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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    Crop Wild Relatives (CWRs) in Nederland
    Hoekstra, R. ; Treuren, R. van; Hintum, T.J.L. van - \ 2016
    wilde verwanten - genetische bronnen van plantensoorten - conservering - ex-situ conservering - in-situ conservering - natuurgebieden - genenbanken - nederland - wild relatives - plant genetic resources - conservation - ex situ conservation - in situ conservation - natural areas - gene banks - netherlands
    http://www.cwrnl.nl
    Flinke uitbreiding genenbank voor Nederlandse paardenrassen
    Hoving, A.H. ; Wit, A.A.C. de; Sulkers, H. - \ 2016
    Zeldzaam huisdier 41 (2016)1. - ISSN 0929-905X - p. 20 - 21.
    genenbanken - paardenrassen - genetische diversiteit - zeldzame rassen - gene banks - horse breeds - genetic diversity - rare breeds
    Het Centrum voor Genetische Bronnen Nederland (CGN) bewaart sperma
    van Nederlandse paardenrassen in de genenbank voor landbouwhuisdieren.
    Doel is het veiligstellen van de genetische diversiteit binnen
    de paardenrassen.
    Genetische diversiteit van de door essentaksterfte geplaagde gewone es
    Copini, P. ; Kopinga, J. ; Laros, I. ; Bovenschen, J. ; Buiteveld, J. - \ 2016
    Vakblad Natuur Bos Landschap (2016)april. - ISSN 1572-7610 - p. 14 - 17.
    chalara fraxinea - fraxinus excelsior - schimmelziekten - resistentie van variëteiten - genetische diversiteit - rassenlijsten - genenbanken - bosbeheer - chalara fraxinea - fraxinus excelsior - fungal diseases - varietal resistance - genetic diversity - descriptive list of varieties - gene banks - forest administration
    Essenzaadbronnen op de Rassenlijst Bomen hebben een hoge genetische diversiteit. Dat is een belangrijk kwaliteitsaspect van teeltmateriaal en speelt een cruciale rol in het aanpassingsvermogen van soorten aan een veranderend klimaat en nieuwe ziekten en plagen. De huidige generatie essenbossen heeft te kampen met de veelal desastreuze gevolgen van essentaksterfte. Uit onderzoek blijkt dat resistentie tegen deze ziekte genetisch bepaald is, en dat een klein deel van de essen goed bestand is tegen de ziekte. Deze genetische basis biedt hoop om een
    nieuwe generatie essen te selecteren die bestand is tegen de ziekte, met behoud van de genetische diversiteit.
    Populatieanalyse Groninger Paard
    Hoving, A.H. ; Vernooij, Kelly ; berg, Rozemarijn van den; Windig, Jack - \ 2015
    Zeldzaam huisdier 40 (2015)4. - ISSN 0929-905X - p. 18 - 19.
    paardenrassen - nederland - fokdoelen - groninger paard - populaties - genetica - inteelt - verwantschap - genenbanken - horse breeds - netherlands - breeding aims - groningen horse - populations - genetics - inbreeding - kinship - gene banks
    We prijzen Nederlandse paardenrassen zoals het Groninger paard niet alleen omdat ze onderdeel van ons cultuurhistorisch erfgoed zijn maar ook vanwege hun veelzijdigheid en betrouwbare karakter. Helaas is de populatie klein. Dan is een goed doordacht fokbeleid nodig voor het behoud van genetische diversiteit en een gezonde populatie
    Zeldzame Nederlandse konijnenrassen in de genenbank
    Hoving, A.H. ; Renes, J. ; Taks, A. - \ 2015
    Zeldzaam huisdier 40 (2015)2. - ISSN 0929-905X - p. 20 - 21.
    rassen (dieren) - genetische bronnen van diersoorten - genenbanken - konijnen - zeldzame rassen - dierveredeling - bevruchtingsvermogen - sperma - ingevroren sperma - breeds - animal genetic resources - gene banks - rabbits - rare breeds - animal breeding - fertilizing ability - semen - frozen semen
    In 2014 is van de meeste zeldzame Nederlandse konijnenrassen sperma ingevroren en opgeslagen in de genenbank. Dit kon gerealiseerd worden dankzij samenwerking tussen konijnenfokkers, het Centrum voor Genetische Bronnen Nederland van Wageningen UR (CGN), Kleindier Liefhebbers Nederland (KLN) en de Stichting Zeldzame Huisdierrassen (SZH).
    Zaad langer goed zonder zuurstof
    Groot, S.P.C. - \ 2014
    Resource: weekblad voor Wageningen UR (2014). - ISSN 1874-3625
    opslag van zaden - zaden - vacuümverpakking - zuurstof - genenbanken - koudeopslag - vochtigheid - seed storage - seeds - vacuum packaging - oxygen - gene banks - cold storage - humidity
    Zaden zijn het beste houdbaar als je ze koel en droog bewaart. Maar het kan nog veel beter: zuurstofloos. Dat toont onderzoek van Steven Groot (PRI) en collega’s aan.
    Winning en cryoconservering van sperma van zeldzame Nederlandse konijnenrassen voor de genenbank
    Hoving-Bolink, A.H. ; Wit, A.A.C. de; Sulkers, H. ; Zuidberg, C.A. ; Hulsegge, B. ; Woelders, H. ; Hiemstra, S.J. - \ 2014
    Wageningen : Centrum voor Genetische Bronnen Wageningen UR (CGN rapport 32) - 37
    rapporten - konijnen - rassen (dieren) - conservering - kunstmatige inseminatie - ingevroren sperma - sperma - genenbanken - zeldzame rassen - reports - rabbits - breeds - conservation - artificial insemination - frozen semen - semen - gene banks - rare breeds
    In dit rapport wordt beschreven welke activiteiten CGN in samenwerking met de SZH, KLN en individuele fokkers hebben ondernomen om genetisch materiaal van konijnenrassen veilig te stellen in de genenbank. Op basis van literatuur en praktijkervaringen is een protocol voor spermawinning en spermaverwerking (cryoconservering) vastgesteld. Een dergelijk protocol was niet beschikbaar in de Nederlandse bedrijfsmatige konijnenhouderij omdat daar uitsluitend met vers sperma gewerkt wordt en niet met ingevroren sperma. Het rapport eindigt met een beschrijving van de resultaten van de spermawinning.
    Conserving the genetic diversity of Bolivian wild potatoes
    Cadima Fuentes, X. - \ 2014
    Wageningen University. Promotor(en): Marc Sosef, co-promotor(en): Ronald van den Berg; Rob van Treuren. - Wageningen : Wageningen University - ISBN 9789462571686 - 229
    solanum - bolivia - wilde verwanten - gewassen - genetische bronnen van plantensoorten - conservering - ex-situ conservering - in-situ conservering - genenbanken - biosystematiek - genetische diversiteit - verzamelmissies - solanum - bolivia - wild relatives - crops - plant genetic resources - conservation - ex situ conservation - in situ conservation - gene banks - biosystematics - genetic diversity - collecting missions

