Champoiseau, P. 2006. Xanthomonas albilineans, l’agent causal de l’échaudure des feuilles de la canne à sucre : caractérisation et variabilité génétique du pouvoir pathogène, en Guadeloupe et dans le monde. PhD Thesis, Life Sciences. Université des Antilles et de la Guyane, Guadeloupe, France, 171 p.

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Abstract: Xanthomonas albilineans is the causal agent of sugarcane leaf scald, a disease that occurs in at least 60 geographical locations in the world. Impact of the disease can be very severe (yield losses, plant death) when susceptible sugarcane varieties are infected by the pathogen. During the last two decades, outbreaks of the disease have been reported in several geographical areas, including Guadeloupe. Control of the disease and of the pathogen evolution can be achieved through breeding and screening of resistant sugarcane varieties. However, to insure long-term control of the disease, it is essential to determine the variabilityof X. albilineans and, in particular, the variations in the mechanisms of pathogenicity. 
Three main factors involved in pathogenicity of X. albilineans have been identified: i) production of a toxin called albicidin, ii) symptom expression on leaves and iii) colonization of the sugarcane stalk. Albicidin plays a key role in symptom incitation by the pathogen. According to several authors, the toxin may also facilitate sugarcane stalk colonization. First studies of the genetic base of albicidin production by strain Xa23R1, from Florida, lead to the identification of three regions of the pathogen’s genome. These regions include 22 ORFs (albI to albXX) involved or potentially involved in biosynthesis of the toxin. So far, no hrp or avr genes that were identified in most other phytopathogenic bacteria have been found in X. albilineans. Therefore, other genes that play a key role in pathogenicity of this pathogen remain to be identified.
In the first part of this thesis, we looked for a relationship between variability of genes involved or potentially involved in albicidin biosynthesis and variability of the factors known to be involved in pathogenicity of X. albilineans. Ten haplotypes and 2 major genetic groups, called ALB-RFLP571-A and ALB-RFLP571-B, were identified among 137 strains of X. albilineans from 27 geographical areas. Almost all strains of the pathogen that were isolated during the last 15 years in geographical areas where leaf scald outbreaks were reported belonged to group ALB-RFLP571-B. Additionally, a strong relationship was found between these 2 genetic groups and the AFLP and RFLP groups that were previously described for this pathogen. Variability in albicidin produced in vitro by X. albilineans was shown and albivars were identified among the 139 bacterial strains used in this study. However, no relationship between this variability and genetic groups ALB-RFLP571-A and ALB-RFLP571-B was found. Different pathogenicity groups, based on symptom severity (pathotypes) and pathogen population density in the stalk (colovars), were identified among 21 strains of X. albilineans which represented different albivars and genetic groups identified in this study. No relationship between these pathogenicity groups and the ALB-RFLP571-A and ALB-RFLP571-B groups was found. Nevertheless, these results suggested that sugarcane stalk colonization by X. albilineans involves other factors than albicidin, and the research of these factors is described in the second part of this thesis.
In the second part of this thesis, we aimed to identify and to characterize the variability of new genes involved in pathogenicity of X. albilineans. Two techniques were used with 19 strains of the pathogen from Guadeloupe, representing different pathotypes (based on intensity of sugarcane stalk colonization and severity of disease symptoms), but that were genetically identical (based on RFLP data of the albicidin biosynthesis genes or the whole bacterial genome): 
i) AFLP analysis of the whole genome with 16 selective primer combinations. Variability among strains and 2 major genetic groups were identified, but no relationship between this genetic variability and variability in pathogenicity of X. albilineans was found.
ii) PCR amplification of genes involved in pathogenicity of other bacterial plant pathogens closely related to X. albilineans, and particularly X. campestris pv. campestris and Xylella fastidiosa. Forty primer combinations representing 40 genes were used, but only three genes (pilB, rpfA et xpsE) could be amplified from X. albilineans. No difference in the nucleotide sequence of these genes in 9 strains of X. albilineans differing in pathogenicity was found. Phylogenetic study based on sequences of these three genes and two housekeeping genes revealed that X. albilineans represents a distinct group between the X. campestris group and Xylella fastidiosa, another xylem-invading bacterium. 
Sequencing of the whole genome of strain GPEPC73, isolated during this thesis, is in progress at Genoscope in Evry/France. Obtaining and deciphering the whole sequence of the genome of X. albilineans is the next step for the comprehension of the genetic basis of X. albilineans pathogenicity, and for better management of sugarcane resistance against leaf scald disease in Guadeloupe, and in the world.

Key words: Sugarcane, leaf scald, Xanthomonas albilineans, pathogenicity, toxin, albicidin, disease severity, stalk colonization, genetic diversity, pathogenicity genes, RFLP, AFLP, PCR.