Do yams (Dioscorea spp.) host endogenous viral sequences ?

Yams (Dioscoreae sp) are important food commodities in tropical and subtropical areas of Africa, the Caribbean, South America and the Pacific where they play a key role in food security. Yams are vegetatively propagated crops. The use of infected vegetative propagules and uncontrolled introductions of infected germplasm promotes the spread of viruses in yam-growing areas, causing significant reduction in tuber yield and quality. Control strategies rely primarily on diagnostic and the use of virus-free germplasm, but their implementation is currently hampered by the high prevalence level of potyviruses and badnaviruses in yam germplasm and the overall partial knowledge of virus species infecting yams. Moreover, the presence of endogenous pararetrovirus sequences (EPRVs) in Dioscorea spp, which is suspected [1] but has not yet been formally demonstrated, could also hamper the implementation of reliable indexing tests and control strategies, especially if yams host infectious EPRVs. The presence of EPRVs in cultivated and wild yams was investigated in the yam germplasm collection of the Tropical Plant Biological Ressource Center (CRB-PT) managed by INRA in Guadeloupe. This collection currently hosts 500 accessions representing 15 distinct species. PCR-based screenings were performed on Dioscorea alata, D. trifida, D. rotundata-cayenensis and wild yam accessions using badnavirus-specific primers [2], caulimovirus-specific primer [3] and primers specific of a newly described genus within the family Caulimoviridae tentatively named dionyvirus (Geering et al., unpublished). Phylogenetic analyses were performed, allowing a study of the diversity of yam badnavirus, caulimovirus and dionyvirus sequences. Southern blot experiments were also performed in order to explore the nature (endogenous vs episomal) of these sequences. (Texte intégral

Improved diagnosis tools for the detection of yam virus in the sanitation process and unveil virus-free accessions for producers' exchange

French West Indies Biological Resources Centre for Tropical Plants (CRB-PT) maintains several germplasm collections of tropical crops and wild relatives, including a collection of more than 450 yam accessions (Dioscorea spp) in vitroculture. The purpose of this Centre is to conserve this biodiversity and distribute virus-free germplasm to end users. To this aim, virus populations infecting conserved accessions have been characterized and the diversity of intra and inter-species highlighted through the SafePGR project. Thus, three new virus generi have been found out (Ampelovirus, Macluravirus and Sadwavirus) besides those existing (Badnavirus [1], Potyvirus [2] and Potexvirus [3]). Efficient extraction method and appropriate detection tools have been created and/or optimized, then implemented for an initial diagnosis of the in vitro collection. Prevalence shown that more than 75% of yam accessions are infected by Potyvirus, 80% of D. alata, the most cultivated yam, are infected by the new yam virus Ampelovirus and Macluravirus are only present in D. alata. Only 14 accessions remained free of viruses, but the majority of the collection contained one, two or more of viruses, so the necessity to sanitize the infected germplasm. The sanitation process consists to submit shoots to thermotherapy at 34°C, then in excising apical meristem to obtain the regeneration of a new plant, expecting to be free of viruses. Using optimized detection tools, each new plant is diagnosed for the six viral generi. Up to now, the sanitation process leads to the achievement of 8 accessions completely virus-free. The development and yield of this improved plant material have to be evaluated by comparison of infected and sanitized accessions

Les espèces d'oiseaux nicheuses menacées de Guadeloupe, Petites Antilles : évaluation par l'application au niveau régional des critères de la liste rouge de l'UICN

L'amélioration des connaissances sur les oiseaux de Guadeloupe acquises ces trente dernières années sur l'évaluation de leur diversité, sur leurs populations et sur leurs densités ainsi que sur les menaces pesant sur elles a conduit à une meilleure connaissance de leur statut. Deux cent quarante et une espèces ont été reportées de Guadeloupe incluant 84 espèces nicheuses dont une endémique. Dix autres espèces qui avaient autrefois été nicheuses ne nichent plus, trois d'entre elles étant éteintes mondialement et 4 ayant disparu de l'archipel. L'analyse des populations et l'évolution récente observée ont conduit l'UICN à classer 3 espèces sur sa liste rouge, une vulnérable (Cichlerminieri lberminieri) et deux proches de menacées (Fulica caribea et l'endémique Melanerpes berminieri). L'application des critères de liste rouge au niveau régional en Guadeloupe conduit à lister 19 espèces nicheuses supplémentaires. D'autres espèces n'ont pu être évaluées faute d'information adéquate. Ainsi, même si la richesse de la diversité de la Guadeloupe évaluée par le nombre d'espèces d'oiseaux nicheuses reste élevée, plus du quart d'entre elles sont menacées régionalement Différentes raisons peuvent être invoquées mais l'impact des activités humaines reste la raison majeure. Les connaissances disponibles sont suffisantes pour proposer des mesures conservatoires sans avoir besoin d'attendre des données supplémentaires. Mais, cela nécessiterait une coopération étroite entre tous les acteurs impliqués. (Texte intégral

