The Plant Pathology Journal

The Korean Society of Plant Pathology (한국식물병리학회)
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A New Approach Using the SYBR Green-Based Real-Time PCR Method for Detection of Soft Rot Pectobacterium odoriferum Associated with Kimchi Cabbage

  • Yong Ju, Jin (Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Dawon, Jo (Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Soon-Wo, Kwon (Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Samnyu, Jee (Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration) ;
  • Jeong-Seon, Kim (Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Jegadeesh, Raman (Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Soo-Jin, Kim (Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration)
  • Received : 2022.09.29
  • Accepted : 2022.11.06
  • Published : 2022.12.01
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Abstract

Pectobacterium odoriferum is the primary causative agent in Kimchi cabbage soft-rot diseases. The pathogenic bacteria Pectobacterium genera are responsible for significant yield losses in crops. However, P. odoriferum shares a vast range of hosts with P. carotovorum, P. versatile, and P. brasiliense, and has similar biochemical, phenotypic, and genetic characteristics to these species. Therefore, it is essential to develop a P. odoriferumspecific diagnostic method for soft-rot disease because of the complicated diagnostic process and management as described above. Therefore, in this study, to select P. odoriferum-specific genes, species-specific genes were selected using the data of the P. odoriferum JK2.1 whole genome and similar bacterial species registered with NCBI. Thereafter, the specificity of the selected gene was tested through blast analysis. We identified novel species-specific genes to detect and quantify targeted P. odoriferum and designed specific primer sets targeting HAD family hydrolases. It was confirmed that the selected primer set formed a specific amplicon of 360 bp only in the DNA of P. odoriferum using 29 Pectobacterium species and related species. Furthermore, the population density of P. odoriferum can be estimated without genomic DNA extraction through SYBR Green-based real-time quantitative PCR using a primer set in plants. As a result, the newly developed diagnostic method enables rapid and accurate diagnosis and continuous monitoring of soft-rot disease in Kimchi cabbage without additional procedures from the plant tissue.

Keywords

Acknowledgement

This work was carried out with the support of the National Institute of Agricultural Sciences (Project No. PJ01679902), Rural Development Administration, Republic of Korea.

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