    Abstract thesis Ximena Cadima Fuentes (to be defended on 8 Dec 2014):

    Conserving the genetic diversity of Bolivian wild potatoes

    The wild relatives of potatoes (Solanum sect. Petota) form the genetic reservoir for the improvement of the cultivated potato. Bolivia harbours 39 wild taxa of these wild potatoes, 21 of which are endemic species. This study aimed to evaluate to what level the current ex situ and in situ management efforts have conserved the genetic diversity of Bolivian wild potato species, and what recommendations can be formulated for improvement.

    The current conservation status of Bolivian endemic wild potato species was assessed using both the globally accepted IUCN criteria and a methodology developed within the framework of the UNEP/GEF-Crop Wild Relative Project (CWR Project). These two methods led to different estimates of threat status for some of the species. Spatial analysis allowed to distinguish eight priority areas for in situ conservation of the 21 Bolivian endemic wild potato species. These areas represent a high concentration of endemic species and have a relatively low level of threat, but only one of them has a conservation status. This is a first step to direct the conservation efforts for wild potato species.

    The genetic stability and diversity of material from different species under ex situ management was evaluated using microsatellite markers. The analysis was performed on accessions that went through a process of seed regeneration and multiplication during ex situ conservation. Genetic changes between different generations of ex situ germplasm were observed for the majority, but not all, of the investigated species. Potential causes of these changes include genetic drift and contamination resulting from human error during regeneration. The populations generated under ex situ conditions were also compared with re-collected in situ populations from the same location or area as the original collection. The results showed highly significant differences in all cases. Potential causes for these differences are changes during ex situ maintenance, sampling effects during collecting and in situ genetic change over time.

    The integrated conservation of Bolivian wild potatoes requires a combination of in situ and ex situ activities. The principle recommendation for the in situ conservation is to move from a passive to an active approach, where conservation areas are prioritized, conservation plans are designed according to the type of area (protected area or agro-ecosystem) and local stake holders are involved. To make sure that ex situ material provides a good representation of the in situ genetic variability, regular re-collecting of species with few accessions (and therefore less variability), endangered in situ, and with known or potential favorable traits is necessary. Gene bank management procedures should follow the FAO gene bank standards and this should be monitored by a national body responsible for genetic resources. And finally, periodic monitoring of the genetic integrity should be implemented as part of good practices during regeneration procedures in order to detect possible changes and to help combat human errors.

