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Widely known as the "tree of life", coconut (Cocos nucifera L.) provides a bountiful source for making a wide variety of healthy foods and industrial items. Its cultivation, however, has been encountering seriously destructive issues including lethal diseases and natural adversities which are currently distressing livelihoods of millions of small-holder farmers around the world. There is an urgent mandate to resolve these issues by meeting sustainable seedling production, facilitating genetic conservation, as well as developing disease identification and modern breeding. This book introduces improvements in coconut biotechnology by covering the advances in micropropagation, germplasm conservation, and molecular pathogenic diagnosis. This comprehensive volume will be a useful source of information and references to researchers, graduate students, agricultural developers, and scholars in the plant sciences. In order to benefit general readers, the book also covers fundamental aspects of biology, diversity, and evolution of this marvelous palm species.

Yam (Dioscorea spp.) is an important crop in tropical and subtropical regions. Many viruses have been recently identified in yam, hampering genetic conservation and safe international exchanges of yam germplasm. We report on the implementation of reliable and cost-effective PCR-based detection tools targeting eight different yam-infecting viruses. Viral indexing of the in vitro yam collection maintained by the Biological Resources Center for Tropical Plants (BRC-TP) in Guadeloupe (French West Indies) unveiled a high prevalence of potyviruses, badnaviruses, Dioscorea mosaic associated virus (DMaV) and yam asymptomatic virus 1 (YaV1) and a high level of coinfections. Infected yam accessions were subjected to a combination of thermotherapy and meristem culture. Sanitation levels were monitored using PCR-based and high-throughput sequencing-based diagnosis, confirming the efficacy and reliability of PCR-based detection tools. Sanitation rates were highly variable depending on viruses. Sixteen accessions were successfully sanitized, paving the way to safe yam germplasm exchanges and the implementation of clean seed production programs worldwide.

In Africa, it is mostly the informal seed system that ensures farmers’ seed supply. This is partly because the formal seed systems are not always effective in meeting demand for new seed varieties. Sometimes informal seed recycling and exchange of improved sorghum varieties will take place alongside formal initiatives, as is the case in southern Mali. Focusing on one particular village in the Dioila district, we analyze the efficacy of farmers’ strategies for preserving varietal seed purity and genetic integrity of an improved inbred-line (Soumba variety). Six seed lots of Soumba, recycled for two to six years by farmers using different practices, were collected and assessed in on-station trials in order to compare their agronomic performance and phenotypic purity (off-type plant frequencies) with control versions of the variety. Additionally, 30 panicle samples were randomly collected from five farmer fields sown with recycled Soumba and assessed for phenotypic purity in a progeny nursery and investigated for molecular diversity using 12 SSR markers. A total of 150 panicles from five other non-Soumba varieties were collected in the village in order to investigate eventual gene flow and its potential genetic consequences for the Soumba variety. In fields sown with recycled Soumba seed, between 2% and 14% of plants showed phenotypic deviations from the typical Soumba variety. The progeny nursery and SSR marker analysis verified the presence of the off-type plants observed in the field. The STRUCTURE program revealed admixtures with other varieties in 23% of Soumba plants, confirming the presence of gene flow. Gene diversity values in Soumba samples ranged from 0.006 for the commercial sample to 0.257 for recycled samples. Introgression and contamination were best minimized when (1) farmers had received specific training in seed production, (2) they could take advantage of isolated fields and (3) they could practise true-to-type panicle selection. Farmers were generally able to maintain the phenotype, as well as sustain or even improve yield performance of their Soumba variety while at the same time genetically enriching their seed stock.

The management of diversity for conservation and breeding is of great importance for all plant species and is particularly true in perennial species, such as the coffee Coffea canephora. This species exhibits a large genetic and phenotypic diversity with six different diversity groups. Large field collections are available in the Ivory Coast, Uganda and other Asian, American and African countries but are very expensive and time consuming to establish and maintain in large areas. We propose to improve coffee germplasm management through the construction of genetic core collections derived from a set of 565 accessions that are characterized with 13 microsatellite markers. Core collections of 12, 24 and 48 accessions were defined using two methods aimed to maximize the allelic diversity (Maximization strategy) or genetic distance (Maximum- Length Sub-Tree method). A composite core collection of 77 accessions is proposed for both objectives of an optimal management of diversity and breeding. This core collection presents a gene diversity value of 0.8 and exhibits the totality of the major alleles (i.e., 184) that are present in the initial set. The seven proposed core collections constitute a valuable tool for diversity management and a foundation for breeding programs. The use of these collections for collection management in research centers and breeding perspectives for coffee improvement are discussed.

A simple and efficient cryopreservation protocol for coconut zygotic embryos has been developed. Embryos were inoculated in Petri dishes on medium containing 3.2 M glucose, which were placed in hermetically closed containers containing 80 or 160 g silica gel for 48 or 24 h. Moisture content of embryos at the end of this treatment varied between 0.25 and 0.65 g g(-1) DW, depending on the accession. Embryos were then transferred for cryopreservation by rapid immersion of cryotubes in liquid nitrogen. After rapid re-warming, embryos were transferred to culture medium containing Eeuwens mineral elements for germination. This protocol was applied to ten accessions representative of coconut genetic diversity, with germination percentages of cryopreserved embryos between 13.7% and 74.7%.

A better knowledge of factors organizing crop genetic diversity in situ increases the efficiency of diversity analyses and conservation strategies, and requires collaboration between social and biological disciplines. Four areas of anthropology may contribute to our understanding of the impact of social factors on crop diversity: ethnobotany, cultural, cognitive and social anthropology. So far, most collaborative studies have been based on ethnobotanical methods, focusing on farmers’ individual motivations and actions, and overlooking the effects of farmer’s social organization per se. After reviewing common shortcomings in studies on sorghum and maize, this article analyzes how social anthropology, through the analysis of intermarriage, residence and seed inheritance practices, can contribute to studies on crop genetic diversity in situ. Crop varieties are thus considered social objects and socially based sampling strategies can be developed. Such an approach is justified because seed exchange is built upon trust and as such seed systems are embedded in a pre-existing social structure and centripetally oriented as a function of farmers’ social identity. The strong analogy between farmers’ cultural differentiation and crop genetic differentiation, both submitted to the same vertical transmission processes, allows proposing a common methodological framework for social anthropology and crop population genetics, where the classical interaction between genetic and environmental factors, G × E, is replaced by a three-way interaction G × E × S, where “S” stands for the social differentiation factors.

