title: Identification and validation of polymorphic microsatellite loci for the analysis of Phytophthora nicotianae populations.
abstract: A large number of SSR loci were screened in the genomic assemblies of 14 different isolates of Phytophthora nicotianae and primers were developed for amplification of 17 markers distributed among different contigs. These loci were highly polymorphic and amplified from genetically distant isolates of the pathogen. Among these, nine were further validated using a multiplexed genotyping assay with differentially labeled primers (FAM or HEX) to allow for duplex PCR amplification. The use of reverse primers with a 5' PIG tail was important to increase the quality and reliability of the analyses. A total of 46 alleles were detected in 5 tester isolates of P. nicotianae representing the breadth of diversity in the species. Furthermore, a high incidence of heterozygosity was determined with two alleles detected in 67% of the primer/isolate combinations. Three different alleles where detected for a single locus/isolate combination, indicating variation in ploidy. These markers represent a valuable new tool for the characterization of populations of P. nicotianae.
authors.affiliation: Dipartimento di Agraria, Università degli Studi Mediterranea, Località Feo di Vito, 89122 Reggio Calabria, Italy.
authors.forename: Antonio
authors.initials: A
authors.lastname: Biasi
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, 1636 East Alisal Street, 93905 Salinas, CA, United States.
authors.forename: Frank
authors.initials: F
authors.lastname: Martin
authors.affiliation: Dipartimento di Agraria, Università degli Studi Mediterranea, Località Feo di Vito, 89122 Reggio Calabria, Italy. Electronic address: lschena@unirc.it.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Schena
mesh_terms: D000483:Alleles; D017931:DNA Primers; D005838:Genotype; D018895:Microsatellite Repeats; D010838:Phytophthora / Q000235:genetics*; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D015203:Reproducibility of Results; D013045:Species Specificity
chemical_list: D017931:DNA Primers
keywords: Microsatellites; P. nicotianae; Phytophthora parasitica; SSRs