1,059 results on '"PRI Biodiversity and Breeding"'
Search Results
2. Natural loss-of-function mutation of EDR1 conferring resistance to tomato powdery mildew in Arabidopsis thaliana accession C24
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PBR Resistance in Solanaceae ,downy mildew ,kinase ,plants ,cloning ,food and beverages ,mechanism ,PBR Breeding for Resistance in Solanaceae ,microsatellites ,PRI Biodiversity and Breeding ,defense ,Plant Breeding ,PBR Biodiversiteit en Genetische Variatie ,salicylic-acid ,Laboratorium voor Plantenveredeling ,PRI Biodiversiteit en Veredeling ,evolution ,EPS ,gene ,PBR Biodiversity and genetic variation - Abstract
To screen for potentially novel types of resistance to tomato powdery mildew Oidium neolycopersici, a disease assay was performed on 123 Arabidopsis thaliana accessions. Forty accessions were fully resistant, and one, C24, was analysed in detail. By quantitative trait locus (QTL) analysis of an F2 population derived from C24 × Sha (susceptible accession), two QTLs associated with resistance were identified in C24. Fine mapping of QTL-1 on chromosome 1 delimited the region to an interval of 58¿kb encompassing 15 candidate genes. One of these was Enhanced Disease Resistance 1 (EDR1). Evaluation of the previously obtained edr1 mutant of Arabidopsis accession Col-0, which was identified because of its resistance to powdery mildew Golovinomyces cichoracearum, showed that it also displayed resistance to O.¿neolycopersici. Sequencing of EDR1 in our C24 germplasm (referred to as C24-W) revealed two missing nucleotides in the second exon of EDR1 resulting in a premature stop codon. Remarkably, C24 obtained from other laboratories does not contain the EDR1 mutation. To verify the identity of C24-W, a DNA region containing a single nucleotide polymorphism (SNP) unique to C24 was sequenced showing that C24-W contains the C24-specific nucleotide. C24-W showed enhanced resistance to O.¿neolycopersici compared with C24 not containing the edr1 mutation. Furthermore, C24-W displayed a dwarf phenotype, which was not associated with the mutation in EDR1 and was not caused by the differential accumulation of pathogenesis-related genes. In conclusion, we identified a natural edr1 mutant in the background of C24.
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- 2015
3. Combined biotic and abiotic stress resistance in tomato
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Yuling Bai, Gerard van der Linden, Christos Kissoudis, Richard Finkers, Rawnaq Chowdhury, Sjaak van Heusden, Clemens C. M. van de Wiel, and Richard G. F. Visser
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plant-disease ,Population ,Plant Science ,Horticulture ,Biology ,Plant disease resistance ,phenotypic plasticity ,salinity tolerance ,Laboratorium voor Plantenveredeling ,PRI Biodiversiteit en Veredeling ,Genetics ,education ,Abiotic component ,education.field_of_study ,salt tolerance ,solanum-lycopersicon ,Abiotic stress ,fungi ,food and beverages ,abscisic-acid ,Biotic stress ,Plant disease ,PRI Biodiversity and Breeding ,Plant Breeding ,Ion homeostasis ,Agronomy ,climate-change ,oidium-neolycopersici ,powdery mildew ,EPS ,botrytis-cinerea ,Agronomy and Crop Science ,Powdery mildew - Abstract
Abiotic and biotic stress factors are the major constrains for the realization of crop yield potential. As climate change progresses, the spread and intensity of abiotic as well as biotic stressors is expected to increase, with increased probability of crops being exposed to both types of stress. Shielding crops from combinatorial stress requires a better understanding of the plant’s response and its genetic architecture. In this study, we evaluated resistance to salt stress, powdery mildew and to both stresses combined in tomato, using the Solanum habrochaites LYC4 introgression line (IL) population. The IL population segregated for both salt stress tolerance and powdery mildew resistance. Using SNP array marker data, QTLs were identified for salt tolerance as well as Na+ and Cl− accumulation. Salt stress increased the susceptibility of the population to powdery mildew in an additive manner. Phenotypic variation for disease resistance was reduced under combined stress as indicated by the coefficient of variation. No correlation was found between disease resistance and Na+ and Cl− accumulation under combined stress Most genetic loci were specific for either salt stress tolerance or powdery mildew resistance. These findings increase our understanding of the genetic regulation of responses to abiotic and biotic stress combinations and can provide leads to more efficiently breeding tomatoes and other crops with a high level of disease resistance while maintaining their performance in combination with abiotic stress.
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- 2015
4. Transport of Nutrients Determines Growth in Tissue Culture; Why apple shoots grow rapidly and tulip shoots grow slowly
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PRI Biodiversity and Breeding ,PRI Biodiversiteit en Veredeling ,fungi ,food and beverages - Abstract
Tulip growth in vitro is seriously impaired by inferior transport in the shoots. As a result, tulip cannot be micropropagated commercially using conventional means. In contrast, apple shoots show high transport and are easily micropropagated.
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- 2015
5. Host plant resistance towards the cabbage whitefly in Brassica oleracea and its wild relatives
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Pelgrom, K. T B, Broekgaarden, C., Voorrips, R. E., Bas, N., Visser, R. G F, Vosman, B., Sub Plant-Microbe Interactions, Plant Microbe Interactions, Sub Plant-Microbe Interactions, and Plant Microbe Interactions
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PBR Non host and insect resistance ,Age dependent resistance ,0106 biological sciences ,Centrum voor Genetische Bronnen Nederland ,Plant Science ,Whitefly ,tomato ,Horticulture ,Plant disease resistance ,01 natural sciences ,Crop ,03 medical and health sciences ,Aleyrodes proletella ,Laboratorium voor Plantenveredeling ,food ,PRI Biodiversiteit en Veredeling ,tabaci ,cultivars ,Genetics ,aleyrodes-proletella homoptera ,Field evaluations ,insect-resistance ,Plant breeding ,Cultivar ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,fruticulosa ,biology ,Savoy cabbage ,fungi ,food and beverages ,Trichomes ,populations ,biology.organism_classification ,food.food ,PRI Biodiversity and Breeding ,Plant Breeding ,Agronomy ,Brassica oleracea ,glucosinolate polymorphism ,Agronomy and Crop Science ,PBR Non host en Insectenresistentie ,010606 plant biology & botany - Abstract
The cabbage whitefly (Aleyrodes proletella) is a phloem-feeding insect that is a serious problem in Brassica oleracea crops like Brussels sprouts, kale and savoy cabbage. In order to develop whitefly-resistant varieties it is essential to identify effective sources of resistance. In this study, we screened a large collection of 432 accessions, including wild material and landraces of Brassica oleracea as well as crop wild relatives, to determine whitefly performance in a no-choice field experiment. Putatively resistant accessions were further tested under greenhouse conditions. Resistant accessions were identified among B. oleracea var. capitata (cabbage) landraces and in the species B. villosa, B. incana and B. montana. Whereas resistance in cabbage is only expressed in plants of at least 12 weeks old, some wild relatives were already starting to express resistance at 6 weeks. This could open up possibilities for breeding cabbages that are resistant at a young(er) plant age. Our research also shows again the importance of crop wild relatives for finding pest resistances.
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- 2014
6. An updated conventional- and a novel GM potato late blight R gene differential set for virulence monitoring of Phytophthora infestans
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G.J.T. Kessel, Marjan Bergervoet, Suxian Zhu, Vivianne G. A. A. Vleeshouwers, Jack H. Vossen, L.P. Kodde, Evert Jacobsen, Maarten Nijenhuis, and Richard G. F. Visser
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disease resistance ,durable resistance ,united-states ,population ,Virulence ,Plant Science ,Horticulture ,Plant disease resistance ,diversity ,tissue culture and gene transfer ,PBR Siergewassen ,PBR Biodiversiteit en Genetische Variatie ,Laboratorium voor Plantenveredeling ,PRI Biodiversiteit en Veredeling ,PBR Siergewassen, Tissue Culture ,solanum-bulbocastanum ,Botany ,Genetics ,Solanum bulbocastanum ,Blight ,Tissue Culture ,rxlr effectors ,Oomycete ,biology ,resistance genes ,Entomology & Disease Management ,fungi ,food and beverages ,PBR Ornamentals ,PBR Ornamentals, tissue culture and gene transfer ,R gene ,biology.organism_classification ,Centrum Ecosystemen ,PRI Biodiversity and Breeding ,Centre for Ecosystem Studies ,Plant Breeding ,Phytophthora infestans ,EPS ,races ,Solanum ,PBR Biodiversity and genetic variation ,Agronomy and Crop Science ,pathogen - Abstract
Late blight is an important disease in potato that is caused by the oomycete Phytophthora infestans. In the past, Solanum demissum late blight resistance (R) genes were introgressed into cultivated potato (Solanum tuberosum). Eleven of these resistant plants were selected to characterize the virulence spectrum of individual P. infestans isolates and to monitor the dynamics of virulence in P. infestans populations. These plants are referred to as the Mastenbroek and Black differential sets. It has long been assumed that each differential plant contained one single R gene. In the current study and previous studies, however, most Mastenbroek differential plants were shown to harbor multiple R gene(s), which blurs virulence typing of late blight isolates. In order to acquire more accurate virulence profiles, we extended the Mastenbroek differential set with Solanum spp. plants harboring reduced R gene complexity and with plants containing recently identified R genes from related but different Solanum species. In addition, a differential set of ten Genetically Modified (GM) plants harboring single late blight R genes in the same genetic background (Desiree). By analyzing the virulence spectra of recently collected isolates using both newly described differential sets, we found that the GM Desiree differential set was more accurate for isolate virulence typing than the conventional (extended) differential set. Besides, the GM Desiree differential set was shown to be useful as trap plants to isolate novel P. infestans strains and to monitor virulence towards particular R genes in P. infestans populations `on site´. Legislative restrictions are, however, limiting the use of the GM Desiree differential set.
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- 2014
7. Isolation and characterization of H7N9 avian influenza A virus from humans with respiratory diseases in Zhejiang, China
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Yuelong Shu, Zhiping Chen, Yanjun Zhang, Huakun Lv, Qiong Ge, Jiankang Han, Haiyan Mao, Ju-ying Yan, Shichang Xia, Guoqiu Zhao, Yi Sun, Yan Feng, Enfu Chen, Yi-yu Lu, Liming Gong, Fang Xu, Xinying Wang, Changping Xu, Zhang-Nv Yang, Jian Gao, Yin Chen, Li Hui, Zhen Li, Koch Guus, Baoxiang Xu, and Lei Zhang
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Male ,Cancer Research ,Hemagglutination ,Chick Embryo ,adaptation ,Influenza A Virus, H7N9 Subtype ,medicine.disease_cause ,Avian Influenza A Virus ,PRI Biodiversiteit en Veredeling ,Cluster Analysis ,Phylogeny ,Phylogenetic tree ,Reverse Transcriptase Polymerase Chain Reaction ,pathogenesis ,poultry ,transmission ,Middle Aged ,Virology & Molecular Biology ,polymerase ,Infectious Diseases ,host ,RNA, Viral ,Crop and Weed Ecology ,Adult ,China ,Virus Cultivation ,Genome, Viral ,Biology ,Real-Time Polymerase Chain Reaction ,determinant ,Virus ,Virology ,Influenza, Human ,substitution ,medicine ,Animals ,Humans ,Leerstoelgroep Gewas- en onkruidecologie ,Whole genome sequencing ,Embryonated ,Sequence Analysis, DNA ,Hemagglutination Inhibition Tests ,Influenza A virus subtype H5N1 ,Virologie & Moleculaire Biologie ,PRI Biodiversity and Breeding ,Microscopy, Electron ,amino-acid ,human infection - Abstract
In 2013, the novel reassortant avian-origin influenza A (H7N9) virus was reported in China. Through enhanced surveillance, infection by the H7N9 virus in humans was first identified in Zhejiang Province. Real-time reverse-transcriptase-polymerase-chain-reaction (RT-PCR) was used to confirm the infection. Embryonated chicken eggs were used for virus isolation from pharyngeal swabs taken from infected human patients. The H7N9 isolates were first identified by the hemagglutination test and electron microscopy, then used for whole genome sequencing. Bioinformatics software was used to construct the phylogenetic tree and for computing the mean rate of evolution of the HA gene in H7Nx and NA in HxN9. Two novel H7N9 avian influenza A viruses (A/Zhejiang/1/2013 and A/Zhejiang/2/2013) were isolated from the positive infection cases. Substitutions were found in both Zhejiang isolates and were identified as human-type viruses. All phylogenetic results indicated that the novel reassortant in H7N9 originated in viruses that infected birds. The sequencing and phylogenetic analysis of the whole genome revealed the mean rate of evolution of the HA gene in H7NX to be 5.74E-3 (95% Highest posterior density: 3.8218E-3 to 7.7873E-3) while the NA gene showed 2.243E-3 (4.378E-4 to 3.79E-3) substitutions per nucleotide site per year. The novel reassortant H7N9 virus was confirmed by molecular methods to have originated in poultry, with the mutations occurring during the spread of the H7N9 virus infection. Live poultry markets played an important role in whole H7N9 circulation.
