Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Wat is erfelijkheid?
    Maurice - Van Eijndhoven, M.H.T. ; Oldenbroek, Kor - \ 2015
    Zeldzaam huisdier 40 (2015)3. - ISSN 0929-905X - p. 10 - 12.
    heritability - rassen (dieren) - dierveredeling - dna - eigenschappen - spermatozoön - eicellen - bevruchting - genen - allelen - homozygoten - heterozygoten - mutaties - genetische merkers - heritability - breeds - animal breeding - dna - properties - spermatozoa - ova - fertilization - genes - alleles - homozygotes - heterozygotes - mutations - genetic markers
    Eigenschappen van dieren zijn in meer of mindere mate erfelijk. Ze gaan over van ouders op nakomelingen. Maar ervaren fokkers weten dat in de fokkerij 1+1 geen 2 is. Welke wetmatigheden en welke toevalligheden spelen een rol in de erfelijkheid? Wat heeft het DNA-onderzoek ons daar recentelijk over geleerd en wat kunnen we daarmee?
    Bloedgroepen bij rundvee. Deel 4: Bloedgroepen bij Roodbont Fries Vee, Brandroden en Lakenvelders
    Oldenbroek, J.K. ; Buys, K. - \ 2014
    Zeldzaam huisdier 39 (2014)4. - ISSN 0929-905X - p. 10 - 11.
    rundveerassen - bloedgroepen - rassen (dieren) - zeldzame rassen - genetische merkers - rundveeteelt - afstamming - cattle breeds - blood groups - breeds - rare breeds - genetic markers - cattle farming - parentage
    Onderzoekers gebruikten bloedgroepenonderzoek om genetische verschillen tussen rassen te bestuderen. Fokkers van zeldzame rassen, zoals Roodbont Fries vee, Brandrood en Lakenvelder, hebben dit aangegrepen om te zien of ze echt een bijzonder ras in handen hadden.
    Towards marker assisted breeding in garden roses: from marker development to QTL detection
    Vukosavljev, M. - \ 2014
    Wageningen University. Promotor(en): Richard Visser; Rene Smulders, co-promotor(en): Paul Arens. - Wageningen : Wageningen University - ISBN 9789462571341 - 245
    rosa - rozen - siergewassen - tuinen - marker assisted breeding - loci voor kwantitatief kenmerk - genetische merkers - rosa - roses - ornamental crops - gardens - marker assisted breeding - quantitative trait loci - genetic markers

    Over the last few decades the rose market in Eastern Europe showed a steady growth, which indicates that there is increasing demand for new cultivars that are adapted to the climate as well as to the customs and beauty criterion of that region. One of the possibilities to speed up breeding is to implement marker assisted selection (MAS). Implementation of MAS requires a specific infrastructure (molecular markers, knowledge on genetics of important traits, genetic maps) which is not yet available for tetraploid roses. In this thesis I developed some of the prerequisites for MAS in roses and discuss when and how MAS could have a positive effect on accelerating breeding and/or reducing the costs of the breeding process.

    The first step in understanding the structure of the genepool of garden roses was to evaluate the relatedness among available cultivars. For the first time genetic diversity among modern garden rose cultivars was evaluated (Chapter 2) using a set of 24 microsatellite markers covering most chromosomes. A total of 518 different alleles were obtained in a set of 138 rose cultivars. Genetic differentiation among types of garden roses (Fst=0.022) was four times that found among cut roses, and similar in magnitude to the differentiation among breeders, due to the fact that horticultural groups and breeders overlap largely in classification. In terms of genetic diversity cut roses can be considered as a subgroup of the garden roses. Winter hardy Canadian garden rose cultivars (Explorer roses) showed the least similarities to European roses, and introgression from wild species for winter hardiness was clearly visible. Roses of two breeding programmes (Harkness and Olesen) shared a similar genepool. Comparison of the differentiation among linkage groups indicated that linkage group 5 is potentially a region containing important QTLs for winter hardiness. Linkage group 6 contains the largest amount of genetic diversity, while linkage group 2 is the most differentiated among types of garden roses.

    Garden roses, as well as many other important crops (wheat, potato, strawberry, etc.) are polyploid. Genetic analyses of polyploids is complex as the same locus is present on multiple homologous chromosomes. SSR markers are suitable for mapping in segregating populations of polyploids as they are multi-allelic, making it possible to detect different alleles of the same locus on all homologous chromosomes. If a SSR marker gives fewer alleles than the ploidy level, quantification of allele dosages increases the information content. In Chapter 3 I showed the power of this approach. Alleles were scored quantitatively using the area under the peaks in ABI electropherograms, and allele dosages were inferred based on the ratios between the peak areas for two alleles in reference cases in which these two alleles occurred together. We resolved the full progeny genotypes, generated more data and mapped markers more accurately, including markers with “null” alleles.

    Even though SSR markers are one of the most appropriate marker systems for genetic studies in polyploids still few hurdles complicate (reduce) their implementation. The first major hurdle in developing microsatellite markers, the cloning step, has been overcome by next generation sequencing techniques. The second hurdle is the testing step to differentiate polymorphic from non-polymorphic loci. The third hurdle, somewhat hidden, is that only those polymorphic markers that detect a large effective number of alleles in the germplasm to be studied, are sufficiently informative to be deployed in multiple studies. Both selection steps are laborious and still done manually. In Chapter 4 I present a strategy in which we first screen sequence reads from multiple genotypes for repeats that show the most variation in length, 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 did not amplify but all others were polymorphic. Ten loci amplified more than one locus, indicating duplicated genes or gene families. Completely avoiding this will be difficult, as the range of numbers of predicted alleles of highly polymorphic single- and multi-locus markers largely overlapped. Of the remainder, half were duplicates, indicating the difficulty of correctly filtering short sequence reads containing repeat sequences. The remaining 18 markers were all highly polymorphic, amplifying between 6 and 20 alleles in the 11 tetraploid garden roses. This strategy therefore represents a major step forward in the development of highly polymorphic microsatellite markers.

    Despite that garden roses are economically very important ornamentals, breeding is still mostly conventional, mainly due to tetraploidy and the lack of genetic maps and knowledge about the genetic base of important traits. Furthermore, crosses with unintended parents occur regularly and detection of these is not always straightforward, especially when genetically related varieties are used. Moreover, in polyploids detection of off-type offspring often relies on detecting differences in allele dosage rather than the presence of new alleles. In Chapter 5 I applied the WagRhSNP Axiom rose SNP array to generate 10,000s of SNPs for parentage analysis and to generate a dense genetic map in tetraploid rose. I described a method to separate progeny into putative populations which share parents, even if one of the parents is unknown, using PCO analysis and sets of markers for which allele dosages are incompatible. Subsequently, dense SNP maps were generated for a biparental and a self-pollinated mapping population with one parent in common. I confirmed a tetrasomic mode of inheritance for these crosses and created a starting point for implementation of marker-assisted breeding in garden roses by QTL analysis for important morphological traits (recurrent blooming and prickle shape).

