Gene profiling in partially resistant and susceptible near-Isogenic tomatoes in response to late blight in the field

Molecular Plant Pathology

Volumn 14, Issue 2, 2013, Pages 171-184

  Cai, Guohong ^a,b   Restrepo, Silvia ^a,c   Myers, Kevin ^a   Zuluaga, Paola ^a   Danies, Giovanna ^a   Smart, Christine ^a   Fry, William ^a  

^a Cornell University ^*  (United States)

^b The State University of New Jersey   (United States)

^c UNIVERSIDAD DE LOS ANDES   (Colombia)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; CLUSTER ANALYSIS; DISEASE RESISTANCE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE SILENCING; GENETIC ASSOCIATION; GENETICS; GENOTYPE; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MICROBIOLOGY; PHYSIOLOGICAL STRESS; PHYSIOLOGY; PHYTOPHTHORA INFESTANS; PLANT DISEASE; PLANT GENE; PLANT VIRUS; REAL TIME POLYMERASE CHAIN REACTION; TOMATO; VIROLOGY;

CLUSTER ANALYSIS; DISEASE RESISTANCE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE SILENCING; GENES, PLANT; GENETIC ASSOCIATION STUDIES; GENOTYPE; LYCOPERSICON ESCULENTUM; PHYTOPHTHORA INFESTANS; PLANT DISEASES; PLANT VIRUSES; REAL-TIME POLYMERASE CHAIN REACTION; RNA, MESSENGER; STRESS, PHYSIOLOGICAL;

LYCOPERSICON ESCULENTUM; PHYTOPHTHORA INFESTANS;

EID: 84871802335     PISSN: 14646722     EISSN: 13643703     Source Type: Journal    
DOI: 10.1111/j.1364-3703.2012.00841.x     Document Type: Article

References (32)

