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Browsing by study line "Växtproduktionsvetenskaper"

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  • Määttänen, Satu (2020)
    Agroforestry, a widespread land-use in tropics and especially in tropical drylands, is gaining increasing attention due its carbon sequestration and storage potential. Majority of African countries acknowledge agroforestry as a national climate change mitigation and adaptation strategy. Despite the large extent of African drylands and the commonness and importance of agroforestry systems to dryland livelihoods, these systems are scarcely studied and research on dryland African agroforestry carbon stocks are few. The aim of the study was to compare carbon stocks of three land-uses: Vitellaria paradoxa dominated parkland (PL), improved agroforestry system (IA) and, as a control, abandoned land (AL), to study carbon allocation between and within the land-uses and to examine the variability of biomass estimates of different allometric equations used in carbon inventory in West African Sahel. Study was conducted in two villages in Yorosso, Southern Mali. Carbon stocks accounted were woody above- and belowground biomass, litter and top-soil organic carbon. Allometric equations and root-to-shoot ratios were used for woody biomass measurement. Comparison of biomass estimations of different allometric equations and root-to-shoot-ratios was conducted by using multiple equations for the dataset. Total system carbon stocks were 24.7 MgC haˉ¹, 29.9 MgC haˉ¹ and 42.2 MgC haˉ¹, for PL, AL and IA, respectively, with statistically significant difference between PL and IA. Top-soil organic carbon (SOC) was important carbon pool, accounting 34.8 % of total system carbon in PL and IA, and 49.6 % in AL. There were no statistically significant differences on the SOC/biomass C ratios between the land-uses. PL had lower SOC stocks than IA or AL, difference being statistically significant. The reason for lower SOC stock of PL could not be explained in this study. IA had larger woody biomass carbon stocks (27.0 MgC haˉ¹) than PL (15.5 MgC haˉ¹ ) and AL (14.4 MgC haˉ¹), but the difference was not statistically significant due to the similar density of large mature trees in all of the land-uses and partly due to the large woody biomass variation within the land-uses. In all of the land-uses, most of biomass carbon was stored in large mature trees and in two species: V. paradoxa and Parkia biglobosa. Large woody individuals had major impact on the land-use level carbon stocks. For carbon conservation, these individuals should be preserved and spared even during land-use change. Despite relatively large density, young trees and shrubs stored diminutive amount of carbon compared to mature trees. As the currently young planted trees in IA will grow and mature in the future, the woody biomass carbon stocks of the system will increase significantly. Lack of regeneration observed in PL threatens the sustainability of the system and its carbon stocks. Future carbon storage potential of AL depends on the regeneration potential of large tree species. Comparison of different allometric equations for tree biomass estimation revealed substantial variation. The choice of allometric equation used affects the obtained results, hampering the comparison of studies using different equations. Commonly used root-to-shoot ratios vary on their estimations, and most probably by underestimating root biomass. There is a clear need for specialised and standard carbon inventory methods for drylands and agroforestry systems.
  • McPartlin, Maria (2020)
    Cellular agriculture is a novel food production technology that utilizes tissue engineering techniques to culture muscle cells to make cultured meat, or microbes and fermenting to create proteins such as casein, albumin and collagen which can be processed to products similar to milk and egg white for example. This thesis aims to explore the challenges that cellular agriculture faces in terms of policy, politics and the society mainly in a Finnish context, but also observing EU regulations. These challenges were investigated by interviewing altogether 15 representatives of stakeholder groups, which are political parties, government administration, organizations of policy executioners, NGO’s, food-tech companies, -funds and research centres. The data from the interviews was transcribed and processed in Atlas.ti-software using the analysis of qualitative content -method. The processed data was then analysed using the analysis of a specialist interview -method. The study revealed that specialists agree that cellular agriculture products will follow EU Novel Food regulations, but that cellular agriculture might have to overcome some regulation-related challenges. Challenges might also arise from markets, consumers and competing with conventionally produced food. Some believed cellular agriculture to have a negative impact on the Finnish society in the form of eroding rural livelihoods, and that the production will be in the hands of large corporations. Many stated that they do not believe cellular agriculture will surpass conventional agriculture, but that it will become just another food innovation. Some believed cellular agriculture offers great possibilities in the form of more sustainable food production. Many of the statements of the interviewees reflected current events already underway in the cellular agriculture and alternative protein field. The challenges cellular agriculture will face are multifaceted, and more information is still needed, especially on the societal effects of cellular agriculture.
