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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    Pathogen manipulation of chloroplast function triggers a light-dependent immune recognition
    Gao, Chuyun ; Xu, Huawei ; Huang, Jie ; Sun, Biying ; Zhang, Fan ; Savage, Zachary ; Duggan, Cian ; Yan, Tingxiu ; Wu, Chih Hang ; Wang, Yuanchao ; Vleeshouwers, Vivianne G.A.A. ; Kamoun, Sophien ; Bozkurt, Tolga O. ; Dong, Suomeng - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)17. - ISSN 0027-8424 - p. 9613 - 9620.
    Chloroplast - Disease resistance - Light - NLR - Potato blight

    In plants and animals, nucleotide-binding leucine-rich repeat (NLR) proteins are intracellular immune sensors that recognize and eliminate a wide range of invading pathogens. NLR-mediated immunity is known to be modulated by environmental factors. However, how pathogen recognition by NLRs is influenced by environmental factors such as light remains unclear. Here, we show that the agronomically important NLR Rpi-vnt1.1 requires light to confer disease resistance against races of the Irish potato famine pathogen Phytophthora infestans that secrete the effector protein AVRvnt1. The activation of Rpi-vnt1.1 requires a nuclear-encoded chloroplast protein, glycerate 3-kinase (GLYK), implicated in energy production. The pathogen effector AVRvnt1 binds the full-length chloroplast-targeted GLYK isoform leading to activation of Rpi-vnt1.1. In the dark, Rpi-vnt1.1-mediated resistance is compromised because plants produce a shorter GLYK-lacking the intact chloroplast transit peptide-that is not bound by AVRvnt1. The transition between full-length and shorter plant GLYK transcripts is controlled by a light-dependent alternative promoter selection mechanism. In plants that lack Rpi-vnt1.1, the presence of AVRvnt1 reduces GLYK accumulation in chloroplasts counteracting GLYK contribution to basal immunity. Our findings revealed that pathogen manipulation of chloroplast functions has resulted in a light-dependent immune response.

    Selective breeding for high natural antibody level increases resistance to avian pathogenic Escherichia coli (APEC) in chickens
    Berghof, T.V.L. ; Matthijs, M.G.R. ; Arts, J.A.J. ; Bovenhuis, H. ; Dwars, R.M. ; Poel, J.J. van der; Visker, M.H.P.W. ; Parmentier, H.K. - \ 2019
    Developmental and Comparative Immunology 93 (2019). - ISSN 0145-305X - p. 45 - 57.
    APEC - Breeding - Chicken - Disease resistance - Escherichia coli - Natural antibody

    Keyhole limpet hemocyanin (KLH)-binding natural antibody (NAb) titers in chickens are heritable, and higher levels have previously been associated with a higher survival. This suggests that selective breeding for higher NAb levels might increase survival by means of improved general disease resistance. Chickens were divergently selected and bred for total NAb levels binding KLH at 16 weeks of age for six generations, resulting in a High NAb selection line and a Low NAb selection line. To for test differences in disease resistance, chickens were challenged with avian pathogenic Escherichia coli (APEC) in two separate experiments. Chickens at 8 days of age received one of four intratracheal inoculations of 0.2 mL phosphate buffered saline (PBS): 1) mock inoculate, 2) with 0.2 mL PBS containing 108.20 colony-forming units (CFU)/mL APEC, 3) with 0.2 mL PBS containing 106.64 CFU/mL APEC, and 4) with 0.2 mL PBS containing 107.55 CFU/mL APEC. Mortality was recorded during 7 days post inoculation. Overall, 50–60% reduced mortality was observed in the High line compared to the Low line for all APEC doses. In addition, morbidity was determined of the surviving chickens at 15 days of age. The High line had lower morbidity scores compared to the Low line. We conclude that selective breeding for high KLH-binding NAb levels at 16 weeks of age increase APEC resistance in early life. This study and previous studies support the hypothesis that KLH-binding NAb might be used as an indicator trait for to selective breed for general disease resistance in an antigen non-specific fashion.

    The role of tomato WRKY genes in plant responses to combined abiotic and biotic stresses
    Bai, Yuling ; Sunarti, Sri ; Kissoudis, Christos ; Visser, Richard G.F. ; Linden, C.G. van der - \ 2018
    Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
    Abiotic stress - Biotic stress - Combined stresses - Disease resistance - Effector-triggered immunity (ETI) - PAMP-triggered immunity (PTI)

    In the field, plants constantly face a plethora of abiotic and biotic stresses that can impart detrimental effects on plants. In response to multiple stresses, plants can rapidly reprogram their transcriptome through a tightly regulated and highly dynamic regulatory network where WRKY transcription factors can act as activators or repressors. WRKY transcription factors have diverse biological functions in plants, but most notably are key players in plant responses to biotic and abiotic stresses. In tomato there are 83 WRKY genes identified. Here we review recent progress on functions of these tomato WRKY genes and their homologs in other plant species, such as Arabidopsis and rice, with a special focus on their involvement in responses to abiotic and biotic stresses. In particular, we highlight WRKY genes that play a role in plant responses to a combination of abiotic and biotic stresses.

