A risk assessment framework for seed degeneration: Informing an integrated seed health strategy for vegetatively propagated crops

Phytopathology

Volumn 107, Issue 10, 2017, Pages 1123-1135

  Thomas Sharma, S ^a,b   Andrade Piedra, J ^c   Carvajal Yepes, M ^d   Hernandez Nopsa, J F ^a,e   Jeger, M J ^f   Jones, R A C ^g   Kromann, P ^h   Legg, J P ⁱ   Yuen, J ^j   Forbes, G A ^k   Garrett, K A ^a,e  

^a KANSAS STATE UNIVERSITY   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c INTERNATIONAL POTATO CENTER   (Peru)

^d INTERNATIONAL CENTER FOR TROPICAL AGRICULTURE CIAT   (Colombia)

^e UNIVERSITY OF FLORIDA   (United States)

^f IMPERIAL COLLEGE LONDON   (United Kingdom)

^g UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^h International Potato Centre Quito   (Ecuador)

ⁱ International Institute of Tropical Agriculture   (Tanzania)

^j SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^k International Potato Center   (China)

more..

Author keywords

Banana; Cassava; Environmental heterogeneity; Positive selection; Potato; Root crops; Seed degeneration; Seed health; Simulation models; Sweetpotato; Tuber crops; Vegetative propagation; Yam

Indexed keywords

AGRICULTURAL LAND; AGRICULTURE; COMPUTER SIMULATION; CROP; MANIHOT; MICROBIOLOGY; MUSA; PHYSIOLOGY; PLANT DISEASE; PLANT SEED; POTATO; PREVENTION AND CONTROL; RISK ASSESSMENT; THEORETICAL MODEL; WEATHER;

AGRICULTURE; COMPUTER SIMULATION; CROPS, AGRICULTURAL; FARMS; MANIHOT; MODELS, THEORETICAL; MUSA; PLANT DISEASES; RISK ASSESSMENT; SEEDS; SOLANUM TUBEROSUM; WEATHER;

EID: 85032623878     PISSN: 0031949X     EISSN: None     Source Type: Journal    
DOI: 10.1094/PHYTO-09-16-0340-R     Document Type: Article

References (61)

