Search

Background: Scientific literature carries a wealth of information crucial for research, but only a fraction of it is present as structured information in databases and therefore can be analyzed using traditional data analysis tools. Natural language processing (NLP) is often and successfully employed to support humans by distilling relevant information from large corpora of free text and structuring it in a way that lends itself to further computational analyses. For this pilot, we developed a pipeline that uses NLP on biological literature to produce knowledge networks. We focused on the flesh color of potato, a well-studied trait with known associations, and we investigated whether these knowledge networks can assist us in formulating new hypotheses on the underlying biological processes. Results: We trained an NLP model based on a manually annotated corpus of 34 full-text potato articles, to recognize relevant biological entities and relationships between them in text (genes, proteins, metabolites and traits). This model detected the number of biological entities with a precision of 97.65% and a recall of 88.91% on the training set. We conducted a time series analysis on 4023 PubMed abstract of plant genetics-based articles which focus on 4 major Solanaceous crops (tomato, potato, eggplant and capsicum), to determine that the networks contained both previously known and contemporaneously unknown leads to subsequently discovered biological phenomena relating to flesh color. A novel time-based analysis of these networks indicates a connection between our trait and a candidate gene (zeaxanthin epoxidase) already two years prior to explicit statements of that connection in the literature. Conclusions: Our time-based analysis indicates that network-assisted hypothesis generation shows promise for knowledge discovery, data integration and hypothesis generation in scientific research. [ABSTRACT FROM AUTHOR]

Late blight, caused by Phytophthora infestans , remains the most devastating disease in potato resulting in economic costs that sum up 5.2 billion euros, globally. The use of resistant varieties is a powerful, viable and environmentally friendly alternative or supplement for the current, commonly deployed chemical control strategies. In this study, we set out to improve the susceptible potato variety Desiree by transformation with single or multiple late blight ( R ) resistance genes. Rpi-sto1 , Rpi-vnt1.1 and a stack of Rpi-sto1 : Rpi-vnt1.1 : Rpi-blb3, were transformed and eight, eight, and ten independent transformants (events) respectively, were selected because of absence of vector backbone, low T-DNA copy number, responsiveness to the cognate Avr effectors, P. infestans resistance in detached leaf assays (DLAs) and preliminary field experiments. The performance of the selected events was studied under field conditions in The Netherlands and Belgium, after P. infestans inoculation and/or to natural late blight infection during two consecutive growing seasons. All selected events were more resistant than the non-transformed susceptible reference clone. The different individual R genes, however, contributed to different levels of resistance. The selected events were also compared to conventionally bred late blight resistant varieties with (partially) known R gene content. Generally, it was found that plants with single R genes showed a lower level of resistance than plants with R gene stacks. Only the events harbouring three late blight R genes remained unaffected until the end of the growing season, in both locations and in both growing seasons. [ABSTRACT FROM AUTHOR]

Various transcriptional networks and plant hormones have been implicated in controlling different aspects of potato tuber formation. Due to its broad impact on many plant developmental processes, a role for auxin in tuber initiation has been suggested but never fully resolved. Here, auxin concentrations were measured throughout the plant prior to and during the process of tuber formation. Auxin levels increase dramatically in the stolon prior to tuberization and remain relatively high during subsequent tuber growth, suggesting a promoting role for auxin in tuber formation. Furthermore, in vitro tuberization experiments showed higher levels of tuber formation from axillary buds of explants where the auxin source (stolon tip) had been removed. This phenotype could be rescued by application of auxin on the ablated stolon tips. In addition, a synthetic strigolactone analogue applied on the basal part of the stolon resulted in fewer tubers. The experiments indicate that a system for the production and directional transport of auxin exists in stolons and acts synergistically with strigolactones to control the outgrowth of the axillary stolon buds, similar to the control of above-ground shoot branching. [ABSTRACT FROM AUTHOR]

