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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Trichome Independent Resistance against Western Flower Thrips in Tomato
Bac-Molenaar, Johanna A. ; Mol, Selena ; Verlaan, Maarten G. ; Elven, Joke van; Kim, Hye Kyong ; Klinkhamer, Peter G.L. ; Leiss, Kirsten A. ; Vrieling, Klaas - \ 2019
Plant and Cell Physiology 60 (2019)5. - ISSN 0032-0781 - p. 1011 - 1024.
Insect resistance - Metabolite profiles - QTL mapping - Tomato - Trichome-derived volatiles - α-Tomatine

Western flower thrips (WFT) are a major pest on many crops, including tomato. Thrips cause yield losses, not only through feeding damage, but also by the transmission of viruses of which the Tomato Spotted Wilt Virus is the most important one. In cultivated tomato, genetic diversity is extremely low, and all commercial lines are susceptible to WFT. Several wild relatives are WFT resistant and these resistances are based on glandular trichome-derived traits. Introgression of these traits in cultivated lines did not lead to WFT resistant commercial varieties so far. In this study, we investigated WFT resistance in cultivated tomato using a F2 population derived from a cross between a WFT susceptible and a WFT resistant cultivated tomato line. We discovered that this WFT resistance is independent of glandular trichome density or trichome-derived volatile profiles and is associated with three QTLs on chromosomes 4, 5 and 10. Foliar metabolic profiles of F3 families with low and high WFT feeding damage were clearly different. We identified α-tomatine and a phenolic compound as potential defensive compounds. Their causality and interaction need further investigation. Because this study is based on cultivated tomato lines, our findings can directly be used in nowadays breeding programs.

Reduced dietary intake of micronutrients with antioxidant properties negatively impacts muscle health in aged mice : Reduced dietary intake of micronutrients
Dijk, Miriam Van; Dijk, Francina J. ; Hartog, Anita ; Norren, Klaske Van; Verlaan, Sjors ; Helvoort, Ardy Van; Jaspers, Richard T. ; Luiking, Yvette - \ 2018
Journal of cachexia, sarcopenia and muscle 9 (2018)1. - ISSN 2190-5991 - p. 146 - 159.
Background. Inadequate intake of micronutrients with antioxidant properties is common among older adults and has been associated with higher risk of frailty, adverse functional outcome, and impaired muscle health. However, a causal relationship is less well known. The aim was to determine in old mice the impact of reduced dietary intake of vitamins A/E/B6/B12/folate, selenium, and zinc on muscle mass, oxidative capacity, strength, and physical activity (PA) over time. Methods. Twenty-one-month-old male mice were fed either AIN-93-M (control) or a diet low in micronutrients with antioxidant properties (=LOWOX-B: 50% of mouse recommended daily intake of vitamins A, E, B6, and B12, folate, selenium, and zinc) for 4 months. Muscle mass, grip strength, physical activity (PA), and general oxidative status were assessed. Moreover, muscle fatigue was measured of m. extensor digitorum longus (EDL) during an ex vivo moderate exercise protocol. Effects on oxidative capacity [succinate dehydrogenase (SDH) activity], muscle fibre type, number, and fibre cross-sectional area (fCSA) were assessed on m. plantaris (PL) using histochemistry. Results. After 2 months on the diet, bodyweight of LOWOX-B mice was lower compared with control (P < 0.0001), mainly due to lower fat mass (P < 0.0001), without significant differences in food intake. After 4 months, oxidative status of LOWOX-B mice was lower, demonstrated by decreased vitamin E plasma levels (P < 0.05) and increased liver malondialdehyde levels (P = 0.018). PA was lower in LOWOX-B mice (P < 0.001 vs. control). Muscle mass was not affected, although PL-fCSA was decreased (~16%; P = 0.028 vs. control). SDH activity and muscle fibre type distribution remained unaffected. In LOWOX-B mice, EDL force production was decreased by 49.7% at lower stimulation frequencies (P = 0.038), and fatigue resistance was diminished (P = 0.023) compared with control. Conclusions. Reduced dietary intake of vitamins A, E, B6, and B12, folate, selenium, and zinc resulted in a lower oxidative capacity and has major impact on muscle health as shown by decreased force production and PA, without effects on muscle mass. The reduced fCSA in combination with similar SDH activity per fibre might explain the reduced oxidative capacity resulting in the increased fatigue after exercise in LOWOX-B mice.