1. Alba, R., Fei, Z.J., Payton, P., Liu, Y., Moore, S.L., Debbie, P., Cohn, J., D'Ascenzo, M., Gordon, J.S., Rose, J.K.C., Martin, G., Tanksley, S.D., Bouzayen, M., Jahn, M.M. and Giovannoni, J. (2004) ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development. Plant J. 39, 697-714.
2. Avrova, A.O., Taleb, N., Rokka, V.M., Heilbronn, J., Campbell, E., Hein, I., Gilroy, E.M., Cardle, L., Bradshaw, J.E., Stewart, H.E., Fakim, Y.J., Loake, G. and Birch P.R. (2004) Potato oxysterol binding protein and cathepsin B are rapidly up-regulated in independent defence pathways that distinguish R gene-mediated and field resistances to Phytophthora infestans. Mol. Plant Pathol. 5, 45-56.
3. Bombarely, A., Menda, N., Tecle, I.Y., Buels, R.M., Strickler, S., Fischer-York, T., Pujar, A., Leto, J., Gosselin, J. and Mueller, L.A. (2011) The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res. 39, D1149-D1155.
4. Corpas, F.J., Barroso, J.B. and del Rio, L.A. (2001) Peroxisomes as a source of reactive oxygen species and nitric oxide signal molecules in plant cells. Trends Plant Sci. 6, 145-150.
5. Dalal, K.B., Salunkhe, D.K. and Olson, L.E. (1966) Certain physiological and biochemical changes in greenhouse-grown tomatoes (Lycopersicon esculentum Mill). J. Food Sci. 31, 461-467.
6. Edwards, E.J., Osborne, C.P., Stromberg, C.A., Smith, S.A., Bond, W.J., Christin, P.A., Cousins, A.B., Duvall, M.R., Fox, D.L., Freckleton, R.P., Ghannoum, O., Hartwell, J., Huang, Y., Janis, C.M., Keeley, J.E., Kellogg, E.A., Knapp, A.K., Leakey, A.D., Nelson, D.M., Saarela, J.M., Sage, R.F., Sala, O.E., Salamin, N., Still, C.J. and Tipple, B. (2010) The origins of C4 grasslands: integrating evolutionary and ecosystem science. Science, 328, 587-591.
7. Eshed, Y. and Zamir, D. (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics, 141, 1147-1162.
8. Falconer, D.S. and Mackay, T.F.C. (1996) Introduction to Quantitative Genetics. Harlow, Essex: Longman Group Ltd.
9. Fry, W. (2008) Phytophthora infestans: the plant (and R gene) destroyer. Mol. Plant Pathol. 9, 385-402.
10. Gillespie, J.H. and Turelli, M. (1989) Genotype-environment interactions and the maintenance of polygenic variation. Genetics, 121, 129-138.
11. Gu, Y.Q., Yang, C., Thara, V.K., Zhou, J. and Martin, G.B. (2000) Pti4 is induced by ethylene and salicylic acid, and its product is phosphorylated by the Pto kinase. Plant Cell, 12, 771-786.
12. Haverkort, A.J., Boonekamp, P.M., Hutten, R., Jacobsen, E., Lotz, L.A.P., Kessel, G.T., Visser, R.G.F. and van der Vossen, E.A.G. (2008) Societal costs of late blight in potato and prospects of durable resistance through cisgenic modification. Potato Res. 51, 47-57.
13. Krug, H. and Fink, M. (1989) Transferability of plant reaction parameters to climate-growth chambers, greenhouses, field. Acta Hortic. 248, 401-408.
14. Kumagai, M.H., Donson, J., Dellacioppa, G., Harvey, D., Hanley, K. and Grill, L.K. (1995) Cytoplasmic inhibition of carotenoid biosynthesis with virus-derived RNA. Proc. Natl. Acad. Sci. USA, 92, 1679-1683.
15. Liu, Y., Schiff, M. and Dinesh-Kumar, S.P. (2002) Virus-induced gene silencing in tomato. Plant J. 31, 777-786.
16. Morey, J.S., Ryan, J.C. and van Dolah, F.M. (2006) Microarry validation factors influencing correlation between oligonucleotide microarrays and real-time PCR. Biol. Proced. Online, 8, 175-193.
17. Moskin, J. (2009) Outbreak of fungus threatens tomato crop. The New York Times (18 July New York edition A16).
