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Resistance Gene Analogues as a Tool for Rapid Identification and Cloning of Disease Resistance Genes in Plants 3 A Review

Journal of Plant Biochemistry and Biotechnology volume 18, pages 1–11 (2009)Cite this article

Abstract

Most of the disease resistance genes (R-genes) discovered in plants have conserved functional domains, predominantly among them are nucleotide binding sites (NBS) and leucine rich repeats (LRR). The sequence information of the conserved domains can be invariably used to mine similar sequences from other plant species, using degenerate and specific primers for their amplification in a polymerase chain reaction. Such derived sequences, known as Resistance Gene Analogues (RGAs), can serve as molecular markers for rapid identification and isolation of R-genes. Besides, they can also provide clues about the evolutionary mechanism of resistance genes and the interaction involved in pathogen recognition. In the recent years, this sequence-homology based approach has been used extensively for the cloning and mapping of RGAs in cereals, pulses, oilseeds, coffee, spices, forest trees and horticultural crops. In this article, the current status of cloning of RGAs from different crops has been reviewed. A general method of RGA cloning and its modifications like NBS-profiling and AFLP-NBS have also been discussed along with examples. Further, it has been suggested that the RGAs cloned in various crops would be a useful genomic resource for developing cultivars with durable resistance to diseases in different crop breeding programmes.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

Avr:

Avirulence

BLB:

Bacterial leaf blight

CAPS:

Cleaved amplified polymorphic sequence

DR:

Defense response

EST:

Expressed sequence tag

LRR:

Leucine rich repeat

NBS:

Nucleotide binding site

PCR:

Polymerase chain reaction

R:

Resistance

RFLP:

Restriction fragment length polymorphism

RGA:

Resistance gene analogue

STS:

Sequence tagged sites

TIR:

Toll and interleukin-1 receptor

References

  1. Liu J, Liu X, Dai, L & Wang G, J Gene Genom, 34 (2007) 765.

    Article  Google Scholar 

  2. Sharma TR, Madhav MS, Jana TK, Pandit A, Singh A, Upreti HC, Gaikwad K & Singh NK, Mol Genet Genom, 274 (2005) 569.

    Article  CAS  Google Scholar 

  3. Hammond-Kosack KE & Jones JDG, Annu Rev Plant Physiol Plant Mol Biol, 48 (1997) 575.

    Article  PubMed  CAS  Google Scholar 

  4. Johal GS & Briggs SP, Science, 258 (1992) 985.

    Article  PubMed  CAS  Google Scholar 

  5. Pan O, Wendel J & Fluhr R, J Mol Evol, 50 (2000) 203.

    PubMed  CAS  Google Scholar 

  6. Madhav MS, Plaha P, Singh NK & Sharma TR, J Phyotopathol, (2008) doi: 10.1111/j.1439-0434.2008.01487.x

    Google Scholar 

  7. Whitham S, Dinesh-Kumar SP, Choi D, Hehl R, Corr C & Baker B, Cell, 78 (1994) 1101.

    Article  PubMed  CAS  Google Scholar 

  8. Traut TW, Eur J Biochem, 222 (1994) 9.

    Article  PubMed  CAS  Google Scholar 

  9. Inohara N, Koseki T, Lin JIM, del Peso L, Lucas PC, Chen FF, Ogura Y & Nunez G, J Biol Chem, 275 (2000) 27823.

    PubMed  CAS  Google Scholar 

  10. Warren RF, Henk A, Mowery P, Holub E & Innes RW, Plant Cell, 10 (1998) 1439.

    PubMed  CAS  Google Scholar 

  11. Ellis J, Lawrence G, Ayliffe M, Anderson P, Collins N, Finnegan J, Frost D, Luck J & Piyor T, Annu Rev Phytopathol, 35 (1997) 271.

    Article  PubMed  CAS  Google Scholar 

  12. Kobe B & Deisenhofer J, Trends Biochem Sci, 19 (1994) 415.

    Article  PubMed  CAS  Google Scholar 

  13. Martin GB, Brommonshcenkel SH, Chunwonge J, Frary A, Ganal MW, Spivey R, Wu T, Earle ED & Tanksley SD, Science, 262 (1993) 1432.

    Article  PubMed  CAS  Google Scholar 

  14. Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu LH, Fauquet C & Ronald P, Science, 270 (1995) 1804.

    Article  PubMed  CAS  Google Scholar 

  15. Jones DA, Thomas CM, Hamnad-Kosack KE, Balint-Kurti PS & Jones JDG, Science, 266 (1994) 789.

    Article  PubMed  CAS  Google Scholar 

  16. Kanazin V, Marek IF & Shoemaker RC, Proc Natl Acad Sci, USA, 93 (1996) 11746.

    Article  PubMed  CAS  Google Scholar 

  17. Leister D, Kurth J, Laurie DA, Yano M, Sasaki T, Devos K, Graner A & Schulzelefert P, Proc Natl Acad Sci, USA, 95 (1998) 370.

