Genomic approaches to plant disease resistance

Current Opinion in Plant Biology

Volumn 3, Issue 2, 2000, Pages 125-131

  Michelmore, Richard ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EMBRYOPHYTA;

EID: 0034055553     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5266(99)00050-3     Document Type: Review

References (65)

1. Barakat A., Matassi G., Bernardi G. Distribution of genes in the genome of Arabidopsis thaliana and its implications for the genome organization of plants. Proc Natl Acad Sci USA. 95:1998;10044-10049.
2. Panstruga R., Buschges R., Piffanelli P., Schulze-Lefert P. A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Res. 26:1998;1056-1062.
3. National, Science, Foundation: Plant, Genome, Research, Program, Collaborative, Research, and Infrastructure, Projects., URLs, http://www.nsf.gov/bio/pubs/awards/genome98 .htm and http://www.nsf.gov/bio/pubs/awards/genome99.htm.
4. Michelmore R.W., Meyers B.C. Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res. 8:1998;1113-1130. This review combines inferences from molecular, structural and population genetic studies to propose a model for the slow (rather than rapid) evolution of resistance-gene specificities based on ideas previously developed for genes in the vertebrate major histocompatibility complex.
5. van der Biezen E.A., Jones J.D.G. Plant disease resistance proteins and the gene-for-gene concept. Trends Biochem Sci. 23:1998;454-456.
6. Bevan M., Bancroft I., Bent E., Love I., Goodman H., Dean C., Bergkamp R., Dirkse W., Van Staveren M., Stiekema W.et al. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature. 391:1998;485-488.
7. ••], illustrates the wealth of information on resistance genes already in the databases and the power of in silico analyses. It also exemplifies some of the complexities of analyzing families of sequences as divergent as those that form resistance genes.
8. Botella M.A., Coleman M.J., Hughes D.E., Nishimura M.T., Jones J.D.G., Somerville S.C. Map positions of 47 Arabidopsis sequences with sequence similarity to disease resistance genes. Plant J. 12:1997;1197-1211.
9. Aarts M.G.M., Hekkert B.L., Holub E.B., Beynon J.L., Stiekema W.J., Pereira A. Identification of R-gene homologous DNA fragments genetically linked to disease resistance loci in Arabidopsis thaliana. Mol Plant-Microbe Interact. 11:1998;251-258.
10. Speulman E., Bouchez D., Holub E.B., Beynon J.L. Disease resistance gene homologs correlate with disease resistance loci of Arabidopsis thaliana. Plant J. 14:1998;467-474. One of several papers using PCR with degenerate oligonucleotide primers that recognize sequences that are conserved in resistance genes. All of the PCR products were mapped to known clusters of resistance genes using arrayed genomic clones rather than segregation analysis. This is a harbinger of the rapid candidate-gene approach to cloning of resistance genes in other species.
11. Kunkel B.N. A useful weed put to work- genetic analysis of disease resistance in Arabidopsis thaliana. Trends Genet. 12:1996;63-69.
12. Holub E.B. Organization of resistance genes in Arabidopsis. Crute I.R., Holub E.B., Burdon J. The Gene-for-Gene Relationship in Host-Parasite Interactions. 1997;5-26 CAB International, Wallingford, UK.
13. ••]. They identify the coiled-coil motif as more characteristic of the non-TIR class of resistance proteins than a leucine zipper. The paper also includes a description of a PCR-based search for TIR-type NBS-LRR-encoding genes in the grasses.
14. ••].
15. Parniske M., Hammond-Kosac K.E., Golstein C., Thomas C.M., Jones D.A., Harrison K., Wulff B.B., Jones J.D. Novel disease resistance specificities result from sequence exchange between tandemly repeated genes at the Cf-4/9 locus of tomato. Cell. 91:1997;821-832.
16. Salmeron J.M., Oldroyd G.E., Rommens C.M., Scofield S.R., Kim H.S., Lavelle D.T., Dahlbeck D., Staskawicz B.J. Tomato Prf is a member of the leucine-rich repeat class of plant disease resistance genes and lies embedded within the Pto kinase gene cluster. Cell. 86:1996;123-133.
17. Meyers B.C., Chin D.B., Shen K.A., Sivaramakrishnan S., Lavelle D.O., Zhang Z., Michelmore R.W. The major resistance gene cluster in lettuce is highly duplicated and spans several megabases. Plant Cell. 10:1998;1817-1832.
18. Meyers B.C., Shen K.A., Rohani P., Gaut B.S., Michelmore R.W. Receptor-like genes in the major resistance locus of lettuce are subject to divergent selection. Plant Cell. 10:1998;1833-1846. One of several papers that followed Parnsike et al. [15] in providing evidence for divergent selection on the putative solvent-exposed residues of the LRR. This paper describes statistical tests for determining the significance of such data.