  • Valdebenito Alamar, Nerea (2021)
    Despite their immobile nature, their ability for adaptation allows plants to face harmful conditions from the environment to successfully survive and reproduce. Plant cells sense and integrate signals from the environment and activate response mechanisms. Participants in these mechanisms are the receptor-like protein kinases (RLKs) and a subgroup of RLKs, the cysteine-rich receptor-like kinases (CRKs). Members of this family have been associated with functions related to environmental stress responses in plants. CRK2 is one interesting member of the CRK clade of RLKs. While roles of CRK2 in the response to biotic and abiotic stimuli have been recently described, many aspects of the diverse functions of CRK2 remain elusive. The reduced size of the crk2 mutant suggests that developmental processes are affected by the absence of the protein. One of the objectives of this work was to analyse potential reasons for the smaller size of crk2. The difference in plant size could be due to a reduced number of cells. Results from the analysis of young cotyledons showed that the smaller plant size is not due to a reduced cell number in leaves when compared to Arabidopsis thaliana (Arabidopsis) ecotype Columbia (Col-0). Another way to understand the processes in which a protein is involved is to target possible interaction partners. Therefore, genotyping and analysis of growth phenotypes of T-DNA insertion mutant lines for candidate interaction partners for CRK2 was performed. The results revealed smaller phenotype for a nitrate transporter (NRT1.7) mutant in fresh weight and rosette area whereas for a protein kinase (QSK1) mutant, higher fresh weight but reduced rosette area was observed compared to Col-0. Generation of constructs for fusion protein expression and purification revealed the possibility of expressing tagged cytoplasmic regions of these proteins for further analysis of protein-protein interaction through kinase assays due to the kinase activity of CRK2. Generation of fluorescent-tagged proteins from the candidate interaction partners allowed for localization studies via confocal microscopy to determine the co-localization to the plasma membrane of these proteins with CRK2, which is located to plasma membrane under standard growth conditions. The co-localization results suggest that the proteins NRT1.7 and QSK1 colocalize with CRK2, which is a step forward in the verification of their possible interaction in planta. The smaller size of the nrt1.7 and qsk1 mutants indicates that the lack of these proteins affects plant development.
  • Hani, Umama (2021)
    To determine the role of metalloprotease EGY1 and hormone signalling pathways in PSII repair cycle, a mutant named white because of early senescence was identified having 4bp deletion in EGY1. To further characterize the growth responses in white mutant, two suppressors (white suppressor 1 and white suppressor 2), mutated in STAY GREEN1 (SGR1) which prevents chlorophyll degradation, restored the normal white phenotype was identified upon suppressor mutant screens. This study investigated the effect of chloroplast translation inhibitors (lincomycin/chloramphenicol) and MV (methyl viologen) on photosynthesis in Arabidopsis thaliana single and double white mutants. Furthermore, a second goal was to verify the correct identification of the mutations in white suppressor 1 and white suppressor 2. Western blotting and pulse amplitude modulated fluorimeter (PAM) was used to quantify the D1 protein (reaction core of PSII) levels and photochemical efficiency (Fv/Fm) respectively. Immunoblotting revealed a pronounced decrease in D1 levels for both white and egy1. PAM results showed a high tolerance of white mutant towards lincomycin/chloramphenicol. The white suppressors complemented the lincomycin/chloramphenicol tolerance of white mutant. The white mutant was highly MV sensitive. This MV response was altered in white double mutants (white ein2-1, white sr1-4D and white rcd1-4), suggesting that hormone signalling was involved in the response to MV. The decreased abundance of D1 in the white mutant suggests a role for EGY1 in PSII assembly and D1 turnover under light stress. In all assays (immunoblotting and PAM), the white mutant and egy1-2 gave the same results, this confirms the correct identification of the white mutant as a new egy1 allele. The successful restoration of lincomycin /chloramphenicol tolerance by white suppressors (S1 and S2), implicates that chlorophyll breakdown impacts on correct photosynthesis function. The suppressors S1 and S2 were transformed with wildtype SGR1, which restored the white mutant phenotype. Thus, the suppressor phenotype was caused by mutations in SGR1.
  • Hadid, Feras (2021)
    The growing demand for crop products caused by population growth and climate change encourages plant scientists to investigate sustainable strategies to tackle such problems. Translating the knowledge of plant molecular mechanisms into applicable practices in the field would help in improving the plants' efficiency and productivity. The size of a plant's shoot apical meristem (SAM) is an important factor in biomass production and crop productivity. Besides, understanding the molecular regulation of the shoot apical meristem would help to know more about the 3D growth innovations of different plant families across the kingdom. This thesis aimed to study the regulation mechanisms of the meristem activity in Gerbera, the model organism of the Asteraceae family that has an informative phylogenetic position to understand evolutionary events. The inflorescence of Gerbera is highly resembling clv3 mutants in Arabidopsis. CLV3 peptide is involved in maintaining the meristem activity, these differences between the two species suggested an evolutionary modification for this pathway. GhCLV3-GhWUS signaling components in Gerbera hybrida were identified following bioinformatics approaches. Then sequence comparisons and phylogenetic analyses between Gerbera sequences and other species were performed. The coding sequence of GhCLV1 was cloned to expression vectors. The expression pattern analysis of the receptors was performed by RT-PCR and RNA-seq data. The results suggest that GhCLV1 is an important factor in maintaining the enlarged inflorescence meristem in Gerbera. Also, all the other receptors were expressed at different levels suggesting their contribution in the GhCLV3-GhWUS pathway and inflorescence termination.
