Biotic and abiotic factors altogether affect the spread of the vectored emerging disease, Yellow leaf of sugarcane, in Guadeloupe.

Yellow leaf of sugarcane caused by the Sugarcane yellow leaf virus (SCYLV), a polerovirus, is an emerging disease in the tropical island of Guadeloupe. It was first detected in 1996 as a possible result of multiple introductions of infected plant material in the germplasm collection of CIRAD, in which three distinct genotypes of the virus have been identified so far. Despite a large distribution of the main vector of SCYLV, the aphid Melanaphis sacchari, in Guadeloupe, average field contamination remains relatively low compared to contamination within the germplasm collection, in which incidence of the virus and number of infected accessions increased by 3.5 from 2003 to 2006. In this study we investigated the impact of diverse environmental factors and genetic diversity of the host and the virus on spread of SCYLV in six distinct geographic locations in Guadeloupe, including 24 fields of plant cane and first ratoon crops planted with five different sugarcane cultivars. Mean values of disease incidence (DI) in all fields were 7.4 and 10.8 (percent of positives samples) in plant cane and first ratoon crops, respectively, as determined by tissue blot immunoassay (TBIA). Two distinct geographical areas were identified in Guadeloupe based on DI values: Marie-Galante, a small island of approximately 61 square miles located 20 miles from Guadeloupe where DI was almost absent (1 positive out of 1700 samples); and the east of the Guadeloupe Basse-Terre, a recent sugarcane growing area, where DI in plant cane crop was significantly higher (18 to 20) comparatively to DI in ancient sugarcane growing areas for the same cultivar (2 to 10). In ancient sugarcane growing areas, DI varied greatly between fields from 2 to 35%. As expected, DI in all fields varied between plant cultivars, revealing differential behaviors of sugarcane genotypes to virus infection. Interestingly, most of virus samples collected from all fields, using the TBIA positive leaves identified in this study, and analyzed by RT-PCR were of one dominant genotype, and virus diversity was not related to virus incidence. Similarly, virus incidence was not linked to the solely one observation of plant colonization by aphid, as determined by the monitoring of populations of M. sacchari during samplings. However, in ancient sugarcane growing areas disease incidence, was significantly correlated to rainfall in the first weeks following sugarcane plantation in the field. Indeed, rainfall thus explained up to 25% (P = 0.039) and 32% (P = 0.018) of DI variations observed in plant cane and first ratoon crops, respectively, as determined by multiple coefficient correlation analysis. It is strongly presumed that rainfall affect dynamic of SCYLV vector populations, directly, or, indirectly, affect predator populations of the vector and development of grasses that can modify aphid behavior. Obviously, spread of a vectored emerging virus disease in a tropical environment is driven by multifactor components that need to be addressed when modeling epidemics. (Texte integral

Modélisation de répartitions d'occurrences spatio-temporelles et épidémiologie végétale

Les processus ponctuels temporel, spatial et spatio-temporel sont utilisés depuis un certain nombre d'années dans des domaines tels que la biologie, l'épidémiologie, la sismologie, la neurologie afin de modéliser des séries d'occurrences d'événements. Notre étude concerne l'apport des modèles de mélange de processus ponctuels dans de telles modélisations. Elle fait également apparaître l'utilité de l'approche bayésienne pour apprécier la variabilité associée à certains facteurs environnementaux. Le lien avec les lois à priori stick-breaking telles que le processus de Dirichlet est présente. Une illustration est fournie avec l'étude de la propagation de la maladie de la feuille jaune de la canne à sucre. La répartition spatio-temporelle des cannes à sucre infectées par le Sugar Cane Yellow Leaf Virus (SCYLV) est étudiée dans une parcelle, saine lors de la plantation, située en Guadeloupe. Notre objectif principal est de caractériser puis de modéliser la dissémination du SCYLV au sein de cette parcelle. (Résumé d'auteur

Variation in sugarcane cultivar host range of Sugarcane yellow leaf virus genotypes in Guadeloupe