    Restriction associated DNA-genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen-mediated selection
    Buckley, James ; Holub, Eric B. ; Koch, Marcus A. ; Vergeer, Philippine ; Mable, Barbara K. - \ 2018
    BMC Genomics 19 (2018)1. - ISSN 1471-2164
    Arabidopsis lyrata - Balancing selection - Disease resistance - Genome scan - Mating system - Pathogens - Polymorphism - R-genes - RAD-seq

    Background: Genome scans based on outlier analyses have revolutionized detection of genes involved in adaptive processes, but reports of some forms of selection, such as balancing selection, are still limited. It is unclear whether high throughput genotyping approaches for identification of single nucleotide polymorphisms have sufficient power to detect modes of selection expected to result in reduced genetic differentiation among populations. In this study, we used Arabidopsis lyrata to investigate whether signatures of balancing selection can be detected based on genomic smoothing of Restriction Associated DNA sequencing (RAD-seq) data. We compared how different sampling approaches (both within and between subspecies) and different background levels of polymorphism (inbreeding or outcrossing populations) affected the ability to detect genomic regions showing key signatures of balancing selection, specifically elevated polymorphism, reduced differentiation and shifts towards intermediate allele frequencies. We then tested whether candidate genes associated with disease resistance (R-gene analogs) were detected more frequently in these regions compared to other regions of the genome. Results: We found that genomic regions showing elevated polymorphism contained a significantly higher density of R-gene analogs predicted to be under pathogen-mediated selection than regions of non-elevated polymorphism, and that many of these also showed evidence for an intermediate site-frequency spectrum based on Tajima's D. However, we found few genomic regions that showed both elevated polymorphism and reduced FST among populations, despite strong background levels of genetic differentiation among populations. This suggests either insufficient power to detect the reduced population structure predicted for genes under balancing selection using sparsely distributed RAD markers, or that other forms of diversifying selection are more common for the R-gene analogs tested. Conclusions: Genome scans based on a small number of individuals sampled from a wide range of populations were sufficient to confirm the relative scarcity of signatures of balancing selection across the genome, but also identified new potential disease resistance candidates within genomic regions showing signatures of balancing selection that would be strong candidates for further sequencing efforts.

    Selection on resilience improves disease resistance and tolerance to infections
    Mulder, H.A. ; Rashidi, H. - \ 2017
    Journal of Animal Science 95 (2017)8. - ISSN 0021-8812 - p. 3346 - 3358.
    Breeding program - Disease resilience - Disease resistance - Response to selection - Selection index - Tolerance to infections
    Response to infection in animals has 2 main mechanisms: resistance (ability to control pathogen burden) and tolerance (ability to maintain performance given the pathogen burden). Selection on disease resistance and tolerance to infections seems a promising avenue to increase productivity of animals in the presence of disease infections, but it is hampered by a lack of records of pathogen burden of infected animals. Selection on resilience (ability to maintain performance regardless of pathogen burden) may, therefore, be an alternative pragmatic approach, because it does not need records of pathogen burden. Therefore, the aim of this study was to assess response to selection in resistance and tolerance when selecting on resilience compared with direct selection on resistance and tolerance. Monte Carlo simulation was used combined with selection index theory to predict responses to selection. Using EBV for resilience in the absence of records for pathogen burden resulted in favorable responses in resistance and tolerance to infections, with higher responses in tolerance than in resistance. If resistance and tolerance were unfavorably correlated, lower selection responses were obtained, especially in resistance. When the genetic correlation was very unfavorable, the selection response in tolerance became negative. Results showed that lower selection responses in resistance and tolerance were obtained when the frequency of disease outbreaks was 10% rather than 50% of the contemporary groups. The efficiency of selection on EBV for resilience compared with selection on EBV for resistance and tolerance was, however, not affected by the frequency of disease outbreaks. When records on pathogen burden were available, selection responses in resistance, tolerance, and the total breeding goal were 3 to 28%, 66 to 398%, and 2 to 11% higher, respectively, than when using the EBV for resilience, showing a clear benefit of recording pathogen burden. This study shows that selection on resilience is a pragmatic way of increasing disease resistance and tolerance to infections in the absence of records on pathogen burden, but recording pathogen burden would yield higher selection responses in resistance and tolerance.
    Approaches for evaluation of resistance to European canker (Neonectria ditissima) in apple
    Garkava-Gustavsson, L. ; Ghasemkhani, M. ; Zborowska, A. ; Englund, J.E. ; Lateur, M. ; Weg, E. van de - \ 2016
    Acta Horticulturae 1127 (2016). - ISSN 0567-7572 - p. 75 - 81.
    Disease resistance - Fruit tree canker - Malus × domestica - Nectria galligena - Phenotyping - Susceptibility