    Winter hardiness is a complex trait and one of the most important limiting factors for garden rose growth and distribution in areas characterized by a continental climate. In Chapter 6 research was undertaken to determine the genetic regions underlying winter hardiness of garden roses, and to generate markers linked to them. For this purpose we exposed two segregating populations, RNDxRND and RNDxHP, to temperatures below -15C in a cold chamber and in the field in Serbia. The frost damage in the hardened plants was estimated directly at the phenotypic level (proportion of dieback) and at the non-visible physiological level indirectly (through the potential for meristem production in spring; regrowth). For winter hardiness we detected two tentative QTLs in the RNDxRND population and two tentative QTLs in the RNDxHP population, of which one was the same in both populations. The ability of plants to regrow in spring was associated to genomic regions on three linkage groups of the RNDxRND population, and on two different linkage groups in the RNDxHP population. A comparison of the ability for regrowth and level of damage caused by low temperature revealed that these two traits are inherited independently and that the final cold tolerance depends on the plant’s ability to withstand low temperature and to regrow fast in spring.

    In résumé, this thesis resulted in the development of basic tools (a fast strategy for polymorphic SSR marker development), basic methods/concepts for genetic analyses in polyploids (quantification of SSR allele dosage, distinguishing outliers from population in polyploid crops, dense SNP map generation and QTL study in tetraploids), and knowledge on genetics of important traits in rose (relatedness among modern garden roses (genetic diversity approach), mode of inheritance, occurrence of selfing, QTLs for morphological traits (recurrent blooming and prickle shape) and dissection of winter hardiness (level of damage caused by low temperature and regrowth)). Additionally, potential use of markers in every phase of rose breeding was discussed (Chapter 7). All these aspects contribute to a solid basis for marker assisted breeding in (garden) rose.

    Elicitin-triggerd apoplastic immunity against late blight in potato
    Du, J. - \ 2014
    Wageningen University. Promotor(en): Richard Visser; Evert Jacobsen, co-promotor(en): Vivianne Vleeshouwers. - Wageningen : Wageningen University - ISBN 9789462570092 - 140
    solanum tuberosum - aardappelen - plantenziekteverwekkende schimmels - phytophthora infestans - ziekteresistentie - genen - schimmeleiwit - genetische merkers - bio-informatica - plantenveredeling - solanum tuberosum - potatoes - plant pathogenic fungi - phytophthora infestans - disease resistance - genes - fungal protein - genetic markers - bioinformatics - plant breeding
    Bloedgroepen bij rundvee als DNA-merkers
    Oldenbroek, J.K. - \ 2014
    Zeldzaam huisdier 39 (2014)1. - ISSN 0929-905X - p. 10 - 13.
    rundveerassen - bloedgroepen - rundveeteelt - rassen (dieren) - zeldzame rassen - genetische merkers - afstamming - antigenen - cattle breeds - blood groups - cattle farming - breeds - rare breeds - genetic markers - parentage - antigens
    Om vast te stellen of de afstamming van een fokdier klopte, werd tussen 1940 en 1990 wereldwijd het bloedgroepenonderzoek gebruikt. In een reeks artikelen willen we aangeven welke inzichten het bloedgroepenonderzoek gegeven heeft in de genetische samenstelling van de zeldzame Nederlandse runderrassen FH, Fries roodbont, MRIJ, Groninger blaarkop en Lakenvelder. Hier het eerste artikel.
    Salmon tracing: Genotyping to trace back escapees from salmon aquaculture
    Blonk, R.J.W. - \ 2014
    Yerseke : IMARES (Report / IMARES Wageningen UR C029/14) - 15
    zalm - zalmteelt - aquacultuur - genetische merkers - genotyping - salmon - salmon culture - aquaculture - genetic markers - genotyping
    The overall objective of the project is to assign an escaped salmon back to the farm responsible for the escape with near 100% accuracy. In this report, the potential of a set of genetic markers to assign an escaped salmon was determined for a set of 12 polymorphic microsatellite markers, provided by Nofima, and by using stochastic simulation. Also, the effect of different numbers of sires, and the effect of pooling of multiple sires in crosses was determined.
    Analysis of Tomato spotted wilt virus effector-triggered immunity
    Ronde, D. de - \ 2013
    Wageningen University. Promotor(en): Just Vlak, co-promotor(en): Richard Kormelink. - S.l. : s.n. - ISBN 9789461737212 - 190
    tomatenbronsvlekkenvirus - plantenvirussen - ziekteresistentie - immuniteit - virulentie - genkartering - genetische merkers - genetische analyse - capsicum annuum - paprika's - tomato spotted wilt virus - plant viruses - disease resistance - immunity - virulence - gene mapping - genetic markers - genetic analysis - capsicum annuum - sweet peppers

    ResistanceinCapsicumagainsttheTomatospottedwiltvirus(TSWV),typespeciesof the Tospovirusgenuswithinthe Bunyaviridaefamily,employsthe singledominant resistancegeneTsw.Thisresistance hasmeanwhilebeenbrokenbyresistance breaking (RB) TSWV isolates and is causing increasing problems in many different (Capsicumcultivating)countries.Theresearchdescribedhereaimedtoidentify andcharacterise theviralproteintriggeringTswresistanceandprovidefurther insightintothemechanismofTsw-mediatedresistance.Knowledgegainedfrom thegeneticandphenotypiccharacterisationofTsw-resistancebreakingisolateswas usedtodevelopdiagnosticmarkersfordetectionofTsw-breakingpathotypesin fieldcultivations.

    TheNSsRNAsilencingsuppressor(RSS)proteinwasidentifiedastheavirulence determinant ofTsw-mediatedresistance(Chapter2).WhiletheNSsproteinfrom theTSWVresistanceinducer(RI)isolatewasactiveasRNAsilencingsuppressorand avirulencedeterminant,theNSsproteinfromtwodifferentTSWVRBisolateslacked bothfunctionsasevidencedfromtransientassays.Surprisingly,thecorresponding resistancebreakingvirusisolatesstillexhibitedRNAisuppressoractivity. Noneof the other viral proteins were able to aid in the transient recovery of RSS activity. Electrophoreticmobilityshift assays(EMSAs)usingplantextractscontaining transientlyexpressedNSsproteinsshowedashift ofsiRNAswithNSsRI,indicative forbinding,butnotwithNSsRB.InagreementwiththelocalleafRSSassaysusinga virusinfection,plantextractsofvirusinfectedleaveswereabletoshiftthesiRNAs, showing recovery of the RSS activityduring virus infection.

    The linkage of RNAi suppression and avirulence in NSs was further investigated bymutationalanalysis(Chapter3).AlargesetofNSsmutantswasgeneratedusing alaninesubstitutions ofauthenticTSWVNSsaminoacidsandwastestedfortheir abilitytotriggerTsw-mediatedHRandabilitytosuppressRNAi.Theseassaysshowed thatthe N-terminaldomainofNSscarried mostimportantresiduesinvolvedwith bothactivities. However,singlemutationscouldbeintroducedthatdisruptedone function,whilemaintainingtheotheroneandviceversaindicatingthatRSSactivity andavirulencewerenotfunctionally linked.SwappingofdomainsbetweenNSsRI andNSsRB notonlyconfirmedtheimportanceoftheN-terminaldomainbutalso thespecificitywithintheTSWVspecies,sincedomainswapsbetweenNSsRIandNSs fromGRSV,arelatedbutdistinct Tospovirus,couldnottransfertheAvrphenotype toGRSV.MutationofaGW/WG-motifintheNterminalregionofNSsRI leadtoa lossofbothfunctionsandindicatedthatthismotif, knowntobeinvolvedinAGO1 interactionof other viral RSS, was of biological relevance for TSWV NSs.

    Theputativeinteraction ofAGO1andNSswasinvestigatedbyusingdifferent approaches to co-immunoprecipitate (Co-IP) on transiently co-expressed tagged- AGO1and(His-)NSs(Chapter4).Initialindicationsforsuchinteraction were obtained,howeverfurthersupportforthisputativeinteraction willhavetocome fromcomplementaryexperiments,e.g. Yeast-2-hybrid (Y2H), FRET-FLIM or BiFC.

