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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.

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Exploiting wild relatives of S. lycopersicum for quality traits
Víquez Zamora, A.M. - \ 2015
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Sjaak van Heusden; Arnaud Bovy. - Wageningen : Wageningen University - ISBN 9789462574410 - 167
solanum lycopersicum - tomaten - solanum pimpinellifolium - wilde verwanten - germplasm - kenmerken - gewaskwaliteit - genomica - genetische kartering - plantenveredeling - tomatoes - wild relatives - traits - crop quality - genomics - genetic mapping - plant breeding
The conservation and use of crop genetic resources for food security
Khoury, C.K. - \ 2015
Wageningen University. Promotor(en): Paul Struik, co-promotor(en): A. Jarvis. - Wageningen : Wageningen University - ISBN 9789462574427 - 302
genetische bronnen van plantensoorten - genetische diversiteit - germplasm - landbouwontwikkeling - klimaatadaptatie - wilde verwanten - ex-situ conservering - voedselzekerheid - plant genetic resources - genetic diversity - agricultural development - climate adaptation - wild relatives - ex situ conservation - food security - cum laude
Cum laude graduation
Among the factors hindering the conservation of crop genetic resources is a lack of essential information regarding this diversity. Questions include: (a) what is the status of diversity in our food systems, and where are the greatest vulnerabilities?, (b) where can genetic diversity be found that can be useful in increasing productivity and mitigating these vulnerabilities?, (c) is this genetic diversity available in the present and in the long term?, and (d) what steps are needed to improve the ability for researchers to access genetic resources critical for present and future crop improvement? This thesis aims to contribute to the knowledge required to answer these questions through an exploration of the need for, potential of, challenges and constraints regarding, and necessary steps to enhance the conservation and use of crop genetic diversity.
Genetic and morphological diversity of okra (Abelmoschus esculentus [L.] Moench.) genotypes and their possible relationships, with particular reference to Greek landraces
Kyriakopoulou, O.G. ; Arens, P.F.P. ; Pelgrom, K.T.B. ; Karapanos, I. ; Bebeli, P. ; Passam, H.C. - \ 2014
Scientia Horticulturae 171 (2014). - ISSN 0304-4238 - p. 58 - 70.
numerical-analysis - germplasm - aflp - collection - cultivars - stability - patterns - distance - markers - plants
Despite its high economic value in many countries (especially in developing regions of the tropics and sub-tropics), okra has received little attention with respect to its source of origin and genetic diversity, particularly at the molecular level. Phenotypic description (morphology, pod characteristics and seed germination) and AFLP (amplified fragment length polymorphism) analysis were performed on Greek and international genotypes. Whereas morphological descriptors did not separate the accessions according to their geographical origin, AFLP analysis revealed a low level (12%) of polymorphism and distinct geographical groupings. Greek germplasm separated into three distinct groups with no overlap between them on the basis of molecular markers. A higher degree of genetic heterogeneity was found (UPGMA analysis) among the accessions of the Boyiatiou group than in the Pylaias group, whereas the occurrence of some common phylogenetic characteristics made separation on the basis of morphology alone difficult. The results from AFLP markers indicate that Greek germplasm constitutes a significant pool of variation with respect to morphological parameters, pod characteristics and seed germinability. Moreover, differences in seed germination among phenotypes may relate to their geographical origin (mainland or islands).
The International Lactuca database
Treuren, R. van; Menting, F.B.J. - \ 2014
plant genetic resources, gene banks
The International Lactuca Database includes accessions of species belonging to the genus Lactuca, but also a few accessions belonging to related genera. Passport data can be searched on-line or downloaded. Characterization and evaluation data can be accessed via the downloading section. Requests for seed material from accessions included in the database should be directed to the institute that maintains the accession. An overview of the holding institutes is provided in the section "contributors". The database concentrates on passport data of all Lactuca species of germplasm collections worldwide
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.
Quantitative methods for sampling of germplasm collections : getting the best out of molecular markers when creating core collections
Odong, T.L. - \ 2012
Wageningen University. Promotor(en): Fred van Eeuwijk, co-promotor(en): Theo van Hintum; Hans Jansen. - [S.l.] : s.n. - ISBN 9789461732095 - 152
bemonsteren - germplasm - genenbanken - genetische bronnen van plantensoorten - statistiek - moleculaire merkers - statistische steekproeftechnieken - gewassen - sampling - gene banks - plant genetic resources - statistics - molecular markers - statistical sampling techniques - crops

This thesis addresses the issue of how special players (crisis entrepreneurs)
try to generate attention to a latent crisis and how government communication
can contribute to identifying and interpreting such a crisis.
