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(2023)Täsmäviljelyn yleistyminen on lisännyt tarvetta maaperän spatiaalisen vaihtelun kartoittamiselle, ja tämän myötä markkinoille on tullut erilaisia maaperäkartoitusmenetelmiä. Tämän tutkimuksen tavoitteena oli selvittää, pystytäänkö gammasäteilyn mittaamiseen perustuvalla SoilOptix-maaperäkartoitusmenetelmällä estimoida pellon sisäistä pH-arvon, helppoliukoisen fosforin sekä mangaanin vaihtelua. Tutkimus toteutettiin Forssassa sijaitsevalla peltolohkolla, jossa yhteensä 48 mittauspisteen maa-analyysituloksista ja SoilOptix-menetelmän pistemäisistä estimaateista tehtiin korrelaatioanalyysejä ja pistekaavioita. Myös gammasäteilyraakadatan toistettavuutta havainnoitiin visuaalisesti. Työn toinen tavoite oli selvittää, vähensikö peltolohkolle tehty täsmäkalkitus pellon sisäistä satovaihtelua ja ravinnevaihtelua. Tämän selvittämiseksi analysoitiin puimurin satokartoitusaineistoja vuoden 2020 kevätrapsin (Brassica napus ssp. oleifera (Moench) Metzg.) ja vuoden 2022 kevätvehnän (Triticum aestivum L.) puinneista. SoilOptix-menetelmällä ei pystytty estimoida peltolohkon sisäistä vaihtelua minkään koejäsenen osalta. Kalkitus ei oleellisesti vähentänyt peltolohkon sisäistä satovaihtelua, mutta ravinnevaihtelua se vähensi. Eri vuosien gammasäteilyn raakadatassa oli samankaltaisuuksia visuaaliseen havainnointiin pohjautuen. Syyt heikkojen korrelaatioiden taustalla eivät ole ilmeiset, ja ne vaatisivat lisätutkimusta. Erityinen kiinnostuksen kohde olisi menetelmässä kerätyn raakadatan lukuarvot, joita ei tässä tutkimuksessa saatu tarkastella. Johtopäätöksenä todetaan selvä lisätutkimuksen tarve menetelmälle.
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(2018)The Khwe San, the residents of Bwabwata National Park (BNP), were hunter-gatherers who used to acquire their food by hunting and collecting veld food in the past. However, they are not allowed to practice their traditional methods anymore due to the status of the park as a national park and the army trying to prevent increased poaching in the bush. Nowadays they are highly dependent on food aid provided by the Namibian government. In addition, small-scale subsistence agriculture is practiced but due to drought and wild animals, harvests are insufficient to meet required food demand on a daily basis. The objective of this research was to investigate gardening opportunities of the Khwe San in the Eastern part of BNP. The data were collected through semi-structured interviews with 38 respondents and several stakeholders. Four different groups were found which were home gardeners, community gardeners, participants of gardening workshop and non-gardeners. The data were analysed using a thematic content analysis, a SPPS statistic programme and a sustainable rural livelihoods framework. In addition, one positive deviance gardener was selected, and his production methods is described in more detail. The main results highlighted the importance of having gardens. All the respondents indicated that gardening is important or very important in terms of food production and income generation. However, the majority of the residents are willing to have home gardens due to the challenges of community gardens in the past e.g. the lack of cooperation, jealousy and stealing as well as the lack of needed goods. Current challenges are that there are only one or two water sources in each village and the distances from the boreholes to gardens are long, which complicates irrigation. In addition, poor fences and lack of seeds and tools are the major challenges that home gardeners face. Future training should include specific things because the interviews showed that the general gardening knowledge is presented. As a conclusion, the focus of gardening should be on home gardens, not on community gardens due to their challenges. However, in order to make gardening sustainable, several activities need to be addressed, including an active agriculture extension officer for monitoring, training on specific things and seed distribution provided by the government. In addition, the gardening support needs to be aimed to dedicated people who are willing to practice gardening