  • Michel, Matthieu (2020)
    Hybrid wheat has been the focus of much research for its potential high yield, high protein content and better resistance to biotic and abiotic stresses. Nowadays, only CHA (Chemical Hybridizing Agent) method is used to induce male sterility at a commercial scale. However, this technique is hard to implement on a large production scale and other methods have been investigated for several years. CMS (Cytoplasmic Male Sterility) has been shown to be a promising way to develop hybrid wheat. However, one downside of the technique is the challenging breeding stage step and the associated conversion and restoration process. To fully express the potential gain in yield, the restoration of the cytoplasmic sterility must be complete for the F1 to be fully fertile. In this study, we investigated different methods to assess fertility restoration in nursery and compared the results with the trial notations. The collected data were also used to feed a genomic selection model to predict the behavior of untested hybrids. The results showed a high experimental error of the bagging method originated mostly from human manipulation. The visual scoring showed higher repeatability but was poorly correlated with trial score. A deeper study of the trial scoring revealed an interesting effect coming from the female and an expression of sterility for commercial lines and CHA hybrid checks. Good prediction accuracies were found for genomic selection on both methods, however deeper studies and cross prediction are needed. The multilocation trials remained the best option to score fertility restoration
  • Qin, Kaiyue Jr (2020)
    Strawberries (Fragaria sp.) are perennial plants that belong to Rosaceae family. According to flowering habit, strawberries are classified as seasonal flowering and perpetual flowering strawberries. Environmental factors regulate flowering in plants. Among them, photoperiod and temperature are two important cues to affect flowering in strawberries. Besides, FT is a general flowering activator in many plant species. This thesis explored the flowering habits and FT expression level of two diploid strawberries F. bucharica and F. nilgerrensis under short and long day at cool temperature at 11 °C. The results were compared with F. vesca which has been studied earlier. After 2, 4 and 6 weeks of cool temperature (11 °C) treatment, all F. vesca and the majority of F. bucharica flowered regardless of photoperiod. As for F. nilgerrensis, there was no floral induction under SD and 20 % flowering rate after 6 weeks of LD treatment. After 4 weeks of the treatment, the expression of FT was down-regulated in F. vesca and F. bucharica compared with control groups under long day at 20 °C. In conclusion, the cool temperature at 11 °C induced flowering both in F. vesca and F. bucharica. The photoperiod affected flowering in F. vesca, while not in F. bucharica. As for F. nilgerrensis, the treatments were not strongly inductive for flowering. It may need more time for floral induction. The FT1 expression was down regulated after 4-week cool temperature treatments in F. vesca and F. bucharica, which was negatively correlated with flower induction. The photoperiod and temperature significantly affect branch crown formation in F. nilgerrensis, while the temperature had significant effects on runner formation and leaf formation in these three species.
  • Huhdanmäki, Tuukka (2021)
    CRISPR-Cas9 is one variant of newly emerging technologies utilizing targeted mutagenesis based on Cas family proteins and guide RNA that enable binding and modifying selected target sequence. The aim of the master’s thesis was to compare different methods of CRISPR-Cas9 induced gene editing in the genus Nicotiana and other secondary protocols necessary to identify successful mutations. PDS1 and PDS2 genes coding phytoene desaturase in plants were selected as target genes as mutant genotype produce visually identifiable photobleaching phenotype. CRISPR-Cas9 ribonucleoprotein complex mediated transformation uses separately produced Cas9 protein and guide RNA that when combined perform transient gene editing in cell. This method was planned to be used but Cas9 protein was challenging to produce in soluble form and final transformation was not achieved. This study suggests that acquiring ready-to-use Cas9 protein might be preferable choice when targeting only few transformations with CRISPR-Cas9 RNP-complex. Agrotransformation is well established method for genus Nicotiana and using Single Transcriptional Unit CRISPR-Cas9 system it is straightforward procedure from plasmid design to transformation. Successfully transformed plants were redeemed from transient agroinfiltration and stable agrotransformation experiments. Off-target mutations are possible and selective outbreeding may be needed. This method lacks the several advantages of CRISPR-Cas9 RNP-complex such as instant gene editing in cell, avoiding RNA interference and transformation over species boundaries, but is simple and functional in genus Nicotiana. Successful mutations were detected using commercial T7E1 and with natural CEL I endonuclease from celery extract. Celery extract can be used as cost-effective alternative to T7E1 for verifying or replicating previously confirmed results.
