing traditional Cre/loxP system in conjunction with a virally mediated Cre expression. More specifically, primary cortical cultures, derived from Dicer flox/+ mice embryos, were transduced with Cre expressing lentiviral vectors (lenti-hSYN-T2A-Cre) to delete the “floxed” Dicer allele. To establish optimal parameters for the procedure, we analysed recombination efficiency under different transduction conditions. The most efficient recombination was achieved after 5 days of induction in cultures. However, we observed that DicerHET genotype did not attenuate survival of the cells, as assessed by immunohistochemistry. Further, as a proof of concept, we exposed the DicerHET cultures to pre-formed fibrils (PFFs) - a PD related stressor that causes αSyn aggregation. pSer129-αSyn-positive LB-like aggregates were detected in all the PFF-treated cultures, however, with a greater accumulation in the DicerHET cultures. Interestingly, increased aggregation was not accompanied by increased cell death, suggesting that DicerHET genotype does not increase vulnerability of cortical neurons to pSer129-αSyn aggregation. Based on our earlier studies we presume that DA neurons may bear a specific vulnerability towards the age-related Dicer depletion. More conclusive evidence on this intriguing relationship could be provided in future research using the DicerHET model that can be readily applied to primary DA cultures.
  • Lassi, Juho (2020)
    Oat (Avena Sativa L.) has been second most cultivated crop in Finland. Oat has been Finland’s most exported grain for several years and its use for human consumption has increased because of dietary benefits. Oat is well suited for northern growing conditions and there has been long tradition for oat breeding in Finland. High yield has been important breeding goal but because the new use purposes, also other quality parameters have more attention in breeding. According to statistics, the average oat yield was 3293 kg/ha in years 2002-2016. The average yields have not changed in past 15 years in farm level. Yield and quality formation of four Finnish oat varieties (Iiris, Meeri, Niklas ja Steinar) and two Central-European oat varieties (Canyon and Harmony) was studied during growing season 2016. The field experiment was carried out at Elimäki in southern Finland. Different characteristics were measured and calculated during the growing season. Dry matter accumulation, growing rhythm, lodging and plant height were determined. Also yield, harvest index, grain filling rate, grading, thousand kernel weight and other quality parameters were determined. Suitability for milling use were studied from the oat varieties. Study was conducted in field as a completely randomized plot experiment with three replicants. Number of growing days correlated positively with yield. The last maturated varieties, Canyon, Harmony and Iiris, produced highest yield and best quality. These highest yielding varieties did not thoug have the highest harvest index. Length of grain filling period correlated positively with thousand kernel weight and grading result which all are also important quality features for oat milling industry. A correlation between grain size and hectoliter weight was not observed in this study.
  • Jämsä, Titta (2020)
    Tämän tutkielman tavoitteena oli selvittää suomalaisen emolehmätuotannon tuottavuutta kuvaavia tunnuslukuja. Emolehmätuotantoa tarvitaan, koska lypsylehmien määrä pienenee ja näin ollen myös lihantuotantoon käytettävissä olevien maitorotuisten vasikoiden määrä. Emolehmien määrä on noussut Suomessa lähes 20 % kymmenen viime vuoden aikana. Emolehmän tärkein tuotos on elävä vasikka, joka saadaan vieroitettua menestyksekkäästi ja riittävän isossa vieroituspainossa suhteessa emon painoon. Naudanlihantuotannon hiilijalanjälkeen on viime vuosina kiinnitetty yhä enemmän huomiota ja