The Plant Pathology Journal

The Korean Society of Plant Pathology (한국식물병리학회)
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Race- and Isolate-specific Molecular Marker Development through Genome-Realignment Enables Detection of Korean Plasmodiophora brassicae Isolates, Causal agents of Clubroot Disease

  • Received : 2017.12.20
  • Accepted : 2018.08.30
  • Published : 2018.12.01
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Abstract

Clubroot is one of the most economically important diseases of the Brassicaceae family. Clubroot disease is caused by the obligate parasite Plasmodiophora brassicae, which is difficult to study because it is nonculturable in the laboratory and its races are genetically variable worldwide. In Korea, there are at least five races that belongs to four pathotype groups. A recent study conducted in Korea attempted to develop molecular markers based on ribosomal DNA polymorphism to detect P. brassicae isolates, but none of those markers was either race-specific or pathotype-specific. Our current study aimed to develop race- and isolate-specific markers by exploiting genomic sequence variations. A total of 119 markers were developed based on unique variation exists in genomic sequences of each of the races. Only 12 markers were able to detect P. brassicae strains of each isolate or race. Ycheon14 markers was specific to isolates of race 2, Yeoncheon and Hoengseong. Ycheon9 and Ycheon10 markers were specific to Yeoncheon isolate (race 2, pathotype 3), ZJ1-3, ZJ1-4 and ZJ1-5 markers were specific to Haenam2 (race 4) isolate, ZJ1-35, ZJ1-40, ZJ1-41 and ZJ1-49 markers were specific to Hoengseong isolate and ZJ1-56 and ZJ1-64 markers were specific to Pyeongchang isolate (race 4, pathotype 3). The PCR-based sequence characterized amplified region (SCAR) markers developed in this study are able to detect five Korean isolates of P. brassicae. These markers can be utilized in identifying four Korean P. brassicae isolates from different regions. Additional effort is required to develop race- and isolate-specific markers for the remaining Korean isolates.

Keywords

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Fig. 1. Alignment of whole genome sequences of Plasmodiophora brassicae. (A) Alignment of five isolates: the dotted rectangles in Yeoncheon and ZL1 indicate the regions where isolate-specific markers were targeted. (B) Identified Yeoncheon- and ZJ1-specific markers regions are highlighted by black arrows.

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Fig. 2. Three markers specific to the Yeocheon (Ycheon 9 and Ycheon 10), Yeocheon and Hoengseong (Ycheon14) isolates of race 2. Akimeki is a control host. R, race; P, pathotype.

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Fig. 3. Three markers showing specificity to the Haenam2 isolate of race 4 and pathotype 4. Akimeki, a Japanese Chinese cabbage cultivar, was a control host. R, race; P, pathotype.

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Fig. 4. Four markers showing specificity to the Hoengseong isolate of race 2 and pathotype 1. Akimeki, a Japanese Chinese cabbage cultivar, was a control host. R, race; P, pathotype.

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Fig. 5. Four markers showing specificity to the Pyeongchang isolate of race 4 and pathotype 3. Akimeki, a Japanese Chinese cabbage cultivar, was a control host. R, race; P, pathotype.

Table 1. Plasmodiophora brassicae isolates used for comparing genome sequences. Sequences of e3 and ZJ-1 isolates were compared to four Korean isolates

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Table 2. Forward and reverse primer sequences used to identify Korean Plasmodiophra brassicae isolates

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