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- 2014
8. Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals
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M. Vukosavljev, Richard G. F. Visser, Marinus J. M. Smulders, W.P.C. van 't Westende, Paul Arens, G.D. Esselink, and P. Cox
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construction ,Genotyping Techniques ,Molecular Sequence Data ,in-silico ,Locus (genetics) ,Biology ,Rosa ,l ,DNA sequencing ,diversity ,Laboratorium voor Plantenveredeling ,PRI Biodiversiteit en Veredeling ,Genotype ,Genetics ,Polymorphic Microsatellite Marker ,Gene family ,Allele ,Ecology, Evolution, Behavior and Systematics ,Repetitive Sequences, Nucleic Acid ,rose ,est-ssr markers ,variability ,transferability ,Computational Biology ,Genetic Variation ,Sequence Analysis, DNA ,PRI Biodiversity and Breeding ,Plant Breeding ,Genetic marker ,identification ,Microsatellite ,genetic-linkage maps ,Transcriptome ,Microsatellite Repeats ,Biotechnology - Abstract
The first hurdle in developing microsatellite markers, cloning, has been overcome by next generation sequencing. The second hurdle is testing to differentiate polymorphic from non-polymorphic loci. The third hurdle, somewhat hidden, is that only polymorphic markers with a large effective number of alleles are sufficiently informative to be deployed in multiple studies. Both steps are laborious and still done manually. We have developed a strategy in which we first screen reads from multiple genotypes for repeats that show the most length variants, and only these are subsequently developed into markers. We validated our strategy in tetraploid garden rose using Illumina paired-end transcriptome sequences of 11 roses. Out of 48 tested two markers failed to amplify but all others were polymorphic. Ten loci amplified more than one locus, indicating duplicated genes or gene families. Completely avoiding duplicated loci will be difficult because the range of numbers of predicted alleles of highly polymorphic single- and multi-locus markers largely overlapped. Of the remainder, half were replicate markers (i.e., multiple primer pairs for one locus), indicating the difficulty of correctly filtering short reads containing repeat sequences. We subsequently refined the approach to eliminate multiple primer sets to the same loci. The remaining 18 markers were all highly polymorphic, amplifying on average 11.7 alleles per marker (range = 6 to 20) in 11 tetraploid roses, exceeding the 8.2 alleles per marker of the 24 most polymorphic markers genotyped previously. This strategy, therefore, represents a major step forward in the development of highly polymorphic microsatellite markers.
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- 2014
9. Genetic diversity of nitrogen use efficiency in spinach (Spinacia oleraces L.) cultivars using the Ingestad model on hydroponics
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Asako Kawai, Edith T. Lammerts van Bueren, Rafael Chan-Navarrete, C. Gerard van der Linden, and Oene Dolstra
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vegetables ,Specific leaf area ,growth ,Plant Science ,Horticulture ,Photosynthesis ,Laboratorium voor Plantenveredeling ,Dry weight ,allocation ,PRI Biodiversiteit en Veredeling ,Relative growth rate ,Genetics ,Cultivar ,crop plants ,photosynthesis ,biology ,fungi ,food and beverages ,biology.organism_classification ,Hydroponics ,PE&RC ,yield ,nitrate accumulation ,PRI Biodiversity and Breeding ,Plant Breeding ,nutrition ,Agronomy ,Shoot ,Spinach ,acid ,leaves ,EPS ,Agronomy and Crop Science - Abstract
Spinach is a leafy vegetable that requires a high N fertilization to have a satisfactory yield and quality, in part because it has poor nitrogen use efficiency (NUE). Therefore, there is a need to breed for cultivars with an excellent NUE. To this end the genetic diversity for NUE-related traits was studied in a diverse set of commercial cultivars. This set was evaluated in a hydroponic system using the Ingestad model; the system was set at a relative growth rate of 0.14 and 0.18 g g-1 day-1 (low and high N, respectively). Experiments were performed at low and high plant density. Traits monitored for single plants included fresh and dry weight, leaf area, specific leaf area, dry weight ratio between root and shoot, and chlorophyll content. The high density experiment showed more genotypic variation for the observed traits than the low density one. Biomass production was considerably lower at low than at high N. Path analysis revealed that leaf area had the highest direct effect on NUE, while specific leaf area was an important trait determining variation in NUE at low N. Slow and fast growing genotypes were shown to use different strategies to utilize N, and these strategies are expressed differently at high and low N availability. This indicates that improving spinach for NUE is feasible using the analysed genotypes as source material, and different strategies can be targeted for adaptation of spinach cultivars to low N conditions.
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- 2014
10. Activation tagging of ATHB13 in Arabidopsis thaliana confers broad-spectrum disease resistance
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Michela Appiano, Annelies E. H. M. Loonen, Dongli Gao, Yuling Bai, Robin P. Huibers, Xi Chen, Anne-Marie A. Wolters, and Richard G. F. Visser
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Arabidopsis ,Pseudomonas syringae ,Plant Science ,transcription factors hahb1 ,Plant Epidermis ,Laboratorium voor Plantenveredeling ,Gene Expression Regulation, Plant ,PRI Biodiversiteit en Veredeling ,Disease Resistance ,Oligonucleotide Array Sequence Analysis ,Genetics ,food and beverages ,General Medicine ,Plants, Genetically Modified ,Phenotype ,powdery mildew resistance ,Oomycetes ,expression patterns ,vegetative storage protein ,oidium-neolycopersici ,PBR Biodiversity and genetic variation ,Powdery mildew ,Signal Transduction ,Biology ,Plant disease resistance ,PBR Biodiversiteit en Genetische Variatie ,Ascomycota ,Stress, Physiological ,plant defense ,Animals ,nudix hydrolase ,Plant Diseases ,Homeodomain Proteins ,PBR Resistance in Solanaceae ,Leucine Zippers ,Hyaloperonospora arabidopsidis ,Arabidopsis Proteins ,Abiotic stress ,Gene Expression Profiling ,Biotic stress ,biology.organism_classification ,PBR Breeding for Resistance in Solanaceae ,cell-death ,Plant Leaves ,PRI Biodiversity and Breeding ,Mutagenesis, Insertional ,Plant Breeding ,salicylic-acid ,Aphids ,Downy mildew ,EPS ,Agronomy and Crop Science ,hd-zip - Abstract
Powdery mildew species Oidium neolycopersici (On) can cause serious yield losses in tomato production worldwide. Besides on tomato, On is able to grow and reproduce on Arabidopsis. In this study we screened a collection of activation-tagged Arabidopsis mutants and identified one mutant, 3221, which displayed resistance to On, and in addition showed a reduced stature and serrated leaves. Additional disease tests demonstrated that the 3221 mutant exhibited resistance to downy mildew (Hyaloperonospora arabidopsidis) and green peach aphid (Myzus persicae), but retained susceptibility to bacterial pathogen Pseudomonas syringae pv tomato DC3000. The resistance trait and morphological alteration were mutually linked in 3221. Identification of the activation tag insertion site and microarray analysis revealed that ATHB13, a homeodomain-leucine zipper (HD-Zip) transcription factor, was constitutively overexpressed in 3221. Silencing of ATHB13 in 3221 resulted in the loss of both the morphological alteration and resistance, whereas overexpression of the cloned ATHB13 in Col-0 and Col-eds1-2 backgrounds resulted in morphological alteration and resistance. Microarray analysis further revealed that overexpression of ATHB13 influenced the expression of a large number of genes. Previously, it was reported that ATHB13-overexpressing lines conferred tolerance to abiotic stress. Together with our results, it appears that ATHB13 is involved in the crosstalk between abiotic and biotic stress resistance pathways.
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- 2014
11. Phenomics and genomics tools for facilitating brassica crop improvement
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PRI Biodiversity and Breeding ,PBR Non host and insect resistance ,Plant Breeding ,PRI Biodiversiteit en Veredeling ,PBR Non host en Insectenresistentie - Published
- 2015
12. Genetic mapping of semi-polar metabolites in pepper fruits (Capsicum sp.): towards unravelling the molecular regulation of flavonoid quantitative trait loci
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Enny Sudarmonowati, Ric C. H. de Vos, Ana Carolina Maisonnave Arisi, Yuni Wahyuni, Ana-Rosa Ballester, Jos Molthoff, Marcela Viquez Zamora, Raoul J. Bino, Roeland E. Voorrips, Vanessa Stahl-Hermes, Awang Maharijaya, and Arnaud G. Bovy
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mQTL ,Candidate gene ,Metabolite ,Population ,AFSG Stafafdelingen (FBR) ,annuum ,Plant Science ,Quantitative trait locus ,Biology ,Article ,chemistry.chemical_compound ,Laboratorium voor Plantenveredeling ,Metabolomics ,Gene mapping ,Semi-polar metabolites ,PRI Biodiversiteit en Veredeling ,expression ,Botany ,Pepper ,Genetics ,MYB12 ,Laboratorium voor Plantenfysiologie ,education ,l. var. acuminatum ,Molecular Biology ,Naringenin chalcone ,biodiversity ,Flavonoids ,education.field_of_study ,F2 population ,glycosides ,food and beverages ,frankliniella-occidentalis ,mass-spectrometry ,metabolomics ,PRI Biodiversity and Breeding ,Plant Breeding ,capsaicinoid content ,Biochemistry ,chemistry ,BIOS Applied Metabolic Systems ,AFSG Staff Departments (FBR) ,Capsicum ,Agronomy and Crop Science ,Laboratory of Plant Physiology ,tomato fruit ,Biotechnology - Abstract
Untargeted LCMS profiling of semi-polar metabolites followed by metabolite quantitative trait locus (mQTL) analysis was performed in ripe pepper fruits of 113 F2 plants derived from a cross between Capsicum annuum AC1979 (no. 19) and Capsicum chinense No. 4661 Selection (no. 18). The parental accessions were selected based on their variation in fruit morphological characteristics and fruit content of some target phytonutrients. Clear segregation of fruit colour and fruit metabolite profiles was observed in the F2 population. The F2 plants formed three clusters based on their metabolite profiles. Of the total of 542 metabolites, 52 could be annotated, including a range of flavonoids, such as flavone C-glycosides, flavonol O-glycosides and naringenin chalcone, as well as several phenylpropanoids, a capsaicin analogue, fatty acid derivatives and amino acid derivatives. Interval mapping revealed 279 mQTLs in total. Two mQTL hotspots were found on chromosome 9. These two chromosomal regions regulated the relative levels of 35 and 103 metabolites, respectively. Analysis also revealed an mQTL for a capsaicin analogue, located on chromosome 7. Confirmation of flavonoid mQTLs using a set of six flavonoid candidate gene markers and their corresponding expression data (expression QTLs) indicated the Ca-MYB12 transcription factor gene on chromosome 1 and the gene encoding flavone synthase (FS-2) on chromosome 6 as likely causative genes determining the variation in naringenin chalcone and flavone C-glycosides, respectively, in this population. The combination of large-scale metabolite profiling and QTL analysis provided valuable insight into the genomic regions and genes important for the production of (secondary) metabolites in pepper fruit. This will impact breeding strategies aimed at optimising the content of specific metabolites in pepper fruit. Electronic supplementary material The online version of this article (doi:10.1007/s11032-013-9967-0) contains supplementary material, which is available to authorized users.