emolehmiin perustuvan lihantuotannon tuottavuutta parantamalla voidaan pienentää myös kasvihuonekaasupäästöjä. Emolehmätuotannon tuottavuutta kuvaavia tunnuslukuja ovat hiehojen poikimaikä, poikimaväli, poikimaprosentti, vasikkakuolleisuus, elinikäistuotos ja poistoikä. Nämä analysoitiin Ruokaviraston nautarekisterin tietojärjestelmistä saatavasta datasta vuosilta 1995-2014. Aineiston tilastollinen analysointi toteutettiin SAS-ohjelmalla. Keskimääräisten tunnuslukujen lisäksi analysoitiin rotukohtaiset erot sekä emolehmätilojen parhaimman ja heikoimman neljänneksen väliset erot. Emolehmähiehot poikivat keskimäärin 27,5 kuukauden iässä. Poikimaväli oli keskimäärin 378 päivää. Angus-rodun hiehojen poikimaikä oli matalin ja lehmien poikimaväli lyhyin lähes koko analysointijakson ajan. Limousinen poikimaikä oli korkein ja poikimaväli pisin. Parhaan neljänneksen tiloilla hiehot poikivat keskimäärin 22 kuukauden iässä ja heikoimman neljänneksen tiloilla yli 42 kuukauden iässä. Poikimavälin keskiarvo parhaan neljänneksen tiloilla oli 364 päivää ja heikoimman neljänneksen tiloilla 400 päivää. Poikimaprosentti oli keskimäärin lähes 86 prosenttia. Anguksen poikimaprosentti oli korkein koko analysointijakson ajan. Parhaan neljänneksen karjoissa poikimaprosentti oli keskimäärin 96 % ja heikoimman neljänneksen karjoissa 73 %. Vasikkakuolleisuus oli keskimäärin 6,2 %. Sonnivasikoiden kuolleisuus oli lähes 2 %-yksikköä suurempi kuin lehmävasikoiden. Ensikoilla vasikkakuolleisuus oli suurempi kuin vanhemmilla lehmillä. Vasikkakuolleisuus oli suurin charolais-rodulla. Emolehmän elinikäistuotos oli keskimäärin 4,4 tuotettua vasikkaa. Elinikäistuotos oli paras anguksella ja limousinella ja heikoin simmentalilla. Poistoiän keskiarvo oli 6,8 vuotta. Korkein poistoikä oli limousinella ja matalin simmentalilla. Tilakohtaiset vaihtelut tuotantotuloksissa olivat suuria. Tuotannon tulisi olla riittävän tehokasta, jotta se olisi ympäristöllisesti kestävää ja emolehmätuotannon hiilijalanjälkeä saataisiin entisestään pienennettyä.
  • Sarviaho, Katri (2019)
    The aim of this study was to estimate the genetic parameters of elk hunting traits in Jämthunds. There were nineteen traits under consideration. Heritabilities, repeatabilities, and genetic and phenotypic correlations were estimated for the traits. Also, coefficient of inbreeding and genetic trends were estimated. The data consisted of results from official elk hunting trials collected by Suomen Harmaahirvikoirajärjestö ry in 2012-2016. There were 46 221 results, from which 23 335 of Jämthunds. The pedigree data was provided by The Finnish Kennel Club and it included 31 544 Jämthunds. Significance of the fixed effects was estimated using F-test in analysis of variance with RStudio 1.0.136. The pedigree was pruned with RelaX2 1.54-pedigree analysis programme. Variance components were estimated with DMU-package using AI-REML-approach. The estimated heritabilities were low and varied between 0.00 and 0.047. The highest heritability was obtained for search and the lowest for obedience during work. Genetic correlations varied from -0.25 to 0.98, and the strongest were estimated for most of the bark related traits. The genetic trend has been positive in all traits, except for obedience traits. The coefficient of inbreeding for dogs born in 2016 was approximately 7.03 %, and the coefficient of inbreeding has decreased 0.26 % in the last decade. There are multiple non-genetic factors that affect the traits, and the data is based on subjectively evaluated variables. It is possible to improve genetic evaluation by collecting more information on trial conditions, by using the whole scale of points during the evaluation, and by making more objective evaluations of the traits. The estimated breeding values of the important traits can be used in selection of the parent of the next generation.
