Cloning genes and QTLs for disease resistance in cereals

Genomics-Assisted Crop Improvement

Volumn 2, Issue , 2007, Pages 103-127

  Keller, Beat ^a   Bieri, Stéphane ^a   Bossolini, Eligio ^a   Yahiaoui, Nabila ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77955053526     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4020-6297-1_5     Document Type: Chapter

References (96)

1. Akhunov E, Akhunova A, Dvorak J (2005) BAC libraries of Triticum urartu, Aegilops speltoides and Ae. tauschii, the diploid ancestors of polyploid wheat. Theor Appl Genet 111:1617-1622
2. Allouis S, Moore G, Bellec A, Sharp R, Faivre Rampant P, Mortimer L, Pateyron S, Foote TN, Griffiths S, Caboche M, Chalhoub B (2003) Construction and characterisation of a hexaploid wheat (Triticum aestivum L.) BAC library from the reference germplasm 'Chinese Spring'. Cereal Res Commun 31:331-338
3. Ayliffe MA, Lagudah ES (2004) Molecular genetics of disease resistance in cereals. Ann Bot 94:765-773
4. Bai JF, Pennill LA, Ning JC, Lee SW, Ramalingam J, Webb CA, Zhao BY, Sun Q, Nelson JC, Leach JE, Hulbert SH (2002) Diversity in nucleotide binding site-leucine-rich repeat genes in cereals. Genome Res 12:1871-1884
5. Baumberger N, Ringli C, Keller B (2001) The chimeric leucine-rich repeat/extensin cell wall protein LRX1 is required for root hair morphogenesis in Arabidopsis thaliana. Genes Dev 15:1128-1139
6. Bennetzen JL, Ma J (2003) The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol 6:128-133
7. Bieri S, Mauch S, Shen Q-H, Peart J, Devoto A, Casais C, Ceron F, Schulze S, Steinbiss H-H, Shirasu K, Schulze-Lefert P (2004) RAR1 positively controls steady state levels of barley MLA resistance proteins and enables sufficient MLA6 accumulation for effective resistance. Plant Cell 16:3480-3495
8. Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165-1177
9. Brueggeman R, Rostoks N, Kudrna D, Kilian A, Han F, Chen J, Druka A, Steffenson B, Kleinhofs A (2002) The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases. Proc Natl Acad Sci USA 99:9328-9333
10. Brunner S, Fengler K, Morgante M, Tingey S, Rafalski A (2005) Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17:343-360
11. Bryan GT, Wu KS, Farrall L, Jia Y, Hershey P et al (2000) A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell 12:2033-2046
12. Bulgarelli D, Collins NC, Tacconi G, Dellaglio E, Brueggeman R, Kleinhofs A, Stanca AM, Vale G (2004) High genetic-resolution mapping of the leaf stripe resistance gene Rdg2a in barley. Theor Appl Genet 108:1401-1408
13. Büschges R, Hollricher K, Panstruga R, Simons G, Wolter M, Frijters A, Van Daelen R, Van Der Lee T, Diergaarde P, Groenendijk J, Topsch S, Vos P, Salamini F, Schulze-Lefert P (1997) The barley Mlo gene: a novel control element of plant pathogen resistance. Cell 88:695-705
14. Cenci A, Chantret N, Kong X, Gu Y, Anderson OD, Fahima T, Distelfeld A, Dubcovsky J (2003) Construction and characterization of a half million clone BAC library of durum wheat (Triticum turgidum ssp. durum). Theor Appl Genet 107:931-939
15. Collins N, Drake J, Ayliffe M, Sun Q, Ellis J, Hulbert S, Pryor T (1999) Molecular characterization of the maize Rp1-D rust resistance haplotype and its mutants. Plant Cell 11:1365-1376
16. De Lorenzo G, D'Ovidio R, Cervone F (2001) The role of polygalacturonase-inhibiting proteins (PGIPS) in defense against pathogenic fungi. Ann Rev Phytopathol 39:313-335
17. Douchkov D, Nowara D, Zierold U, Schweizer, P (2005) A high-throughput gene-silencing system for the functional assessment of defense-related genes in barley epidermal cells. Mol Plant Microbe Interact 18:755-761
18. Dubin HJ, Gilchrist L, Reeves J, McNab A, (eds) (1997) Fusarium head scab: global status and prospects. CIMMYT, Mexico, DF, Mexico. 130 p