  • Mosalam, Mohamed (2021)
    The objectives of the study were to assess the efficiency of transient expression of sgRNA/Cas9 construct in Petunia V26, where sgRNA targeted a cytosine deaminase gene (CodA) that converts 5-fluorocytosine into the toxic compound 5-fluorouracil. Disrupting CodA by transient expression of sgRNA/Cas9 introduced a conditional negative selection system that allowed plants with mutated CodA to regenerate on media containing 5-fluorocytosine. The single transcriptional unit vector pMOH2 was designed to carry two amplified sgRNAs guiding Cas9 targeting at HinfI cutting sites. The expression vector was transformed into Petunia V26 using Agrobacterium tumefaciens (pGV2260). Successful mutations were detected on 62.5 mg/L 5-fluorocytosine. Large numbers of in vitro shoots were regenerated from the transformed leaves on a modified MS-media containing 1 mg/L zeatin. The study revealed that transient expression of the sgRNA/Cas9 construct is efficient and can be used to target other genes in Petunia V26. pMOH2 targeted its sites successfully, and proved that CodA can be used as a conditional negative selection marker to detect cells with an edited genome.
  • Mäkinen, Arttu Tapio (2021)
    Crop monitoring in commercial indoor farming is a commonly used method in assessing the general productivity of the cultivated plants. This assessment practice is typically conducted manually by greenhouse workers and is sometimes supplemented by certain hand-held or stationary devices. An interesting example of novel device-assisted crop monitoring technologies utilizes digital imaging devices and computer-driven image analysis algorithms that have been prominently employed within the field of plant phenotyping. In the context of botanical studies, they have been used in e.g. characterizing various complex interactions between the genotypes of important food crops and their agronomic traits in specific prevailing environmental conditions. Additionally, image-based data acquisition technologies also present very interesting prospects for precision agriculture management practices. They could be harnessed to scan entire greenhouse compartments continuously and acquire massive amounts of data on multiple morphological and physiological aspects of crop growth and development in a non-destructive fashion. The acquired data could be implemented into mathematical greenhouse control models and utilized in a plethora of useful applications, including e.g. estimating and predicting biomass production and yield, detecting and localizing potential abiotic/biotic stress symptoms at an early stage, and ultimately enhancing overall crop production efficiency. In this thesis, these imaging technologies were explored in practice by designing and constructing a growth chamber embedded with automatic climate control and a low-cost multispectral imaging subsystem. The final assembly was tested by conducting a simple experiment involving drought-stressed sweet basil plants (Ocimum basilicum L. cv. ‘Genovese’) to determine how early drought-stress related symptoms could be detected purely from multispectral images. While the system carried out the tasks of automated climate control and continuous image capture adequately, the implemented approach in drought-stress detection was deemed unsuccessful. Significant differences between drought-stressed plants and their respective controls were not observed until visible symptoms were present. This was assumed to be due to incompatibility of the camera module’s spectral sensitivity in detecting changes in water content in plant tissue.
  • Qiu, Yachen (2021)
    Onion (Allium cepa L.) is an important vegetable, which provides major nutritional benefits. In Finland, basal rot caused by Fusarium fungal species (FBR) has become the most destructive disease of onion in recent years. It causes damping off and stunted growth on onion seedlings and root death and abscission and bulb rot on mature onions. The average onion crop loss caused by basal rot has been up to 10% in conventional farming and as high as 30% in organic farming. In this study, a seedling assay was conducted to test the virulence of different Fusarium isolates on a commercial onion cultivar. The study goals were, primarily, to find out which of the Fusarium isolates, originating from onion and crop rotation plants grown in Finland, are pathogenic, and secondly, to compare the virulence of different isolates. Altogether 115 Fusarium isolates were tested for virulence on onion seedlings in a greenhouse. Fifty-five of the tested isolates of F. oxysporum, F. proliferatum and F. redolens were more or less virulent. 19.4% of F. oxysporum isolates, 35.3% of F. proliferatum isolates and 18.2% of F. redolens isolates showed high virulence. Among the aggressive pathogens isolated from onion samples, F. oxysporum f.sp. cepae is still the dominant onion pathogen, F. proliferatum is a new pathogen on onion in Finland, and relatively more aggressive than F. oxysporum. The F. solani and F. tricinctum isolates tested did not have any detrimental effects on the onion seedling health or growth. In order to control FBR in Finland, avoiding planting onion in the infested soils, growing onions from local seedlings to avoid new contamination and storing onions at cold temperatures are recommended.
