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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    The origin and widespread occurrence of Sli-based self-compatibility in potato
    Clot, Corentin R. ; Polzer, Clara ; Prodhomme, Charlotte ; Schuit, Cees ; Engelen, Christel J.M. ; Hutten, Ronald C.B. ; Eck, Herman J. van - \ 2020
    Theoretical and Applied Genetics (2020). - ISSN 0040-5752

    Self-compatible (SC) diploid potatoes allow innovative potato breeding. Therefore, the Sli gene, originally described in S. chacoense, has received much attention. In elite S. tuberosum diploids, spontaneous berry set is occasionally observed. We aimed to map SC from S. tuberosum origin. Two full-sib mapping populations from non-inbred diploids were used. Bulks were composed based on both pollen tube growth and berry set upon selfing. After DNA sequencing of the parents and bulks, we generated k-mer tables. Set algebra and depth filtering were used to identify bulk-specific k-mers. Coupling and repulsion phase k-mers, transmitted from the SC parent, mapped in both populations to the distal end of chromosome 12. Intersection between the k-mers from both populations, in coupling phase with SC, exposed a shared haplotype of approximately 1.5 Mb. Subsequently, we screened read archives of potatoes and wild relatives for k-mers specific to this haplotype. The well-known SC clones US-W4 and RH89-039-16, but surprisingly, also S. chacoense clone M6 were positives. Hence, the S. tuberosum source of SC seems identical to Sli. Furthermore, the candidate region drastically reduced to 333 kb. Haplotype-specific KASP markers were designed and validated on a panel of diploid clones including another renown SC dihaploid G254. Interestingly, k-mers specific to the SC haplotype were common in tetraploid varieties. Pedigree information suggests that the SC haplotype was introduced into tetraploid varieties via the founder “Rough Purple Chili”. We show that Sli is surprisingly widespread and indigenous to the cultivated gene pool of potato.

    Cracker shape modifies ad libitum snack intake of crackers with cheese dip
    Eck, Arianne Van; Stratum, Anouk Van; Achlada, Dimitra ; Goldschmidt, Benoît ; Scholten, Elke ; Fogliano, Vincenzo ; Stieger, Markus ; Bolhuis, Dieuwerke - \ 2020
    The British journal of nutrition (2020). - ISSN 0007-1145
    ad libitum snack intake - composite foods - oral processing behaviour - shape - snacks

    Food and energy intake can be effectively lowered by changing food properties, but little is known whether modifying food shape is sufficient to influence intake. This study investigated the influence of cracker shape and cheese viscosity on ad libitum intake of cracker-cheese combinations. Forty-four participants (13 males, 23±3 years, BMI 21±2 kg/m2) participated in four late afternoon snack sessions [2x2 randomized crossover design]. Iso-caloric crackers were baked into flat squares and finger-shape cylindrical sticks and combined with a cheese dip varying in viscosity. Approximately 80 crackers and 500 g cheese dip were served in separate large bowls. Participants consumed crackers with cheese dip ad libitum while watching a movie of 30 minutes. Dipping behaviour and oral processing behaviour were measured simultaneously by hidden balances under the cheese bowls and video recordings. Cracker intake (28±1 crackers) of cracker-cheese combinations was not influenced by cracker shape. Cheese intake of cracker-cheese combinations was 15% higher for flat squared than finger-shape crackers (131 kJ, p=0.016), as a larger amount of cheese was scooped with flat squared crackers (2.9±0.2 vs. 2.3±0.1 g cheese per dip, p<0.001), and showed higher eating rate and energy intake rate (p<0.001). Eating rate over snacking time decreased by reducing bite frequency (p<0.001) while cheese dip size remained fairly constant (p=0.12). Larger energy intake from condiments was facilitated by increased cracker surface, and this did not trigger earlier satiation. Changing food carrier surface may be a promising approach to moderate energy intake of often high energy dense condiments, sauces and toppings.