19. Feuillet C, Travella S, Stein N, Albar L, Nublat A, Keller B (2003) Map-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome. Proc Natl Acad Sci USA 100:15253-15258
20. Fu H, Dooner H (2002) Intraspecific violation of genetic conlinearity and its implications in maize. Proc Natl Acad Sci USA 99:9573-9578
21. Grant MR, McDowell JM, Sharpe AG, De Torres Zabala M, Lydiate DJ, Dangl JL (1998) Independent deletions of a pathogen-resistance gene in Brassica and Arabidopsis. Proc Natl Acad Sci USA 95:15843-15848
22. Guyot R, Yahiaoui N, Feuillet C, Keller B (2004) In silico comparative analysis reveals a mosaic conservation of genes within a novel colinear region in wheat chromosome 1AS and rice chromosome 5S. Funct Integr Genomics 4:47-58
23. Halterman DA, Wise RP (2004) A single-amino acid substitution in the sixth leucine-rich repeat of barley MLA6 and MLA13 alleviates dependence on RAR1 for disease resistance signaling. Plant J 38:215-226
24. Halterman D, Zhou FS, Wei FS, Wise RP, Schulze-Lefert P (2001) The MLA6 coiled-coil, NBS-LRR protein confers AvrMla6-dependent resistance specificity to Blumeria graminis f.sp. hordei in barley and wheat. Plant J 25:335-348
25. Halterman DA, Wei FS, Wise RP (2003) Powdery mildew-induced Mla mRNAs are alternatively spliced and contain multiple upstream open reading frames. Plant Physiol 131:558-567
26. Holzberg S, Brosio P, Gross C, Pogue GP (2002) Barley stripe mosaic virus-induced gene silencing in a monocot plant. Plant J 30:315-327
27. Horvath H, Rostoks N, Brueggeman R, Steffenson B, Von Wettstein D, Kleinhofs A (2003) Genetically engineered stem rust resistance in barley using the Rpg1 gene. Proc Natl Acad Sci USA 100:364-369
28. Hu GS, Richter TE, Hulbert SH, Pryor T (1996) Disease lesion mimicry caused by mutations in the rust resistance gene rp1. Plant Cell 8:1367-1376
29. Huang L, Brooks SA, Li W, Fellers JP, Trick HN, Gill BS (2003) Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of bread wheat. Genetics 164:655-664
30. Isidore E, Scherrer B, Bellec A, Budin K, Faivre-Rampant P, Waugh R, Keller B, Caboche M, Feuillet C, Chalhoub B (2005a) Direct targeting and isolation of genes of interest using an improved pooled BAC libraries cloning and screening strategy. Funct Integr Genomics 5:97-103
31. Isidore E, Scherrer B, Chalhoub B, Feuillet C, Keller B (2005b) Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels. Genome Res 15:526-536
32. Iyer AS, McCouch SR (2004) The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. Mol Plant Microbe Interact 17:1348-1354
33. Janda J, Bartos J, Safar J, Kubalakova M, Valarik M, Cihalikova J, Simkova H, Caboche M, Sourdille P, Bernard M, Chalhoub B, Dolezel J (2004) Construction of a subgenomic BAC library specific for chromosomes 1D, 4D and 6D of hexaploid wheat. Theor Appl Genet 109:1337-1345
34. Jiang GH, Xia ZH, Zhou YL, Wan J, Li DY, Chen RS, Zhai WX, Zhu LH (2006) Testifying the rice bacterial blight resistance gene xa5 by genetic complementation and further analyzing xa5 (Xa5) in comparison with its homology TFIIA gamma 1. Mol Gen Genet 275:354-366
35. Jorgensen JH (1993) Coordinator's reports: disease and pest resistance genes. Barley Genet Newsl 22:10-133
36. Keller B, Feuillet C, Yahiaoui N (2005) Map-based isolation of disease resistance genes from bread wheat: cloning in a supersize genome. Genet Res Camb 85:93-100
37. Kota R, Spielmeyer W, McIntosh RA, Lagudah ES (2006) Fine genetic mapping fails to dissociate durable stem rust resistance gene Sr2 from pseudo-black chaff in common wheat (Triticum aestivum L.). Theor Appl Genet 112:492-499
38. Kuang H, Woo SS, Meyers BC, Nevo E, Michelmore RW (2004) Multiple genetic processes result in heterogeneous rates of evolution within the major cluster disease resistance genes in lettuce. Plant Cell 16:2870-2894
