Detection of RNA viruses in potato seed-tubers from northern Antioquia (Colombia)
Palavras-chave:
plant viruses, RNAseq, RT-qPCR, seed certification, SolanaceaeResumo
The most important viruses infecting potato in Colombia are PVY, PLRV, PVS, PYVV, PVV, PVX, PMTV, and PVB. Unfortunately, recent investigations on the health status of uncertified and certified seed-tubers of Solanum tuberosum cv. Diacol Capiro and Solanum phureja cv. Criolla Colombia used by farmers in eastern Antioquia (Colombia) have revealed alarming levels of infection by these viruses in all types of seeds distributed in the region. A similar study on northern Antioquia, testing all these eight viruses has not been performed. To close this gap, we present a complementary study on the prevalence of viruses in seed-tubers distributed and commercialized in this region using a combination of RT-qPCR and high-throughput sequencing. Our results further confirm the poor quality of seed-tubers used in Colombia and suggests infection by tobacco necrosis virus D (TNV-D), which is the first report for this virus in Colombia.
Referências
Agindotan BO, Shiel PJ & Berger PH (2007) Simultaneous detection of potato viruses, PLRV, PVA, PVX and PVY from dormant potato tubers by TaqMan real-time RT-PCR. Journal of Virological Methods, 142:01-09.
Agronet (2021) Red de información y comunicación del sector Agropecuario Colombiano. Available at: . Accessed on: October 15th, 2021.
Álvarez D, Gutiérrez P & Marín M (2016) Caracterización molecular del Potato virus V (PVV) infectando Solanum phureja mediante secuenciación de nueva generación. Acta Biológica Colombiana, 21:521-531.
Álvarez D, Gutiérrez-Sánchez P & Marín-Montoya M (2017) Genome sequencing of Potato yellow vein virus (PYVV) and development of a molecular test for its detection. Bioagro, 29:03-14.
Álvarez N, Jaramillo H, Gallo Y, Gutiérrez P & Marín M (2018) Molecular characterization of Potato virus Y (PVY) and Potato virus V (PVV) isolates naturally infecting Cape gooseberry (Physalis peruviana) in Antioquia, Colombia. Agronomía Colombiana, 36:13-23.
Boratyn GM, Thierry-Mieg D, Busby B & Madden TL (2019) Magic-BLAST, an accurate DNA and RNA-seq aligner for long and short reads. BMC Bioinformatics, 20:405.
Bushmanova E, Antipov D, Lapidus A & Prjibelski AD (2019) rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. GigaScience, 8:01-13.
Díaz-Cruz GA, Smith CM, Wiebe KF & Cassone BJ (2017) First complete genome sequence of Tobacco necrosis virus D isolated from soybean and from North America. Genome Announcements, 5:e00781.
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32:1792-1797.
EPPO Global Database (1999) Tobacco necrosis virus (TNV000). Available at: <https://gd.eppo.int/taxon/TNV000/documents>. Accessed on: April 25th, 2021.
Fedepapa (2019) Informe de gestión. Vigencia 2019. Available at: <https://fedepapa.com/wp-content/uploads/2020/05/INFORME-DE-GESTIO%CC%81N-VIGENCIA-2019.pdf>. Accessed on: October 20th, 2021.
Frost KE, Groves RL & Charkowski AO (2013) Integrated control of potato pathogens through seed potato certification and provision of clean seed potatoes. Plant Disease, 97:1268-1280.
Gallo Y, Sierra A, Donaire L, Aranda MA, Gutiérrez PA & Marín MA (2019) Coinfección natural de virus de ARN en cultivos de papa (Solanum tuberosum subsp. Andigena) en Antioquia (Colombia). Acta Biológica Colombiana, 24:546-560.
Gallo Y, Marín M & Gutiérrez PA (2020) Detection of RNA viruses in Cape gooseberry (Physalis peruviana L.) by RNAseq using total RNA and dsRNA inputs. Archives of Phytopathology and Plant Protection, 53:395-413.
Gallo Y, Marín M & Gutiérrez PA (2021a) Detection of RNA viruses in Solanum quitoense by high-throughput sequencing (HTS) using total and double stranded RNA inputs. Physiological and Molecular Plant Pathology, 113:101570.
Gallo Y, Sierra A, Marín M & Gutiérrez PA (2021b) Prevalencia de cinco virus de ARN en tubérculos-semilla de papa cultivados en Antioquia (Colombia). Biotecnología en el Sector Agropecuario y Agroindustrial, 19:66-78.
García D, Olarte MA, Gutiérrez P & Marín MA (2016) Detección serológica y molecular del Potato virus X (PVX) en tubérculos-semilla de papa (Solanum tuberosum L. y Solanum phureja Juz. y Bukasov) en Antioquia. Revista Colombiana de Biotecnología, 18:104-111.