1. Andersen, K. F., Buddenhagen, C. E., Rachkara, P., Gibson, R., Kalule, S., Phillips, D., and Garrett, K. A. 2017. Analyzing key nodes and epidemic risk in seed networks: Sweetpotato in Northern Uganda. bioRxiv (preprint). Online: https://doi.org/10.1101/107359
2. Aritua, V., Legg, J. P., Smit, N., and Gibson, R. W. 1999. Effect of local inoculum on the spread of sweet potato virus disease: limited infection of susceptible cultivars following widespread cultivation of a resistant sweet potato cultivar. Plant Pathol. 48:655-661.
3. Berger, R. D. 1977. Application of epidemiological principles to achieve plant disease control. Annu. Rev. Phytopathol. 15:165-183.
4. Bertschinger, L. 1992. Modelling of potato virus pathosystems by means of quantitative epidemiology. PhD thesis. Swiss Federal Institute of Technology, Zurich, Switzerland.
5. Bertschinger, L., Keller, E. R., and Gessler, C. 1995. Characterization of the virus × temperature interaction in secondarily infected potato plants using EPIVIT. Phytopathology 85:815-819.
6. Blomme, G., Jacobsen, K., Ocimati, W., Beed, F., Ntamwira, J., Sivirihauma, C., Ssekiwoko, F., Nakato, V., Kubiriba, J., Tripathi, L., Tinzaara, W., Mbolela, F., Lutete, L., and Karamura, E. 2014. Fine-tuning banana Xanthomonas wilt control options over the past decade in East and Central Africa. Eur. J. Plant Pathol. 139:271-287.
7. Carvajal-Yepes, M., Olaya, C., Lozano, I., Cuervo, M., Castano, M., and Cuellar, W. J. 2014. Unraveling complex viral infections in cassava (Manihot esculenta Crantz) from Colombia. Virus Res. 186:76-86.
8. Cox, C. M., Bockus, W. W., Holt, R. D., Fang, L., and Garrett, K. A. 2013. Spatial connectedness of plant species: potential links for apparent competition via plant diseases. Plant Pathol. 62:1195-1204.
9. Coyne, D. L., Claudius-Cole, A. O., Kenyon, L., and Baimey, H. 2010. Differential effect of hot water treatment on whole tubers versus cut setts of yam (Dioscorea spp.). Pest Manag. Sci. 66:385-389.
10. DiFonzo, C. D., Ragsdale, D. W., and Radcliffe, E. B. 1995. Potato leafroll virus spread in differentially resistant potato cultivars under varying aphid densities. Am. Potato J. 72:119-132.
11. Fankhauser, C. 2000. Seed-transmitted diseases as constraints for potato production in the tropical highlands of Ecuador. PhD thesis. Swiss Federal Institute of Technology, Zurich, Switzerland.
12. Fargette, D., Colon, L. T., Bouveau, R., and Fauquet, C. 1996. Components of resistance of cassava to African cassava mosaic virus. Eur. J. Plant Pathol. 102:645-654.
13. Fargette, D., and Vie, K. 1995. Simulation of the effects of host resistance, reversion, and cutting selection on incidence of African cassava mosaic virus and yield losses in cassava. Phytopathology 85:370-375.
14. Franklin, J. 2009. Mapping species distributions: spatial inference and prediction. Cambridge University Press, Cambridge, U.K.
15. Frost, K. E., Groves, R. L., and Charkowski, A. O. 2013. Integrated control of potato pathogens through seed potato certification and provision of clean seed potatoes. Plant Dis. 97:1268-1280.
16. Garrett, K. A. 2012. Information networks for disease: commonalities in human management networks and within-host signalling networks. Eur. J. Plant Pathol. 133:75-88.
17. Garrett, K. A., Dobson, A. D. M., Kroschel, J., Natarajan, B., Orlandini, S., Tonnang, H. E. Z., and Valdivia, C. 2013. The effects of climate variability and the color of weather time series on agricultural diseases and pests, and decision-making for their management. Agric. For. Meteorol. 170: 216-227.
18. Gergerich, R. C., Welliver, R. A., Gettys, S., Osterbauer, N. K., Kamenidou, S., Martin, R. R., Golino, D. A., Eastwell, K., Fuchs, M., Vidalakis, G., and Tzanetakis, I. E. 2015. Safeguarding fruit crops in the age of agricultural globalization. Plant Dis. 99:176-187.
19. Gibson, R. W., and Otim-Nape, G. W. 1997. Factors determining recovery and reversion in mosaic-affected African cassava mosaic virus resistant cassava. Ann. Appl. Biol. 131:259-271.
20. Gibson, R. W., and Kreuze, J. F. 2014. Degeneration in sweetpotato due to viruses, virus-cleaned planting material and reversion: a review. Plant Pathol. 64:1-15.