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(2018)Syftet med avhandlingen var att med statistiska metoder utreda ifall, och i så fall hur och hur kraftigt LIR-gårdarnas gårdsarealer påverkar dess lönsamhet. I den första delen undersöktes hur gårdens nettovinst per hektar i medeltal påverkas av gårdsarealen. I den andra delen undersöktes hur styckkostnaden för vårvete, maltkorn, vårraps och havre påverkas av gårdsarealen. Dessutom jämfördes gårdsarealens påverkan på lönsamheten med andra variablers påverkan för att ge proportioner åt fenomenet. Enligt teorin om stordriftsfördelar skulle styckkostnaderna sjunka till följd av att företagets storlek växer. Vid en viss storlek har alla fördelar utnyttjats och styckkostnaden börjar stiga igen då företaget växer ytterligare. Kurvan som beskriver styckkostnaden i förhållande till företagets storlek kallas för LRAC-kurvan och vanligtvis antar den en U- eller L-form beroende på hurudana stordriftsfördelar det finns att utnyttja. Materialet bestod av LIR-gårdarnas ekonomiska resultat för åren 2006 till och med 2015. LIR står för lantbrukssällskapets individuella rådgivning och är en rådgivartjänst som erbjuds av Nylands svenska lantbrukssällskap åt växtodlingsgårdar i Nyland. Det totala antalet observationer var 602. Metoden som användes var multipel linjär regressionsanalys. Som estimator användes OLS och WLS. Med hjälp av denna metod estimerades modeller som förklarade nettovinsten per hektar och styckkostnaden för tidigare nämnda grödor med bl.a. gårdsarealen som oberoende variabel. Regressionsanalyserna erhöll relativt höga förklaringsgrader. Den L-formade LRAC-kurvan visade sig passa bäst för det undersökta materialet. Gårdsarealen hade en signifikant inverkan på den beroende variabelns variation i fyra regressionsanalyser av fem. De andra variablerna förutom gårdsarealen som ingick i regressionsmodellerna verkade också signifikant påverka den beroende variabeln. Sammanfattningsvis innebär undersökningens resultat att gårdsarealen inverkar signifikant positivt på lönsamheten. Det förekommer inte heller starka antydningar om att det förekommer stordriftsnackdelar på de undersökta gårdarna. Däremot verkar odlingsgrödan göra skillnad ifall det finns stordriftsfördelar att utnyttja eller inte. Det kunde också konstateras att andra variabler har en större betydelse för lönsamheten än vad gårdsarealen har.
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(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.
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(2020)Usp45 is the major secreted protein in Lactococcus lactis. Protein’s 27-aa signal peptide (SPUsp45) is widely used for increased secretion and improved yields of heterologous proteins. L. lactis, previously used mainly in food production, has gained increasing popularity in gene technology and, thanks to extensive research, became a Gram-positive model organism alongside Bacillus subtilis. Despite the widespread use of its signal peptide, the biological role of Usp45 protein remains largely a mystery. The aim of this study was to test whether decreased translation of the naturally highly secreted Usp45 protein would lead to improved secretion of desired heterologous proteins. The hypothesis was that high levels of secreted Usp45 cause the Sec translocon becoming a bottleneck and by reducing this strain on the secretion route, the capacity to secrete other proteins could increase. Based on literature, usp45 is not part of the L. lactis core genome and was assumed to be non-vital. To study this, the L. lactis strain NZ9000 was transformed with the plasmid pLEB805 which contains a nisin inducible antisense-usp45 gene (ASusp45) resulting in strain LAC455. The effect of antisense-RNA mediated silencing on growth and morphology of the cells was observed as well as the changes in quantity and quality of secreted proteins in ASusp45 induced cells. The secretion of heterologous proteins was tested with bacteriocins leucocin A and C that were introduced to the cells in expression vectors. This study brought new information on the function of the usp45 gene in L. lactis. The results show that the silencing of the usp45 gene leads to retarded growth rate, multifold ingrowth of the cell wall, aggregation of the cells and the leakage of cytoplasmic proteins leading to loss of viability of the cells. These results demonstrate that Usp45 is vital for the structure of the cell wall, cell separation and normal chain formation, and it probably acts as a vital peptidoglycan hydrolase.