Comparative genomics provides a tool to utilize the exponentially increasing sequence information from model plants to clone agronomically important genes from less studied crop species. Plant disease resistance (R) loci frequently lack synteny between related species of cereals and crucifers but appear to be positionally well conserved in the Solanaceae. In this report, we adopted a local RGA approach using genomic information from the model Solanaceous plant tomato to isolateR3a, a potato gene that confers race-specific resistance to the late blight pathogenPhytophthora infestans.R3ais a member of theR3complex locus on chromosome 11. Comparative analyses of theR3complex locus with the correspondingI2complex locus in tomato suggest that this is an ancient locus involved in plant innate immunity against oomycete and fungal pathogens. However, theR3complex locus has evolved after divergence from tomato and the locus has experienced a significant expansion in potato without disruption of the flanking colinearity. This expansion has resulted in an increase in the number ofRgenes and in functional diversification, which has probably been driven by the co-evolutionary history betweenP. infestansand its host potato. Constitutive expression was observed for theR3agene, as well as some of its paralogues whose functions remain unknown. [ABSTRACT FROM AUTHOR]

Gene expression during the potato (Solanum tuberosum) tuber lifecycle was monitored by cDNA-amplified fragment-length polymorphism, and several differentially expressed transcript-derived fragments were isolated. One fragment, named TDFL431, showed high homology to a copper (Cu) chaperone for Cu/zinc superoxide dismutase (CCS). The Ccs protein is responsible for the delivery of Cu to the Cu/zinc superoxide dismutase enzyme. The potato CCS (StCCS) full-length gene was isolated, and its sequence was compared with CCSs from other species. The promoter region of this gene was isolated, fused to the firefly luciferase coding sequence, and used for transformation of potato plants. The highest level of StCCSluciferase expression was detected in the cortex of stem (like) tissues, such as stem nodes, stolons, and tubers; lower levels were detected in roots and flowers. The StCCS promoter contains regions highly homologous to several plant cis-acting elements. Three of them are related to auxin response, whereas four others are related to response to various stresses. Induction of the StCCS promoter was analyzed on 18 media, differing in hormone, sugar, and Cu content. StCCS expression was induced by auxin, gibberellins (GA[sub 4+7]), fructose, sucrose, and glucose and was inhibited by relatively high concentrations of Cu. [ABSTRACT FROM AUTHOR]

Potato (Solanum tuberosum) is an important food crop consumed all over the world, but it is generally sensitive to drought conditions. One of the major physiological processes affected by drought stress is carbon partitioning: the plant's choice of where to allocate its photoassimilates. Our aim was to investigate the molecular factors and possible bottlenecks affecting carbon partitioning during drought. We studied potato cultivars with contrasting drought responses in the greenhouse in the years 2013–2015, and further investigated the expression of genes involved in carbon partitioning and metabolite levels. Our results indicate that one of the most severe effects of drought stress on potato is the arrest of stolon differentiation and formation of tubers. We also identified some physiological traits like stomatal conductance and chlorophyll content as affecting carbon assimilation, partitioning and eventual tuber yield. The gene expressions and biochemical analyses highlight the various tissues prioritized by the plant for assimilate transport during drought stress, and give indications of what distinguishes drought tolerance and sensitivity of cultivated potato. Some of the key genes studied (like Sucrose synthase and Sucrose transporters) may be inclusive breeding targets for drought tolerance in potato. • Sugar export from source leaves, not its availability, is key in drought tolerance. • Tuber initiation arrest can alter carbon transport to underground tissues. • Starch storage in leaves is a limitation to potato tuber yield under drought. [ABSTRACT FROM AUTHOR]

Highlights • Increasing the daily light integral (DLI) accelerates flower bud appearance in potato. • Increasing DLI decreases the number of leaves formed before the inflorescence. • Faster flowering under high DLI is not controlled by flowering time gene StSP3D. Abstract Little is known on the environmental control of potato flowering. With recent developments in potato breeding, and the growing interest in true potato seed production, more knowledge on potato flowering is required. This research aims to elucidate the effect of the daily light integral (DLI: the accumulated light throughout a day) on potato flower initiation time and investigate which mechanisms underlie this control. We grew potato plants in climate chambers to compare flower initiation under different DLIs in short and long days. We measured the time until the first appearance of the flower buds and the number of leaves formed before the inflorescence. Furthermore, gene expression changes of the potato flowering time gene StSP3D were measured, and potato plants silenced in StSP3D were used to determine whether DLI mediated flowering time was regulated through StSP3D. Additionally, we determined sucrose and starch concentrations and measured the transcription levels of StTPS1 , a gene involved in sugar mediated flowering control. Increasing DLI clearly accelerated flowering in potato. The role of carbohydrates (sucrose and starch) and StTPS1 in DLI-accelerated flowering was inconclusive. Although StSP3D was upregulated under high DLI, transgenic lines silenced in StSP3D also showed accelerated flowering under higher DLIs. We therefore conclude that high DLI accelerates potato flowering and this acceleration happens independently of StSP3D upregulation. [ABSTRACT FROM AUTHOR]