  • Xhelilaj, Kaltra (2021)
    Potyviruses are positive-sense single-stranded RNA viruses that can alter several functions of their host plants and consequently, cause significant economic losses in the infected crop plants. During the viral infection, the host transcriptome changes. Stress related genes are triggered, and genes allowing for susceptibility are target for viral-induced modifications. Therefore, in this study, we investigated whether the expression of potential proviral genes SUO1, AGO1, and the major antiviral player AGO2 change in Nicotiana benthamiana (N. benthamiana) in response to potato virus A (PVA; genus Potyvirus) infection. Moreover, we aimed to determine whether helper component protease (HCPro) and active replication have a role in the transcriptional regulation of these genes. Leaves infected with PVA tagged with Renilla luciferase were collected at 3, 6, and 9 days postinoculation, and the viral gene expression was quantified with a dual-luciferase assay. Total RNA was isolated, cDNA was synthesized, and samples were analyzed through qPCR. BLAST hit results revealed that N. benthamiana has three homologs of the SUO1 gene. qPCR data showed no significant change in neither the expression of SUO1 homologs nor the expression of AGO1 during wild-type PVA infection. Moreover, the lack of HCPro or viral replication did not affect the expression of these genes. On the other hand, the expression of AGO2 was approximately 6 and 5 fold up-regulated at 6 and 9 days post-inoculation, respectively. In contrast with the wild-type PVA infection, the mutated viruses had a pronounced effect on AGO2 transcripts at 3 days post-inoculation. Replication-deficient viral RNA increased AGO2 expression circa four-fold, followed by the HCPro-deficient viral RNA increasing expression circa two-fold. AGO2, the major player involved in antiviral defense, was up-regulated during the wild-type infection. Active viral replication and functional HCPro played a role in AGO2 regulation. However, Agrobacterium infiltration can be accounted for interfering with the interpretation of the AGO2 results. Although SUO1 and AGO1 may be potential genes allowing for susceptibility, this study revealed that the PVA infection does not affect the mRNA expression of these genes. Furthermore, it is concluded that active HCPro and viral replication do not have a role in the expression of these genes on mRNA level. To have a clearer view, integrating small RNA, mRNA, and protein quantification analysis of SUO1 homologs will be necessary. Keywords
  • Gauranvi (2021)
    It is important to study the factors which inhibit the cultivation of major crops which serve as a source of food and feed, with various other medicinal values as well. One of these factors is soil degradation and infertility which could be due to high amounts of toxic elements or unfavourable pH conditions. Faba bean is one such crop and is widely affected by the acidity and aluminium toxicity in soil. In this study, an effort has been made to observe the varying tolerance of faba bean accessions and understand the underlying mechanisms used by them under stress conditions. The accessions selected were Aurora, Babylon and Kassa. Each accession was subjected to three treatments and were grown in pH 7 (control), pH 4.5 (acid treatment) and pH 4.5 + Al3+ (aluminium treatment). The pH of peat for acidic treatment was reduced to 4.5 using Sulphuric acid (H2SO4) and for aluminium treatment, Aluminium sulphate (Al2(SO4)3) was added in addition to the acid. At 16 Day after Sowing (DAS) and 30 DAS the physiological data was collected which comprised of chlorophyll concentration (SPAD value), stomatal conductance, leaf temperature and photosynthesis rate. At 35 DAS, the experiment terminated and the shoot data (fresh and dry weights of leaves and stem; and leaf area) of each plant was recorded. Then the root data (tap root length, quality and quantity of nodules and photographs of roots) was taken for each plant. ICP samples for peat, shoot and shoot were also analysed. The data collected were subjected to analysis of variance using R version 4.0.3. (means separated by 5% significance level). From the plant data, Aurora was found to be tolerant. Kassa was sensitive (especially the roots) and Babylon was sensitive to both acid and aluminium treatments. The ICP results provided the reason for this tolerance pattern and a higher concentration of elements needed for plant growth such as P and S were found to be higher in aluminium and acid treatments.