The potential gene flow between a crop and its wild relatives is largely determined by the overlaps in their ecological and geographical distributions. Ecogeographical databases are therefore indispensable tools for the sustainable management of genetic resources. In order to expand our knowledge of Sorghum bicolor distribution in Kenya, we conducted in situ collections of wild, weedy and cultivated sorghum. Qualitative and quantitative morphological traits were measured for each sampled wild sorghum plant. Farmers' knowledge relating to the management of sorghum varieties and autecology of wild sorghum was also obtained. Cluster analysis supports the existence of several wild sorghum morphotypes that might correspond to at least three of the five ecotypes recognized in Africa. Intermediate forms between wild and cultivated sorghum belonging to the S. bicolor ssp. drummondii are frequently found in predominantly sorghum growing areas. Crop-wild gene flow in sorghum is likely to occur in many agroecosystems of Kenya.

Genetic resource conservation is widely acknowledged as important. The implementation of conservation requires an insight into the distribution of genetic diversity at the scale of small regions or villages. We present an analysis of rice diversity at such a scale, in a region where traditional farming still prevails. Regional allelic diversity was comparable to that noted worldwide for Asian rice (Oryza sativa), but not as high for African rice (O. glaberrima). Each village pooled more than half of the regional allelic diversity. Genetic differentiation between varieties from the same village accounted for 70% of the regional variation. The differentiation associated with lowland and upland rice-growing ecosystems was 23%, while that associated with differences between villages within the same ecosystem was 7%. In the upland ecosystem, geographical distance had a significant effect on theFSTbetween pairs of villages. In the lowland ecosystem, differences in soil salinity between villages affectedFST. Genetic diversity within a single village may have up to three components: an ancientglaberrimacomponent shared with neighbouring or ethnically related villages; a relatively ancientsativacomponent which was hardly or no longer shared with other villages due to local differentiation; and a recently introducedsativacomponent shared with other villages. Genetic resource conservation could be achieved, in terms of allelic diversity, through stratified sampling according to described genetic differentiation factors, whereas current farming systems must be preserved to ensure conservation of the diversity of allelic associations.

L'article décrit l'ensemble des activités se rapportant aux cacaoyers (Theobroma cacao L.) spontanés du sud-est de la Guyane, depuis leur découverte en 1729 jusqu'aux perspectives découlant de leur étude récente : prospections scientifiques (1987, 1990, 1995), matériel collecté et distribué, sauvegarde en Guyane, caractérisation, étude de la variabilité et de la structuration génétique des populations, sélection et étude de leur valeur en croisement. Une synthèse des recherches menées en Guyane et ailleurs (France, Trinidad, Côte-d'Ivoire, etc.) et des principaux résultats obtenus est présentée. La conclusion insiste sur l'intérêt de ce nouveau matériel en amélioration génétique du Cacaoyer, en particulier pour ses grandes potentialités quant à la productivité, le rapport production/vigueur, les résistances à certaines maladies et la qualité du cacao produit.

Xanthosoma sagittifolium (L.) Schott (Araceae) is a monocotyledon aroid native to the tropical Americas, but its original place of domestication is still unknown. It is widely distributed throughout tropical regions in Africa, Southeast Asia, and Oceania. It is an allogamous species cultivated exclusively by vegetative propagation, preventing any possible genetic recombination. Its adaptive capacity is therefore almost nonexistent, and it is vulnerable to various pathogens such as dasheen mosaic virus (DMV ) or Pythium myriotylum Drechsler ( Lebot, 2009 ). Genetic resources are therefore of great value and need to be carefully identifi ed, conserved, and protected. To date, the molecular genetic diversity of this plant has been investigated using only RAPD markers ( Schnell et al., 1999 ; Offei et al., 2004 ) within a limited number of accessions and across restricted areas. The management of ex situ collections and the accurate identifi cation of clones are often hampered by the lack of effi cient markers. Present knowledge on wild crop relatives, population genetics, and spatial distribution of this species is insuffi cient and limited. It is therefore necessary to develop highly polymorphic codominant markers in X. sagittifolium . Microsatellites or simple sequence repeats (SSRs) are highly polymorphic markers that are codominant and widespread in the genome. Such characteristics make them useful for a large range of applications in genetics. Consequently, they have been developed for a large number of plant species. Here, we present the fi rst set of polymorphic nuclear microsatellite markers suitable for germplasm diversity studies and further genetic conservation in X. sagittifolium . Additionally, the microsatellite primers that gave good results were tested for cross-amplifi cation in related Xanthosoma and Caladium species.

The genetic diversity of endemic Madagascan Coffea species has not received any considerable attention, despite the high extinction threat facing most of the species on the island. In order to address this shortfall, we assessed and compared the genetic diversity and allelic richness of ex situ and in situ populations for four selected species, and 18 ex situ populations maintained at the Kianjavato Coffee Research Station. We also investigated the possibility of in situ and ex situ hybridization events for Madagascan coffee, both within and between species. For these purposes, we used 18 nuclear microsatellite markers, on a total of 37 Coffea populations (4 in situ and 33 ex situ) representing a total of 398 genotypes (96 in situ and 302 ex situ) for 23 species. Our study showed (1) strong differentiation be- tween Madagascan Coffea species; (2) good differentiation between all the populations studied, including those from the same locality (even when the area of the locality was restricted); (3) good evidence for both in situ and ex situ hybridization, although in situ hybridization appeared to be limited; (4) much higher genetic diversity within in situ collections compared to ex situ collections; and (5) that, despite limitations, the Kianjavato Coffee Research Station collection is an extremely valuable resource of Madagascan coffee germplasm. Recommendations for in situ and ex situ germplasm conservation are discussed.