    Article  PubMed  CAS  Google Scholar 

  18. Dixon MS, Jones DA, Keddle JS, Thomas CM, Harrison K & Jones JDG, Cell, 84 (1996) 451.

    Article  PubMed  CAS  Google Scholar 

  19. Ori N, Eshed Y, Paran I, Presting G, Aviv D, Tanksley S, Zamir D & Fluhr R, Plant Cell, 9 (1997) 521.

    PubMed  CAS  Google Scholar 

  20. Shen KA, Meyers BC, Islam-Faridi MN, Chin DB, Stelly DM & Michelmore RW, Mol Plant-Microbe Interact, 11 (1998) 815.

    Article  PubMed  CAS  Google Scholar 

  21. Huh J, Kang B, Nahm S, Kims S, Ha K, Lee MH & Kim BD, Theor Appl Genet, 102 (2001) 524.

    Article  CAS  Google Scholar 

  22. Thorup TA, Tanyolac B, Livingstone KD, Poposky S, Paran I & Jahn M, Proc Natl Acad Sci, USA, 97 (2000) 11192.

    Article  PubMed  CAS  Google Scholar 

  23. Botella MA, Cleman MJ, Hughes DE, Nishimura MT, Jones JDG & Somerville SC, Plant J, 12 (1997) 1197.

    Article  PubMed  CAS  Google Scholar 

  24. Aarts MGM, Hekkert BL, Holub EB, Beynon JI, Stiekema WJ & Pereira A, Mol Plant-Microbe Interact, 11 (1998) 251.

    Article  PubMed  CAS  Google Scholar 

  25. Speulman E, Boucherz D, Holub EB & Beynon JL, Plant J, 14 (1998) 467.

    Article  PubMed  CAS  Google Scholar 

  26. Dixon RA & Harrison MJ, Adv Genet, 28 (1990) 165.

    Article  PubMed  CAS  Google Scholar 

  27. Hulbert SH, Webb CA, Smith SM & Sun O, Annu Rev Phytopathol, 39 (2001) 285.

    Article  PubMed  CAS  Google Scholar 

  28. Bryne PF, McMullen MD, Snook ME, Musket TA, Theuri JM, Widstrom NW, Wiseman BR & Coef EH, Proc Natl Acad Sci, USA, 93 (1996) 8820.

    Article  Google Scholar 

  29. Dixon R, Nature, 411 (2001) 843.

    Article  PubMed  CAS  Google Scholar 

  30. Epple P, Aple K & Bohlmann H, Plant Cell, 9 (1997) 509.

    PubMed  CAS  Google Scholar 

  31. Hain R, Reif HJ, Krause E, Langebortels R, Kindl H, Varnam B, Wiese W, Schmelzer E, Schreier PH, Stocker RH & Stenzel K, Nature, 361 (1993) 153.

    Article  PubMed  CAS  Google Scholar 

  32. McMullen MD, Bryne PF, Snook BR, Wiseman BR, Lee EA, Widstrom NW & Coe EH, Proc Natl Acad Sci, USA, 95 (1998) 1996.

    Article  PubMed  CAS  Google Scholar 

  33. Wu G, Shortt BJ, Lawrence EB, Leon J, Fitzsimmons KC, Levine EB, Raskin I & Shah DM, Plant Physiol, 115 (1997) 427.

    PubMed  CAS  Google Scholar 

  34. Walling LL, J Plant Growth Regulators, 19 (2000) 195.

    CAS  Google Scholar 

  35. McMullen MD & Simcox K, Mol Plant-Microbe Interact, 8 (1995) 811.

    Article  CAS  Google Scholar 

  36. Wang G, Mackill DJ, Bonman JM, McCouch SR & Nelson RJ, Mol Genet Genom, 265 (1994) 310.

    Google Scholar 

  37. Faris JD, Li WL, Lin DJ, Chen PD & Gill BS, Theor Appl Genet, 98 (1999) 219.

    Article  CAS  Google Scholar 

  38. Pflieger S, Lefebvre V, Caranta C, Blattes A, Goffinet B & Palloix A, Genome, 42 (1999) 1100.

    Article  PubMed  CAS  Google Scholar 

  39. Geffroy V, Sevignac M, de Oliveira J, Fouilloux G, Skroch P, Thoquet P, Gepts P, Langin T & Dron M, Mol PlantMicrobe Interact, 3 (2000) 287.

