title: Detection of Ribosomal DNA Sequence Polymorphisms in the Protist Plasmodiophora brassicae for the Identification of Geographical Isolates.
abstract: Clubroot is a soil-borne disease caused by the protistPlasmodiophora brassicae(P. brassicae). It is one of the most economically important diseases ofBrassica rapaand other cruciferous crops as it can cause remarkable yield reductions. UnderstandingP. brassicaegenetics, and developing efficient molecular markers, is essential for effective detection of harmful races of this pathogen. Samples from 11 Korean field populations ofP. brassicae(geographic isolates), collected from nine different locations in South Korea, were used in this study. Genomic DNA was extracted from the clubroot-infected samples to sequence the ribosomal DNA. Primers and probes forP. brassicaewere designed using a ribosomal DNA gene sequence from a Japanese strain available in GenBank (accession number AB526843; isolate NGY). The nuclear ribosomal DNA (rDNA) sequence ofP. brassicae, comprising 6932 base pairs (bp), was cloned and sequenced and found to include the small subunits (SSUs) and a large subunit (LSU), internal transcribed spacers (ITS1 and ITS2), and a 5.8s. Sequence variation was observed in both the SSU and LSU. Four markers showed useful differences in high-resolution melting analysis to identify nucleotide polymorphisms including single- nucleotide polymorphisms (SNPs), oligonucleotide polymorphisms, and insertions/deletions (InDels). A combination of three markers was able to distinguish the geographical isolates into two groups.
authors.affiliation: Department of Horticulture, Sunchon National University, Suncheon 540-950, Korea. rawnak.2010@gmail.com.
authors.forename: Rawnak
authors.initials: R
authors.lastname: Laila
authors.affiliation: Department of Horticulture, Sunchon National University, Suncheon 540-950, Korea. gpb21bau@gmail.com.
authors.forename: Arif Hasan Khan
authors.initials: AH
authors.lastname: Robin
authors.affiliation: Department of Horticulture, Sunchon National University, Suncheon 540-950, Korea. ykw7685@naver.com.
authors.forename: Kiwoung
authors.initials: K
authors.lastname: Yang
authors.affiliation: Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea. kjchoi@krict.re.kr.
authors.forename: Gyung Ja
authors.initials: GJ
authors.lastname: Choi
authors.affiliation: Department of Horticulture, Sunchon National University, Suncheon 540-950, Korea. jipark@sunchon.ac.kr.
authors.forename: Jong-In
authors.initials: JI
authors.lastname: Park
authors.affiliation: Department of Horticulture, Sunchon National University, Suncheon 540-950, Korea. nis@sunchon.ac.kr.
authors.forename: Ill-Sup
authors.initials: IS
authors.lastname: Nou
mesh_terms: D001483:Base Sequence; D029741:Brassica rapa / Q000469:parasitology*; D004275:DNA, Ribosomal / Q000235:genetics*; D014644:Genetic Variation; D010802:Phylogeny; D010935:Plant Diseases / Q000469:parasitology*; D056909:Plasmodiophorida / Q000235:genetics* / Q000302:isolation & purification; D011110:Polymorphism, Genetic; D011528:Protozoan Infections / Q000469:parasitology; D056910:Republic of Korea
chemical_list: D004275:DNA, Ribosomal
keywords: Plasmodiophora brassicae; geographical isolates; intraspecific polymorphism; ribosomal DNA; sequence variation; single-nucleotide polymorphism