Cacao (Theobroma cacao L.) is the main source for chocolate with an annual production of four million tons worldwide. This Neotropical tree crop was domesticated inMesoamerica as far back as 3,000 years ago. Knowledge of genetic diversity and population structure in farmer varieties of cacao in the center of domestication is essential for sustainable production of fine-flavored cacao beans and contributes to in situ/onfarm conservation of farmer varieties. Based on 70 single nucleotide polymorphism markers, we analyzed 84 fine-flavored farmer varieties collected from traditional cacao farms in Honduras and Nicaragua. The study also included 31 clones from the international cacao collections to serve as references. The SNP based multilocus matching identified six synonymous groups, including 14 Criollo and two Amelonado varieties. A moderately high level of genetic diversity was observed in these farmer varieties, indicating the possibility to further explore intra-population variation and breed for fine-flavored cocoa. Multivariate analysis showed clustering of the 84 farmer accessions in five genetic groups: ancient Criollo, Amelonado, Trinitario (including Nicaragua Trinitario and Honduras Trinitario) and Upper Amazon Forastero (only one accession). The Honduras Trinitario differed from the Nicaragua Trinitario group. The clustering results largely supported the perceived classification of cacao by local farmers and researchers, which was mainly based on morphological traits. However, the well known traditional variety ''Indio'' in this region was identified as synonymous with Amelonado. Parentage analysis showed that the variety ''Indio'' (or Amelonado) contributed more to the Trinitario type farmer varieties, whereas ancient Criollo had less influence. The present study demonstrates the efficacy of using a small set of SNP makers for cacao germplasm characterization, and further depicts the diverse origins and parentage in farmer varieties from Mesoamerica. This information thus will be highly useful for conservation and utilization of cacao germplasm from this region.

By summarizing surveys conducted on 27 islands of the Pacific region, this chapter reports some traditional knowledge associated with coconut genetic resources and explains how this knowledge has strongly contributed to formulating the concepts and strategies in the conservation of genetic resources. Polynesians have used small islands as conservation areas for their coconut varieties. Since 1930, the number of coconut palms increased but the varieties mixed and the related traditional knowledge dwindled. Based on traditional Polynesian knowledge, the Polymotu concept uses the geographical isolation of special sites for the conservation and reproduction of varieties of coconut. For instance, when isolated site on island is planted with one variety of coconut, breeding occurs only within this variety and certified drupes are then available to farmers. In 2009, the Polymotu concept was included in the global coconut conservation strategy developed by the International Coconut Genetic Resources Network. However, traditional coconut varieties and associated knowledge are continuing to disappear. Decision-makers at the local, national and intenational levels should adopt effective portfolios of strategies and gender-sensitive guidelines to ensure both the effective conservation of coconut genetic resources and associated knowledge, and the availability of diversified planting material for replanting programs.

Mieux connaître les dynamiques de l'agrobiodiversité est nécessaire pour intégrer sa préservation et sa valorisation dans les stratégies d'augmentation de la productivité agricole. La dynamique de la diversité variétale du riz a été analysée dans la région de Vakinankaratra, Madagascar, en 2006, à travers des enquêtes collectives et individuelles auprès d'un échantillon de 1 050 exploitations réparties dans 32 villages, et par la collecte et la caractérisation des variétés de riz utilisées dans ces villages. La richesse variétale moyenne des villages (10,9) et des exploitations (2,2) est comparable à celle qui est observée dans d'autres agrosystèmes traditionnels, mais on observe une grande variabilité régionale dont les déterminants sont l'altitude, les systèmes agraires, les rizicultures pratiquées et la richesse des exploitations. Il existe une grande disparité dans la fréquence d'utilisation des variétés, un grand nombre de variétés " mineures " étant utilisées par moins de 10 % des exploitations. La gestion des semences se caractérise par l'absence de sélection pour la pureté variétale mais aussi par l'élimination des grains mal remplis. L'adoption de nouvelles pratiques de gestion des variétés et des semences, associée au développement récent de la riziculture pluviale, montre l'ouverture de ces agriculteurs aux innovations. Les perspectives du maintien de la diversité génétique in situ sont discutées.

In the present study, the efficiency of two cryopreservation strategies for oil palm (Elaeis guineensis Jacq.) was compared. If extracted from rehydrated kernels, 65% of the embryos desiccated to around 0.3 g H2O/g DW developed into plantlets after cryopreservation. In contrast, only 25% of embryos (0.12 g H2O/g DW) extracted from cryopreserved dry kernels developed into plantlets. However, this value was increased to 63% if kernels were partially rehydrated before freezing until the water content of embryos reached 0.3 g H2O/g DW. This study emphasizes the importance of partial rehydration of oil palm embryos before cryopreservation.

Pour plusieurs sociétés de par le monde, la sécurité alimentaire repose encore aujourd'hui sur une agriculture familiale. L'objectif de cette thèse est de décrire et d'analyser comment les agriculteurs font face à la variabilité climatique. Le versant est du Mont Kenya est caractérisé par une forte variabilité climatique, sociale et culturelle. Les systèmes agricoles intègrent une diversité d'espèces et de variétés. Sans irrigation, ils dépendent exclusivement de la pluviométrie. Une double approche comparative a été utilisée pour isoler les facteurs sociaux et environnementaux dans notre analyse, en comparant trois altitudes (750 m, 950 m et 1100 m) et deux sociétés (Mwimbi et Tharaka). La diversité au niveau inter et intra spécifique est structurée en fonction de l'altitude et des communautés. Le savoir traditionnel des agriculteurs concernant les climats passés s'avère précis lorsqu'on le compare aux données pluviométriques. Avec l'adoption du maïs au détriment du sorgho et du mil, l'évolution des systèmes de cultures a induit un risque plus élevé aujourd'hui qu'auparavant de perdre des variétés lors des sécheresses. Cependant, l'effet négatif de la variabilité climatique n'est pas homogène; les agriculteurs, par leur savoir et leurs pratiques, atténuent l'effet de la variabilité climatique sur les plantes cultivées. Les dates de semis sont variables pour garantir l'humidité adéquate pour la germination des graines en début de saison des pluies. L'adaptabilité génétique des semences diffèrent fort probablement selon les communautés, certaines évoluant depuis plusieurs années en zones très arides (Tharaka à 750 m) alors que d'autres sont plus adaptées à des climats plus cléments (Mwimbi à 1100 m). Les agriculteurs font donc face à la variabilité climatique avec des ressources génétiques qu'ils gèrent et reproduisent historiquement. L'interaction des facteurs sociaux, écologiques, historiques et génétiques devraient davantage être considérée dans les programmes d'amélioration variétale pour faire face à la variabilité climatique.