39. Leister D, Kurth J, Laurie DA, Yano M, Sasaki T, Devos K, Graner A, Schulze-Lefert P (1998) Rapid reorganization of resistance gene homologues in cereal genomes. Proc Natl Acad Sci USA 95:370-375
40. Lijavetzky D, Muzzi G, Wicker T, Keller B, Wing R, Dubcovsky J (1999) Construction and characterization of a bacterial artificial chromosome (BAC) library for the A genome of wheat. Genome 42:1176-1182
41. Liu S, Anderson JA (2003a) Marker assisted evaluation of Fusarium head blight resistant wheat germplasm. Crop Sci 43:760-766
42. Liu S, Anderson JA (2003b) Targeted molecular mapping of a major wheat QTL for Fusarium head blight resistance using wheat ESTs and synteny with rice. Genome 46:817-823
43. Lu H-J, Faris JD (2006) Macro- and microcolinearity between the genomic region of wheat chromosome 5B containing the Tsn1 gene and the rice genome. Funct Integr Genomics 6:90-103
44. Lu H-J, Fellers JP, Friesen TL, Meinhardt SW, Faris JD (2006) Genomic analysis and marker development for the Tsn1 locus in wheat using bin-mapped ESTs and flanking BAC contigs. Theor Appl Genet 112:1132-1142
45. Luo MC, Thomas C, You FM, Hsiao J, Ouyang S, Buell CR, Malandro M, McGuire PE, Anderson OD, Dvorak J (2003) High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82:378-389
46. Mago R, Miah H, Lawrence GJ, Wellings CR, Spielmeyer W, Bariana HS, McIntosh RA, Pryor AJ, Ellis JG (2005) High-resolution mapping and mutation analysis separate the rust resistance genes Sr31, Lr26 and Yr9 on the short arm of rye chromosome 1. Theor Appl Genet 112:41-50
47. Mammadov JA, Steffenson BJ, Saghai Maroof MA (2005) High-resolution mapping of the barley leaf rust resistance gene Rph5 using barley expressed sequence tags (ESTs) and synteny with rice. Theor Appl Genet 111:1651-1660
48. McDonald BA, Linde C (2002) Pathogen population genetics, evolutionary potential, and durable resistance. Ann Rev Phytopathol 40:349-379
49. McDowell JM, Dhandaydham M, Long TA, Aarts MGM, Goff S, Holub EB, Dangl JL (1998) Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP8 locus of Arabidopsis. Plant Cell 10:1861-1874
50. McIntosh RA, Wellings CR, Parks RF (1995). (In: Cloud-Guest A, Jeans K) (eds) Wheat rusts: an atlas of resistance genes. Kluwer, Dordrecht, pp 1-200
51. McIntosh RA, Yamzaki Y, Devos KM, Dubcovsky J, Rogers WJ (2003) Catalogue of gene symbols for wheat. In: Pognat NE, Romano M, Pogna E, Galterio G (eds) Proceedings of the 10th International Wheat Genetics Sysmposium, Istituto Sperimentale per la Cerealicoltura Paestum, Italy pp 1-34
52. Meyers BC, Shen KA, Rohani P, Gaut BS, Michelmore RW (1998) Receptor-like genes in the major resistance locus of lettuce are subject to divergent selection. Plant Cell 10:1833-1846
53. Monosi B, Wisser RJ, Pennill L, Hulbert SH (2004) Full-genome analysis of resistance gene homologues in rice. Theor Appl Genet 109:1434-1447
54. Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, Rafalski A (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37:997-1002
55. Moullet O, Zhang HB, Lagudah ES (1999) Construction and characterisation of a large DNA insert library from the D genome of wheat. Theor Appl Genet 99:305-313
56. Nilmalgoda SD, Cloutier S, Walichnowski AZ (2003) Construction and characterization of a bacterial articial chromosome (BAC) library of hexaploid wheat (Triticum aestivum L.) and validation of genome coverage using locus-specific primers. Genome 46:870-878
57. Nürnberger T, Brunner F, Kemmerling B, Piater L (2004) Innate immunity in plants and animals: striking similarities and obvious differences. Immunol Rev 198:249-266
58. Oerke E-C, Dehne H-W (1997) Global crop production and the efficacy of crop protection - current situation and future trends. Europ J Plant Pathol 103:203-215