In chapter 1, I show how crisis communication is an activity that is often
associated with organizations. This study takes a different view. It is based
on the concept that strategic crisis communication is used by those in
the immediate environment to achieve certain goals. In society, certain
individuals and groups can decide to oppose and denounce a given crisis.
Some of those involved often start signalling the risk of an impending
crisis before any such crisis has actually developed. In this study, I refer
to individuals who generate signals of this kind as ‘crisis entrepreneurs’.
These crisis entrepreneurs typically take the initiative when it comes to
airing their concerns about a potential crisis situation. However, such individuals
often have to deal with certain interactional problems that make it
difficult for them to raise the issue of a crisis. They have to deal with certain
‘interactional’ challenges, while running the risk that their signals will
not be picked up. For instance, they can be held responsible for raising the
problem in question. They can be accused of bearing some degree of personal
responsibility for the problem, through negligence, incompetence,
or laziness, for example. In this study, I have explored the way in which
crisis entrepreneurs issue signals. This is an attempt to identify the problems
that they encounter as they attempt to draw people’s attention to a
given crisis. The goal of this study is to enhance our understanding of crisis
entrepreneurs’ interactional problems. The study makes use of the ‘discursive
perspective’, which is based on the discursive psychological approach
developed in the 1990s by two British social psychologists, Derek Edwards
and Jonathan Potter. To date, this interaction-based approach has seldom
been used in the context of crisis communication.
Chapter 2 underlines the value of examining the way in which stakeholders
within an organization’s environment raise the issue of a crisis.
In terms of crises as a phenomenon, it is important to do justice to
the dynamics of risks and crises. In essence, this is about what happens
in the course of interactions. In such an environment, it is vital for an
organization to keep pace with those in its surroundings if it is to observe
signals in interaction with this dynamic environment. This requires a
view of crisis communication that allows sufficient scope for the interactional
Chapter 3 explores various elements that characterize crises in general,
while describing a particularly significant phase - the latent crisis. I have
identified two forms of latent crisis, a lingering form and a creeping form.
These two forms differ chiefly in terms of the dynamics involved. While
the dynamics of both types exhibit both peaks and troughs, there are differences.
Lingering crises are entirely lacking in dynamism for extended
periods of time. The dynamics of creeping crises, on the other hand, tend to
increase gradually.
After describing the theoretical framework of the study, chapter 4 proceeds
to explore the theoretical and methodological scope of discursive
psychology, in terms of an interactional approach to crisis communication.
Discursive psychology offers the valuable option of using discourse analysis
to examine the social context of risks from the standpoint of everyday
reality. A discursive perspective characteristically focuses on a) everyday
interactions that are not shaped by the study itself and b) the transactions
that, either consciously or unconsciously, feature in such interactions.
The discursive perspective offers a specific form of discourse analysis that
communications professionals can use to understand how those in the
environment express their ideas relative to others. The significance of this
is that it can help professionals to understand the specific interactional
problems facing crisis entrepreneurs. These involve dealing with certain
‘interactional’ challenges, while running the risk that their signals will not
be picked up.
Chapter 5 discusses the two cases selected for this study. The selected
case domain is education in the Netherlands. I have investigated the ways
in which crisis entrepreneurs have signalled problems in this sector. I used
discourse analysis (Edwards, 1997; Potter, 1992) to first examine the interactional
efforts of those behind collective social movements, then those of
individual whistleblowers. To this end, I studied an interview with Matthé
Sjamaar, the rector of a secondary school, which was published in Onderwijsblad
(education journal) in May 1998. I also examined the manifesto of
Beter Onderwijs Nederland (better education for the Netherlands; BON),
which was published in the NRC Handelsblad newspaper in June 2006. Both
sources raised the issue of a crisis. One of the criteria that I used in selecting
these texts was whether the crisis entrepreneur in question had the ability
to influence the public debate. In both cases, both local and national media
responded to the statements made by these crisis entrepreneurs. Using a
discursive response analysis, I explored the way in which newspapers dealt
with the interactional problems faced by these crisis entrepreneurs.
Chapters 6 and 7 form the empirical part of this study. The analysis identified
three important discursive activities that are carried out by crisis
entrepreneurs. These are: 1. demonstrating the validity of the problem,
2. establishing the messenger’s credibility, and 3. creating the belief in a
solution. The analysis showed that Matthé Sjamaar creates indirectly undetermined
others in the environment as being partly responsible for the
cause of the problem, while exhibiting a degree of fatalism and holding out
no prospect of a solution. He makes an indefinite-side group responsible
for the problems. He shows he can not control the problem because it is
too large. He creates the crisis as an isolated entity. They are merely the
facts which he shows, which are independent of him. He suggests that he
has done a lot of hard work and now others have to do something.