    Severaladditional TSWVisolateswereanalysedthatbesidestheknownresistance inducing-and resistance breaking-phenotype showed a temperature-dependent phenotype(Chapter5).IsolatesclassifiedtothistypeexhibitedanRIphenotypeat standardgreenhouseconditions (~22°C)whileatelevatedtemperatures(≥28°C), butstillbelowtemperaturesthatinactivatedtheR-geneproduct(≥31°C),wereable tobreaktheresistance.Viruschallengingassaysatvariousconditionsindicatedthat inductionofTswresistanceatalower temperaturebythesesocalledtemperature dependentresistancebreakingisolates(TempRB)involveddenovosynthesisofthe avirulenceprotein,i.e.NSs,andthat proteinfoldingmight play arole. NSsproteins clonedandexpressedfromthisadditional newsetofTSWVresistanceinducing, resistancebreakingandtemperature dependentresistancebreakingisolates revealedvariableresultsregardless oftheircorrespondingvirusphenotype,when tested for their abilitytoinduceTsw-mediated HR andsuppress RNAi at normal greenhouseconditions(22°C).However,similarassaystoanalysetheiractivity attheelevatedtemperature(28°C)failedwhenusingAgrobacteriummediated transientassays.Sofar,themechanismoftemperature dependencyhasnotbeen clarified yetandneedsfurtherinvestigation.Usingtheinformationobtained,a diagnostictoolwasdevelopedtoscreenforthepotential presenceofresistance breakingisolatesofTSWVusingreversetranscription-polymerasechainreaction amplification(RT-PCR).Aprimersetwasdesignedtargetinganimportantcodon ataaposition79andshowedtobeabletodistinguishRB-isolatesfromRI-isolates. However,afewRB-isolatesstillescapedfromdetection indicatingthelimitedand conditionaluse of this tool.

    In summary, NSs has been identified as Avr-determinant of Tsw-mediated resistance,butthisfunctionisnottightlylinkedtoitsRNAisuppressor-activity. Preliminarydataindicateaputativeinteraction betweenAGO1andNSs.Besides the typicalRIandRBphenotypes,athirdphenotypicclassofTSWVisolates has beenidentified thatexhibitsatemperaturedependencyontriggeringTsw- mediatedresistance andpossiblyinvolvesanalteredproteinfoldingofNSs.A diagnostic toolhasbeendevelopedtodetectresistancebreakingisolatesinthe fieldbasedonRT-PCR,butthistoolstillallowsforescapesofRBisolates.Theresults onNSsarediscussedinlightofitsroleaseffectorwithinthe‘Zig-zag-model’of planthostdefenceresponses.Finally,TSWVNSsisbriefly discussedandcompared totheanimal-infecting(NSs)paralogsoftheBunyaviridaefamily,alsoinlightof functional andstructuralhomologiesbetweenthesensorsofinnateimmunityin plant(R-genes)and animal (NLRs/TLRs) cell systems.

    QTL-based physiological modelling of leaf photosynthesis and crop productivity of rice (Oryza sativa L.) under well-watered and drought environments
    Gu, J. - \ 2013
    Wageningen University. Promotor(en): Paul Struik; H. Wang, co-promotor(en): Xinyou Yin; Tjeerd-Jan Stomph. - S.L. : s.n. - ISBN 9789461735300 - 181
    oryza sativa - fotosynthese van het kroondak - gewasproductie - stress omstandigheden - loci voor kwantitatief kenmerk - genetische merkers - plantenveredeling - simulatiemodellen - oryza sativa - canopy photosynthesis - crop production - stress conditions - quantitative trait loci - genetic markers - plant breeding - simulation models

    Key words: Drought, ecophysiological crop modelling, GECROS, genotype, G×E interaction, modelling, Oryza sativa L., photosynthesis, quantitative trait locus, rice.

    Improving grain yield of rice (Oryza sativa L.) crop for both favourable and stressful environments is the main breeding objective to ensure food security. The objective of this study was to amalgamate crop modelling and genetic analysis, to create knowledge and insight useful in view of this breeding objective.

    Photosynthesis is fundamental to biomass production, but the process is very sensitive to abiotic stresses, including drought. Upland rice cv. Haogelao, lowland rice cv. Shennong265, and 94 of their introgression lines (ILs) were studied under drought and well-watered conditions to analyse the genetics of leaf photosynthesis. After correcting for microclimate fluctuations, significant genetic variation was found in this population, and 1-3 quantitative trait loci (QTLs) were detected per photosynthesis-related trait. A major QTL was mapped near marker RM410 on Chromosome 9 and was consistent for phenotyping at flowering and grain filling, under drought and well-watered conditions, and across field and greenhouse experiments. These results suggest that photosynthesis at different phenological stages and under different environmental conditions is, at least to some extent, influenced by the same genetic factors.

    To understand the physiological regulation of genetic variation and resulting QTLs for photosynthesis detected in the first study, 13 ILs were carefully selected as representatives of the population, based on the QTLs for leaf photosynthesis. These 13 ILs were studied under moderate drought and well-watered conditions in the experiment where combined gas exchange and chlorophyll fluorescence data were collected to assess CO2 and light response curves. Using these curves, seven parameters of a photosynthesis model were estimated to dissect photosynthesis into stomatal conductance (gs), mesophyll conductance (gm), electron transport capacity (Jmax), and Rubisco carboxylation capacity (Vcmax). Genetic variation in light saturated photosynthesis and the major QTL of photosynthesis on Chromosome 9 were mainly associated with variation in gs and gm. Furthermore, relationships between these parameters and leaf nitrogen or dry matter per unit area were shown valid for variation across genotypes and across water treatments. In view of these results and literature reports, it was argued that variation in photosynthesis due to environmental conditions and to genetic variation shares common physiological mechanisms.

    QTL analyses were further extended to other physiological parameters of rice. Molecular marker-based estimates of these traits from estimated additive allele effects were used as input tothe mechanistic crop model GECROS. This marker/QTL-based modelling approach showed the ability of predicting genetic variation of crop performance within ILs for a diverse set of field conditions. This approach also showed the potential of extrapolating to a large population of recombinant inbred lines from the same parents. Most importantly, this model approach may improve the efficiency of marker-assisted selection, as it provides a tool to rank the relative importance of the identified markers in determining final yield under specific environmental conditions.

    To examine the extent to which natural genetic variation in photosynthesis can contribute to increasing biomass production and yield of rice, the GECROS crop model was used again to analyse the impact of genetic variation in photosynthesis on crop biomass production. It was shown that in contrast to other studies a genetic variation in photosynthesis of 25% can be scaled up equally to crop level, resulting in an increase in biomass of 22-29% across different locations and years. The difference with earlier studies seems related to the fact that variation in both Rubisco-limited and electron transport-limited photosynthesis were observed in our IL population.

    This thesis has contributed to closing the gap between genotype and phenotype by integrating crop physiology and genetics through an innovative QTL/marker-based modelling approach. This approach can contribute to making the use of genomics much more efficient in practical plant breeding.

