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Article

Detection of four RNA viruses in commercial and informal potato seed tubers in Antioquia (Colombia)

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Pages 273-294 | Received 27 Jul 2020, Accepted 20 Sep 2020, Published online: 05 Oct 2020

References

  • AGRONET. 2018. Red de Información y Comunicación del Sector Agropecuario Colombiano. [accessed 2018 Sept 15]. http://www.agronet.gov.co/estadistica/Paginas.
  • Alfaro JP, Franco L. 2015. Potato Virus Y (PVY) y Potato Yellow Vein Virus (PYVV) en infecciones mixtas no causan síntomas atípicos en plantas de papa. Rev Fac Cien Bas. 11(2):26–37.
  • Álvarez J, Cotes J, Marín M. 2011. Detección molecular de virus en material de siembra de tomate de árbol en Colombia. Rev Protección Veg. 26(2):80–91.
  • Álvarez D, Gutiérrez P, Marín M. 2017. Secuenciación del genoma del Potato yellow vein virus (PYVV) y desarrollo de una prueba molecular para su detección. Bioagro. 29(1):3–14.
  • Barrero RA, Napier KR, Cunnington J, Liefting L, Keenan S, Frampton RA, Szabo T, Bulman S, Hunter A, Ward L, et al. 2017. An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids. BMC Bioinf. 18(1):26.
  • Broadbent L, Gregory PH, Tinsley TW. 1950. Roguing potato crops for virus diseases. Ann Appl Biol. 37(4):640–650.
  • Cháves G, Cubillos K, Guzmán-Barney M. 2014. First report of recombination in potato yellow vein virus (PYVV) in Colombia. Trop Plant Pathol. 39(3):234–241.
  • Chomczynski P, Sacchi N. 1987. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 162(1):156–159.
  • Cox BA, Jones RAC. 2012. Effects of tissue sampling position, primary and secondary infection, cultivar, and storage temperature and duration on the detection, concentration and distribution of three viruses within infected potato tubers. Australasian Plant Pathol. 41(2):197–210.
  • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792–1797.
  • FAOSTAT. 2018. Food and agriculture data. [accessed 2018 Sept 15]. http://www.fao.org/faostat/en/#home.
  • Forbes GA, Charkowski A, Andrade-Piedra J, Parker ML, Schulte-Geldermann E. 2020. Potato seed systems. In: Campos H, Ortiz O, editors. The potato crop. Cham, Switzerland: Springer.
  • Frost KE, Groves RL, Charkowski AO. 2013. Integrated control of potato pathogens through seed potato certification and provision of clean seed potatoes. Plant Dis. 97(10):1268–1280.
  • Gallo Y, Gutiérrez PA, Marín M. 2013. Detection of PMTV using polyclonal antibodies raised against a capsid-specific peptide antigen. Rev Fac Nac Agron Medellín. 66:6999–7008.
  • García NA, Gutiérrez PA, Marín MA. 2013. Detección y cuantificación del Potato mop-top virus (PMTV) en Colombia mediante qRT-PCR. Acta Agron. 62(2):120–128.
  • 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. Rev Colomb Biotecnol. 18(1):104–111.
  • Gil JF, Cotes JM, Marín M. 2011a. Incidencia de potyvirus y caracterización molecular de PVY en regiones productoras de papa (Solanum tuberosum L.) de Colombia. Rev Colomb Biotecnol. 13(1):85–93.
  • Gil JF, Cotes JM, Marín M. 2011b. Incidencia y caracterización molecular del Potato leafroll virus (PLRV) en las principales regiones productoras de papa de Colombia. Fitosanidad. 15(1):17–24.
  • Gil JF, Cotes JM, González EP, Marín M. 2011c. Caracterización genotípica de aislamientos colombianos del potato mop-top virus (PMTV, Pomovirus). Actual Biol. 33 (94):69–84.
  • Gil JF, Cotes JM, Marín M. 2012. Detección y caracterización molecular del Virus X de la Papa (PVX) en regiones productoras de papa de Colombia. Rev. Protección Veg. 27(2):69–76.
  • Gil JF, Cotes JM, Marín M. 2013a. Detección serológica y caracterización molecular de Potato virus S (PVS, Carlavirus) en cultivos de papa de Colombia. Rev Biol Trop. 61(2):565–575.
  • Gil JF, Cotes JM, Marín M. 2013b. Incidencia visual de síntomas asociados a enfermedades virales en cultivos de papa de Colombia. Rev Biot Agrop. 11(2):101–110.
  • 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 Res. 54(3):253–266.
  • Gish W, States DJ. 1993. Identification of protein coding regions by database similarity search. Nat Genet. 3(3):266–272.
  • 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. Agron Colomb. 28(2):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. Am J Potato Res. 89(6):438–447.
  • Halterman D, Charkowski A, Verchot J. 2012. Potato viruses and seed certification in the USA to provide healthy propagated tubers. Pest Tech. 6(1):1–14.
