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Genetisch gemodificeerde gewassen (GM-gewassen) worden in Europa moeilijk geaccepteerd. De geschiedenis van de weerstand laat zien dat deze bij een klein deel van de bezwaarden te maken heeft met het modificatieproces zelf. Het overgrote deel keert zich veeleer tegen het gebruik van landbouwkundig nuttige transgenen uit virussen en bacteria, en van transgene selectiegenen die onder meer resistentie tegen een antibioticum of een herbicide geven. Al deze genen worden transgenen genoemd omdat ze uit organismen komen die niet kruisbaar zijn met de doelplant. In de beginperiode van de transgenese waren alleen deze transgenen beschikbaar. Inmiddels kan de, ook maatschappelijk belangrijke, versnelling van het klassieke plantenveredelingsproces eveneens worden gerealiseerd met cisgenen en intragenen. De huiver die nog in het publieke en politieke debat doorklinkt, krijgt daardoor een steeds meer irrationeel karakter. Een meer adequate EU-regelgeving wordt daardoor belemmerd

Op 20 juni 2011 promoveerde Hendrik Rietman aan Wageningen University (WUR) op zijn proefschrift getiteld: “Putting the Phytophthora infestans genome sequence at work; multiple novel avirulence and potato resistance gene candidates revealed”. Zijn promotor, Prof. Dr. Richard G. F. Visser, en co-promotor, Dr. Ir. Vivianne G. A. A. Vleeshouwers, zijn beiden verbonden aan de leerstoelgroep Plantenveredeling van de WUR, waar ook het onderzoek werd uitgevoerd. Tevens is er samengewerkt met de leerstoelgroep Fytopathologie (WUR), het Sainsbury Lab en het James Hutton Instituut (beiden gevestigd in het Verenigd Koninkrijk). Financiering was afkomstig van het ‘Parapluplan Phytophthora’ en WUR Plantenveredeling.

Resistentie tegen Botrytis cinerea is gevonden in wilde verwanten van tomaat en deze resistentie was meestal kwantitatief. Het doel van dit promotieonderzoek was om kwantitatieve loci (QTLs) te identificeren die bijdragen aan resistentie tegen B. cinerea. Met behulp van DNA-merkertechnologie en een populatie van introgressie-lijnen zijn tien QTLs geïdentificeerd. Geen van de afzonderlijke QTLs resulteerde in een niveau van resistentie dat overeen kwam de resistente ouder Solanum habrochaites LYC4. Dit betekent dat QTLs gecombineerd zullen moeten worden om Botrytis cinerea-resistente tomaten te verkrijgen. Dankzij de ontwikkelde DNA-merkers kunnen de geïdentificeerde chromosoomfragmenten met resistentiegenen nu gericht ingekruist worden.

Key words: Capsicum, Bemisia tabaci, trichome density, cuticle thickness Whitefly is economically one of the most threatening pests of pepper worldwide, which is mainly caused by its ability to transmit many different viruses. In this research, we characterized pepper germplasm to identify whitefly-resistant accessions that will form the basis for future resistance breeding. Forty-four pepper accessions representing four species (Capsicum annuum, C. frutescens, C. chinense, C. baccatum) were screened for resistance to whiteflies. Screening parameters were adult survival (AS) and oviposition rate (OR) in a no-choice test and whitefly, egg and nymphal density in free-choice tests. To combine parameters in free-choice tests, a plant resistance value was calculated. The results show that AS and OR were significantly different among accessions and were positively correlated, which was also the case for the parameters in the free-choice tests. Accessions identified as highly resistant in no-choice and free-choice tests generally were C. annuum. Whitefly density and OR correlated positively with trichome density and negatively with cuticle thickness of leaves.

Key words: Capsicum, Bemisia tabaci, trichome density, cuticle thickness Whitefly is economically one of the most threatening pests of pepper worldwide, which is mainly caused by its ability to transmit many different viruses. In this research, we characterized pepper germplasm to identify whitefly-resistant accessions that will form the basis for future resistance breeding. Forty-four pepper accessions representing four species (Capsicum annuum, C. frutescens, C. chinense, C. baccatum) were screened for resistance to whiteflies. Screening parameters were adult survival (AS) and oviposition rate (OR) in a no-choice test and whitefly, egg and nymphal density in free-choice tests. To combine parameters in free-choice tests, a plant resistance value was calculated. The results show that AS and OR were significantly different among accessions and were positively correlated, which was also the case for the parameters in the free-choice tests. Accessions identified as highly resistant in no-choice and free-choice tests generally were C. annuum. Whitefly density and OR correlated positively with trichome density and negatively with cuticle thickness of leaves.

Op 20 juni 2011 promoveerde Hendrik Rietman aan Wageningen University (WUR) op zijn proefschrift getiteld: “Putting the Phytophthora infestans genome sequence at work; multiple novel avirulence and potato resistance gene candidates revealed”. Zijn promotor, Prof. Dr. Richard G. F. Visser, en co-promotor, Dr. Ir. Vivianne G. A. A. Vleeshouwers, zijn beiden verbonden aan de leerstoelgroep Plantenveredeling van de WUR, waar ook het onderzoek werd uitgevoerd. Tevens is er samengewerkt met de leerstoelgroep Fytopathologie (WUR), het Sainsbury Lab en het James Hutton Instituut (beiden gevestigd in het Verenigd Koninkrijk). Financiering was afkomstig van het ‘Parapluplan Phytophthora’ en WUR Plantenveredeling.

Resistentie tegen Botrytis cinerea is gevonden in wilde verwanten van tomaat en deze resistentie was meestal kwantitatief. Het doel van dit promotieonderzoek was om kwantitatieve loci (QTLs) te identificeren die bijdragen aan resistentie tegen B. cinerea. Met behulp van DNA-merkertechnologie en een populatie van introgressie-lijnen zijn tien QTLs geïdentificeerd. Geen van de afzonderlijke QTLs resulteerde in een niveau van resistentie dat overeen kwam de resistente ouder Solanum habrochaites LYC4. Dit betekent dat QTLs gecombineerd zullen moeten worden om Botrytis cinerea-resistente tomaten te verkrijgen. Dankzij de ontwikkelde DNA-merkers kunnen de geïdentificeerde chromosoomfragmenten met resistentiegenen nu gericht ingekruist worden.

In het project DuRPh van Wageningen UR worden bestaande aardappelrassen door middel van cisgenese en stapeling van R-genen resistent gemaakt tegen de aardappelziekte. In dit artikel worden de principes van DuRPh uitgelegd en de aanpak en eerste resultaten gepresenteerd.

Door het screenen van lijnen en wilde verwanten van tarwe, is een nieuw resistentiegen tegen STB (Septoria tritici blotch) gevonden.

In 2006 startte Wageningen UR (University & Research centre) daarom in opdracht van het ministerie van Landbouw, Natuur en Voedselkwaliteit het tienjarige onderzoekproject DuRPh (Duurzame Resistentie tegen Phytophthora). In dit project worden bestaande aardappelrassen door middel van ‘cisgenese’ resistent gemaakt tegen de aardappelziekte. Daarbij bouwen onderzoekers van Wageningen UR verschillende zogenaamde R-genen tegelijkertijd bij de aardappel in, waardoor de resistentie waarschijnlijk veel langer stand kan houden. De ambitie van het onderzoek is om het mogelijk te maken dat veredelingsbedrijven rassen kunnen (laten) ontwikkelen waarmee het gebruik van anti-Phytophthoramiddelen met 80% vermindert. Deze brochure geeft een beeld van de vorderingen van het onderzoek over de eerste vijf jaar. Daarnaast gaat zij in op een deel van de internationale problematiek: de beschikbaarheid van resistente aardappelrassen in de ontwikkelingslanden en ontwikkelde landen.