Sarcopenia in older mice is characterized by a decreased anabolic response to a protein meal
Dijk, Miriam van; Nagel, Jolanda ; Dijk, Francina J. ; Salles, Jerôme ; Verlaan, Sjors ; Walrand, Stephane ; Norren, Klaske van; Luiking, Yvette - \ 2017
Archives of Gerontology and Geriatrics 69 (2017). - ISSN 0167-4943 - p. 134 - 143.
Ageing - Anabolic resistance - Geriatric skeletal muscle - Muscle function - Sarcopenia

Ageing is associated with sarcopenia, a progressive decline of skeletal muscle mass, muscle quality and muscle function. Reduced sensitivity of older muscles to respond to anabolic stimuli, i.e. anabolic resistance, is part of the underlying mechanisms. Although, muscle parameters have been studied in mice of various ages/strains; the aim was to study if mice display similar deteriorating processes as human ageing. Therefore, 10,16,21 and 25 months-old C57BL6/6J male mice were studied to measure parameters of sarcopenia and factors contributing to its pathophysiology, with the aim of characterizing sarcopenia in old mice. Muscle mass of the hind limb was lower in 25 as compared to 10 month-old mice. A significant decrease in physical daily activity, muscle grip strength and ex vivo muscle maximal force production was observed in 25 compared to 10 month-old mice. The muscle anabolic response to a single protein meal showed increased muscle protein synthesis in young, but not in old mice, indicative to anabolic resistance. However, by increasing the protein content in meals, anabolic resistance could be overcome, similar as in human elderly. Additionally, aged mice showed higher fasted insulin and hepatic malondialdehyde (MDA) levels (=marker oxidative stress). This study shows clear characteristics of sarcopenia that coincide with anabolic resistance, insulin resistance and oxidative stress in 25 month-old C57/BL6 male mice, similar to human ageing. Furthermore, similar decline in muscle mass, strength and function was observed in this aged-mice-model. These observations offer potential for the future to explore in old mice the effects of interventions targeting sarcopenia.

Low leucine, branched chain amino acid and essential amino acid blood levels are associated with low muscle mass, strength and function
Borg, S. ter; Luiking, Y.C. ; Verlaan, Sjors ; Boirie, Y. ; Schols, Jos M.G.A. ; Groot, C.P.G.M. de - \ 2016
Decreased risk of sarcopenia with high levels of leucine, essential amino acids, EPA, and 25-hydroxyvitamin D
Borg, S. ter; Luiking, Y.C. ; Verlaan, Sjors ; Boirie, Y. ; Schols, Jos M.G.A. ; Groot, C.P.G.M. de - \ 2016
Improved muscle function and quality after diet intervention with leucine-enriched whey and antioxidants in antioxidant deficient aged mice
Dijk, Miriam van; Dijk, Francina J. ; Bunschoten, Annelies ; Dartel, Dorien A.M. van; Norren, Klaske van; Walrand, Stephane ; Jourdan, Marion ; Verlaan, Sjors ; Luiking, Yvette - \ 2016
Oncotarget 7 (2016)14. - ISSN 1949-2553 - p. 17338 - 17355.
