Multiplex real-time PCR for detection, identification and quantification of ‘ Candidatus Liberibacter solanacearum’ in potato plants with zebra chip

• Published in: Journal of microbiological methods 2009-07, Vol.78 (1), p.59-65
• Main Authors: Li, Wenbin, Abad, Jorge A., French-Monar, Ronald D., Rascoe, John, Wen, Aimin, Gudmestad, Neil C., Secor, Gary A., Lee, Ing-Ming, Duan, Yongping, Levy, Laurene
• Format: Article
• Language: English
• Subjects: Bacterial plant pathogens; Bactericera cockerel; Bacteriological methods and techniques used in bacteriology; Bacteriology; Biological and medical sciences; Capsicum; Citrus; DNA, Bacterial - genetics; DNA, Ribosomal - genetics; Fundamental and applied biological sciences. Psychology; Lycopersicon esculentum; Microbiology; Molecular Sequence Data; Phloem-limited bacterium; Phytopathology. Animal pests. Plant and forest protection; Plant Diseases - microbiology; Plants - microbiology; Polymerase Chain Reaction - methods; Rhizobiaceae - classification; Rhizobiaceae - genetics; Rhizobiaceae - isolation & purification; RNA, Ribosomal, 16S - genetics; Solanum tuberosum; Solanum tuberosum - microbiology; α-proteobacteria
• ISSN: 0167-7012; 1872-8359
• DOI: 10.1016/j.mimet.2009.04.009

The new Liberibacter species, ‘ Candidatus Liberibacter solanacearum’ (Lso) recently associated with potato/tomato psyllid-transmitted diseases in tomato and capsicum in New Zealand, was found to be consistently associated with a newly emerging potato zebra chip (ZC) disease in Texas and other southwestern states in the USA. A species-specific primer LsoF was developed for both quantitative real-time PCR (qPCR) and conventional PCR (cPCR) to detect and quantify Lso in infected samples. In multiplex qPCR, a plant cytochrome oxidase (COX)-based probe-primer set was used as a positive internal control for host plants, which could be used to reliably access the DNA extraction quality and to normalize qPCR data for accurate quantification of the bacterial populations in environment samples. Neither the qPCR nor the cPCR using the primer and/or probe sets with LsoF reacted with other Liberibacter species infecting citrus or other potato pathogens. The low detection limit of the multiplex qPCR was about 20 copies of the target 16S rDNA templates per reaction for field samples. Lso was readily detected and quantified in various tissues of ZC-affected potato plants collected from fields in Texas. A thorough but uneven colonization of Lso was revealed in various tissues of potato plants. The highest Lso populations were about 3 × 10 8 genomes/g tissue in the root, which were 3-order higher than those in the above-ground tissues of potato plants. The Lso bacterial populations were normally distributed across the ZC-affected potato plants collected from fields in Texas, with 60% of ZC-affected potato plants harboring an average Lso population from 10 5 to 10 6 genomes/g tissue, 4% of plants hosting above 10 7 Lso genomes/g tissue, and 8% of plants holding below 10 3 Lso genomes/g tissue. The rapid, sensitive, specific and reliable multiplex qPCR showed its potential to become a powerful tool for early detection and quantification of the new Liberibacter species associated with potato ZC, and will be very useful for the potato quarantine programs and seed potato certification programs to ensure the availability of clean seed potato stocks and also for epidemiological studies on the disease.