In 2006 startte Wageningen UR (University & Research centre) daarom in opdracht van het ministerie van Landbouw, Natuur en Voedselkwaliteit het tienjarige onderzoekproject DuRPh (Duurzame Resistentie tegen Phytophthora). In dit project worden bestaande aardappelrassen door middel van ‘cisgenese’ resistent gemaakt tegen de aardappelziekte. Daarbij bouwen onderzoekers van Wageningen UR verschillende zogenaamde R-genen tegelijkertijd bij de aardappel in, waardoor de resistentie waarschijnlijk veel langer stand kan houden. De ambitie van het onderzoek is om het mogelijk te maken dat veredelingsbedrijven rassen kunnen (laten) ontwikkelen waarmee het gebruik van anti-Phytophthoramiddelen met 80% vermindert. Deze brochure geeft een beeld van de vorderingen van het onderzoek over de eerste vijf jaar. Daarnaast gaat zij in op een deel van de internationale problematiek: de beschikbaarheid van resistente aardappelrassen in de ontwikkelingslanden en ontwikkelde landen.

Genetisch gemodificeerde gewassen (GM-gewassen) worden in Europa moeilijk geaccepteerd. De geschiedenis van de weerstand laat zien dat deze bij een klein deel van de bezwaarden te maken heeft met het modificatieproces zelf. Het overgrote deel keert zich veeleer tegen het gebruik van landbouwkundig nuttige transgenen uit virussen en bacteria, en van transgene selectiegenen die onder meer resistentie tegen een antibioticum of een herbicide geven. Al deze genen worden transgenen genoemd omdat ze uit organismen komen die niet kruisbaar zijn met de doelplant. In de beginperiode van de transgenese waren alleen deze transgenen beschikbaar. Inmiddels kan de, ook maatschappelijk belangrijke, versnelling van het klassieke plantenveredelingsproces eveneens worden gerealiseerd met cisgenen en intragenen. De huiver die nog in het publieke en politieke debat doorklinkt, krijgt daardoor een steeds meer irrationeel karakter. Een meer adequate EU-regelgeving wordt daardoor belemmerd

Genetisch gemodificeerde gewassen (GM-gewassen) worden in Europa moeilijk geaccepteerd. De geschiedenis van de weerstand laat zien dat deze bij een klein deel van de bezwaarden te maken heeft met het modificatieproces zelf. Het overgrote deel keert zich veeleer tegen het gebruik van landbouwkundig nuttige transgenen uit virussen en bacteria, en van transgene selectiegenen die onder meer resistentie tegen een antibioticum of een herbicide geven. Al deze genen worden transgenen genoemd omdat ze uit organismen komen die niet kruisbaar zijn met de doelplant. In de beginperiode van de transgenese waren alleen deze transgenen beschikbaar. Inmiddels kan de, ook maatschappelijk belangrijke, versnelling van het klassieke plantenveredelingsproces eveneens worden gerealiseerd met cisgenen en intragenen. De huiver die nog in het publieke en politieke debat doorklinkt, krijgt daardoor een steeds meer irrationeel karakter. Een meer adequate EU-regelgeving wordt daardoor belemmerd

Meer dan de helft van alle bekende insecten leeft van planten. Niet alleen insecten passen zich aan hun voedsel aan. Ook de plant wapent zich tegen zijn belagers. Hoe is deze situatie ontstaan? Hoe verdedigen planten zich tegen insectenvraat, en hoe 'ontmantelen' sommige insecten deze verdediging?

Meer dan de helft van alle bekende insecten leeft van planten. Niet alleen insecten passen zich aan hun voedsel aan. Ook de plant wapent zich tegen zijn belagers. Hoe is deze situatie ontstaan? Hoe verdedigen planten zich tegen insectenvraat, en hoe 'ontmantelen' sommige insecten deze verdediging?

In 2006 startte Wageningen UR het tienjarige project DuRPh: Duurzame Resistentie tegen Phytophthora. In het project wordt gebruikt gemaakt van cisgenese: het inbrengen van genen van de eigen (of een verwante) soort door middel van genetische modificatie. In deze brochure wordt ingegaan op de achtergronden van DuRPh: het terugdringen van het gebruik van pesticiden en de daarmee samenhangende milieubelasting en kosten. Men hoopt dat cisgenese wel aanvaard zal worden, in tegenstelling tot genetische modificatie waarbij vreemde genen in de plant ingebracht worden.

In 2006 startte Wageningen UR het tienjarige project DuRPh: Duurzame Resistentie tegen Phytophthora. In het project wordt gebruikt gemaakt van cisgenese: het inbrengen van genen van de eigen (of een verwante) soort door middel van genetische modificatie. In deze brochure wordt ingegaan op de achtergronden van DuRPh: het terugdringen van het gebruik van pesticiden en de daarmee samenhangende milieubelasting en kosten. Men hoopt dat cisgenese wel aanvaard zal worden, in tegenstelling tot genetische modificatie waarbij vreemde genen in de plant ingebracht worden.

Partial resistance to leaf rust ( Puccinia hordei Otth) in barley is a quantitative resistance that is not based on hypersensitivity. This resistance hampers haustorium formation and results in a long latency period in greenhouse tests. The resistance is due to genes with relatively small, quantitative effects, located on so called quantitative trait loci (QTL). A detailed chromosome map of barley, containing 3,258 molecular markers, was constructed and used as a platform to compare the genetic positions of QTLs across different mapping populations. This confirmed that partial resistance in barley to P. hordei is controlled by a high diversity of genes, each mapping population segregating for a different set of QTLs. Another consensus map was constructed that gathered together 775 barley microsatellite markers. The introgression of single QTL-allele or combination of QTL-alleles in near isogenic lines (NILs) allowed us to confirm the effect of three target QTLs ( Rphq2 , Rphq3 and Rphq4 ) in seedling disease tests performed in greenhouse compartments and in field disease tests. The use of several leaf rust isolates revealed the clear isolate-specific effect of Rphq4 . Gene Rphq2 was easy to detect in seedlings of the corresponding NILs and was located in a physical region of high recombination. The position of Rphq2was refinedto a 0.1 cM genetic interval that corresponds probably with only a relatively short stretch of DNA. This makes it feasible to pick the gene up from a bacterial DNA (BAC) library in not too distant future.

