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Identification of molecular markers associated with sweet potato resistance to sweet potato virus disease in Kenya

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Abstract

Sweet potato virus disease (SPVD), a result of the co-infection of whitefly transmitted Sweet potato chlorotic stunt virus (genus Crinivirus, family Closteroviridae) and the aphid transmitted Sweet potato feathery mottle virus (genus Potyvirus, family Potyviridae), is the most destructive disease of sweet potato in East Africa. A study was conducted to establish if genotypes identified as resistant or susceptible to SPVD in Kenya could be distinguished using molecular markers. A total of 47 unrelated sweet potato genotypes were selected from germplasm collections and classified into two phenotypic groups as resistant or susceptible to SPVD. Genotype selection was based on disease severity or days to symptom development in plants following graft inoculation. Amplified fragment length polymorphism (AFLP) marker profiles were generated for each individual and used in association studies to identify markers suitable for classifying the two pre-defined phenotypic groups. Analysis of molecular variance showed significant (P < 0.002) variation between the two groups using 206 polymorphic AFLP markers. Discriminant analysis and logistic regression statistical methods were used to select informative markers, and to develop models that would classify the two phenotypic groups. A training set of 30 genotypes consisting of 15 resistant and 15 susceptible were used to develop classification models. The remaining 17 genotypes were used as a test set. Four markers, which gave 100% correct classification of the training set and 94% correct classification of the test set, were selected by both statistical methods.

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References

  • Abad JA, Moyer JW (1992) Detection and distribution of sweet potato feathery mottle virus in sweet potato by in vitro-transcribed RNA probes (riboprobes), membrane immunobinding assay and direct blotting. Phytopathology 82:300–305

    Article  Google Scholar 

  • Alicai T, Fenby NS, Gibson RW, Adipala E, Vetten HJ, Foster GD, Seal SE (1999) Occurrence of two serotypes of sweet potato chlorotic stunt virus in East Africa. Phytopathology 48:718–726

    CAS  Google Scholar 

  • Aluko GK (2003) Genetic mapping of agronomic traits from the interspecific cross of Oryza sativa L. and Oryza glaberrima Steud. Ph.D. dissertation (EDT-1110103-143019), Louisiana State University, Baton Rouge

  • Aritua V, Adipala E, Carey EE, Gibson RW (1998a) The incidence of sweet potato virus disease and virus resistance of sweet potato grown in Uganda. Ann Appl Biol 132:399–411

    Google Scholar 

  • Aritua V, Alicai T, Adipala E, Carey EE, Gibson RW (1998b) Aspects of resistance to sweet potato virus disease in sweet potato. Ann Appl Biol 132:387–398

    Google Scholar 

  • Cali BB, Moyer JW (1981) Purification, serology and particle morphology of two russet crack strains of sweet potato feathery mottle virus. Phytopathology 64:210–218

    Google Scholar 

  • Capdevielle FM (2001) Evaluation of discriminant analysis procedure combining agronomic and molecular marker information for germplasm improvement in rice. MS thesis. Louisiana State University, Baton Rouge

    Google Scholar 

  • Capdevielle FM, Aluko GK, Balzarini M, Oard JH (2000) Application of molecular markers and discriminant analysis to identify rice lines with contrasting phenotypes for agronomic traits. In: Khush GS, Brar DS, Hardy B (eds) Proceedings of the fourth international rice and genetics symposium. International Rice Research Institute, Los Banos, Philippines, p 216 (abstr.)

  • Carey EE, Gibson RW, Fuentes S, Machmud M, Mwanga ROM, Turyamureeba G, Zhang L, Ma D, Abo El-Abbas F, El-Bedewy R, Salazar LF (1999) The causes and control of virus diseases in developing countries: is sweet potato virus disease the main problem? In: Impact on a changing world. International Potato Center Report for 1997–1998, Pages 241–248

  • CIP (2001) Techniques in plant virology in CIP. In: Salazar LF, Jayasinghe U (eds) CIP, Lima, Peru

  • Cohen J, Loebenstein G (1991) Role of whitefly-transmitted agent in infection of sweet potato by cucumber mosaic virus. Plant Dis 75:291–292

    Article  Google Scholar 

  • Cruz-Castillo JG, Ganeshanandam S, Mackay BR, Lawes GS, Lawoko CRO, Wooley DJ (1994) Applications of canonical discriminant analysis in horticultural research. Hortscience 29:1115–1119

    Google Scholar 

  • Dasgupta I, Malathi VG, Mukherjee SK (2003) Genetic engineering for virus resistance. Curr Sci 84:341–354

    CAS  Google Scholar 

  • Di Feo L, Nome SF, Biderbost E, Fuentes S, Salazar L (2000) Etiology of sweet potato chlorotic dwarf disease in Argentina. Plant Dis 84:35–39

    Article  Google Scholar 

  • Ebdon JS, Petrovic AM, Schwager SJ (1998) Evaluation of discriminant analysis in identification of low and high water use in Kentucky Bluegrass cultivars. Crop Sci 38:152–157

