Browsing by Subject "414 Agricultural biotechnology"

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  • Mollerup, Filip; Aumala, Ville; Parikka, Kirsti Maria; Mathieu, Yan; Brumer, Harry; Tenkanen, Tiina Maija; Master, Emma (2019)
    Copper radical alcohol oxidases belonging to auxiliary activity family 5, subfamily 2 (AA5_2) catalyze the oxidation of galactose and galactosides, as well as aliphatic alcohols. Despite their broad applied potential, so far very few AA5_2 members have been biochemically characterized. We report the recombinant production and biochemical characterization of an AA5_2 oxidase from Penicillium rubens Wisconsin 54-1255 (PruAA5_2A), which groups within an unmapped clade phylogenetically distant from those comprising AA5_2 members characterized to date. PruAA5_2 preferentially oxidized raffinose over galactose; however, its catalytic efficiency was 6.5 times higher on glycolaldehyde dimer compared to raffinose. Deep sequence analysis of characterized AA5_2 members highlighted amino acid pairs correlated to substrate range and conserved within the family. Moreover, PruAA5_2 activity spans substrate preferences previously reported for AA5 subfamily 1 and 2 members, identifying possible functional overlap across the AA5 family.
  • Razeq, Fakhria M.; Jurak, Edita; Stogios, Peter J.; Yan, Ruoyu; Tenkanen, Maija; Kabel, Mirjam A.; Wang, Weijun; Master, Emma R. (2018)
    Background: Acetylated 4-O-(methyl) glucuronoxylan (GX) is the main hemicellulose in deciduous hardwood, and comprises a beta-(1 -> 4)-linked xylopyranosyl (Xylp) backbone substituted by both acetyl groups and alpha-(1 -> 2)-linked 4-O-methylglucopyranosyluronic acid (MeGlcpA). Whereas enzymes that target singly acetylated Xylp or doubly 2,3-O-acetyl-Xylp have been well characterized, those targeting (2-O-MeGlcpA) 3-O-acetyl-Xylp structures in glucuronoxylan have remained elusive. Results: An unclassified carbohydrate esterase (FjoAcXE) was identified as a protein of unknown function from a polysaccharide utilization locus (PUL) otherwise comprising carbohydrate-active enzyme families known to target xylan. FjoAcXE was shown to efficiently release acetyl groups from internal (2-O-MeGlcpA) 3-O-acetyl-Xylp structures, an activity that has been sought after but lacking in known carbohydrate esterases. FjoAcXE action boosted the activity of alpha-glucuronidases from families GH67 and GH115 by five and nine times, respectively. Moreover, FjoAcXE activity was not only restricted to GX, but also deacetylated (3-O-Araf)2-O-acetyl-Xylp of feruloylated xylooligomers, confirming the broad substrate range of this new carbohydrate esterase. Conclusion: This study reports the discovery and characterization of the novel carbohydrate esterase, FjoAcXE. In addition to cleaving singly acetylated Xylp, and doubly 2,3-O-acetyl-Xylp, FjoAcXE efficiently cleaves internal 3-O-acetyl-Xylp linkages in (2-O-MeGlcpA)3-O-acetyl-Xylp residues along with densely substituted and branched xylooligomers; activities that until now were missing from the arsenal of enzymes required for xylan conversion.
  • Whitaker, Vance M.; Knapp, Steven J.; Hardigan, Michael A.; Edger, Patrick P.; Slovin, Janet P.; Bassil, Nahla V.; Hytönen, Timo; Mackenzie, Kathryn K.; Lee, Seonghee; Jung, Sook; Main, Dorrie; Barbey, Christopher R.; Verma, Sujeet (2020)
    The cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, originating nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry has become the most widely cultivated fruit crop in the world, universally appealing due to its sensory qualities and health benefits. The recent publication of the first high-quality chromosome-scale octoploid strawberry genome (cv. Camarosa) is enabling rapid advances in genetics, stimulating scientific debate and provoking new research questions. In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture. Among these are the origins of the genome, characterization of genetic variants, and big data approaches to breeding. Key areas of research in molecular biology will include the control of flowering, fruit development, fruit quality, and plant–pathogen interactions. In order to realize this potential as a global community, investments in genome resources must be continually augmented.