    Toggenburger in de genenbank. NOG nieuws (interview)
    Schenk, M. ; Sulkers, H. ; Hulsegge, B. ; Hoving-Bolink, A.H. - \ 2013
    Geitenhouderij 17 (2013)6. - ISSN 0165-9812 - p. 34 - 35.
    nederlandse toggenburgergeit - geitenrassen - genetische bronnen van diersoorten - sperma - genenbanken - dutch toggenburg - goat breeds - animal genetic resources - semen - gene banks
    Het Centrum voor Genetische Bronnen Nederland (CGN) van Wageningen UR richt zich op behoud en bevordering van duurzaam gebruik van genetische diversiteit van soorten die van belang zijn voor de landbouw en de bosbouw en verzamelt daarvoor genetisch materiaal van planten, (zeldzame) landbouwhuisdieren en bomen. In dat kader heeft CGN de Landelijke Fokgroep Toggenburger benaderd met de vraag om medewerking te verlenen aan de winning van sperma van Toggenburger bokken. Door opslag van genetisch materiaal van de Nederlandse Toggenburger geit in de genenbank wordt ook dit ras veiliggesteld.
    Report of ad hoc meeting of the Chairs, Vice-Chairs and Central Crop Database Managers of the ECPGR Solanaceae and Cucurbits Working Groups
    Díez Niclós, M.J. ; Valcárcel, J.V. ; Íñigo, A.G. ; Dooijeweert, W. van; Menting, F. ; Weerden, G. van der; Daunay, M. - \ 2013
    Valencia, Spain : ECPGR - 5
    genenbanken - databanken - solanaceae - cucurbitaceae - werkgroepen - gene banks - databases - solanaceae - cucurbitaceae - working groups
    The scope of this two-day ad hoc meeting was to explore the possibility to abandon Central Crop Databases (CCDBs) and focus on EURISCO, in order to avoid duplication of data and working efforts. The main facilities of both systems were discussed. Current progress concerning the selection of Most Appropriate Accessions (MAAs) was reviewed for Solanaceae and Cucurbits and possible plans for the new phase of ECPGR (Phase IX, 2014-2018) were discussed.
    Conservation and sustainable use of animal genetic resources
    Hiemstra, S.J. - \ 2013
    Lelystad : Centre for genetic resources (CGN) - 6
    genetische bronnen van diersoorten - genetische diversiteit - agrobiodiversiteit - huisdieren - cryopreservering - genenbanken - cultureel erfgoed - voedselzekerheid - animal genetic resources - genetic diversity - agro-biodiversity - domestic animals - cryopreservation - gene banks - cultural heritage - food security
    Genetic diversity is the basis of agriculture. Adapting populations of domestic animals through breeding is impossible withot genetic diversity. Genetic diversity is part of the history of mankind and is essential for future improvements in agricultural production.
    Winning en opslag van sperma van zeldzame Nederlandse schapen- en geitenrassen in de genenbank (2001-2012)
    Hoving, A.H. ; Sulkers, H. ; Zuidberg, C.A. ; Hulsegge, B. ; Woelders, H. ; Wit, A.A.C. de; Hiemstra, S.J. - \ 2013
    Lelystad : Centrum voor Genetische Bronnen Wageningen UR (CGN rapport / Centrum voor Genetische Bronnen Nederland 29) - 30
    schapenrassen - geitenrassen - zeldzame rassen - schapenhouderij - geitenhouderij - spermaconservering - genetische bronnen van diersoorten - dierveredeling - genenbanken - sheep breeds - goat breeds - rare breeds - sheep farming - goat keeping - semen preservation - animal genetic resources - animal breeding - gene banks
    In de periode 2001-2012 is in een aantal acties genetisch materiaal van Nederlandse schapen- en geitenrassen opgenomen in de genenbank voor landbouwhuisdieren. In totaal zijn er ruim 34.000 doses rammen- en bokkensperma van 12 rassen opgeslagen in de genenbank. In dit rapport wordt beschreven welke activiteiten het Centrum voor Genetische Bronnen Nederland in de periode 2001-2012 heeft ondernomen om genetisch materiaal van schapen- en geitenrassen veiliig te stellen in de genenbank. De eerste actie vond plaats in 2001-2002, net na de MKZ-crisis, die duidelijk maakte dat er een reëel gevaar is dat een groot deel van de heideschapen bij een dergelijke dierziekte kan verdwijnen. Na deze eerste actie is het aantal doses sperma van diverse schapen- en geitenrassen verder uitgebreid in de periode 2003-2012. Naast de heideschaaprassen zijn het Melkschaap, de Zwartbles, de Blauwe Texelaar, de Nederlandse Landgeit en de Nederlandse Bonte en Witte geit toegevoegd aan de genenbank.