    Article  Google Scholar 

  • Esbenshade PR, Moyer JW (1982) Indexing system for sweet potato feathery mottle virus in sweet potato using enzyme-linked immunosorbent assay. Plant Dis 66:911–913

    Article  Google Scholar 

  • Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distance among DNA halotypes: An application to human mitochondrial DNA restriction data. Genetics 131:479–491

    PubMed  CAS  Google Scholar 

  • Fahima T, Roder MS, Wendehake K, Kirzhner VM, Nevo E (2002) Microsatellite polymorphism in natural populations of wild emmer wheat, Triticum dicoccoides, in Israel. Theor Appl Genet 104:17–29

    Article  PubMed  CAS  Google Scholar 

  • Fajardo DS, LaBonte DR, Jarret RL (2002) Identifying and selecting for genetic diversity in Papua New Guinea sweetpotato Ipomoea batatas (L.) Lam. germplasm collected as botanical seed. Genet Res Crop Evol 49:463–470

    Article  Google Scholar 

  • Geddes AMW (1990) The relative importance of crop pests in sub-Saharan Africa. Natural Resources Institute Bulletin No 36. NRI, Kent, UK, p 69

    Google Scholar 

  • Gibson RW, Mpembe I, Alicai T, Carey EE, Mwanga ROM, Seal SE, Vetten HJ (1998) Symptoms, aetiology and serological analysis of sweet potato virus disease in Uganda. Plant Pathol 47:95–102

    Article  Google Scholar 

  • Gibson RW, Mwanga ROM, Kasule S, Mpembe I, Carey EE (1997) Apparent absence of viruses in most symptomless field—grown sweet potato in Uganda. Ann Appl Biol 130:481–490

    Google Scholar 

  • Gichuki ST, Berenyi M, Zhang D, Hermann M, Schmidt J, Glossl J, Burg K (2003) Genetic diversity of sweetpotato [Ipomoea batatas (L.) Lam] in relationship to geographic sources as assessed with RAPD markers. Genet Res Crop Evol 50:429–437

    Article  CAS  Google Scholar 

  • Gutierrez DL, Fuentes S, Salazar LF (2003) Sweet potato virus disease: distribution, incidence, and effect on sweet potato yield in Peru. Plant Dis 87:297–302

    Article  Google Scholar 

  • Hahn SK, Terry ER, Leuschner K (1981) Resistance of sweet potato to virus complex. Exp Agric 15:252–256

    Google Scholar 

  • Hoyer U, Maiss E, Jelkmann W, Lesemann W, Vetten HJ (1996) Identification of the coat protein gene of a sweet potato sunken vein closterovirus isolate from Kenya and evidence for a serological relationship among geographically diverse closterovirus isolates from sweet potato. Phytopathology 86:744–750

    Article  CAS  Google Scholar 

  • Huff DR, Peakall R, Smouse PE (1993) RAPD variation within and among natural populations of outcrossing buffalograss (Buchloe dactyloides (Nutt) Engelm). Theor Appl Genet 86:927–934

    Article  CAS  Google Scholar 

  • Karyeija RF, Gibson RW, Valkonen JPT (1998a) Resistance to sweet potato virus disease (SPVD) in wild East African Ipomoea. Ann Appl Biol 133:39–44

    Google Scholar 

  • Karyeija RF, Gibson RW, Valkonen JPT (1998b) The significance of sweet potato feathery mottle virus in subsistence sweet potato production in Africa. Plant Dis 82:4–15

    Article  Google Scholar 

  • Karyeija RF, Kreuze JF, Gibson RW, Valkonen JPT (2000) Synergistic interactions of a potyvirus and a phloem-limited crinivirus in sweet potato plants. Virology 269:26–36

    Article  PubMed  CAS  Google Scholar 

  • Kokkinos CD, Clark CA (2006a) Real-time PCR assays for detection and quantification of sweetpotato viruses. Plant Dis 90:783–788

    Article  CAS  Google Scholar 

  • Kokkinos CD, Clark CA (2006b) Interactions among sweet potato chlorotic stunt virus and different potyviruses and potyvirus strains infecting sweetpotato in the United States. Plant Dis 90:1347–1352

    Article  Google Scholar 

  • Kreuze JF, Karyeija RF, Gibson RW, Valkonen JPT (2000) Comparisons of coat protein gene sequences show that East African isolates of sweet potato feathery mottle virus form a genetically distinct group. Arch Virol 145:567–574

    Article  PubMed  CAS  Google Scholar 

  • Li R, Salih S, Hurtt S (2004) Detection of geminiviruses in sweetpotato by polymerase chain reaction. Plant Dis 88:1347–1351

    Article  CAS  Google Scholar 

  • Mcharo M, LaBonte DR, Mwanga ROM, Kreigner A (2005) Associating molecular markers with virus resistance to classify sweetpotato genotypes. J Am Soc Hort Sci 130:355–359