  • Webb, Anne; Cottage, Amanda; Wood, Thomas; Khamassi, Khalil; Hobbs, Douglas; Gostkiewicz, Krystyna; White, Mark; Khazaei, Hamid; Ali, Mohamed; Street, Daniel; Duc, Gerard; Stoddard, Fred L.; Maalouf, Fouad; Ogbonnaya, Francis C.; Link, Wolfgang; Thomas, Jane; O'Sullivan, Donal M. (2016)
    Faba bean (Vicia faba L.) is a globally important nitrogen-fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence-based consensus map was used to explore synteny with the most closely related crop species, lentil and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2-cM interval of Vf chromosome 2 which was highly colinear with Mt3. The obvious candidate gene from 78 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40-1 gene controlling anthocyanin production in Medicago and resequencing of the Vf orthologue showed a putative causative deletion of the entire 50 end of the gene.
  • Stoddard, Fred; Mäkelä, Pirjo; Puhakainen, Tuula Anneli (INTECHopen, 2011)
  • Kamarainen, A.; Jokinen, K.; Linden, L. (2020)
    The addition of Sphagnum to peat-based growing media ('Sphagnum replacement') influences plant performance. The primary physical effect of Sphagnum addition appears to be enhanced water retention. Good performance of plants cultivated in Sphagnum seems partly explainable in terms of its water retention properties. The large body of nutrient solution retained in Sphagnum can delay disadvantageous changes in its concentration during cultivation. The physical quantity of Sphagnum per unit volume, i.e. its bulk density, governs the volume of retained water and thus determines the strength of effects contributing to plant performance. When subjected to severe drought, plants cultivated in Sphagnum did not show clear signs of water deficit up to at least 1,572 hPa of matric suction, which is the estimated wilting point for plants grown in light peat. Using Sphagnum to replace peat in the growing medium appears advantageous to plants not only during drought but also during ordinary greenhouse cultivation.
  • University of Helsinki, Department of Agricultural Sciences; Al-Khayri, Jameel M.; Jain, Shri Mohan; Johnson, Dennis V.; (Springer, 2019)
  • Mäkelä, Pirjo (2005)
  • Haliloglu, Kamil; Hosseinpour, Arash; Cinisli, Kağan Tolga; Ozturk, Halil Ibrahim; Ozkan, Guller; Pour-Aboughadareh, Alireza; Poczai, Péter (2020)
    Salinity is an edaphic stress that dramatically restricts worldwide crop production. Nanomaterials and plant growth-promoting bacteria (PGPB) are currently used to alleviate the negative effects of various stresses on plant growth and development. This study investigates the protective effects of different levels of zinc oxide nanoparticles (ZnO-NPs) (0, 20, and 40 mg L-1) and PGPBs (no bacteria, Bacillus subtilis, Lactobacillus casei, Bacillus pumilus) on DNA damage and cytosine methylation changes in the tomato (Solanum lycopersicum L. 'Linda') seedlings under salinity stress (250 mM NaCl). Coupled Restriction Enzyme Digestion-Random Amplification (CRED-RA) and Randomly Amplified Polymorphic DNA (RAPD) approaches were used to analyze changes in cytosine methylation and to determine how genotoxic effects influence genomic stability. Salinity stress increased the polymorphism rate assessed by RAPD, while PGPB and ZnO-NPs reduced the adverse effects of salinity stress. Genomic template stability was increased by the PGPBs and ZnO-NPs application; this increase was significant when Lactobacillus casei and 40 mg L-1 of ZnO-NPs were used.A decreased level of DNA methylation was observed in all treatments. Taken together, the use of PGPB and ZnO-NPs had a general positive effect under salinity stress reducing genetic impairment in tomato seedlings.
  • Tavakoli, Kamand; Pour-Aboughadareh, Alireza; Kianersi, Farzad; Poczai, Péter; Etminan, Alireza; Shooshtari, Lia (2021)
    Targeted nucleases are powerful genomic tools to precisely change the target genome of living cells, controlling functional genes with high exactness. The clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9) genome editing system has been identified as one of the most useful biological tools in genetic engineering that is taken from adaptive immune strategies for bacteria. In recent years, this system has made significant progress and it has been widely used in genome editing to create gene knock-ins, knock-outs, and point mutations. This paper summarizes the application of this system in various biological sciences, including medicine, plant science, and animal breeding.