    Use of genetic markers in pig breeding programs
    Coster, A. - \ 2013
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Henk Bovenhuis; Henri Heuven. - S.l. : s.n. - ISBN 9789461734426 - 152
    varkens - dierveredeling - varkensfokkerij - genetische merkers - marker assisted breeding - stamboom - genomica - loci voor kwantitatief kenmerk - worpgrootte - pigs - animal breeding - pig breeding - genetic markers - marker assisted breeding - pedigree - genomics - quantitative trait loci - litter size

    The objective of this thesis was to investigate the use of genetic markers in commercial pig breeding, with a special emphasis on genomically imprinted genes. For the latter purpose, an association study was undertaken to identify genomically imprinted QTL related to sow fertility traits in two commercial pig populations. Furthermore, several simulation studies were performed to evaluate methods to estimate breeding values with marker data. Finally, a new method was designed to estimate the parental origin of marker alleles in crossed populations when the pedigree is unknown.

    The association study involved approximately sows from two commercial pig populations. The sows were genotyped for SNP markers, of which were finally used. The results revealed one SNP with a significant imprinting effect on the trait litter size in one population. The imprinting effect of this SNP was not significant in the other population but its effect was similar. The SNP was located close to the gene DIO3, which has a known imprinting status. Furthermore, several SNP with significant additive and dominance effects were found in both populations.

    The simulation studies were designed to evaluate the effect of the number of genes and the relative importance of these genes on the trait on performance of distinct methods to estimate breeding values with markers. Results of the first study showed that the performance of these methods is affected by gene number and size. Results of the second study continued on these results and showed that genetic gain achievable by selecting on breeding values estimated by these methods strongly depends on the number of genes and their relative size.

    Knowledge of parental origin of marker or gene alleles is of crucial importance to study genomically imprinted genes. A method based on the Dirichlet Process was designed to estimate the parental origin of SNP alleles in crossed populations. The method performed better than methods that did not account crossbreeding, and the performance of the method was strongly improved when some genotypes of some parental individuals were available in the data.

    The last chapter evaluated the influence of genomic imprinting on genetic parameters of genes. An important conclusion of this chapter is that genomically imprinted genes have less variance compared to similar, non-imprinted genes. This lower variance leads to lower power of statistical methods to detect these genes and lower genetic gain achievable in breeding programs. On the other hand, however, genomically imprinted genes could be effectively used in crossbreeding programs.

    Rationalization of a genebank cucumber collection with SSR markers
    Dooijeweert, W. van; Treuren, R. van - \ 2012
    genenbanken - komkommers - cucumis sativus - simple sequence repeats (ssr) - moleculaire genetica - genetische merkers - gene banks - cucumbers - cucumis sativus - simple sequence repeats - molecular genetics - genetic markers
    The cucumber (Cucumis sativus) collection of the Centre for Genetic Resources, the Netherlands (CGN) consists of 937 accessions. The collection mainly includes old cultivars but also contains landraces and the crop wild relative C. sativus var. hardwickii. Passport data were updated in 2002, and used to rationalize the collection. Recently, the main part of the collection was screened for microsatellite (SSR) variation.
    Genetic diversity and population structure of cucumber (Cucumis sativus L.)
    Lv, J. ; Qi, J. ; Shi, Q. ; Shen, D. ; Zhang, S. ; Shao, G. ; Li, H. ; Sun, Z. ; Weng, Y. ; Shang, Y. ; Gu, X. ; Li, X. ; Zhu, X. ; Zhang, J. ; Treuren, R. van; Dooijeweert, W. van; Zhang, Z. ; Huang, S. - \ 2012
    PLoS ONE 7 (2012)10. - ISSN 1932-6203 - 9
    genetische diversiteit - cucumis sativus - komkommers - populatiegenetica - genenbanken - dna-fingerprinting - germplasm - genetische merkers - vruchtgroenten - groenten - genetic diversity - cucumis sativus - cucumbers - population genetics - gene banks - dna fingerprinting - germplasm - genetic markers - fruit vegetables - vegetables - genome - map
    Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.
    Development of genomic resources for ornamental lilies (Lilium L.)
    Shahin, A. - \ 2012
    Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Jaap van Tuyl; Paul Arens. - S.l. : s.n. - ISBN 9789461733009 - 169
    lilium - sierplanten - plantenveredeling - transcriptomica - genetische kartering - genotyping - genetische merkers - nucleotidenvolgordes - genomica - lilium - ornamental plants - plant breeding - transcriptomics - genetic mapping - genotyping - genetic markers - nucleotide sequences - genomics

    Lily (Lilium L.) is a perennial bulbous ornamental, belonging to subclass Monocotyledonae and family Liliaceae. Lily, according to statistics of Dutch auctions, is the fifth most important cut flower and the second in flower bulbs based on acreage. This species has been extensively used for cytogenetic studies, but molecular genetic studies are limited. The heterogenic nature and the very complex and huge genome (36 Gb) of lily might be the reason for this. To improve the efficiency of breeding and selection in this species, and set up the basis for genetic studies in Lilium, genomic resources are needed.

    Next generation sequencing (NGS) technology (454 pyro-sequencing) was used to sequence the transcriptomes (RNA-seq) of four lily cultivars: ‘Connecticut King’, ‘White Fox’, ‘Star Gazer’, and Trumpet that belong to the four most important hybrid groups: Asiatic, Longiflorum, Oriental, and Trumpet respectively. Successfully, 52,172 unigenes with an average length of 555 bp were developed and used for a wide range of genetic and genomic studies: SNP marker identification for genetic mapping, gene annotation, and comparative genomic studies.

    Combining NGS with SNP genotyping techniques to accelerate genetic studies is of considerable interest in different species. In this study, thousands of SNPs out of the 52,172 lily unigenes were identified. Genotyping technique KASPar (KBiosciences competitive Allele Specific PCR) was used to genotype two lily mapping populations: ‘LA (L. longiflorum ‘White Fox’ x Asiatic hybrid ‘Connecticut King’) and AA (‘Connecticut King’ x ‘Orlito’) using 225 SNP markers selected from ‘Connecticut King’ unigenes. Genotyping success rate was 75.5% (170 SNP markers worked), polymorphic SNP rate was 45% (102 SNP markers), and mapped SNP marker rate was 42% (94 SNP mapped) in LA population and 38% (85 SNP mapped) in AA population. Thus, we validated a subset of the putative SNP makers and showed the usability of this type of markers to improve genetic maps for complex genomes like that of lily.

    The SNP markers together with the available AFLP (amplified fragment length polymorphisms), DArT (diversity arrays technology), and NBS (nucleotide binding site) markers were used to build reference genetic maps for these two lily populations. These maps represent the first reasonably saturated maps that cover 89% of the lily genome with an average marker density of one marker per 4 cM. The availability of more SNP markers for genotyping, opens the door for further enriching these genetic maps and thus improve the marker density.