- Published
- 2013
13. Genetic diversity and structure in a collection of tulip cultivars assessed by SNP markers
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Jianjun Liu, Paul Arens, P.J.J. Bijman, Arwa Shahin, Nan Tang, and Jaap M. van Tuyl
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Genetic diversity ,biology ,liliaceae ,conservation ,population-structure ,food and beverages ,Horticulture ,biology.organism_classification ,Genetic analysis ,Tulipa gesneriana ,PRI Biodiversity and Breeding ,power ,Plant Breeding ,single nucleotide polymorphisms ,Genetic distance ,PRI Biodiversiteit en Veredeling ,Genetic marker ,Genetic structure ,Botany ,identification ,program ,Cultivar ,genome ,Hybrid - Abstract
Although tulip is one of the most important bulbous crops worldwide, the genetic background of most cultivars is unclear at present. The purposes of this study are to investigate genetic diversity and to identify the genetic structure and relationships among tulip cultivars. A total of 236 polymorphic single nucleotide polymorphisms (SNPs) were obtained from ‘Kees Nelis’ and ‘Cantata’, from which 121 SNPs with a minor allele frequency above 0.1 were selected for genetic analysis. The total observed heterozygosity ( Ho ) among the 72 accessions was 0.35, Ho of cultivar groups ranged from 0.22 ( Tulipa fosteriana ) to 0.43 ( Tulipa gesneriana × T. fosteriana hybrids). Rather small genetic distances were found among T. gesneriana cultivar groups which are defined according to flowering time and morphology. In both PCoA (principle coordinate analysis) and STRUCTURE analysis, the 72 accessions were separated into three clusters ( F ST = 0.208, P F ST = 0.072, P = 0.02). T. gesneriana × T. fosteriana hybrid breeding lines were easily identified as admixed individuals in STRUCTURE analysis, by means of which cultivar ‘Purissima’ and ‘Flair’ were also inferred as hybrids.
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- 2013
14. Metabolomics and molecular marker analysis to explore pepper (Capsicum sp.) biodiversity
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K.T.B. Pelgrom, Enny Sudarmonowati, Raoul J. Bino, Yuni Wahyuni, Yury Tikunov, Arnaud G. Bovy, Awang Maharijaya, Ana-Rosa Ballester, and Ric C. H. de Vos
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Volatiles ,Semi-polar compounds ,AFLP ,Metabolite ,Endocrinology, Diabetes and Metabolism ,Clinical Biochemistry ,hs-spme ,AFSG Stafafdelingen (FBR) ,Biology ,tomato ,Biochemistry ,chemistry.chemical_compound ,Metabolomics ,Laboratorium voor Plantenveredeling ,Metabolite profiling ,acyclic diterpene glycosides ,PRI Biodiversiteit en Veredeling ,Molecular marker ,Genetic variation ,Pepper ,Botany ,Laboratorium voor Plantenfysiologie ,constituents ,volatile fraction ,Pungency ,food and beverages ,fruit ,mass-spectrometry ,Terpenoid ,PRI Biodiversity and Breeding ,Plant Breeding ,capsaicinoid content ,chemistry ,chinense ,BIOS Applied Metabolic Systems ,annuum l ,Amplified fragment length polymorphism ,Original Article ,AFSG Staff Departments (FBR) ,EPS ,Capsicum ,Laboratory of Plant Physiology - Abstract
An overview of the metabolic diversity in ripe fruits of a collection of 32 diverse pepper (Capsicum sp.) accessions was obtained by measuring the composition of both semi-polar and volatile metabolites in fruit pericarp, using untargeted LC-MS and headspace GC-MS platforms, respectively. Accessions represented C. annuum, C. chinense, C. frutescens and C. baccatum species, which were selected based on variation in morphological characters, pungency and geographic origin. Genotypic analysis using AFLP markers confirmed the phylogenetic clustering of accessions according to Capsicum species and separated C. baccatum from the C. annuum-C. chinense-C. frutescens complex. Species-specific clustering was also observed when accessions were grouped based on their semi-polar metabolite profiles. In total 88 semi-polar metabolites could be putatively identified. A large proportion of these metabolites represented conjugates of the main pepper flavonoids (quercetin, apigenin and luteolin) decorated with different sugar groups at different positions along the aglycone. In addition, a large group of acyclic diterpenoid glycosides, called capsianosides, was found to be highly abundant in all C. annuum genotypes. In contrast to the variation in semi-polar metabolites, the variation in volatiles corresponded well to the differences in pungency between the accessions. This was particularly true for branched fatty acid esters present in pungent accessions, which may reflect the activity through the acyl branch of the metabolic pathway leading to capsaicinoids. In addition, large genetic variation was observed for many well-established pepper aroma compounds. These profiling data can be used in breeding programs aimed at improving metabolite-based quality traits such as flavour and health-related metabolites in pepper fruits. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-012-0432-6) contains supplementary material, which is available to authorized users.
- Published
- 2013
15. Comparative analysis of Solanum stoloniferum responses to probing by the green peach aphid Myzus persicae and the potato aphid Macrosiphum euphorbiae
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fungi ,food and beverages ,manduca-sexta lepidoptera ,host nicotiana-attenuata ,arabidopsis-thaliana ,molecular-interactions ,PE&RC ,Laboratorium voor Entomologie ,PRI Biodiversity and Breeding ,Plant Breeding ,phloem-feeding insects ,salivary secretions ,plant defense ,PRI Biodiversiteit en Veredeling ,microarray analysis ,Laboratory of Entomology ,brevicoryne-brassicae ,resistance gene mi - Abstract
Plants protect themselves against aphid attacks by species-specific defense mechanisms. Previously, we have shown that Solanum stoloniferum Schlechtd has resistance factors to Myzus persicae Sulzer (Homoptera: Aphididae) at the epidermal/mesophyll level that are not effective against Macrosiphum euphorbiae Thomas (Homoptera: Aphididae). Here, we compare the nymphal mortality, the pre-reproductive development time, and the probing behavior of M. persicae and M. euphorbiae on S. stoloniferum and Solanum tuberosum L. Furthermore, we analyze the changes in gene expression in S. stoloniferum 96 hours post infestation by either aphid species. Although the M. euphorbiae probing behavior shows that aphids encounter more probing constrains on phloem activitieslonger probing and salivation time on S. stoloniferum than on S. tuberosum, the aphids succeeded in reaching a sustained ingestion of phloem sap on both plants. Probing by M. persicae on S. stoloniferum plants resulted in limited feeding only. Survival of M. euphorbiae and M. persicae was affected on young leaves, but not on senescent leaves of S. stoloniferum. Infestation by M. euphorbiae changed the expression of more genes than M. persicae did. At the systemic level both aphids elicited a weak response. Infestation of S. stoloniferum plants with a large number of M. persicae induced morphological changes in the leaves, leading to the development of pustules that were caused by disrupted vascular parenchyma and surrounding tissue. In contrast, an infestation by M. euphorbiae had no morphological effects. Both plant species can be regarded as good host for M. euphorbiae, whereas only S. tuberosum is a good host for M. persicae and S. stoloniferum is not. Infestation of S. stoloniferum by M. persicae or M. euphorbiae changed the expression of a set of plant genes specific for each of the aphids as well as a set of common genes.
- Published
- 2013
16. Betula PR-10 protein (PR-10) gene, PR-10-01A01.01 allele, partial cds
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PRI Bioscience ,PRI Biodiversity and Breeding ,Plant Breeding ,Laboratorium voor Plantenveredeling ,PRI Biodiversiteit en Veredeling ,EPS-4 ,Betula sp - Published
- 2016
17. Phytophthora in planta induced O3 (ipiO) gene, partial cds
- Subjects
PRI Biodiversity and Breeding ,Phytophthora mirabilis ,Plant Breeding ,Biointeracties and Plant Health ,Laboratorium voor Plantenveredeling ,EPS-2 ,Phytophthora infestans ,PRI Biodiversiteit en Veredeling ,Laboratory of Phytopathology ,PRI Biointeractions en Plantgezondheid ,hytophthora phaseoli ,Laboratorium voor Phytopathologie - Published
- 2016
18. Identification of loci affecting accumulation of secondary metabolites in tomato fruit of a Solanum lycopersicum × Solanum chmielewskii introgression line population
- Author
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Ana-Rosa Ballester, Ruud A. de Maagd, Yury Tikunov, Jos Molthoff, Ric C. H. de Vos, Silvana Grandillo, Arnaud G. Bovy, Sjaak van Heusden, and Marcela Viquez-Zamora
- Subjects
0106 biological sciences ,0301 basic medicine ,QTL analysis ,PBR Breeding for Quality ,Metabolite ,Population ,Introgression ,Chromosome 9 ,Plant Science ,Biology ,Quantitative trait locus ,lcsh:Plant culture ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Alkaloids ,Laboratorium voor Plantenveredeling ,PRI Biodiversiteit en Veredeling ,Botany ,lcsh:SB1-1110 ,BIOS Plant Development Systems ,education ,Gene ,Flavonoids ,education.field_of_study ,Tomato (Solanum lycopersicum) ,Phenylpropanoid ,fungi ,food and beverages ,Introgression lines ,biology.organism_classification ,PRI Biodiversity and Breeding ,Plant Breeding ,030104 developmental biology ,chemistry ,BIOS Applied Metabolic Systems ,Solanum ,EPS ,010606 plant biology & botany - Abstract
Semi-polar metabolites such as flavonoids, phenolic acids, and alkaloids are very important health-related compounds in tomato. As a first step to identify genes responsible for the synthesis of semi-polar metabolites, quantitative trait loci (QTLs) that influence the semi-polar metabolite content in red-ripe tomato fruit were identified, by characterizing fruits of a population of introgression lines (ILs) derived from a cross between the cultivated tomato Solanurn lycopersicum and the wild species Solanurn chmielewskii. By analyzing fruits of plants grown at two different locations, we were able to identify robust metabolite QTLs for changes in phenylpropanoid glycoconjugation on chromosome 9, for accumulation of flavonol glycosides on chromosome 5, and for alkaloids on chromosome 7. To further characterize the QTLs we used a combination of genome sequencing, transcriptomics and targeted metabolomics to identify candidate key genes underlying the observed metabolic variation.
- Published
- 2016
19. Triticinae alpha-gliadin storage protein gene, partial cds
- Subjects
PRI Bioscience ,PRI Biodiversity and Breeding ,Triticum monococcum ,Plant Breeding ,Laboratorium voor Plantenveredeling ,Food Chemistry ,PRI Biodiversiteit en Veredeling ,Centrum voor Genetische Bronnen Nederland ,Levensmiddelenchemie ,Triticinae ,Aegilops sp ,VLAG - Published
- 2016
20. Macrofungal diversity in Colombian Amazon forests varies with regions and regimes of disturbance
- Author
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A. Esperanza Franco-Molano, Teun Boekhout, Gerben Straatsma, and Carlos A. López-Quintero
- Subjects
rain-forest ,Mycobiota ,leaf-litter ,Biodiversity ,Slash-and-burn ,Rainforest ,Biology ,geographical gradients ,molecular characterization ,PRI Biodiversiteit en Veredeling ,Ecosystem ,tree species richness ,Ecology, Evolution, Behavior and Systematics ,biodiversity ,Nature and Landscape Conservation ,tropical forests ,WIMEK ,Ecology ,Amazon rainforest ,Plant litter ,PRI Biodiversity and Breeding ,fungal diversity ,climate-change ,Alpha diversity ,alpha-diversity - Abstract
Here we present the results of fungal biodiversity studies from some selected Colombian Amazon forests in relationship to plant biodiversity and successional stages after slash and burn agriculture. Macrofungal diversity was found to differ between forests occurring in two regions (Araracuara vs Amacayacu) as well as between flooded forests and terra firme forests in the Amacayacu region. Macrofungal biodiversity differed between regeneration states of different age in the Araracuara region. Suitable substrates, especially dead wood that occurred as a result of recent slash and burn agriculture, resulted in the formation of many sporocarps of wood-inhabiting species. Putative ectomycorrhizal species were found in a dipterocarp forest. Fifty two percent of the macrofungal species could not be identified to the species level, but could be assigned to a genus, and it is likely that a significant portion of these represent species new to science. Long term studies are needed to obtain a comprehensive and complete understanding of the diversity and functioning of mycobiota in Amazon forest ecosystems.
