Assessment of the genetic diversity among strains of Xanthomonas cynarae by randomly amplified polymorphic DNA analysis and development of specific characterized amplified regions for the rapid identification of X-cynarae

The randomly amplified polymorphic DNA (RAPD) method was used to investigat e the genetic diversity in Xanthomonas cynarae, which causes bacterial brac t spot disease of artichoke. This RAPD analysis was also intended to identi fy molecular markers characteristic of this species, in order to develop PC R-based markers which can be used to detect this pathogenic bacterium in ar tichoke fields. Among the 340 RAPD primers tested, 40 were selected on thei r ability to produce reproducible and reliable fingerprints in our genetic background. These 40 primers produced almost similar patterns for the 37 X. cynarae strains studied, different from the fingerprints obtained for othe r Xanthomonas species and other xanthomonad-like bacteria isolated from art ichoke leaves. Therefore, X. cynarae strains form a homogeneous genetic gro up. However, a little DNA polymorphism within this species was observed and the collection of X. cynarae isolates was divided into two groups (one con taining three strains, the second one including all other strains). Out of seven RAPD markers characteristic of X. cynarae that were cloned, four did not hybridize to the genomic DNA of strains belonging to other Xanthomonas species. These four RAPD markers were converted into PCR markers (specific characterized amplified regions [SCARs]); they were sequenced, and a PCR pr imer pair was designed for each of them. Three derived SCARs are good candi dates to develop PCR-based tests to detect X. cynarae in artichoke fields.