SNP markers identify widely distributed clonal lineages of Phytophthora colocasiae in Vietnam, Hawaii and Hainan Island, China

Mycologia. Jul-Aug 2014;106(4):676-85. doi: 10.3852/13-165. Epub 2014 Jun 3.

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.

Keywords: SNP; loss of heterozygosity; population genetics.

MeSH terms

  • China
  • Colocasia / parasitology*
  • DNA Primers / genetics
  • Genetic Markers
  • Genetic Variation
  • Genetics, Population
  • Genotype
  • Geography
  • Hawaii
  • Islands
  • Loss of Heterozygosity
  • Phytophthora / genetics*
  • Plant Diseases / parasitology*
  • Polymorphism, Single Nucleotide / genetics*
  • Sequence Analysis, DNA
  • Vietnam

Substances

  • DNA Primers
  • Genetic Markers