  • Ruotanen, Päivi (2020)
    Patellar luxation is a typical orthopaedic disorder in small sized dogs. Patella can luxate either medially or laterally, medial luxation being by far more common than the lateral luxation. PL is considered hereditary since certain breeds have great susceptibility to get the condition, and the symptoms may occur at young age. PL is diagnosed by following the so-called Putnam’s scale where the stifle joint is palpated and manipulated. PL is graded from 0=normal…4=permanent luxation. The aim of this study was to estimate the variance components and the heritability of PL, to visualize PL’s genetic trend and to calculate the genetic correlation between left and right stifle and between PL and hip dysplasia (HD) in Japanese Spitz. The PL, HD and pedigree data were provided by the Finnish Kennel Club. Data were modified with both R-program and Microsoft Office Excel. The pedigree check was performed with RelaX2 program and variance component analyses were done with DMU program using the restricted maximum likelihood method. Heritabilities (h2) were from very low to low depending on the model and breed. When the dependent variable was the mean of left and right patellae of an individual the lowest heritability was in the Pomeranian h2=0.03 and highest in the Chihuahua h2=0.18. The genetic correlation of left and right patellae was 1 in all breeds which suggests that they are genetically the same trait. In the Japanese Spitz the genetic correlation between PL and HD was -0.05. The genetic trend of PL was favorable in the Chihuahua and the Japanese Spitz. In the Pomeranian the trend was negative and neutral in the Finnish Spitz. Based on the results, the selection against PL has not been efficient. In future, patellae health should be controlled by using breeding indexes because the heritability of PL is low. Also, improvements in phenotyping could lead to more accurate selection.
  • Hämäläinen, Aurora (2020)
    The traditional method of estimating inbreeding is based on pedigree information, which only considers the known common ancestors of the animals. In recent years, the animal breeding sector has introduced new genomic tools in breeding schemes. The aim of this study was to estimate and compare the level of inbreeding in Finnish Yorkshire and Finnish Landrace pigs using pedigree and genomic methods. Data consisted of pedigree and genotype information from both breeds. In pedigree data there were 503 315 Landrace and 549 296 Yorkshire animals after pruning for pedigree completeness and errors in the data. In the genotype data, there were 522 individuals of Landrace and 934 individuals of Yorkshire animals after pruning. Inbreeding coefficients (FPED) were estimated from pedigree data using RelaX2 program and for genomic data using PLINK by detecting runs of homozygosity (FROH). Percentage of homozygosity (FPH) was also studied from genomic data. Yearly rate of inbreeding based on pedigree raised steadily. Average inbreeding coefficients from year 2014 were 0.10 for Landrace and 0.15 for Yorkshire. The average inbreeding coefficient based on ROHs for animals born in year 2014 were 0.21 for Landrace and 0.25 for Yorkshire animals. Correlation between pedigree-based estimate and genomic-based FROH was found to be quite low for both breeds; 0.51 for Landrace and 0.58 for Yorkshire. The correlation between the two genomic based methods FROH and FPH was high, 0.86 for Landrace and 0.89 for Yorkshire. The level of inbreeding was found to be quite high in both breeds. The genomic-based estimates were higher overall than pedigree-based estimates, which indicates that pedigree data are missing some common ancestors. Based on the results, the level of inbreeding in Finnish pig breeds should be monitored to maintain sufficient genetic diversity in the populations.
  • Das, Bishwajit (2020)
    Asteraceae comprises of approximately 10% of all angiosperm plant species. These species are well known for their highly compressed inflorescences known as capitula which consists of morphologically different types of flowers: ray, trans and disc flowers. This immense morphological difference excels Gerbera as an ideal plant to study flower type differentiations. Even though this complex process is governed by several genes, the ray flower identity is believed to be greatly influenced by GhCYC3 promoter mediated gene regulations. In previous studies two TCP transcription factors (TF): GhCIN1and GhCIN2, and two MADS TFs: GAGA1 and RCD5 were identified as the potential upstream regulators of GhCYC3. So, the aim of this study is to test whether these potential upstream regulators physically bind to GhCYC3 promoter in in vitro conditions. In order to achieve the goal, these transcription factor proteins from Gerbera hybrida were successfully expressed in E. coli and purified as fusion proteins to maltose-binding protein (MBP). Physical binding of the purified fusion proteins to the putative target DNA sites in the promoter region of GhCYC3 gene was tested by electrophoretic mobility shift assay (EMSA). The results showed that none of the gerbera transcription factors (GhCIN1, GhCIN2, GAGA1 and RCD5) bind to their putative target sites under the condition tested in this study. However, it might not be justifiable to deduce that these TFs do not interact with GhCYC3 promoter. The absence of in vitro interaction between the tested TFs and GhCYC3 promoter might be caused by either lack of proper folding and activity of the TFs or absence of co-factors which are available in vivo.