    Article  Google Scholar 

  40. Leister D, Ballvora A, Salamini F & Gebhardt C, Nature Genet, 14 (1998) 421.

    Article  Google Scholar 

  41. Leister D, Kurth J, Laurie DA, Yano M, Sasaki T, Graner A & Schulze-Lefert P, Theor Appl Genet, 98 (1999) 509.

    Article  CAS  Google Scholar 

  42. Seah S, Sivasithampatam K, Karakoisis A & Lagudah ES, Theor Appl Genet, 97 (1996) 937.

    Article  Google Scholar 

  43. Mago R, Nair S & Mohan M, Theor Appl Genet, 99 (1999) 50.

    Article  CAS  Google Scholar 

  44. Wang S & Xiao X, Plant Breed, 121 (2002) 203.

    Article  CAS  Google Scholar 

  45. Kumar SP, Dalal V, Singh NK & Sharma TR, J Phytopathol, 155 (2007) 273.

    Article  CAS  Google Scholar 

  46. Mohler V, Klahr A, Wenzel G & Schwarz G, Theor Appl Genet, 105 (2002) 364.

    Article  PubMed  CAS  Google Scholar 

  47. Madsen LH, Collins NC, Rakwalska M, Backes G, Sandal N, Krusell L, Jensen J, Waterman EH, Jahoor A, Ayliffe M, Pryor AJ, Langridge P, Schulze-Lefert P & Stougaard J, Mol Genet Genom, 269 (2003) 150.

    CAS  Google Scholar 

  48. Ramlingam J, Vera Cruz CM, Kukreja K, Chitoor JM, Wu JL, Lee SW, Baraoldan M, George ML Cohen MB, Hulbert SH, Leach JE & Leung H, Mol Plant-Microbe Interact, 16 (2003) 14.

    Article  Google Scholar 

  49. Collins NC, Webb CA, Seah S, Ellis, JG, Hulbert SH, & Prypr A, Mol Plant-Microbe Interact, 11 (1998) 968.

    Article  PubMed  CAS  Google Scholar 

  50. McFadden HG, Lehmensiek A & Lagudah ES, Theor Appl Genet, 113 (2006) 987

    Article  PubMed  CAS  Google Scholar 

  51. Xie C, Sun O, Ni Z, Yang T, Nevo E & Fahima T, Plant Breed, 123 (2008) 198.

    Article  Google Scholar 

  52. Seishi I, Grassland Sci, 51 (2005) 63.

    Article  Google Scholar 

  53. Radwan O, Bouzidi MF, Vear F, Philippon J, De Labrouhe DT, Nicolas P & Mouzeyar S, Theor Appl Genet, 106 (2003)1438.

    PubMed  CAS  Google Scholar 

  54. Fourmann M, Chariot F, Froger N, Delourme R & Brunei D, Genome, 44 (2001) 1083.

    PubMed  CAS  Google Scholar 

  55. Kanazin V, Marek IF & Shoemaker RC, Proc Natl Acad Sci, USA, 93 (1996) 11746.

    Article  PubMed  CAS  Google Scholar 

  56. Yu YG, Buss GR, Saghai-Maroof MA, Proc Natl Acad Sci, USA, 93 (1996) 11751.

    Article  PubMed  CAS  Google Scholar 

  57. Rivkin MI, Vallejos CE & McClean PE, Genome, 42 (1999) 41.

    Article  PubMed  CAS  Google Scholar 

  58. Lopez CE, Acosta IF, Jara C, Pedraza F, Gaitan-Solis E, Gallego G, Beebe S & Thome J, Phytopathology, 93 (2003) 88.

    Article  PubMed  CAS  Google Scholar 

  59. Cordero JC & Skinner DZ, Theor Appl Genet, 104 (2002) 1283.

    Article  PubMed  CAS  Google Scholar 

  60. Yaish MWF, Saenz de Miera LE & Perez de la Vega M, Genome, 47 (2004) 650.

    Article  PubMed  CAS  Google Scholar 

  61. Huettel B, Santra D, Muehlbauer FJ & Kahl G, Theor Appl Genet, 105 (2002) 479.

    Article  PubMed  CAS  Google Scholar 

  62. He L, Du C, Covaleda L, Xu Z, Robinson AF, Yu JZ, Kohel RJ & Zhang H B, Mol Plant-Microbe Interact, 17 (2004) 1234.

    Article  PubMed  CAS  Google Scholar 

  63. Zhang J, Yuanb Y, Niua C, Hinchliffec DJ, Lua Y, Yub S, Percyd RG, Ulloae R & Cantrell RG, Crop Sci, 47 (2007) 180.

    Article  CAS  Google Scholar 

  64. Hunger S, DiGaspero G, Mohring S, Bellin D, Schafer-Pregl R, Borchardt DC, Durel CE, Werber M, Weisshaar B, Salamini F & Schneider K, Genome, 46 (2003) 70.