Antioxidants - Fatigue - Gerotarget - Sarcopenia - Skeletal muscle

Antioxidant (AOX) deficiencies are commonly observed in older adults and oxidative stress has been suggested to contribute to sarcopenia. Here we investigate if 1) low levels of dietary antioxidants had a negative impact on parameters of muscle mass, function and quality, and 2) to study if nutritional interventions with AOX and/ or leucine-enriched whey protein could improve these muscle parameters in aged mice. 18-months-old mice were fed a casein-based antioxidant-deficient (lowox) diet or a casein-based control-diet (CTRL) for 7 months. During the last 3 months, lowoxmice were subjected to either: A) continued lowox, b) supplementation with vitamin A/E, Selenium and Zinc (AOX), c) substitution of casein with leucine-enriched whey protein (PROT) or d) a combination of both AOX and PROT (TOTAL). After 7 months lowox-mice displayed lower muscle strength and more muscle fatigue compared to CTRL. Compared to lowox-mice, PROT-mice showed improved muscle power, grip strength and less muscle fatigue. AOX-mice showed improved oxidative status, less muscle fatigue, improved grip strength and mitochondrial dynamics compared to lowox-mice. The TOTAL-mice showed the combined effects of both interventions compared to lowox-mice. In conclusion, nutritional intervention with AOX and/or leucine-enriched whey protein can play a role in improving muscle health in a AOXdeficient mouse model.

Response to the 'Letter to the Editor on the Maastricht Sarcopenia Study'
Borg, Sovianne ter; Verlaan, Sjors ; Groot, Lisette C.P.G.M. de; Vries, Jeanne H.M. de; Meijboom, Saskia ; Mijnarends, Donja M. ; Luiking, Yvette C. ; Schols, Jos M.G.A. - \ 2016
Journal of the American Medical Directors Association 17 (2016)1. - ISSN 1525-8610 - p. 557 - 558.
Differences in nutriënt intake and biochemical nutriënt status between sarcopenic and nonsarcopenic older adults - results from the Maastricht Sarcopenia Study
Borg, S. ter; Groot, C.P.G.M. de; Mijnarends, D. ; Vries, J.H.M. de; Verlaan, S. ; Meijboom, S. ; Luiking, Y.C. ; Schols, J.M.G.A. - \ 2016
Journal of the American Medical Directors Association 17 (2016)5. - ISSN 1525-8610 - p. 393 - 401.
Background There is growing evidence of a relationship between nutrients and muscle mass, strength, and physical performance. Although nutrition is seen as an important pillar of treating sarcopenia, data on the nutritional intake of sarcopenic older adults are limited. Objective To investigate potential nutritional gaps in the sarcopenic population, the present study compared nutrient intake and biochemical nutrient status between sarcopenic and nonsarcopenic older adults. Design The Maastricht Sarcopenia Study included 227 community-dwelling older adults (≥65 years) from Maastricht, 53 of whom were sarcopenic based on the European Working Group on Sarcopenia in Older People algorithm. Habitual dietary intake was assessed with a food frequency questionnaire and data on dietary supplement use were collected. In addition, serum 25-hydroxyvitamin D, magnesium and α-tocopherol/cholesterol, plasma homocysteine and red blood cell n-3, and n-6 fatty acids profiles were assessed. Nutrient intake and biochemical nutrient status of the sarcopenic groups were compared with those of the nonsarcopenic groups. The robustness of these results was tested with a multiple regression analysis, taking into account between-group differences in characteristics. Results Sarcopenic older adults had a 10%–18% lower intake of 5 nutrients (n-3 fatty acids, vitamin B6, folic acid, vitamin E, magnesium) compared with nonsarcopenic older adults (P < .05). When taking into account dietary supplement intake, a 19% difference remained for n-3 fatty acids intake (P = .005). For the 2 biochemical status markers, linoleic acid and homocysteine, a 7% and 27% difference was observed, respectively (P < .05). The higher homocysteine level confirmed the observed lower vitamin B intake in the sarcopenic group. Observed differences in eicosapentaenoic acid and 25-hydroxyvitamin D between the groups were related to differences in age and living situation. Conclusions Sarcopenic older adults differed in certain nutritional intakes and biochemical nutrient status compared with nonsarcopenic older adults. Dietary supplement intake reduced the gap for some of these nutrients. Targeted nutritional intervention may therefore improve the nutritional intake and biochemical status of sarcopenic older adults.