    The genetic maps were used to map and understand the genetic of several horticultural traits in Lilium. Fusarium oxysporum and lily mottle virus (LMoV) are considered as very serious diseases in Lilium and as such present important targets for breeding. Six putative QTLs (quantitive trait loci) were identified for Fusarium resistance in AA population, from which QTL1 was the strongest (explains ~25 % of phenotypic variation). In LA population, QTL1 was also confirmed. Thus, QTL1 is a strong and reliable QTL in both populations and it can be used to develop markers for most of the Fusarium resistance for molecular assisted breeding (MAB) applications. The LMoV was mapped as a marker on the AA genetic maps, however, no close markers to this trait (i.e. distance of the closest marker to LMoV was 9 cM) were identified yet. Several ornamental traits: lily flower color ‘carotene’ (LFCc), flower spots (lfs), stem color (LSC), antherless phenotype (lal), and flower direction (up-side facing, lfd) were phenotyped and mapped. Some of these traits showed to be recessive traits (spots, antherless, and flower direction) and controlled by a single gene. Developing markers for recessive traits is valuable since such markers allow the identification of suitable breeding parents so the presence of the recessive trait can be either enhanced or repressed. A more complex trait is flower longevity because it is a function of: the number of buds per inflorescence, the expansion and opening of the buds, the life span of the individual flowers, and also the life-span of the leaves. Moreover, senescence in Lilium is ethylene-insensitive and the regulator(s) of its vase life is not known yet. Our study showed that vase life of individual lily flowers increased significantly by the exogenous application of sugars. Abscisic acid (ABA) level, furthermore, increased dramatically in lily flowers at senescence compared with anthesis. This indicates that ABA might be the main regulator of vase life in lily. However, more experiments should be conducted to prove this conclusion.

    The genomic resources developed for lily together with genomic resources developed for Tulipa L., in the same way, offered a valuable source of information to conduct comparative genomic studies within and between these two genera. We initiated the first step towards linking molecular genetic maps of Lilium and Tulipa using transcriptome sequences generated by 454 pyro-sequencing. Orthologous genes between lily and tulip were identified (10,913 unigenes) based on sequence data of four lily cultivars and five tulip cultivars. Next, common SNP and EST-SSR markers between the parents of lily mapping populations (AA and LA population) and the parents of tulip mapping population (‘Kees Nelis’ (T. gesneriana) x ‘Cantata’ (T. fosteriana)) based on these orthologous sequences were generated. A total of 229 common SNP and 140 common EST-SSR markers were identified. Genotyping and mapping these markers in the populations of both genera will link the genetic maps of Lilium and Tulipa and thus allow insight into the preservation of gene order, structure, and ‘putative’ functional homology in addition to evolutionary processes.

    Also, these genomic resources can be used to increase the resolution of, and support for, phylogenetic trees. We selected a set of orthologous genes of Lilium (19 genes, 11,766 bp containing 433 polymorphic sites), of Tulipa (20 genes, 10,347 bp containing 216 polymorphic sites), and of the orthologous genes between the two genera (7 genes, 5,790 bp containing 587 polymorphic sites). These sets are uniquely present in the sequences and informative in estimating the genetic divergence of the two genera, thus they can be used to genotypes more species per genera to build genera and maybe family trees later on. The nucleotide polymorphism rate of Lilium was twice as high as that of Tulipa, on average one substitution per 26 bp for Lilium compared with one substitution per 48 bp for Tulipa. NGS provide a valuable source for large numbers of phylogenetic informative substitutions that might revolutionize the phylogenetic, population genetic, and biodiversity studies. However, the use of bi-allelic information from multiple loci in phylogenetic studies is still challenging and it needs to be studied further.

    Moreover, having such high numbers of sequence data, allows us to test some evolutionary hypotheses such as positive selection: selection during domestication/breeding processes might be imprinted in the species genome, which can be examined based on omega (dn/ds) values. The higher the omega value the stronger the indication of positive selection. Positive selection was recorded in Lilium and Tulipa genomes when this small subset of gene contigs (46) of the two genera was tested. Our hypothesis could not be confirmed, however to draw final conclusions on this matter, omega values for many more genes of the two genera have to be measured.

    Finally, a wealth of putative molecular markers (SNPs and SSRs) has become available that can have direct applications for breeding in these genera. SNP markers are important since they are user friendly, efficient, transferable, and co-dominant markers. Applying high throughput genotyping technology to genotype the two lily populations improved the coverage of the two genetic maps. Also, genotyping the same SNP markers in the two populations facilitated the comparisons between the linkage groups of the two populations and will allow the construction of a consensus map. Consequently, exchange of genetic knowledge (mainly QTLs) between the two populations will be easier. The thousands of SNPs identified in the genome of the four lily cultivars opens the door for combining the current linkage mapping studies with association studies which will have a direct impact on improving the resolution of mapping and on MAB applications in Lilium.

    Multiplex SSR analysis of Phytophthora infestans in different countries and the importance for potato breeding
    Li, Y. - \ 2012
    Wageningen University. Promotor(en): Evert Jacobsen, co-promotor(en): Theo van der Lee; D.E.L. Cooke. - S.l. : s.n. - ISBN 9789461732798 - 206
    solanum tuberosum - aardappelen - plantenveredeling - plantenziekteverwekkende schimmels - phytophthora infestans - microsatellieten - populaties - ziekteresistentie - genetische merkers - moleculaire merkers - bio-informatica - genomica - plant-microbe interacties - solanum tuberosum - potatoes - plant breeding - plant pathogenic fungi - phytophthora infestans - microsatellites - populations - disease resistance - genetic markers - molecular markers - bioinformatics - genomics - plant-microbe interactions