This publication provides information and guidance on safe movement and duplication of coconut (Cocos nucifera L.) germplasm using embryo culture transfer protocols. It represents the main output of a project aiming at validating and applying the adapted protocol to provide users with an up-to-date, reliable method for effectively transferring coconut germplasm. Most importantly, embryo transfer offers an important facility for duplicating unique accessions housed in certain coconut genebanks in other genebanks to minimise the risk of losing them.

International audience; Le quinoa (Chenopodium quinua Willd.), cultivé de façon traditionnelle par les populations andines depuis plus de 5000 ans, est devenu une production marginale au Chili. Pourtant, il est l'unique espèce cultivable de l'altiplano et son extension jusqu'au sud de Temuco a généré une grande diversité de l'espèce. L'objectif du projet IMAS (Impact des modalités d'accès aux semences) fut donc d'analyser les pratiques de gestion des ressources génétiques en quinoa in situ dans les trois principales zones de production et les facteurs susceptibles d'influencer ces pratiques, dans un futur plus ou moins proche. Un travail conceptuel basé sur le développement d'un modèle type multi-agents (ABM: Agent-Based Models) générique a permis de décrire les acteurs et leurs règles de prise de décision. Des simulations informatiques permettent d'analyser l'impact de scénarios prospectifs. Nous utilisons des jeux de rôles pour partager notre représentation du système, valider le modèle de façon participative et dialoguer autour des scénarios avec des acteurs aux points de vue différenciés (chercheurs, institutions et agriculteurs). Les jeux de rôles et simulations des scénarios sont une version simplifiée de la réalité avec un nombre réduit et orienté des variables d'entrée. Les processus de prise de décision sont conservés et les variables de sortie servent de base à une discussion sur les dynamiques. Un locus est mis sur l'évolution de l'agrobiodiversité dans l'analyse de l'impact des différents scénarios. Une perspective de cette plateforme de dialogue est d'amorcer une nouvelle phase de recherche-action orientée par la volonté des acteurs en faveur d'un scénario en particulier avec l'appui de la recherche.

Protocols are proposed for the low (-20°C) and ultra-low (-80°C) temperature storage of coconut (Cocos nucifera L.) embryos. A tissue dehydration step prior to storage, and a rapid warming step upon recovery optimized the protocol. The thermal properties of water located within the embryos were monitored using differential scanning calorimetry (DSC). In the most efficient version of the protocol, embryos were dehydrated under a sterile air flow in a dehydration solution containing glucose (3.33 M) and glycerol (15%) for16 hours. This protocol decreased the embryo water content from 77 to 29% FW and at the same time reduced the amount of freezable water down to 0.03%. The dehydrated embryos could be stored for up to 3 weeks at -20°C (12 % producing normal plants upon recovery) or 26 weeks at -80°C (28% producing normal plants upon recovery). These results indicate that it is possible to store coconut germplasm on a medium term basis using an ultra-deep freezer unit. However for more efficient, long term storage, cryopreservation remains the preferred option.