59. Piffanelli P, Ramsay L, Waugh R, Benabdelmouna A, D'Hont A, Hollricher K, Jorgensen JH, Schulze-Lefert P, Panstruga R (2004) A barley cultivation-associated polymorphism conveys resistance to powdery mildew. Nature 430:887-891
60. Qu SH, Liu GF, Zhou B, Bellizzi M, Zeng LR, Dai LY, Han B, Wang GL (2006) The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat protein and is a member of a multigene family in rice. Genetics 172:1901-1914
61. Richter TE, Pryor TJ, Bennetzen JL, Hulbert SH (1995) New rust resistance specificities associated with recombination in the Rp1 complex in maize. Genetics 141:373-381
62. Rosewarne GM, Singh RP, Huerta-Espino J, William HM, Bouchet S, Cloutier S, McFadden H, Lagudah ES (2006) Leaf tip necrosis, molecular markers and (31-proteasome subunits associated with the slow rusting resistance genes Lr46/Yr29. Theor Appl Genet 112:500-508
63. Safar J, Bartos J, Janda J, Bellec A, Kubalakova M, Valarik M, Pateyron S, Weiserova J, Tuskova R, Cihalikova J, Vrana J, Simkova H, Faivre-Rampant P, Sourdille P, Caboche M, Bernard M, Dolezel J, Chalhoub B (2004) Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J 39:960-968
64. Salvi S, Tuberosa R (2005) To clone or not clone plant QTLs: present and future challenges. Trends Plant Sci 10:297-304
65. Saxena KMS, Hooker AL (1968) On structure of a gene for disease resistance in maize. Proc Natl Acad Sci USA 61:1300-1305
66. Scherrer B, Isidore E, Klein P, Kim J, Bellec A, Chalhoub B, Keller B, Feuillet C (2005) Large-intraspecific haplotype variability at the Rph7 locus results from rapid and recent divergence in the barley genome. Plant Cell 17:361-374
67. Schnurbusch T, Paillard S, Schori A, Messmer M, Schachermayr G, Winzeler M, Keller B (2004a) Dissection of quantitative and durable leaf rust resistance in Swiss winter wheat reveals a major resistance QTL in the Lr34 chromosomal region. Theor Appl Genet 108:477-484
68. Schnurbusch T, Bossolini E, Messmer M, Keller B (2004b) Tagging and validation of a major quantitative trait locus for leaf rust resistance and leaf tip necrosis in winter wheat cultivar Forno. Phytopathology 94:1036-1041
69. Schulze-Lefert P, Bieri S (2005) Recognition at a distance. Science 308:506-508
70. Schweizer P, Pokorny J, Abderhalden O, Dudler R (1999) A transient assay system for the functional assessment of defense-related genes in wheat. Mol Plant Microbe Interact 12:647-654
71. Scofield SR, Huang L, Brandt AS, Gill BS (2005) Development of a virus-induced gene-silencing system for hexaploid wheat and its use in functional analysis of the Lr21-mediated leaf rust resistance pathway. Plant Physiol 138:2165-2173
72. Shen QH, Zhou F, Bieri S, Haizel T, Shirasu K, Schulze-Lefert P (2003) Recognition specificity and RAR1/SGT1 dependence in barley Mla disease resistance genes to the powdery mildew fungus. Plant Cell 15:732-744
73. Shen B, Wang DM, McIntyre CL, Liu CJ (2005) A 'Chinese Spring' wheat (Triticum aestivum L.) bacterial artificial chromosome library and its use in the isolation of SSR markers for targeted genome regions. Theor Appl Genet 111:1489-1494
74. Shirasu K, Nielsen K, Piffanelli P, Oliver R, Schulze-Lefert P (1999) Cell-autonomous complementation of mlo resistance using a biolistic transient expression system. Plant J 17:293-299
75. Smith SM, Hulbert SH (2005) Recombination events generating a novel Rp1 race specificity. Mol Plant Microbe Interact 18:220-228
76. Smith SM, Pryor AJ, Hulbert SH (2004) Allelic and haplotypic diversity at the Rp1 rust resistance locus of maize. Genetics 167:1939-1947
77. Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu LH, Fauquet C, Ronald P (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270:1804-1806