  • Lipping, Sanna (2021)
    Kaivannaisfosfori on merkittävin fosfaattilannoitteiden lähde maailman maataloudessa. Fosforia on kuitenkin rajallinen määrä maapallolla ja kaivannaisfosforin varannot uhkaavat ehtyä 50-500 vuoden aikana. Maailman maatalous joutuu sopeutumaan tulevaisuudessa kaivannaisfosforin vähenemiseen, jolloin fosforin talteen saaminen erilaisin kierrätysmenetelmin tulee olemaan merkittävä kiertotalouden osa. Kierrätyslannoitteiden mahdollisuuksia on yleisesti tutkittu viime aikoina paljon, mutta niiden vaikutusta kauran fosforin ottoon on tutkittu melko vähän. Tämän tutkimuksen tarkastelun kohteena oli kauran (Avena sativa. L Obelix) fosforin otto vuosina 2017 ja 2018 Uudellamaalla sijaitsevalla koelohkolla. Tutkittavina kierrätyslannoitteina olivat lihaluujauho, matokomposti, mädätejäännös ja ammoniumsulfaatti. Kontrollina tutkimuksessa olivat väkilannoiteruutu sekä lannoittamaton ruutu. Koepellon lannoitushistoria oli suomalaisittain tyypillinen ja pellon fosforitaso oli tutkimuksen alkuvaiheessa luokiteltu hyväksi tai korkeaksi. Vuoden 2017 kasvukausi oli pitkäaikaiseen keskiarvoon (1981-2010) nähden kylmä ja sateinen, kun taas vuosi 2018 oli erityisen lämmin ja kuiva. Tämän tutkimuksen perusteella näillä kierrätyslannoitteilla ei ollut merkitsevää eroa kauran fosforin ottoon kumpanakaan vuonna verrattuna väkilannoitteeseen tai lannoittamattomaan käsittelyyn. Merkitsevä ero näkyi kuitenkin vuoden 2017 fosforin otossa lihaluujauhon ja mädätejäännöksen välillä (p=0,0159 vertailussa lannoittamattoman käsittelyn ja p=0,0206 vertailussa väkilannoitekäsittelyn kanssa). Maaperän fosforitaseissa ei havaittu merkitseviä eroja käsittelyiden välillä. Kierrätyslannoitekäsittelyiden välillä havaittiin merkitsevä ero niiden vaikutuksessa maaperän pH-arvoon (p=0,045 vertailussa lannoittamattoman ruudun ja p=0,036 vertailussa väkilannoitekäsittelyn kanssa) vuonna 2018. Tukeyn HSD-testissä ei kuitenkaan tapahtunut jakaantumista eri alajoukkoihin. Koepellon ennestään hyvä ravinnetilanne on voinut vaikuttaa kokeessa tasaamalla eroja eri käsittelyiden välillä.
  • Taniwan, Steven (2020)
    Norway spruce is commonly cultivated throughout Europe, Russia, and Japan. Cultivation of Norway spruce often faces the issue of fungal diseases, one of which is cherry rust disease caused by Thekopsora areolata. The gene model MA_10g0010 encoding an uncharacterized peroxidase (PabPrx86) has previously been associated with the presence of this pathogen. The aim of this study was to describe and assay the protein produced from this gene model, observe its localization in the cell, and determine its relative expression level in different tissues of Norway spruce. Experiments were performed by isolating the full length cDNA for PabPrx86 and cloning the cDNA into destination vectors pEAQ-HT-DEST1 and pK7FWG2 leading to a hypertranslatable transcript and a C-terminal GFP fusion, respectively. The plasmid constructs were transformed to Agrobacterium tumefaciens and agro-infiltrated to Nicotiana benthamiana. In addition, the relative expression level of this gene in different spruce tissues at different times of the year was determined using the qRT-PCR method. Sequencing showed that there were two allelic variants of this gene in the spruce individual sampled for RNA. Results showed that both alleles code for a peroxidase with basic pI. Subcellular localization with the GFP tag detected that PabPrx86 protein was located out of cytoplasm, indicating that the protein was translated in the ER-ribosomes, whereas relative expression level analysis revealed that PabPrx86 was highest expressed in the bud and lateral bud in June. Peroxidases are known to relate with plant defense, but further experiments are required to determine the role of PabPrx86 in Norway spruce and what the association with T. areolata means.
  • Ghimire, Sadikshya (2021)
    Fusarium proliferatum has recently become a major threat to onion, which is an important food crop for food security and has a significant role in the agricultural sector. This fungus is found causing rots and producing mycotoxin fumonisin that, if ingested, can cause carcinogenic effects in humans and fatal diseases in animals. F. proliferatum has been identified as a pathogen causing rots and wilts in many plants in several countries, and recently some isolates of this pathogen were also found in Finland causing basal rot in onion. Though F. proliferatum has wide adaptability and pathogenicity, there are research gaps on this newly emerging pathogen, which is mostly limited to some specific hosts such as maize. There is a lack of knowledge of its infection mechanisms and mycotoxin production dynamics in onion. This experimental work was conducted at the University of Helsinki, Finland, to study the nature of pathogenicity and toxin gene expression of F. proliferatum in laboratory conditions as a function of time. Spore suspensions of three isolates of F. proliferatum, Fpr047, Fpr049, and Fpr919, were prepared and used as inoculums that were injected into healthy organically grown onions, which were then stored in dark for five weeks. Control bulbs were inoculated with sterile water. Pathogen virulence, based on symptom development, and fungal colonization in the onion tissues were determined at five different time points and the toxin gene expression was determined at three time points. Colonization levels were determined by real-time PCR using primers binding to the intergenic spacer (IGS) region of F. proliferatum. A part of the IGS region of the three isolates was sequenced to study the diversity between the isolates. All the tested isolates were found to be virulent, and they colonized the onions after one week from inoculation. However, the isolate Fpr919 appeared different from the other two in terms of symptom severity. It was more aggressive than the other two, causing disease symptoms earlier and causing more severe rot symptoms in the infected bulbs. It also had nucleotide sequence variations in the IGS region in comparison with the other two isolates, suggesting genetic diversity. No significant differences were observed between the isolates in the fungal colonization levels. Expression of FUM1 gene and a putative virulence gene SIX2-1 was detected by RT-RT-PCR in most of the infected tissue samples. The results obtained signify that F. proliferatum is a pathogen with the potential of producing fumonisin toxin in onion, suggesting the need for further molecular study on this fungus to control the disease and prevent mycotoxin contamination in plant products.