    Genetische bronnen bieden sleutel bij aanpassing klimaat
    Buiteveld, J. ; Vries, S.M.G. de - \ 2013
    De Boomkwekerij 13 (2013). - ISSN 0923-2443 - p. 22 - 23.
    genetische bronnen van plantensoorten - bomen - rassen (planten) - plantenverzamelingen - houtachtige planten - zaad verzamelen - klimaatverandering - genenbanken - gegevens verzamelen - informatieontsluiting - plant genetic resources - trees - varieties - plant collections - woody plants - seed collection - climatic change - gene banks - data collection - information retrieval
    Ten behoeve van een wereldwijd onderzoek zijn de genetische bronnen van bomen en struiken in Nederland in kaart gebracht. Om te kunnen omgaan met klimaatverandering in de komende decennia, is er immers genetische diversiteit nodig.
    The seed hunter in het spoor van Vavilov (interview met C. Kik)
    Zanderink, R. ; Kik, C. - \ 2013
    Slow Food Magazine 6 (2013)1. - ISSN 1878-4682 - p. 10 - 14.
    genetische bronnen van plantensoorten - wilde planten - zaad verzamelen - genenbanken - groenten - plant genetic resources - wild plants - seed collection - gene banks - vegetables
    Er moet voor een veredelaar een grote variatie aan plantmateriaal aanwezig zijn om uit te kunnen putten zodat onze gewassen, die vaak bestaan uit monoculturen, voor de toekomst veiliggesteld worden. Het vinden van die variatie is het werk van seed hunters of zadenverzamelaars. Eén van die seed hunters is de Wageningse onderzoeker Chris Kik, hoofdcurator van het Centrum voor Genetische Bronnen in Nederland (CGN) in Wageningen.
    Development of best practices for ex situ conservation of radish germplasm in the context of the crop genebank knowledge base
    Thormann, M. ; Yang, Q. ; Allender, C. ; Bas, N. ; Campbell, G. ; Dulloo, M.E. ; Ebert, A.W. ; Lohwasser, U. ; Pandey, C. ; Robertson, L.D. ; Spellman, O. - \ 2013
    Genetic Resources and Crop Evolution 60 (2013)4. - ISSN 0925-9864 - p. 1251 - 1262.
    genetische bronnen van plantensoorten - radijsjes - raphanus - ex-situ conservering - genenbanken - databanken - best practices - groenten - plant genetic resources - radishes - raphanus - ex situ conservation - gene banks - databases - best practices - vegetables - seed longevity - raphanus-sativus - storage - temperature - pollinators - prediction
    Information about crop-specific best practices for ex situ conservation of plant genetic resources has been difficult to find until recently. The CGIAR, together with national and regional partners, started to fill that gap by publishing best practices on the crop genebank knowledge base (CGKB -http://cropgenebank.sgrp.cgiar.org/), a website specifically developed and officially launched in 2010 to provide easy access to knowledge about all aspects of ex situ conservation of specific crops to genebank managers and ex situ conservation researchers. A collaborative study, undertaken by Bioversity International with eight national and international genebanks, utilized the framework provided by the CGKB to develop and publish radish conservation best practices. This paper focuses on two aspects of this study: (1) Differences in procedures and practices in radish conservation currently applied in five key genebank activities, namely, acquisition of germplasm, viability testing and monitoring, seed drying, seed storage, and regeneration. While in a few cases genebanks agreed on a specific best practice to recommend, in others it was not desirable to identify one practice as superior to another, therefore a range of existing practices is described as a variety of equivalent options. The results highlight the importance of proactive genebank management aimed at meeting the standards within the specific context in which a genebank operates. (2) The framework and template provided by the CGKB in guiding the development of genebank best practices, and the CGKB as an excellent resource to widely and freely share best practices with the global community to support the effective management of crop genebanks.
    Cryo conservering van sperma van zeldzame Nederlandse eendenrassen
    Zuidberg, C.A. ; Wit, A.A.C. de; Hoving, A.H. ; Woelders, H. ; Sulkers, H. ; Hiemstra, S.J. - \ 2012
    Wageningen : Centrum voor Genetische Bronnen (CGN rapport 24) - 25