    Article  PubMed  CAS  Google Scholar 

  65. Lein JC, Asbach K, Tian Y, Schulte D, Li C, Koch G, Jung C & Cai D Genome, 50 (2007) 61.

    Article  PubMed  CAS  Google Scholar 

  66. Leister D, Ballvora A, Salamini F & Gebhardt C, Nature Genet, 14 (1998) 421.

    Article  Google Scholar 

  67. Brugmans B, Wouters D, van Os H, Hutten R, van der Linden G, Visser RG, van Eck HJ & van der Vossen EA, Theor Appl Genet, 2008 (In Press).

    Google Scholar 

  68. Shen KA, Meyers BC, Nurul Islam-Faridi M, Chin DB, Stelly DM & Michelmore RW, Mol Plant-Microbe Interact, 11 (1998) 815.

    Article  PubMed  CAS  Google Scholar 

  69. Lee SY, Seo JS, Rodriguez-Lanetty M & Lee DH, Mol Genet Genom, 269 (2003) 101.

    CAS  Google Scholar 

  70. Calenge F, Van der Linden GC, Van de Weg E, Schouten HJ, Van Arkel G, denance C & Durel CE, Theor Appl Genet, 110 (2005) 660.

    Article  PubMed  CAS  Google Scholar 

  71. Donald TM, Pellerone F, Adam-Blondon AF, Bouquet A, Thomas MR & Dry IB, Theor Appl Genet, 104 (2002) 610.

    Article  PubMed  CAS  Google Scholar 

  72. Mahanil S, Reisch BI, Owens CL, Thipyapong P & Laosuwan P, Am J Enol Vitic, 58 (2007) 484.

    CAS  Google Scholar 

  73. Hayes A J & Saghai Maroof M A, Theor Appl Genet, 100 (2000)1279.

    Article  CAS  Google Scholar 

  74. Peia X, Lia S, Jiangb Y, Zhanga Y, Wanga Z & Jia S, Plant Sci, 172 (2007) 1166.

    Article  Google Scholar 

  75. Azhar M & Heslop-Harrison JS, Cytogenet Genome Res, 121(2008) 59.

    Article  PubMed  CAS  Google Scholar 

  76. Hermann S, Brumbley S & McIntyre C L, Aust Plant Pathol, 35 (2006) 631.

    Article  CAS  Google Scholar 

  77. Xu O, Wen X & Deng X, Theor Appl Genet, 111 (2005) 819.

    Article  PubMed  CAS  Google Scholar 

  78. Anja H & Thomas D, Physiol Plant, 129 (2007) 775.

    Article  Google Scholar 

  79. Pflieger S, Lefebvre V, Caranta C, Blattes A, Goffinet B & Palloix A, Genome, 42 (1999) 1100.

    Article  PubMed  CAS  Google Scholar 

  80. Noir S, Combes MC, Anthony F & Lashermes P, Mol Genet Genom, 265 (2001) 654.

    Article  CAS  Google Scholar 

  81. Nair A R & Thomas G, Theor Appl Genet, 116 (2007) 123.

    Article  CAS  Google Scholar 

  82. Noir S, Combes MC, Anthony F & Lashermes P, Mol Genet Genom, 265 (2001) 654.

    Article  CAS  Google Scholar 

  83. Zhang O, Zhang ZY, Lin SZ, Zhang HO, Lin YZ, An XM, Li Y & Li HX, Plant Biol, 10 (2008) 310.

    Article  PubMed  CAS  Google Scholar 

  84. Diaz V & Ferrer E, Genome, 46 (2003) 404.

    Article  PubMed  CAS  Google Scholar 

  85. Van der Linden CG, Wouters DCAE, Mihalka V, Kochieva EZ, Smulders MJM, Vosman B, Theor Appl Genet, 109 (2004) 384.

    Article  PubMed  Google Scholar 

  86. Egea-Gilabert C, Dickinson MJ, Bilotti G & Candela ME, Biol Plant, 47(2003)27.

    Article  CAS  Google Scholar 

  87. You M, Boersma JG, Buirchell BJ, Sweetingham MW Siddique KH, and H. Yang H, Cell Mol Biol Lett, 10 (2005)123.

    PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi, 110 012, India

    T. R. Sharma, Alok Das & S. P. Kumar

  2. Division of Genetics, Indian Agriculture Research Institute, Pusa Campus, New Delhi, 110 012, India

    M. L. Lodha

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  1. T. R. Sharma
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  2. Alok Das
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  4. M. L. Lodha
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Correspondence to T. R. Sharma.

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Sharma, T.R., Das, A., Kumar, S.P. et al. Resistance Gene Analogues as a Tool for Rapid Identification and Cloning of Disease Resistance Genes in Plants 3 A Review. J. Plant Biochem. Biotechnol. 18, 1–11 (2009). https://doi.org/10.1007/BF03263289

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