  • Hernández-Gúzman AK, Gúzman-Barney MM. 2014. Detección del virus del amarillamiento de las nervaduras de la hoja de la papa en diferentes órganos de Solanum tuberosum grupo Phureja cv Criolla Colombia utilizando RT-PCR convencional y en tiempo real. Rev Colomb Biotecnol. 26(1):74–85.
  • Hill SA, Jackson EA. 1984. An investigation of the reliability of ELISA as a practical test for detecting potato leaf roll virus and potato virus Y in tubers. Plant Pathol. 33(1):21–26.
  • ICA. 2015. Resolución 3168 de 2015. [accessed 2018 Sept 10]. https://www.ica.gov.co/getattachment/4e8c3698-8fcb-4e42-80e7-a6c7acde9bf8/2015R3168.aspx.
  • Imbeaud S, Graudens E, Boulanger V, Barlet X, Zaborski P, Eveno E, Mueller O, Schroeder A, Auffray C. 2005. Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces. Nucleic Acids Res. 33(6):e56.
  • Ioannou N. 1989. Production of seed potatoes in Cyprus: the effects of roguing and planting date on the spread of potato leaf roll virus, tuber yield, and infestation by potato tuber moth. Potato Res. 32(3):331–339.
  • Jones S, Baizan-Edge A, MacFarlane S, Torrance L. 2017. Viral diagnostics in plants using next generation sequencing: computational analysis in practice. Front Plant Sci. 8:1770.
  • Kadian MS, Ilangantileke S, Arif M, Hossain M, Roder W, Sakha BM, Singh SV, Farrooq K, Mazeen ACM. 2007. Status of potato seed systems in South West Asia (SWA). Potato J. 34:25–30.
  • Karasev AV, Gray SM. 2013. Continuous and emerging challenges of Potato virus Y in potato. Annu Rev Phytopathol. 51(1):571–586. https://10.1146/annurev-phyto-082712-102332.
  • Kerlan C. 2008. Potato viruses. In: Mahy BW, van Regenmortel MH, editors. Desk encyclopedia of plant and fungal virology. Oxford: Academic Press; p. 458–471.
  • Kogovšek P, Kladnik A, Mlakar J, Znidarič MT, Dermastia M, Ravnikar M, Pompe-Novak M. 2011. Distribution of Potato virus Y in potato plant organs, tissues, and cells. Phytopathology. 101(11):1292–1300.
  • Lacroix C, Renner K, Cole E, Seabloom EW, Borer ET, Malmstrom CM. 2016. Methodological guidelines for accurate detection of viruses in wild plant species. Appl Environ Microbiol. 82(6):1966–1975.
  • Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol. 25(7):1307–1320.
  • Li B, Dewey CN. 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinf. 12:323.
  • MacDiarmid R, Rodoni B, Melcher U, Ochoa-Corona F, Roossinck M. 2013. Biosecurity implications of new technology and discovery in plant virus research. PLoS Pathog. 9(8):e1003337.
  • Madden LV, Hughes G. 1999. Sampling for plant disease incidence. Phytopathology. 89(11):1088–1103.
  • Marín M, Gutiérrez P. 2016. Principios de virologia molecular de plantas tropicales. Bogotá: Corpoica.
  • Martínez H, Espinal C, Salazar M, Barrios C. 2005. La cadena de la papa en Colombia: una mirada global de su estructura y dinámica 1991–2005. MADR. [accessed 2018 Jan 10]. http://bibliotecadigital.agronet.gov.co/handle/11348/6325.
  • Medina HC, Gutiérrez PA, Marín MA. 2015. Detección del Potato virus Y (PVY) en tubérculos de papa mediante TAS-ELISA y qRT-PCR en Antioquia (Colombia). Bioagro. 27(2):83–92.
  • Medina HC, Gutiérrez PA, Marín MA. 2017. Detection and sequencing of Potato virus Y (PVY) and Potato leafroll virus (PLRV) in a volunteer plant of Solanum tuberosum L. cv. Diacol-Capiro. Acta Agron. 66(4):625–532.
  • 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 Agron. 65(2):204–210.
  • Muñoz D, Gutiérrez PA, Marín MA. 2016a. Detección y caracterización molecular del Potato virus Y (PVY) en cultivos de papa (Solanum tuberosum L.) del norte de Antioquia, Colombia. Rev Prot Veg. 31:9–19.
  • Muñoz D, Gutiérrez P, Marín M. 2016b. Detection and genome characterization of Potato virus Y isolates infecting potato (Solanum tuberosum L.) in La Union Antioquia, Colombia. Agron Colomb. 34(3):317–328.
  • Muñoz L, Gutiérrez PA, Marín M. 2017. Secuenciación del genoma completo del Potato yellow vein virus (PYVV) en tomate (Solanum lycopersicum) en Colombia. Acta Biol Colomb. 22(1):5–17.
  • Navarrete I, Panchi N, Andrade Piedra J. 2017. Health quality of seed potato and yield losses in Ecuador. Rev ALAP. 21(2):69–88.
  • Nie X, Singh RP. 2001. A novel usage of random primers for multiplex RT-PCR detection of virus and viroid in aphids, leaves, and tubers. J Virol Methods. 91(1):37–49.
