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Staff Publications

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TIVO-Traceerbaarheid van Individuele Varkens in de Organische keten. Een brug naar kennisdeling - Eindrapport
Wognum, P.M. ; Erp, T. van - \ 2013
TIVO - 51
rfid - dna-fingerprinting - varkens - varkenshouderij - naspeurbaarheid - duurzame veehouderij - biologische voedingsmiddelen - varkensvlees - biologische landbouw - dna fingerprinting - pigs - pig farming - traceability - sustainable animal husbandry - organic foods - pigmeat - organic farming
In dit rapport worden de resultaten van het TIVO-project (Traceerbaarheid van Individuele Varkens in de Organische keten) gepresenteerd. De resultaten worden geplaatst in de context van nationale en internationale ontwikkelingen. De resultaten worden in twee delen besproken: DNA-profilering en RFID ten behoeve van individuele elektronische identificatie. Beide trajecten waren gericht op het verbeteren van de traceerbaarheid van biologisch varkensvlees en aantonen van authenticiteit. Een tweede prioriteit was het verbeteren van informatie-uitwisseling in de toeleverketen, zodat inzicht mogelijk wordt in de prestaties van producten en processen en verbeteringen kunnen worden aangebracht.
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 - cucumbers - population genetics - gene banks - dna fingerprinting - 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.
On some surprising statistical properties of a DNA fingerprinting technique called AFLP
Gort, G. - \ 2010
University. Promotor(en): A. Stein; Fred van Eeuwijk. - [S.l. : S.n. - ISBN 9789085855378 - 154
planten - statistische analyse - dna-fingerprinting - genomen - biometrie - moleculaire genetica - dna - aflp - biostatistiek - toegepaste statistiek - plants - statistical analysis - dna fingerprinting - genomes - biometry - molecular genetics - amplified fragment length polymorphism - biostatistics - applied statistics
AFLP is a widely used DNA fingerprinting technique, resulting in band absence - presence profiles, like a bar code. Bands represent DNA fragments, sampled from the genome of an individual plant or other organism. The DNA fragments travel through a lane of an electrophoretic gel or microcapillary system, and are separated by length, with shorter fragments traveling further. Multiple individuals are simultaneously fingerprinted on a gel. One of the applications of AFLP is the estimation of genetic similarity between individuals, e.g. in diversity and phylogenetic studies. In that case, profiles of two individuals are compared, and the fraction of shared (comigrating) bands is calculated, e.g. using the Dice similarity coefficient. Two comigrating bands may share the same fragment, but band sharing could also be due to chance, if two equally sized, but different fragments are amplified. This is called homoplasy. Homoplasy biases similarity coefficients. Homoplasy could also occur within a lane, if two different fragments of equal length are amplified, resulting in a single band. We call this collision. The main objective of this thesis is the study of collision and homoplasy in AFLP. The length distribution of AFLP fragments plays an important role. This distribution is highly skewed with more abundant short fragments. By simulation the expected similarity for unrelated genotypes is calculated. As much as 40% of the bands may be shared by chance in case of profiles with 120 bands. The collision problem is analogous to the birthday problem, which has a surprising solution. The collision problem is even more extreme, making it even more surprising. Profiles with only 19 bands contain collision(s) with probability 1/2. These findings have consequences for practice. In some cases it is better to prevent the occurrence of collisions by decreasing the number of bands, in other cases a correction for homoplasy and collision is preferred. Modified similarity coefficients are proposed, that estimate the fraction of homologous fragments, correcting for homoplasy and collision. Partially related to homoplasy and collision, we study the codominant scoring of AFLP in association panels. Examples of AFLP in lettuce and tomato serve as illustrations.
Construction and use of a physical map of potato
Borm, T.J.A. - \ 2008
University. Promotor(en): Richard Visser, co-promotor(en): Herman van Eck. - S.l. : S.n. - ISBN 9789085852377 - 139
solanum tuberosum - moleculaire kartering - genetische kartering - genomen - dna-fingerprinting - dna-bibliotheken - genetische merkers - maximale aannemelijkheid - moleculaire merkers - marker assisted breeding - aflp - molecular mapping - genetic mapping - genomes - dna fingerprinting - dna libraries - genetic markers - maximum likelihood - molecular markers - amplified fragment length polymorphism
Feeding the growing world population is one of the biggest challenges for the 21st century.