  • Rehman, Attiq ur (2020)
    Wheat (Triticum aestivum L.) is one of the major crops in the world and an important agricultural commodity in Finland with various uses. Fusarium head blight (FHB) is a deadly disease of cereal crops and with the gradual increase in temperature and precipitation, it is becoming alarming to Finnish agriculture. Deoxynivalenol (DON) is a vomitoxin produced by Fusarium graminearum species during the FHB infection and is hazardous to health if taken in larger quantities by humans and animals. European Union has legalized the maximum allowed DON content in wheat flour for human consumption at 1.75 ppm. Various types of resistance against FHB are known till date, including tolerance and escape from the disease. Anther extrusion (AE) is a highly heritable trait in wheat and is mechanistically involved in resistance against FHB by preventing the availability of nutrients for the fungus. Other traits such as heading, maturity, and height have shown correlations with FHB incidence and severity in previous studies. Genomic information is crucial to identify markers to accelerate wheat breeding programs against FHB. This experiment was conducted at Boreal Plant Breeding Ltd. Finland using 198 spring wheat breeding lines in a row-and-column design with three replications in an artificially spawn-inoculated F. graminearum field. The goal of the project was to evaluate the genetic diversity for various agronomic and FHB-resistance traits and to estimate correlations among them. A genome-wide association study was also performed by using 11,987 SNP markers to investigate any marker-trait association(s) in the spring wheat breeding germplasm. Larger phenotypic variability was observed in both agronomic and FHB-resistance related traits. Many spurious associations were found with general linear models (Naïve and Q model). No marker-trait associations were observed among the traits in mixed linear model (K) after including kinship as a covariate. Cryptic relatedness among breeding lines has shown a significant role during association mapping. An unexpected negative correlation was found between DON and Fusarium severity indicating inaccuracies in phenotyping. A negative phenotypic and genotypic correlation was found between AE and DON. Future studies on the validation of AE as a phenotypic marker against DON accumulation is recommended. Repeating the experiment with the inclusion of more lines with Fhb1 gene in homozygous state might be helpful in finding reliable associations for FHB-resistance related traits.
  • Delemme, Romain (2021)
    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.
  • Salovaara, Anna-Kaisa (2019)
    Jääsalaattia (Lactuca sativa var. crispa L.) tuotetaan ympärivuotisesti kasvihuoneessa ja se on kuluttajien keskuudessa suosittu lehtivihannes. Jääsalaatti kerää monien muiden lehtivihannesten tapaan nitraattia ja sen nitraattipitoisuudet voivat nousta melko suuriksikin. Jääsalaatin nitraattipitoisuuteen vaikuttavat useat eri tekijät, kuten laji, lajike, lannoitustaso ja valon intensiteetti. Tehokkailla nitraattipitoisuuden hallintakeinoilla voidaan parantaa tuottajan mahdollisuuksia vaikuttaa sadon laatuun. Valtaosa ravinnon mukana saatavasta nitraatista on peräisin lehtivihanneksista. Euroopan unioni on asettanut katteen alla kasvatetun salaatin nitraattipitoisuudelle talvi- ja kesäkauden raja-arvot. Nitraatti on ihmisen terveydelle haitallinen yhdiste, sillä osa siitä muuttuu elimistössä nitriitiksi, mikä kasvattaa etenkin pienten lasten methemoglobinemian riskiä. Glysiinibetaiini on osmolyytti ja solun metabolian kanssa yhteensopiva yhdiste. Monet viljelykasvit