The media portrayed Rector Sjamaar as symbolizing a problem that was
primarily a personal issue. BON, on the other hand, presents itself as a collective
that is committed to achieving better education in the Netherlands.
The writers display insight and overview of the education problem and
create the association to BON as a group consisting of ‘outspoken thinkers’
who are not hindered by doubts. The authors set themselves superior
in their attitude towards the education reformers. The writers poses the
problem as clear and relevant to everyone and so they create their own
need for existence. So now they start a movement and give voice to something
that has long been going on: BON is the solution to turn the tide. We
can jointly fate a twist. Various media sources reinforced this image, portraying
this social movement as the solution to the problem.
The study has shown that crisis entrepreneurs may differ in terms of the
strategies used and the interactional problems encountered. The solutions
put forward by BON have proved more effective than those suggested by
Rector Sjamaar. As a result, the discursive activities pursued by the former
have been more successful than those of the latter. The diverse reactions
exhibited by the media sources in this study serve to underline the precarious
nature of a crisis entrepreneur’s operation. For instance, the analysis
shows that rather than focusing on the authenticity of his signal, the
responses to Matthé Sjamaar’s article dismiss his views as a purely private
emotion. Based on this study, I show that the Rector’s initiative was undermined
by his presentation of the problem. It failed to trigger a general
sense of crisis as a result of segregation. BON fared very differently, as the
problem of educational reform is already widely recognized. Moreover, as
the analysis shows, BON’s spokespersons are important actors in this connection.
Ad and Marijke Verbrugge have put forward polarizing arguments,
in which they distance themselves from the New Learning concept. These
views have clearly been taken on board by supporters and opponents in the
debate triggered by these authors. The study has also shown that certain
interactional problems are not necessarily inevitable, but that such problems
can be triggered by crisis entrepreneurs themselves. Its content is
inextricably linked to people’s goals in making specific comments.
Chapter 8 summarizes the main observations in this thesis. It shows
that the problems created by raising the issue of a latent crisis are not
purely substantive in nature (‘is this crisis genuine?’), there is also an interactional
aspect (for example, ‘how do I get people to accept the urgency
and validity of the problem?’). My study provides a greater understanding
of the course that crises can take. It also shows that crisis entrepreneurs
can be seen as dynamic elements within society. They express dissenting
views, and launch new initiatives through various forms of traditional and
electronic media. This process can be very instructive. Communications
professionals can better understand how crises develop among those in
their environment if they are aware of the types of interactional problems,
and the types of responses, that can result from raising the issue of a crisis.
Moreover, this might also help communications professionals to achieve
better outcomes in their dealings with crisis entrepreneurs.
A discursive approach is valuable in this respect because it shows how
certain themes in communication can deal with policy development. This
approach can lead to a better hold on these themes in practice and can
provide another perspective to widespread failure of interaction between
government and citizens. The government is often unable to understand
what the citizen means, because their interactional problems are not recognized.
Knowledge of their doubts on an issue, can help the organization
to acquire a better understanding of objections – from inside and
out – against a particular policy. A discourse analysis of the interactional
contributions of crisis entrepreneurs may give a rich and structured insight
into latent crisis supply, including the strategies, interactional problems
and reactions of the actors involved and how they are able to recognize a
potential crisis.

To Serve and Conserve: strengthening germplasm evaluation to focus on users' needs
Hintum, T.J.L. van - \ 2011
genenbanken - gegevensbeheer - germplasm - germplasm uitgiften - plantenveredeling - gene banks - data management - germplasm releases - plant breeding
Powerpointpresentatie over het gebruik van genenbanken: focus op wat de gebruiker nodig heeft.
Identification of a new resistance gene to septoria tritici blotch in wheat
Tabib Ghaffary, M.S. ; Fan's, J.D. ; Friesen, T.L. ; Kema, G.H.J. - \ 2010
Gewasbescherming 41 (2010)3. - ISSN 0166-6495 - p. 151 - 151.
tarwe - mycosphaerella graminicola - genetisch bepaalde resistentie - genen - germplasm - resistentieveredeling - wheat - genetic resistance - genes - resistance breeding
Door het screenen van lijnen en wilde verwanten van tarwe, is een nieuw resistentiegen tegen STB (Septoria tritici blotch) gevonden.