Potato, being the fourth crop in the human diet, after maize, wheat and rice, plays an
important role in this respect. Like other crops, potato is exposed to a range of potentially
yield-reducing factors: Pathogens, a (possibly changing) bad climate and averse soil
conditions. Research into the response of potato to these influences, often determined by
hereditary factors, is necessary to meet a growing demand for potatoes. A map of
genetically determined properties is crucial for this research. Several techniques are
available to produce maps – each with it's own merits and demerits, resulting in maps of
different qualities and with different resolutions. Two often used mapping techniques are
genetic mapping, where the inheritance of multiple traits (“markers”) is studied in
offspring using statistical analysis and the markers ordered accordingly, and physical
mapping on the basis of “Bacterial Artificial Chromosome” (BAC) libraries. BAC
libraries consist of a large number of individual bacterial strains (BAC clones), each
containing a randomly sampled section of DNA of the organism being studied. By
comparing individual BAC clones with each other, finding out where the donor organism's
(the organism being studied) DNA sections overlap, the BAC clones can be ordered into
groups or “contigs”. Comparison is often done on the basis of so called fingerprints – a
pattern consisting of DNA fragments of different lengths, resembling a bar-code pattern. A
similarity in fingerprint patterns between two BAC clones indicates that the BAC clones
contain similar (overlapping) sections of the donor organism's DNA. Recently an ultra
dense genetic map has been published, containing more than 10,000 markers produced
using “Amplified Fragment Length Polymorphism” (AFLPTM) marker technology. The
integrated physical and genetic map that is the subject of this thesis extends this genetic
map, and is in itself the starting point for determining the detailed DNA sequence of
potato, as is currently being undertaken by an international scientific collaboration within
the Potato Genome Sequencing Consortium (PGSC, http://www.potatogenome.net).
First step in creating this integrated physical and genetic map was creation, fingerprinting
and characterization of a BAC library, as described in chapter two. BACs were
individually fingerprinted using an AFLP based protocol, and (amongst others) these
AFLP BAC-fingerprints were compared to a theoretical model of the distribution of
fragment lengths in AFLP fingerprints to determine if fingerprinting was successful.
Correction and refinement of some of the mapping algorithms that were used to create the
genetic map are discussed in chapters three and four, resulting in refined genetic map
locations for the AFLP markers and the capability to process marker scores containing
arbitrary types of scoring ambiguities while conserving all available information. An
extension to the basic principle offers the possibility to also map AFLP markers derived
from different chromosomes that are indistinguishable on the basis of their AFLP
fragment length alone.
In chapter five, systematic differences in AFLP BAC fingerprints are discussed that are
caused by the use of different machines for capillary electrophoresis, by the use of
different fluorescent DNA labels and by different capillary position. These systematic
differences are (partially) corrected by using the (abundant) AFLP fingerprints of BAC
clones containing (part of) the potato chloroplast genome as a reference sample.
By ordering the AFLP fingerprints of individual BAC clones on the basis of fingerprint
similarity, a physical map is produced that is integrated with the genetic map using a
novel, ultra efficient, procedure described in chapter six. This procedure, “AFLP contig
matching” uses intricate experimental design and combinatorial analysis to obtain an
integrated physical and genetic map with the least amount of effort.
Het gebruik van DNA-barcodes voor de routinematige analyse van nematodengemeenschappen als indicator voor biologische bodemkwaliteit
Helder, J. ; Elsen, S.J.J. van den; Mooijman, P.J.W. ; Rybarczyk-Mydlowska, K.D. ; Pomp, H. ; Holterman, M.H.M. ; Megen, H.H.B. van; Bongers, A.M.T. ; Bakker, J. - \ 2008
Gewasbescherming 39 (2008)Suppl.. - ISSN 0166-6495 - p. 8 S - 9 S.