    Combine nicely, consume wisely : The role of single food properties in oral processing behavior, intake and sensory perception of composite foods
    Eck, Arianne van - \ 2020
    Wageningen University. Promotor(en): V. Fogliano; M. Stieger, co-promotor(en): E. Scholten. - Wageningen : Wageningen University - ISBN 9789463953467 - 241
    Warts wars : The resistant potatoes strike back
    Prodhomme, Charlotte - \ 2020
    Wageningen University. Promotor(en): R.G.F. Visser, co-promotor(en): J.H. Vossen; H.J. van Eck. - Wageningen : Wageningen University - ISBN 9789463952934 - 278

    Potato wart disease, caused by the obligate biotrophic Chytrid fungus Synchytrium endobioticum, is one of the most important quarantine diseases of potato. This disease was named after the symptoms caused by the pathogen, which are the proliferation of meristematic tissues leading to the formation of warts, mainly on the below-ground sprouts of potato plants. The quarantine status of S. endobioticum is due to the production of spores that can remain viable in the soil for more than 40 years, the lack of chemical control and the severe yield losses. In Europe, more than 40 different pathotypes of S. endobioticum have been recorded and only resistance to pathotype 1 is commonly deployed in the breeding germplasm. The breeding and cultivation of potato varieties resistant to a wider spectrum of pathotypes is crucial for quarantine practice to reduce the propagation of the pathogen. Therefore, the identification of genes bringing resistance to the most frequent pathotypes of the pathogen and the development of diagnostic markers for marker assisted selection (MAS) is urgently needed.

    In this thesis, genes involved in resistance to pathotypes 1, 2, 6 and 18 of S. endobioticum were identified to make an inventory of the different resistance sources at hand for potato breeders. In Chapter 2, we investigated the distribution of the pathotype 1 resistance in a variety panel representative of the potato breeding material. Breeding programs of the 20th century were very successful in producing varieties resistant to pathotype 1 as 77% of the panel varieties were found to be resistant. To identify markers linked with pathotype 1 resistance, we used previously produced genotypic and phenotypic data to perform a Genome-Wide Association Study (GWAS). The GWAS resulted in the identification of markers associated with pathotype 1 resistance on the north arm of chromosome 11. In this region, the major effect gene Sen1 was previously identified. Sen1 is the main source of pathotype 1 resistance in the variety panel and no common ancestral donor could be identified due to the inability to define identity-by-descent (IBD).

    As we faced limitations to design markers fully diagnostic for pathotype 1 resistance using the GWAS approach, we aimed to develop new tools to identify haplotype specific SNPs. In Chapter 3, we developed a new set of workflows, called Comparative Subsequence Sets Analysis (CoSSA), for the genetic analysis of traits of interest and the identification of haplotype specific SNPs. CoSSA can be used for any crop as it is suitable for polyploids and can be used with or without a reference genome. We applied CoSSA to identify Sen3, a dominant gene conferring resistance to all tested pathotypes. Sen3 was fine-mapped to the resistance gene cluster C76 on the north arm of chromosome 11.

    Furthermore, we used CoSSA for the fine-mapping of Sen1 in Chapter 4. Sen1 was mapped to the same R gene cluster as Sen3. We performed a candidate gene analysis and showed that Sen1 encodes a nucleotide-binding domain, leucine rich containing (NLR) protein from the TNL group. The two identified candidate genes were cloned and tested in complementation assays with AvrSen1, the S. endobioticum effector protein which triggers Hypersensitive Responses (HR) in Sen1 plants. These findings will serve as novel tools to study the interactions between potato and S. endobioticum.

    In Chapter 5, we made an, as complete as possible at this moment, inventory of the dominant potato wart disease resistance (Sen) genes and QTLs present in the potato breeding germplasm. We combined the GWAS and CoSSA strategies to identify two new major genes, Sen4 and Sen5, which are involved in resistance to pathotypes 2, 6 and 18. We also identified several wart disease resistance QTLs which, in combination with the dominant genes, can contribute to improve resistance to the higher pathotypes. To avoid any confusion between the previously and newly identified QTLs, we introduced a new naming system which allows to differentiate each resistant haplotype identified. Finally, we screened a broad panel of potato varieties and wild Solanum species for the genes Sen1, Sen2, Sen3, Sen4 and Sen5.

    To put it in a nutshell, a complete picture of the major potato wart disease resistance sources present in the breeding germplasm is given in this thesis. Haplotype specific markers have been designed for all the major genes and QTLs mapped, which will facilitate the breeding of resistant varieties. Finally, the development of CoSSA will facilitate the mapping of traits of interest and the design of haplotype specific markers for any crop.

