Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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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 - \ 2018
Plant Biotechnology Journal (2018). - ISSN 1467-7644
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.

Quantitative Trait Loci in Solanaceae species
Kuzniar, Arnold ; Singh, G. - \ 2018
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
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.
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
Effect of physical damage and storage of pineapple fruits on their suitability for juice production
Hounhouigan, M.H. ; Linnemann, A.R. ; Ingenbleek, P.T.M. ; Soumanou, M.M. ; Trijp, H.C.M. van; Boekel, T. van - \ 2014
Journal of Food Quality 37 (2014)4. - ISSN 0146-9428 - p. 268 - 273.
ascorbic-acid content - vitamin-c content - orange - temperature - potato - fresh
This study evaluated the suitability of physically damaged pineapples, variety “MD2,” that were stored for up to 9 days at 20C for the production of fresh pineapple juice. Fresh pineapples were bruised and cut in different ways. The study showed an interaction effect of the physical damage treatments and storage duration on juice pH, total soluble solids and sucrose content. However, bruising and cutting treatments did not affect the physicochemical qualities and vitamin C content of the fresh juice. Furthermore, storage of pineapple fruits for up to 9 days was accompanied by an increase of glucose and fructose.
Development and evaluation of Taqman assays for the differentiation of Dickeya (sub)species
Wolf, J.M. van der; Haas, B.H. de; Hoof, R.A. van; Haan, E.G. de; Bovenkamp, G.W. van den - \ 2014
European Journal of Plant Pathology 138 (2014)4. - ISSN 0929-1873 - p. 695 - 709.
complete genome sequence - syn. erwinia-chrysanthemi - potato - strains - pcr - relatedness - polymerase - clade - crops - hosts
TaqMan assays were developed for the detection of seven Dickeya species, namely D. dianthicola, D. dadantii, D. paradisiaca, D. chrysanthemi, D. zeae, D. dieffenbachiae and D. solani. Sequences of the gene coding for dnaX were used for the design of primers and probes. In studies with axenic cultures of bacteria, the assays were highly specific and only reacted with strains of the target species, and not with non-target bacteria, including those belonging to other Dickeya species and other genera. The detection thresholds for DNA extracted from pure cultures of target strains ranged from 10 to 100 fg. The TaqMan assays for D. dianthicola and D. solani were more extensively evaluated as part of a method validation procedure. The threshold level for target bacteria added to a potato peel extract diluted ten-times in a semi-selective broth, was strain dependent and ranged from 1,000 to 100,000 cfu/ml. The coefficients of variation for repeatability and reproducibility were low and results were largely independent of the type of substrate, i.e. potato tuber or carnation leaf extracts. However, during routine testing of seed potatoes, false-positive reactions were found with the assay for D. solani. The use of the TaqMan assays for inspection of plant propagation material, ecological studies and studies on the effect of control strategies in disease management strategies is discussed
Novel applications of motif-directed profiling to identify disease resistance genes in plants
Vossen, J.H. ; Dezhsetan, S. ; Esselink, D. ; Arens, M. ; Sanz, M.J. ; Verweij, W. ; Verzaux, E. ; Linden, C.G. van der - \ 2013
Plant Methods 9 (2013). - ISSN 1746-4811
nucleotide-binding-site - kinase-like protein - phytophthora-infestans - conferring resistance - fusarium-oxysporum - diploid avena - potato - map - loci - encodes
Background: Molecular profiling of gene families is a versatile tool to study diversity between individual genomes in sexual crosses and germplasm. Nucleotide binding site (NBS) profiling, in particular, targets conserved nucleotide binding site-encoding sequences of resistance gene analogs (RGAs), and is widely used to identify molecular markers for disease resistance (R) genes. Results: In this study, we used NBS profiling to identify genome-wide locations of RGA clusters in the genome of potato clone RH. Positions of RGAs in the potato RH and DM genomes that were generated using profiling and genome sequencing, respectively, were compared. Largely overlapping results, but also interesting discrepancies, were found. Due to the clustering of RGAs, several parts of the genome are overexposed while others remain underexposed using NBS profiling. It is shown how the profiling of other gene families, i.e. protein kinases and different protein domain-coding sequences (i.e., TIR), can be used to achieve a better marker distribution. The power of profiling techniques is further illustrated using RGA cluster-directed profiling in a population of Solanum berthaultii. Multiple different paralogous RGAs within the Rpi-ber cluster could be genetically distinguished. Finally, an adaptation of the profiling protocol was made that allowed the parallel sequencing of profiling fragments using next generation sequencing. The types of RGAs that were tagged in this next-generation profiling approach largely overlapped with classical gel-based profiling. As a potential application of next-generation profiling, we showed how the R gene family associated with late blight resistance in the SH*RH population could be identified using a bulked segregant approach. Conclusions: In this study, we provide a comprehensive overview of previously described and novel profiling primers and their genomic targets in potato through genetic mapping and comparative genomics. Furthermore, it is shown how genome-wide or fine mapping can be pursued by choosing different sets of profiling primers. A protocol for next-generation profiling is provided and will form the basis for novel applications. Using the current overview of genomic targets, a rational choice can be made for profiling primers to be employed.