- Published
- 2012
21. Genomic organisation of the Mal d 1 gene cluster on linkage group 16 in apple
- Author
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Eric van de Weg, Anna Rosa Iorio, Stefano Tartarini, Sander Peters, Giulia Pagliarani, Roberta Paris, Stefano Del Duca, Paul Arens, Pagliarani G., Paris R., Iorio A.R., Tartarini S., Del Duca S., Arens P., Peters S., and van de Weg E.
- Subjects
PRU P 1 ,Pseudogene ,scab resistance ,cloning ,Plant Science ,Biology ,Genome ,Article ,bet v 1 ,resistance locus ,ALLERGEN ,PRI Biodiversiteit en Veredeling ,Arabidopsis ,Gene cluster ,expression ,Genetics ,Malus × domestica ,Gene family ,PR-10 ,MALUS X DOMESTICA ,Molecular Biology ,Gene ,Cloning ,Bacterial artificial chromosome ,x-domestica borkh ,BAC CLONE ,biology.organism_classification ,PRI Biodiversity and Breeding ,Plant Breeding ,arabidopsis ,major allergen ,birch pollen allergen ,Prunus ,Agronomy and Crop Science ,duplicate genes ,Biotechnology - Abstract
European populations exhibit progressive sensitisation to food allergens, and apples are one of the foods for which sensitisation is observed most frequently. Apple cultivars vary greatly in their allergenic characteristics, and a better understanding of the genetic basis of low allergenicity may therefore allow allergic individuals to increase their fruit intake. Mal d 1 is considered to be a major apple allergen, and this protein is encoded by the most complex allergen gene family. Not all Mal d 1 members are likely to be involved in allergenicity. Therefore, additional knowledge about the existence and characteristics of the different Mal d 1 genes is required. In the present study, we investigated the genomic organisation of the Mal d 1 gene cluster in linkage group 16 of apple through the sequencing of two bacterial artificial chromosome clones. The results provided new information on the composition of this family with respect to the number and orientation of functional and pseudogenes and their physical distances. The results were compared with the apple and peach genome sequences that have recently been made available. A broad analysis of the whole apple genome revealed the presence of new genes in this family, and a complete list of the observed Mal d 1 genes is supplied. Thus, this study provides an important contribution towards a better understanding of the genetics of the Mal d 1 family and establishes the basis for further research on allelic diversity among cultivars in relation to variation in allergenicity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9588-4) contains supplementary material, which is available to authorized users.
- Published
- 2012
22. A potato pathogenesis-related protein gene, StPRp27, contributes to race-nonspecific resistance against Phytophthora infestans
- Author
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Jun Liu, Zhendong Tian, Conghua Xie, Xiaolei Shi, and Edwin A. G. van der Vossen
- Subjects
quantitative resistance ,Phytophthora infestans ,late blight resistance ,Population ,population ,Nicotiana benthamiana ,broad-spectrum resistance ,Breeding ,Plant disease resistance ,Real-Time Polymerase Chain Reaction ,tobacco ,r-gene ,PRI Biodiversiteit en Veredeling ,solanum-bulbocastanum ,expression ,Tobacco ,Botany ,Genetics ,Solanum bulbocastanum ,Gene Silencing ,education ,Molecular Biology ,DNA Primers ,Disease Resistance ,Plant Diseases ,Plant Proteins ,Solanum tuberosum ,Pathogenesis-related protein ,education.field_of_study ,biology ,EPS-2 ,fungi ,food and beverages ,General Medicine ,R gene ,biology.organism_classification ,infection ,PRI Biodiversity and Breeding ,identification ,Phytophthora - Abstract
Late blight caused by Phytophthora infestans is the most important disease of potato. Many efforts have been made to understand molecular mechanism of the durable resistance to address the challenge raised by rapid evolution of the pathogen. A pathogenesis related protein (PR) gene StPRp27 was previously isolated from the potato leaves challenged by P. infestans. The sequence analysis and expression pattern reveal that StPRp27 may be associated with resistance to P. infestans. In present research, transient expression of StPRp27 in Nicotiana benthamiana enhanced resistance to P. infestans isolates 99189 and PY23 indicating its potential contribution to the disease resistance. These findings were also confirmed by over-expression of StPRp27 in potato cv. E-potato 3, which significantly slowed down the development of the disease after inoculation with a mixture of P. infestans races. Further, silencing of StPRp27 homologous genes in N. benthamiana harboring dominant Phytophthora resistance gene Rpi-blb1 or Rpi-blb2 showed no effects on the resistance triggered by these R genes. Our results suggest that StPRp27 contributes to a race-nonspecific resistance against P. infestans by inhibiting the disease development and has a potential use in selection and breeding for durable resistance to late blight.
- Published
- 2011
23. Anthocyanin production as a potential visual selection marker during plant transformation
- Author
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Evert Jacobsen, Sabaz Ali Khan, Cyril Brendolise, Henk J. Schouten, Richard G. F. Visser, C.M. Helderman, Andrew C. Allan, Y. Wu, Luisa M. Trindade, and A.J. Kortstee
- Subjects
Anthocyanin ,Light ,Genetically modified crops ,transgenic plants ,Plant Roots ,Anthocyanins ,Tissue Culture Techniques ,chemistry.chemical_compound ,Laboratorium voor Plantenveredeling ,Gene Expression Regulation, Plant ,Kanamycin ,PRI Biodiversiteit en Veredeling ,Transgenes ,Promoter Regions, Genetic ,genes ,transcription factor ,biology ,EPS-3 ,food and beverages ,Plants, Genetically Modified ,Fragaria ,dna transformation ,Malus ,Shoot ,Plant Shoots ,Plasmids ,Biotechnology ,Genetic Markers ,Agrobacterium ,agrobacterium ,Genes, Plant ,Transformation, Genetic ,expression ,Botany ,Genetics ,Malus x domestica ,Alleles ,Selectable marker ,Solanum tuberosum ,Original Paper ,Methanol ,fungi ,biology.organism_classification ,cultures ,Plant Leaves ,PRI Biodiversity and Breeding ,Alternative selection marker ,Fragaria ananassa ,Plant Breeding ,Transformation (genetics) ,chemistry ,efficiency ,regeneration ,Animal Science and Zoology ,EPS ,biosynthesis ,Agronomy and Crop Science - Abstract
A mutant allele of the transcription factor gene MYB10 from apple induces anthocyanin production throughout the plant. This gene, including its upstream promoter, gene coding region and terminator sequence, was introduced into apple, strawberry and potato plants to determine whether it could be used as a visible selectable marker for plant transformation as an alternative to chemically selectable markers, such as kanamycin resistance. After transformation, red coloured calli, red shoots and red well-growing plants were scored. Red and green shoots were harvested from apple explants and examined for the presence of the MYB10 gene by PCR analysis. Red shoots of apple explants always contained the MYB10 gene but not all MYB10 containing shoots were red. Strawberry plants transformed with the MYB10 gene showed anthocyanin accumulation in leaves and roots. No visible accumulation of anthocyanin could be observed in potato plants grown in vitro, even the ones carrying the MYB10 gene. However, acid methanol extracts of potato shoots or roots carrying the MYB10 gene contained up to four times higher anthocyanin content than control plants. Therefore anthocyanin production as result of the apple MYB10 gene can be used as a selectable marker for apple, strawberry and potato transformation, replacing kanamycin resistance. Electronic supplementary material The online version of this article (doi:10.1007/s11248-011-9490-1) contains supplementary material, which is available to authorized users.
- Published
- 2011
24. Functional analysis and expression profiling of HcrVf1 and HcrVf2 for development of scab resistant cisgenic and intragenic apples
- Author
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Frans A. Krens, Remmelt Groenwold, Sameer Joshi, Henk J. Schouten, Evert Jacobsen, and Jan G. Schaart
- Subjects
Resistance ,promoters ,Plant Science ,Laboratorium voor Plantenveredeling ,Gene Expression Regulation, Plant ,PRI Biodiversiteit en Veredeling ,Malus × domestica ,Plant Immunity ,Promoter Regions, Genetic ,cluster ,real-time pcr ,Genetics ,biology ,GMO ,Reverse Transcriptase Polymerase Chain Reaction ,EPS-2 ,plants ,Venturia inaequalis ,General Medicine ,Plants, Genetically Modified ,Phenotype ,Malus ,linkage ,Nucleic Acid Amplification Techniques ,Cisgenesis ,Agrobacterium ,agrobacterium ,Genes, Plant ,Article ,Ascomycota ,Gene ,Plant Diseases ,receptor-like genes ,Gene Expression Profiling ,venturia-inaequalis ,fungi ,Promoter ,Nucleic acid amplification technique ,biology.organism_classification ,vf gene ,PRI Biodiversity and Breeding ,Gene expression profiling ,Plant Breeding ,Apple scab ,sequences ,Agronomy and Crop Science - Abstract
Apple scab resistance genes, HcrVf1 and HcrVf2, were isolated including their native promoter, coding and terminator sequences. Two fragment lengths (short and long) of the native gene promoters and the strong apple rubisco gene promoter (PMdRbc) were used for both HcrVf genes to test their effect on expression and phenotype. The scab susceptible cultivar ‘Gala’ was used for plant transformations and after selection of transformants, they were micrografted onto apple seedling rootstocks for scab disease tests. Apple transformants were also tested for HcrVf expression by quantitative RT-PCR (qRT-PCR). For HcrVf1 the long native promoter gave significantly higher expression that the short one; in case of HcrVf2 the difference between the two was not significant. The apple rubisco gene promoter proved to give the highest expression of both HcrVf1 and HcrVf2. The top four expanding leaves were used initially for inoculation with monoconidial isolate EU-B05 which belongs to race 1 of V. inaequalis. Later six other V. inaequalis isolates were used to study the resistance spectra of the individual HcrVf genes. The scab disease assays showed that HcrVf1 did not give resistance against any of the isolates tested regardless of the expression level. The HcrVf2 gene appeared to be the only functional gene for resistance against Vf avirulent isolates of V. inaequalis. HcrVf2 did not provide any resistance to Vf virulent strains, even not in case of overexpression. In conclusion, transformants carrying the apple-derived HcrVf2 gene in a cisgenic as well as in an intragenic configuration were able to reach scab resistance levels comparable to the Vf resistant control cultivar obtained by classical breeding, cv. ‘Santana’. Electronic supplementary material The online version of this article (doi:10.1007/s11103-011-9749-1) contains supplementary material, which is available to authorized users.
