Development of Loop-Mediated Isothermal Amplification Assay for Rapid Detection and Analysis of the Root-Knot Nematode Meloidogyne hapla in Soil

A Rapid PCR-LAMP Assay for the Early Detection of Lasiodiplodia theobromae from Basal Stem Rot-Infected Passion Fruit Plants

Lasiodiplodia theobromae is an emerging threat and the main pathogenic fungi associated with basal stem rot of passion fruit in Guangxi Zhuang Autonomous Region, China. Current pathogen identification protocols are labor-intensive and time-consuming, emphasizing the need for more efficient methods to enable precise surveillance of L. theobromae for early detection and warning. The present study sought to develop a rapid colorimetric LAMP assay for early detection and surveillance of L. theobromae in passion fruit plants. For that, amplifications of ITS locus were performed on fungal genomic DNA using conventional PCR, with the specific primer pair ITS1 and ITS4. The hydroxy naphthol blue (HNB)-dependent colorimetric LAMP assay was then optimized by varying primer sets, inner primers concentration, reaction temperatures and incubation time. A microbial lysis buffer was employed to extract genomic DNA from stems infected with L. theobromae. The prime LAMP primer set targeting the ITS region of L. theobromae was designed and an HNB based colorimetric LAMP assay was optimized. Various optimization parameters were evaluated, with the optimal conditions determined as 1.6 μM of each FIB and BIP, 0.2 μM of each F3 and B3, and incubation at 65 °C for 40 min. This ITS-based LAMP assay could effectively distinguish L. theobromae from less dominant pathogens in passion fruits with a detection limit of 3 pg for ITS locus amplicons. Our proposed method utilizing a microbial lysis buffer enables rapid and cost-effective detection of L. theobromae DNA in early-infected passion fruit plants, eliminating the need for microbial cultivation and DNA purification.

Development of colorimetric and fluorescent closed tube LAMP assay using simplified extraction for diagnosis of Meloidogyne enterolobii in root tissues

Meloidogyne enterolobii, a guava root-knot nematode, is a highly virulent pest in tropical and subtropical regions causing galls or knots in roots of diverse plant species posing a serious threat to agriculture. Managing this nematode is challenging due to limitations in conventional identification based on isolation and microscopic classification requiring expertise and time. A colorimetric and fluorescent LAMP assay using simplified extraction method targeting rDNA-ITS region was developed to detect M. enterolobii DNA. The Men-LAMP assay exhibits simple procedure and achievable outcomes directly from root gall samples within 75 to 80 min, using a simplified Worm Lysis Buffer Plus (WLB +) extraction and the LAMP assay. The results could be interpreted using color and fluorescence without requiring post-amplification to minimize any possibility of contamination. The specificity showed no cross amplification with other plant-parasitic nematodes, a sensitivity was limited to 2.89 ng/μL. Our study proposes a sensitive, specific and time-efficient diagnostic tool for M. enterolobii infection as an alternative promising method for rapid and effective diagnosis at point-of-service to manage and control of M. enterolobii in export plants that can contribute to the degradation of trade restrictions and streamline of the international quarantine inspection process.

Colorimetric LAMP Assay for Detection of Xanthomonas phaseoli pv. manihotis in Cassava Through Genomics: A New Approach to an Old Problem

Bacterial blight caused by Xanthomonas phaseoli pv. manihotis (Xpm) is considered the main bacterial disease that affects cassava, causing significant losses when not properly managed. In the present study, a fast, sensitive, and easy-to-apply method to detect Xpm via colorimetric loop-mediated isothermal amplification (LAMP) was developed. To ensure the use of a unique-to-the-target pathovar core region for primer design, 74 complete genomic sequences of Xpm together with different bacterial species and pathovars were used for comparative genomics. A total of 42 unique genes were used to design 27 LAMP primer sets, from which nine primers were synthesized, and only one (Xpm_Lp1 primer set) showed sufficient efficiency in preliminary tests. The sensitivity, assessed by a serial dilution of the type strain (IBSBF 278) DNA, yielded high sensitivity, detecting up to 100 fg. The LAMP primers showed high specificity, did not cross-react with other bacterial species or other pathovars tested, and amplified only the Xpm isolates. Tests confirmed the high efficiency of the protocol using infected or inoculated macerated cassava leaves without the need for additional sample treatment. The LAMP test developed in this study was able to detect Xpm in a fast, simple, and sensitive way, and it can be used to monitor the disease under laboratory and field conditions.

Development of a Rapid, Accurate, and On-Site Detection Protocol for Red Imported Fire Ants, Solenopsis invicta (Hymenoptera: Formicidae)

A rapid, accurate, and on-site molecular diagnostic protocol for red imported fire ants (Solenopsis invicta, Si) was developed using loop-mediated isothermal amplification (LAMP) assays. Si11977 (GenBank accession no. MK986826) was confirmed to be a Si-specific gene. Four-primer Si11977-LAMP (4pSi-LAMP) and six-primer Si11977-LAMP (6pSi-LAMP) assays specifically detected Si. The reaction time of 6pSi-LAMP assays was reduced by 5 min compared with 4pSi-LAMP assays. The optimal amount of polymerase and the detection limit for the 6pSi-LAMP assays were 0.1 unit/μL and 5 fg/μL, respectively. In addition, a method for extracting genomic DNA from ant tissues within 2 to 3 min and a protocol for performing on-site LAMP assays using a car heating mug and a LAMP observation box were described. The on-site Si detection protocol used in this study was possible within 30 min from DNA extraction to species identification.