  • Smaragdov, M. G.; Kudinov, A. A. (2020)
    Background Due to the advent of SNP array technology, a genome-wide analysis of genetic differences between populations and breeds has become possible at a previously unattainable level. The Wright's fixation index (F-st) and the principal component analysis (PCA) are widely used methods in animal genetics studies. In paper we compared the power of these methods, their complementing each other and which of them is the most powerful. Results Comparative analysis of the power Principal Components Analysis (PCA) and F-st were carried out to reveal genetic differences between herds of Holsteinized cows. Totally, 803 BovineSNP50 genotypes of cows from 13 herds were used in current study. Obtained F-st values were in the range of 0.002-0.012 (mean 0.0049) while for rare SNPs with MAF 0.0001-0.005 they were even smaller in the range of 0.001-0.01 (mean 0.0027). Genetic relatedness of the cows in the herds was the cause of such small F-st values. The contribution of rare alleles with MAF 0.0001-0.01 to the F-st values was much less than common alleles and this effect depends on linkage disequilibrium (LD). Despite of substantial change in the MAF spectrum and the number of SNPs we observed small effect size of LD - based pruning on F-st data. PCA analysis confirmed the mutual admixture and small genetic difference between herds. Moreover, PCA analysis of the herds based on the visualization the results of a single eigenvector cannot be used to significantly differentiate herds. Only summed eigenvectors should be used to realize full power of PCA to differentiate small between herds genetic difference. Finally, we presented evidences that the significance of F-st data far exceeds the significance of PCA data when these methods are used to reveal genetic differences between herds. Conclusions LD - based pruning had a small effect on findings of F-st and PCA analyzes. Therefore, for weakly structured populations the LD - based pruning is not effective. In addition, our results show that the significance of genetic differences between herds obtained by F-st analysis exceeds the values of PCA. Proposed, to differentiate herds or low structured populations we recommend primarily using the F-st approach and only then PCA.
  • Trouvelot, Sophie; Héloir, Marie-Claire; Poinssot, Benoît; Gauthier, Adrien; Paris, Franck; Guillier, Christelle; Combier, Maud; Tdra, Lucie; Daire, Xavier; Adrian, Marielle (2014)
    Increasing interest is devoted to carbohydrates for their roles in plant immunity. Some of them are elicitors of plant defenses whereas other ones act as signaling molecules in a manner similar to phytohormones. This review first describes the main classes of carbohydrates associated to plant immunity, their role and mode of action. More precisely, the state of the art about perception of “PAMP, MAMP and DAMP type” oligosaccharides is presented and examples of induced defense events are provided. A particular attention is paid to the structure / activity relationships of these compounds. The role of sugars as signaling molecules, especially in plant microbe interactions, is also presented. Secondly, the potentialities and limits of foliar sprays of carbohydrates to stimulate plant immunity for crop protection against diseases are discussed, with focus on the roles of the leaf cuticle and phyllosphere microflora.
  • Bidabadi, Siamak Shirani; Jain, S. Mohan (2020)
    Plants generally have the highest regenerative ability because they show a high degree of developmental plasticity. Although the basic principles of plant regeneration date back many years, understanding the cellular, molecular, and physiological mechanisms based on these principles is currently in progress. In addition to the significant effects of some factors such as medium components, phytohormones, explant type, and light on the regeneration ability of an explant, recent reports evidence the involvement of molecular signals in organogenesis and embryogenesis responses to explant wounding, induced plant cell death, and phytohormones interaction. However, some cellular behaviors such as the occurrence of somaclonal variations and abnormalities during the in vitro plant regeneration process may be associated with adverse effects on the efficacy of plant regeneration. A review of past studies suggests that, in some cases, regeneration in plants involves the reprogramming of distinct somatic cells, while in others, it is induced by the activation of relatively undifferentiated cells in somatic tissues. However, this review covers the most important factors involved in the process of plant regeneration and discusses the mechanisms by which plants monitor this process.