Partial resistance to leaf rust ( Puccinia hordei Otth) in barley is a quantitative resistance that is not based on hypersensitivity. This resistance hampers haustorium formation and results in a long latency period in greenhouse tests. The resistance is due to genes with relatively small, quantitative effects, located on so called quantitative trait loci (QTL). A detailed chromosome map of barley, containing 3,258 molecular markers, was constructed and used as a platform to compare the genetic positions of QTLs across different mapping populations. This confirmed that partial resistance in barley to P. hordei is controlled by a high diversity of genes, each mapping population segregating for a different set of QTLs. Another consensus map was constructed that gathered together 775 barley microsatellite markers. The introgression of single QTL-allele or combination of QTL-alleles in near isogenic lines (NILs) allowed us to confirm the effect of three target QTLs ( Rphq2 , Rphq3 and Rphq4 ) in seedling disease tests performed in greenhouse compartments and in field disease tests. The use of several leaf rust isolates revealed the clear isolate-specific effect of Rphq4 . Gene Rphq2 was easy to detect in seedlings of the corresponding NILs and was located in a physical region of high recombination. The position of Rphq2was refinedto a 0.1 cM genetic interval that corresponds probably with only a relatively short stretch of DNA. This makes it feasible to pick the gene up from a bacterial DNA (BAC) library in not too distant future.

Tomato early blight (EB) caused by the fungus Alternaria solani is a field disease with a worldwide distribution, including Indonesia. The disease is currently controlled using frequent applications of fungicides. The use of resistant cultivar would be an attractive way to reduce fungicide application. The aims of the research are to support breeding of EB resistance cultivars for the Indonesian market, by identifying EB resistance genes effective in Indonesia and developing markers for MAS.In Chapter 1 the literature on A. solani, EB and resistance is reviewed. On the fungal side pathogenicity and genetic variation have been widely investigated. However, the existence of different physiological races has not been convincingly demonstrated or disproved. Reliable methods of screening are available for use in resistance breeding. Intensive screening of tomato accessions worldwide has shown that strong resistance is not available in the cultivated tomato but only in wild species. Resistance to A. solani is expressed quantitatively and is polygenically inherited. For that reason classical breeding has not been able to achieve high levels of resistance, and undesirable traits from the donors have been introgressed as well. Recently QTLs have been mapped in a few resistance sources, which could facilitate transferring such quantitative resistance genes and circumvent the problem of unfavourable linkage drag once markers tightly linked to the QTLs have been obtained.In Chapter 2 a resistance test method involving droplet inoculation is described, which is an adaptation of an existing but hardly-used technique. This method has advantages in comparison with the more widely used spray inoculation method, including a clear distinction between lesions caused by A. solani and necroses of 1eaf loss due to other causes, and an objective measurement of damage in contrast to subjective scoring. In the droplet inoculation method leaflets of intact plants are inoculated with droplets of an A. solani conidial suspension in water or an agar solution. Lesions are assessed quantitatively by measuring the length and the perpendicular width. In this way objective and accurate assessments, which are prerequisites for QTL analysis, can be achieved. This inoculation method was used to screen a collection of 54 tomato accessions for resistance to an Indonesian A. solani isolate,S. arcanum LA2157 is highly resistant to A. solani in the glasshouse screening tests. The genetics of the resistance in this wild relative of tomato was further studied using a QTL mapping approach (Chapter 3). The mapping population consisted of 176 F2 plants. A linkage map consisting of 12 linkage groups covering 1179 cM was based on 379 markers (33 SSR, 21 SNP and 316 AFLP markers). All linkage groups could be assigned to the 12 tomato chromosomes. About half of the markers showed deviation from the expected 1:2:1 segregation ratio. The F2 population was phenotyped in a glasshouse in Netherlands with an Indonesian isolate of A. solani. EB resistance was evaluated with respect to lesion size (LS) and related parameters (relative area under the lesion expansion curve [RAULEC] and percentage of small lesions [PSmL]). The derived F3 lines (156) were tested in a field in Indonesia. Percentage of EB index (PEBI) was assessed at six times and relative area under the disease progress curve (RAUDPC) was calculated. A total of six QTLs with a range of LOD scores 3.6 to 16.4 were mapped on chromosomes 1, 2, 5, 6, 7 and 9. Three of the QTLs showed effects in both tests despite differences in experimental method and observed traits. For the first time, three QTLs for resistance affecting the development of stem lesions, another disease symptom caused by the fungus on the main and secondary stems of the plant, were identified, which completely overlapped with QTL regions for early blight resistance. Two QTLs on chromosomes 2 and 9, which explained 7 to 16% of the phenotypic variation for EB resistance and 31% for stem lesion resistance, are recommended to be used in tomato breeding programs for resistance to A. solani.

Tomato early blight (EB) caused by the fungus Alternaria solani is a field disease with a worldwide distribution, including Indonesia. The disease is currently controlled using frequent applications of fungicides. The use of resistant cultivar would be an attractive way to reduce fungicide application. The aims of the research are to support breeding of EB resistance cultivars for the Indonesian market, by identifying EB resistance genes effective in Indonesia and developing markers for MAS.In Chapter 1 the literature on A. solani, EB and resistance is reviewed. On the fungal side pathogenicity and genetic variation have been widely investigated. However, the existence of different physiological races has not been convincingly demonstrated or disproved. Reliable methods of screening are available for use in resistance breeding. Intensive screening of tomato accessions worldwide has shown that strong resistance is not available in the cultivated tomato but only in wild species. Resistance to A. solani is expressed quantitatively and is polygenically inherited. For that reason classical breeding has not been able to achieve high levels of resistance, and undesirable traits from the donors have been introgressed as well. Recently QTLs have been mapped in a few resistance sources, which could facilitate transferring such quantitative resistance genes and circumvent the problem of unfavourable linkage drag once markers tightly linked to the QTLs have been obtained.In Chapter 2 a resistance test method involving droplet inoculation is described, which is an adaptation of an existing but hardly-used technique. This method has advantages in comparison with the more widely used spray inoculation method, including a clear distinction between lesions caused by A. solani and necroses of 1eaf loss due to other causes, and an objective measurement of damage in contrast to subjective scoring. In the droplet inoculation method leaflets of intact plants are inoculated with droplets of an A. solani conidial suspension in water or an agar solution. Lesions are assessed quantitatively by measuring the length and the perpendicular width. In this way objective and accurate assessments, which are prerequisites for QTL analysis, can be achieved. This inoculation method was used to screen a collection of 54 tomato accessions for resistance to an Indonesian A. solani isolate,S. arcanum LA2157 is highly resistant to A. solani in the glasshouse screening tests. The genetics of the resistance in this wild relative of tomato was further studied using a QTL mapping approach (Chapter 3). The mapping population consisted of 176 F2 plants. A linkage map consisting of 12 linkage groups covering 1179 cM was based on 379 markers (33 SSR, 21 SNP and 316 AFLP markers). All linkage groups could be assigned to the 12 tomato chromosomes. About half of the markers showed deviation from the expected 1:2:1 segregation ratio. The F2 population was phenotyped in a glasshouse in Netherlands with an Indonesian isolate of A. solani. EB resistance was evaluated with respect to lesion size (LS) and related parameters (relative area under the lesion expansion curve [RAULEC] and percentage of small lesions [PSmL]). The derived F3 lines (156) were tested in a field in Indonesia. Percentage of EB index (PEBI) was assessed at six times and relative area under the disease progress curve (RAUDPC) was calculated. A total of six QTLs with a range of LOD scores 3.6 to 16.4 were mapped on chromosomes 1, 2, 5, 6, 7 and 9. Three of the QTLs showed effects in both tests despite differences in experimental method and observed traits. For the first time, three QTLs for resistance affecting the development of stem lesions, another disease symptom caused by the fungus on the main and secondary stems of the plant, were identified, which completely overlapped with QTL regions for early blight resistance. Two QTLs on chromosomes 2 and 9, which explained 7 to 16% of the phenotypic variation for EB resistance and 31% for stem lesion resistance, are recommended to be used in tomato breeding programs for resistance to A. solani.

