Comparative sequence analysis of the region harboring the hardness locus in barley and its colinear region in rice

Plant Physiology

Volumn 136, Issue 2, 2004, Pages 3177-3190

  Caldwell, Katherine S ^a,b,c   Langridge, Peter ^b   Powell, Wayne ^a  

^a SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^b UNIVERSITY OF ADELAIDE   (Australia)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOMES; CROPS; MATHEMATICAL MODELS;

COMPARATIVE SEQUENCE ANALYSIS; ENDOSPERM TEXTURE; GENE DUPLICATIONS;

GENES;

BARLEY; CHROMOSOMES; GENES; MATHEMATICAL MODELS; TRANSLOCATION;

HORDEUM VULGARE; HORDEUM VULGARE SUBSP. VULGARE; ORYZA SATIVA; POACEAE;

SPACER DNA;

ARABIDOPSIS; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BARLEY; COMPARATIVE STUDY; CONTIG MAPPING; GENE; GENE EXPRESSION REGULATION; GENETICS; GENOME; MOLECULAR EVOLUTION; MOLECULAR GENETICS; RICE; TRANSPOSON;

ARABIDOPSIS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CONTIG MAPPING; DNA TRANSPOSABLE ELEMENTS; DNA, INTERGENIC; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; HORDEUM; MOLECULAR SEQUENCE DATA; ORYZA SATIVA;

EID: 16544383364     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.104.044081     Document Type: Article

References (84)