  • Okeyo GO, Sharma K, Atieno E, Narla RD, Miano DW, Schulte-Geldermann E. 2018. Effectiveness of positive selection in managing seed-borne potato viruses. JAS. 10(3):71–80.
  • Pecman A, Kutnjak D, Gutiérrez-Aguirre I, Adams I, Fox A, Boonham N, Ravnikar M. 2017. Next generation sequencing for detection and discovery of plant viruses and viroids: Comparison of two approaches. Front Microbiol. 13(8):1998.
  • Peiman M, Xie C. 2006. Sensitive detection of potato viruses, PVX, PLRV and PVS, by RT-PCR in potato leaf and tuber. Austral Plant Disease Notes. 1(1):41–46.
  • Priegnitz U, Lommen WJM, Onakuse S, Struik PC. 2019. A farm typology for adoption of innovations in potato production in Southwestern Uganda. Front Sustain Food Syst. 3:68.
  • Riascos M, Gutiérrez PA, Marín MA. 2018. Identificación molecular de Potyvirus infectando cultivos de papa en el oriente de Antioquia (Colombia). Acta Biol Colomb. 23(1):39–50.
  • RStudio Team. 2015. RStudio: Integrated development for R. [accessed 2018 June 10]. http://www.rstudio.com.
  • Salazar LF. 1996. Potato viruses and their control. Lima: International Potato Center.
  • Salazar LF. 2006. Emerging and re-emerging potato diseases in the Andes. Potato Res. 49(1):43–47.
  • Sánchez de Luque C, Corzo P, Pérez O. 1991. Incidencia de virus de papa y su efecto sobre el rendimiento en tres zonas agroecológicas de Colombia. Rev ALAP. 4:36–51.
  • Schulte-Geldermann E, Gildemacher PR, Struik PC. 2012. Improving seed health and seed performance by positive selection in three Kenyan potato varieties. Am J Potato Res. 89(6):429–437.
  • 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. J Virol Methods. 55(1):133–143.
  • Singh M, Singh RP, Fageria MS, Nie X, Coffin R, Hawkins G. 2013. Optimization of a Real-Time RT-PCR assay and its comparison with ELISA, conventional RT-PCR and the grow-out test for large scale diagnosis of Potato virus Y in dormant potato tubers. Am J Potato Res. 90(1):43–50.
  • Singh RK, Chakrabarti SK, Buckseth T. 2018. Technologies and sustainability of protected cultivation for Hi-valued vegetable crops. In: Kumar S, Patel NB, Saravaiya SN, Patel BN, editors. Recent innovations in potato seed production. India: Navsari Agricultural University; p. 237–245.
  • Taliansky M, Mayo MA, Barker H. 2003. Potato leafroll virus: a classic pathogen shows some new tricks. Mol Plant Pathol. 4(2):81–89.
  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 30(12):2725–2729.
  • Thiele G. 1999. Informal potato seed systems in the Andes: Why are they important and what should we do with them? World Dev. 27(1):83–99.
  • Thomas-Sharma S, Abdurahman A, Ali S, Andrade‐Piedra JL, Bao S, Charkowski AO, Crook D, Kadian M, Kromann P, Struik PC, et al. 2016. Seed degeneration in potato: the need for an integrated seed health strategy to mitigate the problem in developing countries. Plant Pathol. 65(1):3–16.
  • Thomas-Sharma S, Andrade-Piedra J, Carvajal Yepes M, Hernandez Nopsa JF, Jeger MJ, Jones RAC, Kromann P, Legg JP, Yuen J, Forbes GA, et al. 2017. A risk assessment framework for seed degeneration: Informing an integrated seed Health strategy for vegetatively propagated crops. Phytopathology. 107(10):1123–1135.
  • UNECE. 2004. Overview of national schemes for seed potato certification. [accessed 2020 Feb 20]. http://www.unece.org/fileadmin/DAM/trade/agr/wgroups/ge_06/ncs_schemes/ncs_all_2004_03_31.pdf.
  • Vallejo D, Gutiérrez PA, Marín MA. 2016. Genome characterization of a Potato virus S (PVS) variant from tuber sprouts of Solanum phureja Juz. et Buk. Agron Colomb. 34(1):51–60.
  • Valverde RA, Nameth ST, Jordan RL. 1990. Analysis of double-stranded RNA for plant virus diagnosis. Plant Dis. 74(3):255–258.
  • Villamil A, Cuellar WJ, Guzmán M. 2014. Natural co-infection of Solanum tuberosum crops by the Potato yellow vein virus and potyvirus in Colombia. Agron Colomb. 32(2):213–223.
  • Villamor D, Ho T, Al Rwahnih M, Martin R, Tzanetakis I. 2019. High throughput sequencing for plant virus detection and discovery. Phytopathology. 109(5):716–725.
  • Visser M, Bester R, Burger JT, Maree HJ. 2016. Next-generation sequencing for virus detection: covering all the bases. Virol J. 13:85.
  • Wang B, Ma Y, Zhang Z, Wu Z, Wu Y, Wang Q, Li M. 2011. Potato viruses in China. Crop Prot. 30(9):1117–1123.
  • 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. Am J Potato Res. 91(3):304–311.

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