Biomarkers of nutrition status in sarcopenic older adults - results from the Maastricht Sarcopenia Study
Borg, S. ter; Mijnarends, D. ; Verlaan, S. ; Schols, J.M.G.A. ; Groot, C.P.G.M. de; Luiking, Y.C. - \ 2015
In: Book of Abstracts 12th European Nutrition Conference (FENS). - Berlin : Karger - p. 371 - 371.
Introduction: Nutrition is an important pillar of treating sarcopenia. Multiple studies indicate a relationship between nutrients and muscle mass, strength and physical performance. Data are, however, limited on whether sarcopenic older adults differ in their nutrition status, compared to non-sarcopenic older adults. Objectives: The present study compared biomarkers of nutrition status between sarcopenic and non-sarcopenic older adults. Method / Design: The cross-sectional Maastricht Sarcopenia Study (MaSS) included 227 older adults (= 65 years), recruited in different community care settings in Maastricht, the Netherlands. Sarcopenia was defined using the European Working Group on Sarcopenia in Older People algorithm. Characteristics like Mini- Nutritional Assessment (MNA) and Mini-Mental State Examination (MMSE) were recorded. Serum 25-hydroxyvitamin D, magnesium and a-tocopherol (adjusted for cholesterol), red blood cell fatty acid profile and homocysteine were selected regarding their relationship with muscle parameters. Statistical inference was performed with ttest and ANOVA for inclusion of covariates. Results: Sarcopenic older adults differed significantly in age (p
Macronutrient intake and inadequacies of community-dwelling older adults, a systematic review
Borg, S.J. ter; Verlaan, S. ; Mijnarends, D. ; Schols, J.M.G.A. ; Groot, C.P.G.M. de; Luiking, Y.C. - \ 2015
Annals of Nutrition & Metabolism 66 (2015)4. - ISSN 0250-6807 - p. 242 - 255.
dietary-protein intake - dependent elderly population - nutritional-status - cognitive function - physical-activity - food-consumption - body-composition - energy-intake - people - health
Background: Anorexia of ageing may predispose older adults to under-nutrition and protein energy malnutrition. Studies, however, report a large variation in nutrient inadequacies among community-dwelling older adults. Summary: This systematic review provides a comprehensive overview of the energy and macronutrient intakes and possible inadequacies in community-dwelling older adults. PubMed and EMBASE were screened up to December 2013; data from national nutrition surveys were added. Forty-six studies were included, following the PRISMA guideline. Key Messages: Mean daily energy intake was 8.9 MJ in men and 7.3 MJ in women. Mean daily carbohydrate and protein intakes were 46 and 15 En% in men and 47 and 16 En% in women, respectively. Mean daily total fat, saturated fatty acid (SFA), mono-unsaturated fatty acid (MUFA) and poly-unsaturated fatty acid intakes were respectively 34, 13, 13 and 5-6 En%. The carbohydrates and MUFA intakes are below the acceptable macronutrient distribution ranges (AMDR). Fat intake is relatively high, and SFA intake exceeds the upper-AMDR. Based on the estimated average requirement (EAR) cut-point method, 10-12% of older adults do not meet the EAR for protein. To interpret a possible energy imbalance additional information is needed on physical activity, energy expenditure and body weight changes. This systematic review indicates a suboptimal dietary macronutrient distribution and a large variation in nutrient intakes among community-dwelling older adults.
