title: SNP markers identify widely distributed clonal lineages of Phytophthora colocasiae in Vietnam, Hawaii and Hainan Island, China.
abstract: Taro (Colocasia esculenta) is an important food crop, and taro leaf blight caused by Phytophthora colocasiae can significantly affect production. Our objectives were to develop single nucleotide polymorphism (SNP) markers for P. colocasiae and characterize populations in Hawaii (HI), Vietnam (VN) and Hainan Island, China (HIC). In total, 379 isolates were analyzed for mating type and multilocus SNP profiles including 214 from HI, 97 from VN and 68 from HIC. A total of 1152 single nucleotide variant (SNV) sites were identified via restriction site-associated DNA (RAD) sequencing of two field isolates. Genotyping with 27 SNPs revealed 41 multilocus SNP genotypes grouped into seven clonal lineages containing 2-232 members. Three clonal lineages were shared among countries. In addition, five SNP markers had a low incidence of loss of heterozygosity (LOH) during asexual laboratory growth. For HI and VN, >95% of isolates were the A2 mating type. On HIC, isolates within single clonal lineages had A1, A2 and A0 (neuter) isolates. The implications for the wide dispersal of clonal lineages are discussed.
authors.affiliation: Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee.
authors.forename: Sandesh
authors.initials: S
authors.lastname: Shrestha
authors.affiliation: Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, and China Agricultural University, Beijing.
authors.forename: Jian
authors.initials: J
authors.lastname: Hu
authors.affiliation: Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee.
authors.forename: Rebecca Trout
authors.initials: RT
authors.lastname: Fryxell
authors.affiliation: National Center for Genome Resources, Santa Fe, New Mexico.
authors.forename: Joann
authors.initials: J
authors.lastname: Mudge
authors.affiliation: Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee klamour@utk.edu.
authors.forename: Kurt
authors.initials: K
authors.lastname: Lamour
mesh_terms: D002681:China; D031060:Colocasia / Q000469:parasitology*; D017931:DNA Primers / Q000235:genetics; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D005843:Geography; D006254:Hawaii; D062312:Islands; D019656:Loss of Heterozygosity; D010838:Phytophthora / Q000235:genetics*; D010935:Plant Diseases / Q000469:parasitology*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014744:Vietnam
chemical_list: D017931:DNA Primers; D005819:Genetic Markers
keywords: SNP; loss of heterozygosity; population genetics