Comparative sequence analysis of the sorghum Rph region and the maize Rp1 resistance gene complex

Plant Physiology

Volumn 130, Issue 4, 2002, Pages 1728-1738

  Ramakrishna, Wusirika ^a   Emberton, John ^a   SanMiguel, Phillip ^b   Ogden, Matthew ^a   Llaca, Victor ^c   Messing, Joachim ^c   Bennetzen, Jeffrey L ^a  

^a PURDUE UNIVERSITY   (United States)

^b PURDUE UNIVERSITY   (United States)

^c RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENES;

GENOMIC STRUCTURE;

PLANTS (BOTANY);

EMBRYOPHYTA; SORGHUM BICOLOR; ZEA; ZEA MAYS;

EID: 0036909636     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.014951     Document Type: Article

References (59)

1. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402
2. Anderson PA, Lawrence GJ, Morrish BC, Ayliffe MA, Finnegan EJ, Ellis JG (1997) Inactivation of the flax rust resistance gene M associated with loss of a repeated unit within the leucine-rich repeat coding region. Plant Cell 9: 641-651
3. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
4. Ayliffe MA, Collins NC, Ellis JG, Pryor A (2000) The maize rp1 rust resistance gene identifies homologues in barley that have been subjected to diversifying selection. Theor Appl Genet 100: 1144-1154
5. Bennetzen JL (1996) The contributions of retroelements to plant genome organization, function and evolution. Trends Microbiol 4: 347-353
6. Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomes: Microcolinearity and its many exceptions. Plant Cell 12: 1021-1029
7. Bennetzen JL, Hulbert SH (1992) Organization, instability and evolution of plant disease resistance genes. Plant Mol Biol 20: 575-578
8. Bennetzen JL, Qin MM, Ingels S, Ellingboe AH (1988) Allele-specific and mutator-associated instability at the rp1 disease-resistance locus of maize. Nature 332: 369-370
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. Caicedo AL, Schaal BA, Kunkel BN (1999) Diversity and molecular evolution of the RPS2 resistance gene in Arabidopsis thaliana. Proc Natl Acad Sci USA 96: 302-306
11. Chen MS, SanMiguel P, Bennetzen JL (1998) Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148: 435-443
12. 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
13. Devos KM, Brown JKM, Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12: 1075-1079
14. Dodds PN, Lawrence GJ, Ellis JG (2001) Contrasting modes of evolution acting on the complex N locus for rust resistance in flax. Plant J 27: 439-453
15. Dubcovsky J, Ramakrishna W, SanMiguel P, Busso C, Yan L, Shiloff B, Bennetzen J (2001) Comparative sequence analysis of colinear barley and rice BACs. Plant Physiol 125: 1342-1353
16. Ellis J, Dodds P, Pryor T (2000a) Structure, function and evolution of plant disease resistance genes. Curr Opin Plant Biol 3: 278-284
17. Ellis J, Dodds P, Pryor T (2000b) The generation of plant disease resistance gene specificities. Trends Plant Sci 5: 373-379
18. Feuillet C, Keller B (1999) High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci USA 96: 8265-8270
19. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95: 1971-1974
20. Gallego F, Feuillet C, Messmer M, Penger A, Graner A, Yano M, Sasaki T, Keller B (1998) Comparative mapping of the two wheat leaf rust resistance loci Lr1 and Lr10 in rice and barley. Genome 41: 328-336
21. Gaut BS, Doebley JF (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci USA 88: 2060-2064
22. Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci USA 93: 10274-10279
23. Hu G, Hulbert SH (1994) Evidence for the involvement of gene conversion in meiotic instability of the Rp1 rust resistance genes of maize. Genome 37: 742-746
24. Hulbert SH, Bennetzen JL (1991) Recombination at the rp1 locus of maize. Mol Gen Genet 226: 377-382
25. Jiang JM, Hulbert SH, Gill BS, Ward DC (1996) Interphase fluorescence in situ hybridization mapping: A physical mapping strategy for plant species with large complex genomes. Mol Gen Genet 252: 497-502
26. Kilian A, Chen J, Han F, Steffenson B, Kleinhofs A (1997) Towards map-based cloning of the barley stem rust resistance genes Rpg1 and rpg4 using rice as an intergenomic cloning vehicle. Plant Mol Biol 35: 187-195
27. Klein P, Klein RR, Cartinhour S, Ulanch P, Dong J, Obert J, Morishige DT, Schlueter S, Childs K, Ale M (2000) A high-throughput AFLP-based method for constructing integrated genetic and physical maps: Progress toward a sorghum genome map. Genome Res 10: 789-807
28. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 17: 1244-1245
