RLP/K enrichment sequencing; a novel method to identify receptor-like protein (RLP) and receptor-like kinase (RLK) genes
Lin, Xiao ; Armstrong, Miles ; Baker, Katie ; Wouters, Doret ; Visser, Richard G.F. ; Wolters, Pieter J. ; Hein, Ingo ; Vleeshouwers, Vivianne G.A.A. - \ 2020
New Phytologist 227 (2020)4. - ISSN 0028-646X - p. 1264 - 1276.
genotyping by sequencing (GBS) - pattern recognition receptor (PRR) - Phytophthora infestans - potato - receptor-like kinase (RLK) - receptor-like protein (RLP) - RenSeq - RLP/K enrichment sequencing (RLP/KSeq)
The identification of immune receptors in crop plants is time-consuming but important for disease control. Previously, resistance gene enrichment sequencing (RenSeq) was developed to accelerate mapping of nucleotide-binding domain and leucine-rich repeat containing (NLR) genes. However, resistances mediated by pattern recognition receptors (PRRs) remain less utilized. Here, our pipeline shows accelerated mapping of PRRs. Effectoromics leads to precise identification of plants with target PRRs, and subsequent RLP/K enrichment sequencing (RLP/KSeq) leads to detection of informative single nucleotide polymorphisms that are linked to the trait. Using Phytophthora infestans as a model, we identified Solanum microdontum plants that recognize the apoplastic effectors INF1 or SCR74. RLP/KSeq in a segregating Solanum population confirmed the localization of the INF1 receptor on chromosome 12, and led to the rapid mapping of the response to SCR74 to chromosome 9. By using markers obtained from RLP/KSeq in conjunction with additional markers, we fine-mapped the SCR74 receptor to a 43-kbp G-LecRK locus. Our findings show that RLP/KSeq enables rapid mapping of PRRs and is especially beneficial for crop plants with large and complex genomes. This work will enable the elucidation and characterization of the nonNLR plant immune receptors and ultimately facilitate informed resistance breeding.
Genotypic and phenotypic characterization of Phytophthora infestans in South Korea during 2009–2016 reveals clonal reproduction and absence of EU_13_A2 genotype
Choi, Jang Gyu ; Hong, Su Young ; Kessel, Geert J.T. ; Cooke, David E.L. ; Vossen, Jack H. ; Cho, Ji Hong ; Im, Ju Seong ; Park, Young Eun ; Cho, Kwang Soo - \ 2020
Plant Pathology 69 (2020)5. - ISSN 0032-0862
genotype - late blight - phenotype - potato - SSR
In order to better understand the Phytophthora infestans population structure in South Korea, 172 isolates were collected between 2009 and 2016 from four major potato cultivation areas. Fungicide (metalaxyl and dimethomorph) response, mating type, and microsatellite (SSR) genetic fingerprints were analysed to characterize these isolates. Ten isolates collected in Gyeongnam Province, which specializes in protected winter cultivation in polytunnels, were A2 mating type. All other isolates were A1 mating type. Overall, 42% of the isolates were resistant to metalaxyl, and 43% were sensitive. All isolates were sensitive to dimethomorph. From the SSR fingerprints, 45 distinct genotypes were identified, which could be clustered into four clonal lineages: KR_1_A1, KR_2_A2, SIB-1, and US-11. KR_1_A1 was the predominant P. infestans genotype in South Korea. KR_2_A2 was only found in Gyeongnam Province; all isolates were A2 mating type and resistant to metalaxyl. SIB-1 was dominant until 2013 but its frequency has gradually decreased in more recent years. US-11 was first found in 2014, after which its frequency has increased to become codominant with KR_1_A1. The calculated standardized index of association (IA) suggests that the South Korean P. infestans population is undergoing clonal reproduction. When compared with populations of P. infestans from the Netherlands, it has less genetic diversity and the dominant Netherlands P. infestans genotype, EU_13_A2 (Blue_13), was not found in South Korea. Such monitoring of the pathogen population contributes to a more efficient integrated pest management-based control strategy for potato late blight control in South Korea.