    CAS  Google Scholar 

  • Mcharo M, LaBonte, Oard JH, Kays JS, McLaurin WJ (2004) Linking quantitative traits with AFLP markers in sweetpotato using discriminant analysis. Acta Hort 637:285–293

    CAS  Google Scholar 

  • Mcharo TM (2005) Associating molecular markers with phenotypes in sweetpotatoes and Liriopogons using multivariate statistical modelling. Ph.D. dissertation (ETD-03142005-155707), Louisiana State University, Baton Rouge

  • Mihovilovich E, Humberto AM, Salazar LF (2000) Combining ability for resistance to sweet potato feathery mottle virus. HortScience 35:1319–1320

    Google Scholar 

  • Mukasa SB, Rubaihayo SB, Valkonen JPT (2006) Interactions between a crinivirus, an ipomovirus and a potyvirus in coinfected sweetpotato plants. Plant Pathol 55:458–467

    Article  CAS  Google Scholar 

  • Mwanga ROM, Kriegner A, Cervantes JFC, Zhang DP, Moyer JW, Yencho GC (2002a) Resistance of sweet potato chlorotic stunt virus and sweet potato feathery mottle virus is mediated by two separate recessive genes in sweetpotato. J Am Soc Hort Sci 127:798–806

    CAS  Google Scholar 

  • Mwanga ROM, Odongo B, Turyamureeba G, Alajo A (2003) Release of six sweetpotato cultivars (‘Naspot 1’ to ‘Naspot 6’) in Uganda. HortScience 38:475–476

    Google Scholar 

  • Mwanga ROM, Yencho GC, Moyer JW (2002b) Diallel analysis of sweetpotato for resistance to sweet potato virus disease. Euphytica 128:237–248

    Article  CAS  Google Scholar 

  • Njeru R, Jones RAC, Sivasithamparam K, Jones MGK (1995) Resistance to subterranean clover mottle virus in subterranean clover results from restricted cell-to-cell movement. Aust Agric Res 46:633–643

    Article  Google Scholar 

  • Okada Y, Saito A, Nishigushi M, Kimura T (2001) Virus resistance in transgenic sweetpotato [Ipomoea batatas L. (Lam)] expressing the coat protein gene of sweet potato feathery mottle virus. Theor Appl Genet 103:743–751

    Article  CAS  Google Scholar 

  • Rosenblatt M (1956) Remarks on some nonparametric estimates of a density function. Ann Math Stat 27:565–572

    Google Scholar 

  • SAS Institute Inc. (1999) SAS/STAT user’s guide. SAS Institute Inc., Cary, NC

    Google Scholar 

  • SAS Institute Inc. (2001) The SAS system for windows v8. SAS Institute Inc., Cary, NC

    Google Scholar 

  • Vetten HJ, Hoyer U, Maiss E, Lesenmann DE, Jelkmann W (1996) Serological detection and discrimination of geographically diverse isolates of sweet potato sunken vein closterovirus. Phytopathology 11:100, 891 (abstract)

    Google Scholar 

  • Wambugu FM (2003) Development and transfer of genetically modified virus-resistant sweet potato for subsistence farmers in Kenya. Nutr Rev 61:S110–S113

    Article  PubMed  Google Scholar 

  • Wroth JM, Jones RAC (1992) Subterranean clover mottle sobomovirus: its host range, resistance in subterranean clover and transmission through seed and by grazing by animals. Ann Appl Biol 121:329–343

    Article  Google Scholar 

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Acknowledgments

This work is an output from a research project funded by the McKnight Foundation Collaborative Crop Research Program and the Louisiana Board of Regents. The authors thank Suzanne Hurtt, Simon Gichuki and Sammy Agili for their assistance in getting the germplasm from Kenya to USA through the Plant Germplasm Quarantine Office of USDA-ARS, Beltsville, MD; Crindi Loschinkohl, Ruhui Li, and Suzanne Hurtt for their assistance in DNA extractions and Mary Bowen for her technical assistance in AFLP analysis.

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Authors and Affiliations

  1. Kenya Agricultural Research Institute, Biotechnology Centre, 14733, Nairobi , 00800, Kenya

    Douglas W. Miano

  2. School of Plant, Environmental and Soil Sciences, Louisiana State Univ. Agricultural Center, Louisiana Agricultural Experimental Station, Baton Rouge, LA, 70803, USA

    Douglas W. Miano & Don R. LaBonte

  3. Department of Plant Pathology and Crop Physiology, Louisiana State Univ. Agricultural Center, Louisiana Agricultural Experimental Station, Baton Rouge, LA, 70803, USA

    Christopher A. Clark

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  1. Douglas W. Miano
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  2. Don R. LaBonte
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Correspondence to Douglas W. Miano.

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Miano, D.W., LaBonte, D.R. & Clark, C.A. Identification of molecular markers associated with sweet potato resistance to sweet potato virus disease in Kenya. Euphytica 160, 15–24 (2008). https://doi.org/10.1007/s10681-007-9495-2

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  • DOI: https://doi.org/10.1007/s10681-007-9495-2

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