- Published
- 2011
25. Genetic mapping in Lilium: mapping of major genes and quantitative trait loci for several ornamental traits and disease resistances
- Subjects
construction ,pollination ,durum-wheat ,EPS-4 ,zea-mays ,food and beverages ,dart ,markers ,linkage map ,PRI Biodiversity and Breeding ,Plant Breeding ,Laboratorium voor Plantenveredeling ,wild relatives ,PRI Biodiversiteit en Veredeling ,diversity arrays technology ,segregation distortion - Abstract
Construction of genetic linkage maps for lily was achieved using two populations, LA and AA that share one parent ‘Connecticut King’. Three different molecular marker systems (AFLP™, DArT and NBS profiling) were used in generating linkage maps for ‘Connecticut King’. The LA and the AA populations consist of 20 and 21 linkage groups (LGs), respectively. Average density between markers was 3.9 cM for the LA and 5 cM for the AA population. Several horticultural traits were mapped for the first time in Lilium and showed to be single gene based. We propose to name these genes as LFCc for flower colour, lfs for flower spots, LSC for stem colour, lal for antherless phenotype and lfd for flower direction whereby upper and lower case names refer to dominant and recessive genes, respectively. Additionally, resistance to Lily mottle virus (LMoV) was mapped as a locus on LG AA10. For Fusarium resistance, the Kruskal–Wallis test identified six putative quantitative trait loci (QTL) in the AA population of which one QTL (explaining 25% of the variation in resistance) could be confirmed by interval mapping
- Published
- 2011
26. High resolution mapping of a novel late blight resistance gene Rpi-avll, from the wild Bolivian species Solanum avilesii
- Subjects
quantitative resistance ,EPS-2 ,phytophthora-infestans ,qtl ,rflp ,marker-assisted selection ,microsatellites ,potato-virus-y ,PRI Biodiversity and Breeding ,Plant Breeding ,cultivated potato ,disease-resistance ,Laboratorium voor Plantenveredeling ,PRI Biodiversiteit en Veredeling ,bulbocastanum - Abstract
Both Mexico and South America are rich in Solanum species that might be valuable sources of resistance (R) genes to late blight (Phytophthora infestans). Here, we focus on an R gene present in the diploid Bolivian species S. avilesii. The genotype carrying the R gene was resistant to eight out of 10 Phytophthora isolates of various provenances. The identification of a resistant phenotype and the generation of a segregating population allowed the mapping of a single dominant R gene, Rpi-avl1, which is located in an R gene cluster on chromosome 11. This R gene cluster is considered as an R gene “hot spot”, containing R genes to at least five different pathogens. High resolution mapping of the Rpi-avl1 gene revealed a marker co-segregating in 3890 F1 individuals, which may be used for marker assisted selection in breeding programs and for further cloning of Rpi-avl1
- Published
- 2011
27. Transcriptomic profiling of citrus fruit peel tissues reveals fundamental effects of phenylpropanoids and ethylene on induced resistance
- Subjects
penicillium-digitatum sacc ,plant defense responses ,food and beverages ,grapefruit ,microarray data ,acquired-resistance ,gene-expression ,infection ,PRI Biodiversity and Breeding ,Plant Breeding ,uv-irradiation ,PRI Biodiversiteit en Veredeling ,phenylalanine ammonia-lyase ,BIOS Applied Metabolic Systems ,decay resistance - Abstract
Penicillium spp. are the major postharvest pathogens of citrus fruit in Mediterranean climatic regions. The induction of natural resistance constitutes one of the most promising alternatives to avoid the environmental contamination and health problems caused by chemical fungicides. To understand the bases of the induction of resistance in citrus fruit against Penicillium digitatum, we have used a 12k citrus cDNA microarray to study transcriptional changes in the outer and inner parts of the peel (flavedo and albedo, respectively) of elicited fruits. The elicitor treatment led to an over-representation of biological processes associated with secondary metabolism, mainly phenylpropanoids and cellular amino acid biosynthesis and methionine metabolism, and the down-regulation of genes related to biotic and abiotic stresses. Among phenylpropanoids, we detected the over-expression of a large subset of genes important for the synthesis of flavonoids, coumarins and lignin, especially in the internal tissue. Furthermore, these genes and those of ethylene biosynthesis showed the highest induction. The involvement of both phenylpropanoid and ethylene pathways was confirmed by examining changes in gene expression and ethylene production in elicited citrus fruit. Therefore, global results indicate that secondary metabolism, mainly phenylpropanoids, and ethylene play important roles in the induction of resistance in citrus fruit.
- Published
- 2011
28. De ontwikkeling van een informatiesysteem voor invasieve plantensoorten
- Subjects
geïntroduceerde soorten ,plant dispersal ,databases ,ecological risk assessment ,inventarisaties ,ecologische risicoschatting ,PE&RC ,risk management ,Biosystematiek ,PRI Biodiversity and Breeding ,introduced species ,Plant Breeding ,verspreiding van planten ,inventories ,PRI Biodiversiteit en Veredeling ,Biosystematics ,risicobeheersing ,Laboratory of Nematology ,databanken ,Laboratorium voor Nematologie - Abstract
De laatste decennia kent de Nederlandse flora een sterke toename van exoten. Soorten die door een sterke uitbreiding of verdichting van hun areaal overlast veroorzaken, worden invasieve soorten genoemd. De overlast van invasieve soorten (vaak kortweg invasieven genoemd) kan bestaan uit economische schade en gezondheids- en/of veiligheidsproblemen. Het Ministerie van Landbouw, Natuur en Voedselkwaliteit heeft daarom het Uitvoeringsconsortium Invasieve Plantensoorten een FES‑subsidie verleend om in vier jaar tijd een informatiesysteem over potentieel invasieve exotische plantensoorten op te zetten. Doel is informatie aan te leveren op basis waarvan ingeschat kan worden hoe groot de kans is dat exotische soorten zich bij introductie in Nederland invasief zullen gaan gedragen. Daarnaast is het doel hulp te bieden bij het herkennen van zulke soorten als ze worden geïmporteerd. Het informatiesysteem is ondergebracht in Q-bank.
- Published
- 2011
29. A pipeline for high throughput detection and mapping of SNPs from EST databases
- Author
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C. Gerard van der Linden, Jifeng Tang, Ben Vosman, Herman J. van Eck, Jack A. M. Leunissen, Richard G. F. Visser, and A. M. Anithakumari
- Subjects
construction ,haplotype ,Bioinformatics ,markers ,Single-nucleotide polymorphism ,Plant Science ,Biology ,computer.software_genre ,Molecular Inversion Probe ,Article ,Illumina GoldenGate assay ,Laboratorium voor Plantenveredeling ,Gene mapping ,EST database ,PRI Biodiversiteit en Veredeling ,single-nucleotide polymorphisms ,Bioinformatica ,Genetics ,SNP ,genome ,Molecular Biology ,Genotyping ,Database ,EPS-3 ,QualitySNP ,linkage maps ,map-based cloning ,food and beverages ,Tag SNP ,SNP genotyping ,PRI Biodiversity and Breeding ,Plant Breeding ,varieties ,potato ,Agronomy and Crop Science ,computer ,discovery ,Biotechnology ,SNP array - Abstract
Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic variation that can be used as molecular markers. The SNPs that are hidden in sequence databases can be unlocked using bioinformatic tools. For efficient application of these SNPs, the sequence set should be error-free as much as possible, targeting single loci and suitable for the SNP scoring platform of choice. We have developed a pipeline to effectively mine SNPs from public EST databases with or without quality information using QualitySNP software, select reliable SNP and prepare the loci for analysis on the Illumina GoldenGate genotyping platform. The applicability of the pipeline was demonstrated using publicly available potato EST data, genotyping individuals from two diploid mapping populations and subsequently mapping the SNP markers (putative genes) in both populations. Over 7000 reliable SNPs were identified that met the criteria for genotyping on the GoldenGate platform. Of the 384 SNPs on the SNP array approximately 12% dropped out. For the two potato mapping populations 165 and 185 SNPs segregating SNP loci could be mapped on the respective genetic maps, illustrating the effectiveness of our pipeline for SNP selection and validation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-009-9377-5) contains supplementary material, which is available to authorized users.
- Published
- 2010
30. Biochemical and molecular analysis of pink tomatoes: deregulated expression of the gene encoding transcription factor SlMYB12 leads to pink tomato fruit colour
- Author
-
Cathie Martin, Jos Molthoff, Marieke Ykema, Ric C. H. de Vos, Arnaud G. Bovy, Pasquale Tripodi, Silvana Grandillo, Josefina-Patricia Fernandez-Moreno, Diego Orzaez, Bas te Lintel Hekkert, Ana-Rosa Ballester, Antonio Granell, and Jos Heldens
- Subjects
Physiology ,Population ,Plant Science ,arabidopsis-thaliana ,Biology ,in-vivo ,anthocyanin ,PRI Biodiversiteit en Veredeling ,Botany ,Gene expression ,Genetics ,inheritance ,MYB ,flavonoid biosynthesis ,education ,Gene ,Naringenin chalcone ,Regulation of gene expression ,education.field_of_study ,fungi ,carotenoids ,food and beverages ,health ,biology.organism_classification ,mutations ,PRI Bioscience ,PRI Biodiversity and Breeding ,Flavonoid biosynthesis ,metabolome ,Solanum ,accumulation - Abstract
The color of tomato fruit is mainly determined by carotenoids and flavonoids. Phenotypic analysis of an introgression line (IL) population derived from a cross between Solanum lycopersicum ‘Moneyberg’ and the wild species Solanum chmielewskii revealed three ILs with a pink fruit color. These lines had a homozygous S. chmielewskii introgression on the short arm of chromosome 1, consistent with the position of the y (yellow) mutation known to result in colorless epidermis, and hence pink-colored fruit, when combined with a red flesh. Metabolic analysis showed that pink fruit lack the ripening-dependent accumulation of the yellow-colored flavonoid naringenin chalcone in the fruit peel, while carotenoid levels are not affected. The expression of all genes encoding biosynthetic enzymes involved in the production of the flavonol rutin from naringenin chalcone was down-regulated in pink fruit, suggesting that the candidate gene underlying the pink phenotype encodes a regulatory protein such as a transcription factor rather than a biosynthetic enzyme. Of 26 MYB and basic helix-loop-helix transcription factors putatively involved in regulating transcription of genes in the phenylpropanoid and/or flavonoid pathway, only the expression level of the MYB12 gene correlated well with the decrease in the expression of structural flavonoid genes in peel samples of pink- and red-fruited genotypes during ripening. Genetic mapping and segregation analysis showed that MYB12 is located on chromosome 1 and segregates perfectly with the characteristic pink fruit color. Virus-induced gene silencing of SlMYB12 resulted in a decrease in the accumulation of naringenin chalcone, a phenotype consistent with the pink-colored tomato fruit of IL1b. In conclusion, biochemical and molecular data, gene mapping, segregation analysis, and virus-induced gene silencing experiments demonstrate that the MYB12 transcription factor plays an important role in regulating the flavonoid pathway in tomato fruit and suggest strongly that SlMYB12 is a likely candidate for the y mutation.
- Published
- 2010
31. Genetic diversity studies on Fusarium asiaticum isolates collected from barley in China show a clear substructure associated with their geographic origin
- Subjects
PRI Biodiversity and Breeding ,wheat fields ,PRI Biodiversiteit en Veredeling ,Bioint Moleculair Phytopathology ,mycotoxins ,deoxynivalenol ,food and beverages ,graminearum clade ,genetic diversity ,populations ,scab ,head blight pathogen - Abstract
Fusarium head blight (FHB) can affect wheat and barley and is a devastating disease caused by a complex of Fusarium species. Here we report on a large-scale survey on the genetic diversity of isolates collected from barley in China. Ten VNTR markers were tested on a representative set of 40 isolates covering 14 sampling areas along the Yangtze River. VNTR4 and VNTR7, with 13 and 6 alleles, each were applied to a total of 1106 single-spore isolates to reveal the population structure of F. asiaticum. The F. asiaticum population showed high genetic diversity and a clear genotypic substructure within China. Pairwise comparisons of allele frequencies between the mountainous provinces of Sichuan and Chongqing in Western China, Hubei Province in the centre or the eastern provinces of Zhejiang, Jiangsu and Shanghai showed significant differences. Even between counties of the same province, significant differences between allele frequencies were found (P
- Published
- 2010
32. Identification of tomato phosphatidylinositol-specific phospholipase-C (PI-PLC) family members and the role of PLC4 and PLC6 in HR and disease resistance
- Subjects
hypersensitive response ,EPS-2 ,phosphatidic-acid ,fungi ,food and beverages ,plasma-membrane ,arabidopsis-thaliana ,cell-death ,signaling pathways ,moss physcomitrella-patens ,Laboratorium voor Phytopathologie ,PRI Biodiversity and Breeding ,pollen-tube growth ,Plant Breeding ,Laboratorium voor Plantenveredeling ,PRI Biodiversiteit en Veredeling ,Laboratory of Phytopathology ,cladosporium-fulvum ,diacylglycerol pyrophosphate - Abstract
The perception of pathogen-derived elicitors by plants has been suggested to involve phosphatidylinositol-specific phospholipase-C (PI-PLC) signalling. Here we show that PLC isoforms are required for the hypersensitive response (HR) and disease resistance. We characterised the tomato [Solanum lycopersicum (Sl)] PLC gene family. Six Sl PLC-encoding cDNAs were isolated and their expression in response to infection with the pathogenic fungus Cladosporium fulvum was studied. We found significant regulation at the transcriptional level of the various SlPLCs, and SlPLC4 and SlPLC6 showed distinct expression patterns in C. fulvum-resistant Cf-4 tomato. We produced the encoded proteins in Escherichia coli and found that both genes encode catalytically active PI-PLCs. To test the requirement of these Sl PLCs for full Cf-4-mediated recognition of the effector Avr4, we knocked down the expression of the encoding genes by virus-induced gene silencing. Silencing of SlPLC4 impaired the Avr4/Cf-4-induced HR and resulted in increased colonisation of Cf-4 plants by C. fulvum expressing Avr4. Furthermore, expression of the gene in Nicotiana benthamiana enhanced the Avr4/Cf-4-induced HR. Silencing of SlPLC6 did not affect HR, whereas it caused increased colonisation of Cf-4 plants by the fungus. Interestingly, Sl PLC6, but not Sl PLC4, was also required for resistance to Verticillium dahliae, mediated by the transmembrane Ve1 resistance protein, and to Pseudomonas syringae, mediated by the intracellular Pto/Prf resistance protein couple. We conclude that there is a differential requirement of PLC isoforms for the plant immune response and that Sl PLC4 is specifically required for Cf-4 function, while Sl PLC6 may be a more general component of resistance protein signalling.