  • Ruokolainen, Satu; Ng, Yan Peng; Broholm, Suvi K.; Albert, Victor A.; Elomaa, Paula; Teeri, Teemu H. (2010)
  • Poczai, Péter; Amiryousefi, Ali; Hyvönen, Jaakko Tapani; Sablok, Gaurav (2018)
    Tomato (Solanum lycopersicon) is one of the most important crops worldwide with 177 million tonnes produced over 4.7 million ha. Compared to many other crops plant used in commercial production show very little genetic variation due to selection for a limited set of traits during its domestication. This group consisting of 13 inter-crossable diploid (2n = 2x = 24) species under extensive taxonomic studies, is an important source of traits and genes for tomato improvement. Tomato is the most intensively studied solanaceous species both in terms of its genetics and genomics. In addition to marker, sequence, and bioinformatic resources, various molecular genetic tools for functional analyses have been developed extensively. It is surprizing that these large-scale genome-sequencing initiatives generated quasi-complete plastid sequences, which were later discarded as non-target contamination without further analysis. They provide an untapped treasure trove of plastid genomic in raw read archives and other repositories for tomatoes. Chloroplast DNA is organized in compact gene-rich genomes, which are present in high copy number within plant cells. In Solanaceae plastid gene content and synteny are highly conserved, which is also preserved to some level in the intergenic spacer regions (IGS & ITS). In the present study, we utilized high-throughput sequencing data to gather a transcriptome based nuclear matrix and to assemble complete plastid genome sequences for all species of the core tomato clade (Solanum sect. Lycopersicon). We compare the genome organization, structure and phylogenetic relationships based on these data and investigate incongruences found between nuclear and plastid genomic trees. Our study allowed us to construct the first interspecific analysis including all species of wild tomatoes based on entire plastid sequences and compare genomic rearrangements with congeneric taxa. We found that plastome based trees provide strong support for two major groups in the tomato clade with S. pennellii and S. habrochaites in two distinct groups with the rest of the species. On the other hand, these two species form a clade in a basal position as compared with other tomato species in the phylogenetic analyses based on nuclear genes. This topological incongruence observed might be caused by the chloroplast capture event. In this process, a new combination of nuclear and chloroplast genomes were formed through inter-species hybridization and subsequent backcrosses with S. pennellii and S. habrochaites. Cross-species transfer of the chloroplast from one species to another has been reported among hybridizing plant groups, but it has not been hypothesised previously in Solanaceae.
  • Kajala, Ilkka; Shi, Qiao; Nyyssölä, Antti; Maina, Ndegwa; Hou, Yaxi; Katina, Kati; Tenkanen, Maija; Juvonen, Riikka (2015)
    Wheat bran offers health benefits as a baking ingredient, but is detrimental to bread textural quality. Dextran production by microbial fermentation improves sourdough bread volume and freshness, but extensive acid production during fermentation may negate this effect. Enzymatic production of dextran in wheat bran was tested to determine if dextran-containing bran could be used in baking without disrupting bread texture. The Weissella confusa VTT E-90392 dextransucrase gene was sequenced and His-tagged dextransucrase Wc392-rDSR was produced in Lactococcus lactis. Purified enzyme was characterized using 14C-sucrose radioisotope and reducing value-based assays, the former yielding Km and Vmax values of 14.7 mM and 8.2 μmol/(mg∙min), respectively, at the pH optimum of 5.4. The structure and size of in vitro dextran product was similar to dextran produced in vivo. Dextran (8.1% dry weight) was produced in wheat bran in 6 h using Wc392-rDSR. Bran with and without dextran was used in wheat baking at 20% supplementation level. Dextran presence improved bread softness and neutralized bran-induced volume loss, clearly demonstrating the potential of using dextransucrases in bran bioprocessing for use in baking.
  • Koskela, Elli A.; Hytonen, Timo (Springer International Publishing AG, 2018)
    Compendium of Plant Genomes
    Strawberries (Fragaria sp.) are small perennial plants capable of both sexual reproduction through seeds and clonal reproduction via runners. Because vegetative and generative developmental programs are tightly connected, the control of flowering is presented here in the context of the yearly growth cycle. The rosette crown of strawberry consists of a stem with short internodes produced from the apical meristem. Each node harbors one trifoliate leaf and an axillary bud. The fate of axillary buds is dictated by environmental conditions; high temperatures and long days (LDs) promote axillary bud development into runners, whereas cool temperature and short days (SDs) favor the formation of branch crowns. SDs and cool temperature also promote flowering; under these conditions, the main shoot apical meristem is converted into a terminal inflorescence, and vegetative growth is continued from the uppermost axillary branch crown. The environmental factors that regulate vegetative and generative development in strawberries have been reasonably well characterized and are reviewed in the first two chapters. The genetic basis of the physiological responses in strawberries is much less clear. To provide a point of reference for the flowering pathways described in strawberries so far, a short review on the molecular mechanisms controlling flowering in the model plant Arabidopsis is given. The last two chapters will then describe the current knowledge on the molecular mechanisms controlling the physiological responses in strawberries.