UAV-based Multispectral & Thermal dataset for exploring the diurnal variability, radiometric & geometric accuracy for precision agriculture
Kallimani, Christina ; Heidarian Dehkordi, Ramin ; Evert, Frits van; Kooistra, Lammert ; Rijk, Bert - \ 2020
Wageningen University & Research
multispectral - thermal infrared - diurnal variability - unmanned aerial vehicles (UAV) - precision agriculture - wheat - potato - barley
To explore the diurnal variations, radiometric and geometric accuracy of UAV-based data for precision agriculture, a comprehensive dataset was created in a one-day field campaign (21 June 2017). The multi-sensor data set covers wheat, barley & potato experimental fields, located in Wageningen University and Research (WUR) farm maintained by Unifarm. UAV-based images were collected with several sensors over the experimental area, starting from 7:25am and ending at 20:00pm local solar time. The dataset consists of images collected by 9 flights with senseFly MSP4C, 9 with Parrot Sequoia, 2 with Slant Range P3, 5 with DJI Zenmuse X3 NIR, 4 with the senseFly Thermo-map and 1 with the RGB Sony WX-220. Additionally, validation measurements at radiometric calibration plates and plant sample locations were taken with a Cropscan handheld spectrometer and a tec5 Handyspec spectrometer. The dataset consists of the validation measurements, the raw images and the processed orthomosaics (both with and without geometric correction).
Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence
Pasanen, M. ; Waleron, M. ; Schott, Thomas ; Cleenwerck, I. ; Misztak, Agieszka ; Waleron, Krzysztof ; Pritchard, L. ; Bakr, Ramadan ; Degefu, Yeshtila ; Wolf, J.M. van der; Vandamme, Peter ; Pirhonen, M. - \ 2020
International Journal of Systematic and Evolutionary Microbiology 70 (2020)4. - ISSN 1466-5026 - p. 2440 - 2448.
Pectobacterium - Pectobacterium parvum - Salmonella SPI-1 T3SS - potato - soft rot - virulence
Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second clade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421T (CFBP 8630T=LMG 30828T) is suggested as a type strain.
Tracking disease resistance deployment in potato breeding by enrichment sequencing
Armstrong, Miles R. ; Vossen, Jack ; Lim, Tze Yin ; Hutten, Ronald C.B. ; Xu, Jianfei ; Strachan, Shona M. ; Harrower, Brian ; Champouret, Nicolas ; Gilroy, Eleanor M. ; Hein, Ingo - \ 2019
Plant Biotechnology Journal 17 (2019)2. - ISSN 1467-7644 - p. 540 - 549.
breeding - crops - disease resistance genes - dRenSeq - potato - tracking of NLRs
Following the molecular characterisation of functional disease resistance genes in recent years, methods to track and verify the integrity of multiple genes in varieties are needed for crop improvement through resistance stacking. Diagnostic resistance gene enrichment sequencing (dRenSeq) enables the high-confidence identification and complete sequence validation of known functional resistance genes in crops. As demonstrated for tetraploid potato varieties, the methodology is more robust and cost-effective in monitoring resistances than whole-genome sequencing and can be used to appraise (trans) gene integrity efficiently. All currently known NB-LRRs effective against viruses, nematodes and the late blight pathogen Phytophthora infestans can be tracked with dRenSeq in potato and hitherto unknown polymorphisms have been identified. The methodology provides a means to improve the speed and efficiency of future disease resistance breeding in crops by directing parental and progeny selection towards effective combinations of resistance genes.
AgMIP's Global Gridded Crop Model Intercomparison (GGCMI) phase 1 output data set: CGMS-WOFOST potato
Hoek, Steven ; Wit, Allard de - \ 2018
Wageningen University and Research
AgMIP - GGCMI - crop model - historical simulations - global - potato - CGMS-WOFOST
This is model output from CGMS-WOFOST for potato as part of AgMIP's Global Gridded Crop Model Intercomparison (GGCMI) phase 1 output data set. The data have been generated following the modeling protocol of Elliott et al. (2015) and has been used to evaluate the models (Müller et al., 2017). A data description paper has been published in Scientific Data (Müller et al. 2019).
Quantitative Trait Loci in Solanaceae species
Kuzniar, Arnold ; Singh, G. - \ 2018
Wageningen University & Research
plant breeding - plant genetics - quantitative trait locus - QTL - genetic marker - trait - Solanaceae - tomato - potato - FAIR data - RDF - SQLite - csv
This tar archive contains experimental data on Quantitative Trait Loci (QTLs) mapped in Solanacea species. In particular, the QTL data were extracted from tomato- and potato-specific literature using the QTL TableMiner++ tool, and the resulting data were made available in machine-readable and semantically-interoperable formats: SQLite database (.db); comma-separated value file (.csv); RDF/Turle file (.ttl).