In this study, we analyze 31 transgenic lines and their respective untransformed background lines to determine the transgene effects on targeted structures including the pectin components rhamnogalacturonan I (RG-I) and homogalacturonan (HG), neutral side chains (galactan/arabinangalactan), acetylation of pectin, and cellulose level. Modification arising from the pectin backbone- or pectin side chain transgenic lines either increased or decreased the HG:RG-I ratio, side chain length, and methyl esterification of pectin in the tuber cell wall. The pectin esterification transgenic line exhibited only limited side effects. The cellulose level-targeting transgenic lines yielded an unexpectedly high HG:RG-I ratio and longer pectic side chains. These results clearly demonstrate that in effects of a transgene are not restricted to the direct activity of the targeted enzyme but have consequences for the structure of the cell wall matrix. Analysis of whole cell wall structure is therefore necessary to assess the complete effect, direct and indirect, of a transgene. [ABSTRACT FROM AUTHOR]

Abstract: GA biosynthesis and catabolism has been shown to play an important role in regulating tuberization in potato. Active GAs are inactivated in the stolon tips shortly after induction to tuberization. Overexpression of a GA inactivation gene results in an earlier tuberization phenotype, while reducing expression of the same gene results in delayed tuberization. In addition, overexpression of genes involved in GA biosynthesis results in delayed tuberization, while decreased expression of those genes results in earlied tuberization. The final step in GA biosynthesis is catalysed by StGA3ox1 and StGA3ox2 activity, that convert inactive forms of GA into active GA1 and GA4. In this study we cloned StGA3ox2 gene in an RNAi construct and used this construct to transform potato plants. The StGA3ox2 silenced plants were smaller and had shorter internodes. In addition, we assayed the concentrations of various GAs in the transgenic plants and showed an altered GA content. No difference was observed on the time point of tuber initiation. However, the transgenic clones had increased number of tubers with the same yield, resulting in smaller average tuber weight. In addition, we cloned the promoter of StGA3ox2 to direct expression of the GUS reporter gene to visualize the sites of GA biosynthesis in the potato plant. Finally, we discuss how changes of several GA levels can have an impact on shoot, stolon and tuber development, as well as the possible mechanisms that mediate feed-forward and feed-back regulation loops in the GA biosynthetic pathway in potato. [Copyright &y& Elsevier]

Abstract: In the post-genomic era, high-throughput technologies have led to data collection in fields like transcriptomics, metabolomics and proteomics and, as a result, large amounts of data have become available. However, the integration of these ∼omics data sets in relation to phenotypic traits is still problematic in order to advance crop breeding. We have obtained population-wide gene expression and metabolite (LC–MS) data from tubers of a diploid potato population and present a novel approach to study the various ∼omics datasets to allow the construction of networks integrating gene expression, metabolites and phenotypic traits. We used Random Forest regression to select subsets of the metabolites and transcripts which show association with potato tuber flesh color and enzymatic discoloration. Network reconstruction has led to the integration of known and uncharacterized metabolites with genes associated with the carotenoid biosynthesis pathway. We show that this approach enables the construction of meaningful networks with regard to known and unknown components and metabolite pathways. [Copyright &y& Elsevier]