Keywords:Strigahermonthica , Sorghum bicolor , selection measures, resistance, tolerance, genotypes.This thesis presents a study on the interaction between the parasitic weed Striga(S.hermonthica [Del.] Benth.) and the cereal crop sorghum ( S. bicolor [L.]Moench).Its main objective was to find suitable measures for the selection of breeding material (crop genotypes) with superior levels of resistance or superior levels of tolerance to Striga.To meet this objective the physiological background of tolerance, the relation between Striga infestation, infection and yield loss and the effect of host genotype on Striga parasitism and reproductionwere studied.These host-parasite interactions were studied with 4-10 different sorghum genotypes differing in level and mechanism of defence against Striga . Field experiments carried out inMaliwere used for yield assessments and development and validation of selection measures. Through pot and agar-gel experiments, aboveground resistance measures were validated with observations on belowground stages. Pot experimentation was also used to create infection response curves and to measure photosynthesis and chlorophyll fluorescence to develop tolerance measures.Strigaparasitism and reproduction, and the detrimental effect of Striga on crop yield can significantly be reduced through crop genotype choice. Maximum aboveground Striga number is a reliable selection measure for resistance. Striga flowerstalk dry weight can be used to identify genotypes that reduce Striga reproduction. The maximum relative yield loss is a suitable selection measure for tolerance in susceptible genotypes, while for more resistant genotypes the relative yield loss per Striga infection seems more appropriate. For these tolerance measures, yield assessment of nearby uninfected controls is indispensable. Chlorophyll fluorescence, more precisely photochemical quenching and electron transport rate, may enable screening for tolerance without this requirement.

Potato is the most important non-cereal crop in the world. Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating disease of potato. In the mid-191h century, P. infestans attacked the European potato fields and this resulted in a widespread famine in Ireland. Late blight remains the No.l constraint to potato production and causes a yearly multi-billion US$ loss globally. In Europe and North America, late blight con trol heavily relies on the use of chemicais, which is hardly affordable to farmers in developing countries and also raises considerabie environmental concerns in the developed countries.Use of host resistance is ecologically the most sustainable way of disease management. Disease resistance (R) genes exist in a wide range of wild species of the genera Solanum. One wild species, Solanum demissum, became the donor of most characterized R genes due to its crossability with the cultivated species S. tuberosum. However, these race-specific genes (Rl-Rll) didn't enable satisfactory protection under the current deployment scheme. Breeders either turned to other wild species or adopted a so-called 'R-gene-free' approach to explore quantitative resistance. Unfortunately, neither alternative offered a solution to late blight control and did not result in commercial release of cultivars with durable resistance.At the end of the 20th century, biological research entered the genomics era, landmarked by the Human Genome Project and by the Arabidopsis and rice genome sequencing initiatives. Genomics also became the new frontier of research in potato and P. infestans. This scientific development is deepening and broadening our understanding of the biology of the host and the pathogen and is facilitating isolation of key genes involved in the interaction. The genetically modified organism (GMO) strategy allows a much more efficient application of these genes than time-consuming conventional breeding. This thesis deals with the isolation, characterization, and deployment of host R genes with the expectation to achieve an ecologically and economically sound control of late blight.The potato-P.infestans interaction follows the gene-for-gene model, that is, resistance only occurs when a host R gene and its corresponding avirulence (Avr) gene in the pathogen are both present. Several disease testing methods have been developed for determination of the gene-for-gene interaction between potato andP. infestans. In vitro inoculation was developed as a quick, space-effective, and accurate assay (Chapter 2). The method exploits the amenability of potato for tissue culture and the suitability of the in vitro environment for late blight disease development.ltsspecificity and reliability was confirmed by comparison with the well-established detached-Ieaf assay. Currently, in vitro inoculation is routinely used in phenotyping of segregating populations, resistance testing of transformants for functional complementation, and screening of new R genes in a wide range of wild germplasms.The investigation of host resistance was focused on the R3 complex locus on the distal part of chromosome I\. The R3 complex locus segregated in a potato mapping population, which was used to construct the potato ultra-high dense (UHD) map saturated with over 10,000 amplified fragment length polymorphism (AFLP) markers. Using a population of 1748 plants, we constructed a high-resolution genetic map at the R3 complex locus. The combination of fine-mapping and accurate disease testing with specific P. infestans isolates resulted in the unexpected discovery that the R3 complex locus is composed of two functionally distinct genes, R3a and R3b, which are 0.4 cM apart and have both been introgressed from S. demissum (Chapter 3). Each gene was localized into a genetic interval of 0.25 cM, providing the starting point for map-based cloning.Plant R gene families undergo fast evolution, resulting in considerable intraand inter-specific variation. Plant disease resistance (R) loci frequently lack synteny between related species of cereals and crucifers but appear to be positionally well conserved in the Solanaceae. Comparative genomics provides a tooi to utilize the exponentially increasing sequence information from model plants to clone agronomically important genes from less studied crop species. We were keen to investigate whether this tooi can enable new R gene cloning by a case study. The comparative study revealed that the potato late blight R3 locus and the tomato Fusarium wilt 12 locus were derived from an ancestrallocus involved in plant innate immunity. We adopted alocal RGA approach using DNA sequences of the 12 gene to isolate the R3a gene (Chapter 4).l2 and R3a share 88% and 83% identities at the DNA and protein level, respectively. R3a is a member of the R3 complex locus. Comparative physical mapping disclosed that the potato R3 complex locus underwent a significant expansion after divergence from tomato without disruption of the flanking colinearity. This expansion resulted in an increase in the number of R genes and functional diversification.lnterestingly, the differential evolution of the ancient R locus in the two closely related species is well correlated with the contrasting evolutionary potentials of the pathogens with which 12 and R3 interact.Fusarium oxysporum is a soilborne fungus with low genotype diversity, whereas the late blight pathogen P. infestans is notorious in its ability to move and mutate. An intriguing question is whyS. demissum.aspecies that appears to contain only easily-broken R genes, can display durable resistance at the population level in its natural environment. The polymorphism of parasite recognition capacity in a host population will restrict most isolates of the parasite to grow on most hosts. Allelism is an efficient way of creating recognition polymorphism. We made another unexpected discovery that the R3 complex locus has very high allelic diversity and that the R5 -R 11 resistant specificities all contain a distinct allelic version (Chapter 5). Sequence exchange between alleles and diversifying selection are the major driving forces of this allelic recogntion polymorphism to P. infestans. Remarkably, the genomic structure of the R3 complex locus favors the creation of new resistance specificity by reshuffling of elements from the two clusters (R3a and R3b). The multiple allelism of the R3 complex locus may be a natural mechanism of S. demissum to suppress late blight epidemics and should be mimicked in resistance breeding. We suggest that R-gene polyculture via the GMO approach should be the future paradigm of R gene deployment in late blight controI.Potato breeding for late blight resistance was one of the earliest mankind practices in combating plant pathogens by means of genetic improvement but the disease has not been controlled by resistance breeding so faro The non-durable nature of S. demissum R genes apparently disappointed most breeders and the blame of easily-broken R genes even led to the unsuccessful R-gene-free approach. However, from an evolutionary and ecological point of view, single R genes can never defeat pathogens such as P. infestans with extremely high evolutionary risk. We propose that the community rethinks its strategy of R gene deployment in late blight disease management. R gene monoculture is obviously not recommended. R gene pyramiding is currently practiced by breeders but this strategy is basically the same as R gene monoculture since it creates uniformity in host resistance specificity in the field, which will be eventually broken by the fast-evolving pathogen. R gene polyculture should be the strategy of the future. However, we should soberly realize that host resistance might be high enough for survival of the plant population but it alone might never offer a protection that meets the economical threshold. Integrated pest management should include R gene polyculture as the central element, cultivation measures, and limited chemical applications To provide this central element, we need to clone more R genes. Our discovery of the multiple allelism of the R3 potato late blight resistance complex and molecular characterization of one of its allelic versions will offer a possibility to a dozen R genes in the near future and then to deploy them in a potato field using marker-free GMO techniques.