Data from global field experiments for potato simulations
Raymundo, Rubi ; Asseng, Senthold ; Prasad, Rishi ; Kleinwechter, Ulrich ; Condori, Bruno ; Bowen, Walter ; Wolf, J. ; Olesen, Jørgen E. ; Dong, Qiaoxue ; Zotarelli, Lincoln ; Gastelo, Manuel ; Alva, Ashok ; Travasso, Maria ; Arora, Vijay - \ 2018
Wageningen University & Research
potato - field experimental data - simulations
Interspecies Respect and Potato Conservation in the Peruvian Cradle of Domestication
Angé, Olivia ; Chipa, Adrian ; Condori, Pedro ; Ccoyo, Aniceto Ccoyo ; Mamani, Lino ; Pacco, Ricardo ; Quispe, Nazario ; Quispe, Walter ; Sutta, Mariano - \ 2018
Conservation and Society 16 (2018)1. - ISSN 0972-4923 - p. 30 - 40.
affect - agrobiodiversity - Andes - conservation - Cuzco Highlands - ethics - interspecies sociality - non-human charisma - Peru - potato - respect
This paper explores people and tuber affective encounters, as they unfold in a biodiversity conservation programme in the Peruvian Andes. It draws on ethnographic data from the Potato Park, renowned worldwide as one of the most successful in-situ initiatives for the conservation of biocultural diversity. Concerned with interspecies relations, the paper focusses on the circulation of respeto that is both an affect and a normative stance posited locally as necessary for the conservation of the potato. Addressing first expressions of respeto in daily potato practices by highland peasants, the paper then explores its importance within the context of the Park's conservation policy. Agricultural investigations and seed-banking are indeed enmeshed in activities intended to intensify potato-people regard. Throughout the paper, the concept of non-human charisma is used to point out the different kinds of potato appraisals experienced in the Park; as well as how the Park concretely works toward human beings' learning 'how to be affected' by tuber agrobiodiversity. The article finally explains how potato affective agency is extended beyond the Park, to reach the international scene. Exploring the Potato Park from the perspective of respeto, and using charisma as a heuristic tool, it enlightens a mode of conservation initiative; creating flourishing ecologies through affective encounters, that cannot be accounted for with an instrumental approach.
Potato late blight field resistance from QTL dPI09c is conferred by the NB-LRR gene R8
Jiang, Rui ; Li, Jingcai ; Tian, Zhendong ; Du, Juan ; Armstrong, Miles ; Baker, Katie ; Tze-Yin Lim, Joanne ; Vossen, Jack H. ; He, Huan ; Portal, Leticia ; Zhou, Jun ; Bonierbale, Merideth ; Hein, Ingo ; Lindqvist-Kreuze, Hannele ; Xie, Conghua - \ 2018
Journal of Experimental Botany 69 (2018)7. - ISSN 0022-0957 - p. 1545 - 1555.
dRenSeq - field resistance - late blight - map-based cloning - potato - R gene
Following the often short-lived protection that major nucleotide binding, leucine-rich-repeat (NB-LRR) resistance genes offer against the potato pathogen Phytophthora infestans, field resistance was thought to provide a more durable alternative to prevent late blight disease. We previously identified the QTL dPI09c on potato chromosome 9 as a more durable field resistance source against late blight. Here, the resistance QTL was fine-mapped to a 186 kb region. The interval corresponds to a larger, 389 kb, genomic region in the potato reference genome of Solanum tuberosum Group Phureja doubled monoploid clone DM1-3 (DM) and from which functional NB-LRRs R8, R9a, Rpi-moc1, and Rpi-vnt1 have arisen independently in wild species. dRenSeq analysis of parental clones alongside resistant and susceptible bulks of the segregating population B3C1HP showed full sequence representation of R8. This was independently validated using long-range PCR and screening of a bespoke bacterial artificial chromosome library. The latter enabled a comparative analysis of the sequence variation in this locus in diverse Solanaceae. We reveal for the first time that broad spectrum and durable field resistance against P. infestans is conferred by the NB-LRR gene R8, which is thought to provide narrow spectrum race-specific resistance.