    Distribution of P1(D1) wart disease resistance in potato germplasm and GWAS identification of haplotype-specific SNP markers
    Prodhomme, Charlotte ; Vos, Peter G. ; Paulo, Maria João ; Tammes, Jasper E. ; Visser, Richard G.F. ; Vossen, Jack H. ; Eck, Herman J. van - \ 2020
    Theoretical and Applied Genetics (2020). - ISSN 0040-5752

    Key message: A Genome-Wide Association Study using 330 commercial potato varieties identified haplotype specific SNPmarkers associated with pathotype 1(D1) wart disease resistance. Abstract: Synchytrium endobioticum is a soilborne obligate biotrophic fungus responsible for wart disease. Growing resistant varieties is the most effective way to manage the disease. This paper addresses the challenge to apply molecular markers in potato breeding. Although markers linked to Sen1 were published before, the identification of haplotype-specific single-nucleotide polymorphisms may result in marker assays with high diagnostic value. To identify hs-SNP markers, we performed a genome-wide association study (GWAS) in a panel of 330 potato varieties representative of the commercial potato gene pool. SNP markers significantly associated with pathotype 1 resistance were identified on chromosome 11, at the position of the previously identified Sen1 locus. Haplotype specificity of the SNP markers was examined through the analysis of false positives and false negatives and validated in two independent full-sib populations. This paper illustrates why it is not always feasible to design markers without false positives and false negatives for marker-assisted selection. In the case of Sen1, founders could not be traced because of a lack of identity by descent and because of the decay of linkage disequilibrium between Sen1 and flanking SNP markers. Sen1 appeared to be the main source of pathotype 1 resistance in potato varieties, but it does not explain all the resistance observed. Recombination and introgression breeding may have introduced new, albeit rare haplotypes involved in pathotype 1 resistance. The GWAS approach, in such case, is instrumental to identify SNPs with the best possible diagnostic value for marker-assisted breeding.

    Nanoparticles for “two color” 19F magnetic resonance imaging: Towards combined imaging of biodistribution and degradation
    Koshkina, Olga ; White, Paul B. ; Staal, Alexander H.J. ; Schweins, Ralf ; Swider, Edyta ; Tirotta, Ilaria ; Tinnemans, Paul ; Fokkink, Remco ; Veltien, Andor ; Riessen, N.K. van; Eck, Ernst R.H. van; Heerschap, Arend ; Metrangolo, Pierangelo ; Baldelli Bombelli, Francesca ; Srinivas, Mangala - \ 2020
    Journal of Colloid and Interface Science 565 (2020). - ISSN 0021-9797 - p. 278 - 287.
    F MRI - Degradation - Fluorocarbons - Fractal nanoparticles - PLGA - SANS

    The use of polymeric nanoparticles (NPs) as therapeutics has been steadily increasing over past decades. In vivo imaging of NPs is necessary to advance the therapeutic performance. 19F Magnetic Resonance Imaging (19F MRI) offers multiple advantages for in vivo imaging. However, design of a probe for both biodistribution and degradation has not been realized yet. We developed polymeric NPs loaded with two fluorocarbons as promising imaging tools to monitor NP biodistribution and degradation by 19F MRI. These 200 nm NPs consist of poly(lactic-co-glycolic acid) (PLGA) loaded with perfluoro-15-crown-5 ether (PFCE) and PERFECTA. PERFECTA/PFCE-PLGA NPs have a fractal sphere structure, in which both fluorocarbons are distributed in the polymeric matrix of the fractal building blocks, which differs from PFCE-PLGA NPs and is unique for fluorocarbon-loaded colloids. This structure leads to changes of magnetic resonance properties of both fluorocarbons after hydrolysis of NPs. PERFECTA/PFCE-PLGA NPs are colloidally stable in serum and biocompatible. Both fluorocarbons show a single resonance in 19F MRI that can be imaged separately using different excitation pulses. In the future, these findings may be used for biodistribution and degradation studies of NPs by 19F MRI in vivo using “two color” labeling leading to improvement of drug delivery agents.