1. Ahn S, Tanksley SD (1993) Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 90: 7980-7984
2. Akhunov ED, Goodyear AW, Geng S, Qi LL, Echalier B, Gill BS, Miftahudin, Gustafson JP, Lazo G, Chao SM, et al (2003) The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genome Res 13: 753-763
3. 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
4. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9: 211-215
5. Baurnert M, Maycox PR, Navone F, DeCarnilli P, Jahn R (1989) Synaptobrevin: an integral membrane protein of 18,000 Daltons present in small synaptic vesicles of rat brain. EMBO J 8: 379-384
6. Beecher B, Smidansky ED, See D, Blake TK, Giroux MJ (2001) Mapping and sequence analysis of barley hordoindolines. Theor Appl Genet 102: 833-840
7. Bennett MD, Leitch IJ (1995) Nuclear DNA amounts in angiosperms. Ann Bot (Lond) 76: 113-176
8. Bennett MD, Leitch IJ (1997) Nuclear DNA amounts in angiosperms: 583 new estimates. Ann Bot (Lond) 80: 169-196
9. Bennett MD, Smith JB, Heslop-Harrison JS (1982) Nuclear DNA amounts in angiosperms. Proc R Soc Lond B Biol Sci 216: 179-199
10. Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 12: 1021-1029
11. 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
12. Bennetzen JL, Ramakrishna W (2002) Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Mol Biol 48: 821-827
13. Blochet JE, Chevalier C, Forest E, Pebaypeyroula E, Gautier MF, Joudrier P, Pezolet M, Marion D (1993) Complete amino-acid-sequence of puroindoline: a new basic and cystine-rich protein with a unique tryptophan-rich domain, isolated from wheat endosperm by Triton X-114 phase partitioning. FEBS Lett 329: 336-340
14. Brunner S, Keller B, Feuillet C (2003) A large rearrangement involving genes and low-copy DNA interrupts the microcollinearity between rice and barley at the Rph7 locus. Genetics 164: 673-683
15. Chantret N, Center A, Sabot F, Anderson O, Dubcovsky J (2004) Sequencing of the Triticum monococcum hardness locus reveals good microcolinearity with rice. Mol Gen Genet 271: 377-386
16. Chen MS, SanMiguel P, Bennetzen JL (1998) Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148: 435-443
17. Chen YA, Scheller RH (2001) SNARE-mediated membrane fusion. Nat Rev Mol Cell Biol 2: 98-106
18. Clark LG, Zhang WP, Wendel JF (1995) A phylogeny of the grass family (Poaceae) based on Ndhf -sequence data. Syst Bot 20: 436-460
19. Crepet WL, Feldman GD (1991) The earliest remains of grasses in the fossil record. Am J Bot 78: 1010-1014
20. Delseny M (2004) Re-evaluating the relevance of ancestral shared synteny as a tool for crop improvement. Curr Opin Plant Biol 7: 1-6
21. Devos KM, Gale MD (1997) Comparative genetics in the grasses. Plant Mol Biol 35: 3-15
22. Distelfeld A, Uauy C, Olmos S, Schlatter AR, Dubcovsky J, Fahima T (2004) Microcolinearity between a 2-cM region encompassing the grain protein content locus Gpc-6B1 on wheat chromosome 6B and a 350-kb region on rice chromosome 2. Funct Integr Genomics 4: 59-66
23. Dixon RA, Harrison MJ, Paiva NL (1995) The isoflavonoid phytoalexin pathway; from enzymes to genes to transcription factors. Physiol Plant 93: 385-392
24. Dixon RA, Lamb CJ, Masoud S, Sewalt VJH, Paiva NL (1996) Metabolic engineering: prospects for crop improvement through the genetic manipulation of phenylpropanoid biosynthesis and defense responses. A review. Gene 179: 61-71
25. Dixon RA, Paiva NL (1995) Stress-induced phenylpropanoid metabolism. Plant Cell 7: 1085-1097
26. Druka A, Kudrna D, Han F, Kilian A, Steffenson B, Frisch D, Tomkins J, Wing R, Kleinhofs A (2000) Physical mapping of the barley stem rust resistance gene rpg4. Mol Gen Genet 264: 283-290
27. Dubcovsky J, Ramakrishna W, SanMiguel PJ, Busso CS, Yan LL, Shiloff BA, Bennetzen JL (2001) Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiol 125: 1342-1353
28. Dubreil L, Gaborit T, Bouchet B, Gallant DJ, Broekaert WF, Quillien L, Marion D (1998) Spatial and temporal distribution of the major isoforms of puroindolines (puroindoline-a and puroindoline-b) and non specific lipid transfer protein (ns-LTPle(1)) of Triticum aestivum seeds: relationships with their in vitro antifungal properties. Plant Sci 138: 121-135
29. Ewing B, Green P (1998) Base calling of automated sequencer traces using phred. II: error probabilities. Genome Res 8: 186-194
30. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I: accuracy assessment. Genome Res 8: 175-185
31. 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
32. Feuillet C, Keller B (2002) Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann Bot (Lond) 89: 3-10
33. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95: 1971-1974
34. Gill KS, Gill BS, Endo TR, Boyko EV (1996) Identification and high-density mapping of gene-rich regions in chromosome group 5 of wheat. Genetics 143: 1001-1012
35. Goff SA, Ricke D, Lan TH, Presting G, Wang RL, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 296: 92-100
36. Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8: 195-202
37. Gu YQ, Anderson OD, Londeore CF, Kong X, Chibbar RN, Lazo GO (2003) Structural organization of the barley D-hordein locus in comparison with orhtologous region of wheat genomes. Genome 46: 1084-1097
38. 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
39. Han F, Kilian A, Chen JP, Kudrna D, Steffenson B, Yamamoto K, Matsumoto T, Sasaki T, Kleinhofs A (1999) Sequence analysis of a rice BAC covering the syntenous barley Rpg1 region. Genome 42: 1071-1076
40. Han F, Kleinhofs A, Ullrich SE, Kilian A, Yano M, Sasaki T (1998) Synteny with rice: analysis of barley malting quality QTLs and rpg4 chromosome regions. Genome 41: 373-380
41. Keller B, Feuillet C (2000) Colinearity and gene density in grass genomes. Trends Plant Sci 5: 246-251
42. 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
43. Krishnamurthy K, Balconi C, Sherwood JE, Giroux MJ (2001) Wheat puroindolines enhance fungal disease resistance in transgenic rice. Mol Plant Microbe Interact 14: 1255-1260