    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-19th century, P. infestans attacked the European potato fields and this resulted in a widespread famine in Ireland and other parts of Europe. Late blight remains the most important pathogen to potato and causes a yearly multi-billion US dollar loss globally. In Europe and North America, late blight control heavily relies on the use of chemicals, which is hardly affordable to farmers in developing countries and also raises considerable environmental concerns in the developed countries.
    The structure of P. infestans populations can change quickly by migration, sexual recombination and sub-clonal variation. Migration and the reconvening of the two mating types considerably raised the level of genetic diversity in the global P. infestans population, leading to a more variable population with a presumed higher level of adaptability as compared to the previously, purely asexually, reproducing population. How can the P. infestans population efficiently be monitored with such diverse genotypes? A high-throughput, high-resolution and easy-handled set of markers would be favorable for this purpose. Few genetic markers, if any, have found such widespread use as SSRs. Sequencing allows the identification of large numbers of microsatellites by bioinformatics. So far, however, only a limited number of informative microsatellite loci had been described for P. infestans and none have been mapped. This thesis first describes the development and mapping of SSR markers in P. infestans and integration with other SSRs to generate a multiplex SSR set and its application in the population analysis of P. infestans from four countries are described with the developed multiplex SSRs. Finally, the use of this knowledge in resistance breeding of potato is shortly indicated and discussed.
    Chapter 1 describes the historic population changes of P. infestans at the global level and the current population trends. It summarizes microsatellite as favorite molecular markers for studying pathogen population diversity and assesses monitoring of population dynamics in more detail for resistance breeding in potato.
    The selection and identification of new SSR markers is presented in Chapter 2. From EST and genomic sequences from P. infestans we identified 300 non-redundant SSR loci by a bioinformatic screening pipeline. Based on the robustness, level of polymorphism and map position eight SSR markers were selected, which were assembled in two multiplex PCR sets and labeled with two different fluorescent dyes to allow scoring after single capillary electrophoresis.
    This successful multiplex SSR approach encouraged the development of fast, accurate and high-throughput genotyping, in an one-step multiplex PCR method to facilitate worldwide screening of P. infestans populations. Published SSRs and the 8 new SSRs were integrated. All these SSR markers were re-evaluated and the 12 most informative SSRs were selected to set up a standard set for global application (Chapter 3). The 12-plex SSRs are distributed over different chromosomes, significantly increasing the resolution of genotyping compared to the previous set of 8 SSRs. The 12-plex SSRs were integrated to one-step fluorescence-based multiplex reaction, which plays a key role to facilitate highly paralleled genotyping and efficient dissection of the more complex P. infestans populations. This multiplex PCR for P. infestans populations is (i) simple, as only one PCR is needed to perform multi-locus typing with twelve markers; (ii) rapid, as the genotyping results can be available in 1 day; and (iii) reproducible and adapted to different laboratories. The genotyping data from different geographic populations were submitted to the Euroblight database. With the same SSR set and the bin set, a comparable global database can easily be achieved.
    As indicated earlier, more recent analyses of P. infestans populations highlight the appearance of many new genotypes via migration and/or sexual recombination. To practice the newly developed 12-plex SSR set and dissect the current population structure, several P. infestans populations from 4 different continents were selected for analysis. These include Chinese (Chapter 4), Dutch (Chapter 5), Ecuadorian (Chapter 6) and Tunisian (Chapter 7) populations.
    China has become the largest potato producing country not only for potato cultivation area but also in Megaton potato production. Interprovincial trade of consumption and seed potatoes is very important and frequent in China. Although both, the A1 and A2 mating types are found in China, to this date, no evidence of an active sexual cycle based on changes in allele frequency was found. With the ten SSRs, a large genotypic survey of in nation-wide collection of 228 P. infestans isolates was performed (Chapter 4). One of the three dominant clonal lineages CN-04 (A2) in this Chinese population was genetically similar to a major clonal lineage identified in Europe, called “Blue_13” with A2 mating type. It was not possible to critically assess the origin of this clonal lineage. This study is the first report of “Blue_13” outside Europe. The virulence spectrum of selected Chinese P. infestans isolates showed seven different virulence spectra varying from 3 to 10 differentials. The CN04 genotypes were identified as more aggressive and more virulent genotypes, one of whom had the full virulence pattern after using the potato differential set. Within the Chinese P. infestans population, the genotypes strongly clustered according to their six sampling provinces, which seems not to be influenced by the frequent interprovincial trading activities of seed potatoes. The mating type ratio and the SSR allele frequencies indicate that in China the contribution of the sexual cycle to P. infestans on population dynamics is minimal. It was concluded that the migration through asexual propagules and the generation of sub-clonal variation are the dominant driving factors behind the Chinese P. infestans population structure.
    The Netherlands has a long history of population studies on local P. infestans isolates and a substantial amount of commercial potato varieties growing in the field. One decade (2000-2009) of isolate sampling in 5 different regions provided the basis for a good understanding of the population dynamics in the Netherlands (Chapter 5). The surveyed population revealed the presence of several clonal lineages and a group of sexual progenies. The major clonal lineage with A2 mating type is known as “Blue_13”, but also two distinct clonal lineages with A1 mating type in this study have been identified. This survey witnesses that the Dutch population was undergoing dramatic changes in the ten years under study. The most notable change was the emergence and spread of A2 mating type strain “Blue_13”. The results emphasize the importance of the sexual cycle in generating genetic diversity and the importance of the asexual cycle as the propagation- and dispersal mechanism for successful genotypes. In addition to the neutral SSR markers a molecular marker for the virulence of isolates on potato lines that contain the Rpi-blb1 R-gene has been developed. Using this Avr-blb1 marker and the corresponding virulence assay we report, for the first time, the presence of Rpi-blb1 breaker isolates in the Netherlands even before a Rpi-blb1 containing resistant variety was introduced. The 12 breaker isolates only occurred in sexual progeny. So far the asexual spread of such virulent isolates has been limited because of the absence of Rpi-blb1 containing varieties in the field.
    Remarkably, on the other end of the world in the Andes, the region of potato origin, the situation is far less complex as far as P. infestans is concerned. There are more than 400 potato landraces in Ecuador and the planting habit by local farmers by traditional cultivation at small scale in the highlands is different from potato cultivation in other potato countries in North America or Europe (Chapter 6). Phytophthora isolates in Ecuador belong to two closely related species, P. infestans (on potato and tomato) and P. andina (on non-tuber bearing host), but SSR analysis of 66 isolates indicated that the two species are separated in two clearly distinguished genetic groups. Two ancient clonal lineages of P. infestans appeared to be dominant in Ecuador one is found only on tomato the other one only on potato. Within the potato isolates, but not in the tomato isolates, there is a large sub-clonal variation caused by (partial) polyploidization and loss of alleles.
    In Tunisia, potato is cultivated in three to four partly overlapping seasons while tomato is grown either in greenhouses or as aerial crop in most potato producing regions. Chapter 7 revealed, among 165 isolates of five regions, the presence of a major clonal lineage (NA-01, A1 mating type, Ia mtDNA haplotype) that seems to consist of races that are relatively simple. Another highly genetic diverse group of isolates was found containing more complex races and isolates with both mating types. Season clustering indicated that at least some of the new genotypes generated by sexual reproduction overlapped between seasons and such a sexual progeny may play an important role in the next season epidemics. On tomato, mostly asexual progeny was identified with two mtDNA haplotypes but less nuclear genotypes, compared to potato. This study shows that the P. infestans population is currently changing, and the old clonal lineage is being replaced by a more complex, genetically diverse and sexually propagating population in two sub-regions in Tunisia. Despite the massive import of potato seeds from Europe, the P. infestans population in Tunisia is still clearly distinct from the European population.
    Chapter 8 discusses the application of microsatellites in monitoring genetic diversity of late blight and the potential use in resistance breeding. Monitoring of the local P. infestans population for new virulent genotypes with the differential potato set in combination with screening for effector variation, allows early detection of adaptation of certain genotypes within the P. infestans population to particular resistance genes in a specific region. This provides the possibilities to determine which broad spectrum R-genes are still useful in order to adapt the control strategy by resistance breeding to the new situation. One way of doing that is to replace the existing varieties by other varieties with stacked non-broken R-genes obtained by marker assisted selection or to add additional R-genes to existing (R-gene containing) varieties by transformation. In a transgenic or cisgenic approach, additional broad spectrum R-genes could be added by re-transformation. As we have shown, the right R-gene management strategy in potato breeding, but also in potato production, should include the direct monitoring of local pathogen populations by using the differential set and the 12-plex SSR set.

    Gensignalen voor voerefficiëntie en methaanemissie = Genomic selection to improve feed efficiency and reduce methane emission
    Haas, Y. de; Calus, M.P.L. ; Mulder, H.A. ; Haan, M.H.A. de; Bannink, A. ; Dijkstra, J. ; Windig, J.J. ; Veerkamp, R.F. - \ 2011
    Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 450) - 26
    melkveehouderij - melkkoeien - dierveredeling - fokwaarde - genetische merkers - rundveevoeding - voederwaardering - efficiëntie - dosering - methaan - emissie - dairy farming - dairy cows - animal breeding - breeding value - genetic markers - cattle feeding - feed evaluation - efficiency - dosage - methane - emission
    There are many possibilities to breed for improved feed efficiency and reduced methane emission of dairy cattle. However, the results are not that reliable yet to be implemented directly.
    Genetic dissection of drought tolerance in potato
    Anithakumari, A.M. - \ 2011
    Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Gerard van der Linden. - [S.l.] : S.n. - ISBN 9789085858379 - 152
    solanum tuberosum - aardappelen - droogteresistentie - genetische analyse - diploïdie - single nucleotide polymorphism - genetische merkers - kwantitatieve kenmerken - loci voor kwantitatief kenmerk - genetische kartering - plantenveredeling - solanum tuberosum - potatoes - drought resistance - genetic analysis - diploidy - single nucleotide polymorphism - genetic markers - quantitative traits - quantitative trait loci - genetic mapping - plant breeding

    Drought is the most important cause of crop and yield loss around the world. Breeding for

    drought tolerance is not straightforward, as drought is a complex trait. A better understanding

    of the expression of drought traits, the genes underlying the traits and the way these genes

    interact will significantly increase the success of breeding for drought tolerance.

