Browsing by department "Department of Agricultural Sciences"

The objective of this study was to develop functional method for producing doupled-haploid plants for faba bean. Microspore culture is an advanced method to produce doubled-haploids and it is based on the totipotent nature of plant cells, since even a microspore, which is an immature pollen cell with haploid genome, can develop into a plant. This plant is either haploid or doupled haploid depending on whether there has been chromosome doubling or not and because the chromosomes either do not have pairs or the pairs are pure copies of each other, the plant is completely homozygous. Doubled haploids are already used in breeding programs with several crops such as wheat, barley and oilseed rape. Faba bean is an important legume for food, feed and crop rotation. Together with other legumes it has the potential to replace soybean imports entirely in Finland. Faba bean yield stability and anti-nutritional factors restrain its use and active breeding is required to improve the crop. In Finland, where pea and faba bean are the only grain legumes actively cultivated, the breeding of faba bean has been recently reactivated and its objectives are earliness, higher yield, protein content and improved quality factors. Big bottle neck in faba bean breeding is the creation of pure homozygote lines because the partial cross-breeding in the species sets restrains for the procedure. In this study promising pea and chick pea protocols that were developed in 2009 and an efficient rapeseed protocol were applied with faba bean. The interaction of various stress treatments and two different induction media with five genotypes of faba bean on microspore culture were analysed. Pro-embryos and cell divisions were observed from the cultures. Heat shock was the most effective stress treatment. Effects of density and induction medium were high and cultivar’s low tannin content seemed to impact positively to induction efficiency. These results suggest that for faba bean microspore culture is as suitable method as anther culture is and that there is hope to produce doubled-haploid faba beans in the future.

Nitrogen leaching is the main cause of nitrogen loss from Finnish agricultural soils. Nitrogen leaching can exceed 20 kg/ha/year. The Finnish waters and the Baltic Sea are affected by nitrogen leaching due to that nitrogen increases algae blooming. Studies have shown that the loss of nitrogen can be decreased by cultivating catch crops. Nitrogen leaching can in some cases be decreased by up to 90 %. In Finland catch crops are seldom grown. Catch crops are thought to be too costly and time consuming. The aim of this study was to investigate how efficiently winter wheat, rye and winter turnip rape function as catch crops and what effect the preceding crops of fallow, barley and peas have on autumn sown crops, with regard to nitrogen levels. A three year-long field experiment was established in 2010 at Viikki research farm in Helsinki. Winter wheat, rye and winter turnip rape were cultivated as catch crops; the preceding crops were fallow in 2010-2011 and barley and pea in 2011-2012. In 2012 winter wheat, rye and winter turnip rape were cultivated with fallow, peas and barley as preceding crops. In this study the soil’s mineral nitrogen content was measured before sowing in autumn and in spring. In 2010-2011 the soil’s mineral nitrogen content was also measured after harvest. The nitrogen content of the plants was measured in autumn. The seed quality and the seed yield were also measured. In autumn 2011 the mineral nitrogen content of the soil was higher after barley than after peas. However, there was more mineral nitrogen after cultivating fallow, compared to peas and barley in autumn 2012. The loss of mineral nitrogen between autumn 2010 and spring 2011 was slight. The nitrogen loss was greatest where winter turnip rape was cultivated, due to the plant’s high nitrogen assimilation. Winter turnip rape accumulated much more nitrogen than rye and winter wheat, whereas rye accumulated more nitrogen than winter wheat in 2010 and 2011. Mineral nitrogen loss between autumn 2011 and spring 2012 was high, over 80 % of the nitrogen was lost due to heavy rainfall and a mild winter.

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.