International audience; Since 2007, research institutes and grapevine collections from 17 countries of Europe, Caucasus and North Africa are working together for the conservation, characterization and management of grapevine genetic resources. The initial work consisted in inventorying and describing the varieties in the partners’ collections, using standardized morphological, agronomic, and molecular descriptors, and to link the information into a unique European web-database. The growing database contains today passport data from 25.000 living accessions, of which 2.500 are linked to photos and 1.600 are characterized for 48 OIV descriptors and 9 microsatellite markers. The project is also working on 448 old autochthonous varieties that have presented a regional interest in the past but are not clearly identified. Comparing their microsatellite fingerprint with the total database will enable us to find if they are original resources and to uniquely define their traits. The database website is open for consultation, with different levels of access that allows indept searches but also confidentiality, according to the user needs. At the end of 2010, the fingerprint data will also be online, so that other collections or professionals can check their own varieties against the referenced varieties to verify names and true-to-typeness. The final objective of the European project is to promote an optimized conservation scheme of the Vitis germplasm, involving ex-situ, cryo- and on-farm conservation, so that the resources are permanently maintained, easily accessible and field-tested in a pertinent agricultural context. This network of resources will also provide plant material as a basis for biotechnology, genomic and breeding research.; Depuis 2007, les institutes de recherche et les collections de vigne de 17 pays d’Europe, du Caucase et d’Afrique du Nord collaborent pour la conservation, la caractérisation et la gestion des ressources génétiques de vigne. Le travail initial a consisté à inventorier et décrire les variétés des partenaires, en utilisant des descripteurs morphologiques, agronomiques et moléculaires standard, et liant l’information dans une base de données européenne unique. La base de données grandissante contient aujourd’hui les données passeport de 25.000 accessions vivantes, dont 2.500 sont décrites par des photos et 1.600 sont caractérisées pour 48 descripteurs OIV et 9 marqueurs microsatellite. Le projet travaille également sur 448 variétés autochtones ayant présenté un intérêt régional dans le passé mais mal identifiées. Comparer leur profile microsatellite avec l’ensemble des données nous permettra de déterminer leur originalité et de définir de manière non-équivoque leurs caractéristiques. La base de données est ouverte au public, et prévoit des niveaux d’accès différents, pour permettre les recherches approfondies ainsi que la confidentialité, selon les besoins de l’utilisateur. Fin 2010, les données moléculaires seront également publiques, permettant aux professionnels de vérifier la conformité de leurs variétés. 3 L’objectif final du projet européen est de promouvoir un schéma optimal de conservation des ressources de vigne, impliquant conservation ex-situ, la cryo-preservation et la conservation à la ferme, pour pérenniser les ressources de vigne, les rendre facilement accessibles et les tester dans leur contexte agricole. Ce réseau de ressources fournira également le matériel de base pour la recherché en biotechnologie, génomique et sélection.; Dal 2007, gli istituti di ricerca e le collezioni di vite di 17 paesi d’Europa, del Caucaso e del Nord-Africa collaborano per la conservazione, la caratterizzazione e la gestione delle risorse genetiche della vite. Inizialmente, il lavoro ha consistito nell’inventario e la descrizione delle varietà delle collezioni partner, utilizzando descrittori morfologici, agronomici e molecolari standardizzati, le cui informazioni sono poi inserite in un unico database Europeo. Il database sta crescendo e contiene oggi i dati passaporto di 25.000 varietà viventi, di cui 2.500 sono descritte da foto e 1.600 da 48 descrittori OIV e 9 marcatori microsatelliti. Il progetto sta inoltre lavorando su 448 antiche varietà autoctone che hanno presentato un interesse regionale nel passato, ma che sono mal identificate. Comparare il loro profilo genetico con il database permetterà di determinare la loro originalità e di definire inequivocabilmente le loro caratteristiche. Il database e’ accessibile al pubblico, e prevede diversi livelli di accesso permettendo una ricerca approfondita e allo stesso tempo la confidentialità, secondo i bisogni degli utilizzatori. Alla fine del 2010, la base dei marcatori molecolari sarà ugualmente aperta, permettendo cosi’ ai professionisti di verificare la conformità delle loro varietà. L’obiettivo finale del progetto europeo e’ di organizzare uno schema ottimale di conservazione delle risorse di Vitis, facendo ricorso a metodi ex-situ, di crio-preservazione e conservazione in fattoria, permettendo la perenizzazione delle risorse, rendendole facilmente accessibili e analizzandole nel contesto agricolo. Questa rete di collaborazione potrà anche provvedere materiale di base per la ricerca in biotecnologia, genomica e selezione.

Corresponding author. Present address: The Muhammadiyah University of Purwokerto, Biology Education Department, Kampus Dukuhwaluh, Purwokerto 53182, Indonesia. Fax: +61 62281637239. E-mail address: Sisunandar@ump.ac.id (Sisunandar). Present address: Indonesian Oil Palm Research Institute, Jl Brigjen Katamso 51, Medan, North Sumatera, Indonesia; International audience; Cryopreservation of coconut can be used as a strategy to back up the establishment of living collections which are expensive to maintain and are under constant threat from biotic and abiotic factors. Unfortunately, cryopreservation protocols still need to be developed that are capable of producing a sizeable number of field-grown plants. Therefore, we report on the development of an improved cryopreservation protocol which can be used on a wide range of coconut cultivars. The cryopreservation of zygotic embryos and their recovery to soil-growing plants was achieved through the application of four optimised steps viz.: (i) rapid dehydration; (ii) rapid cooling; (iii) rapid warming and recovery in vitro and (iv) acclimatisation and soil-supported growth. The thermal properties of water within the embryos were monitored using differential scanning calorimetry (DSC) in order to ensure that the freezable component was kept to a minimum. The feasibility of the protocol was assessed using the Malayan Yellow Dwarf (MYD) cultivar in Australia and then tested on a range of cultivars which were freshly harvested and studied in Indonesia. The most efficient protocol was one based on an 8-h rapid dehydration step followed by rapid cooling step. Best recovery percentages were obtained when a rapid warming step and an optimised in vitro culture step were used. Following this protocol, 20% (when cryopreserved 12 days after harvesting) and 40% (when cryopreserved at the time of harvest) of all MYD embryos cryopreserved could be returned to normal seedlings growing in soil. DSC showed that this protocol induced a drop in embryo fresh weight to 19% and significantly reduced the amount of water remaining that could produce ice crystals (0.1%). Of the 20 cultivars tested, 16 were found to produce between 10% and 40% normal seedlings while four cultivars generated between 0% and 10% normal seedlings after cryopreservation. This new protocol is applicable to a wide range of coconut cultivars and is useful for the routine cryopreservation of coconut genetic resources.

