A comparative analysis of RNA isolation methods optimized for high-throughput detection of viral pathogens in California’s regulatory and disease management program for citrus propagative materials Tyler Dang 1 , Sohrab Bodaghi 1 , Fatima Osman 2 , Jinbo Wang 1,3 , Tavia Rucker 1 , Shih-Hua Tan 1 , Amy Huang 1 , Deborah Pagliaccia 1 , Stacey Comstock 1 , Irene Lavagi-Craddock 1 , Kiran R. Gadhave 1,4 , Paulina Quijia-Lamina 1 , Arunabha Mitra 1 , Brandon Ramirez 1 , Gerardo Uribe 1 , Alexandra Syed 1 , Sarah Hammado 1 , Iman Mimou 1 , Roya Campos 1 , Silva Abdulnour 1 , Michael Voeltz 1 , Jinhwan Bae 1 , Emily Dang 1 , Brittany Nguyen 1 , Xingyu Chen 1 , Noora Siddiqui 1 , Yi Tien Hsieh 1 , Shurooq Abu-Hajar 1 , Joshua Kress 5 , Kristina Weber 5 and Georgios Vidalakis 1 * 1 Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States, 2 Department of Plant Pathology, University of California, Davis, Davis, CA, United States, 3 United States Department of Agriculture-APHIS-Biotechnology Risk Analysis Program, Riverdale, MD, United States, 4 Texas A&M, Department of Entomology Agrilife Research, Amarillo, TX, United States, 5 California Department of Food and Agriculture Nursery Services Program, Sacramento, CA, United States Citrus germplasm programs can benefit from high-throughput polymerase chain reaction (PCR)-based methods for the detection of graft-transmissible pathogens in propagative materials. These methods increase diagnostic capacity, and thus contribute to the prevention of disease spread from nurseries to citrus orchards. High quality nucleic acids, as determined by purity, concentration, and integrity, are a prerequisite for reliable PCR detection of citrus pathogens. Citrus tissues contain high levels of polyphenols and polysaccharides, which can affect nucleic acid quality and inhibit PCR reactions. Various commercially available RNA isolation methods are used for citrus and include: phenol-chloroform (TRIzol ® , Thermo Fisher Scientific); silica columns (RNeasy ® Plant Mini Kit, Qiagen); and magnetic beads-based methods (MagMAX™-96 Viral RNA Isolation Kit, Thermo Fisher Scientific). To determine the quality of RNA and its impact on the detection of Frontiers in Agronomy frontiersin.org 01 OPEN ACCESS EDITED BY David Ezra, Agricultural Research Organization (ARO), Israel REVIEWED BY Giorgio Gambino, National Research Council (CNR), Italy Garima Singh, Pachhunga University College, India *CORRESPONDENCE Georgios Vidalakis vidalg@ucr.edu SPECIALTY SECTION This article was submitted to Disease Management, a section of the journal Frontiers in Agronomy RECEIVED 02 April 2022 ACCEPTED 08 July 2022 PUBLISHED 18 August 2022 CITATION Dang T, Bodaghi S, Osman F, Wang J, Rucker T, Tan S-H, Huang A, Pagliaccia D, Comstock S, Lavagi-Craddock I, Gadhave KR, Quijia-Lamina P, Mitra A, Ramirez B, Uribe G, Syed A, Hammado S, Mimou I, Campos R, Abdulnour S, Voeltz M, Bae J, Dang E, Nguyen B, Chen X, Siddiqui N, Hsieh YT, Abu-Hajar S, Kress J, Weber K and Vidalakis G (2022) A comparative analysis of RNA isolation methods optimized for high-throughput detection of viral pathogens in California’s regulatory and disease management program for citrus propagative materials. Front. Agron. 4:911627. doi: 10.3389/fagro.2022.911627 TYPE Original Research PUBLISHED 18 August 2022 DOI 10.3389/fagro.2022.911627