Fine mapping of the Ph-3 gene conferring resistance to late blight (Phytophthora infestans) in tomato
Zhang, C.Z. ; Liu, L. ; Zheng, Z. ; Sun, Y.Y. ; Zhou, L.X. ; Yang, Y.H. ; Cheng, F. ; Zhang, Z.H. ; Wang, X.W. ; Huang, S.W. ; Xie, B.Y. ; Du, Y.C. ; Bai, Y. ; Li, J.M. - \ 2013
Theoretical and Applied Genetics 126 (2013)10. - ISSN 0040-5752 - p. 2643 - 2653.
species solanum-pimpinellifolium - disease resistance - united-states - potato - cloning - virus - accession - effectors - genomics - venturii
Late blight, caused by the oomycete pathogen Phytophthora infestans (Mont.) de Bary, is a devastating disease for tomato and potato crops. In the past decades, many late blight resistance (R) genes have been characterized in potato. In contrast, less work has been conducted on tomato. The Ph-3 gene from Solanum pimpinellifolium was introgressed into cultivated tomatoes and conferred broad-spectrum resistance to P. infestans. It was previously assigned to the long arm of chromosome 9. In this study, a high-resolution genetic map covering the Ph-3 locus was constructed using an F-2 population of a cross between Solanum lycopersicum CLN2037B (containing Ph-3) and S. lycopersicum LA4084. Ph-3 was mapped in a 0.5 cM interval between two markers, Indel_3 and P55. Eight putative genes were found in the corresponding 74 kb region of the tomato Heinz1706 reference genome. Four of these genes are resistance gene analogs (RGAs) with a typical nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 domain. Each RGA showed high homology to the late blight R gene Rpi-vnt1.1 from Solanum venturii. Transient gene silencing indicated that a member of this RGA family is required for Ph-3-mediated resistance to late blight in tomato. Furthermore, this RGA family was also found in the potato genome, but the number of the RGAs was higher than in tomato.
Genetic progress in Dutch crop yields
Rijk, H.C.A. ; Ittersum, M.K. van; Withagen, J.C.M. - \ 2013
plant breeding and genetics - winter wheat - spring barley - potato - sugar beet - crop yield - genetic improvement
This dataset contains the underlying data for the study: Rijk, B., Ittersum, M. van, Withagen, J. "Genetic progress in Dutch crop yields". Field Crops Research 149 (2013) 262–268,
Genomic analysis of the native European Solanum species, S. dulcamara
Agostino, N.D. ; Golas, T. ; Geest, H. van; Bombarely, A. ; Dawood, T. ; Zethof, J. ; Driedonks, N. ; Wijnker, T.G. ; Bargsten, J. ; Nap, J.P. ; Mariani, C. ; Rieu, I. - \ 2013
BMC Genomics 14 (2013). - ISSN 1471-2164 - 14 p.
phytophthora-infestans - solanaceae - identification - evolution - polymorphism - sequence - tomato - potato - genes
Background - Solanum dulcamara (bittersweet, climbing nightshade) is one of the few species of the Solanaceae family native to Europe. As a common weed it is adapted to a wide range of ecological niches and it has long been recognized as one of the alternative hosts for pathogens and pests responsible for many important diseases in potato, such as Phytophthora. At the same time, it may represent an alternative source of resistance genes against these diseases. Despite its unique ecology and potential as a genetic resource, genomic research tools are lacking for S. dulcamara. We have taken advantage of next-generation sequencing to speed up research on and use of this non-model species. Results - In this work, we present the first large-scale characterization of the S. dulcamara transcriptome. Through comparison of RNAseq reads from two different accessions, we were able to predict transcript-based SNP and SSR markers. Using the SNP markers in combination with genomic AFLP and CAPS markers, the first genome-wide genetic linkage map of bittersweet was generated. Based on gene orthology, the markers were anchored to the genome of related Solanum species (tomato, potato and eggplant), revealing both conserved and novel chromosomal rearrangements. This allowed a better estimation of the evolutionary moment of rearrangements in a number of cases and showed that chromosomal breakpoints are regularly re-used. Conclusion - Knowledge and tools developed as part of this study pave the way for future genomic research and exploitation of this wild Solanum species. The transcriptome assembly represents a resource for functional analysis of genes underlying interesting biological and agronomical traits and, in the absence of the full genome, provides a reference for RNAseq gene expression profiling aimed at understanding the unique biology of S. dulcamara. Cross-species orthology-based marker selection is shown to be a powerful tool to quickly generate a comparative genetic map, which may speed up gene mapping and contribute to the understanding of genome evolution within the Solanaceae family.
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