Assessing the genetic variation of Ty-1 and Ty-3 alleles conferring resistance to tomato yellow leaf curl virus in a broad tomato germplasm
Caro Rios, C.M. ; Verlaan, M.G. ; Julian, O. ; Finkers, H.J. ; Wolters, A.M.A. ; Hutton, S.F. ; Scott, J.W. ; Kormelink, R.J.M. ; Visser, R.G.F. ; Diez, M.J. ; Perez-de-Castro, A. ; Bai, Y. - \ 2015
Molecular Breeding 35 (2015). - ISSN 1380-3743 - 13 p.
Tomato yellow leaf curl virus (TYLCV) hampers tomato production worldwide. Our previous studies have focussed on mapping and ultimately cloning of the TYLCV resistance genes Ty-1 and Ty-3. Both genes are derived from Solanum chilense and were shown to be allelic. They code for an RNA-dependent RNA polymerase (RDR) belonging to the RDR¿ type defined by a DFDGD catalytic domain. In this study, we first fine-mapped the TYLCV resistance in S. chilense LA1932, LA1960 and LA1971. Results showed that chromosomal intervals of the causal genes in these TYLCV-resistant accessions overlap and cover the region where Ty-1/Ty-3 is located. Further, virus-induced gene silencing was used to silence Ty-1/Ty-3 in tomato lines carrying TYLCV resistance introgressed from S. chilense LA1932, LA1938 and LA1971. Results showed that silencing Ty-1/Ty-3 compromised the resistance in lines derived from S. chilense LA1932 and LA1938. The LA1971-derived material remained resistant upon silencing Ty-1/Ty-3. Further, we studied the allelic variation of the Ty-1/Ty-3 gene by examining cDNA sequences from nine S. chilense-derived lines/accessions and more than 80 tomato cultivars, landraces and accessions of related wild species. The DFDGD catalytic domain of the Ty-1/Ty-3 gene is conserved among all tomato lines and species analysed. In addition, the 12 base pair insertion at the 5-prime part of the Ty-1/Ty-3 gene was found not to be specific for the TYLCV resistance allele. However, compared with the susceptible ty-1 allele, the Ty-1/Ty-3 allele is characterized by three specific amino acids shared by seven TYLCV-resistant S. chilense accessions or derived lines. Thus, Ty-1/Ty-3-specific markers can be developed based on these polymorphisms. Elevated transcript levels were observed for all tested S. chilenseRDR alleles (both Ty-1 and ty-1 alleles), demonstrating that elevated expression level is not a good selection criterion for a functional Ty-1/Ty-3 allele.
Micronutrient intakes and potential inadequacies of community-dwelling older adults: a systematic review
Borg, S. ter; Verlaan, S. ; Hemsworth, J. ; Mijnarends, D. ; Schols, J.M.G.A. ; Luiking, Y.C. ; Groot, C.P.G.M. de - \ 2015
The British journal of nutrition 113 (2015)8. - ISSN 0007-1145 - p. 1195 - 1206.
vitamin-d status - elderly-people - cognitive function - dietary assessment - nutritional-status - nutrient intake - food-consumption - intake adequacy - united-states - energy-intake
Micronutrient deficiencies and low dietary intakes among community-dwelling older adults are associated with functional decline, frailty and difficulties with independent living. As such, studies that seek to understand the types and magnitude of potential dietary inadequacies might be beneficial for guiding future interventions. We carried out a systematic review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. Observational cohort and longitudinal studies presenting the habitual dietary intakes of older adults ( = 65 years) were included. Sex-specific mean (and standard deviation) habitual micronutrient intakes were extracted from each article to calculate the percentage of older people who were at risk for inadequate micronutrient intakes using the estimated average requirement (EAR) cut-point method. The percentage at risk for inadequate micronutrient intakes from habitual dietary intakes was calculated for twenty micronutrients. A total of thirty-seven articles were included in the pooled systematic analysis. Of the twenty nutrients analysed, six were considered a possible public health concern: vitamin D, thiamin, riboflavin, Ca, Mg and Se. The extent to which these apparent inadequacies are relevant depends on dynamic factors, including absorption and utilisation, vitamin and mineral supplement use, dietary assessment methods and the selection of the reference value. In light of these considerations, the present review provides insight into the type and magnitude of vitamin and mineral inadequacies.