Potato is the most important non-cereal crop in the world. Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating disease of potato. In the mid-191h century, P. infestans attacked the European potato fields and this resulted in a widespread famine in Ireland. Late blight remains the No.l constraint to potato production and causes a yearly multi-billion US$ loss globally. In Europe and North America, late blight con trol heavily relies on the use of chemicais, which is hardly affordable to farmers in developing countries and also raises considerabie environmental concerns in the developed countries.Use of host resistance is ecologically the most sustainable way of disease management. Disease resistance (R) genes exist in a wide range of wild species of the genera Solanum. One wild species, Solanum demissum, became the donor of most characterized R genes due to its crossability with the cultivated species S. tuberosum. However, these race-specific genes (Rl-Rll) didn't enable satisfactory protection under the current deployment scheme. Breeders either turned to other wild species or adopted a so-called 'R-gene-free' approach to explore quantitative resistance. Unfortunately, neither alternative offered a solution to late blight control and did not result in commercial release of cultivars with durable resistance.At the end of the 20th century, biological research entered the genomics era, landmarked by the Human Genome Project and by the Arabidopsis and rice genome sequencing initiatives. Genomics also became the new frontier of research in potato and P. infestans. This scientific development is deepening and broadening our understanding of the biology of the host and the pathogen and is facilitating isolation of key genes involved in the interaction. The genetically modified organism (GMO) strategy allows a much more efficient application of these genes than time-consuming conventional breeding. This thesis deals with the isolation, characterization, and deployment of host R genes with the expectation to achieve an ecologically and economically sound control of late blight.The potato-P.infestans interaction follows the gene-for-gene model, that is, resistance only occurs when a host R gene and its corresponding avirulence (Avr) gene in the pathogen are both present. Several disease testing methods have been developed for determination of the gene-for-gene interaction between potato andP. infestans. In vitro inoculation was developed as a quick, space-effective, and accurate assay (Chapter 2). The method exploits the amenability of potato for tissue culture and the suitability of the in vitro environment for late blight disease development.ltsspecificity and reliability was confirmed by comparison with the well-established detached-Ieaf assay. Currently, in vitro inoculation is routinely used in phenotyping of segregating populations, resistance testing of transformants for functional complementation, and screening of new R genes in a wide range of wild germplasms.The investigation of host resistance was focused on the R3 complex locus on the distal part of chromosome I\. The R3 complex locus segregated in a potato mapping population, which was used to construct the potato ultra-high dense (UHD) map saturated with over 10,000 amplified fragment length polymorphism (AFLP) markers. Using a population of 1748 plants, we constructed a high-resolution genetic map at the R3 complex locus. The combination of fine-mapping and accurate disease testing with specific P. infestans isolates resulted in the unexpected discovery that the R3 complex locus is composed of two functionally distinct genes, R3a and R3b, which are 0.4 cM apart and have both been introgressed from S. demissum (Chapter 3). Each gene was localized into a genetic interval of 0.25 cM, providing the starting point for map-based cloning.Plant R gene families undergo fast evolution, resulting in considerable intraand inter-specific variation. Plant disease resistance (R) loci frequently lack synteny between related species of cereals and crucifers but appear to be positionally well conserved in the Solanaceae. Comparative genomics provides a tooi to utilize the exponentially increasing sequence information from model plants to clone agronomically important genes from less studied crop species. We were keen to investigate whether this tooi can enable new R gene cloning by a case study. The comparative study revealed that the potato late blight R3 locus and the tomato Fusarium wilt 12 locus were derived from an ancestrallocus involved in plant innate immunity. We adopted alocal RGA approach using DNA sequences of the 12 gene to isolate the R3a gene (Chapter 4).l2 and R3a share 88% and 83% identities at the DNA and protein level, respectively. R3a is a member of the R3 complex locus. Comparative physical mapping disclosed that the potato R3 complex locus underwent a significant expansion after divergence from tomato without disruption of the flanking colinearity. This expansion resulted in an increase in the number of R genes and functional diversification.lnterestingly, the differential evolution of the ancient R locus in the two closely related species is well correlated with the contrasting evolutionary potentials of the pathogens with which 12 and R3 interact.Fusarium oxysporum is a soilborne fungus with low genotype diversity, whereas the late blight pathogen P. infestans is notorious in its ability to move and mutate. An intriguing question is whyS. demissum.aspecies that appears to contain only easily-broken R genes, can display durable resistance at the population level in its natural environment. The polymorphism of parasite recognition capacity in a host population will restrict most isolates of the parasite to grow on most hosts. Allelism is an efficient way of creating recognition polymorphism. We made another unexpected discovery that the R3 complex locus has very high allelic diversity and that the R5 -R 11 resistant specificities all contain a distinct allelic version (Chapter 5). Sequence exchange between alleles and diversifying selection are the major driving forces of this allelic recogntion polymorphism to P. infestans. Remarkably, the genomic structure of the R3 complex locus favors the creation of new resistance specificity by reshuffling of elements from the two clusters (R3a and R3b). The multiple allelism of the R3 complex locus may be a natural mechanism of S. demissum to suppress late blight epidemics and should be mimicked in resistance breeding. We suggest that R-gene polyculture via the GMO approach should be the future paradigm of R gene deployment in late blight controI.Potato breeding for late blight resistance was one of the earliest mankind practices in combating plant pathogens by means of genetic improvement but the disease has not been controlled by resistance breeding so faro The non-durable nature of S. demissum R genes apparently disappointed most breeders and the blame of easily-broken R genes even led to the unsuccessful R-gene-free approach. However, from an evolutionary and ecological point of view, single R genes can never defeat pathogens such as P. infestans with extremely high evolutionary risk. We propose that the community rethinks its strategy of R gene deployment in late blight disease management. R gene monoculture is obviously not recommended. R gene pyramiding is currently practiced by breeders but this strategy is basically the same as R gene monoculture since it creates uniformity in host resistance specificity in the field, which will be eventually broken by the fast-evolving pathogen. R gene polyculture should be the strategy of the future. However, we should soberly realize that host resistance might be high enough for survival of the plant population but it alone might never offer a protection that meets the economical threshold. Integrated pest management should include R gene polyculture as the central element, cultivation measures, and limited chemical applications To provide this central element, we need to clone more R genes. Our discovery of the multiple allelism of the R3 potato late blight resistance complex and molecular characterization of one of its allelic versions will offer a possibility to a dozen R genes in the near future and then to deploy them in a potato field using marker-free GMO techniques.

