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

Authors

Wenbin Li, USDA-APHIS-PPQ-CPHST
Jorge A. Abad, USDA-APHIS-PPQ-PHP-PSPI
Ronald D. French-Monar, Texas A&M
John Rascoe, USDA-APHIS-PPQ-PHP
Aimin Wen, North Dakota State University
Neil C. Gudmestad, North Dakota State University
Gary A. Secor, North Dakota State University
Ing-Ming Lee, USDA-ARS
Yongping Duan, USDA-ARSFollow
Laurene Levy, USDA-APHIS-PPQ-CPHST

Date of this Version

2009

Comments

Published in Journal of Microbiological Methods 78 (2009) 59–65.

Abstract

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 ZCaffected 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 3×10⁸ 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 10⁵ to 10⁶ genomes/g tissue, 4% of plants hosting above 10⁷ Lso genomes/g tissue, and 8% of plants holding below 10³ 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.