Au Burkina Faso, les paysans gèrent une grande diversité variétale de sorgho dans différentes conditions agro-écologiques. Le but de cette étude est de décrire et analyser les diversités agro-morphologique et génétique de variétés locales de sorghos collectées en 2003 et 2004 dans trois régions agricoles du Burkina Faso (le Centre-nord, le Centre-ouest et la Boucle du Mouhoun), d'identifier les forces majeures qui influent sur leurs évolutions et de proposer des méthodes de gestion et de valorisation de la diversité. Deux approches à la fois agro-morphologique et génétique ont servi à caractériser la diversité inter-variétale et intra-variétale. La caractérisation inter variétale a été conduite avec 124 variétés locales à l'aide de 28 caractères agro-morphologiques et 29 marqueurs microsatellites. Quatre vingt quatorze pour cent (94,4 %) des variétés locales appartiennent à la race botanique Guinea composée de deux sous races : les gambicum 96,6 % et les margaritiferum 3,4 %. Les Bicolor et Durra-Bicolor représentent chacun 0,8 %. Quatre pour cent (4 %) des variétés n'ont pu être rattachés à un groupe botanique ; ceux-ci seraient des hybrides de Guinea. Les variétés à grains blancs représentent 74,2 %, celles à grains orangés 13,7 %, et celles à grains rouges 12,1 %. La plus grande part de la diversité est expliquée par le facteur variété, significatif pour tous les caractères, en particulier pour le cycle (R² = 0,84) et le poids de 1000 grains (R² = 0,79). En dehors de la durée de cycle, les facteurs " village et zone agro-écologique " ont une faible influence sur la diversité agro-morphologique, structurée en cinq groupes dont un groupe de sorghos précoces à grain rouge. Ces groupes ont été discriminés sur les critères de vitrosité du grain, de longueur de cycle et de panicule ainsi que de poids de 1000 grains. Le taux de polymorphisme génétique est de 79,3 %, avec une diversité allélique de 4,9 allèles par locus et une diversité génétique de 0,37. La diversité génétique à l'instar de la diversité agro-morphologique est aléatoirement répartie et ne respecte aucun critère. Les Guinea margaritiferum apparaissent génétiquement distincts des Guinea gambicum. Les variétés à grain rouge constituent un groupe génétiquement homogène. La différenciation génétique est faible entre les villages (Fst=0,06) et entre les zones agro-écologiques (Fst=0,04). C'est plutôt la couleur de grain avec un Fst=0,08 qui apparaît comme le principal facteur de structuration. La caractérisation intra-variétale a été réalisée avec dix variétés à grain blanc de la race Guinea gambicum, choisies parmi les 124 variétés de la caractérisation inter-variétale. Ces variétés présentent des cycles différents, et sont soumises à des modes de gestion différents dans les espaces agraires. Onze caractères agro-morphologiques et douze marqueurs microsatellites ont servi à caractériser la variabilité de 25 panicules par variété. Les niveaux de diversité intra-variétale diffèrent de manière plus ou moins importante entre les variétés. Les plus faibles variances agro-morphologiques ont été observées au sein des variétés précoces, et les plus fortes variances au sein des variétés tardives. Les variétés précoces sont nettement discriminées des variétés tardives et intermédiaires sur les critères de durée de cycle, de longueur de panicule, de productivité et de poids moyen de 1000 grains. Le taux de polymorphisme génétique est de 100 %, avec une diversité allélique de 5,7 allèles par locus, et une diversité génétique de 0,53. Les plus fortes valeurs de polymorphisme comme de diversité génétique sont observées au sein des variétés tardives. La différenciation génétique globale est forte (Fst=0,39). Génétiquement les variétés précoces constituent un groupe à part, bien différencié des variétés de cycles intermédiaire et tardif, entre lesquelles la différenciation est faible (Fst=0,06). Le taux d'allogamie est de 22 %. Cette étude a montré que les niveaux de diversité agro

Crop species are characterised by their intimate association with human populations, their history and their practices and needs. In long domesticated crops, migration can have expanded gradually within continents and jumped between continents, shaping global patterns of diversity and adaptation. Sorghum (Sorghum bicolor bicolor) is one such case of very successful crop, which was domesticated in Subsahelian Africa and is now grown throughout the world. Here we review conclusions of recent studies conducted at various geographical scales (field, village, region, country, continent), sometimes including temporal variation, and practised at the level of morpho-agronomic traits, whole-genome molecular markers as well as selected candidate genes. Local diversity in the area of sorghum origin is almost as large as whole-species diversity, with peripheral regions displaying specific genotypic combinations corresponding to distinct races, but very limited specific genic diversity. This pattern of diversity is accompanied with a generally low level of linkage disequilibrium, which is confined to genome segments within the Mb range. A focus on certain genes involved in cereal grain quality revealed cases of novel alleles that appeared during the course of migration outside the centre of origin, being likely selected by the action of the farmers, highlighted the potential of neo-diversity for crop diversification. The diversity of human groups acts together with the agro-ecological factors to shape the structure of sorghum genetic diversity. As detailed in a village in Cameroon, introgression occurs among weedy types and cultivated types, yielding an array of intermediates; farmers identify and name them, and actively select against certain morphotypes, but several practices unconsciously favour gene flow. Based on a study covering 79 villages in Niger, no genetic erosion occurred over a 26 year period; farmers' management can preserve the diversity despite recurrent and severe drought periods and major social changes. The tremendous diversity maintained by farmers in traditional agroecosystems of Western Africa supports the development of crop improvement approaches making broad use of local germplasm in decentralized breeding programs.(Texte intégral)

The genetic diversity of coconut (Cocos nucifera L.) is being lost due to a combination of pest and disease attack and natural disasters. Consequently, there is a need to undertake germplasm conservation before further loss occurs. Since coconut has a large, recalcitrant seed (sensitive to desiccation), it cannot be stored in traditional ways using a seed bank. Cryopreservation is now seen as an important storage approach although available techniques need further improvement. Given the importance of embryo maturity to the success of cryopreservation in other species, the effect of coconut embryo maturity upon cryopreservation success was investigated using two cultivars (Nias Yellow Dwarf and Takome Tall). After cryopreservation, using a new four-step protocol (rapid desiccation, rapid freezing, rapid thawing, and recovery and acclimatization S2 SPEAKER ABSTRACTS for 16 wk in the glasshouse), we found that that embryos isolated from an 11-mo-old fruit gave the highest number of normal seedlings (ca. 28%) when compared to counterparts excised from younger or older fruits. In addition, the results showed that the fruit could be stored for up to 3 wk prior to the isolation of embryos before their performance in cryopreservation was compromised. No morphological and cytological abnormalities were observed in the seedlings recovered from 11-mo-old cryopreserved embryos when compared to their un-cryopreserved counterparts. Genetic and epigenetic testing using microsatellite and global DNA methylation rates could not detect any significant differences between genomic DNA isolated from seedlings recovered from cryopreserved compared to their un-cryopreserved counterparts [S-008]. (Texte intégral)

Rice varietal diversity was assessed in Guinea on the basis of surveys of 1679 farms located in 79 villages of the four natural regions of the country. The descriptors used were the number of known varieties, the number of cultivated varieties and Shannon's diversity and evenness index. On the basis of their use rates, varieties were classified as major or minor types at the village scale and as regionally and/or nationally eminent varieties at these scales. Varietal diversity was high, especially in forest Guinea and lower Guinea. Diversity pattern was typical of the subsistence farming system. The high share of local variety reflected the predominance of low management and low input cropping systems. The presence of improved varieties confirms farmers' openness to innovation and to the government policy of promoting improved varieties. Regional diversity reflected the agro-ecological diversity and specificities of each region, the history and the extent of rice-growing systems, and the importance of rice in the local diet. Recent dissemination of NERICA varieties has not caused any reduction of pre-existing varieties. The short-duration NERICA are mainly used as a complement to the long-duration traditional varieties and thus enhance varietal diversity. Risks of diversity erosion seem limited in the current setting of farming system and diversity structure. However, at the village level, the diversity pattern is fragile as the proportion of farmers who used each variety of the village is low and heterogeneous. A continuous monitoring of the dynamics of rice varietal diversity in Guinea is needed.