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(2018)Cereal β-glucan, or (1→3)(1→4)-β-D-glucan, has unique viscous and gelling properties, which are related to its physiological effects. The increased viscosity in human gastrointestinal tract by β-glucan is considered a key factor for its health benefits. However, the possible gelling ability of β-glucan in human intestine and its relation to the physiological functionality have not been investigated. The aims of this study were to investigate the possible structure formation of β-glucan at physiological conditions and to understand gelation difference between oat and barley β-glucan (OBG and BBG, respectively). Additionally, the effects of phytate and molecular weight (MW) on structure formation of β-glucan were studied. Oat (ROBG14, ROBG22) and barley bran concentrates (RBBG18) were used for in vitro studies in upper gut model. OBG14 was extracted from oat concentrates and used for further producing phytate-removed OBG (PR-OBG) or enzymatically degraded OBG (ENZ-OBG). The effect of phytate or molecular weight on gelation of beta-glucan was studied by comparing the gelation of PR-OBG or ENZ-OBG to OBG14 after 2 h and 1 d. The effect of β-glucan source was studied with medium viscosity oat (MOBG) and barley (MBBG) β-glucan with same molecular weight and concentration on day 1 and day 4. The extracted samples were first dissolved at physiological T 37°C for 2 h and the gel properties of the samples were measured with oscillatory measurements. OBG showed more structure formation than BBG at low concentrations in both studies with in vitro digestion model and extracted β-glucan samples at physiological temperature. In vitro RBBG18 (β-glucan content of the in vitro extract 0.6%) showed liquid-like behavior and no hysteresis obtained, indicating no structure formation. ROBG14 (β-glucan content 0.5%) and ROBG22 (β-glucan content 0.6%) showed entangled network, with similar crossover frequencies, 0.07 and 0.1 Hz, respectively. 1.5% MOBG showed liquid-like behavior on day 1, but storage modulus (G’) increased during storage. The undissolved particles in watery medium of MBBG indicated 37°C was not enough for partial dissolution which could lead to gel. At the same concentration (1%), both PR-OBG and OBG14 showed weak gel structure, with slightly higher G’ in PR-OBG. This indicated that phytate is not the reason for better gelation of OBG than BBG, which was hypothesized due to higher residual phytate in OBG than BBG. ENZ-OBG (0.7%) had lower G’ than OBG14 (0.7%), which indicated more structure formed in higher MW OBG at 2 h. To conclude, OBG is more prone to structure formation than BBG at physiological conditions. Phytate was not the reason for better gelation of OBG than BBG.
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(2023)The current trend in the food and forest industries is to utilize sustainable and renewable products. One such product is galactoglucomannans (GGM), water-soluble hemicelluloses covering 25–35 % of the dry wood mass. GGM can be extracted from spruce sawdust or branches using a safe and environmentally friendly pressurized hot water extraction (PHWE) method. Deacetylation of GGM happening during extraction and concentration by membrane filtration at alkali conditions possibly enables gel formation. This thesis aims to observe if low acetyl GGM has the ability to form a gel and which factors have an impact on its gelation and gel properties. Low acetyl PHWE GGM powders were provided by the Natural Resources Institute of Finland (Luke). The GGM solutions at different pH values (4, 7, and 10) and solid concentration levels (5, 10, and 15 %) were prepared using a magnetic stirring rod and then ultrasonicated (50% amplitudes for 5 min). Viscosity, rheological properties, water holding capacity (WHC), hardness, and adhesiveness were measured on days 1, 2, 3, and 5 during storage at room temperature (22 °C). The results showed that GGM was able to form a gel at all investigated conditions, except for the samples at pH 4 and a solid concentration of 5 %. GGM solutions at high pH (7–10) and solid concentrations (10–15%) formed gels without ultrasonication. All GGM gels had high WHC (≥ 90 %). Gel viscosity increased with prolonging of storage time and increased solid concentration. The frequency sweep analyses showed that all investigated samples had a gel-like behavior. Gel hardness and adhesiveness increased in all the samples during storage and increased solid concentration. The thesis demonstrated that low acetyl GGM could form a gel, which could be used as a gelling agent, where solid concentration and pH impacted to gel structure. Thus, the study could widen industrial applications of GGM or at least engage interest.