Keywords:Strigahermonthica , Sorghum bicolor , selection measures, resistance, tolerance, genotypes.This thesis presents a study on the interaction between the parasitic weed Striga(S.hermonthica [Del.] Benth.) and the cereal crop sorghum ( S. bicolor [L.]Moench).Its main objective was to find suitable measures for the selection of breeding material (crop genotypes) with superior levels of resistance or superior levels of tolerance to Striga.To meet this objective the physiological background of tolerance, the relation between Striga infestation, infection and yield loss and the effect of host genotype on Striga parasitism and reproductionwere studied.These host-parasite interactions were studied with 4-10 different sorghum genotypes differing in level and mechanism of defence against Striga . Field experiments carried out inMaliwere used for yield assessments and development and validation of selection measures. Through pot and agar-gel experiments, aboveground resistance measures were validated with observations on belowground stages. Pot experimentation was also used to create infection response curves and to measure photosynthesis and chlorophyll fluorescence to develop tolerance measures.Strigaparasitism and reproduction, and the detrimental effect of Striga on crop yield can significantly be reduced through crop genotype choice. Maximum aboveground Striga number is a reliable selection measure for resistance. Striga flowerstalk dry weight can be used to identify genotypes that reduce Striga reproduction. The maximum relative yield loss is a suitable selection measure for tolerance in susceptible genotypes, while for more resistant genotypes the relative yield loss per Striga infection seems more appropriate. For these tolerance measures, yield assessment of nearby uninfected controls is indispensable. Chlorophyll fluorescence, more precisely photochemical quenching and electron transport rate, may enable screening for tolerance without this requirement.

In het kader van het onderzoeksprogramma 'Biologische productiesystemen in de akkerbouw en vollegrondsgroenteteelt' is de afgelopen vier jaar onderzoek gedaan naar de mogelijkheden die veredeling kan bieden om het wortelstelsel van uien te verbeteren. Dit lijkt mogelijk door specifieke soortkruisingen met stengelui (Japanse bladui) en Allium roylei, met als bijkomend voordeel dat naast de selectie op een beter type wortelstelsel ook geselecteerd kan worden op resistentie tegen de bladschimmels valse meeldauw en bladvlekkenziekte. Een opvallend onderzoeksresultaat was het effect van arbusculaire mycorrhiza (AM) op het verbeteren van het wortelstelsel en de productiviteit van stengelui, en mogelijk ook ui

In het kader van het onderzoeksprogramma 'Biologische productiesystemen in de akkerbouw en vollegrondsgroenteteelt' is de afgelopen vier jaar onderzoek gedaan naar de mogelijkheden die veredeling kan bieden om het wortelstelsel van uien te verbeteren. Dit lijkt mogelijk door specifieke soortkruisingen met stengelui (Japanse bladui) en Allium roylei, met als bijkomend voordeel dat naast de selectie op een beter type wortelstelsel ook geselecteerd kan worden op resistentie tegen de bladschimmels valse meeldauw en bladvlekkenziekte. Een opvallend onderzoeksresultaat was het effect van arbusculaire mycorrhiza (AM) op het verbeteren van het wortelstelsel en de productiviteit van stengelui, en mogelijk ook ui

Plants are continuously exposed to a wide variety of pathogens. However, all plant species are non-hosts for the majority of the potential plant pathogens. The genetic dissection of non-host resistance is hampered by the lack of segregating population from crosses between host and non-host species, since hardly any non-host is crossable with a host. We have studied the non-host resistance in Lactuca saligna (wild lettuce) to lettuce downy mildew ( Bremia lactucae ). L. saligna is one of the few examples of a non-host species that is crossable with a related host species, L. sativa (lettuce). Based on this interspecific cross, segregating populations have been developed for genetical analysis of the non-host resistance. To map the resistance, we have used two strategies in which we make use of DNA markers to genotype plants. As no accurate linkage map was available for lettuce, we started with the construction of a linkage map of L. saligna´L. sativa . In Chapter 2, the development of an integrated linkage map, based on two populations, is described. To acquire DNA markers, AFLP analyses have been performed on the F 2 populations of the crosses L. saligna CGN 5271 ´L. sativa Olof and L. saligna CGN 11341´L. sativa Norden. Based on these AFLP analyses the polymorphism rate between L. saligna and L. sativa is estimated to be 81%. A linkage map was constructed that comprises 12 SSRs and 476 AFLP markers over 854 cM in nine linkage groups (n=9). Since the markers are randomly spread over all chromosomes, we assume this map is an accurate representative of both parental genomes and very useful for Marker Assisted Selection.The first mapping strategy for downy mildew resistance is described in Chapter 3. In that study, we have performed a QTL analysis on 126 F 2 plants of a cross between the resistant L. saligna CGN 5271 and the susceptible L. sativa Olof. For this QTL analysis all 126 F 2 plants have been tested for resistance in four disease tests with two complex Bremia races (NL14 and NL16). The F 2 population showed a wide and continuous range of resistance levels from completely resistant to completely susceptible. Evidence is presented for a quantitative resistance against both Bremia races as well as for a race-specific resistance against Bremia race NL16 and not against NL14. These disease test data sets have been combined with DNA marker data of all 126 F 2 plants that had already been obtained for the construction of the linkage map. QTL mapping revealed a qualitative gene ( R39 ) explaining the race-specific resistance and three QTLs ( RBQ1 , RBQ2 and RBQ3 ) explaining the quantitative resistance. The qualitative gene R39 is a dominant gene that gives nearly complete resistance to race NL16 in L. saligna CGN 5271 and therefore it shows features similar to Dm genes (dominant race specific genes that give a complete resistance to d owny m ildew). The three QTLs explain 51% of the quantitative resistance against NL14, which indicates that probably not all QTLs have been detected in this F 2 population.In addition to this rather classical F 2 mapping strategy, we have performed an alternative mapping strategy based on the development and characterization of a set of Backcross Inbred Lines (BILs). These BILs are genetically nearly completely like L. sativa but contain a single chromosome substitution segment of L. saligna CGN 5271 (Chapter 4). Starting from an F 1 plant, BILs have been developed by four to five generations of backcrosses and one generation of selfing. All backcrosses from F 1 to BC 4 were made randomly without intentional selection. Marker Assisted Selection was started in the BC 4 generation. Finally, a set of 29 lines was obtained that covers 95% of the L. saligna genome, comprising 16 lines with a single homozygous introgression (BILs), one line with two homozygous introgressions, five lines with heterozygous single introgressions and seven lines with two or more heterozygous introgressions. Several chromosome regions showed severe distorted segregation in the F 2 population. Based on segregation ratios in backcross lines, we were able to explain distorted segregations of three chromosome regions observed in the F 2 population by genetic loci that are involved in pollen- or egg cell fitness.When seed of the first developed BILs was available, a disease test had been set up to test if the BILs, which carried QTLs as identified in the F 2 population, showed enhanced levels of quantitative resistance indeed. Nine BILs (or nearly-BILs) have been tested for resistance to Bremia race NL16. They covered together 31% of the L. saligna parental genome. Two resistance loci detected in the F 2 population ( R39 and RBQ3 ) have been confirmed in the disease test on the BILs. R39 is a dominant gene, which gives a complete resistance against Bremia race NL16. RBQ3 reduces the infection severity of the susceptible L. sativa by 49% ten days post inoculation. The quantitative effects from the resistance genes in these BILs were higher than expected from the F 2 mapping results. No conclusive comparisons of RBQ2 could have been made, as the introgression in the backcross line was not homozygous. RBQ1 has not been tested. Most exciting, the BIL method revealed a new resistance locus on Chromosome 8 with a 77% reduction on the infection severity compared to the susceptible control ten days post inoculation. We conclude that the BIL mapping method can reveal new QTLs unnoticed in the F 2 mapping method and it enables a quantification of the resistance gene effect in a L. sativa background.To extend our knowledge about the non-host resistance of L. saligna to Bremia , we have compared the genetics of non-host resistance to Bremia in L. saligna CGN 5271 with another accession L. saligna CGN 11341. The two accessions show a 39% AFLP polymorphism rate. We have analyzed the non-host resistance of L. saligna CGN 11341 by disease tests and DNA marker analyses on an F 2 and BC 1 population. Disease tests with Bremia races NL14 and NL16 showed a wide range of infection severity scores from resistant to susceptible to both races. The majority of plants had a similar resistance level to both Bremia races. These findings imply that the resistance of L. saligna is quantitatively expressed and is probably race non-specific. A few F 2 and BC 1 plants were completely resistant against Bremia race NL16 and rather susceptible to race NL14. QTL mapping revealed that a major resistance gene that was located on Chromosome 9 explains this race-specific resistance. This gene is designated R39b , as it may be different from R39 .No additional QTLs have been detected in this small F 2 population (n= 54). However, F 2 plants with L. saligna CGN 11341 alleles at loci of RBQ1 , RBQ2 , RBQ3 and RBQ4 mapped in L. saligna CGN 5271, were more resistant than F 2 plants with L. sativa alleles at these loci. In conclusion, we state that it is very likely that the same genes explain the resistances to Bremia in both L. saligna accessions. A backcross program for a set of Backcross Inbred Lines (BIL) that cover R39b and loci for putative QTLs, is in progress.In the last chapter of this thesis the basic results of the study have been discussed. We adduce that non-host resistance in L. saligna is not explained by accumulation of race-specific major resistance genes ( Dm genes) but by a resistance mechanism based on QTLs. Further, we have made a comparison for efficiency of four breeding methods to introgress the resistance genes from L. saligna . Based on this study, we conclude that twice as many resistance genes are introgressed when Marker Assisted Selection is used. Finally, several recommendations concerning research on non-host resistance and the applications of Backcross Inbred Lines have been suggested.