UDP-glucose 4-epimerases (UGE) catalyze the reversible conversion of UDP-glucose to UDP-galactose. Two potato UGE genes (StUGE45 and StUGE51) were isolated from a potato cDNA library using the Arabidopsis thaliana UGE1 cDNA as a probe. The cDNA clones cluster differently in a phylogenetic tree of plant epimerases. StUGE51 showed higher expression than StUGE45, particularly, in older tubers, flowers, stems and in vitro plants. Transgenic potato plants were generated to examine the effect of modified UGE expression on the amount of cell wall galactose. Sense expression of the two StUGE clones in potato gave plants with no overt developmental phenotype. In contrast to WT plants, a large number of transformants had the ability to overcome the toxic effect of galactose in the culture medium during in vitro growth. The UGE45 transformants showed a clear correlation of increased UGE RNA expression levels with this tolerance to galactose, whereas the UGE51 transformants did not. The elevated UGE expression in the transformants resulted in an increased galactose content in potato tuber cell walls. This effect was more profound for the UGE45 transformants than for the UGE51 ones. Our results suggest that the two potato UGEs have different biochemical properties, and that they have a different function in plant development. [Copyright &y& Elsevier]

Four potato cellulose synthase (CesA) homologs (StCesA1, 2, 3 and 4) were isolated by screening a cDNA library made from developing tubers. Based on sequence comparisons and the fact that all four potato cDNAs were isolated from this single cDNA-library, all four StCesA clones are likely to play a role in primary cell wall biosynthesis. Several constructs were generated to modulate cellulose levels in potato plants in which the granule-bound starch synthase promoter was used to target the modification to the tubers. The StCesA3 was used for up- and down-regulation of the cellulose levels by sense (SE-StCesA3) and antisense (AS-StCesA3) expression of the complete cDNA. Additionally, the class-specific regions (CSR) of all four potato cellulose synthase genes were used for specific down-regulation (antisense) of the corresponding CesA genes (csr1, 2, 3 and 4). None of the transformants showed an overt developmental phenotype. Sections of tubers were screened for altered cell wall structure by Fourier Transform Infrared microspectroscopy (FTIR) and exploratory Principal Component Analysis (PCA), and those plants discriminating from WT plants were analysed for cellulose content and monosaccharide composition. Several transgenic lines were obtained with mainly decreased levels of cellulose. These results show that the cellulose content in potato tubers can be reduced down to 40% of the WT level without affecting normal plant development, and that constructs based on the CSR alone are specific and sufficient to down-regulate cellulose biosynthesis. [Copyright &y& Elsevier]

The potato tuber life cycle involves several developmental stages including tuberisation, tuber growth, dormancy and sprouting. Gene expression during the potato tuber life cycle has been monitored using a RNA fingerprinting technique termed cDNA-AFLP. The expression profile of the nearly 2000 transcript derived fragments (TDFs) was analysed and general conclusions concerning the different stages of tuber life cycle and tissue specificity were drawn. Comparison of 116 TDFs isolated and sequenced to the NCBI databases indicated that most of the genes expressed during tuber life cycle are involved in defence, stress, storage and signal transduction pathways. In order to identify time and tissue specific regulatory elements, the TDFs were further screened for their time and tissue specific expression and the putative promoters corresponding to the twelve differentially expressed TDFs were isolated. Comparison of the 12 upstream sequences to all described cis-acting elements resulted in the identification of 12 know cis-acting elements: two general cis-elements, one enhancer and nine specific boxes. These specific cis-elements have been characterised in other plant species and they respond to light, sugars and hormones such as gibberellins, auxins and abscisic acid (ABA). All these environmental factors play an important role during the potato tuber life cycle. [Copyright &y& Elsevier]

Abstract: Two transgenic potato lines, csr2–1 and csr4–8 that contained two different antisense cellulose synthase (CesA) genes, csr2 and csr4, respectively were crossed. The aim, amongst others, was to investigate the possibility of generating double transformants to validate a hypothetical presence of the proteins of the two CesA genes in the same cellulose synthase enzyme complex. SYBR-Green quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) assays were carried out on four CesA gene transcripts (CesA1, 2, 3, and 4) in the wild type genetic background, and on the two antisense CesA gene transcripts (CesA2 and 4) in the progeny resulting from the cross between the two transgenic potato lines. The quantitative RT-PCR analyses revealed different expression patterns of the two CesA genes. The CesA2 mRNA was shown to be relatively more abundant than CesA4 mRNA, regardless of the genetic background, suggesting that the two proteins are not present in the same enzyme complex. [Copyright &y& Elsevier]