bodembeheer - gewasbescherming - nematoda - nematodenbestrijding - monitoring - dna-fingerprinting - analytische methoden - bodemkwaliteit - soil management - plant protection - nematode control - dna fingerprinting - analytical methods - soil quality
Genetische identificatie en detectie van Erwinia carotovora subsp. carotovora (Ecc)
Speksnijder, A.G.C.L. ; Wolf, J.M. van der; Doorn, J. van - \ 2008
pectobacterium carotovorum subsp. carotovorum - plantenziekteverwekkende bacteriën - bacterieziekten - gewasbescherming - genetische merkers - aardappelen - detectie - dna-fingerprinting - plant pathogenic bacteria - bacterial diseases - plant protection - genetic markers - potatoes - detection - dna fingerprinting
Met genetische fingerprint-technieken wordt gezocht naar moleculaire merkers. Op basis van deze merkers kunnen specifieke moleculaire toetsen ontwikkeld worden voor keuringsdiensten en onderzoeksinstellingen. De ontwikkeling van een detectiestrategie van Ecc heeft geleid tot positieve identificatie van bacteriezieke planten waarin voorheen geen Erwinia gedetecteerd kon worden
Makkelijker volgen van het Phytophthora infestans
Kessel, G.J.T. ; Lee, T. van der - \ 2007
solanum tuberosum - aardappelen - phytophthora infestans - genetische merkers - dna-fingerprinting - potatoes - genetic markers - dna fingerprinting
Onderzoek naar het met behulp van bio-informatica opsporen van SSR-merkers in het P. infestans-genoom, het ontwerpen van primers voor deze SSR-merkers, het op de genetische koppelingskaart positioneren van de meest informatieve merkers en deze samenbrengen in een multiplexset
Genetic diversity analysis using lowly polymorphic dominant markers: The example of AFLP in pigs.
Foulley, J.L. ; Schriek, M. van; Groenen, M.A.M. ; Heuven, H.C.M. - \ 2006
Journal of Heredity 97 (2006)3. - ISSN 0022-1503 - p. 244 - 252.
dierveredeling - varkens - varkensrassen - rasverschillen - genetische diversiteit - genetische afstand - genetische analyse - genetische merkers - dna-fingerprinting - genfrequentie - dna-vermenigvuldiging - genetische polymorfie - genetische bronnen van diersoorten - aflp - animal breeding - pigs - pig breeds - breed differences - genetic diversity - genetic distance - genetic analysis - genetic markers - dna fingerprinting - gene frequency - dna amplification - genetic polymorphism - animal genetic resources - amplified fragment length polymorphism - population diversity - selective neutrality - distance - frequency
DNA markers are commonly used for large-scale evaluation of genetic diversity in farm animals, as a component of the management of animal genetic resources. AFLP markers are useful for such studies as they can be generated relatively simply; however, challenges in analysis arise from their dominant scoring and the low level of polymorphism of some markers. This paper describes the results obtained with a set of AFLP markers in a study of 59 pig breeds. AFLP fingerprints were generated using four primer combinations (PC), yielding a total of 148 marker loci, and average harmonic mean of breed sample size was 37.3. The average proportion of monomorphic populations was 63% (range across loci: 3%-98%). The moment-based method of Hill and Weir (2004, Mol Ecol 13:895-908) was applied to estimate gene frequencies, gene diversity (F ST), and Reynolds genetic distances. A highly significant average FST of 0.11 was estimated, together with highly significant PC effects on gene diversity. The variance of FST across loci also significantly exceeded the variance expected under the hypothesis of AFLP neutrality, strongly suggesting the sensitivity of AFLP to selection or other forces. Moment estimates were compared to estimates derived from the square root estimation of gene frequency, as currently applied for dominant markers, and the biases incurred in the latter method were evaluated. The paper discusses the hypotheses underlying the moment estimations and various issues relating to the biallelic, dominant, and lowly polymorphic nature of this set of AFLP markers and to their use as compared to microsatellites for measuring genetic diversity
Indicatie genetische variatie hoofdrassen paprika ten behoeve van verbetering uniformiteit : verslag van een pilot-studie
Smulders, M.J.M. ; Westende, W.P.C. van 't; Schoot, J.R. van der; Vosman, B. - \ 2004
Wageningen : Plant Research International - 11
capsicum annuum - plantenvermeerdering - genetische variatie - dna-fingerprinting - weefselkweek - glastuinbouw - vruchtgroenten - propagation - genetic variation - dna fingerprinting - tissue culture - greenhouse horticulture - fruit vegetables
Morfologisch vertonen paprikarassen bij telers soms een gebrek aan uniformiteit. Dit kan een effect zijn van milieuomstandigheden, maar zou (deels) het gevolg kunnen zijn van genetische variatie in de rassen. In het laatste geval zou men de uniformiteit binnen een paprika-ras kunnen verhogen door weefselkweek. Doel van deze korte studie was om vast te stellen of genetische variatie kan worden vastgesteld in paprikarassen met behulp van DNA fingerprint-technieken. Het is een pilot studie, met kleine aantallen bemonsterde planten, zodat het percentage afwijkende planten niet exact kan worden bepaald.