Plants are continuously exposed to a wide variety of pathogens. However, all plant species are non-hosts for the majority of the potential plant pathogens. The genetic dissection of non-host resistance is hampered by the lack of segregating population from crosses between host and non-host species, since hardly any non-host is crossable with a host. We have studied the non-host resistance in Lactuca saligna (wild lettuce) to lettuce downy mildew ( Bremia lactucae ). L. saligna is one of the few examples of a non-host species that is crossable with a related host species, L. sativa (lettuce). Based on this interspecific cross, segregating populations have been developed for genetical analysis of the non-host resistance. To map the resistance, we have used two strategies in which we make use of DNA markers to genotype plants. As no accurate linkage map was available for lettuce, we started with the construction of a linkage map of L. saligna´L. sativa . In Chapter 2, the development of an integrated linkage map, based on two populations, is described. To acquire DNA markers, AFLP analyses have been performed on the F 2 populations of the crosses L. saligna CGN 5271 ´L. sativa Olof and L. saligna CGN 11341´L. sativa Norden. Based on these AFLP analyses the polymorphism rate between L. saligna and L. sativa is estimated to be 81%. A linkage map was constructed that comprises 12 SSRs and 476 AFLP markers over 854 cM in nine linkage groups (n=9). Since the markers are randomly spread over all chromosomes, we assume this map is an accurate representative of both parental genomes and very useful for Marker Assisted Selection.The first mapping strategy for downy mildew resistance is described in Chapter 3. In that study, we have performed a QTL analysis on 126 F 2 plants of a cross between the resistant L. saligna CGN 5271 and the susceptible L. sativa Olof. For this QTL analysis all 126 F 2 plants have been tested for resistance in four disease tests with two complex Bremia races (NL14 and NL16). The F 2 population showed a wide and continuous range of resistance levels from completely resistant to completely susceptible. Evidence is presented for a quantitative resistance against both Bremia races as well as for a race-specific resistance against Bremia race NL16 and not against NL14. These disease test data sets have been combined with DNA marker data of all 126 F 2 plants that had already been obtained for the construction of the linkage map. QTL mapping revealed a qualitative gene ( R39 ) explaining the race-specific resistance and three QTLs ( RBQ1 , RBQ2 and RBQ3 ) explaining the quantitative resistance. The qualitative gene R39 is a dominant gene that gives nearly complete resistance to race NL16 in L. saligna CGN 5271 and therefore it shows features similar to Dm genes (dominant race specific genes that give a complete resistance to d owny m ildew). The three QTLs explain 51% of the quantitative resistance against NL14, which indicates that probably not all QTLs have been detected in this F 2 population.In addition to this rather classical F 2 mapping strategy, we have performed an alternative mapping strategy based on the development and characterization of a set of Backcross Inbred Lines (BILs). These BILs are genetically nearly completely like L. sativa but contain a single chromosome substitution segment of L. saligna CGN 5271 (Chapter 4). Starting from an F 1 plant, BILs have been developed by four to five generations of backcrosses and one generation of selfing. All backcrosses from F 1 to BC 4 were made randomly without intentional selection. Marker Assisted Selection was started in the BC 4 generation. Finally, a set of 29 lines was obtained that covers 95% of the L. saligna genome, comprising 16 lines with a single homozygous introgression (BILs), one line with two homozygous introgressions, five lines with heterozygous single introgressions and seven lines with two or more heterozygous introgressions. Several chromosome regions showed severe distorted segregation in the F 2 population. Based on segregation ratios in backcross lines, we were able to explain distorted segregations of three chromosome regions observed in the F 2 population by genetic loci that are involved in pollen- or egg cell fitness.When seed of the first developed BILs was available, a disease test had been set up to test if the BILs, which carried QTLs as identified in the F 2 population, showed enhanced levels of quantitative resistance indeed. Nine BILs (or nearly-BILs) have been tested for resistance to Bremia race NL16. They covered together 31% of the L. saligna parental genome. Two resistance loci detected in the F 2 population ( R39 and RBQ3 ) have been confirmed in the disease test on the BILs. R39 is a dominant gene, which gives a complete resistance against Bremia race NL16. RBQ3 reduces the infection severity of the susceptible L. sativa by 49% ten days post inoculation. The quantitative effects from the resistance genes in these BILs were higher than expected from the F 2 mapping results. No conclusive comparisons of RBQ2 could have been made, as the introgression in the backcross line was not homozygous. RBQ1 has not been tested. Most exciting, the BIL method revealed a new resistance locus on Chromosome 8 with a 77% reduction on the infection severity compared to the susceptible control ten days post inoculation. We conclude that the BIL mapping method can reveal new QTLs unnoticed in the F 2 mapping method and it enables a quantification of the resistance gene effect in a L. sativa background.To extend our knowledge about the non-host resistance of L. saligna to Bremia , we have compared the genetics of non-host resistance to Bremia in L. saligna CGN 5271 with another accession L. saligna CGN 11341. The two accessions show a 39% AFLP polymorphism rate. We have analyzed the non-host resistance of L. saligna CGN 11341 by disease tests and DNA marker analyses on an F 2 and BC 1 population. Disease tests with Bremia races NL14 and NL16 showed a wide range of infection severity scores from resistant to susceptible to both races. The majority of plants had a similar resistance level to both Bremia races. These findings imply that the resistance of L. saligna is quantitatively expressed and is probably race non-specific. A few F 2 and BC 1 plants were completely resistant against Bremia race NL16 and rather susceptible to race NL14. QTL mapping revealed that a major resistance gene that was located on Chromosome 9 explains this race-specific resistance. This gene is designated R39b , as it may be different from R39 .No additional QTLs have been detected in this small F 2 population (n= 54). However, F 2 plants with L. saligna CGN 11341 alleles at loci of RBQ1 , RBQ2 , RBQ3 and RBQ4 mapped in L. saligna CGN 5271, were more resistant than F 2 plants with L. sativa alleles at these loci. In conclusion, we state that it is very likely that the same genes explain the resistances to Bremia in both L. saligna accessions. A backcross program for a set of Backcross Inbred Lines (BIL) that cover R39b and loci for putative QTLs, is in progress.In the last chapter of this thesis the basic results of the study have been discussed. We adduce that non-host resistance in L. saligna is not explained by accumulation of race-specific major resistance genes ( Dm genes) but by a resistance mechanism based on QTLs. Further, we have made a comparison for efficiency of four breeding methods to introgress the resistance genes from L. saligna . Based on this study, we conclude that twice as many resistance genes are introgressed when Marker Assisted Selection is used. Finally, several recommendations concerning research on non-host resistance and the applications of Backcross Inbred Lines have been suggested.