Potato StCONSTANS-like1 Suppresses Storage Organ Formation by Directly Activating the FT-like StSP5G Repressor
Abelenda, José A. ; Cruz-Oró, Eduard ; Franco-Zorrilla, José Manuel ; Prat, Salomé - \ 2016
Current Biology 26 (2016)7. - ISSN 0960-9822 - p. 872 - 881.
CONSTANS - FLOWERING LOCUS T - potato - tuberigen
The CONSTANS-FT pathway defines a core module for reproductive transition in both long-day (LD) and short-day (SD) plants. Changes in the transcriptional function of the CONSTANS (CO) protein have been proposed to mediate differential SD activation of FLOWERING LOCUS T (FT) orthologs in SD plants. Potato Andigena genotypes have an obligate SD requirement for tuber formation, and this photoperiodic response correlates with activation of the FT StSP6A gene in leaves. The potato StCOL1 factor represses expression of this mobile tuberization signal, but the control mechanism is poorly understood. Here, we analyzed StCOL1 diurnal oscillation and protein accumulation at different photoperiods and light wavelengths. We observed that the potato StCOL1 gene peaked at dawn and that, in contrast to the Arabidopsis AtCO homolog, the light receptor phyB is necessary for protein stabilization in the light. Reduced StCOL1 levels in RNAi lines strongly correlated with downregulated expression of an additional potato FT family member, StSP5G. Co-regulated StCOL1 and StSP5G expression suggested that StCOL1 activates this target directly rather than controlling StSP6A expression. By hybridization of a universal protein-binding microarray, we established that StCOL1 binds a TGTGGT element, and we found that immunoprecipitated StCOL1 protein fractions were enriched in StSP5G promoter fragments bearing this element. We show that StSP5G represses tuberization in LD conditions and that this FT-like homolog suppresses StSP6A gene expression. Rewiring StCOL1 transcriptional function from direct activation of the StSP6A inducer signal to the control of an FT-like repressor thus mediates the strict SD requirement of Andigena plants for tuberization.
Immune activation mediated by the late blight resistance protein R1 requires nuclear localization of R1 and AVR1
Du, Y. ; Berg, J. ; Govers, F. ; Bouwmeester, K. - \ 2015
New Phytologist 207 (2015)3. - ISSN 0028-646X - p. 735 - 747.
disease-resistance - phytophthora-infestans - arabidopsis-thaliana - innate immunity - plant immunity - receptor - recognition - potato - gene - component
Resistance against oomycete pathogens is mainly governed by intracellular nucleotide-binding leucine-rich repeat (NLR) receptors that recognize matching avirulence (AVR) proteins from the pathogen, RXLR effectors that are delivered inside host cells. Detailed molecular understanding of how and where NLR proteins and RXLR effectors interact is essential to inform the deployment of durable resistance (R) genes. Fluorescent tags, nuclear localization signals (NLSs) and nuclear export signals (NESs) were exploited to determine the subcellular localization of the potato late blight protein R1 and the Phytophthora infestans RXLR effector AVR1, and to target these proteins to the nucleus or cytoplasm. Microscopic imaging revealed that both R1 and AVR1 occurred in the nucleus and cytoplasm, and were in close proximity. Transient expression of NLS- or NES-tagged R1 and AVR1 in Nicotiana benthamiana showed that activation of the R1-mediated hypersensitive response and resistance required localization of the R1/AVR1 pair in the nucleus. However, AVR1-mediated suppression of cell death in the absence of R1 was dependent on localization of AVR1 in the cytoplasm. Balanced nucleocytoplasmic partitioning of AVR1 seems to be a prerequisite. Our results show that R1-mediated immunity is activated inside the nucleus with AVR1 in close proximity and suggest that nucleocytoplasmic transport of R1 and AVR1 is tightly regulated.