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(2012)The literature review describes the characteristics, uses and probiotic potential of propionibacteria and gives an overview of proteomic methods focusing on 2-DE studies related to probiotic bacteria and P. freudenreichii. The aim of the experimental part was to use 2-DE to obtain proteome maps of two strains of P. freudenreichii and detect inter-strain differential protein expression. The influence of a number of parameters on the quality of 2-D gels was also investigated. The pH 3-7 and pH 3-11 NL proteome maps obtained displayed 305 and 356 spots, respectively, and detected the differential expression of 60 and 72 spots, respectively. The 3-11 NL proteome map showed spot over-crowding in the pH 4-6 region. Addition of 50 mM dithiothreitol (DTT) to the samples prior to isoelectric focusing (IEF) and an increase of IPG buffer concentration greatly improved spot resolution. Silver staining achieved higher spot counts than Coomassie staining. The influence of the number of lysis cycles on protein extraction was marginal, while lower protein sample loads produced superior 2-D gels. Results show that data from 2-DE proteome maps can provide an overview of inter-strain differential protein expression in P. freudenreichii. The optimal 2-DE experimental setup would include pH 4-7 IPG strips, a low protein load and inclusion of DTT in the IEF sample, as well as silver staining for spot visualisation.
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(2017)Gender diversity in the workforce describes the equal representation of men and women in terms of ratio. Raising importance of the concept due to changing societal norms has allowed researchers to explore the mostly positive effect gender diversity, especially in leadership level, has on a company’s performance. Despite all the benefits, women in the forest-based sector are still underrepresented. This study aims to understand the underlying reasons for female underrepresentation in the forestry sector and to identify solutions to improve the situation. The study explored the barriers and enablers that hindered or supported female career development in the forestry industry and investigated possible solutions in light of sector’s future goals. In-depth elite interviewing was selected as the method of data collection. Ten interviews with senior level female leaders of seven forestry companies in Finland and Sweden were conducted face-to-face or over the phone. The qualitative content analysis of data identified most common barriers faced by women in their careers: a) discrimination, exclusion, and stereotyping due to masculine company culture, b) balancing work and family due to inflexible working hours and lack of remote work possibilities. Moreover, it recognised the importance of competence development and support systems as the enabling aspects of women careers in the industry. In addition to further understanding gender effect in the forestry sector, the study allowed to look into the future of the sector through the eyes of female leaders. The findings of the study are in line with previous research that identified the career advancement barriers and enablers in other industries. However, culture-specific issues posing a challenge to female career development and promoting exclusion, such as sauna and hunting traditions, were identified. Additionally, the importance of a personal support system was highlighted in the study. The critical role of the forestry sector and the bioeconomy in the sustainable global future was recognised by all study participants. The ability of forestry companies to adapt to future needs and to become a part of modern society will require them to rethink old concepts, modernise the image and allow for a more diverse company culture to foster in all organisational levels.
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(2007)Virusinduced gene silencing (VIGS) vectors based on tobacco rattle virus (TRV) are now widely used for characterizing the function of plant genes. However, previous TRV vectors using RNA2 to carry the targeted gene sequence had difficulties to induce gene silencing on some plant species (Gerbera hybrida etc.) due to the obstacle of RNA2 movement. To achieve efficient gene silencing in those species, it is necessary to develop new TRV vectors, in which the targeted gene will be included in TRV RNA1 and the 16K gene will be replaced. Based on TRV RNA1, two new VIGS vectors M1 and M2 were developed through deletion part of 16K gene. Another mutant 16Kstop was also constructed to carry an early terminator in the 4th codon of 16K gene. The infectivity and gene silencing efficiency of the new constructs were assessed through a series of infection experiments. It was found that the infectivity of M1 and M2 was lower than wild TRV RNA1. M1 and M2 could induce PDS gene silencing on Nicotiana benthamiana, but their gene silencing efficiency was limited as compared with previous TRV VIGS vectors in which the PDS gene fragment was contained in RNA2. We also found that the 16K gene sequence, rather than the 16K protein, was required for efficient virus movement and accumulation.