Stammen identificeren met vingerafdrukken
Hendrickx, P.M. ; Sonnenberg, A.S.M. - \ 2003
Paddestoelen : onafhankelijk vakblad voor Nederland en België 2003 (2003)17. - ISSN 1380-359X - p. 9 - 9.
eetbare paddestoelen - agaricus - dna-fingerprinting - databanken - soortendiversiteit - verzamelingen - edible fungi - dna fingerprinting - databases - species diversity - collections
PPO-databank met stammencollectie wordt middels genetische fingerprint geidentificeert op soortechtheid
Toets spoort mozaiekvirus in amaryllis beter op: bolbloemen - Hippeastrum.
Derks, A.F.L.M. - \ 2002
Vakblad voor de Bloemisterij 57 (2002)38. - ISSN 0042-2223 - p. 56 - 57.
potplanten - snijbloemen - amaryllis - hippeastrum - plantenvirussen - plantenziekten - diagnostische technieken - dna - dna-fingerprinting - bloembollen - biotechnologie - glastuinbouw - ornamental bulbs - pot plants - cut flowers - plant viruses - plant diseases - diagnostic techniques - dna fingerprinting - biotechnology - greenhouse horticulture
De nieuwe PCR-toets (Polymerase Chain Reaction) is gevoeliger voor het aantonen van virussen in amaryllis dan de conventionele ELISA-toets. De nieuwe toets, het aantal virussen en de virusziektebeelden komen uitgebreid aan de orde in dit artikel
Zooming in on the lettuce genome: species relationships in Lactuca s.l., inferred from chromosomal and molecular characters
Koopman, W.J.M. - \ 2002
University. Promotor(en): Jos van der Maesen; Evert Jacobsen; Ronald van den Berg. - S.l. : s.n.] - ISBN 9789058086761 - 196 p.
lactuca - asteraceae - fylogenie - fylogenetica - klassering volgens erfelijke eigenschappen - herbaria - chromosome banding - dna - dna-fingerprinting - genomen - karyotypen - plantenveredeling - phylogeny - phylogenetics - cladistics - dna fingerprinting - genomes - karyotypes - plant breeding
<em><p>Lactuca</em> sativa (cultivated lettuce) is the world's most important leafy salad vegetable. Apart from <em>L. sativa</em> , the genus <em>Lactuca</em> contains ca. 75 wild species, potentially useful to improve, for example, taste, texture, and disease resistance of cultivated lettuce. The wild species <em>L. serriola</em> (Prickly Lettuce), <em>L. saligna</em> (Least Lettuce), and <em>L. virosa</em> (Great Lettuce) are commonly used for lettuce improvement.</p><p> In preliminary experiments, we established that there is a close connection between evolutionary distances of wild species relative to cultivated lettuce, and their position in the lettuce gene pool (i.e., the possibility to hybridize them with cultivated lettuce). In the present thesis, we established evolutionary relationships among <em>L. sativa</em> and 22 wild species in order to predict this position.</p><p> We determined that <em>L. sativa</em> , <em>L. serriola</em> , <em>L. dregeana</em> , and <em>L. altaica</em> are closely related, and can be regarded as conspecific. <em>L. aculeata</em> is closely related to them, but is a distinct species. <em>L. serriola</em> , <em>L. dregeana</em> , <em>L. altaica,</em> and <em>L. aculeata</em> occupy the primary gene pool of cultivated lettuce. They can be easily hybridized with cultivated lettuce, and thus are readily accessible gene sources for lettuce improvement. <em>L. saligna</em> and <em>L. virosa</em> are less closely related to <em>L. sativa</em> , and occupy the secondary gene pool (i.e. hybridization with <em>L. sativa</em> is possible, but difficult). All primary and secondary gene-pool species can be classified in <em>Lactuca</em> sect. <em>Lactuca</em> subsect. <em>Lactuca</em> . We found that all tertiary gene-pool species (hybridization with <em>L. sativa</em> only possible with radical techniques) can be classified in the remaining sections of the genus <em>Lactuca</em> (sections <em>Phaenixopus</em> , <em>Mulgedium,</em> and <em>Lactucopsis</em> ). These sections are the most promising sources of wild species for future improvement of cultivated lettuce. In the experiments, the tertiary gene-pool species were represented by <em>L. viminea</em> , <em>L. tatarica</em> , <em>L. sibirica</em> , and <em>L. quercina</em> . Surprisingly, the species classified in <em>Lactuca</em> sect. <em>Lactuca</em> subsect. <em>Cyanicae</em> are not evolutionary close to cultivated lettuce. They are not part of the lettuce gene pool, and should be excluded from <em>Lactuca</em> .