21. Gibson, R. W., Wasswa, P., and Tufan, H. A. 2014. The ability of cultivars of sweetpotato in East Africa to ‘revert’ from Sweet potato feathery mottle virus infection. Virus Res. 186:130-134.
22. Gildemacher, P. R., Demo, P., Barker, I., Kaguongo, W., Woldegiorgis, G., Wagoire, W. W., Wakahiu, M., Leeuwis, C., and Struik, P. C. 2009. A description of seed potato systems in Kenya, Uganda and Ethiopia. Am. J. Potato Res. 86:373-382.
23. Gildemacher, P. R., Schulte-Geldermann, E., Borus, D., Demo, P., Kinyae, P., Mundia, P., and Struik, P. C. 2011. Seed potato quality improvement through positive selection by smallholder farmers in Kenya. Potato Res. 54: 253-266.
24. Grimm, V., Berger, U., DeAngelis, D. L., Polhill, J. G., Giske, J., and Railsback, S. F. 2010. The ODD protocol: a review and first update. Ecol. Modell. 221:2760-2768.
25. Gross, L. J. 2013. Use of computer systems and models. Pages 213-220 in: Encyclopedia of Biodiversity, 2nd Ed., S. A. Levin, ed. Vol. 2. Academic Press, Waltham, MA.
26. Hernandez Nopsa, J. F., Buddenhagen, C. E., Andersen, K. F., Andrade-Piedra, J., Forbes, G. A., Kromann, P., Thomas-Sharma, S., Useche, P., and Garrett, K. A. 2017. Epidemic network analysis for mitigation of invasive pathogens in seed systems: Potato in Ecuador. bioRxiv (preprint). Online: https://doi.org/10.1101/107367.
27. Hernandez Nopsa, J. F., Daglish, G. J., Hagstrum, D. W., Leslie, J. F., Phillips, T. W., Scoglio, C., Thomas-Sharma, S., Walter, G. H., and Garrett, K. A. 2015. Ecological networks in stored grain: Key postharvest nodes for emerging pests, pathogens, and mycotoxins. BioScience 65: 985-1002.
28. Hilker, F. M., Allen, L. J. S., Bokil, V. A., Briggs, C. J., Feng, Z., Garrett, K. A., Gross, L. J., Hamelin, F. M., Jeger, M. J., Manore, C. A., Power, A. G., Redinbaugh, M. G., Rúa, M. A., and Cunniffe, N. J. 2017. Modelling virus coinfection to inform management of maize lethal necrosis in Kenya. Phytopathology 107:1095-1108.
29. Holt, J., Jeger, M. J., Thresh, J. M., and Otim-Nape, G. W. 1997. An epidemiological model incorporating vector population dynamics applied to African cassava mosaic virus disease. J. Appl. Ecol. 34:793-806.
30. Hughes, G., and Madden, L. V. 2002. Some methods for eliciting expert knowledge of plant disease epidemics and their application in cluster sampling for disease incidence. Crop Prot. 21:203-215.
31. Jones, R. A. C. 2006. Control of plant virus diseases. Adv. Virus Res. 67: 205-244.
32. Jones, R. A. C. 2016. Future scenarios for plant virus pathogens as climate change progresses. Adv. Virus Res. 95:87-147.
33. Knol, A. B., Slottje, P., van der Sluijs, J. P., and Lebret, E. 2010. The use of expert elicitation in environmental health impact assessment: a seven step procedure. Environ. Health 9:19.
34. Kreuze, J. F., Perez, A., Untiveros, M., Quispe, D., Fuentes, S., Barker, I., and Simon, R. 2009. Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses. Virology 388:1-7.
35. Lamichhane, J. R., Barzman, M., Booij, K., Boonekamp, P., Desneux, N., Huber, L., Kudsk, P., Langrell, S. R. H., Ratnadass, A., Ricci, P., Sarah, J.-L., and Messean, A. 2015. Robust cropping systems to tackle pests under climate change. A review. Agron. Sustain. Dev. 35:443-459.
36. Legg, J. 1999. Emergence, spread and strategies for controlling the pandemic of cassava mosaic virus disease in east and central Africa. Crop Prot. 18: 627-637.
37. Legg, J. P., Jeremiah, S. C., Obiero, H. M., Maruthi, M. N., Ndyetabula, I., Okao-Okuja, G., Bouwmeester, H., Bigirimana, S., Tata-Hangy, W., Gashaka, G., Mkamilo, G., Alicai, T., and Kumar, P. L. 2011. Comparing the regional epidemiology of the cassava mosaic and cassava brown streak virus pandemics in Africa. Virus Res. 159:161-170.
38. Legg, J. P., Kumar, P. L., Makeshkumar, T., Tripathi, L., Ferguson, M., Kanju, E., Ntawuruhunga, P., and Cuellar, W. 2015. Cassava virus diseases: Biology, epidemiology, and management. Adv. Virus Res. 91:85-142.
39. Levins, R. 1966. The strategy of model building in population biology. Am. Sci. 54:421-431.
40. Mac Nally, R. 2007. Consensus weightings of evidence for inferring breeding success in broad-scale bird studies. Austral Ecol. 32:479-484.