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(2019)Mycosporines and mycosporine-like amino acids (MAAs) are small-molecules that provide UV protection in a broad range of organisms. Cyanobacteria produce a diverse set of MAA chemical variants, many of which are glycosylated. Even though the biosynthetic pathway for the production of a common cyanobacterial MAA, shinorine, is known, the biosynthetic origins of the glycosylated variants remains unclear. In this work, bioinformatics analyses were performed to catalogue the genetic diversity encoded in the MAA gene clusters in cyanobacterial genomes and identify a set of enzymes that might be involved in MAA biosynthesis. A total of 211 cyanobacterial genomes were found to contain the MAA gene cluster, with six containing glycosyltransferase genes within the gene cluster. Afterwards, 38 strains from the University of Helsinki Culture Collection were tested for the production of MAAs using QTOF-LC/MS analyses. This resulted in the identification of several novel glycosylated MAA chemical variants from Nostoc sp. UHCC 0302, which contained a 7.4 kb MAA biosynthetic gene cluster consisting of 7 genes, including two for glycosyltransferases and one for dioxygenase. Heterologous expression of this gene cluster in Escherichia coli TOP10 resulted in the production of a glycosylated porphyra-334 variant of 509 m/z by the transformant cells, showing that colanic acid biosynthesis glycosyltransferases can catalyse the addition of hexose to MAAs. These results suggested a biosynthetic route for the production of glycosylated MAAs in cyanobacteria and allowed to propose a putative role for dioxygenases in MAA biosynthesis. Further characterization of additional glycosyltransferases is necessary to improve our understanding of glycosylated MAA biosynthesis and functionality, which could be applied to large scale processes and be used in industrial applications.
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(2012)Class IIa (pediocin-like) bacteriocins are a major group of bacteriocins produced by lactic acid bacteria (LAB) characterised by their antilisterial activity. As a protective LAB strain for meat products, Leuconostoc carnosum 4010 kills Listeria by producing two class IIa bacteriocins, the well characterised leucocin A (LeuA) and the less studied leucocin C (LecC). Although the amino acid sequence of the secreted LecC has been published, the genes required for its production remain unknown. The aims of this study were to characterise the genes needed for LecC production and to express the lecC gene in Lactococcus lactis. The lecC gene was localised by Southern blot in a large plasmid different from the one harbouring LeuA genes in Ln. carnosum 4010 genome. Five genes in two operons were identified mainly by PCR-based methods and sequencing, namely, the structural gene (lecC) with a 72-bp signal sequence, the immunity gene (lecI) encoding a 97-aa immunity protein, two genes lecTS for an ABC transporter and the gene lecX for an accessory protein. The immunity function of LecI was demonstrated by expressing the lecI gene in LecC sensitive Listeria monocytogenes. Compared to the wild type, LecI-producing Listeria was more tolerant to LecC, thus corroborating the immunity function of LecI. For heterologous expression of LecC, the lecC gene was fused to the lactococcal usp45 signal sequence in the nisin-selectable and nisin-inducible food-grade secretion vector pLEB690. Consequently, bioactive LecC was secreted efficiently by the recombinant Lc. lactis. In conclusion, novel genes for the production of LecC in Ln. carnosum 4010 were identified. The findings indicate that LecC is produced by a dedicated system independent of LeuA. The successful production of functional LecC in Lc. lactis offers an attractive approach for the future application of bacteriocins in food production.
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(2009)Genetic composition of Theobroma cacao L., including 60 Nicaraguan farmers accessions, was investigated using nine microsatellite (SSR) markers. Fourteen breeders accessions from Experimental Center “El Recreo”, INTA, Nicaragua, two Criollos accession from CATIE, Costa Rica, and two accessions from Ecuador were included as reference material. The average PIC value (0.78) indicated a high power of discrimination for the nine loci used. A total of 155 alleles were detected at the nine loci. The number of alleles per marker ranged from 10 to 22 with a means of 17.22 alleles per locus. A heterozygosity deficiency (HExp < HObs) was registered for all microsatellite loci. The average expected heterozygosity was=0.68 among Nicaraguan farmers accessions. The Analysis of molecular variance (AMOVA) showed a low level of differentiation among populations. The genetic distances determined for the groups of farmers accessions RAAS and Pacifico Sur are closely similar, while a great genetic distance was observed between RAAN and RAAS groups. The cluster analysis presented a strong genetic relation between the Criollo 13 from CATIE and farmers accession MAT0404. The principal component analysis showed that 7 farmers accession from Nicaragua are genetically related with the accessions Criollo 13 and Yucatan from the international accessions. The present study suggested a good possibility to select farmers accessions to be included in breeding programs, especially those accessions related to know Criollo accessions.