    eenden - cryopreservering - spermatozoön - genenbanken - genetische bronnen van diersoorten - spermaconservering - sperma - ex-situ conservering - zeldzame rassen - nederland - ducks - cryopreservation - spermatozoa - gene banks - animal genetic resources - semen preservation - semen - ex situ conservation - rare breeds - netherlands
    The Centre for Genetic Resources, the Netherlands (CGN) has the aim to store genetic materials of farm animal genetic resources in the gene bank, including semen of native Dutch duck breeds. CGN will store these valuable genetic resources in the gene bank to be able to recreate the breeds or to support in situ conservation of the breed in case of calamities. For every species research has to be done in order to find the optimal protocol for semen collection and cryo conservation. In this report of the cryopreservation activities on duch breeds in 2011 and 2012 are reported. In this report is described how breeds and animals were chosen, how the protocol for semen collection is developed, which research is done for collecting and freezing the semen and how many straws were cryopreserved in 2011 and 2012. The Dutch 'krombek' (Hook Bill duck) and the 'witborst' (North Holland White Bibbed duck) are endangered breeds and considered as our living heritage. Priority was given to these two breeds. Finally more than 900 straws from 39 animals were stored in the gene bank.
    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.
    Report of a Working Group on Solanaceae : first meeting of the Working group and ad hoc meeting of the database managers, 14-17 Februari 2012, Menemen, Turkey
    Dooijeweert, W. van; Maggioni, L. ; Daunay, M.C. ; Lipman, E. - \ 2012
    Menemen, Turkey : Biodiversity International - 38
    solanaceae - genenbanken - genetische bronnen van plantensoorten - gewassen - databanken - genetische diversiteit - plantenverzamelingen - solanaceae - gene banks - plant genetic resources - crops - databases - genetic diversity - plant collections
    The Solanaceae Working Group (WG) of the European Cooperative Programme for Plant Genetic Resources (ECPGR) has established six databases for the crops that form its mandate. These include three major crops (Eggplant, Pepper and Tomato) and three minor crops (Cyphomandra, Pepino and Physalis). The ad hoc meeting of the Solanaceae Database (DB) Managers took place on 14 February 2012, prior to the meeting of the whole Solanaceae WG from 15 to 17 February. Willem van Dooijeweert, Chair of the WG, welcomed the DB Managers and explained the objectives of the meeting. The idea of the ad hoc meeting of DB Managers was brought up at an ad hoc meeting of the Vegetables Network Coordinating Group (18 April 2008, Wageningen, The Netherlands), as a response to the requirement of the initiative for “A European Genebank Integrated System” (AEGIS) that each WG submit lists of accessions for inclusion in the European Collection. The meeting was seen as an opportunity for the five attending DB Managers to exchange knowledge and discuss problems related to the management of the databases and, in particular, to prepare for AEGIS. After the one-day meeting, the DB Managers would propose a common vision of the selection process of European Accessions at the WG meeting that was to follow. Ahead of their meeting, the DB Managers had compiled Excel working files containing all data of each crop, which were extracted from the European Plant Genetic Resources Catalogue (or European Internet Search Catalogue, EURISCO) and the Central Crop Databases (CCDBs).
    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.
    An ecogeographic analysis of Oryza series Sativae in Asia and the Pacific
    Banaticla-Hilario, M.C.N. - \ 2012
    Wageningen University. Promotor(en): Marc Sosef, co-promotor(en): Ronald van den Berg; K.L. McNally. - S.l. : s.n. - ISBN 9789461733788 - 237
    oryza - oryza sativa - oryza nivara - genetische bronnen van plantensoorten - plantengeografie - plantenecologie - diversiteit - in-situ conservering - plantenmorfologie - taxonomie - genetica - genenbanken - azië - oryza - oryza sativa - oryza nivara - plant genetic resources - phytogeography - plant ecology - diversity - in situ conservation - plant morphology - taxonomy - genetics - gene banks - asia