  • Asikainen, Aava (2019)
    Research on phosphorus (P) fertilization of white cabbage has been limited even though white cabbage is an important field vegetable in Finland. The quantities of phosphorus recommended in Finland when cultivating white cabbage are relatively large and excessive fertilization increases the risk of runoff to water systems. Scientific research is needed to determine fertilization levels that ensure good yields while reducing risks to the environment. The effects of P fertilization on yield, phosphorus uptake and phosphorus balance of white cabbage were studied in two soils of different P status in Piikkiö, Finland. The experiment on soil with loamy sand texture and high P status consisted of four fertilization treatments between 0-32 kg P ha-1 while the experiment on clay parcel with relatively low P status consisted of five treatments between 0-100 kg P ha-1, including a starter treatment. Yield, plant P content and P uptake were unaffected by the treatments. Yield was 83-87 t ha-1 on high P soil and 66-69 t ha-1 on low P soil. In high P soil, uptake of P by the plants was 50 kg ha-1 and field P balance was negative in all treatments. In low P soil, uptake was 40-45 kg ha-1 and P balance was positive starting from treatment level 30 kg P ha-1. It is likely that P fertilization levels based on the maximum limits set by the national Agri-environmental Programme are unnecessarily high for white cabbage. A level of fertilization equaling the P uptake of the yield can be recommended.
  • Tuominiemi, Antti (2020)
    The sequencing methods used to study the genome of organisms have become cheaper, resulting in a significant increase in the amount of genomic data available. Knowing the nucleic acid sequence of the DNA does not tell much about an organism. Not without first annotating the genome, which means searching for the locations of genes and defining their products. The programs used for annotation make mistakes and their results must be evaluated in various ways. The vast amount of genomic data encourages fast production of new annotations and this can increase human made errors. Some annotation programs use gene databases, so the number of wrongly annotated genes they contain may increase in the future if the quality control of annotations is not improved. This study examines correlation between selected quality measures and the quality of annotations. The quality metrics used can be divided into two basic types, the first one is based on the basic structures of genes and the second one on comparing the protein product of a gene against a protein database. The study assumes that comparison to a reference is a reliable way to assess the quality of annotations. The comparison is made at genome, exon and nucleotide levels. A single value describing the comparison is calculated at each level. For each gene aligned with a reference gene, sensitivity and specificity are calculated and used to make f-score at the nucleotide level. Four different versions of the wild strawberry (Fragaria vesca) genome and their six annotations were used as data. They were downloaded from the Genome Database for Rosacaea, which is a genome database specializing in rose plants. The correlation coefficients calculated from quality metrics and f-scores were in several cases small but reliable because the p-value was minimal. Correlation coefficients were higher when quality metrics based on protein homology were examined. The correlation coefficient calculated from the mean of the structure-based quality metrics and the f-score received lower values if the studied annotation had a high f-score value. These results detailed in this paper support the view that the selected structure-based quality metrics are not suitable for evaluation of high-grade annotations. They might possibly be used in automated detection of poor-quality annotations. Quality metrics based on protein homology appeared to be promising subjects for further research.
  • Ruuskanen, Jutta (2020)
    Arapaima gigas is one of the world’s largest freshwater fishes and it is native to the Amazon region. The species is over-exploited and sustainable long-term conservation strategies are needed to maintain the genetic diversity of the species. The aim of this study was to analyze the genetic diversity of Peruvian Arapaima gigas populations. The microsatellite data was collected as a part of a three-year project by the Regional Government of San Martín (GORESAM) and Finnish Game and Fisheries Research Institute (FGFRI). The data consisted of 15 microsatellite loci and 324 samples from three populations, Iquitos, Paiche, and Pucallpa. The samples for Iquitos and Pucallpa were collected from populations in the Amazon basin. Samples of Paiche were collected from a captive population in a fish farming research center. The average numbers of alleles and genotypes ranged between 1.9-3.3 and 2.5-4.6, respectively. Population Pucallpa showed the highest average level of heterozygosity (0.41), whereas the lowest level was observed in population Iquitos (0.25). There were altogether 13 loci which showed a statistically significant excess of heterozygosity, and nine loci with significant deficiency of heterozygosity across the three populations. The FIS-values were in accordance with most of the significant deviations indicating the excess or deficiency of heterozygosity. The average FIT-value (0.226) indicated a slight increase of homozygotes. Populations Iquitos and Paiche were on a state of Hardy-Weinberg equilibrium, but population Pucallpa showed a statistically significant deviation from the state of equilibrium. The pairwise FST-values ranged between 0.169-0.373, and they indicate that the three studied populations are genetically different. In addition, the values of Nei’s genetic distance (D) and full-pedigree likelihood analysis indicate a genetic differentiation between the populations. The number of migrants (Nm) between the three populations was estimated based on the mean frequency of private alleles (p(1) = 0.085) and the mean sample size (108 individuals). The number of migrants was 0.273 after the correction for sample size. The genetic diversity within and between the Peruvian populations resembles the results obtained in other studies of Arapaima gigas in the Amazon basin. Sustainable fish farming could offer a solution in maintaining the genetic diversity of the species.