Damage thresholds and population dynamics of Meloidogyne chitwoodi on carrot (Daucus carota) at different seed densities
Heve, W.K. ; Been, T.H. ; Schomaker, C.H. ; Teklu, M.G. - \ 2015
Nematology 17 (2015)5. - ISSN 1388-5545 - p. 501 - 514.
plant-parasitic nematodes - root-knot nematode - partial resistance - potato - cultivars - increase - hapla
Yield loss of carrot (Daucus carota) cv. Nerac caused by Meloidogyne chitwoodi and population dynamics of this nematode were studied using a range of 13 nematode densities at three seed densities (2, 4, 18 seeds pot-1) in a climate-controlled glasshouse. Yield and quality data were fitted to Seinhorst’s yield models. Final population densities were fitted to the population dynamic models for sedentary and free-living nematodes. The tolerance limits for yield loss were 0.34, 0.62 and 0.50, while that of quality were 0.012, 0.142 and 0.813 second-stage juveniles (J2) (g dry soil)-1 at increasing seed densities, respectively. The minimum yield (m), increased with seed density: 0.25, 0.30 and 0.50; the minimum quality yield was 0.10, 0.08 and 0.15 J2 (g dry soil)-1 at increasing seed densities, respectively. Both maximum multiplication rates and maximum population densities increased with increasing seed density but were generally low. Carrot cv. Nerac can be considered a bad host for M. chitwoodi.
Introgression Browser: High throughput whole-genome SNP visualization
Aflitos, S.A. ; Sanchez Perez, G.F. ; Ridder, D. de; Fransz, P. ; Schranz, M.E. ; Jong, J.H.S.G.M. de; Peters, S.A. - \ 2015
The Plant Journal 82 (2015)1. - ISSN 0960-7412 - p. 174 - 182.
in-situ hybridization - alien chromosomes - recombination - tomato - markers - thaliana - potato - identification - organization - improvement
Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not viable. Here, we present the Introgression Browser (IBROWSER), a bioinformatics tool aimed at visualizing introgressions at nucleotide or SNP accuracy. The software selects homozygous SNPs from Variant Call Format (VCF) information and filters out heterozygous SNPs, Multi-Nucleotide Polymorphisms (MNPs) and insertion-deletions (InDels). For data analysis IBROWSER makes use of sliding windows, but if needed it can generate any desired fragmentation pattern through General Feature Format (GFF) information. In an example of tomato (Solanum lycopersicum) accessions we visualize SNP patterns and elucidate both position and boundaries of the introgressions. We also show that our tool is capable of identifying alien DNA in a panel of the closely related S. pimpinellifolium by examining phylogenetic relationships of the introgressed segments in tomato. In a third example, we demonstrate the power of the IBROWSER in a panel of 597 Arabidopsis accessions, detecting the boundaries of a SNP-free region around a polymorphic 1.17 Mbp inverted segment on the short arm of chromosome 4. The architecture and functionality of IBROWSER makes the software appropriate for a broad set of analyses including SNP mining, genome structure analysis, and pedigree analysis. Its functionality, together with the capability to process large data sets and efficient visualization of sequence variation, makes IBROWSER a valuable breeding tool.
Effects of salt on the expansion of starchy snacks: a multiscale analysis
Sman, R.G.M. van der; Broeze, J. - \ 2014
Food & Function 5 (2014)12. - ISSN 2042-6496 - p. 3076 - 3082.
glass-transition - sodium-chloride - aqueous-solutions - mass-transfer - sucrose - extrusion - potato - water - trehalose - mixtures
We investigate the effect of salt on the expansion of starchy snacks during frying by means of a multiscale simulation model. This model has been developed earlier for starchy snacks without salt. The simulation results are analysed by means of the supplemented state diagram. We have found that the optimal expansion for salty snacks occurs under the same conditions as for snacks without salt. This occurs at the moisture content where the 4 bar boiling line intersects the critical isoviscosity line of 1 MPa s. Salt is shown to influence both the boiling line and the critical isoviscosity line, via a change of the glass transition. The optimal moisture content for salty snacks is lower than that of unsalted snacks. We view our findings as important for reformulations of starchy snacks with lower salt levels. Furthermore, the presented tools of the multiscale simulations and supplemented state diagram can generally be used for reformulation problems in structured foods.