Molecular characterization of Secoviridae and Potexvirus infecting yams (Dioscorea spp)

The prevalence of virus species is generally high among vegetatively?propagated crops, because they cannot be sanitized via seed production and therefore accumulate viruses over long periods of time. In yams (Dioscorea spp), viruses belonging to the families Alphaflexiviridae (genus potexvirus), Betaflexiviridae (genus carlavirus), Caulimoviridae (genus badnavirus), Cucumoviridae (genus cucumovirus) and Potyviridae (genera macluravirus and potyvirus) have been characterized so far. However, it is likely that the diversity of viral species infecting this crop remains underestimated. To test this hypothesis, in silico analyses of ESTs of Dioscorea alata were performed and unveiled the existence of sequences corresponding to several known genera of yam viruses, such as badnavirus and macluravirus, and also to families of unknown yam?associated viruses, including Geminiviridae and Secoviridae. This result has prompted a search for yet uncharacterized viruses infecting yams. RT?PCR performed on crude extracts of symptomatic yams (D. alata, D. trifida) following direct binding of viral particles and using available degenerate primers raised distinct amplification products, which were cloned and sequenced. Some of them displayed significant levels of homologies with potexviruses and with viruses of the family Secoviridae. The 3' end of their genomes was successfully amplified by 3' RACE, cloned and sequenced. Sequence analyses and phylogenetic analyses confirmed the existence in yams of new viral species within the genus potexvirus and the family Secoviridae. These results highlight the need to improve the current taxonomy of yam potexviruses and suggest to further explore the diversity of viruses of the family Secoviridae in yams. (Texte intégral

Ziyanm pa ka bout en Gwadloup - never-ending yams in Guadeloupe. Agrobiodiversity use for labour-intensive and sustainable production of graded yam with the “gutter-type tuber-support-container

Yam (Dioscorea spp) is an annual tuber crop which is an important food crops in intertropical diets. Its area of cultivation varies from Japan, Western Africa, to the Caribbean with a wide diversity of cropping systems and cultivars. Among them, the yam cropping system with the “gutter-type tuber-support-container” in Japan allows for a sustainable increase of the graded tuber production. The main objective of this preliminary study is to test the adaptation of this yam cropping system under our Caribbean conditions and to select cultivars adapted to this system. The experiment was set in 2015 on the INRA experimental station in Duclos where 7 cultivars of D. alata were planted in gutters with a high density. The use of the “gutter-type tuber-support-container” coupled to the use of compost and paper mulch can intensify in a sustainable way yam-based cropping systems while avoiding the use of chemicals (mineral fertilizers, herbicides...). First results are promising, especially for 2 cultivars from Vanuatu, called Wanorak and Nepelev, which show very good yields (50t.ha-1) and grade (1 meter length for 1.4 kg in average per tuber). This type of cropping system could represent a sustainable alternative for local communities for instance. We still need to validate these results and to realize a technical-economical analysis of the performance of such system

Towards a better characterization of endogenous badnavirus sequences of yams (Dioscorea spp.)

Yams, and more generallytubers, are very important crops for food security in tropical and subtropical countries.They are propagated vegetativelytherefore they accumulate viruses over long periods of time. Viruses are currently the main constraint for yam production and yam germplasm conservation and distribution. A wide range of badnavirus sequences belonging to 13 distinct viral species were amplified from genomic DNA of severalyam species when using badnavirus degenerate primers [1; 2].However, we consistently observed that the proportion of amplification products raised by PCR performed on total genomic DNA is significantly higher than that raised by direct binding PCR, which has been designed to detect episomal forms of yam badnaviruses.Both observations have fueled suspicion that yams might host endogenous badnavirus sequences, and possibly infectious ones like bananas [3]. Therefore, search for endogenous badnavirus sequences was undertaken in yam accessions conserved in the germplasm collection of the Guadeloupe Tropical Plant Biological Ressource Center (CRB-PT) and the yam quarantine facility in Montpellier (France). Southern blots performed on genomic DNA extracted from uninfected Dioscoreatrifidaand using parts of yam badnavirus genomes as probes confirmed the suspicion of endogenous badnavirus sequences in yam genomes. Furthermore, PCR performed on genomic DNA extracted from healthy seedlings of D. alata and D. rotundata using badnavirus degenerate primers raised amplification products whose sequences fit in the current phylogeny of badnaviruses. Amplification products raised from several of these DNA samples by long-PCR displayedrearrangements such asduplications andreversions which are reminiscent of endogenous badnavirus sequences encountered in the genome of other crops such as banana. Similarly rearranged sequences were raised by rolling circle amplification, which is known to sometime amplify chromosomal sequences. These results suggest that yams do host endogenous sequences of several distinct badnavirus species. (Texte intégral