Key-words: bacterial blight, biological control, biodiversity, endophytic bacteria, L-form, pea, PDRl retrotransposon, Pisum sativum, Pisum abyssinicum, Pseudomonas syringae pv. pisi, race specific resistance, race non-specific resistance, Spanish landraces.Pea bacterial blight (Pseudomonas syringae pv. pisi) occurs worldwide and can cause severe damage under cool and wet conditions particularly at the seedling stage in wintersown crops. Seven Ps. syr. pv. pisi races are currently recognized. There are no resistant cultivars to race 6, which is becoming increasingly important. Current disease control measures include disease avoidance through seed testing and the deployntent of resistant cultivars with race specific resistance gene(s). In the present study two novel control measures were investigated with the potential for integration to give a durable and sustainable disease control. The first was breeding for resistance based on race non-specific resistance present in Pisum abyssinicum, which confers resistance to all races, including race 6. Its mode of inheritance was investigated through a crossing programme with Pisum sativum cultivars. Resistance was controlled by a major recessive gene and a number of modifiers. Progenies of crosses between resistant F5 populations and commercial cultivars are now available. Molecular markers for race non-specific resistance based on a pea retrotransposon marker system were developed. It is suggested that the combination of race specific and race non-specific resistance provides the optimal genetic background for the maximum expression of resistance to all races of the pathogen in all plant parts and under field conditions. The second measure was biological control by endophytic bacteria. Studies on the ecology of endophytic bacteria in pea and identification of efficient indigenous colonizers for potential application in biocontrol have been made. Endophytic population levels were in the range 10 3 -10 6 CFU/g fresh tissue in roots and stems. There was a predominance of Gram-negative bacteria, particularly Pseudomonas sp. and Pantoea agglomerans. Arthrobacter sp. and Curtobacterium sp. were the main Gram-positive bacteria. Factors such as soil type, plant genotype and crop growth stage may significantly influence the diversity and population levels of endophytic bacteria. Future research should focus on the combination and testing of elite breeding lines with selections of disease suppressive endophytic isolates under a variety of field conditions in order to obtain an efficient and durable performance in commercial agriculture.

Key-words: bacterial blight, biological control, biodiversity, endophytic bacteria, L-form, pea, PDRl retrotransposon, Pisum sativum, Pisum abyssinicum, Pseudomonas syringae pv. pisi, race specific resistance, race non-specific resistance, Spanish landraces.Pea bacterial blight (Pseudomonas syringae pv. pisi) occurs worldwide and can cause severe damage under cool and wet conditions particularly at the seedling stage in wintersown crops. Seven Ps. syr. pv. pisi races are currently recognized. There are no resistant cultivars to race 6, which is becoming increasingly important. Current disease control measures include disease avoidance through seed testing and the deployntent of resistant cultivars with race specific resistance gene(s). In the present study two novel control measures were investigated with the potential for integration to give a durable and sustainable disease control. The first was breeding for resistance based on race non-specific resistance present in Pisum abyssinicum, which confers resistance to all races, including race 6. Its mode of inheritance was investigated through a crossing programme with Pisum sativum cultivars. Resistance was controlled by a major recessive gene and a number of modifiers. Progenies of crosses between resistant F5 populations and commercial cultivars are now available. Molecular markers for race non-specific resistance based on a pea retrotransposon marker system were developed. It is suggested that the combination of race specific and race non-specific resistance provides the optimal genetic background for the maximum expression of resistance to all races of the pathogen in all plant parts and under field conditions. The second measure was biological control by endophytic bacteria. Studies on the ecology of endophytic bacteria in pea and identification of efficient indigenous colonizers for potential application in biocontrol have been made. Endophytic population levels were in the range 10 3 -10 6 CFU/g fresh tissue in roots and stems. There was a predominance of Gram-negative bacteria, particularly Pseudomonas sp. and Pantoea agglomerans. Arthrobacter sp. and Curtobacterium sp. were the main Gram-positive bacteria. Factors such as soil type, plant genotype and crop growth stage may significantly influence the diversity and population levels of endophytic bacteria. Future research should focus on the combination and testing of elite breeding lines with selections of disease suppressive endophytic isolates under a variety of field conditions in order to obtain an efficient and durable performance in commercial agriculture.

Door het screenen van lijnen en wilde verwanten van tarwe, is een nieuw resistentiegen tegen STB (Septoria tritici blotch) gevonden.

In het kader van het onderzoeksprogramma 'Biologische productiesystemen in de akkerbouw en vollegrondsgroenteteelt' is de afgelopen vier jaar onderzoek gedaan naar de mogelijkheden die veredeling kan bieden om het wortelstelsel van uien te verbeteren. Dit lijkt mogelijk door specifieke soortkruisingen met stengelui (Japanse bladui) en Allium roylei, met als bijkomend voordeel dat naast de selectie op een beter type wortelstelsel ook geselecteerd kan worden op resistentie tegen de bladschimmels valse meeldauw en bladvlekkenziekte. Een opvallend onderzoeksresultaat was het effect van arbusculaire mycorrhiza (AM) op het verbeteren van het wortelstelsel en de productiviteit van stengelui, en mogelijk ook ui