Second National Report on Plant Genetic Resources for Food and Agriculture, The Netherlands
Visser, L. - \ 2008
Den Haag : Ministerie van Landbouw, Natuur en Voedselkwaliteit - 56
genetische bronnen van plantensoorten - genenbanken - genetische diversiteit - gewassen - biodiversiteit - plantenverzamelingen - germplasm - in-situ conservering - ex-situ conservering - agrobiodiversiteit - plant genetic resources - gene banks - genetic diversity - crops - biodiversity - plant collections - in situ conservation - ex situ conservation - agro-biodiversity
The National Report is considered a strategic policy document. After a general introduction on Dutch agriculture, it describes the state of diversity in the production system and the crop and variety levels due to ongoing developments in agricultural production. Chapters 2 and 3 focus on the in situ Management and ex situ Management of Plant Genetic Resources respectively, explaining why the ex situ approach is relatively important for the country given the current status of its agriculture. Chapter 4 describes the changes in the State of Use over the last decade. Additional information is contained in the chapters on National Programmes, Training and Legislation; Regional and International Collaboration; Access to PGRFA, Benefit-Sharing and Farmers’ Rights, with a final chapter on the Contribution of PGRFA Management to Food Security and Sustainable Development. National stakeholder consultations have contributed to this report.
AFLP analysis reveals a lack of phylogenetic structure within Solanum section Petota
Jacobs, M.M.J. ; Berg, R.G. van den; Vleeshouwers, V. ; Visser, M.E. ; Mank, R. ; Sengers, M. ; Hoekstra, R. ; Vosman, B. - \ 2008
BMC Evolutionary Biology 8 (2008). - ISSN 1471-2148 - 12 p.
restriction site variation - wild potatoes - series relationships - solanaceae - reexamination - germplasm - taxonomy - complex
Background The secondary genepool of our modern cultivated potato (Solanum tuberosum L.) consists of a large number of tuber-bearing wild Solanum species under Solanum section Petota. One of the major taxonomic problems in section Petota is that the series classification (as put forward by Hawkes) is problematic and the boundaries of some series are unclear. In addition, the classification has received only partial cladistic support in all molecular studies carried out to date. The aim of the present study is to describe the structure present in section Petota. When possible, at least 5 accessions from each available species and 5 individual plants per accession (totally approx. 5000 plants) were genotyped using over 200 AFLP markers. This resulted in the largest dataset ever constructed for Solanum section Petota. The data obtained are used to evaluate the 21 series hypothesis put forward by Hawkes and the 4 clade hypothesis of Spooner and co-workers. Results We constructed a NJ tree for 4929 genotypes. For the other analyses, due to practical reasons, a condensed dataset was created consisting of one representative genotype from each available accession. We show a NJ jackknife and a MP jackknife tree. A large part of both trees consists of a polytomy. Some structure is still visible in both trees, supported by jackknife values above 69. We use these branches with >69 jackknife support in the NJ jackknife tree as a basis for informal species groups. The informal species groups recognized are: Mexican diploids, Acaulia, Iopetala, Longipedicellata, polyploid Conicibaccata, diploid Conicibaccata, Circaeifolia, diploid Piurana and tetraploid Piurana. Conclusion Most of the series that Hawkes and his predecessors designated can not be accepted as natural groups, based on our study. Neither do we find proof for the 4 clades proposed by Spooner and co-workers. A few species groups have high support and their inner structure displays also supported subdivisions, while a large part of the species cannot be structured at all. We believe that the lack of structure is not due to any methodological problem but represents the real biological situation within section Petota.
Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China
Li, Yinghui ; Guan, Rongxia ; Liu, Zhangxiong ; Ma, Yansong ; Wang, Lixia ; Li, Linhai ; Lin, Fanyun ; Luan, Weijiang ; Chen, Pengyin ; Yan, Zhe ; Guan, Yuan ; Zhu, Li ; Ning, Xuecheng ; Smulders, M.J.M. ; Li, W. ; Piao, Rihua ; Cui, Yanhua ; Yu, Zhongmei ; Guan, Min ; Chang, Ruzhen ; Hou, Anfu ; Shi, Ainong ; Zhang, Bo ; Zhu, Shenlong ; Qiu, L. - \ 2008
Theoretical and Applied Genetics 117 (2008)6. - ISSN 0040-5752 - p. 857 - 871.