Tomato yellow leaf curl virus resistance by ty-1 involves increased cytosine methylation of viral genomes and is compromised by cucumber mosaic virus infection
Butterbach, P.B.E. ; Verlaan, M.G. ; Dullemans, A.M. ; Lohuis, H. ; Visser, R.G.F. ; Bai, Y. ; Kormelink, R.J.M. - \ 2014
Proceedings of the National Academy of Sciences of the United States of America 111 (2014)35. - ISSN 0027-8424 - p. 12942 - 12947.
short interfering rna - dna methylation - geminivirus al2 - l2 proteins - adenosine kinase - gene - suppression - arabidopsis - plants - locus
Tomato yellow leaf curl virus (TYLCV) and related begomoviruses are a major threat to tomato production worldwide and, to protect against these viruses, resistance genes from different wild tomato species are introgressed. Recently, the Ty-1 resistance gene was identified, shown to code for an RNA-dependent RNA polymerase and to be allelic with Ty-3. Here we show that upon TYLCV challenging of resistant lines carrying Ty-1 or Ty-3, low virus titers were detected concomitant with the production of relatively high levels of siRNAs whereas, in contrast, susceptible tomato Moneymaker (MM) revealed higher virus titers but lower amounts of siRNAs. Comparative analysis of the spatial genomic siRNA distribution showed a consistent and subtle enrichment for siRNAs derived from the V1 and C3 genes in Ty-1 and Ty-3. In plants containing Ty-2 resistance the virus was hardly detectable, but the siRNA profile resembled the one observed in TYLCV-challenged susceptible tomato (MM). Furthermore, a relative hypermethylation of the TYLCV V1 promoter region was observed in genomic DNA collected from Ty-1 compared with that from (MM). The resistance conferred by Ty-1 was also effective against the bipartite tomato severe rugose begomovirus, where a similar genome hypermethylation of the V1 promoter region was discerned. However, a mixed infection of TYLCV with cucumber mosaic virus compromised the resistance. The results indicate that Ty-1 confers resistance to geminiviruses by increasing cytosine methylation of viral genomes, suggestive of enhanced transcriptional gene silencing. The mechanism of resistance and its durability toward geminiviruses under natural field conditions is discussed.
Macronutrient intake and inadequacies in community-dwelling older adults, a systematic review
Borg, S. ter; Groot, C.P.G.M. de; Mijnarends, D. ; Verlaan, S. ; Luiking, Y.C. - \ 2013
Macronutrient intake and inadequacies in community-dwelling older adults, a systematic review
Borg, S. ter; Groot, C.P.G.M. de; Mijnarends, D. ; Verlaan, S. ; Luiking, Y.C. - \ 2013
Assessment of nutrient intake and status in sarcopenia - a pilot study
Borg, S. ter; Mijnarends, D. ; Verlaan, S. ; Vries, J.H.M. de; Meijers, J.M.M. ; Schols, J.M.G.A. ; Groot, C.P.G.M. de; Luiking, Y.C. - \ 2013
Characterization of major resistance genes to Tomato Yellow Leaf Curl Virus
Verlaan, M.G. - \ 2013
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Yuling Bai; Richard Kormelink. - [S.l.] : s.n. - ISBN 9789461735614 - 158
solanum lycopersicum - tomaten - tomatengeelkrulbladvirus - ziekteresistentie - plantenveredeling - genkartering - introgressie - uitschakelen van genexpressie - solanum lycopersicum - tomatoes - tomato yellow leaf curl virus - disease resistance - plant breeding - gene mapping - introgression - gene silencing

Tomato yellow leaf curl disease, a devastating disease of tomato, is caused by a complex of begomoviruses generally referred to as Tomato yellow leaf curl virus (TYLCV). Almost all breeding for TYLCV resistance has been based on the introgression of the Ty-1 and Ty-3 resistance loci derived from Solanum chilense LA1969 and LA1932/LA2779 respectively. The aim of this thesis was to fine map, clone and characterize these two TYLCV resistance genes.