19. Gale M., DeVos K. Plant comparative genetics after 10 years. Science. 282:1998;656-658.
20. DeVos K., Beales J., Nagamura Y., Sasaki T. Arabidopsis-rice: will colinearity allow gene prediction across the eudicot-monocot divide? Genome Res. 9:1999;825-829.
21. van Dodeweerd A.M., Hall C.R., Bent E.G., Johnson S.J., Bevan M.W., Bancroft I. Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana. Genome. 42:1999;887-892.
22. Liester D., Kurth J., Laurie D.A., Yano M., Sasaki T., Graner A., Schulz-Lefert P. Rapid reorganization of resistance gene homologues in cereal genomes. Proc Natl Acad Sci USA. 95:1998;370-375.
23. Stahl E.A., Dwyer G., Mauricio R., Kreitman M., Bergelson J. Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis. Nature. 400:1999;667-671.
24. Grant M.R., McDowell J.M., Sharpe A.G., de Torres Zabala M., Lydiate D.J., Dangl J.L. Independent deletions of a pathogen-resistance gene in Brassica and Arabidopsis. Proc Natl Acad Sci USA. 95:1998;15843-15848.
25. Han F, Kilian A, Chen JP, Kudrna D, Steffenson B, Yamamoto K, Matsumoto T, Sasaki T, Kleinhofs A: Sequence analysis of a rice BAC covering the syntenous barley Rpg1 region. Genome 42:1071-1076.
26. Grube, C.E., Livingstone, K.D., Zamir, D., Paran, I., Fluhr, R., Radwanski, E.R., Landry, L.G., Kyle Jahn, M. Comparative analysis of disease resistance within the Solanaceae. URL http://www.intl-pag.org/pag/7/abstracts/pag7413.html .
27. Shen K.A., Meyers B.C., Islam-Faridi M.N., Chin D.B., Stelly M., Michelmore R.W. Resistance gene candidates identified using PCR with degenerate primers map to resistance genes clusters in lettuce. Mol Plant-Microbe Interac. 11:1998;815-823.
28. Zhong X.-B., Bodeau J., Fransz P.F., Williamson V.M., van Kammen A., de Jong H., Zabel P. FISH to meiotic pachytene chromosomes of tomato reveals the root-knot nematode resistance gene Mi-1 and the acid phosphatase gene Aps-1 to be located near the junction of euchromatin and pericentromeric heterochromatin of chromosome arms 6S and 6L, respectively. Theor Appl Genet. 98:1999;365-370.
29. Leister D., Ballvora A., Salamini F., Gebhardt C. A PCR-based approach for isolating pathogen resistance genes from potato with potential for wide application in plants. Nat Genetics. 14:1996;421-429.
30. Kanazin V., Marek L.F., Shoemaker R.C. Resistance gene analogs are conserved and clustered in soybean. Proc Natl Acad Sci USA. 93:1996;11746-11750.
31. Yu Y.G., Buss G.R., Maroof M.A. Isolation of a superfamily of candidate disease-resistance genes in soybean based on a conserved nucleotide-binding site. Proc Natl Acad Sci USA. 93:1996;11751-11756.
32. Rivkin M.I., Vallejos C.E., McClean P.E. Disease-resistance related sequences in common bean. Genome. 42:1999;41-47.
33. National, Center, for Genome, Resources, Dickerman, A.: Plant Resistance Genes Data Viewer. URL http://www.ncgr.org/rgenes.
34. Mozo T., Dewar K., Dunn P., Ecker J.R., Fischer S., Kloska S., Lehrach H., Marra M., Martienssen R., Meier-Ewert S., Altmann T. A complete BAC-based physical map of the Arabidopsis thaliana genome. Nat Genet. 22:1999;271-275.
35. Cho R.J., Mindrinos M., Richards D.R., Sapolsky R.J., Anderson M., Drenkard E., Dewdney J., Reuber T.L., Stammers M., Federspiel N.et al. Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nature Genet. 23:1999;203-207.
36. Caicedo A.L., Schaal B.A., Kunkel B.N. Diversity and molecular evolution of the RPS2 resistance gene in Arabidopsis thaliana. Proc Natl Acad Sci USA. 96:1999;302-306. This paper describes a broad population genetic treatment of the evolution of the RPS2 locus. This type of study is a forerunner to future analyses of resistance genes in natural populations of Arabidopsis that are likely to provide a great deal of information about the evolution of disease resistance in plants.
37. Sicard D., Woo W.-W., Arroyo-Garcia R., Ochoa O., Nguyen D., Korol A., Nevo E., Michelmore R.W. Molecular diversity at the major cluster of disease resistance genes in cultivated and wild Lactuca spp. Theor Appl Genet. 99:1999;405-418.
38. Ellis J.G., Lawrence G.J., Luck J.E., Dodds P.N. Identification of regions in alleles of the flax rust resistance gene L that determine differences in gene-for-gene specificity. Plant Cell. 11:1999;495-506. This paper describes the elegant dissection of the L gene. It illustrates the potential of studying a truly orthologous series of alleles in contrast to the more complex analyses involving paralogs that comprise clusters of resistance genes in other species.