- Published
- 2010
33. Influence of temperature on plant morphology traits and their relationship to relative growth rate in wild and cultivated Capsicum accessions
- Subjects
Horticultural Supply Chains ,night temperature ,sweet-pepper ,food and beverages ,leaf-area ,Leerstoelgroep Tuinbouwproductieketens ,integration ,PE&RC ,WUR GTB Gewasfysiologie Management en Model ,simulation ,yield ,PRI Biodiversity and Breeding ,Plant Breeding ,Laboratorium voor Plantenveredeling ,PRI Biodiversiteit en Veredeling ,suboptimal temperature - Abstract
Strawberry fruit are susceptible to microbial decay during post-harvest storage. To search for an effective alternative to currently-used fungicides for disease control, we investigated the effect of benzo-(1, 2, 3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH) on fruit decay and the maintenance of quality in strawberries after harvest. Freshly harvested strawberry fruit were treated with 0 (control), 0.05, 0.20 or 0.50 g l-1 BTH for 5 min. BTH treatment at 0.20 g l-1 was most effective at inhibiting fruit decay in strawberry fruit during storage at 5°C, while quality parameters such as total soluble solids contents and titratable acidity were also maintained. Fruit treated with 0.20 g l-1 BTH exhibited reduced microbial populations and higher activities of chitinase and ß-1,3-glucanase. However, treatment with 0.50 g l-1 BTH was ineffective at controlling fruit decay. Our results show that a post-harvest application of an appropriate concentration of BTH treatment was effective in reducing fruit decay and enhanced disease resistance in strawberry fruit. The data obtained suggest that BTH may provide an alternative to control post-harvest decay in strawberry fruit.
- Published
- 2010
34. Intraspecific variation in herbivore community composition and transcriptional profiles in field-grown Brassica oleracea cultivars
- Author
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Marcel Dicke, Ben Vosman, Colette Broekgaarden, Erik H. Poelman, and Roeland E. Voorrips
- Subjects
0106 biological sciences ,Insecta ,mustard oil bomb ,Physiology ,Population Dynamics ,comparative genomics ,Plant Science ,01 natural sciences ,induced resistance ,chemistry.chemical_compound ,Laboratorium voor Plantenveredeling ,Gene Expression Regulation, Plant ,manduca-sexta ,PRI Biodiversiteit en Veredeling ,Cultivar ,species richness ,Laboratory of Entomology ,Plant Proteins ,2 specialist herbivores ,0303 health sciences ,biology ,EPS-2 ,Jasmonic acid ,Community structure ,food and beverages ,Research Papers ,Brevicoryne brassicae ,Brassica oleracea ,microarray ,brevicoryne-brassicae ,Genes, Plant ,Models, Biological ,induced plant vaccination ,Intraspecific competition ,03 medical and health sciences ,Species Specificity ,Botany ,Animals ,030304 developmental biology ,Herbivore ,Gene Expression Profiling ,fungi ,jasmonic acid ,Feeding Behavior ,15. Life on land ,biology.organism_classification ,Laboratorium voor Entomologie ,PRI Biodiversity and Breeding ,Plant Breeding ,chemistry ,Aphids ,Brassicaceae ,gene expression ,nicotiana-attenuata ,herbivorous insects ,Species richness ,insect resistance ,microarray analysis ,010606 plant biology & botany - Abstract
Intraspecific differences in plant defence traits are often correlated with variation in transcriptional profiles and can affect the composition of herbivore communities on field-grown plants. However, most studies on transcriptional profiling of plant–herbivore interactions have been carried out under controlled conditions in the laboratory or greenhouse and only a few examine intraspecific transcriptional variation. Here, intraspecific variation in herbivore community composition and transcriptional profiles between two Brassica oleracea cultivars grown in the field is addressed. Early in the season, no differences in community composition were found for naturally occurring herbivores, whereas cultivars differed greatly in abundance, species richness, and herbivore community later in the season. Genome-wide transcriptomic analysis using an Arabidopsis thaliana oligonucleotide microarray showed clear differences for the expression levels of 26 genes between the two cultivars later in the season. Several defence-related genes showed higher levels of expression in the cultivar that harboured the lowest numbers of herbivores. Our study shows that herbivore community composition develops differentially throughout the season on the two B. oleracea cultivars grown in the field. The correlation between the differences in herbivore communities and differential expression of particular defence-related genes is discussed.
- Published
- 2010
35. SPECIFIC MAPPING OF DISEASE RESISTANCE GENES IN TETRAPLOID CUT ROSES
- Author
-
C.F.S. Koning-Boucoiran, O. Dolstra, C.G. van der Linden, J. van der Schoot, V.W. Gitonga, K. Verlinden, C.A. Maliepaard, and F.A. Krens
- Subjects
Marker-trait association ,Genetics ,education.field_of_study ,Population ,RGA ,food and beverages ,Horticulture ,Biology ,Plant disease resistance ,Rosa ,Genetic linkage map ,NBS profiling markers ,PRI Biodiversity and Breeding ,Plant Breeding ,Laboratorium voor Plantenveredeling ,Powdery mildew ,Gene mapping ,PRI Biodiversiteit en Veredeling ,Genetic marker ,Genetic variation ,Microsatellite ,Amplified fragment length polymorphism ,education - Abstract
Control of fungal diseases is a major constraint of cut-rose cultivation in greenhouses and in transportation around the world. Therefore, development of resistant cultivars is a promising way to reduce the use of chemicals required for controlling the diseases. Genetic analyses and breeding for resistance, however, are hampered by the high degree of heterozygosity and the polyploid nature of cultivated roses. Nucleotide-binding site (NBS) profiling of Van der Linden et al. (2004) was used as a tool enabling a more directed way of studying the genetics of resistance to pathogens responsible for diseases such as powdery mildew. NBS profiling is a multiplex screening technique, producing amplified resistance gene (R-gene) and resistance gene analogue (RGA) fragments by using degenerated primers based on the conserved motifs present in the NBS domain of resistance genes. Since RGAs are abundantly distributed and highly polymorphic within the plant genome, NBS profiling generates multiple markers of putative resistance genes. Twelve NBS degenerated primer/ restriction enzyme combinations were used to genotype the whole rose tetraploid K5 population (Yan, 2005) and its parents. To generate RGA profiles, the restriction enzymes: AluI, HaeIII, Mse and RsaI were used in combination with degenerated primers NBS1, NBS3, and NBS5a6. The profiles were dominantly scored resulting in 106 polymorphic RGA markers which segregated in a 1:1 or 3:1 ratio. Uni-and bi-parental simplex markers will be mapped on the two available AFLP/SSR K5 maps (Yan, 2005) with Joinmap 4.0. The resulting parental tetraploid maps will be used to dissect the genetic variation for resistance to powdery mildew resistance. Additional Rosaceae SSRs mentioned in the literature are currently tested on the K5 population to obtain allelic bridges between the tetraploid and diploid genetic maps in rose and related species in order to align them. These bridges will improve cross-ploidy comparisons in roses in order to strengthen cut rose breeding
- Published
- 2009
36. IDENTIFICATION OF CARNATION VARIETIES USING MICROSATELLITE MARKERS
- Author
-
Paul Arens, L.P. Kodde, G.D. Esselink, W.A. Wietsma, Ben Vosman, Y. Noordijk, and L. Hof
- Subjects
SSR markers ,biology ,Dianthus ,Centrum voor Genetische Bronnen Nederland ,Mutants ,Ploidy level ,Carnation ,Horticulture ,biology.organism_classification ,PRI Biodiversity and Breeding ,PRI Biodiversiteit en Veredeling ,Genetic marker ,Microsatellite ,Identification (biology) ,Cultivar - Abstract
As in many ornamentals, also in carnation the number of varieties in common knowledge is large and identification throughout the chain from breeder to consumer using plant material from different stages and organs may be needed. Results in this study on the use of microsatellite markers from Dianthus caryophyllus L. for the characterization of carnation varieties as well as the construction and evaluation of a molecular database show that these markers show potential for identification purposes
- Published
- 2009
37. Relevance of unilateral and bilateral sexual polyploidization in relation to intergenomic recombination and introgression in Lilium species hybrids
- Author
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Nadeem Khan, Paul Arens, Jaap M. van Tuyl, R. Barba-Gonzalez, Munikote S. Ramanna, and Richard G. F. Visser
- Subjects
lily hybrids ,Introgression ,Context (language use) ,Plant Science ,Horticulture ,Laboratorium voor Plantenveredeling ,Meiosis ,PRI Biodiversiteit en Veredeling ,2n pollen formation ,tetraploid progeny ,Botany ,Genetics ,cytological mechanism ,x asiatic hybrids ,genome composition ,gish analysis ,Hybrid ,Lilium ,biology ,EPS-4 ,food and beverages ,biology.organism_classification ,Sexual reproduction ,PRI Biodiversity and Breeding ,Plant Breeding ,Backcrossing ,diploid potato ,Ploidy ,Agronomy and Crop Science ,bc2 progenies ,distant hybrid - Abstract
Sexual polyploids were induced in diploid (2n = 2x = 24) interspecific F1 hybrids of Longiflorum × Asiatic (LA) and Oriental × Asiatic (OA) Lilium hybrids by backcrossing to Asiatic (AA) parents as well as by sib-mating of the F1 LA hybrids. A majority of the BC1 progenies were triploid and the progenies from sib-mating were tetraploid or near tetraploids. Genomic in situ hybridization (GISH) technique was applied to assess the intergenomic recombination in the BC1 populations of LA and OA hybrids obtained after unilateral sexual polyploidization. A total of 63 LA (LA × AA and AA × LA) and 53 OA hybrids were analysed. LA hybrids were originated through the functioning of 2n gametes either as 2n eggs or 2n pollen while those of OA hybrids originated through functional 2n pollen of diploid OA genotype. In both type of crosses, a majority of the progenies had originated through First Division Restitution (FDR) mechanism of functional 2n gamete either with or without a cross over. However, there were nine LA- and four OA-genotypes where Indeterminate Meiotic Restitution (IMR) was the mechanism of 2n gamete formation. Based on GISH, total amount of introgression of Longiflorum and Oriental genome into Asiatic genome was determined. Most of the BC progenies exhibited recombination and the amount of recombination was higher in LA hybrids as compared to OA hybrids. Intergenomic recombination was also determined cytologically in the 16 plants of sib-mated LA hybrids where both parents had contributed 2n gametes. Based on these results the nature of interspecific lily hybrids obtained from uni- and bilateral sexual polyploidization leading to allotriploid and allotetraploid formation is discussed in the context of introgression and intergenomic recombination.