  • Sharma, Himanshu; Hyvönen, Jaakko; Poczai, Péter (2020)
    Premise Plant invasions are increasing globally, and extensive study of the genetic background of the source and invading populations is needed to understand such biological processes. For this reason, chloroplast microsatellite markers were identified to explore the genetic diversity of the noxious weed Ambrosia trifida (Asteraceae). Methods and Results The complete chloroplast genome of A. trifida was mined for microsatellite loci, and 15 novel chloroplast primers were identified to assess the genetic diversity of 49 Ambrosia samples. The number of alleles amplified ranged from two to six, with an average of 3.2 alleles per locus. Shannon's information index varied from 0.305 and 1.467, expected heterozygosity ranged from 0.178 to 0.645, and the polymorphism information content value ranged from 0.211 to 0.675 (average 0.428). The cross-species transferability of the 15 microsatellite loci was also evaluated in four related Ambrosia species (A. artemisiifolia, A. maritima, A. psilostachya, and A. tenuifolia). Conclusions The novel chloroplast microsatellite markers developed in the current study demonstrate substantial cross-species transferability and will be helpful in future genetic diversity studies of A. trifida and related species.
  • Belachew, Kiflemariam Yehuala; Nagel, Kerstin; Fiorani, Fabio; Stoddard, Frederick Lothrop (2018)
    Background Soil moisture deficiency causes yield reduction and instability in faba bean (Vicia faba L.) production. The extent of sensitivity to drought stress varies across accessions originating from diverse moisture regimes of the world. Hence, we conducted successive greenhouse experiments in pots and rhizotrons to explore diversity in root responses to soil water deficit. Methods A set of 89 accessions from wet and dry growing regions of the world was defined according to the Focused Identification of Germplasm Strategy and screened in a perlite-sand medium under well watered conditions in a greenhouse experiment. Stomatal conductance, canopy temperature, chlorophyll concentration, and root and shoot dry weights were recorded during the fifth week of growth. Eight accessions representing the range of responses were selected for further investigation. Starting five days after germination, they were subjected to a root phenotyping experiment using the automated phenotyping platform GROWSCREEN-Rhizo. The rhizotrons were filled with peat-soil under well watered and water limited conditions. Root architectural traits were recorded five, 12, and 19 days after the treatment (DAT) began. Results In the germplasm survey, accessions from dry regions showed significantly higher values of chlorophyll concentration, shoot and root dry weights than those from wet regions. Root and shoot dry weight as well as seed weight, and chlorophyll concentration were positively correlated with each other. Accession DS70622 combined higher values of root and shoot dry weight than the rest. The experiment in GROWSCREEN-Rhizo showed large differences in root response to water deficit. The accession by treatment interactions in taproot and second order lateral root lengths were significant at 12 and 19 DAT, and the taproot length was reduced up to 57% by drought. The longest and deepest root systems under both treatment conditions were recorded by DS70622 and DS11320, and total root length of DS70622 was three times longer than that of WS99501, the shortest rooted accession. The maximum horizontal distribution of a root system and root surface coverage were positively correlated with taproot and total root lengths and root system depth. DS70622 and WS99501 combined maximum and minimum values of these traits, respectively. Thus, roots of DS70622 and DS11320, from dry regions, showed drought-avoidance characteristics whereas those of WS99501 and Melodie/2, from wet regions, showed the opposite. Discussion The combination of the germplasm survey and use of GROWSCREEN-Rhizo allowed exploring of adaptive traits and detection of root phenotypic markers for potential drought avoidance. The greater root system depth and root surface coverage, exemplified by DS70622 and DS11320, can now be tested as new sources of drought tolerance.
  • Ayvaz, Muavviz; Guven, Avni; Fagerstedt, Kurt Valter (2015)
    Potato crop production in Turkey ranks on the thirteenth place in the world. Toxicity is a problematic issue for some parts of the Turkish soils. Hence, it is very important to clarify the physiological responses of plants to toxic mineral stress. In this study, two different potato cultivars - Solanum tuberosum cv. Resy and Solanum tuberosum cv. Agria - were used as a study material. Excess boron was applied in two different concentrations (5 mmol/L and 12.5 mmol/L) 32 days after planting the tubers. Plants were harvested at the end of 15 days of excess boron application. Chlorophyll fluorescence (Fv/Fm) was measured. Shoot height and shoot-root fresh weight contents were determined. Analyses were carried out for the contents of the endogenous hormones indole-3-acetic acid (IAA) and abscisic acid (ABA) by using gas chromatography-mass spectrophotometry (GS-MS). According to the obtained data, plants' shoot height did not change, whereas the shoot's fresh weight decreased significantly with increasing of the boron concentrations in cv Resy, by applying 12.5 mmol/L boron. With 12.5 mmol/L boron, the photosynthesis was negatively affected in both cultivars. Boron application led to increased endogenous IAA and ABA content in both cultivars. As a result, cv. Resy showed more resistance to excess boron. Findings on the hormone metabolism and chlorophyll fluorescence in different cultivars will shed a light on understanding the physiological response to excess mineral stress.