    The non-cultivated speciesof the genus Oryza can provide a genetic arsenal of useful traits for improving the widely cultivated and consumed Asian rice (O. sativa). The diversity of these valuable plant resources must be well understood to ensure their effective in- and ex-situ conservation. In this thesis, we examined the ecogeographic variations within and between the three species of Oryza series Sativae in Asia and the Pacific. We looked at species differentiation from different spatial scales by analysing sympatric accession pairs of O. meridionalis and O. rufipogon and of O. nivara and O. rufipogon.

    We conducted phenotypic analyses in Chapter 2. The strong influence of ecology on species morphology was demonstrated in the ordination and cluster analyses results where O. meridionalis and O. nivara grouped together and were separated from O. rufipogon. We detected greater differentiation of O. nivara and O. rufipogon in South Asia and positive correlations between spatial and intraspecific (interpopulation) morphological distances in continental Asia. We found significant correlations between geoclimatic factors and certain character measurements within species and observed that seedling height, culm number and diameter, leaf size, and anther length exhibit contrasting responses for O. nivara and O. rufipogon. We confirmed significant morphological differences between the three species, between the South and Southeast Asian populations of O. nivara, and between the Australasian and the non-Australasian populations of O. rufipogon and provided botanical descriptions to delineate O. meridionalis, O. nivara and O. rufipogon morphologically.