    Method for modifying tuber shape in potato
    Eck, H.J. van; Knaap, E.K.M. van der - \ 2020
    Octrooinummer: WO2020008078, gepubliceerd: 2020-01-09.
    The present invention relates to a method for modifying the tuber shape of a potato (Solanum tuberosum) plant comprising genetically engineering the presence or absence or functional activity 5 of the StOFP20 gene. The tuber shape of a potato plant is modified from round to elongate by deletion or inactivation of a functional StOF P20 gene present in the genome of a plant that produces round potatoes to become absent or non-functional. The present invention further relates to a method for modifying the tuber shape of a potato (Solanum tuberosum) plant comprising crossing a potato plant comprising a functional StOF P20 gene With a potato plant lacking a 10 functional StOF P20 gene and subsequently selecting from the F2 progeny of the cross a plant With the desired tuber shape.
    Genome-wide association analysis in tetraploid potato reveals four QTLs for protein content
    Klaassen, Michiel T. ; Willemsen, Johan H. ; Vos, Peter G. ; Visser, Richard G.F. ; Eck, Herman J. van; Maliepaard, Chris ; Trindade, Luisa M. - \ 2019
    Molecular Breeding 39 (2019). - ISSN 1380-3743
    Valorisation of tuber protein is relevant for the potato starch industry to create added-value and reduce impact on the environment. Hence, protein content has emerged as a key quality trait for innovative potato breeders. In this study, we estimated trait heritability, explored the relationship between protein content and tuber under-water weight (UWW), inferred haplotypes underlying quantitative trait loci (QTLs) and pinpointed candidate genes. We used a panel of varieties (N = 277) that was genotyped using the SolSTW 20 K Infinium single-nucleotide polymorphism (SNP) marker array. Protein content data were collected from multiple environments and years. Our genome-wide association study (GWAS) identified QTLs on chromosomes 3, 5, 7 and 12. Alleles of StCDF1 (maturity) were associated with QTLs found on chromosome 5. The QTLs on chromosomes 7 and 12 are presented here for the first time, whereas those on chromosomes 3 and 5 co-localized with loci reported in earlier studies. The candidate genes underlying the QTLs proposed here are relevant for functional studies. This study provides resources for genomics-enabled breeding for protein content in potato.
    “The truth is not in the middle”: Journalistic norms of climate change bloggers
    Eck, Christel W. van; Mulder, Bob C. ; Dewulf, Art - \ 2019
    Global environmental change : human and policy dimensions 59 (2019). - ISSN 0959-3780
    Bloggers - Climate change - Climate change communications - Journalistic norms - Online media
    Climate change has often been presented in a biased way in traditional media outlets, due to journalists’ adherence to the norm of balanced reporting. More generally, journalistic norms shape the selection and composition of news and thereby influence how climate change is covered in traditional media. Climate change coverage is also prominent in new media outlets, such as blogs. The current research aims to identify which journalistic norms are supported in the climate blogosphere, on the basis of 27 interviews with climate change bloggers. The results show that climate change bloggers support the traditional journalistic norms of personalization, dramatization, novelty, authority and order, but not balance. Beyond the traditional journalistic norms, climate change bloggers identify contextualization, clarity, decency, and particularly truth as important journalistic norms. Truth is understood as a multi-dimensional norm comprising objectivity, transparency, and honesty. No differences are identified between norms supported by climate sceptical and climate mainstream bloggers, but each group operationalizes the norms differently. These results challenge and redefine traditional models of journalistic norms, and contribute to theorizing how journalistic norms shape climate change coverage in new media outlets. As such, this research on climate change bloggers and their journalistic norms is crucial for a fuller understanding of current climate change communications.
    Genetic mapping of tuber size distribution and marketable tuber yield under drought stress in potatoes
    Aliche, Ernest B. ; Oortwijn, Marian ; Theeuwen, Tom P.J.M. ; Bachem, Christian W.B. ; Eck, Herman J. van; Visser, Richard G.F. ; Linden, Gerard van der - \ 2019
    Euphytica 215 (2019)11. - ISSN 0014-2336
    Association panel - Drought - Marketable tubers - Modelling - Size - Yield