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(2009)Strawberry (Fragaria × ananassa) is the most important berry crop cultivated in Finland. Due to the species' economic importance, there is a national breeding programme aimed at extending the cropping season from the current one month to up to three months. This could be achieved by growing cultivars which would initiate flowers throughout the summer months, without the requirement of a period of short days as is the case with currently grown cultivars. The cultivated strawberry is an octoploid and therefore has complex patterns of inheritance. It is desirable to study the genetic mechanisms of flowering in the closely related but diploid species F. vesca (L). In the diploid Fragaria, a mutation in a single locus, namely the SEASONAL FLOWERING LOCUS (Sfl), changes the flowering phenotype from seasonal to perpetual flowering. There is also an array of genetic tools available for F. vesca, which facilitate genetic studies at molecular level. Experiments described here aimed at elucidating the identity of the gene which confers perpetual flowering in F. vesca by exploring the flowering characteristics and genotypes of five F2 populations (crosses between seasonal × perpetual flowering cultivars). The study took advantage of a genetic map for diploid Fragaria, publicly available EST and genomic Fragaria sequences and a recently developed BAC library. Sequence information was used for designing gene–specific primers for a host of flowering–related candidate genes, which were subsequently mapped on the diploid Fragaria genetic map. BAC library was screened with molecular markers supposedly located close to the Sfl, with the aim of positionally cloning the Sfl. Segregation of flowering phenotypes in the five F2 populations showed, that the Sfl indeed controls flowering in all the tested cultivars. A genetic map was constructed of the chromosome with the Sfl, and a positional cloning attempt was initiated with the closest flanking markers. 45 gene–specific primers pairs were designed for 21 flowering–related genes, and eight genes were successfully mapped on the diploid Fragaria map. One of the mapped genes, namely PRR7, located very close to the Sfl, and is a potential candidate for the gene that has evaded identification so far.
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(2014)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.
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(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.
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(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.
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(2009)Common bean (Phaseolus vulgaris L.) is one of the most important crops in Nicaraguan agriculture. Bean production is carried out on small scale farms, where farmers generally lack key inputs. Seeds have been identified as the most critical input in bean production. For this reason, national seed program will be a priority during next ten years. Among the four main seed quality components, genetic component has been the least studied. The occurrence of offtype seeds and plants in the cultivar ‘INTA ROJO’ during seed production has hindered the seed certification process and questioned the genetic quality of the cultivars produced in Nicaragua. The present study aimed to compare the genetic composition of different seed categories in the cultivar ‘INTA ROJO’, and to confirm the genetic identity of offtype seeds and plants found in this cultivar. The genotype frequencies of fourty individuals were analyzed using ten microsatellite markers in the following seed categories: Breeder’s seed, foundation seed, registered seed and certified seed. The genotype frequencies were analyzed using Fisher’s exact test, where breeder’s seed was assigned as a reference population. Additionally, twenty offtype seeds and plants, among them the offtype seeds known as “frijol viterra” and “frijol rojo oscuro”, were contrasted with breeder’s seed through pairwise comparisons of genetic distances. The results suggest that changes in genotype frequencies take place during seed production and they are ascribed to the selection pressures caused by environmental differences among production regions and inadequate varietal depuration procedures during seed production. In addition, the offtypes denominated “frijol rojo oscuro” were identified as an unknown cultivar probably derived from natural segregations, mutations and out-crossing among bean seed lots, and in less degree from accidental seed mixtures. In contrast, “frijol viterra” was confirmed to be the same cultivar ‘INTA ROJO’. Its differences in seed weights were associated rather to environmental effects than to genotypic ones. The seed technology implications of these findings and further perspectives are discussed.
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(2010)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.
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(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.
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