In France, cryopreservation is currently used for a limited number of forest tree species, but has been applied yet very little to horticultural or other agricultural species. The CRYOVEG project aims at (1) developing or optimizing cryopreservation techniques in a range of selected species; and (2) establishing a national scientific and technical network of plant biological resource centers (CRBs) using cryopreservation. The project has a network organization, with IRD/INRA Montpellier as the cryopreservation expertise centre and partners in continental France and in overseas departments in charge of genetic resource conservation for various species: INRA Petit Bourg, Guadeloupe (yam); INRA San Giuliano, Corsica (Citrus); INRA Bordeaux (Prunus); INRA Angers (apple and pear); INRA Montpellier (grapevine); INRA Ploudaniel (potato, Brassica); IRD La Réunion (coffee); CIRAD Roujol, Guadeloupe (sugarcane); and CIRAD La Réunion (vanilla, garlic). Deliverables will vary depending on the state-of-the-art of cryopreservation for each species: for potato, yam, sugarcane, garlic, Citrus, Brassica and coffee, optimized protocols will be tested on a range of representative accessions. For grapevine, Prunus, apple, pear and vanilla, operational protocols will be developed. The group will work as a think-tank on the integration of cryopreservation in the national plant genetic resource conservation strategy and an action plan for its implementation will be collectively designed. The project will work towards establishing a French research network on plant genetic resource cryopreservation, open to all partners interested in cryopreservation. The group will prepare research and development projects whose results will be disseminated through European plant genetic resource conservation networks e.g. ECP/ GR). Finally, network members will train French and foreign (from North and South countries) researchers and technicians in cryopreservation techniques. (Conflicts of interest: None declared. Source of funding: This project is supported by a French competitive grant (Call for Projects 2008 ''Biological Resource Centers") of the Consultative Committee for Biological Resources/Infrastructures in the Biology, Health and Agronomy sectors (CCRB/IBiSA).). (Texte intégral)

Genetic resources conserved in vivo in field collections remain exposed to diseases, pest attacks and weather calamities such as hurricanes. in vivo collections have also high maintenance costs and can retain only a limited genetic diversity, particularly among species. The use of tissue culture and crypreservation, which have been developed over the past 30 years helps to overcome these disadvantages. Specifically, cryopreservation (storage at the temperature of liquid nitrogen, - 196°C) is the only technique that ensures the long term, safe and cost effective conservation of genetic resources of vegetatively propagated and non orthodox see plant species are conserved in Cirad la Réunion. In order to ensure their safe, long-term cost is effective conservation, it is necessary to develop cryopreservation techniques. Tropical garlic is our priority crop. Therefore, as mentioned in my application form, cryopreservation techniques will be applied to establish a cryopreserved collection of garlic germplasm in CIRAD La Réunion. This training period had two main objectives : to become acquainted with the cryopreservation techniques, for their futur application to the plants maintained in the Biological Resource Centre ( CRB) under establishment in Cirad la Réunion.

Au Burkina Faso, au Mali, au Niger et a Wante, 1 518 echantillons de sorgho ont ete collectes et analyses a l’aide de marqueurs microsatellites. Les parametres de diversite et de differenciation genetique ont ete estimes a differentes echelles spatiales, depuis celle de la variete locale a celle du pays, pour determiner l’effet des principales forces evolutives sur la diversite genetique du sorgho. Il existe une diversite intra-varietale principalement determinee par la biologie de la reproduction du sorgho et par les derives genetiques engendrees par les effectifs limites d’individus lors de l’introduction d’une variete ou de la selection paysanne de la semence. A l’echelle d’un village, la correlation entre la diversite des noms vernaculaires et la diversite genetique mesuree par les marqueurs microsatellites est faible. Aucune structuration spatiale n’est observee dans des villages distants de plus de 30 kilometres soulignant le caractere tres local des systemes semenciers traditionnels. Au Mali et au Niger, une proportion equivalente et superieure, respectivement, de la diversite genetique du sorgho est observee sur un transect longitudinal qui recoupe essentiellement des divisions ethnolinguistiques, par rapport au transect latitudinal qui recoupe une variabilite agro-ecologique plus grande. La diversite des groupes humains explique donc, en interaction avec les conditions environnementales, la diversite genetique du sorgho in situ. Une grande partie de la diversite presente dans la core collection sorgho du Centre de cooperation internationale en recherche agronomique pour le developpement (Cirad) se retrouve a l’echelle de pays comme le Niger ou le Mali. L’importance de la diversite genetique cultivee par les paysans dans des systemes agricoles restes traditionnels souligne l’utilite des approches de conservation in situ des ressources genetiques. La conciliation des enjeux de conservation et d’amelioration varietale pourrait etre realisee par un recours plus important au germoplasme local dans des programmes de selection decentralises.

Cette mission avait pour but le suivi du programme de sauvegarde de la collection de cacaoyers dans le cadre du projet FIRC Guyane.