García A (2022) Detección molecular y limpieza de virus en material de siembra de Solanum tuberosum y S. phureja. Master Dissertation. Universidad Nacional de Colombia, Medellín. 358p.
Gil JF, Cotes JM, González EP & Marín M (2011) Caracterización genotípica de aislamientos colombianos del potato mop-top virus (PMTV, Pomovirus). Actualidades Biológicas, 33:69-84.
Gil JF, Adams I, Boonham N, Nielsen SL & Nicolaisen M (2016) Molecular and biological characterization of Potato mop-top virus (PMTV, Pomovirus) isolates from the potato-growing regions of Colombia. Plant Pathology, 65:1210-1220.
Gildemacher PR, Schulte-Geldermann E, Borus D, Demo P, Kinyae P, Mundia P & Struik PC (2011) Seed potato quality improvement through positive selection by smallholder farmers in Kenya. Potato Research, 54:253-266.
Giraldo S, Sierra A, Ospina M, Higuita M, Gallo Y, Gutiérrez P & Marín M (2022) Detección y caracterización molecular del potato virus B (PVB) en papa criolla (Solanum phureja) en Antioquia. Acta Biológica Colombiana, 27:258-268.
Gutiérrez PA, Alzate JF & Marín-Montoya MA (2013) Complete genome sequence of a novel potato virus S strain infecting Solanum phureja in Colombia. Archives of Virology, 158:2205-2208.
Gutiérrez P, Mesa HJ & Marín M (2016) Genome sequence of a divergent Colombian isolate of potato virus V (PVV) infecting Solanum phureja. Acta Virologica, 60:49-54.
Gutiérrez P, Rivillas A, Tejada D, Giraldo S, Restrepo A, Ospina M, Cadavid S, Gallo Y & Marín M (2021) PVDP: A portable open source pipeline for detection of plant viruses in RNAseq data. A case study on potato viruses in Antioquia (Colombia). Physiological and Molecular Plant Pathology, 113:101604.
Guyader S & Ducray DG (2002) Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products. Journal of General Virology, 83:1799-1807.
Guzmán M, Román V, Franco L & Rodríguez P (2010) Presencia de cuatro virus en algunas accesiones de la Colección Central Colombiana de papa mantenida en campo. Agronomía Colombiana, 28:225-233.
Guzmán-Barney M, Franco-Lara L, Rodríguez D, Vargas L & Fierro JE (2012) Yield losses in Solanum tuberosum Group Phureja cultivar criolla Colombia in plants with symptoms of PYVV in field trials. American Journal of Potato Research, 89:438-447.
Halterman D, Charkowski A & Verchot J (2012) Potato viruses and seed certification in the USA to provide healthy propagated tubers. Pest Technology, 6:01-14.
ICA (2015) Resolución 3168 de 2015. Available at: <https://www.ica.gov.co/getattachment/4e8c3698-8fcb-4e42-80e7-a6c7acde9bf8/2015R3168.aspx>. Accessed on: September 20th, 2022.
ICTV (2021) International Committee on Taxonomy of Viruses. Available at: <https://ictv.global/msl>. Accessed on: October 20th, 2021.
Kreuze JF, Souza-Dias JAC, Jeevalatha A, Figueira AR, Valkonen JPT & Jones RAC (2020) Viral diseases in potato. In: Campos H & Ortiz O (Eds.) The potato crop. Cham, Springer. pp.389-430.
Kumar R, Kaundal P, Kumar R, Siddappa S, Kumari H, Chandra K, Sharma S & Kumar M (2021) Rapid and sensitive detection of potato virus X by one-step reverse transcription-recombinase polymerase amplification method in potato leaves and dormant tubers. Molecular and Cellular Probes, 58:101743.
MADR (2019) Estrategia de ordenamiento de la producción. Cadena productiva de la papa y su industria. Available at: <https://sioc.minagricultura.gov.co/Papa/Normatividad/Plan%20de%20Ordenamiento%20papa%202019-2023.pdf>. Accessed on: April 25th, 2021.
Mesa ME, González MI, Gutiérrez PA & Marín MA (2016) Diagnóstico serológico y molecular del Potato leafroll virus (PLRV) en tubérculos-semilla de papa en Antioquia. Acta Agronómica, 65:204-210.
Mumford RA, Walsh K, Barker I & Boonham N (2000) Detection of Potato mop top virus and Tobacco rattle virus Using a Multiplex Real-Time Fluorescent Reverse-Transcription Polymerase Chain Reaction Assay. Phytopathology, 90:448-453.
Muñoz L, Gutiérrez-Sánchez PA & Marín-Montoya M (2016a) Detección y secuenciación del genoma del Potato Virus Y (PVY) que infecta plantas de tomate en Antioquia, Colombia. Bioagro, 28:69-80.