Development of a Multiplexed Bead-Based Suspension Array for the Detection and Discrimination of Pospiviroid Plant Pathogens
Brunschot, S.L. van; Bergervoet, J.H.W. ; Pagendam, D.E. ; Weerdt, M. de; Geering, A.D.W. ; Drenth, A. ; Vlugt, R.A.A. van der - \ 2014
PLoS ONE 9 (2014)1. - ISSN 1932-6203
rt-pcr assay - 1st report - greenhouse tomatoes - natural infection - viroid disease - potato - identification - transmission - technology - strain
Efficient and reliable diagnostic tools for the routine indexing and certification of clean propagating material are essential for the management of pospiviroid diseases in horticultural crops. This study describes the development of a true multiplexed diagnostic method for the detection and identification of all nine currently recognized pospiviroid species in one assay using Luminex bead-based suspension array technology. In addition, a new data-driven, statistical method is presented for establishing thresholds for positivity for individual assays within multiplexed arrays. When applied to the multiplexed array data generated in this study, the new method was shown to have better control of false positives and false negative results than two other commonly used approaches for setting thresholds. The 11-plex Luminex MagPlex-TAG pospiviroid array described here has a unique hierarchical assay design, incorporating a near-universal assay in addition to nine species-specific assays, and a co-amplified plant internal control assay for quality assurance purposes. All assays of the multiplexed array were shown to be 100% specific, sensitive and reproducible. The multiplexed array described herein is robust, easy to use, displays unambiguous results and has strong potential for use in routine pospiviroid indexing to improve disease management strategies.
Response of Solanum tuberosum to Myzus persicae infestation at different stages of foliage maturity
Alvarez, A.E. ; Alberti D'Amato, A.M. ; Tjallingii, W.F. ; Dicke, M. ; Vosman, B. - \ 2014
Insect Science 21 (2014)6. - ISSN 1672-9609 - p. 727 - 740.
aphid brevicoryne-brassicae - russian wheat aphid - leaf senescence - hemiptera aphididae - gene-expression - plant defense - macrosiphum-euphorbia - susceptible wheat - arabidopsis - potato
Young leaves of the potato Solanum tuberosum L. cultivar Kardal contain resistance factors to the green peach aphid Myzus persicae (Sulzer) (Hemiptera: Aphididae) and normal probing behavior is impeded. However, M. persicae can survive and reproduce on mature and senescent leaves of the cv. Kardal plant without problems. We compared the settling of M. persicae on young and old leaves and analyzed the impact of aphids settling on the plant in terms of gene expression. Settling, as measured by aphid numbers staying on young or old leaves, showed that after 21 h significantly fewer aphids were found on the young leaves. At earlier time points there were no difference between young and old leaves, suggesting that the young leaf resistance factors are not located at the surface level but deeper in the tissue. Gene expression was measured in plants at 96 h postinfestation, which is at a late stage in the interaction and in compatible interactions this is long enough for host plant acceptance to occur. In old leaves of cv. Kardal (compatible interaction), M. persicae infestation elicited a higher number of differentially regulated genes than in young leaves. The plant response to aphid infestation included a larger number of genes induced than repressed, and the proportion of induced versus repressed genes was larger in young than in old leaves. Several genes changing expression seem to be involved in changing the metabolic state of the leaf from source to sink.
Management of irrigation frequency and nitrogen fertilization to mitigate GHG and NO emissions from drip-fertigated crops
Abalos, D. ; Sanchez-Martin, L. ; Garcia-Torres, L. ; Groenigen, J.W. van; Vallejo, A. - \ 2014
Science of the Total Environment 490 (2014). - ISSN 0048-9697 - p. 880 - 888.
treated pig slurries - oxide emissions - n2o emissions - mediterranean climate - nitric-oxide - soil - water - potato - carbon - field
Drip irrigation combined with split application of fertilizer nitrogen (N) dissolved in the irrigation water (i.e. drip fertigation) is commonly considered best management practice for water and nutrient efficiency. As a consequence, its use is becoming widespread. Some of the main factors (water-filled pore space, NH4+ and NO3-) regulating the emissions of greenhouse gases (i.e. N2O, CO2 and CH4) and NO from agroecosystems can easily be manipulated by drip fertigation without yield penalties. In this study, we tested management options to reduce these emissions in a field experiment with a melon (Cucumis melo L.) crop. Treatments included drip irrigation frequency (weekly/daily) and type of N fertilizer (urea/calcium nitrate) applied by fertigation. Crop yield, environmental parameters, soil mineral N concentrations and fluxes of N2O, NO, CH4 and CO2 were measured during 85 days. Fertigation with urea instead of calcium nitrate increased N2O and NO emissions by a factor of 2.4 and 2.9, respectively (P <0.005). Daily irrigation reduced NO emissions by 42% (P <0.005) but increased CO2 emissions by 21% (P <0.05) compared with weekly irrigation. We found no relation between irrigation frequency and N2O emissions. Based on yield-scaled Global Warming Potential as well as NO cumulative emissions, we conclude that weekly fertigation with a NO3--based fertilizer is the best option to combine agronomic productivity with environmental sustainability. Our study shows that adequate management of drip fertigation, while contributing to the attainment of water and food security, may provide an opportunity for climate change mitigation.
Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family
Resjö, S. ; Ali, A. ; Meijer, H.J.G. ; Seidl, M.F. ; Snel, B. ; Sandin, M. ; Levander, F. ; Govers, F. ; Andreasson, E. - \ 2014
Journal of Proteome Research 13 (2014)4. - ISSN 1535-3893 - p. 1848 - 1859.
tandem mass-spectrometry - protein-kinases - arabidopsis-thaliana - in-vitro - proteomics - identification - expression - potato - organization - specificity
The oomycete Phytophthora infestans is the causal agent of late blight in potato and tomato. Since the underlying processes that govern pathogenicity and development in P. infestans are largely unknown, we have performed a large-scale phosphoproteomics study of six different P. infestans life stages. We have obtained quantitative data for 2922 phosphopeptides and compared their abundance. Life-stage-specific phosphopeptides include ATP-binding cassette transporters and a kinase that only occurs in appressoria. In an extended data set, we identified 2179 phosphorylation sites and deduced 22 phosphomotifs. Several of the phosphomotifs matched consensus sequences of kinases that occur in P. infestans but not Arabidopsis. In addition, we detected tyrosine phosphopeptides that are potential targets of kinases resembling mammalian tyrosine kinases. Among the phosphorylated proteins are members of the RXLR and Crinkler effector families. The latter are phosphorylated in several life stages and at multiple positions, in sites that are conserved between different members of the Crinkler family. This indicates that proteins in the Crinkler family have functions beyond their putative role as (necrosis-inducing) effectors. This phosphoproteomics data will be instrumental for studies on oomycetes and host–oomycete interactions. The data sets have been deposited to ProteomeXchange (identifier PXD000433).
Increased difficulties to control late blight in Tunisia are caused by a genetically diverse Phytophthora infestans population next to the clonal lineage NA-01
Harbaoui, K. ; Hamada, W. ; Li, Y. ; Vleeshouwers, V.G.A.A. ; Lee, T.A.J. van der - \ 2014
Plant Disease 98 (2014)7. - ISSN 0191-2917 - p. 898 - 908.
genotypic diversity - durable resistance - potato - tomato - plant - netherlands - virulence
In Tunisia, late blight caused by Phytophthora infestans is a serious threat to potato and tomato. The Mediterranean weather conditions can be conducive to infection in all seasons and the host crops, tomato and potato, are grown year round. Potato is planted and harvested in two to four overlapping intervals from August to June and tomato is grown both in open fields and in greenhouses. The consequences of these agricultural practices and the massive import of seed potato on the genetic variation of P. infestans are largely unknown. We conducted a survey in which 165 P. infestans isolates, collected from five subregions in Tunisia between 2006 and 2008, on which we studied genotypic diversity through nuclear (simple-sequence repeat [SSR]) markers and combined this with a previous study on their mitochondrial haplotypes (mtDNA). The phylogenetic analysis revealed the presence of a major clonal lineage (NA-01, A1 mating type, mitochondrial haplotype Ia). Isolates belonging to this clonal lineage were found in all regions and showed a relatively simple virulence pattern on a potato differential set carrying different Solanum demissum resistance genes. Apart from isolates belonging to this NA-01 clonal lineage, a group of isolates was found that showed a high genetic diversity, comprising both mating types and a more complex race structure that was found in the regions where late blight on potato was more difficult to control. The population on potato and tomato seems to be under different selection pressures. Isolates collected from tomato showed a low genetic diversity even though potato isolates collected simultaneously from the same location showed a high genetic diversity. Based on the SSR profile comparison, we could demonstrate that the four major clonal lineages found in the Netherlands and also in other European countries could not be found in Tunisia. Despite the massive import of potato seed from Europe, the P. infestans population in Tunisia was found to be clearly distinct