39. Crameri A., Raillard S.A., Bermudez E., Stemmer W.P. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature. 391:1998;288-291.
40. Chang C.C., Chen T.T., Cox B.W., Dawes G.N., Stemmer W.P., Punnonen J., Patten P.A. Evolution of a cytokine using DNA family shuffling. Nat Biotechnol. 17:1999;793-797.
41. Lemieux B., Aharoni A., Schena M. Overview of DNA chip technology. Mol Breeding. 4:1998;277-289.
42. Baldwin D., Crane V., Rice D. A comparison of gel-based, nylon filter and microarray techniques to detect differential RNA expression in plants. Curr Opin Plant Biol. 2:1999;96-103. The authors of this review present a useful comparison of several global expression technologies as well as describing their limitations. The first microarray data for genes altered following challenge by a pathogen is briefly described.
43. Eisen J.A. Phylogenomics. improving functional predictions for uncharacterized genes by evolutionary analysis Genome Res. 8:1998;163-167.
44. Farmer, E.E.: Collaboration with Research Groups Involved in Plant Defense. URL http://www.unil.ch/ibpv/docs/WWWPR/Docs / collaboration.htm This website describes a first generation printed cDNA microarray containing ~150 defense related ESTs of Arabidopsis.
45. Rushton P.J., Somssich I.E. Transcriptional control of plant genes responsive to pathogens. Curr Opin Plant Biol. 1:1998;311-315.
46. Brazma A., Jonassen I., Vilo J., Ukkonen E. Predicting gene regulatory elements in silico on a genomic scale. Genome Res. 8:1998;1202-1215.
47. Thieffry D. From global expression data to gene networks. BioEssays. 21:1999;895-899.
48. Morris S.W., Vernooij B., Titatarn S., Starrett M., Thomas S., Wiltse C.C., Frederiksen R.A., Bhandhufalck A., Hulbert S., Uknes S. Induced resistance responses in maize. Mol-Plant Microbe Interact. 11:1998;643-658.
49. Reymond P., Farmer E.E. Jasmonate and salicylate as global signals for defense gene expression. Curr Opin Plant Biol. 1:1998;404-411.
50. Kitajima S., Sato F. Plant pathogenesis-related proteins. molecular mechanisms of gene expression and protein function J Biochem (Tokyo). 125:1999;1-8.
51. Baulcombe D.C. Fast forward genetics based on virus-induced gene silencing. Curr Opin Plant Biol. 2:1999;109-113.
52. Kumagai M.H., Keller Y., Bouvier F., Clary D., Camara B. Functional integration of non-native carotenoids into chloroplasts by viral-derived expression of capsanthin-capsorubin synthase in Nicotiana benthamiana. Plant J. 14:1998;305-315.
53. Marteinssen R.A. Functional genomics. probing plant gene function and expression with transposons Proc Natl Acad Sci USA. 95:1998;2021-2026.
54. Ori N., Eshed Y., Paran I., Presting G., Aviv D., Tanksley S., Zamir D., Fluhr R. The I2C family from the wilt disease resistance locus I2 belong to the nucleotide binding, leucine-rich repeat superfamily of plant disease resistance genes. Plant Cell. 9:1997;521-532.
55. Clough S.J., Bent A.F. Floral dip. a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana Plant J. 16:1998;735-743.
56. Oldroyd G.E.D., Staskawicz B.J. Genetically engineered broad-spectrum disease resistance in tomato. Proc Natl Acad Sci USA. 95:1998;10300-10305.
57. Tang X., Xie M., Kim Y.J., Zhou J., Klessig D.F., Martin G.B. Overexpression of Pto activates defense responses and confers broad resistance. Plant Cell. 11:1999;15-30.
58. Jones D.A., Jones J.D.G. The role of leucine-rich repeat proteins in plant defenses. Adv Bot Res. 24:1997;90-167.
59. Baker B., Zambryski P., Staskawicz B., Dinesh-Kumar S.P. Signaling in plant-microbe interactions. Science. 276:1997;726-733.
60. Rathjen J.P., Chang J.H., Staskawicz B.J., Michelmore R.W. Activated Pto mediates the AvrPto-dependent hypersensitive disease resistance response in N. benthamiana and tomato. EMBO J. 18:1999;3232-3240.
61. Glazebrook J. Genes controlling expression of defense responses in Arabidopsis. Curr Opin Plant Biol. 2:1999;280-286. This review is a good synthesis of the complex but revealing genetics of plant-pathogen interactions in Arabidopsis.
62. Altschul S.F., Koonin E.V. Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases. Trends Biochem Sci. 23:1998;444-447.
63. Piffanelli P., Devoto A., Schultz-Liefert P. Defense signaling pathways in cereals. Curr Opin Plant Biol. 2:1999;295-300.
64. Chimmaiyan A.M., Chaudhary D., O'Rouke K., Koonin E.V., Dixit V.M. Role of CED-4 in the activation of CED-3. Nature. 338:1997;728-729.
65. Van der Biezen E.A., Jones J.D.G. The NB-ARC domain. a novel signaling motif shared by plant disease resistance gene products and regulators of cell death in animals Curr Biol. 8:1998;R226-R227.