multilocus genotype data - linkage disequilibrium - population-structure - plant introductions - cyst-nematode - ssr markers - molecular diversity - ancestral lines - germplasm - resistance
The Chinese genebank contains 23,587 soybean landraces collected from 29 provinces. In this study, a representative collection of 1,863 landraces were assessed for genetic diversity and genetic differentiation in order to provide useful information for effective management and utilization. A total of 1,160 SSR alleles at 59 SSR loci were detected including 97 unique and 485 low-frequency alleles, which indicated great richness and uniqueness of genetic variation in this core collection. Seven clusters were inferred by STRUCTURE analysis, which is in good agreement with a neighbor-joining tree. The cluster subdivision was also supported by highly significant pairwise F st values and was generally in accordance with differences in planting area and sowing season. The cluster HSuM, which contains accessions collected from the region between 32.0 and 40.5°N, 105.4 and 122.2°E along the central and downstream parts of the Yellow River, was the most genetically diverse of the seven clusters. This provides the first molecular evidence for the hypotheses that the origin of cultivated soybean is the Yellow River region. A high proportion (95.1%) of pairs of alleles from different loci was in LD in the complete dataset. This was mostly due to overall population structure, since the number of locus pairs in LD was reduced sharply within each of the clusters compared to the complete dataset. This shows that population structure needs to be accounted for in association studies conducted within this collection. The low value of LD within the clusters can be seen as evidence that much of the recombination events in the past have been maintained in soybean, fixed in homozygous self-fertilizing landraces.
Crop wild relatives in the Netherlands: actors and protection measures
Hoekstra, R. ; Veller, M.G.P. van; Odé, B. - \ 2008
In: Crop wild relative conservation and use / Maxted, N., Ford-Lloyd, B.V., Kell, S.P., Iriondo, J.M., Dulloo, E., Turok, J., Wallingford : CABI - ISBN 9781845930998 - p. 165 - 177.
gewassen - wilde verwanten - bedreigde soorten - plantenverzamelingen - genetische bronnen van plantensoorten - in-situ conservering - genetische erosie - genetische variatie - botanische tuinen - genenbanken - germplasm - medicinale planten - hulpbronnenbehoud - economische botanie - crops - wild relatives - endangered species - plant collections - plant genetic resources - in situ conservation - genetic erosion - genetic variation - botanical gardens - gene banks - medicinal plants - resource conservation - economic botany
This book text presents methodologies and case studies that provide recommendations for the conservation and use of crop wild relatives. In a national, regional or global context, the status of crop wild relatives, that are closely related to crop plants, is examined. Conservation of crop wild relatives is important to enable these species to be included in plant breeding activities for beneficial traits such as pest or disease resistance and yield improvement.
Path-dependency in plant breeding: challenges facing participatory reforms in the Ethiopian Sorghum Improvement Program
McGuire, S.J. - \ 2008
Agricultural Systems 96 (2008)1-3. - ISSN 0308-521X - p. 139 - 149.
varietal selection - agricultural-research - genetic diversity - knowledge - india - environment - innovation - germplasm - framework - science
Participatory plant breeding (PPB) seeks to involve farmers more closely in crop improvement in order to improve breeding impact. While PPB aims to reform breeding practice, there has been little analysis of the current practice breeding institutions. Such an analysis is necessary, both to understand why a breeding programme works the way it does, and to assess the possibilities of for reforms. This paper develops theories of path-dependency, social construction of technology, and actor-networks to analyse the historical development of the Ethiopian Sorghum Improvement Program (ESIP), a long-running and sophisticated public-sector effort whose outputs have had limited adoption. This analysis explores choices in technology development, the social networks influencing them, and the possibility that established choices become stabilized in a pathway that resists changes to different lines of research and technology development. Applying this analysis to ESIP helps to understand the path-dependency of sorghum breeding, showing how early choices around agroecological classifications, germplasm use, and F1 hybrid development became `locked-in¿, consequently resisting change. Technical constraints, breeding routines, and actor networks all reinforce particular choices from the past, as does the centralized organization of the ESIP team. Most PPB efforts assume that poor breeder awareness of the traits farmers desire is the main reason for low impact, and thus concentrate on addressing this gap. This study points to more fundamental reasons for poor impact, and indicates that institutional change in breeding is unlikely to emerge from a PPB intervention focusing on selection criteria alone. In order to be lasting, reforms need to recognise technical pathways, strengthen the voice of farmers or other beneficiary groups, and engage with dominant policy narratives. This highlights the value of analysing breeding institutions before designing breeding reforms, and the utility of path-dependency for such an analysis.
The international spinach database
Treuren, R. van; Menting, F.B.J. - \ 2007
plant genetic resources, gene banks
The database concentrates on passport data of spinach of germplasm collections worldwide. All available passport data of accessions included in the International Spinach Database are downloadable as zipped Excel file. This zip file also contains the decoding tables, except for the FAO institutes table that is available on the Wiews website (PGR > Download). Characterization and evaluation data generated within the framework of the EU GENRES project entitled "Leafy vegetables germplasm, stimulating use" (AGRI-2006-0262) are also downloadable as zipped Excel file.