Some horses experience a problem called free faecal liquid (FFL). The condition is not characterized by classical diarrhoea but by free liquid that is voided separately from the solid part of the faeces. Problems with FFL include irritation and abrasive lesions in the skin in the rear end. No health issues of more severe character are usually present in these horses, apart from preliminary findings indicating a higher risk of colic when compared to horses without FFL. The reason for why horses develop FFL, and its effects on the horse, are unknown as the subject has not been studied much. It has been suggested that one reason could be in how the horses are fed. It has been speculated that haylage could have an impact on the development of FFL. A study was done with the aim to collect information about feeding and management of horses affected with FFL in Sweden and Norway (n = 100), and to compare faecal composition in horses with and without FFL. This particular part of the study focused on the faecal properties. The objective was to compare chemical composition of the faeces of affected and unaffected horses, in order to detect possible reasons for FFL, which could be studied further. The study was performed with three repeated samplings on all horses. Case and control horses were paired and were housed at the same farm and were fed the same forage. The horse owners were collecting faecal samples using a standardized protocol. The variables examined in faecal samples were dry matter (DM), pH, volume of free liquid after centrifugation, sand, osmolality, acetate, propionate, isobutyrate, n-butyrate and total volatile fatty acid (VFA) concentration of the samples. In samples from the first sampling occasion, differences (P < 0.05) between cases and controls were found in concentration of acetate, isobutyrate and total amount of VFA. Tendencies toward differences (0.10 < P > 0.05) were found in the volume of liquid and sand as well as in n-butyrate concentration. At the second sampling tendencies toward differences were found in the amount of sand and in n-butyrate concentration. In samples from the third sampling a tendency toward difference was present for pH value. All values were or tended to be higher for horses with FFL. Also, clear correlations were found between nearly all the variables. The pH value was found to correlate negatively with osmolality and all the VFAs except for isobutyrate where no correlation was found in any of the sampling occasions. Osmolality was also found to correlate positively with all the VFAs. VFAs correlated positively with one another. The results showed a tendency toward difference in n-butyrate concentration and presence of sand in faecal samples when case and control horses were compared, although not with consistency as samples form the third sampling occasion did not follow results from the first and second samplings. As the results were not constant throughout the study, these two variables may not be reliable when trying to find possible reasons for FFL. Almost all the variables were found to correlate with one another, exception being isobutyrate with pH. As butyrate is a major source of energy for horses and important for the health of the equine intestine, this information could be useful in further studies concerning the possible reasons for FFL.

The Rosaceae family accounts for more than 90% of the total fresh fruit production in Finland and for more than 25% worldwide in 2013. Thus, improving the yield potential of Rosaceae species works in favor of economic growth and food security. To achieve that, expanding the knowledge on Rosaceae species is required. Fragaria vesca (F. vesca), particularly the everbearing F. vesca semperflorens accession ‘Hawaii-4’ (H4), provides several features that makes it formidable as a model organism for the study of physiological processes in Rosaceae species, where the CENTRORADIALIS/TERMINALFLOWER 1/SELF-PRUNING (CETS) genes play a remarkable role. In this Thesis, I have studied the expression patterns and functions of the CETS genes by performing gene expression analysis, generation of H4 transgenic lines and observation on H4 plants (both transgenic and wild type) grown under different sets of conditions. My results confirmed the expression patterns and functions previously reported for F.vesca TERMINAL FLOWER1 and F.vesca FLOWERING LOCUS T1. I showed that F.vesca CENTRORADIALIS-LIKE2 is a floral repressor and demonstrated that F.vesca FLOWERING LOCUS T3 is a flowering promoter. Additionally, our data suggest that F.vesca MOTHER OF FT is directly related with stolon formation and that F.vesca CENTRORADIALIS-LIKE1 is most likely a floral repressor. This new information could be used in the future to improve the efficiency of Rosaceae crops farming by adapting flowering and vegetative responses and also for breeding more productive Rosaceae crops.

Towards the year 2030 in Finland, sustainability issues will be dominated by climate change, the worsening state of the Baltic Sea, technological and technical development, globalization, the degradation of ecosystem services and increasing energy consumption. At the decision-making level, setting strategic objectives towards the year 2030 should consist of increasing energy efficiency, halting the reduction of biodiversity and changing consumption habits. Furthermore, promoting public transportation, limiting greenhouse gas emissions, increasing the proportion of renewable energy sources and linking climate policy to all sustainable development policies should be targeted in strategic long-term planning. This master’s thesis research was implemented as a Delphi study, a method commonly used in futures research. In a Delphi study the expertise of a chosen panel is utilized to gather information on a given topic. The research aimed at investigating the experts’ views on 1) the most important driving forces – changes and trends – affecting sustainable development towards the year 2030 2) the desirability and probability of different sustainability objectives and 3) recognizing the potential political conflicts brought by these strategies. The Delphi study was carried out during February 2010 – April 2010. It consisted of two rounds. The first round questionnaire was sent 43 experts (response rate 56 %). During the second round the most interesting first round results were completed with qualitative arguments (response rate 50 %). The results were analyzed in the manner that the research issues of most interest were 1) the trends having the most importance towards the year 2030 2) the most desirable strategic objectives with a high probability for political conflicts. The results indicate a high risk for political conflict especially with the targets on halting the reduction of biodiversity and changing consumption habits. These two objectives were considered difficult to grasp and often overruled by economic interests. Changing the current societal system based on continuous growth and consumption would require profound alterations in economy, society and individual values. The results also indicate that energy is a key issue for the coming decades: setting strategic objectives for replacing fossil fuels should be among the top priorities of the Finnish national government. Also, in addition for climate change being an important trend, the deviation of rankings in importance among the panel indicated a possibility for social and economic trends to have unexpected, sudden effects as we move towards the year 2030. These include global poverty and inequality, changing age structures and the sustainability of the Finnish economy.

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.

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.

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

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