    Potato is an important food crop, yet it is relatively susceptible to drought. As a first step

    towards identifying the genetic basis for drought tolerance in potato, we make use of diploid

    potato populations that have been genetically well characterized (CxE, SHxRH). The CxE

    population was extensively evaluated for drought tolerance in vitro and for two successive

    years (2008, 2009) under greenhouse conditions and the data were used for QTL mapping.

    For optimal QTL mapping, we expanded the CxE and SHxRH genetic maps with 499 SNP

    markers (two arrays 384 and 768SNP arrays respectively, enriched for putative stress

    tolerance candidate genes). The SNPs were discovered in public EST databases using

    QualitySNP software and detected with the Illumina GoldenGate assay. About 300 SNPs

    served as bridge markers between the CxE and SHxRH maps. This will enable us to make use

    of the extensive genetic and sequence information of the SHxRH population and the RH

    genome sequence. With the availability of the potato genome sequence of the doubled

    monoploid DM1-3 516R44 (DM) (, it was possible to further

    examine the SNP marker loci for paralogs and intron spanning sequences. In total 732 SNP

    marker loci were found to be unique in the potato genome sequence. Many of these SNP

    markers not only served as landmarks on the genetic map but may also as putative genes

    underlying quantitative traits. In addition the validated SNP markers are now utilized as

    anchors in the potato physical map.

    We investigated the possibility of screening potato for relevant drought traits in in vitro

    cultures and evaluated the CxE population for the response to PEG-induced water deficit

    stress and recovery potential after stress. Significant genetic variation was observed for the

    response to drought and for recovery potential. Several shoot and root growth traits were

    measured. In this study the genetic variation and heritability estimates were high to very high

    for the measured traits under control and recovery condition. In total 23 QTLs were detected

    in plants under control, stress and recovery treatments. Interesting putative candidate genes

    that may underly stress response QTLs were identified.

    The drought tolerance evaluation of the CxE population in pots in the greenhouse included

    traits like leaf Relative Water Content, δ13C as a measure of Water Use Efficiency,

    Chlorophyll Fluorescence, Chlorophyll Content, shoot and root biomass and tuber yield. The

    progeny displayed a wide contrast for drought tolerance, with individuals surviving and

    recovering completely after 3 weeks of drought, and others completely wilted beyond

    recovery. Most of the traits had high heritabilities. QTLs effective in multiple treatments and

    years were detected for tuber number, tuber weight, plant height, shoot fresh and dry weight.

    Other QTLs were found to be dependent on the environment: QTL x Environment interaction

    was found for leaf d13C under drought conditions and we speculate that the function of δ13C

    was genetically split into a stomatal and non-stomatal component.

    Many of the QTLs for growth traits measured both in the greenhouse and in in vitro cultures

    were specific to either of the growth conditions. Yet significant QTLs that were detected for

    plant height, shoot dry weight, fresh biomass for plants grown in the greenhouse were also

    found when the population was grown in vitro. These QTLs may be less affected by

    environmental influences, and we may therefore expect that some of these QTLs will be

    relevant under field conditions as well. This also suggests that the in vitro system may be used

    for preliminary selection in breeding programmes for specific performance-related traits.

    The genetic architecture of transcript-level variation for drought response was captured in the

    potato population CxE and mapped as expression QTLs (eQTLs). We anchored the

    differentially expressed genes to the genome sequence of potato, and this enabled us to

    determine whether the transcription of these genes (the eQTLs) is in cis or in trans regulated.

    The combined use of genome-wide detection of eQTLs in combination with genome sequence

    information for gene location has enables us to detect regulatory hot spots for drought

    response in the CxE population. Based on gene ontology annotation, a number of eQTLs were

    detected for genes known to be involved in drought signal transduction and drought-induced

    transcriptional regulation, and for redox genes. Examination of co-localization of eQTLs and

    phenotypic QTLs identified several interesting eQTLs for genes that may be involved in

    specifying the phenotypic QTL, for instance, the eQTL for a gene that was annotated with a

    putative function in the photosystem II light reaction colocalized with trait QTL of

    chlorophyll florescence (Fv/Fm) on chromosome 1, along with other genes involved in 139

    drought response such as heat shock proteins and signaling proteins with known induced

    expression under stress conditions. On chromosome 10, eQTLs for genes involved in carbon

    partitioning, signaling receptor kinases, transcription factors and hormone and lipid

    metabolism were colocalized with phenotypic QTLs for chlorophyll content and stomatal

    component of δ13C. As we have only touched the surface of the information contained in the

    transcriptome dataset combined with the phenotyping data, continued efforts on mining the

    dataset and in depth analysis will most likely reveal more putative candidate genes for QTL


    This thesis constitutes the first knowledge of in vitro and greenhouse screening for drought

    tolerance in potato and has led to the description of important traits for screening and

    selection in breeding for drought tolerance. The QTLs identified in this thesis may be

    interesting targets for potato breeding to improve drought tolerance of the potato crop.

    Furthermore, our results illustrate the power of application of integrated genetic and genomics

    approaches to unravel the molecular components underlying abiotic stress tolerance traits.