    Drought sensitivity of potato leads to a reduction in total tuber yield and marketable yield. An investigation of drought effects on tuber yield attributes will facilitate our understanding of how to reduce such huge yield losses. We have evaluated tuber yield, tuber size distribution and marketable yield of a set of 103 European commercial potato cultivars under irrigated and non-irrigated conditions in the field. The multi-year results from two locations, Connantre, France (2013–2015) and Nieuw-Namen in Zeeland, The Netherlands (2013–2014), were analysed. We used Normal and Gamma Distribution models to describe the tuber size distribution of tuber fresh weight and tuber number, respectively. The interactions among parameters of tuber size distribution and total/marketable tuber yield traits were analysed using correlation matrices and biplots. Finally, we used a 14K Infinium SNP marker array to find associations between the parameters or traits and genetic loci on the potato genome. Late foliage maturity facilitated a wider spread of tuber size distribution in favour of larger-sized tubers. Drought effects on total yield were representative of their impact on marketable yield, however, absolute values of total tuber number may not be indicative of marketable number of tubers. We found significant marker-trait associations between a region on chromosome 3 and the spread of tuber number distribution, size class with maximum tuber number and marketable fractions of tuber number and tuber weight. These findings will contribute to improvement and selection for drought tolerance in potato.

    Shape up! How shape, size and addition of condiments influence eating behavior towards vegetables
    Eck, Arianne Van; Wijne, Christien ; Fogliano, Vincenzo ; Stieger, Markus ; Scholten, Elke - \ 2019
    Food & Function 10 (2019)9. - ISSN 2042-6496 - p. 5739 - 5751.

    Practical approaches to increase consumption of healthy foods such as vegetables are needed. Controlling eating rate is a promising strategy, since faster eating rates have been related to higher food intake. Food properties can be modified to influence eating rates, but little is known about the impact of vegetable dimensions and condiment additions on eating rates of vegetables. This study determined the influence of shape, size and condiment properties on eating behavior towards carrots. Eating behavior (mastication time, number of chews, chewing frequency, eating rate) was determined for carrots with same total weight but different shapes (cube, julienne), and varying in size, number of pieces and aspect ratio. Carrots presented in one large cube required the lowest mastication effort (shortest mastication time, fewest chews) among all pre-cut carrots. Carrot cubes required less mastication effort leading to higher eating rates than carrots julienne. To investigate the effect of condiment addition on eating behavior towards carrots, mayonnaises varying in fat content and viscosity were combined with carrots, and mastication behavior and bolus properties were determined. Mayonnaises, in particular those with high fat content or low viscosity, contributed to faster bolus formation of carrots. Carrots were swallowed with less particles of larger sizes when mayonnaises were added. These results indicate that a specific particle size is not a prerequisite to induce swallowing, and that other bolus properties such as lubrication or cohesiveness trigger the urge to swallow. We conclude that eating behavior towards carrots can be controlled by relatively small changes in both carrot and condiment properties. To increase carrot intake by increasing eating rate, we suggest to avoid cutting of carrots or to add condiments, which could be an effective strategy to increase vegetable consumption or to decrease mastication effort to target the elderly population.

    A model-based approach to analyse genetic variation in potato using standard cultivars and a segregating population. II. Tuber bulking and resource use efficiency
    Khan, Muhammad Sohail ; Yin, Xinyou ; Putten, Peter E.L. van der; Jansen, Hans J. ; Eck, Herman J. van; Eeuwijk, Fred A. van; Struik, Paul C. - \ 2019
    Field Crops Research 242 (2019). - ISSN 0378-4290
    Genotype-by-environment interaction - Heritability - Maturity type - Path coefficient analysis - QTL mapping

    Quantitative differences in tuber bulking of 100 genotypes in a segregating F1 population, their parents (SH, RH) and five contrasting cultivars of potato (Solanum tuberosum) grown in six environments were analysed using a piece-wise expolinear function. Tuber bulking was characterised by three parameters: cm, ED and wmax, where cm and ED were growth rate and effective duration, respectively, of the linear phase of tuber bulking, and wmax was the final tuber dry weight at the end of the linear phase (tE). We also analysed radiation (RUET) and nitrogen use efficiency (NUET), and their relationships with the model parameters. Values of cm and RUET were highest for early-maturing genotypes. Late-maturing genotypes had largest ED and NUET. As a result, wmax was higher in late genotypes than in early genotypes. Most traits exhibited high heritability and high genetic correlations with wmax. Path analysis showed that RUET, cm and a previously quantified parameter for total canopy cover Asum, had a major influence on wmax. Sixteen QTLs were detected for all traits explaining the phenotypic variance by up to 66%. One particular QTL on paternal linkage group V was detected for all traits with a major additive effect and maximum total phenotypic variance. Additional QTLs mostly associated with RH (cm, tE and ED) or both SH-RH linkage groups (NUET, wmax). Our study demonstrates that there are opportunities for improving tuber dry matter yield by selecting an optimal combination of important physiological traits.