Yellow leaf is a widely spread disease of sugarcane that can cause yield losses in susceptible cultivars. This disease is caused by Sugarcane yellow leaf virus (SCYLV) which belongs to the genus Polerovirus (Luteoviridae family). Five different SCYLV genotypes have been described and three of these were found in Guadeloupe (genotypes BRA-PER, CUB and REU). Additionally, variation in infection capacity and virulence exists among SCYLV genotypes. In order to investigate the cultivar host range of SCYLV genotypes occurring in Guadeloupe, we explored the capacity of genotypes BRA-PER, CUB and REU to infect different sets of sugarcane cultivars. A first experiment was performed with 30 cultivars from a breeding plot (non-replicated design). Four leaves were sampled per cultivar, bulked and processed for identification of virus genotype by RT-PCR. A second experiment was performed with 25 cultivars from a core collection of 200 accessions (experimental design with three replications). Ten leaves were sampled per accession and per replication, bulked and processed for identification of virus genotype by RT-PCR. The breeding plot and the core collection were both located at CIRAD's research station in Guadeloupe where disease pressure was high. In both experiments, SCYLV genotypes CUB and REU were found in a larger number of cultivars than genotype BRA-PER. In the second experiment, genotype CUB was present in all SCYLV-infected cultivars and was therefore the virus genotype with the largest cultivar host range. This genotype appears to have the propensity to infect all sugarcane cultivars infected by genotypes BRA-PER and REU. Additionally, cultivar host range varied to some extent between genotypes BRA-PER and REU, suggesting the occurrence of host-ranges specific to these SCYLV genotypes. Variation in sugarcane cultivar host range between SCYLV genotypes may explain, at least in part, the variations in SCYLV incidence and epidemics reported in different sugarcane growing locations. (Résumé d'auteur

Worldwide genetic diversity of Sugarcane white streak virus. [P.43]

Sugarcane white streak virus (SWSV), a novel mastrevirus, was recently discovered using virion-associated nucleic acids (VANA) metagenomics approach from two sugarcane cultivars originating from Egypt ( Candresse et al, PLos ONE 9(7): e102945 ). Systematic diagnosis of plants grown at the CIRAD's sugarcane quarantine station further revealed that SWSV was also infecting sugarcane cultivars originating from Sudan (KN variety) and Réunion Island (R variety). Nine genomes amplified from plants originating from these two locations were cloned and sequenced. The genome organization of these nine genomes was most similar to that of SWSV-B/C strains. Genome-wide pairwise comparisons using Mega6 indicated that the nine isolates share 91.1% pairwise identity. This analysis also showed that each of the three coding region of the genome, movement protein (mp), coat protein (cp) and replication associated protein (rep), contains polymorphic parts. We designed specific primers for amplifying the polymorphic region of each coding region and sequenced them from 40 isolates, including 12 isolates from Réunion Island issued from KN varieties, 7 isolates from Guadeloupe Island issued from KN varieties and 21 isolates from CIRAD's quarantine, including 11 and 10 isolates issued from R and KN varieties, respectively. Phylogenetic analyses based on mp, cp and rep partial genes reveal that the isolates are split into two polymorphic groups that correspond to SWSV-B and SWSV-C strains. However, phylogenetic trees issued from the three genomic regions were not congruent, suggesting recombination events. Interestingly, SWSV-C isolates are more prevalent in R varieties (64%) than in KN varieties (24%). They are also more frequent in KN varieties sampled from Reunion Island (31%) than from KN varieties collected from the two other locations (17%). Reunion Island is the only location sampled where the putative vector of the virus Cicadulina mbila is present, which may account for the strongest prevalence of SWSV-C in this region and for R cultivar contamination. This assumption will need to be confirmed. This new virus already stresses the need to set up efficient diagnostic and sanitation tools in order to detect and clean the infected cultivars for quarantine purposes. (Résumé d'auteur