    European canker is caused by the fungus Neonectria ditissima (Neonectria galligena, formerly Nectria galligena). The disease causes significant losses to apple production in Sweden and many other countries with a temperate wet climate. Application of fungicides and good horticultural practices do not prevent canker damage in nurseries and orchards. Disease outbreaks damage and even completely destroy trees. To date, complete resistance to N. ditissima is not known in apple, but cultivars differ considerably in their level of partial resistance. To be able to conduct breeding for resistance to European canker, reliable plant tests are urgently needed. Differences in resistance to N. ditissima (colonization rate; CR) in apple cultivars were evaluated by wound inoculations with a standardized number of conidia on cut shoots from mature trees placed in a climate chamber and on potted trees in an unheated greenhouse. Infection percentage (Inf%) was assessed by 'natural' inoculations in leaf scars under high infection pressure in the field. All the experiments were carried out over 2 years. Lengths of lesions were measured at regular time intervals on five occasions for shoots and seven occasions for trees. Considerable differences in CR and Inf% were found among the cultivars. The relative levels of resistance obtained are consistent with previous reports for most cultivars. Assessment of CR (area under curve) and Inf% thus proved to be useful tools for evaluation of resistance to European canker. Also, some potentially new sources of resistance were identified.

    RNA interference for functional genomics and improvement of cotton (Gossypium sp.)
    Abdurakhmonov, Ibrokhim Y. ; Ayubov, Mirzakamol S. ; Ubaydullaeva, Khurshida A. ; Buriev, Zabardast T. ; Shermatov, Shukhrat E. ; Ruziboev, Haydarali S. ; Shapulatov, Umidjon ; Saha, Sukumar ; Ulloa, Mauricio ; Yu, John Z. ; Percy, Richard G. ; Devor, Eric J. ; Sharma, Govind C. ; Sripathi, Venkateswara R. ; Kumpatla, Siva P. ; Krol, Sander van der; Kater, Hake D. ; Khamidov, Khakimdjan ; Salikhov, Shavkat I. ; Jenkins, Johnie N. ; Abdukarimov, Abdusattor ; Pepper, Alan E. - \ 2016
    Frontiers in Plant Science 7 (2016)FEB2016. - ISSN 1664-462X
    Antisense - Cotton pest control - Disease resistance - Fiber quality - Gene silencing - Gossypium

    RNA interference (RNAi), is a powerful new technology in the discovery of genetic sequence functions, and has become a valuable tool for functional genomics of cotton (Gossypium sp.). The rapid adoption of RNAi has replaced previous antisense technology. RNAi has aided in the discovery of function and biological roles of many key cotton genes involved in fiber development, fertility and somatic embryogenesis, resistance to important biotic and abiotic stresses, and oil and seed quality improvements as well as the key agronomic traits including yield and maturity. Here, we have comparatively reviewed seminal research efforts in previously used antisense approaches and currently applied breakthrough RNAi studies in cotton, analyzing developed RNAi methodologies, achievements, limitations, and future needs in functional characterizations of cotton genes. We also highlighted needed efforts in the development of RNAi-based cotton cultivars, and their safety and risk assessment, small and large-scale field trials, and commercialization.

    Ectopic expression of Arabidopsis L-type lectin receptor kinase genes LecRK-I.9 and LecRK-IX.1 in Nicotiana benthamiana confers Phytophthora resistance
    Wang, Yan ; Nsibo, D.L. ; Juhar, H.M. ; Govers, Francine ; Bouwmeester, Klaas - \ 2016
    Plant Cell Reports (2016). - ISSN 0721-7714 - 11 p.
    Disease resistance - Interfamily gene transfer - L-type lectin receptor kinases - LecRK - Nicotiana benthamiana - Phytophthora

    Key message: TransgenicNicotiana benthamianalines with constitutive expression of an Arabidopsis lectin receptor kinase gene (LecRK-I.9orLecRK-IX.1) show enhanced resistance toPhytophthorapathogens, demonstrating conserved gene functionality after interfamily transfer.Abstract: In plants, cell surface receptors mediate the first layer of innate immunity against pathogenic microbes. In Arabidopsis several L-type lectin receptor kinases (LecRKs) were previously found to function as Phytophthora resistance components. In this study, we determined the functionality of Arabidopsis LecRK-I.9 or LecRK-IX.1 in Phytophthora resistance when transferred into the Solanaceous plant Nicotiana benthamiana. Multiple transgenic lines were generated for each LecRK gene and molecular analyses revealed variation in transgene copy number, transgene expression levels and LecRK protein accumulation. Infection assays showed that transgenic N. benthamiana plants expressing either Arabidopsis LecRK-I.9 or LecRK-IX.1 are more resistant to Phytophthora capsici and to Phytophthora infestans. These results demonstrate that Arabidopsis LecRK-I.9 and LecRK-IX.1 retained their Phytophthora resistance function when transferred into N. benthamiana. Therefore, these LecRKs have the potential to function as a complementary Phytophthora resistance resource in distantly related plant species next to the canonical Phytophthora resistance genes encoding nucleotide-binding leucine-rich repeat proteins.

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