44. Kurata N, Moore G, Nagamura Y, Foote T, Yano M, Minobe Y, Gale M (1994) Conservation of genome structure between rice and wheat. Biotechnology 12: 276-278
45. La Rota M, Sorrells M (2004) Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Funct Integr Genomics 4: 34-16
46. Li WL, Gill BS (2002) The colinearity of the Sh2/A1 orthologous region in rice, sorghum and maize is interrupted and accompanied by genome expansion in the Triticeae. Genetics 160: 1153-1162
47. Li Y, Baldauf S, Lim EK, Bowles DJ (2001) Phylogenetic analysis of the UDP-glycosyltransferase multigene family of Arabidopsis thaliana. J Biol Chem 276: 4338-4343
48. Miklos GLG, Rubin GM (1996) The role of the genome project in determining gene function: Insights from model organisms. Cell 86: 521-529
49. Moore G, Devos KM, Wang Z, Gale MD (1995) Cereal genome evolution: grasses, line up and form a circle. Curr Biol 5: 737-739
50. Morris CF (2002) Puroindolines: the molecular genetic basis of wheat grain hardness. Plant Mol Biol 48: 633-647
51. Ogura T, Wilkinson AJ (2001) AAA(+) superfamily ATPases: common structure-diverse function. Genes Cells 6: 575-597
52. Panstruga R, Buschges R, Piffanelli P, Schulze-Lefert P (1998) A contiguous 60-kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Res 26: 1056-1062
53. Patel S, Latterich M (1998) The AAA team: related ATPases with diverse functions. Trends Cell Biol 8: 65-71
54. Roberts MA, Reader SM, Dalgliesh C, Miller TE, Foote TN, Fish LJ, Snape JW, Moore G (1999) Induction and characterization of Ph1 wheat mutants. Genetics 153: 1909-1918
55. Ross J, Li Y, Lim EK, Bowles DJ (2001) Higher Plant Glycosyltransferases. Genome Biology 2: 3004.1-3004.6
56. Rostoks N, Park Y-J, Ramakrishna W, Ma J, Druka A, Shiloff BA, SanMiguel PJ, Jiang Z, Brueggeman R, Sandhu D, et al (2002) Genomic sequencing reveals gene content, genomic organization, and recombination relationships in barley. Fund Integr Genomics 2: 51-59
57. Rouves S, Boeuf C, Zwickert-Menteur S, Gautier MF, Joudrier P, Bernard M, Jestin L (1996) Locating supplementary RFLP markers on barley chromosome 7 and synteny with homoeologous wheat group 5. Plant Breed 115: 511-513
58. Sakata K, Nagamura Y, Numa H, Antonio BA, Nagasaki H, Idonuma A, Watanabe W, Shimizu Y, Horiuchi I, Matsumoto T, et al (2002) RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Res 30: 98-102
59. SanMiguel P, Bennetzen JL (1998) Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann Bot (Lond) 82: 37-44
60. m. Funct Integr Genomics 2: 70-80
61. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, et al (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768
62. Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y, et al (2002) The genome sequence and structure of rice chromosome 1. Nature 420: 312-316
63. Shewry PR, Beaudoin F, Jenkins J, Griffiths-Jones S, Mills ENC (2002) Plant protein families and their relationships to food allergy. Biochem Soc Trans 30: 906-910
64. Shields R (1993) Plant genetics: pastoral synteny. Nature 365: 297-298
65. Shirasu K, Schulman AH, Lahaye T, Schulze-Lefert P (2000) A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res 10: 908-915
66. Shirley BW (1996) Flavonoid biosynthesis: 'new' functions for an 'old' pathway. Trends Plant Sci 1: 377-382
67. Simpson CG, Thow G, Clark GP, Jennings SN, Watters JA, Brown JWS (2002) Mutational analysis of a plant branchpoint and polypyrimidine tract required for constitutive splicing of a mini-exon. RNA 8: 47-56
68. Sollner T, Bennett MK, Whiteheart SW, Scheller RH, Rothman JE (1993) A protein assembly-disassembly pathway in vitro that may correspond to sequential steps of synaptic vesicle docking, activation, and fusion. Cell 75: 409-418
69. Sonnhammer ELL, Durbin R (1995) A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167: 1-10
70. Sorrells ME, La Rota M, Bermudez-Kandianis CE, Greene RA, Kantety R, Munkvold JD, Miftahudin, Mahmoud A, Ma XF, Gustafson PJ, et al (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13: 1818-1827
71. Tikhonov AP, SanMiguel PJ, Nakajima Y, Gorenstein NM, 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
72. Trimble WS, Cowan DM, Scheller RH (1988) VAMP-1: a synaptic vesicle-associated integral membrane protein. Proc Natl Acad Sci USA 85: 4538-4542
73. Vicient CM, Suoniemi A, Anamthamat-Jonsson K, Tanskanen J, Beharav A, Nevo E, Schulman AH (1999) Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11: 1769-1784
74. Weber T, Zemelman BV, Mcnew JA, Westermann B, Gmachl M, Parlati F, Sollner TH, Rothman JE (1998) SNAREpins: minimal machinery for membrane fusion. Cell 92: 759-772
75. Wei FS, Wong RA, Wise RP (2002) Genome dynamics and evolution of the Mla (powdery mildew) resistance locus in barley. Plant Cell 14: 1903-1917
76. Wicker T, Matthews DE, Keller B (2002) TREP: a database for Triticeae repetitive element. Trends Plant Sci 7: 561-562
77. 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
78. Wicker T, Yahiaoui N, Guyot R, Schlagenhauf E, Liu ZD, Dubcovsky J, Keller B (2003) Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and A(m) genomes of wheat. Plant Cell 15: 1186-1197
79. Wolfe KH, Gouy ML, Yang YW, Sharp PM, Li WH (1989) Date of the monocot dicot divergence estimated from chloroplast DNA-sequence data. Proc Natl Acad Sci USA 86: 6201-6205
80. Wu J, Yamagata H, Hayashi-Tsugane M, Hijishita S, Fujisawa M, Shibata M, Ito Y, Nakamura M, Sakaguchi M, Yosihara R, et al (2004) Composition and structure of the centromeric region of rice chromosome 8. Plant Cell 16: 967-976
81. Yan L, Echenique V, Busso C, SanMiguel P, Ramakrishna W, Bennetzen JL, Harrington S, Dubcovsky J (2002) Cereal genes similar to Snf2 define a new subfamily that includes human and mouse genes. Mol Gen Genet 268: 488-499
82. Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100: 6263-6268
83. Yu J, Hu SN, Wang J, Wong GKS, Li SG, Liu B, Deng YJ, Dai L, Zhou Y, Zhang XQ, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 296: 79-92
84. 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