  • Lehto-Edwards, Nanna (2020)
    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.
  • Iso-Kokkila, Marijke (2020)
    Barley has been cultivated throughout the world for centuries. During that time, it has experienced different climatic conditions and selective pressure. The consecutive genetic variation gives us a valuable source to explore various components of yield and stress resilience. In this research field experiments were performed on 24 European barley cultivar and landrace genotypes, as well as laboratory experiments on 15 genotypes; 13 cultivated and 2 genetically modified genotypes. The aim of the field tests was to examine the genotypic variation in Finnish weather conditions during two growth seasons in Viikki and to find out how stomatal conductance differs between varieties and whether it can be connected to yield. The aim of the laboratory tests conducted in Tartu was to examine the genotypic variation in the ability of barley seedlings’ stomata to react to changes in environmental conditions with high vapor pressure deficit and abscisic acid treatment. The reason for this study is the ongoing climate change, which challenges breeders to create new resilient varieties for future climatic conditions. In addition to genomic data and genetic tools a wide variety of genotype data is needed to capture valuable traits that different varieties possess. The hypothesis of this study was to find differences in gas exchange, that could be useful considering breeding of resilient barley cultivars adapted to future climatic conditions. The tests conducted in field and laboratory conditions demonstrated, that genotypic variation could be found among here tested barley varieties. In the experiments we found several interesting cultivars, that could be tested further to verify their usefulness in breeding resilient barley cultivars for future climatic conditions.
  • Nyberg, Paulina (2020)
    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.
  • Huttunen, Ari (2020)
    Gibberella zeae (Schwein.) Petch and its asexual form Fusarium graminearum Schwabe is a pathogen of oat, barley, wheat and maize that causes Fusarium head blight in cereals. F. graminearum produces mycotoxins that contaminate yields in humid and warm weather conditions. The pathogen spreads most effectively during its sexual stage. F. graminearum has become more common as a result of climate change and as reduced tillage has become more preferred in cultivation. This research was a part the Fustox Projet in Natural Resources Institute in Jokioinen research station. Develelopment of G.zeae in crop residues was studied. Crop residue samples were collected from no-till and tilled field plots in existing field trials in spring 2013. Occurrence of F. graminearum was studied in barley and oat from no-till and tilled field plots and in oat from a field trial of four tillage methods during the growing season 2013. Efficiency of two fungicides (DMI and DMI+QoI fungicides) were studied in two oat cultivars, barley and spring wheat in MTT Ylistaro research station. Yield samples were also analysed for deoxynivalenol (DON) contamination. Occurrence of the pathogen was determined by incubating straw pieces and kernels in laboratory conditions. Fusarium species were identified by their colony and spore morphology and colour. Contrary to expectations the pathogen was somewhat more prevalent in tilled plots than in reduced tillage. This may be due to greater microbe activity that is capable of decomposing or inhibiting the pathogen in fields with reduced tillage. In this study stem-bases were more infected by the pathogen in reduced tillage. Fungicide treatments were effective in reducing the occurrence of F. graminearum in the field and DON contamination in yield. There were no significant differences between fungicides. The most effective methods of controlling G. zeae and F. graminearum is selection resistant cultivars for cultivation. Careful selection of soil tillage method can also aid in controlling the pathogen.