18. Mueller, L.A., Lankhorst, R.K., Tanksley, S.D., Giovannoni, J.J., White, R., Vrebalov, J., Fei, Z., van Eck, J., Buels, R., Mills, A.A., Menda, N., Tecle, I.Y., Bombarely, A., Stack, S., Royer, S.M., Chang, S.B., Shearer, L.A., Kim, B.D., Jo, S.H., Hur, C.G., Choi, D., Li, C.B., Zhao, J., Jiang, H., Geng, Y., Dai, Y., Fan, H., Chen, J., Lu, F., Shi, J., Sun, S., Chen, J., Yang, X., Lu, C., Chen, M., Cheng, Z., Li, C., Ling, H., Xue, Y., Wang, Y., Seymour, G.B., Bishop, G.J., Bryan, G., Rogers, J., Sims, S., Butcher, S., Buchan, D., Abbott, J., Beasley, H., Nicholson, C., Riddle, C., Humphray, S., McLaren, K., Mathur, S., Vyas, S., Solanke, A.U., Kumar, R., Gupta, V., Sharma, A.K., Khurana, P., Khurana, J.P., Tyagi, A., Sarita, S., Chowdhury, P., Shridhar, S., Chattopadhyay, D., Pandit, A., Singh, P., Kumar, A., Dixit, R., Singh, A., Praveen, S., Dalal, V., Yadav, M., Ghazi, I.A., Gaikwad, K., Sharma, T.R., Mohapatra, T., Singh, N.K., Szinay, D., de Jong, H., Peters, S., van Staveren, M., Datema, E., Fiers, M.W.E.J., van Ham, R.C.H.J., Lindhout, P., Philippot, M., Frasse, P., Regad, F., Zouine, M., Bouzayen, M., Asamizu, E., Sato, S., Fukuoka, H., Tabata, S., Shibata, D., Botella, M.A., Perez-Alonso, M., Fernandez-Pedrosa, V., Osorio, S., Mico, A., Granell, A., Zhang, Z., He, J., Huang, S., Du, Y., Qu, D., Liu, L., Liu, D., Wang, J., Ye, Z., Yang, W., Wang, G., Vezzi, A., Todesco, S., Valle, G., Falcone, G., Pietrella, M., Giuliano, G., Grandillo, S., Traini, A., D'Agostino, N., Chiusano, M.L., Ercolano, M., Barone, A., Frusciante, L., Schoof, H., Jöcker, A., Bruggmann, R., Spannagl, M., Mayer, K.X.F., Guigó, R., Camara, F., Rombauts, S., Fawcett, J.A., Van de Peer, Y., Knapp, S., Zamir, D. and Stiekema, W. (2009) A snapshot of the emerging tomato genome sequence. Plant Genome, 2, 78-92.
19. Nelson, M.D., Gubler, W.D. and Shaw, D.V. (1995) Inheritance of powdery mildew resistance in greenhouse-grown versus field-grown California strawberry progenies. Phytopathology, 85, 421-424.
20. Perry, K.L. and Francki, R.I.B. (1992) Insect-mediated transmission of mixed and reassorted cucumovirus genomic RNAs. J. Gen. Virol. 73, 2105-2114.
21. Rauscher, G., Simko, I., Mayton, H., Bonierbale, M., Smart, C.D., Grunwald, N.J., Greenland, A. and Fry, W.E. (2010) Quantitative resistance to late blight from Solanum berthaultii cosegregates with R(Pi-ber): insights in stability through isolates and environment. Theor. Appl. Genet. 121, 1553-1567.
22. Restrepo, S., Myers, K.L., del Pozo, O., Martin, G.B., Hart, A.L., Buell, C.R., Fry, W.E. and Smart, C.D. (2005) Gene profiling of a compatible interaction between Phytophthora infestans and Solanum tuberosum suggests a role for carbonic anhydrase. Mol. Plant-Microbe Interact. 18, 913-922.
23. Richards, C.L., Rosas, U., Banta, J., Bhambhra, N. and Purugganan, M.D. (2012) Genome-wide patterns of Arabidopsis gene expression in nature. Plos Genet. 8, e1002662.
24. Ros, B., Thummler, F. and Wenzel, G. (2004) Analysis of differentially expressed genes in a susceptible and moderately resistant potato cultivar upon Phytophthora infestans infection. Mol. Plant Pathol. 5, 191-201.
25. Ros, B., Thummler, F. and Wenzel, G. (2005) Comparative analysis of Phytophthora infestans induced gene expression in potato cultivars with different levels of resistance. Plant Biol. 7, 686-693.
26. Rotenberg, D., Thompson, T.S., German, T.L. and Willis, D.K. (2006) Methods for effective real-time RT-PCR analysis of virus-induced gene silencing. J. Virol. Methods, 138, 49-59.
27. Smart, C.D., Tanksley, S.D., Mayton, H. and Fry, W.E. (2007) Resistance to Phytophthora infestans in Lycopersicon pennellii. Plant Dis. 91, 1045-1049.
28. Tusher, V.G., Tibshirani, R. and Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA, 98, 5116-5121.
29. Wang, B.L., Liu, J., Tian, Z.D., Song, B.T. and Xie, C.H. (2005) Monitoring the expression patterns of potato genes associated with quantitative resistance to late blight during Phytophthora infestans infection using cDNA microarrays. Plant Sci. 169, 1155-1167.
30. Wang, H., He, X., Band, M., Wilson, C. and Liu, L. (2005) A study of inter-lab and inter-platform agreement of DNA microarray data. BMC Genomics, 6, 71.
31. Wang, Z.M., Johnsen, K.H. and Lechowicz, M.J. (1999) Is climate simulation in growth chambers necessary? Biotronics, 28, 13-21.
32. Yang, S.F. and Hoffman, N.E. (1984) Ethylene biosynthesis and its regulation in higher-plants. Annu. Rev. Plant Physiol. 35, 155-189.