78. Spielmeyer W, McIntosh RA, Kolmer J, Lagudah ES (2005) Powdery mildew resistance and Lr34/Yr18 genes for durable resistance to leaf and stripe rust cosegregate at a locus on the short arm of chromosome 7D of wheat. Theor Appl Genet 111:731-735
79. Srichumpa P, Brunner S, Keller B, Yahiaoui N (2005) Allelic series of four powdery mildew resistance genes at the Pm3 locus in hexaploid bread wheat. Plant Physiol 139:885-895
80. Stein N, Feuillet C, Wicker T, Schlagenhauf E, Keller B (2000) Subgenome chromosome walking in wheat: a 450-kb physical contig in Triticum monococcum L.spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.). Proc Natl Acad Sci USA 97:13436-13441
81. Stein N, Perovic D, Kumlehn J, Pelliio B, Stracke S, Streng S, Ordon F, Graner A (2005) The eukaryotic translation initiation factor 4E confer multiallelic recessive Bymovirus resistance in Hordeum vulgare (L.). Plant J 42:912-922
82. Sun XL, Cao YL, Yang ZF, Xu CG, Li XH, Wang SP, Zang QF (2004) Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein. Plant J 37:517-527
83. Toumasini L, Yahiaoui N, Srichumpa P, Keller B (2006) Development of functional moleculer markers specific for seven Pm 3 resistance aller and their validation in the bread wheat gene pool. Theor Appl Genet 114:165-175
84. Wang ZX, Yano M, Yamanouchi U, Iwamoto M, Monna L, Hayasaka H, Katayose Y, Sasaki T (1999) The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. Plant J 19:55-64
85. Wei F, Gobelman-Werner K, Morroll SM, Kurth J, Mao L, Wing R, Leister D, Schulze-Lefert P, Wise RP (1999) The Mla (powdery mildew) resistance cluster is associated with three NBS-LRR gene families and suppressed recombination within a 240-kb DNA interval on chromosome 5S (1HS) of barley. Genetics 153:1929-1948
86. Wei F, Wing RA, Wise RP (2002) Genome dynamics and evolution of the Mla (powdery mildew) resistance locus in barley. Plant Cell 14:1903-1917
87. Weibull J, Walther U, Sato K, Habekuss A, Kopahnke D, Proeseler G (2003) Diversity in resistance to biotic stresses. In: von Bothmer R (ed) Diversity in barley (Hordeum vulgare), (elsevier Science BV), Amsterdam, pp 143-178
88. Wicker T, Stein N, Albar L, Feuillet C, Schlagenhauf E, Keller B (2001) Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J 26:307-316
89. Wicker T, Zimmermann W, Perovic D, Paterson AH, Ganal M, Graner A, Stein N (2005) A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats. Plant J 41:184-194
90. Xu Y, McCouch SR, Zhang Q (2005) How can we use genomics to improve cereals with rice as a reference genome? Plant Mol Biol 59:7-26
91. Yahiaoui N, Srichumpa P, Dudler R, Keller B (2004) Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat. Plant J 37:528-538
92. Yahiaoui N, Brunner S, Keller B (2006) Rapid generation of new powdery mildew resistance genes after wheat domestication. Plant J 47:85-98
93. Yoshimura S, Yamanouchi U, Katayose Y, Toki S, Wang ZX, Kono I, Kurata N, Yano M, Iwata N, Sasaki T (1998) Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc Natl Acad Sci USA 95:1663-1668
94. Yu Y, Tomkins JP, Waugh R, Frisch DA, Kudrna D, Kleinhofs A, Brueggeman RS, Muehlbauer GJ, Wise RP, Wing RA (2000) A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theor Appl Genet 101:1093-1099
95. Zeller FJ, Hsam SLK (1998) Progress in breeding for resistance to powdery mildew in common wheat (Triticum aestivum L.). Proceedings of the IX international wheat genetics symposium Saskatoon, Saskatchewan, pp 178-180
96. Zhou FS, Kurth JC, Wei FS, Elliott C, Vale G, Yahiaoui N, Keller B, Somerville S, Wise R, Schulze-Lefert P (2001) Cell-autonomous expression of barley Mla1 confers race-specific resistance to the powdery mildew fungus via a Rar1-independent signaling pathway. Plant Cell 13:337-350