title: Combined use of a new SNP-based assay and multilocus SSR markers to assess genetic diversity of Xylella fastidiosa subsp. pauca infecting citrus and coffee plants.
abstract: Two haplotypes of Xylella fastidiosa subsp. pauca (Xfp) that correlated with their host of origin were identified in a collection of 90 isolates infecting citrus and coffee plants in Brazil, based on a single-nucleotide polymorphism in the gyrB sequence. A new single-nucleotide primer extension (SNuPE) protocol was designed for rapid identification of Xfp according to the host source. The protocol proved to be robust for the prediction of the Xfp host source in blind tests using DNA from cultures of the bacterium, infected plants, and insect vectors allowed to feed on Xfp-infected citrus plants. AMOVA and STRUCTURE analyses of microsatellite data separated most Xfp populations on the basis of their host source, indicating that they were genetically distinct. The combined use of the SNaPshot protocol and three previously developed multilocus SSR markers showed that two haplotypes and distinct isolates of Xfp infect citrus and coffee in Brazil and that multiple, genetically different isolates can be present in a single orchard or infect a single tree. This combined approach will be very useful in studies of the epidemiology of Xfp-induced diseases, host specificity of bacterial genotypes, the occurrence of Xfp host jumping, vector feeding habits, etc., in economically important cultivated plants or weed host reservoirs of Xfp in Brazil and elsewhere.
authors.affiliation: Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), 14080 Córdoba, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Montes-Borrego
authors.affiliation: Departamento de Entomologia e Acarologia, ESALQ, Universidade de São Paulo, Piracicaba, São Paulo 13418-970, Brazil.
authors.forename: Joao R S
authors.initials: JR
authors.lastname: Lopes
authors.affiliation: Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), 14080 Córdoba, Spain.|IAS-CSIC and College of Agriculture and Forestry, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14071-Córdoba, Spain.
authors.forename: Rafael M
authors.initials: RM
authors.lastname: Jiménez-Díaz
authors.affiliation: Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), 14080 Córdoba, Spain.
authors.forename: Blanca B
authors.initials: BB
authors.lastname: Landa
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D001938:Brazil; D002957:Citrus / Q000382:microbiology*; D040503:Coffea / Q000382:microbiology*; D027081:DNA Gyrase / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D014644:Genetic Variation; D005838:Genotype; D054884:Host-Pathogen Interactions; D018895:Microsatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D010935:Plant Diseases / Q000382:microbiology*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA; D044167:Xylella / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D001426:Bacterial Proteins; D017931:DNA Primers; D004269:DNA, Bacterial; D005819:Genetic Markers; D027081:DNA Gyrase
keywords: Citrus variegated chlorosis; coffee leaf scorch; haplotype characterization; host-plant association; vector transmission; xylem-limited bacteria