- Published
- 2009
38. DNA barcoding discriminates the noxious invasive plant species, floating pennywort (Hydrocotyle ranunculoidesL.f.), from non-invasive relatives
- Author
-
Marinus J. M. Smulders, J.R. van der Schoot, C.C.M. van de Wiel, H. Duistermaat, and J. L. C. H. van Valkenburg
- Subjects
biology ,biology.organism_classification ,DNA barcoding ,Biosystematiek ,Invasive species ,DNA sequencing ,PRI Biodiversity and Breeding ,DNA profiling ,PRI Biodiversiteit en Veredeling ,Genus ,Aquatic plant ,Botany ,Genetics ,Biosystematics ,Hydrocotyle ,genetics ,Hydrocotyle ranunculoides ,land plants ,Ecology, Evolution, Behavior and Systematics ,Biotechnology - Abstract
Floating pennywort (Hydrocotyle ranunculoides L.f.), a member of the plant family Araliaceae originating from North America, is an example of an invasive aquatic species posing serious problems to the management of waterways outside of its original distribution area in Australia and Western Europe. As a consequence, its import was banned in the Netherlands. It can be difficult to distinguish H. ranunculoides from other species of the genus on a morphological basis. In this regard, DNA barcoding may become a good alternative once this could be performed on a routine basis. In this study, we show that it is possible to distinguish H. ranunculoides from a series of closely related congeners by using a single plastid DNA sequence, trnH-psbA.
- Published
- 2009
39. Exploiting Knowledge of R/Avr Genes to Rapidly Clone a New LZ-NBS-LRR Family of Late Blight Resistance Genes from Potato Linkage Group IV
- Author
-
Juan Carlos Correa Morales, Marjon Arens, Carolien Ruyter-Spira, Edwin A. G. van der Vossen, Richard G. F. Visser, Anoma Lokossou, Steve C Whisson, Paul R. J. Birch, Gert van Arkel, Tae-Ho Park, and Evert Jacobsen
- Subjects
Leucine zipper ,disease resistance ,quantitative resistance ,Phytophthora infestans ,Physiology ,Molecular Sequence Data ,Nicotiana benthamiana ,Locus (genetics) ,Sequence alignment ,arabidopsis-thaliana ,broad-spectrum resistance ,oomycete effectors ,plant immune-system ,Laboratorium voor Plantenveredeling ,r-gene ,PRI Biodiversiteit en Veredeling ,solanum-bulbocastanum ,Tobacco ,Solanum bulbocastanum ,Amino Acid Sequence ,Cloning, Molecular ,Gene ,Alleles ,Phylogeny ,Plant Diseases ,Plant Proteins ,Solanum tuberosum ,Genetics ,phytophthora-infestans mont ,biology ,EPS-2 ,downy mildew ,Genetic Complementation Test ,fungi ,food and beverages ,General Medicine ,R gene ,Plants, Genetically Modified ,biology.organism_classification ,Immunity, Innate ,PRI Bioscience ,PRI Biodiversity and Breeding ,Plant Breeding ,Multigene Family ,Sequence Alignment ,Agronomy and Crop Science - Abstract
In addition to the resistance to Phytophthora infestans (Rpi) genes Rpi-blb1 and Rpi-blb2, Solanum bulbocastanum appears to harbor Rpi-blb3 located at a major late blight resistance locus on LG IV, which also harbors Rpi-abpt, R2, R2-like, and Rpi-mcd1 in other Solanum spp. Here, we report the cloning and functional analyses of four Rpi genes, using a map-based cloning approach, allele-mining strategy, Gateway technology, and transient complementation assays in Nicotiana benthamiana. Rpi-blb3, Rpi-abpt, R2, and R2-like contain all signature sequences characteristic of leucine zipper nucleotide binding site leucine-rich repeat (LZ-NBS-LRR) proteins, and share amino-acid sequences 34.9% similar to RPP13 from Arabidopsis thaliana. The LRR domains of all four Rpi proteins are highly homologous whereas LZ and NBS domains are more polymorphic, those of R2 being the most divergent. Clear blocks of sequence affiliation between the four functional resistance proteins and those encoded by additional Rpi-blb3 gene homologs suggest exchange of LZ, NBS, and LRR domains, underlining the modular nature of these proteins. All four Rpi genes recognize the recently identified RXLR effector PiAVR2.
- Published
- 2009
40. Development of SNP markers and haplotype analysis of the candidate gene for rhg1, which confers resistance to soybean cyst nematode in soybean
- Author
-
Zhangxiong Liu, M.J.M. Smulders, Chen Zhang, Zulu Ma, Zhongshan Gao, Lijuan Qiu, Yinghui Li, Ruzhen Chang, and Haiyang Nan
- Subjects
Candidate gene ,loci underlying resistance ,Soybean cyst nematode ,Single-nucleotide polymorphism ,Plant Science ,Biology ,Quantitative trait locus ,diversity ,heterodera-glycines ,Laboratorium voor Plantenveredeling ,rice blast resistance ,PRI Biodiversiteit en Veredeling ,single-nucleotide polymorphisms ,Genetics ,Molecular Biology ,Gene ,Haplotype ,dna polymorphism ,biology.organism_classification ,Molecular biology ,PRI Biodiversity and Breeding ,Plant Breeding ,qtls ,Genetic marker ,quantitative trait loci ,Microsatellite ,Agronomy and Crop Science ,metaanalysis ,Biotechnology - Abstract
Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) is one of the most destructive pests in the cultivation of soybean (Glycine max (L.) Merr.) worldwide. Markers based on the SCN resistance gene will enable efficient marker-assisted selection (MAS). We sequenced the candidate gene rhg1 in six resistant and two susceptible soybean genotypes and identified 37 SNPs (single nucleotide polymorphisms) among the sequences, of which 11 were in the coding region. Seven of these 11 SNPs led to changes in the amino acid sequence of the gene. The amino acid sequence we obtained differs from the previously published one by a stretch of 26¿27 amino acids. Six codominant allele-specific SNP markers based on agarose gel detection were developed and tested in 70 genotypes, among which occurred only nine different haplotypes. Two neutrality tests (Tajima¿s D and Fu and Li¿s F) were significant for the six SNP loci in the 70 genotypes, which is consistent with intensive directional selection. A strong LD pattern was detected among five SNPs except 2868T > C. Two SNPs (689C > A and 757C > T) formed one haplotype (689C-757C) that was perfectly associated with SCN resistance. The new allele-specific PCR markers located in the alleged sequence of the rhg1 candidate gene, combined with the microsatellite marker BACR-Satt309, will significantly improve the efficiency of MAS during the development of SCN-resistant cultivars.
- Published
- 2009
41. Molecular diversity of arbuscular mycorrhizal fungi in onion roots from organic and conventional farming systems in the Netherlands
- Author
-
István Parádi, Olga E. Scholten, Guillermo A. Galván, Thomas W. Kuyper, Jacqueline Baar, Karin Burger, and Chris Kik
- Subjects
Allium cepa ,Organic farming ,Centrum voor Genetische Bronnen Nederland ,Biodiversity ,Plant Science ,Biology ,DNA, Ribosomal ,Plant Roots ,soil ,Glomeromycota ,PRI Biodiversiteit en Veredeling ,Mycorrhizae ,Botany ,Onions ,Genetics ,Colonization ,DNA, Fungal ,Molecular Biology ,glomus-intraradices ,Ecology, Evolution, Behavior and Systematics ,Glomus ,Bodembiologie ,Phylogeny ,Soil Microbiology ,phosphate ,Netherlands ,Phylotype ,Original Paper ,Mycorrhizal colonization ,Fungal genetics ,Agriculture ,General Medicine ,Soil Biology ,biology.organism_classification ,PE&RC ,colonization ,crops ,PRI Biodiversity and Breeding ,communities ,plant-growth responses ,impact ,grassland ,Soil microbiology - Abstract
Diversity and colonization levels of naturally occurring arbuscular mycorrhizal fungi (AMF) in onion roots were studied to compare organic and conventional farming systems in the Netherlands. In 2004, 20 onion fields were sampled in a balanced survey between farming systems and between two regions, namely, Zeeland and Flevoland. In 2005, nine conventional and ten organic fields were additionally surveyed in Flevoland. AMF phylotypes were identified by rDNA sequencing. All plants were colonized, with 60% for arbuscular colonization and 84% for hyphal colonization as grand means. In Zeeland, onion roots from organic fields had higher fractional colonization levels than those from conventional fields. Onion yields in conventional farming were positively correlated with colonization level. Overall, 14 AMF phylotypes were identified. The number of phylotypes per field ranged from one to six. Two phylotypes associated with the Glomus mosseae–coronatum and the G. caledonium–geosporum species complexes were the most abundant, whereas other phylotypes were infrequently found. Organic and conventional farming systems had similar number of phylotypes per field and Shannon diversity indices. A few organic and conventional fields had larger number of phylotypes, including phylotypes associated with the genera Glomus-B, Archaeospora, and Paraglomus. This suggests that farming systems as such did not influence AMF diversity, but rather specific environmental conditions or agricultural practices. Electronic supplementary material The online version of this article (doi:10.1007/s00572-009-0237-2) contains supplementary material, which is available to authorized users.
- Published
- 2009
42. Approaches for development of cisgenic apples
- Subjects
PRI Biodiversity and Breeding ,Plant Breeding ,Laboratorium voor Plantenveredeling ,EPS-2 ,PRI Biodiversiteit en Veredeling ,fungi ,food and beverages ,bacteria ,biochemical phenomena, metabolism, and nutrition ,equipment and supplies - Abstract
Introgression of genetic traits from wild apple germplasm (Malus spp.) into commercial apple cultivars is a painstakingly slow process. For e.g. introgression of the Vf gene from Malus floribunda 821 for resistance to apple scab, caused by the fungus Venturia inaequalis, took more than 80 years due to genetic drag and the long juvenile period of apple. In order to speedup the classical breeding, molecular techniques can be applied to enrich existing commercial apple varieties with functional alleles from sexually compatible plants, preventing genetic drag and keeping the genetic makeup of the commercial cultivar. This concept is named “cisgenesis”. This paper describes several approaches and considerations for development of cisgenic apples and stacking of genes. Also we provide an overview of isolated alleles from apple available for cisgenesis at the moment and in the near future
- Published
- 2009
43. Identification and mapping of a new apple scab resistance gene
- Author
-
J.M. Soriano, S. Joshi, R. Groenwold, Y. Noordijk, B. Henken, M. van Kaauwen, and H.J. Schouten
- Subjects
Genetics ,Strain (biology) ,Venturia inaequalis ,DArT markers ,Horticulture ,Biology ,Plant disease resistance ,biology.organism_classification ,SSR ,PRI Biodiversity and Breeding ,Plant Breeding ,Laboratorium voor Plantenveredeling ,Gene mapping ,Malus × domestica ,Apple scab ,Genetic marker ,PRI Biodiversiteit en Veredeling ,Botany ,Microsatellite ,Gene - Abstract
Here we report the identification of a new resistance gene (Vd3) against apple scab (Venturia inaequalis) from the apple selection 1980-015-25 of the breeding program at Plant Research International. This accession also contains the Vf gene. We mapped Vd3, using SSR and DArT markers, on linkage group 1, at a distance of 6 cM from Vf gene, but in repulsion phase to Vf. Based on pedigree analysis and resistance tests, it could be deduced that 1980-015-25 had inherited Vd3 from the founder D3. This gene provides resistance to the highly virulent EU-NL-24 strain of the race 7 of V. inaequalis. This strain has overcome the resistance from both Vf and Vg. However, Vd3 has been not effective against the majority of other V. inaequalis strains we used in our disease tests.