Paving the way for genetic improvement of zinc accumulation in Brassica rapa
Wu, J. - \ 2007
Wageningen University. Promotor(en): Maarten Koornneef, co-promotor(en): Mark Aarts; Xiaowu Wang. - [S.l.] : S.n. - ISBN 9789085047667 - 130
brassica campestris - zinc - genetic improvement - germplasm - quantitative trait loci - genes - gene expression - zink - genetische verbetering - loci voor kwantitatief kenmerk - genen - genexpressie
Brassica rapa L. comprises several vegetable crops, some of which are among the most important vegetables in China, serving as one of the main resources of mineral nutrition for Chinese people. However, the knowledge on the genetics of micronutrient accumulation, including Zn, Fe and Mn, is lacking in B. rapa. By exploring the genetic potential for the improvement of Zn accumulation in B. rapa vegetables I expect to contribute to the reduction of micronutrient malnutrition in China. To characterize the natural variation of Zn accumulation and Zn response upon exposure to different Zn concentrations, I screened a large collection of germplasm representing nine cultivar groups covering the geographic distribution of B. rapa vegetables in China (Chapter 2). The result revealed that there was marked variation in accumulation of Zn (23.2-159.9 µg g-1), Fe (60.3-350.1 µg g-1) and Mn (20.9-53.3 µg g-1) in B. rapa. Zn accumulation correlated with Fe or Mn accumulation both under normal and deficient Zn supply. No significant correlation was detected for the accumulation of these three elements with cultivar groups. A two-fold variation was found for dry-biomass based tolerance to Zn deficiency or excessive Zn. The wide natural variation provides a base for the genetic dissection by quantitative trait locus (QTL) analysis or for developing breeding programs for improved mineral content. QTL analysis is a powerful tool in dissection of complex genetic traits. A doubled haploid (DH) population developed from two Chinese cabbage (B. rapa. ssp. pekinesis) varieties was used for QTL analysis of the accumulation of 11 minerals in leaves and for tolerance to deficient or toxic Zn supplies (Chapter 3). The trait analysis showed significantly positive correlations between the leaf concentrations of the tested minerals, indicating that this must be taken into consideration in breeding programs, especially when toxic minerals (Cd, As) are involved. Seven QTLs were detected for Na, Mg, P, Mn, Zn and Sr leaf concentrations, with an explained variance ranging from 11.1 % to 18.2 % . The tolerance to Zn stress was evaluated by dry shoot biomass of plants grown under different Zn supplies. One common QTL was found affecting Shoot Dry Biomass (SDB) under normal, deficient and excessive Zn supply conditions. An additional QTL was detected for SDB only under Zn excess stress, with an explained variance of 13.0 %. The fact that no major QTL was detected indicates the complexity of the genetic control of the traits, probably involving many loci, each with a limited contribution to mineral accumulation in B. rapa. Furthermore this indicates that the genetic improvement of these traits by classical breeding will be very complicated, as it will require a combination of favourable alleles at many of the genes contributing to the traits. Screening additional populations for larger effect QTLs may provide an alternative. Metal transporters play important roles in maintaining metal homeostasis in plants and are involved in processes of metal uptake, internal transport and storage. Thlaspi caerulescens J&C Presl. is a Zn/Cd/Ni hyperaccumulator, which has been used as a model for plant metal homeostasis research. It has been proposed that the hyperaccumulation is most likely due to the different regulation of the metal homeostasis genes rather than involving genes with novel functions (Van de Mortel et al., 2006). I cloned four metal transporter full-length cDNAs by screening T. caerulescens cDNA libraries, encoding two ZIP transporters (TcZNT5 and TcZNT6, in Chapter 4) and two so-called NRAMP transporters (TcNRAMP3 and TcNRAMP4, in Chapter 5). These four genes showed strongly increased expression in T. caerulescens, as compared to the non-accumulator Arabidopsis thaliana in a wide range of Zn supplies or in the presence of Cd, indicated that these genes were involved in metal hyperaccumulation or tolerance in T. caerulescens. Expression analysis in two T. caerulescens accessions with contrasting Cd accumulation (La Calamine and Ganges) further revealed that their difference in Cd accumulation ability was associated with differences in the regulation of the expression of ZNTs and NRAMPs . Loss of function of the AtZIP5 gene in Arabidopsis increased its tolerance to Cd as measured by reduced root growth, but overexpression of the T. caerulescens orthologue TcZNT5 in Arabidopsis did not lead to any change in phenotype. In contrast, loss of function of AtZIP6 in Arabidopsis did not change its phenotype, but overexpression of the T. caerulescens orthologue TcZNT6 in Arabidopsis increased Cd sensitivity. The Arabidopsis double mutant nramp3 nramp4 showed hypersensitivity to Cd and toxic Zn, in addition to its previously reported hypersensitivity to Fe deficiency. Our study did not reveal functional differences between the T. caerulescens and A. thaliana NRAMPs, which transport the same metals when heterologously expressed in yeast and all four are localized at the vacuolar membrane in plants. Furthermore the phenotype caused by the inactivation of the AtNRAMP3 and AtNRAMP4 genes in Arabidopsis can be rescued by expression of TcNRAMP3. Nevertheless, neither nramp3 nramp4 plants expressing TcNRAMP3, nor wild-type plants expressing TcNRAMP4 at high levels show enhanced Zn or Cd tolerance compared to wild type Arabidopsis. The data presented in this thesis indicate that enhanced Zn accumulation, Zn tolerance or Cd tolerance probably requires elevated and controlled expression of a set of genes, rather than only single metal transporter genes.