    A model-based approach to analyse genetic variation in potato using standard cultivars and a segregating population. I. Canopy cover dynamics
    Khan, Muhammad Sohail ; Struik, Paul C. ; Putten, Peter E.L. van der; Jansen, Hans J. ; Eck, Herman J. van; Eeuwijk, Fred A. van; Yin, Xinyou - \ 2019
    Field Crops Research 242 (2019). - ISSN 0378-4290
    Genotype-by-environment interaction - Haulm growth - Heritability - Maturity type - QTL mapping

    We designed a model to quantify the canopy cover dynamics in potato (Solanum tuberosum L.). It describes the dynamics during the build-up phase, maximum cover phase, and decline phase of canopy development through five parameters defining timing of three phases and maximum canopy cover (vmax). These five parameters were estimated for 100 individuals of an F1 population, their parents, and five standard cultivars, using data from six field experiments, and used to estimate secondary traits, related to duration and area under the canopy cover curve for the three phases. The duration of the canopy build-up phase (DP1) was rather conserved, but the duration of maximum canopy cover (DP2) and the decline phase (DP3) varied greatly, with late maturing genotypes having longer DP2 and DP3 and thus a higher area under the canopy cover curve (Asum). High genetic variability coupled with high heritability was recorded for end of canopy senescence (te), DP2 and Asum. Strong positive phenotypic and genetic correlations were observed between DP2 and te, vmax or Asum indicating that genotypes with longer DP2 could be indirectly obtained by selecting for these traits. Several quantitative trait loci (QTLs) were detected for model traits explaining the variance by up to 74%. Clustering of many QTLs were found on position 18.2 cM on paternal linkage group V with major additive effects. Many additional QTLs with minor effects were mostly associated with maternal linkage groups. Our model approach could be used to exploit available genetic variability in canopy cover dynamics of potato.

    How do static and dynamic sensory perceptions change when foods are consumed with condiments
    Eck, Arianne van; Fogliano, V. ; Galindo-Cuspinera, Verónica ; Scholten, E. ; Stieger, M.A. - \ 2019
    Understanding Genetic Load in Potato for Hybrid Diploid Breeding
    Bachem, Christian W.B. ; Eck, Herman J. van; Vries, Michiel E. de - \ 2019
    Molecular Plant 12 (2019)7. - ISSN 1674-2052 - p. 896 - 898.
    Controlling factors for land productivity under extreme climatic events in continental Europe and the Mediterranean Basin
    Mulder, V.L. ; Eck, C.M. van; Friedlingstein, P. ; Arrouays, D. ; Regnier, P. - \ 2019
    Catena 182 (2019). - ISSN 0341-8162
    Extreme climatic events - Land degradation - Soil functioning - Soil variability - Vegetation activity

    Within the context of achieving Land Degradation Neutrality by 2030, this work studied to which extent soil variability acts as controlling factor for changes in observed land productivity under extreme climatic events. This was done by analysing 30 years of Normalized Difference Vegetation Index (NDVI) data and coinciding extreme warm, dry and their compound events in continental Europe and the Mediterranean Basin. In order to better understand the response of vegetation activity to extreme climatic events in relation to soil functioning, the data was segmented into different climate zones and further studied as a function of land cover and soil type. This study demonstrated that extreme climatic events cause substantial reductions in the NDVI with the maximum median impact up to 31%, one month after the occurrence of an extreme climatic event. However, the magnitude of NDVI drop largely depended on land cover and soil type. Our analysis showed that for soil types with root depth limitations, lower water retention capacity and the absence of specific symbiotic species in the soil, vegetation activity was more impacted by climate extremes compared to soil types having favourable growing conditions. Natural land cover types, especially taiga and boreal forest, were most sensitive. Consequently, with the expected increase in extreme events, the now stable and productive ecosystems may become unstable and less capable to absorb the CO2 in the future, thereby enhancing climate change and land degradation. Therefore, it is important to have mitigation policies tailored towards maintaining soil functioning in vulnerable ecosystems.

    Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; Mapping and pedigree analysis of a potato wart disease resistance gene Sen3
    Prodhomme, Charlotte ; Esselink, Danny ; Borm, Theo ; Visser, Richard G.F. ; Eck, Herman J. Van; Vossen, Jack H. - \ 2019
    Plant Methods 15 (2019)1. - ISSN 1746-4811
    Bulked segregant analysis (BSA) - Diagnostic markers - k-mers - Potato wart disease - Reference genome - Whole genome sequencing (WGS)

    Background: Standard strategies to identify genomic regions involved in a specific trait variation are often limited by time and resource consuming genotyping methods. Other limiting pre-requisites are the phenotyping of large segregating populations or of diversity panels and the availability and quality of a closely related reference genome. To overcome these limitations, we designed efficient Comparative Subsequence Sets Analysis (CoSSA) workflows to identify haplotype specific SNPs linked to a trait of interest from Whole Genome Sequencing data. Results: As a model, we used the resistance to Synchytrium endobioticum pathotypes 2, 6 and 18 that co-segregated in a tetraploid full sib population. Genomic DNA from both parents, pedigree genotypes, unrelated potato varieties lacking the wart resistance traits and pools of resistant and susceptible siblings were sequenced. Set algebra and depth filtering of subsequences (k-mers) were used to delete unlinked and common SNPs and to enrich for SNPs from the haplotype(s) harboring the resistance gene(s). Using CoSSA, we identified a major and a minor effect locus. Upon comparison to the reference genome, it was inferred that the major resistance locus, referred to as Sen3, was located on the north arm of chromosome 11 between 1,259,552 and 1,519,485 bp. Furthermore, we could anchor the unanchored superscaffold DMB734 from the potato reference genome to a synthenous interval. CoSSA was also successful in identifying Sen3 in a reference genome independent way thanks to the de novo assembly of paired end reads matching haplotype specific k-mers. The de novo assembly provided more R haplotype specific polymorphisms than the reference genome corresponding region. CoSSA also offers possibilities for pedigree analysis. The origin of Sen3 was traced back until Ora. Finally, the diagnostic power of the haplotype specific markers was shown using a panel of 56 tetraploid varieties. Conclusions: CoSSA is an efficient, robust and versatile set of workflows for the genetic analysis of a trait of interest using WGS data. Because the WGS data are used without intermediate reads mapping, CoSSA does not require the use of a reference genome. This approach allowed the identification of Sen3 and the design of haplotype specific, diagnostic markers.

    Multicore Liquid Perfluorocarbon-Loaded Multimodal Nanoparticles for Stable Ultrasound and 19F MRI Applied to In Vivo Cell Tracking
    Koshkina, Olga ; Lajoinie, Guillaume ; Baldelli Bombelli, Francesca ; Swider, Edyta ; Cruz, Luis J. ; White, Paul B. ; Schweins, Ralf ; Dolen, Yusuf ; Dinther, Eric A.W. van; Riessen, N.K. van; Rogers, Sarah E. ; Fokkink, Remco ; Voets, Ilja K. ; Eck, Ernst R.H. van; Heerschap, Arend ; Versluis, Michel ; Korte, Chris L. de; Figdor, Carl G. ; Vries, I.J.M. de; Srinivas, Mangala - \ 2019
    Advanced Functional Materials 29 (2019)19. - ISSN 1616-301X
    F MRI - cell therapy - cell tracking - multimodal imaging - perfluorocarbons - ultrasound

    Ultrasound is the most commonly used clinical imaging modality. However, in applications requiring cell-labeling, the large size and short active lifetime of ultrasound contrast agents limit their longitudinal use. Here, 100 nm radius, clinically applicable, polymeric nanoparticles containing a liquid perfluorocarbon, which enhance ultrasound contrast during repeated ultrasound imaging over the course of at least 48 h, are described. The perfluorocarbon enables monitoring the nanoparticles with quantitative 19 F magnetic resonance imaging, making these particles effective multimodal imaging agents. Unlike typical core–shell perfluorocarbon-based ultrasound contrast agents, these nanoparticles have an atypical fractal internal structure. The nonvaporizing highly hydrophobic perfluorocarbon forms multiple cores within the polymeric matrix and is, surprisingly, hydrated with water, as determined from small-angle neutron scattering and nuclear magnetic resonance spectroscopy. Finally, the nanoparticles are used to image therapeutic dendritic cells with ultrasound in vivo, as well as with 19 F MRI and fluorescence imaging, demonstrating their potential for long-term in vivo multimodal imaging.

