2005 Annual Report 4d.Progress report. This report serves to document research conducted under a Specific Cooperative Agreement between ARS and the University of California, Davis. Additional details of the research can be found in the report for the parent project 5302-22000-005-00D, Epidemiology and Control of Xylella Diseases and Their Insect Vectors. Xylella fastidiosa strains isolated from almond leaf scorch diseased orchards in California were grouped into two major genotypes utilizing SNPs in the 16S rDNA sequences, and the two genotypes were correlated with differential pathogenicities of the strains. J. Chen (CDPGRU, Parlier) and cooperator B. Kirkpatrick (UC-Davis) conducted the research. He has characterized genetic differences within and between the two genotypes. Strains of the two genotypes showed noticeable differences in motility and EPS production. Based on the available whole genome sequences, at least 30 piliation genes that could be responsible for twitching motility were identified in the genomes of both genotypes. Sequence analysis showed some genes were remarkably conserved but others varied at a high level. Variations were mainly from SNPs but Indels were also found. PCR primers targeting the piliation genes have been developed and the arraying of these pathogenicity related genes are currently underway. Similarly, genes at the gum operon were also studied and the PCR-Arraying experiment is in progress. A protease gene involving in type V secretion was identified. The 5’ end of this gene possesses a tandem repeat varying between the two genotypes. Variations also occurr within each genotype from the same diseased tree sample, suggesting the instability or the high level of polymorphism of the locus and contrasting to high overall stability of the 16S rDNA and other housekeeping genetic loci. This knowledge and information is being used to design microarrays for accurate and sensitive detection and identification of X. fastidiosa.