The Ty-1 gene has been used in tomato breeding already for almost 20 years. Its exact genetic location was however unknown which made precise marker assisted breeding difficult. Here we have analysed the recombination behavior of the chromosomal region where Ty-1 is introgressed by applying newly developed molecular markers in two F2 populations obtained from two commercial Ty-1 carrying hybrids. A big S. chilense introgression was detected in both populations that coveralmost the whole short arm and a part of the long arm of chromosome 6. In this introgression recombination suppression was detected and Fluorescence in situ Hybridization (FISH) analysis revealed two chromosomal rearrangements between S. lycopersicum and S. chilense LA1969. These rearrangements are most likely the cause of the observed recombination suppression. Using disease tests on progeny of informative recombinants Ty-1 was mapped to a region of approximately 600 kb which partly overlapped with the mapped region for Ty-3, which led to the indication that Ty-1 and Ty-3 could be allelic. Altogether these results nicely demonstrate the usefulness of FISH as a powerful tool to aid in the accurate mapping of genes that are introgressed from wild species into cultivated tomato (Chapter 2).

To further fine map and ultimately clone Ty-1 and Ty-3 more plants were screened for recombination events and consequently recombinant inbred lines were generated. By developing new markers in combination with disease tests both genes were fine mapped to a very small, almost similar genomic region (approximately 70 kb). Using a Tobacco Rattle Virus-Virus Induced Gene Silencing approach, the resistance genes were finally identified. It was shown that Ty-1 and Ty-3 are allelic and that they code for a RNA-dependent RNA polymerase (RDR) belonging to the RDRɣ type which has an atypical DFDGD motif in the catalytic domain. In contrast to the RDRαtype, characterized by a catalytic DLDGD motif, no clear function has yet been described for the RDRɣ type. With the identification of Ty-1/Ty-3, a completely new class of resistance genes was unveiled (Chapter 3).

The Ty-1/Ty-3 allele is characterized by a 4 amino acid insertion at the 5-prime part of the protein and by a catalytic DFDGD motif. The allelic variation of this gene was examined using cDNA from five S. chilense derived lines and using draft assemblies of whole genome sequences from more than 50 tomato cultivars, landraces and related wild species. Tobacco Rattle Virus induced gene silencing was used to silence Ty-1/Ty-3 and altogether showed that resistance was compromised in three out of five S. chilense derived lines tested. One line with resistance derived from S. chilense LA1971 remained resistance after silencing of Ty-1/Ty-3. For another line (8783, derived from LA1932) only 4 out of 13 plants showed symptoms after silencing,but silencing in this line was inefficient because only one out of three PDS controls showed photobleaching. Comparison of the two typical features of the Ty-1/Ty-3 gene showed no sequence variation amongst S. chilense derived lines. The catalytic domain was found to be conserved among all tomato lines and species analysed, while the characteristic 4 amino acid insertion was also observed in three species closely related to S. chilense, e.g.Solanum corneliomulleri, Solanum peruvianum and Solanum huaylasense. This indicated that most S. chilense accessions most likely carry a functional TYLCV resistance locus on chromosome 6, allelic to Ty-1/Ty-3, and Solanum species related to S. chilense could possibly be useful for future TYLCV resistance breeding (Chapter 4).