Muñoz D, Gutiérrez P & Marín M (2016b) Detección y caracterización molecular del Potato virus Y (PVY) en cultivos de papa (Solanum tuberosum L.) del norte de Antioquia, Colombia. Protección Vegetal, 31:09-19.
Porras P & Herrera C (2015) Modelo productivo de la papa variedad Diacol Capiro para el departamento de Antioquia. Mosquera, Corpoica. 92p.
Price WC (1938) Studies on the virus of tobacco necrosis. American Journal of Botany, 25:603.
Raigond B, Verma A, Pathania S, Sridhar J, Kochhar T & Chakrabarti SK (2020) Development of a reverse transcription loop-mediated isothermal amplification for detection of potato virus a in potato and in insect vector aphids. Crop Protection, 137:105296.
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G & Mesirov JP (2011) Integrative Genomics Viewer. Nature Biotechnology, 29:24-26.
Rodríguez LE, Ñustez CE & Estrada N (2009) Criolla Latina, Criolla Paisa y Criolla Colombia, nuevos cultivares de papa criolla para el departamento de Antioquia (Colombia). Agronomía Colombiana, 27:289-303.
Saitou N & Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4:406-425.
Savenkov EI, Sandgren MY & Valkonen JPT (1999) Complete sequence of RNA 1 and the presence of tRNA-like structures in all RNAs of Potato mop-top virus, genus Pomovirus. Journal of General Virology, 80:2779-2784.
Schulte-Geldermann E, Gildemacher PR & Struik PC (2012) Improving seed health and seed performance by positive selection in three Kenyan potato varieties. American Journal of Potato Research, 89:429-437.
Schumpp O, Bréchon A, Brodard J, Dupuis B, Farinelli L, Frei P, Otten P & Pellet D (2021) Large-Scale RT-qPCR diagnostics for seed potato certification. Potato Research, 64:553-569.
Seminario JF, Villanueva-Guevara R & Valdez-Yopla MH (2018) Rendimiento de cultivares de papa (Solanum tuberosum L.) amarillos precoces del grupo Phureja. Agronomía Mesoamericana, 29:639-653.
Sierra A, Gallo Y, Estrada M, Gutiérrez PA & Marín M (2020) Detección molecular de seis virus de ARN en brotes de tubérculos de papa criolla (Solanum phureja) en Antioquia, Colombia. Bioagro, 32:03-14.
Sierra A, Gallo Y, Estrada M, Gutiérrez P & Marín M (2021) Detection of four RNA viruses in commercial and informal potato seed tubers in Antioquia (Colombia). Archives of Phytopathology and Plant Protection, 54:273-294.
Singh RP, Kurz J, Boiteau G & Bernard G (1995) Detection of potato leafroll virus in single aphids by the reverse transcription polymerase chain reaction and its potential epidemiological application. Journal of Virological Methods, 1:133-143.
Smith KM & Bald JG (1935) A description of a necrotic virus disease affecting tobacco and other plants. Parasitology, 27:231-245.
Tamura K (1992) Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Molecular Biology and Evolution, 9:678-687.
Tamura K, Stecher G & Kumar S (2021) MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38:3022-3027.
Teakle DS & Gold AH (1963) Further studies of Olpidium as a vector of tobacco necrosis virus. Virology, 19:310-315.
Thomas-Sharma S, Abdurahman A, Ali S, Andrade-Piedra JL, Bao S, Charkowski AO, Crook D, Kadian M, Kromann P, Struik PC, Torrance L, Garrett KA & Forbes GA (2016) Seed degeneration in potato: the need for an integrated seed health strategy to mitigate the problem in developing countries. Plant Pathology, 65:03-16.
Thomas-Sharma S, Andrade-Piedra J, Carvajal M, Hernandez JF, Jeger MJ, Jones RAC, Kromann P, Legg JP, Yuen J, Forbes GA & Garrett KA (2017) A risk assessment framework for seed degeneration: Informing an integrated seed Health strategy for vegetatively propagated crops. Phytopathology, 107:1123-1135.
Vallejo D, Gutiérrez P & Marín M (2016) Genome characterization of a Potato virus S (PVS) variant from tuber sprouts of Solanum phureja Juz. et Buk. Agronomía Colombiana, 34:51-60.
Yang L, Nie B, Liu J & Song B (2014) A reexamination of the effectiveness of ribavirin on eradication of viruses in potato plantlets in vitro using ELISA and quantitative RT–PCR. American Journal of Potato Research, 91:304-311.
Downloads
Publicado
Como Citar
Edição
Seção
Licença
Este trabalho está licenciado sob uma licença Creative Commons Attribution 4.0 International License.