    Genomic selection in dairy cattle
    Roos, A.P.W. de - \ 2011
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): B.J. Hayes; Roel Veerkamp. - [S.l. : S.n. - ISBN 9789085858539 - 184
    melkvee - selectief fokken - genetische verbetering - veredelingsprogramma's - fokwaarde - genetische merkers - haplotypen - voorspelling - dierveredeling - genexpressieanalyse - genotyping - dairy cattle - selective breeding - genetic improvement - breeding programmes - breeding value - genetic markers - haplotypes - prediction - animal breeding - genomics - genotyping
    The objectives of this Ph.D. thesis were (1) to optimise genomic selection in dairy cattle with respect to the accuracy of predicting total genetic merit and (2) to optimise a dairy cattle breeding program using genomic selection. The study was performed using a combination of real data sets and simulations. Real data sets consisted of dense marker genotypes of progeny tested bulls that had accurate phenotypes derived from their daughters’ performance records. Through cross-validation, the reliability of genomic predictions was assessed for Bayesian models that fitted either marker genotypes, ancestral haplotypes or genomic relationships. Haplotype-based methods gave the most reliable predictions and provided opportunities to limit computer requirements for analysing very large data sets. The reliability of genomic predictions across breeds was studied using simulated marker data. The data was simulated such that it showed the same the patterns of linkage disequilibrium (LD) as observed within and between Holstein, Angus, and Jersey cattle from the Netherlands, Australia, and New Zealand. It was concluded that the most reliable genomic predictions can be obtained when the reference populations of each breed are combined, whereas for diverged breeds at least 300,000 markers are required to ensure that the LD between markers and QTL persists across breeds. Using a simulated genomic selection scheme, it was shown that the annual rate of genetic gain in dairy cattle may double compared to current progeny test schemes, without compromising the rate of inbreeding. To achieve such a high rate of genetic gain, the generation interval needs to be reduced significantly, as young bulls will prove to be superior to progeny tested bulls. It is expected that in the near future many animals will be genotyped and very high marker densities will be inferred by imputation techniques. This may result in genomic predictions that are persistent across breeds and generations. Large scale genotyping of cows may enable genomic selection for novel traits and the integration of genomic information in herd management processes.
    Botrytis-soorten op bloembolgewassen
    Staats, M. ; Kan, J. van - \ 2010
    Gewasbescherming 41 (2010)5. - ISSN 0166-6495 - p. 248 - 249.
    plantenziekten - plantenziekteverwekkende schimmels - botrytis - genetische merkers - bloembollen - verwantschap - waardplanten - voortplanting - genetische diversiteit - plant diseases - plant pathogenic fungi - botrytis - genetic markers - ornamental bulbs - kinship - host plants - reproduction - genetic diversity
    De onderlinge verwantschap en populatie-opbouw van Botrytis-soorten is onderzocht met moleculaire merkers. Er bleek geen relatie te bestaan tussen de verwantschap van de schimmels en hun waardplantsoort. Botrytis-soorten die ‘vuur’ kunnen veroorzaken in bolgewassen planten zich verschillend voort: Botrytis elliptica seksueel en Botrytis tulipae aseksueel. Twee eiwitten die in alle Botrytis-soorten voorkomen bleken in Botrytis elliptica niet essentieel te zijn voor virulentie op lelie.
    De genetica van grauwe schimmelresistentie in tomaat
    Finkers, H.J. - \ 2010
    Gewasbescherming 41 (2010)5. - ISSN 0166-6495 - p. 250 - 252.
    tomaten - solanum lycopersicum - botrytis cinerea - genetisch bepaalde resistentie - wilde verwanten - loci voor kwantitatief kenmerk - genetische merkers - resistentieveredeling - tomatoes - solanum lycopersicum - botrytis cinerea - genetic resistance - wild relatives - quantitative trait loci - genetic markers - resistance breeding
    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.
    The genetics of the metabolome in Brassica rapa
    Pino del Carpio, D. - \ 2010
    Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Guusje Bonnema. - [S.l. : S.n. - ISBN 9789085857211 - 168
    brassica campestris - koolsoorten - metabolieten - genexpressie - genetische regulatie - genotypische variatie - genetische diversiteit - genetische merkers - selectiemethoden - metabolomica - brassica campestris - cabbages - metabolites - gene expression - genetic regulation - genetic variance - genetic diversity - genetic markers - selection methods - metabolomics
    In this thesis the metabolic variation in Brassica rapa is described based on results of metabolic profiling of a core collection of 168 accessions representing the different crop types and geographical origin and a Doubled Haploid population. In Chapter 2 we describe the genetic and phenotypic variation of this core collection to explore the possibility of following association mapping methods to identify genes involved in metabolic regulation. We explored through a genome wide and candidate gene approach different association mapping methods in a core collection in Chapters 3 and 4 respectively and in Chapter 5 we combined the QTL analysis of targeted and untargeted metabolites profiled through LC-MS with expression QTLs following a genetical genomics approach aiming to detect genes underlying the metabolite QTL. The genetic diversity evaluated through the screening of AFLP and SSR markers was correlated with classification of accessions using morphological and metabolic trait values. The relationship between accessions in groups was compared using hierarchical clustering and the STRUCTURE program. Using Random Forests classification a set of metabolites was selected that differentiated the different sub groups as determined by STRUCTURE (Chapter 2). Based on the classification into subpopulations using the STRUCTURE program we included the subpopulations as a correction term in our statistical model for association studies (Chapter 3). Additionally, because of the increasing amount of data that will be soon available through sequencing technology we tested the use of Random Forests in the search for marker-trait association for the isoprenoids pathway. Using the results obtained with the linear models as implemented in TASSEL and the results obtained in Random Forests we found a set of 16 significant markers with potential use for marker assisted selection in breeding for several isoprenoidsThe determination of map positions through synteny prediction and genetic mapping of a group of genes from the glucosinolate pathway lead us to identify Myb28 and MAM as candidate genes mapping under a previously detected major QTL for glucosinolates We followed an association mapping approach to investigate their role in the variation in glucosinolates in the core collection by profiling 37 SSR markers, which included markers linked to these candidate genes and markers distributed along different positions in linkage group A03 (Chapter 4). Interestingly, not only MAM and Myb28, but the AOP and GS-OH genes involved in side chain modification and Myb29 in transcriptional regulation were also associated with glucosinolate levels. A genetical genomics approach was followed to identify candidate genes for variation inmetabolites of six biosynthetic pathways: carotenoids, tocopherols, folates, glucosinolates, flavonoids and phenylpropanoids, based on the co-localization analysis and comparison between metabolic (m)QTLs and expression (e)QTLs (Chapter 5). A Doubled Haploid (DH) population was profiled for metabolite content and variation through targeted and LC-MS untargeted approaches. Additionally, the same population was profiled for transcript variation with a newly developed 105K Cogenics array assembled using mainly EST sequences from three species: B. napus, B. rapa and B. oleracea. Co-localization of eQTLs and mQTLs for several isoprenoids (tocopherols and carotenoids) and glucosinolates lead us to the identification of candidate genes for these pathways. However, further work is needed to identify the gene or genes underlying a major cluster of QTLs for 112 centrotypes derived from the LC-MS untargeted data. The results obtained through this combined approach and considerations that need to be taken into account when performing these types of studies with regard to identification of paralogues and the use of a multi Brassica species microarray for transcript profiling in Brassica rapa are discussed.In the final Chapter, the combined use of core collections encompassing the genetic diversity within B. rapa and biparental DH populations to unravel the genetic regulation of the metabolome are discussed.
    Genetic analysis of protein composition of bovine milk
    Schopen, G.C.B. - \ 2010
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Marleen Visker; Henk Bovenhuis. - [S.l. : S.n. - ISBN 9789085856450 - 189
    zwartbont - melkeiwitten - melkvee - dierveredeling - genetische merkers - fokwaarde - genetische variatie - genexpressieanalyse - holstein-friesian - milk proteins - dairy cattle - animal breeding - genetic markers - breeding value - genetic variation - genomics
    This thesis is part of the Dutch Milk Genomics Initiative, and the general aim was to obtain more insight into the genetic background of bovine milk protein composition. Morning milk samples from roughly 2000 cows were analyzed for the six major milk proteins (αS1-casein, αS2-casein, β-casein, κ-casein, α-lactalbumin and β-lactoglobulin) using capillary zone electrophoresis.
    The estimated genetic parameters for milk protein composition showed that there was considerable genetic variation for milk protein composition and that the genetic correlations among the six major milk proteins were low. There was a strong negative genetic correlation between β-lactoglobulin and total casein in milk. The presence of genetic variation justified the performance of in-depth genetic analyses such as linkage and association mapping. A linkage study was performed to screen the whole bovine genome to identify chromosomal regions affecting milk protein composition. This study resulted in ten chromosomal regions, of which regions on BTA6, 11 and 14 showed the largest effect on milk protein composition. The confidence intervals of these regions were large, in general. Therefore, an association study was performed to narrow down these chromosomal regions and to detect new chromosomal regions affecting milk protein composition. The association study resulted in four main regions on BTA5, 6, 11 and 14, and also new regions were detected. These new regions may, in addition to the four main regions, play a role in the genetic regulation of milk protein synthesis.
    The milk protein composition is important for technological properties of milk. An increase in casein index is preferable for the cheese production. Therefore, four scenario’s, to increase casein index in milk, were discussed. The first scenario has been termed genetic differentiation, the second scenario was genetic selection based on estimated breeding values, the third scenario was genetic selection based on genotypes, and the last scenario was genomic selection. These four scenarios illustrated that there are opportunities to utilize genetic variation in milk protein composition.

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