The Ty-1 gene encoded an RDR and for this reason most likely conferred resistance involving amplification of the siRNA signal. In the last experimental chapter (Chapter 5) this hypothesis was tested. It was shown that upon TYLCV challenging of resistant Ty-1 and Ty-3 lines low virus titers were detected concomitant with the production of relatively high levels of siRNAs. In contrast to the situation in susceptible tomato Moneymaker where high virus titers were observed, but the amount of siRNAs produced lower compared to those in Ty-1 and Ty-3. Analysis of the spatial genomic siRNA distribution showed a consistent and subtle enrichment for siRNAs derived from the CP (V1) and C3 gene in Ty-1 and Ty-3 lines compared with Moneymaker. In tomato plants containing the Ty-2 resistance gene, included as a control and not an RDR, the virus was hardly detectable but the siRNA profile similar to the one observed in TYLCV-challenged susceptible tomato Moneymaker. Furthermore, genome methylation analysis revealed a relative hypermethylation of the TYLCV CP (V1) promoter region in genomic DNA collected from Ty-1 in comparison to susceptible tomato Moneymaker.

Altogether this thesis describes the mapping, cloning and characterization of the TYLCV resistance genes Ty-1 and Ty-3. Future breeding efforts for TYLCV resistance can now exploit in-gene markers and the insights obtained can possibly direct future research and breeding efforts on plant virus resistance (Chapter 6).

The Tomato Yellow Leaf Curl Virus Resistance Genes Ty-1 and Ty-3 Are Allelic and Code for DFDGD-Class RNA–Dependent RNA Polymerases
Verlaan, M.G. ; Hutton, S.F. ; Ibrahem, R.M. ; Kormelink, R.J.M. ; Visser, R.G.F. ; Scott, J.W. ; Edwards, J.D. ; Bai, Y. - \ 2013
Plos Genetics 9 (2013)3. - ISSN 1553-7404
geminivirus al2 - l2 proteins - lycopersicon-chilense - recessive resistance - nicotiana-attenuata - interfering rnas - adenosine kinase - breeding lines - plant-viruses - mottle virus
Tomato Yellow Leaf Curl Virus Disease incited by Tomato yellow leaf curl virus (TYLCV) causes huge losses in tomato production worldwide and is caused by different related begomovirus species. Breeding for TYLCV resistance has been based on the introgression of multiple resistance genes originating from several wild tomato species. In this study we have fine-mapped the widely used Solanum chilense–derived Ty-1 and Ty-3 genes by screening nearly 12,000 plants for recombination events and generating recombinant inbred lines. Multiple molecular markers were developed and used in combination with disease tests to fine-map the genes to a small genomic region (approximately 70 kb). Using a Tobacco Rattle Virus–Virus Induced Gene Silencing approach, the resistance gene was identified. It is shown that Ty-1 and Ty-3 are allelic and that they code for a RNA–dependent RNA polymerase (RDR) belonging to the RDR¿ type, which has an atypical DFDGD motif in the catalytic domain. In contrast to the RDRa type, characterized by a catalytic DLDGD motif, no clear function has yet been described for the RDR¿ type, and thus the Ty-1/Ty-3 gene unveils a completely new class of resistance gene. Although speculative, the resistance mechanism of Ty-1/Ty-3 and its specificity towards TYLCV are discussed in light of the function of the related RDRa class in the amplification of the RNAi response in plants and transcriptional silencing of geminiviruses in plants
TYCLV resistance
Bai, Y. ; Verlaan, M.G. ; Hutton, Samuel - \ 2012
Octrooinummer: WO2012125025, verleend: 2012-09-20.
The invention relates to molecular markers for determining the presence or absence of a gene conferring resistance to tomato yellow leaf curl virus from S. chilense (Ty-1) in a host plant. The invention additionally relates to methods for producing a host plant comprising a gene conferring resistance to tomato yellow leaf curl virus from S. chilense (Ty-1), comprising the analysis of the presence or absence of the molecular markers. The invention further relates to a plant, and parts thereof, that is obtained by a method of the invention.
Cloning of the allelic Tomato Yellow Leaf Curl Virus resistance genes Ty-1 and Ty-3
Verlaan, Maarten - \ 2012
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