- Published
- 2009
44. Essentially Derived Varieties in Ornamentals
- Author
-
Ben Vosman
- Subjects
Rose ,Theoretical computer science ,business.industry ,media_common.quotation_subject ,Authorization ,Microsatellite ,EDV ,Horticulture ,Biology ,Variety (linguistics) ,Conformity ,Biotechnology ,Breeder (cellular automaton) ,PRI Biodiversity and Breeding ,Genetic similarity ,PRI Biodiversiteit en Veredeling ,Plant species ,business ,media_common - Abstract
The concept of Essentially derived varieties (EDVs) was introduced in the UPOV 1991 act to protect the interests of the breeder of the initial variety. When a variety is considered as an EDV, authorisation for commercial exploitation is needed from the breeder of the initial variety. There is considerable debate going on about which approaches to use for determining essential derivation and also which thresh-olds should be used in the different plant species. For determining whether a variety should be considered essentially derived from an existing variety two conceptually different approaches can be taken. The first one is based on genetic conformity, the second is more a forensic approach. For the implementation of the EDV concept using the conformity approach it is important that similarities between unrelated varieties can clearly be separated from essentially derived varieties. In the forensic approach the high genetic similarity between original variety and mutant is taken as a starting point. The basic idea is to calculate the probability that a second, putatively derived, variety would have a profile identical to the initial variety, given an independent breeding history. Both approaches will be illustrated and ways to implement the EDV concept will be discussed
- Published
- 2009
45. ps2, the gene responsible for functional sterility in tomato, due to non-dehiscent anthers, is the result of a mutation in a novel polygalacturonase gene
- Author
-
Danny Schipper, Adriaan W. van Heusden, Richard G. F. Visser, André A. M. van Lammeren, and Benoit Gorguet
- Subjects
Mutant ,plant ,resource ,medicine.disease_cause ,Laboratorium voor Plantenveredeling ,Solanum lycopersicum ,Gene Expression Regulation, Plant ,PRI Biodiversiteit en Veredeling ,RNA Precursors ,site ,Arabidopsis thaliana ,Tissue Distribution ,Phylogeny ,Plant Proteins ,Genetics ,Mutation ,biology ,EPS-2 ,Chromosome Mapping ,General Medicine ,endo-polygalacturonase ,Polygalacturonase ,Biotechnology ,Plant Infertility ,Sterility ,Molecular Sequence Data ,mechanism ,Flowers ,arabidopsis-thaliana ,Polymorphism, Single Nucleotide ,Open Reading Frames ,expression ,medicine ,Amino Acid Sequence ,Gene ,Arabidopsis Proteins ,Alternative splicing ,Wild type ,Laboratorium voor Celbiologie ,Anther dehiscence ,biology.organism_classification ,PRI Biodiversity and Breeding ,Alternative Splicing ,Plant Breeding ,Laboratory of Cell Biology ,Agronomy and Crop Science ,Sequence Alignment ,Biomarkers - Abstract
The recessive mutation ps-2, which appeared spontaneously in tomato, confers functional male sterility due to non-dehiscent anthers. In this study, we isolated and characterized the PS-2 gene. A single nucleotide mutation in a novel tomato polygalacturonase gene is responsible for the ps-2 phenotype. The mutation in ps-2 is responsible for an alternative splicing during maturation of the pre-mRNA, which leads to an aberrant mRNA. Differentiation between ps-2 and wild type (PS-2) anthers only appears in the final developmental stage in which the stomium remains closed in the mutant. To our knowledge, this is the first functional sterility gene isolated in the Solanaceae family. The specific expression of the Arabidopsis homolog of PS-2 in the anther dehiscence zone suggests a conserved mode of action over the plant kingdom, which means that the repression of PS-2 homologs may be a potential way to introduce functional sterility in other species.
- Published
- 2009
46. Molecular breeding for resistance to Phytophthora infestans (Mont.) de Bary in potato (Solanum tuberosum L.): a perspective of cisgenesis
- Author
-
Tae-Ho Park, Vivianne G. A. A. Vleeshouwers, E.A.G. van der Vossen, Evert Jacobsen, and Richard G. F. Visser
- Subjects
quantitative resistance ,Plant Science ,broad-spectrum resistance ,Plant disease resistance ,marker-assisted selection ,globodera-pallida stone ,cultivated potato ,Laboratorium voor Plantenveredeling ,PRI Biodiversiteit en Veredeling ,Cisgenesis ,Botany ,Genetics ,Blight ,Plant breeding ,field-resistance ,late-blight resistance ,Molecular breeding ,biology ,EPS-2 ,fungi ,food and beverages ,biology.organism_classification ,Solanum tuberosum ,gene-cluster ,PRI Biodiversity and Breeding ,Plant Breeding ,disease-resistance ,Phytophthora infestans ,Solanum ,Agronomy and Crop Science ,race-specific resistance - Abstract
Late blight caused by Phytophthora infestans is one of the most devastating diseases in potato cultivation and is mostly controlled by the application of chemicals. However, introduction of combinations of resistance (R) genes conferring broad-spectrum resistance from wild Solanum species into cultivated potatoes is considered the most practical and promising approach to achieve durable resistance. This can be realized via classical breeding or genetic modification (GM). Because classical breeding is very time-consuming and is often hampered by linkage drag, a GM approach seems logic in this heterozygous and vegetatively propagated crop. During the last decades, many R genes have been identified in several wild Solanum species. Some have been cloned and more will follow. When these genes are derived from species crossable with cultivated potato (so-called cisgenes), application in resistance breeding using a GM approach is similar to an introgression breeding approach, in that the exploited genes are indigenous to the crop. Pending deregulation or derogation of cisgenesis, the use of cisgenic R genes would be an ideal strategy to accomplish durable resistance in potato.
- Published
- 2009
47. Development of hypo-allergenic apples: silencing of the major allergen Mal d 1 gene in 'Elstar' apple and the effect of grafting
- Subjects
fungi ,cloning ,malus-domestica ,fruit ,PRI Bioscience ,PRI Biodiversity and Breeding ,controlled food challenge ,bet-v-1 ,PRI Biodiversiteit en Veredeling ,expression ,bacteria ,birch pollen allergen ,double-blind ,protein - Abstract
Many people who are allergic to birch pollen are also allergic to apple fruit, due to cross- allergenicity. Since apples are the most extensively consumed fruit in Europe, it is highly relevant to develop a hypo-allergenic apple. Apples with significantly reduced levels of the allergen, Mal d 1, may allow many apple allergics to eat them without an allergic reaction. We are currently collaborating to develop a hypo-allergenic apple within the European Integrated Research Project, ISAFRUIT (www.isafruit.org). Hypo-allergenic apple plants (Malus × domestica Borkh., ‘Elstar’) with decreased levels of Mal d 1 mRNA were produced by RNA interference (RNAi) technology. Ten genetically modified (GM) apple lines were selected. In vitro plantlets were first transferred to a greenhouse, then grafted onto wild-type M.9 rootstock to promote the development of fruit-producing trees. Levels of Mal d 1 gene silencing were measured repeatedly by quantitative real-time PCR. Compared to leaf samples from wild-type ‘Elstar’, two GM lines showed modest levels of gene silencing (up to 250-fold), whereas the other eight GM lines were significantly silenced (up to10,000-fold) in Mal d 1 gene expression. These levels of silencing were unaffected by grafting, and have been stable over more than 3 years, and throughout all developmental stages.
- Published
- 2009
48. Phytophthora infestans isolates lacking class I ipiO variants are virulent on Rpi-blb1 potato
- Author
-
Chris Maliepaard, Vivianne G. A. A. Vleeshouwers, Klaas Bouwmeester, Theo van der Lee, Nicolas Champouret, Evert Jacobsen, Hendrik Rietman, Peter J. I. van de Vondervoort, Francine Govers, Richard G. F. Visser, Anika Heupink, and Edwin A. G. van der Vossen
- Subjects
Physiology ,Phytophthora infestans ,Population ,Molecular Sequence Data ,late blight resistance ,population-structure ,Nicotiana benthamiana ,broad-spectrum resistance ,Biology ,Plant disease resistance ,Fungal Proteins ,cultivated potato ,Laboratorium voor Plantenveredeling ,PRI Biodiversiteit en Veredeling ,solanum-bulbocastanum ,Botany ,Solanum bulbocastanum ,Blight ,education ,Phylogeny ,Plant Diseases ,Solanum tuberosum ,Genetics ,nevado-de-toluca ,education.field_of_study ,Genetic diversity ,Biointeracties and Plant Health ,Virulence ,EPS-2 ,downy mildew ,Gene Expression Profiling ,fungi ,central mexico ,Genetic Variation ,food and beverages ,General Medicine ,R gene ,biology.organism_classification ,cell-death ,Laboratorium voor Phytopathologie ,PRI Biodiversity and Breeding ,Plant Breeding ,Gene Expression Regulation ,Laboratory of Phytopathology ,PRI Biointeractions en Plantgezondheid ,Agronomy and Crop Science ,mediated plant transformation - Abstract
A strategy to control the devastating late blight disease is providing potato cultivars with genes that are effective in resistance to a broad spectrum of Phytophthora infestans isolates. Thus far, most late blight resistance (R) genes that were introgressed in potato were quickly defeated. In contrast, the Rpi-blb1 gene originating from Solanum bulbocastanum has performed as an exclusive broad-spectrum R gene for many years. Recently, the RXLR effector family ipiO was identified to contain Avr-blb1. Monitoring the genetic diversity of the ipiO family in a large set of isolates of P. infestans and related species resulted in 16 ipiO variants in three distinct classes. Class I and class II but not class III ipiO variants induce cell death when coinfiltrated with Rpi-blb1 in Nicotiana benthamiana. Class I is highly diverse and is represented in all analyzed P. infestans isolates except two Mexican P. infestans isolates, and these were found virulent on Rpi-blb1 plants. In its C-terminal domain, IPI-O contains a W motif that is essential for triggering Rpi-blb1–mediated cell death and is under positive selection. This study shows that profiling the variation of Avr-blb1 within a P. infestans population is instrumental for predicting the effectiveness of Rpi-blb1–mediated resistance in potato.
- Published
- 2009
49. Apical dominance in Alstroemeria cultured in vitro
- Author
-
P. Pumisutapon, Richard G. F. Visser, and G.J.M. de Klerk
- Subjects
chemistry.chemical_classification ,biology ,Apical dominance ,fungi ,EPS-4 ,food and beverages ,Horticulture ,biology.organism_classification ,Rhizome ,PRI Biodiversity and Breeding ,Plant Breeding ,Murashige and Skoog medium ,Laboratorium voor Plantenveredeling ,chemistry ,Auxin ,PRI Biodiversiteit en Veredeling ,Axillary bud ,Alstroemeria ,Shoot ,Botany ,Life Science ,Explant culture - Abstract
Apical dominance in Alstroemeria is studied to develop an improved propagation protocol for this crop. Four types of explants were prepared: an intact rhizome with two intact shoots (+R+2S), an intact rhizome with two decapitated shoots (+R-2S), a decapitated rhizome with two intact shoots (-R+2S), and a decapitated rhizome with two decapitated shoots (-R-2S). The explants were cultivated on solid MS medium with 9 µM 6-benzylaminopurine (BAP). -R-2S explants showed the highest and +R+2S the lowest axillary-bud outgrowth. Outgrowth in -R+2S and +R-2S explants was intermediate. So, axillary buds are released by removal of the rhizome tip and by removal of the shoot tips. In both decapitated shoots and decapitated rhizomes, application of lanolin with 3-indolebutyric acid (IBA) to the cut end restored apical dominance. This indicates that both tips exert an effect via basipetally transported auxin
- Published
- 2009
50. Acceptatie van natuurlijke en genetisch gemodificeerde hypoallergene appels door mensen met het orale allergie syndroom (OAS)
- Subjects
PRI Bioscience ,PRI Biodiversity and Breeding ,Plant Breeding ,Laboratorium voor Plantenveredeling ,PRI Biodiversiteit en Veredeling ,Fruit ,PPO BBF Fruitgewassen - Published
- 2009
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