41. Mallowa, S. O., Isutsa, D. K., Kamau, A. W., and Legg, J. P. 2011. Effectiveness of phytosanitation in cassava mosaic disease management in a post-epidemic area of western Kenya. ARPN J. Ag. Bio. Sci. 6:8-15.
42. Mallowa, S. O., Isutsa, D. K., Kamau, A. W., Obonyo, R., and Legg, J. P. 2006. Current characteristics of cassava mosaic disease in postepidemic areas increase the range of possible management options. Ann. Appl. Biol. 149: 137-144.
43. Martin, T. G., Kuhnert, P. M., Mengersen, K., and Possingham, H. P. 2005. The power of expert opinion in ecological models using Bayesian methods: Impact of grazing on birds. Ecol. Appl. 15:266-280.
44. McGuire, S., and Sperling, L. 2016. Seed systems smallholder farmers use. Food Secur. 8:179-195.
45. McQuaid, C. F., Sseruwagi, P., Pariyo, A., and van den Bosch, F. 2016. Cassava brown streak disease and the sustainability of a clean seed system. Plant Pathol. 65:299-309.
46. Moslonka-Lefebvre, M., Finley, A., Dorigatti, I., Dehnen-Schmutz, K., Harwood, T., Jeger, M. J., Xu, X., Holdenrieder, O., and Pautasso, M. 2011. Networks in plant epidemiology: From genes to landscapes, countries, and continents. Phytopathology 101:392-403.
47. Mwangi, J. K., Nyende, A. B., Demo, P., and Matiru, V. N. 2008. Detection of latent infection by Ralstonia solanacearum in potato (Solanum tuberosum) using stems instead of tubers. Afr. J. Biotechnol. 7:1644-1649.
48. Oberkampf, W. L., Helton, J. C., Joslyn, C. A., Wojtkiewicz, S. F., and Ferson, S. 2004. Challenge problems: uncertainty in system response given uncertain parameters. Reliab. Eng. Syst. Saf. 85:11-19.
49. Parsa, S., Morse, S., Bonifacio, A., Chancellor, T. C. B., Condori, B., Crespo-Perez, V., Hobbs, S. L. A., Kroschel, J., Ba, M. N., Rebaudo, F., Sherwood, S. G., Vanek, S. J., Faye, E., Herrera, M. A., and Dangles, O. 2014. Obstacles to integrated pest management adoption in developing countries. Proc. Natl. Acad. Sci. USA 111:3889-3894.
50. R Core Team. 2016. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
51. Rahman, M. S., and Akanda, A. M. 2008. Impact of PVY and PLRV on growth and yield of second generation seed potato. Bangl. J. Plant Pathol. 24:19-24.
52. Restif, O., Hayman, D. T. S., Pulliam, J. R. C., Plowright, R. K., George, D. B., Luis, A. D., Cunningham, A. A., Bowen, R. A., Fooks, A. R., O’Shea, T. J., Wood, J. L. N., and Webb, C. T. 2012. Model-guided fieldwork: practical guidelines for multidisciplinary research on wildlife ecological and epidemiological dynamics. Ecol. Lett. 15:1083-1094.
53. Salazar, L. F. 1996. Potato viruses and their control. International Potato Center, Lima, Peru.
54. Schulte-Geldermann, E., Gildemacher, P. R., and Struik, P. C. 2012. Improving seed health and seed performance by positive selection in three Kenyan potato varieties. Am. J. Potato Res. 89:429-437.
55. Shaw, M. W., and Pautasso, M. 2014. Networks and plant disease management: Concepts and applications. Annu. Rev. Phytopathol. 52: 477-493.
56. Sisterson, M. S., and Stenger, D. C. 2013. Roguing with replacement in perennial crops: Conditions for successful disease management. Phytopathology 103:117-128.
57. Thiele, G. 1999. Informal potato seed systems in the Andes: Why are they important and what should we do with them? World Dev. 27: 83-99.
58. Thomas‐Sharma, S., Abdurahman, A., Ali, S., Andrade‐Piedra, J., Bao, S., Charkowski, A., Crook, D., Kadian, M., Kromann, P., Struik, P., Torrance, L., Garrett, K. A., and Forbes, G. A. 2016. Seed degeneration in potato: the need for an integrated seed health strategy to mitigate the problem in developing countries. Plant Pathol. 65:3-16.
59. van den Bosch, F., Jeger, M. J., and Gilligan, C. A. 2007. Disease control and its selection for damaging plant virus strains in vegetatively propagated staple food crops; a theoretical assessment. P. Roy. Soc. B-Biol. Sci. 274: 11-18.
60. van der Waals, J. E., Kruger, K., Franke, A. C., Haverkort, A. J., and Steyn, J. M. 2013. Climate change and potato production in contrasting South African agro-ecosystems 3. Effects on relative development rates of selected pathogens and pests. Potato Res. 56:67-84.
61. Yamada, K., Elith, J., McCarthy, M., and Zerger, A. 2003. Eliciting and integrating expert knowledge for wildlife habitat modelling. Ecol. Modell. 165:251-264.