    In Chapter 3, we genotyped the same set of accessions with 29 SSR markers and applied a variety of methods for genetic diversity analysis. Based on ordination and phylogenetic results, we verified that O. meridionalis is a genetically distinct species and that O. nivara and O. rufipogon overlap genetically across their geographic distribution. However, Bayesian clustering analysis recognized local-scale species separation of O. nivara and O. rufipogon implying stronger interspecific gene flow barriers in smaller spatial units. Concurrently, AMOVA indicated that the bulk (64%) of genetic variation in Asia Pacific series Sativae can be found among accessions and the lesser portions within accessions (26%) and among species (10%). We captured contrasting intraspecific variation patterns for O. nivara and O. rufipogon where the former exhibited low diversity, high population differentiation and isolation by distance mainly in South Asia while the latter displayed high diversity, low population differentiation and isolation by distance primarily in continental Southeast Asia. We established that altitude is correlated negatively to accession diversity and positively to local-scale species differentiation. Using Bayesian inference, we identified eight genetically distinct population groups: C1) Indian and Bangladeshi O. nivara; C2) Cambodian O. nivara; C3) Southeast Asian O. rufipogon; C4) O. meridionalis; C5) Nepalese O. nivara; C6) non-Cambodian Southeast Asian O. nivara; C7) Australasian O. rufipogon; and C8) South Asian O. rufipogon. Cluster analysis grouped the aromatic and japonica cultivar groups of O. sativa with O. rufipogon in South Asia and the indica and aus groups with O. nivara from Thailand and Cambodia, respectively. O. nivara from Nepal seemed genetically isolated from the other population groups. We also detected variation patterns that agreed with the results in Chapter 1 such as the South and Southeast Asian divisions of O. nivara, the divergence of Australasian populations from the rest of O. rufipogon and the greater differentiation of O. nivara and O. rufipogon in South Asia.

    In Chapter 4, we conducted artificial crossing experiments to 15 selected parental accessions of O. meridionalis, O. nivara, and O. rufipogon and assessed the extent of several post-pollination isolating mechanisms in Oryza series Sativae. We observed reproductive incompatibility within and between the inbreeding species O. meridionalis and O. nivara and high intraspecific crossability of the outcrossing O. rufipogon where viable and non-sterile F1 hybrids were produced only by combinations with a parental distance that ranged from 1062 to 3813 kilometers. Insular Southeast Asian and/or Australasian accessions of O. rufipogon were the most reproductively successful parents. O. rufipogon exhibited significant pre-zygotic species isolation (in terms of seed set) and reduced post-zygotic isolation, and seemed symmetrically compatible with O. nivara and asymmetrically compatible with O. meridionalis. We obtained few annual hybrids with relatively high fertilities from crosses between O. rufipogon and O. nivara and numerous perennial hybrids with low fertilities from crosses between O. rufipogon and O. meridionalis. Crossability estimates did not show significant correlations with geographic distance between parents. However, we discerned reduced seed set and F1 fertility in interspecific combinations with sympatric parents compared to crosses with non-sympatric parents, indicative of reinforced species isolation in sympatry. We evaluated the F1 offspring of different cross combinations and found a mixture of intermediate and parental character traits in interspecific hybrids.

    We discussed the taxonomic implications of the research results in Chapter 5 where we specifically dealt with the opposing views of lumping or splitting of O. nivara and O. rufipogon. We concluded that these two taxadeserve to be treated as separate species based on the following biosystematic evidence obtained from the thesis: 1) ecological distinction; 2) considerable prezygotic barriers; 3) opposing patterns of gene flow and genetic variation; 4) local-scale genetic divergence and 5) enhanced reproductive barriers under sympatric conditions. We identified ecogeography as a major driving force in the diversification of Oryza series Sativae in Asia and the Pacific and suggested that ecological speciation gave rise to O. nivara and O. rufipogon. We also presented recognizable geographic races within species.

    Ultimately in Chapter 6, we emphasized the importance of our study in several aspects of rice science and identified results that agreed with prior Oryza diversity studies. At the same time, we presented previously unreported morphological and genetic variation patterns that were established in this thesis. We discussed the possible applications of the research results to wild rice conservation, covering in situ strategies as well as gene bank practices. We also highlighted the potential role of O. nivara in Asian rice domestication where it could have either directly given rise to the indica cultivar group or hybridized/introgressed with migrated japonica cultivars in India, eventually leading to the development of indica.

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