</p><p> To determine the evolutionary relationships among <em>L. sativa</em> and its wild relatives, we examined the genomes of the species at various levels, which provided additional information on genome evolution. We established, that in general the genome sizes in the group increased during evolution, while the ratio of AT/GC nucleotides decreased. Genome complexity for species with 2C DNA amounts below 8.5 pg was similar, but species with 2C DNA amounts exceeding 8.5 pg had more complex and less similar genomes. The species from the primary gene pool share a common ancestor, but the genomes of <em>L. sativa</em> / <em>L. serriola</em> , <em>L. saligna</em> , and <em>L. virosa</em> , evolved in different directions.</p><p> The present thesis demonstrates that with the proper combination of techniques, a plant systematic study can provide both practically applicable results and fundamental evolutionary insights, thus bridging the gap between fundamental and applied research.
Biological nitrogen fixation of soybean in acid soils of Sumatra, Indonesia
Waluyo, S.H. - \ 2000
Agricultural University. Promotor(en): W.M. de Vos; L. 't Mannetje; L.T. An. - S.l. : s.n.] - ISBN 9789058082954 - 151 p.
glycine max - sojabonen - bodembiologie - stikstoffixatie - stikstofbindende bacteriën - rhizobium - bradyrhizobium - inoculatie - entstof - biochemische technieken - dna-fingerprinting - stamverschillen - stammen (biologisch) - zaadbehandeling - omhullen - zure gronden - bodemaciditeit - bekalking - sumatra - indonesië - soyabeans - soil biology - nitrogen fixation - nitrogen fixing bacteria - inoculation - inoculum - biochemical techniques - dna fingerprinting - strain differences - strains - seed treatment - pelleting - acid soils - soil acidity - liming - indonesia
<p>The aim of this study is to improve soybean cultivation in transmigration areas, especially in Sitiung, West Sumatra. However, these soils are very acid, and have a high P-fixing capacity. To reduce the amounts of fertilisers, normally 5 - 7 ton lime ha <sup>-1</sup> and 100 kg P as TSP, seed, pelleted with lime (60 kg ha <sup>-1</sup> ) and TSP (10 kg ha <sup>-1</sup> ), was introduced. In this way only 2 ton lime ha <sup>-1</sup> are required.</p><p>Soybean can fix nitrogen (BNF) in symbiosis with ( <em>Brady</em> ) <em>Rhizobium</em> bacteria. However, these acid soils in general, have low numbers of ( <em>Brady</em> ) <em>Rhizobium</em> . By inoculating the soils with ( <em>Brady</em> ) <em>Rhizobium</em> , BNF of soybean, and yield, were considerably improved.</p><p>A study was made of the indigenous ( <em>Brady</em> ) <em>Rhizobium</em> population in view of the following:</p><ul><lem>Although at the beginning the numbers may be low, by repeated soybean cultivation, the numbers will increase, and they may interfere with inoculation of effective ( <em>Brady</em> ) <em>Rhizobium</em> strains.</lem><lem>These indigenous ( <em>Brady</em> ) <em>Rhizobium</em> are adapted to local stress conditions, and they may be useful for the improvement of strains, to be used as inoculants.</lem></ul><p>Using molecular techniques, indigenous strains derived from soil samples from old soybean areas (Java) and from new soybean areas (Sumatra) were classified in more detail. Most likely <em>B. japonicum</em> is the dominant strain in Java while in Sumatra <em>B. elkanii</em> is more present. A <em>Sinorhizobium fredii</em> -like strain was isolated from one soil sample from Java.</p>
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