    Increased virulence of Globodera pallida during repeated rearing on different resistant potato cultivars explained by a simple model
    Beniers, J.E. ; Nöllen, Y. ; Eck, H.J. van; Schouten, H.J. - \ 2019
    Plant Pathology 68 (2019)3. - ISSN 0032-0862 - p. 445 - 453.
    Globodera pallida - model - potato cyst nematodes - resistance - selection - virulence

    Selection for virulence of Globodera pallida on potato cultivars was studied for four generations under controlled conditions. The reproduction rate (Pf/Pi) of a mixed Pa2/3 population increased by a factor of 61 during rearing on the partially resistant potato cv. Darwina compared to rearing on the susceptible cv. Irene. This was a result of selection for virulence on cv. Darwina, and achieving the Hardy–Weinberg equilibrium on cv. Irene. Increased virulence also significantly raised the reproduction rate on several other Solanum genotypes. These changes could be explained reasonably well by the monogenic inheritance of a virulence factor breaking the Grp1 locus. The virulence changes were probably mainly evoked by this gene only, inherited from S. vernei 1-3 or S. vernei 24/20. The Grp1 locus has probably provided the differential S. vernei hybrid (VTn)2 62-33-3 with its resistance to the Pa2 group and not to the Pa3 group. Alternation of cultivars did not halt selection if the cultivars highly differentiated between the Pa2 and Pa3 populations. Only when alternation was with cultivars that harboured a different resistance gene against Pa3 was selection for virulence delayed. Differences in virulence levels (i.e. reproduction rates) within the nematode population determined the rate of selection, not the resistance level itself. Selection of a Pa3 population for three generations on cv. Karakter not only increased the reproduction rate on cv. Karakter itself by a factor 4.2, but also raised the reproduction on other potato genotypes. A simple monogenic model could explain these changes in virulence.

    Adding condiments to foods : How does static and dynamic sensory perception change when bread and carrots are consumed with mayonnaise?
    Eck, Arianne van; Fogliano, Vincenzo ; Galindo-Cuspinera, Verónica ; Scholten, Elke ; Stieger, Markus - \ 2019
    Food Quality and Preference 73 (2019). - ISSN 0950-3293 - p. 154 - 170.
    Bread - Carrot - Condiments - Mayonnaise - RATA - TDS

    Foods with condiments such as bread with spreads or vegetables with dips are frequently consumed. The aim of this study was to understand how dynamic and static sensory perception changes when foods are consumed together with condiments. Two carriers (bread, carrot) varying in hardness were combined with condiments (mayonnaises) varying in fat content and viscosity to obtain model composite foods. Dynamic sensory perception was assessed using Temporal Dominance of Sensations (TDS) with attribute lists describing both carrier- and condiment-related attributes. Static sensory perception was evaluated using Rate-All-That-Apply (RATA) with attribute lists descriptive for either bread, carrot or mayonnaise. Carrier foods (bread, carrot) had a larger influence on dynamic and static sensory perception of carrier-condiment combinations than condiments (mayonnaises). Sensations related to mayonnaises (sour, creamy) were dominant at later stages of consumption when these were combined with harder bread or carrots. Hard bread or carrots reduced intensities of several mayonnaise-related attributes (sour, dairy when combined with bread; creamy, after taste when combined with carrots) to a larger extent than soft bread or carrots. Consumer sensitivity to discriminate between foods was not affected by the presence of other food items when differences in bread, carrots or mayonnaise properties were large. In case of smaller differences between food properties, consumer sensitivity to discriminate between foods declined and depended on the food type it was combined with. We conclude that the product properties of both solid carrier foods and condiments and their interaction during consumption impact dynamic and static sensory perception of carrier-condiment combinations.

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