The distribution of genetic diversity in a Brassica oleracea gene bank collection related to the effects on diversity of regeneration, as measured with AFLPs
Hintum, T.J.L. van; Wiel, C.C.M. van de; Visser, D.L. ; Treuren, R. van; Vosman, B.J. - \ 2007
Theoretical and Applied Genetics 114 (2007)5. - ISSN 0040-5752 - p. 777 - 786.
molecular characterization - germplasm - maintenance - accessions - integrity - dna - l.
The ex situ conservation of plant genetic resources in gene banks involves the selection of accessions to be conserved and the maintenance of these accessions for current and future users. Decisions concerning both these issues require knowledge about the distribution of genetic diversity within and between accessions sampled from the gene pool, but also about the changes in variation of these samples as a result of regenerations. These issues were studied in an existing gene bank collection of a cross-pollinating crop using a selection of groups of very similar Dutch white cabbage accessions, and additional groups of reference material representing the Dutch, and the global white cabbage gene pool. Six accessions were sampled both before and after a standard regeneration. 30 plants of each of 50 accessions plus 6 regeneration populations included in the study were characterised with AFLPs, using scores for 103 polymorphic bands. It was shown that the genetic changes as a result of standard gene bank regenerations, as measured by AFLPs, are of a comparable magnitude as the differences between some of the more similar accessions. The observed changes are mainly due to highly significant changes in allele frequencies for a few fragments, whereas for the majority of fragments the alleles occur in similar frequencies before and after regeneration. It is argued that, given the changes of accessions over generations, accessions that display similar levels of differentiation may be combined safely.
Marker-assisted acquisition and core collection formation: A case study in barley using AFLPs and pedigree data
Treuren, R. van; Tchoudinova, I. ; Soest, L.J.M. van; Hintum, T.J.L. van - \ 2006
Genetic Resources and Crop Evolution 53 (2006)1. - ISSN 0925-9864 - p. 43 - 52.
genetic diversity - cultivars - dna - management - germplasm
A problem that often occurs in deciding which germplasm should be acquired to expand the diversity of a plant genetic resources collection, and which accessions should be included in a core collection, is the lack of proper data. The usefulness of an AFLP-based protocol to assist in acquisition decisions and in core collection formation was examined by using 52 barley cultivars. For validation purposes, pedigree data of the cultivars were used to calculate the 'effective number of origin lines' (n(o1)), a parameter introduced in earlier research that was defined as the number of alleles per locus, not identical by descent, in a set of lines. Two AFLP primer combinations were able to distinguish all 52 cultivars from each other, and to discriminate between spring and winter crop types. Using the year of origin of the cultivars, the historical development of n(o1) showed a stepwise pattern, indicating the periodical release of genetically similar cultivars, alternated by the incorporation of new material. Comparison of AFLP data between cultivars and both their parents was possible in five cases. These comparisons revealed a high likelihood that the correct parents were involved but a rather skewed contribution of parents to offspring, suggesting that backcrossing had been applied. Treating the 25 cultivars that were released before 1980 and played an important role in barley cultivation as a basic collection, and the 27 more recent cultivars as potential candidates for acquisition, n(o1) values generated by a marker-based approach largely followed those using a random approach. Given this poor performance, a marker-based protocol to assist in acquisition decisions was not considered useful for the analysed material. If the 52 cultivars were considered to be the collection from which a core collection had to be selected, the marker-based selection showed much better results compared to a random selection. About half of the total number of origin lines could be captured with a quarter of the collection, indicating the potential utility of AFLPs in core collection formation.