In Maritime Guinea, the interpenetration of upland, lowland and mangrove rice growing ecosystems has found expression in the cohabitation of the two rice cultivated species. Recent changes in cropping practices may lead to the replacement of local varieties by modern high-yielding varieties. In the framework build-up of a strategy for the preservation of local varieties, we analysed the extent, the organisation and the specificities of the rice genetic diversity. One hundred seventy accessions collected in farmers’ fields were genotyped with 11 SSR markers and phenotyped with 26 morpho-physiologic descriptors. The general organisation of rice genetic diversity in Maritime Guinea, and its tight relationship with the rice growing ecosystems were similar to the one observed elsewhere. The two major subspecies of O sativa––indica and tropical japonic––as well as the two major ecotypes of O. glaberrima––“floating” and “upright”––were present. Moreover, an original genetic compartment was detected, highlighting the occurrence of glaberrima × sativa hybridisation. Allelic diversity was found to be comparable to that noted worldwide for indica and japonica groups of O. sativa, but not as large for O. glaberrima. Given its extent, its original compartment, and its potential for inter-specific and inter-subspecific indica × japonica recombination, the preservation of rice genetic diversity in Maritime Guinea deserves special attention.

Rice genetic diversity partitioning between farms, varieties and, within-variety diversity, were analysed in two villages of Maritime Guinea with contrasted agroecological conditions. One thousand and two hundred individual plants belonging to 45 accessions collected in eight farms were genotyped using 10 SSR markers. The molecular variance was evenly shared between and within accessions, while the farm effect was almost nil. Local varieties had a multi-line genetic structure. The number of multilocus genotypes was proportional to the utilisation rate of the variety in the village. The F ST values between different accessions of each variety were significant which indicated low genetic consistency in the variety names. This varietal structure could mainly be explained by the migration phenomenon and the high varietal turnover. Compared to allelic diversity, multilocus genotypic diversity seemed to be the most suitable indicator of the quantitative distribution of diversity at different management scales (accession, farm and village). The within- and between-farm F ST values were in the same order of magnitude. The within-farm diversity was not farm-specific but quantitatively high, i.e. up to 50% of the total genotypic diversity of a given village. Given the relative importance of the within-variety diversity, the in situ approach stands out as the most effective solution. As farms do not host specific diversity the in situ approach could be implemented by working with a small number of farms.

Encapsulation-dehydration is a cryopreservation technique based on the technology developed for producing synthetic seeds, i.e. the encapsulation of expiants in calcium alginate beads. Encapsulated expiants are then precultured in liquid medium with a high sucrose concentration and partially desiccated before freezing. Encapsulating the expiants allowsthe subsequent application of very drastic treatments including preculture with high sucrose concentrations and desiccation to low moisture contents which would be higly damaging or lethal to non-encapsulated samples. An encapsulation-dehydration protocol comprises the following steps: pretreatment, encapsulation, preculture, desiccation, freezing and storage, thawing and regrowth. Encapsulation-dehydration has been applied to around 40 different plant species. The optimization of the successive steps of the encapsulation-dehydration protocol is illustrated for sugarcane apices.

Oil palm seeds have been classified as intermediate with regards to their storage behaviour. Therefore, genetic resources of this species cannot be conserved in the form of dry seeds at low temperature, as is the common practice for orthodox seeds. At present, the traditional ex situ method to preserve genetic resources of oil palm is as whole plants in the field. The establishment of field collections is made easier by the perennial character of this species. However, field collections remain exposed to natural disasters and attacks by pests and pathogens. The advent of biotechnology allows improvements to be made for long-term ex situ conservation of this species, through the storage of zygotic and somatic embryos in liquid nitrogen (-196°C). Research performed at the GeneTrop laboratory (Montpellier, France) has shown that partially desiccated excised mature embryos and whole kernels can be successfully cryopreserved. This approach ensures the conservation of various populations provided that the fertilization is controlled. Another approach uses embryogenic tissues established from elite hybrids or genetically transformed material, thus allowing the conservation of genotypes. A protocol has been developed for the cryopreservation of polyembryonic cultures, which includes a pregrowth treatment of cultures on medium with high sucrose content followed by partial desiccation and rapid freezing. This protocol has been successfully applied to clones of 80 different genotypes, leading to the establishment of a cryobank of oil palm germplasm in the GeneTrop laboratory in 1995. More recently, cryopreservation of embryogenic cell suspensions and of single somatic embryos has been achieved, thus making it possible for the cryopreservation of materials from elite trees. These results illustrate the potential and feasibility of using biotechnology to improve the long-term ex situ conservation of oil palm genetic resources.

Background and Aims The impact of evolutionary forces on insular systems is particularly exacerbated by the remoteness of islands, strong founder effects, small population size and the influence of biotic and abiotic factors. Patterns of molecular diversity were analysed in an island system with Santalum insulare, a sandalwood species endemic to eastern Polynesia. The aims were to evaluate clonality and to study the genetic diversity and structure of this species, in order to understand the evolutionary process and to define a conservation strategy. - Methods Eight nuclear microsatellites were used to investigate clonality, genetic variation and structure of the French Polynesian sandalwood populations found on ten islands distributed over three archipelagos. - Key Results It was found that 58% of the 384 trees analysed were clones. The real size of the populations is thus dramatically reduced, with sometimes only one genet producing ramets by root suckering. The diversity parameters were low for islands (nA = 1·5-5·0; HE = 0·28-0·49). No departure from Hardy-Weinberg proportion was observed except within Tahiti island, where a significant excess of homozygotes was noted in the highland population. Genetic structure was characterized by high levels of differentiation between archipelagos (27% of the total variation) and islands (FST = 0·50). The neighbour-joining tree did not discriminate the three archipelagos but separated the Society archipelago from the other two. - Conclusions This study shows that clonality is a frequent phenomenon in S. insulare. The genetic diversity within populations is lower than the values assessed in species distributed on the mainland, as a consequence of insularity. But this can also be explained by the overexploitation of sandalwood. The differentiation between archipelagos and islands within archipelagos is very high because of the limited gene flow due to oceanic barriers. Delineation of evolutionary significant units and principles for population management are proposed based on this molecular analysis. (Resume d'auteur)