29. Leister DM, Kurth J, Laurie DA, Yano M, Sasaki T, Devos KM, Graner A, Schulze-Lefert P (1998) Rapid reorganisation of resistance gene homologues in cereal genomes. Proc Natl Acad Sci USA 95: 370-375
30. Llaca V, Messing J (1998) Amplicons of maize zein genes are conserved within genic but expanded and constricted in intergenic regions. Plant J 15: 211-220
31. Mao L, Wood TC, Yu Y, Budiman MA, Tomkins J, Sung-Sick W, Sasinowski M, Presting G, Frisch D, Goff S et al. (2000) Rice transposable elements: A survey of 73,000 sequence-tagged-connectors. Genome Res 10: 982-990
32. 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
33. Multani DS, Meeley RB, Paterson AH, Gray J, Briggs SP, Johal GS (1998) Plant-pathogen microevolution: Molecular basis for the origin of a fungal disease in maize. Proc Natl Acad Sci USA 95: 1686-1691
34. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418-426
35. Noel L, Moores TL, van der Biezen EA, Parniske M, Daniels MJ, Parker JE, Jones JDG (1999) Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell 11: 2099-2111
36. Parniske M, Hammond-Kosack KE, Golstein C, Thomas CM, Jones DA, Harrison K, Wulff BBH, Jones JDG (1997) Novel disease resistance specificities result from sequence exchange between tandemly repeated genes at the Cf-4/9 locus of tomato. Cell 91: 821-832
37. Parniske M, Jones JDG (1999) Recombination between diverged clusters of the tomato Cf-9 plant disease resistance gene family. Proc Natl Acad Sci USA 96: 5850-5855
38. Peng Y, Schertz KF, Cartinhour S, Hart GE (1999) Comparative genome mapping of Sorghum bicolor (L.) Moench using an RFLP map constructed in a population of recombinant inbred lines. Plant Breed 118: 225-235
39. Ramakrishna W, Dubcovsky J, Park Y-J, Busso C, Emberton J, SanMiguel P, Bennetzen JL (2002a) Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes. Genetics (in press)
40. Ramakrishna W, Emberton J, Ogden M, SanMiguel P, Bennetzen JL (2002b) Structural analyses of the maize Rp1 complex uncovers numerous sites and unexpected mechanisms of local rearrangement. Plant Cell (in press)
41. Rhoades VH (1935) The location of a gene for disease resistance in maize. Proc Natl Acad Sci USA 21: 243-246
42. 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
43. Salomon S, Puchta H (1998) Capture of genomic and T-DNA sequences during double-strand break repair in somatic plant cells. EMBO J 17: 6086-6095
44. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20: 43-45
45. m. Funct Integr Genom 2: 70-80
46. SanMiguel P, Tikhonov A, Jin Y-K, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768
47. Saxena KMS, Hooker AL (1968) On the structure of a gene for disease resistance in maize. Proc Natl Acad Sci USA 61: 1300-1305
48. Song R, Llaca V, Linton E, Messing J (2001) Sequence, regulation, and evolution of the maize 22-kD α zein gene family. Genome Res 11: 1817-1825
49. Song R, Llaca V, Messing J (2002) Mosaic organization of orthologous sequences in grass genomes. Genome Res 13: 1549-1555
50. Song W-Y, Pi L-Y, Wang G-L, Gardner J, Holsten T, Ronald PC (1997) Evolution of the rice Xa21 disease resistance gene family. Plant Cell 9: 1279-1287
51. Stahl EA, Dwyer G, Mauricio R, Kreitman M, Bergelson J (1999) Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis. Nature 400: 667-671
52. Sudupak MA, Bennetzen JL, Hulbert SH (1993) Unequal exchange and meiotic instability of disease-resistance genes in the rp1 region of maize. Genetics 133: 119-125
53. Sun Q, Collins NC, Ayliffe M, Smith SM, Drake J, Pryor T, Hulbert SH (2001) Recombination between paralogues at the rp1 rust resistance locus in maize. Genetics 158: 433-438
54. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 4876-4882
55. Tikhonov AP, SanMiguel PJ, Nakajima Y, Gorenstein ND, Bennetzen JL, Avramova Z (1999) Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc Natl Acad Sci USA 96: 7409-7414
56. Webb CA, Richter TE, Collins NC, Nicolas M, Trick HN, Pryor T, Hulbert SH (2002) Genetic and molecular characterization of the maize rp3 rust resistance locus. Genetics 162: 381-394
57. Wessler S, Tarpley A, Purugganan M, Spell M, Okagaki R (1990) Filler DNA is associated with spontaneous deletions in maize. Proc Natl Acad Sci USA 87: 8731-8735
58. Wessler SR, Bureau TE, White SE (1995) LTR-retrotransposons and MITES: Important players in the evolution of plant genomes. Curr Opin Genet Dev 5: 814-821
59. Wilson WA, Harrington SE, Woodman WL, Lee M, Sorrells ME, McCouch SR (1999) Inferences on the genome structure of progenitor maize through comparative analysis of rice, maize and the domesticated panicoids. Genetics 153: 453-473