syntetisoivat glysiinibetaiinia vasteena abioottisille stresseille ja se parantaa kasvien stressinkestävyyttä myös eksogeenisesti annettuna. Glysiinibetaiinia saadaan ravinnon mukana esimerkiksi viljatuotteissa ja se on ihmisille turvallinen yhdiste, jota voidaan käyttää myös ravintolisänä. Glysiinibetaiinia eristetään muun muassa sokerijuurikkaan melassista ja sitä voidaan käyttää orgaanisena lannoitteena tai kasvunedistäjänä kasvintuotannossa. Tämän tutkimuksen tavoitteena oli selvittää glysiinibetaiinin käyttömahdollisuuksia jääsalaatin tuotannon edistäjänä. Kasvihuonekokeessa seitsemän vuorokautta kestänyt glysiinibetaiinikäsittely aloitettiin jääsalaattien ollessa 29 vuorokauden ikäisiä. Glysiinibetaiinikäsittelyjen pitoisuudet olivat 0, 1, 7,5 ja 15 mM. Jääsalaatin nitraattipitoisuus, glysiinibetaiinipitoisuus sekä tuore- ja kuivamassa määritettiin 24, 29, 36, 41 ja 49 vuorokauden ikäisistä kasveista. Tutkimus toteutettiin kiertovesiviljelyjärjestelmässä ja glysiinibetaiinikäsittely annettiin ravinneliuoksessa. Jääsalaatit ottivat eksogeenisesti annettua glysiinibetaiinia. Glysiinibetaiinikäsittely pienensi jääsalaatin nitraattipitoisuutta seitsemän vuorokauden käsittelyn jälkeen merkitsevästi kontrolliin verrattuna ja alenema oli suoraan verrannollinen käsittelyn pitoisuuteen. Lisäksi glysiinibetaiinikäsittely pienensi jääsalaatin tuorepainoa ja suurensi kuiva-ainepitoisuutta. Määrityksissä myös jääsalaatin glysiinibetaiinipitoisuuden havaittiin olevan suoraan verrannollinen käsittelyn pitoisuuteen.
  • Haarala, Jaakko (2020)
    Ilmastonmuutos tuo mukanaan Suomeen äärioloja, jotka lisäävät typen huuhtoutumista, mutta myös mahdollisuuksia pidempinä ja lämpimimpinä kasvukausina. Viimeisen kahdenkymmenen vuoden aikana lajikejalostus ei ole kuitenkaan lisännyt käytännön satotasoja, vaan sadot ovat jopa taantuneet. Laskeneet satotasot eivät selity pelkästään laskeneilla typpilannoitustasoilla, ja satokuilua onkin lähdetty ratkaisemaan monimuotoisemmalla viljelykierrolla, joihin sisältyy esimerkiksi härkäpapua. Tutkimuksen tavoitteena oli selvittää esikasvina toimineen härkäpavun (Vicia faba L.) vaikutusta maaperän liukoisiin typpivaroihin ja seuraavien viljelykasvustojen typpidynamiikkaan. Tutkimus toteutettiin Haltialan pellolla satunnaistettuna täydellisten lohkojen kerrannekokeena, jossa käsittelynä oli yhteensä kuusi kasvia ja neljä lannoitustasoa. Kasvustoista mitattiin lehtivihreäpitoisuus, lehtialaindeksi (LAI) sekä määritettiin kuiva-aineen kehittyminen ja koeruuduista otettiin maanäytteet vähintään viidesti kasvukauden aikana. Biomassamääritysten pohjalta analysoitiin kasvinosien typpipitoisuudet ja laskettiin typpisadot. Maanäytteet uutettiin (2M KCl) NH4+- ja NO3--N-pitoisuuksien määrittämiseksi. Kasvustojen typpidynamiikkaa (NUE, UPE, UTE, NHI), typpisatoja ja koeruutujen mineralisaatiota sekä mineraalityppipitoisuuksia vertailtiin lannoitus ja esikasvi taustatekijöinä. Lämmin ja kuiva kasvukausi viivästytti kasvustojen sulkeutumista ja epätasaisuus vaikutti tuloksiin enemmän kuin esikasvi tai lannoitus. Lannoittamattomat kasvustot eivät eronneet tilastollisesti biomassaltaan tai typenotoltaan lannoitetuista. Kasvien typenotto vaikutti enemmän maaperän NO3--N kuin NH4+-N-pitoisuuksiin. Härkäpapuesikasvi lisäsi kauran lehtialan kestoa (LAD). Laskennallinen mineralisaatio oli suurin nollalannoitusruuduissa, keskimäärin 127 N kg ha-1. Kasvustojen UPE, UTE ja NUE jäivät pieniksi maan pintahorisontin ollessa lakastumisrajalla koko kesän. Härkäpavulla on hyvin todennäköisesti vaikutusta maan typpivaroihin, mutta tarkemmat arviot vaativat syvemmälle maahan ulottuvia mittauksia ja edullisemman kasvukauden.