Nucleotide-binding site (NBS) profiling of genetic diversity in durum wheat
Mantovani, P. ; Linden, C.G. van der; Maccaferri, M. ; Sanguineti, M.C. ; Tuberosa, R. - \ 2006
Genome 49 (2006)11. - ISSN 0831-2796 - p. 1473 - 1480.
microsatellite markers - disease resistance - bread wheat - germplasm - aflp - traits - ssr - map
Molecular markers are effective tools to investigate genetic diversity for resistance to pathogens. NBS (nucleotide-binding site) profiling is a OCR (polymerase chain reaction)-based approach to studying genetic variability that specifically targets chromosome regions containing R-genes and R-gene analogues. We used NBS profiling to measure genetic diversity among 58 accessions of durum wheat. Mean polymorphism rates detected using MseI and AluI as restriction enzymes were 34% and 22%, respectively. Mean number of polymorphisms per enzyme-primer combination was equal to 23.8 +/- 5.9, ranging from 13 to 31 polymorphic bands. In total, 96 markers over 190 indicated a good capacity to discriminate between accessions (the polymorphic index content ranging from 0.30 to 0.50). The results obtained with NBS profiling were compared with simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) data of the same set of accessions. The genetic distances computed with 190 NBS profiling markers were in close agreement with those obtained with AFLP and SSR markers (r = 0.73 and 0.76, respectively). Our results indicate that NBS profiling provides an effective means to investigate genetic diversity in durum wheat.
Animal genetic resources conservation in The Netherlands and Europe: Poultry perspective
Woelders, H. ; Zuidberg, C.A. ; Hiemstra, S.J. - \ 2006
Poultry Science 85 (2006)2. - ISSN 0032-5791 - p. 216 - 222.
dierveredeling - pluimvee - kippen - genetische bronnen van diersoorten - conservering - cryopreservering - cryobeschermingsmiddelen - genenbanken - genetische diversiteit - germplasm - in vitro kweek - inseminatie - sperma - spermaconservering - europa - nederland - animal breeding - poultry - fowls - animal genetic resources - conservation - cryopreservation - cryoprotectants - gene banks - genetic diversity - in vitro culture - insemination - semen - semen preservation - europe - netherlands - fowl spermatozoa - frozen - sperm
Increased global use of highly productive breeds of farm animals has been coupled to loss of genetic diversity in most species. In European countries, various governmental, non-governmental, and private organizations try to preserve genetic diversity of livestock in situ (e.g., by stimulating the use of indigenous, rare breeds by farmers; in nature reserves; or in noncommercial farms). In the case of poultry, maintaining in situ populations of the noncommercial (fancy) breeds largely relies on hobby farmers. In addition to in situ conservation, gene banks are being established for ex situ conservation. In at least 2 countries, France and The Netherlands, there are limited collections of frozen semen of rare poultry breeds. Since 2003, the CGN has started with a more systematic effort to collect, freeze, and store semen of indigenous Dutch poultry breeds. At present, the CGN gene bank contains semen of 11 Dutch rare poultry breeds. Also, CGN has performed research on the methodology for cryopreservation of fowl semen. This recent work was focused on finding a suitable replacement for glycerol, which is contraceptive in the hen, as a cryoprotectant. For reasons of hygiene and sample identification, we favored straw freezing, as opposed to the highly effective pellet freezing method. A significant interaction was found between cooling rate and cryoprotectant concentration. Best post-thaw sperm quality was obtained when combining 0.6 mol of dimethylacetamide/L with a cooling rate of +/- 200 degrees C/min. Inseminations, twice per week with 0.3 billion sperm per insemination resulted in 97 and 88% fertilized eggs with fresh and frozen semen, respectively. In 2005, CGN has used this straw freezing method to extend the collection of poultry semen in the Dutch gene bank.
Fragment Length Distributions and Collision Probabilities for AFLP Markers
Gort, G. ; Koopman, W.J.M. ; Stein, A. - \ 2006
Biometrics 62 (2006)4. - ISSN 0006-341X - p. 1107 - 1115.
cumulative distribution-functions - approximation - germplasm
AFLP is a DNA fingerprinting technique frequently used in plant and animal sciences. A drawback of the technique is the occurrence of multiple DNA fragments of the same length in a single AFLP lane, which we name a collision. In this article we quantify the problem. The well-known birthday problem plays a role. Calculation of collision probabilities requires a fragment length distribution (fld). We discuss three ways to estimate the fld: based on theoretical considerations, on in-silico determination using DNA sequence data from Arabidopsis thaliana, or on direct estimation from AFLP data. In the latter case we use a generalized linear model with monotone smoothing of the fragment length probabilities. Collision probabilities are calculated from two perspectives, assuming known fragment counts and assuming known band counts. We compare results for a number of fld's, ranging from uniform to highly skewed. The conclusion is that collisions occur often, with higher probabilities for higher numbers of bands, for more skewed distributions, and, to a lesser extent, for smaller scoring ranges. For a typical plant genome an AFLP with 19 bands is likely to contain the first collision. Practical implications of collisions are discussed. AFLP examples from lettuce and chicory are used for illustration.
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