Structure and evolution of cereal genomes

Current Opinion in Genetics and Development

Volumn 13, Issue 6, 2003, Pages 644-650

  Paterson, Andrew H ^a   Bowers, John E ^a   Peterson, Daniel G ^b   Estill, James C ^a   Chapman, Brad A ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b MISSISSIPPI STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; PRIMER DNA;

ARCHEOLOGY; BACTERIAL ARTIFICIAL CHROMOSOME; BOTANY; CEREAL; CLONING; DIET; DNA SEQUENCE; GENE MAPPING; GENE SEQUENCE; GENE STRUCTURE; GENETIC VARIABILITY; GENOME SIZE; INTERMETHOD COMPARISON; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PLANT; POPULATION; PRIORITY JOURNAL; REVIEW; RICE; SEQUENCE DATABASE; SEQUENCE TAGGED SITE; SINGLE NUCLEOTIDE POLYMORPHISM;

BACTERIA (MICROORGANISMS); EMBRYOPHYTA;

EID: 0344513360     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2003.10.002     Document Type: Review

References (65)

1. Kellogg E.A. Relationships of cereal crops and other grasses. Proc. Natl. Acad. Sci. U.S.A. 95:1998;2005-2010.
2. Harlan JR: Crops and Man. Madison, WI: Crop Science Society of America; 1975.
3. Paterson A., Lin Y.-R., Li Z. Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science. 269:1995;1714-1718.
4. Hu F.Y., Tao D.Y., Sacks E., Fu B.Y., Xu P., Li J., Yang Y., McNally K., Khush G.S., Paterson A.H.et al. Convergent evolution of perenniality in rice and sorghum. Proc. Natl. Acad. Sci. U.S.A. 100:2003;4050-4054.
5. Qi X.Q., Stam P., Lindhout P. Comparison and integration of four barley genetic maps. Genome. 39:1996;379-394.
6. Roder M.S., Korzun V., Wendehake K., Plaschke J., Tixier M.H., Leroy P., Ganal M.W. A microsatellite map of wheat. Genetics. 149:1998;2007-2023.
7. Ming R., Liu S.C., Lin Y.R., da Silva J., Wilson W., Braga D., van Deynze A., Wenslaff T.F., Wu K.K., Moore P.H.et al. Detailed alignment of Saccharum and Sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes. Genetics. 150:1998;1663-1682.
8. Devos K.M., Pittaway T.S., Reynolds A., Gale M.D. Comparative mapping reveals a complex relationship between the pearl millet genome and those of foxtail millet and rice. Theor. Appl. Genet. 100:2000;190-198.
9. Lee M., Sharopova N., Beavis W.D., Grant D., Katt M., Blair D., Hallauer A. Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population. Plant Mol. Biol. 48:2002;453-461.
10. McCouch S.R., Teytelman L., Xu Y.B., Lobos K.B., Clare K., Walton M., Fu B.Y., Maghirang R., Li Z.K., Xing Y.Z.et al. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9:2002;199-207.
11. Sharopova N., McMullen M.D., Schultz L., Schroeder S., Sanchez-Villeda H., Gardiner J., Bergstrom D., Houchins K., Melia-Hancock S., Musket T.et al. Development and mapping of SSR markers for maize. Plant Mol. Biol. 48:2002;463-481.
12. Wu J.Z., Maehara T., Shimokawa T., Yamamoto S., Harada C., Takazaki Y., Ono N., Mukai Y., Koike K., Yazaki J.et al. A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell. 14:2002;525-535 Gene mapping, based on the hybridization of ESTs to large-insert DNA clones, provides many of the benefits of a completed sequence to many cereal genomes at much less time and cost. Although the rice genome will soon be fully sequenced, the methods described are applicable to many additional genomes that may not be sequenced for quite some time yet.
13. Wight C.P., Tinker N.A., Kianian S.F., Sorrells M.E., O'Donoughue L.S., Hoffman D.L., Groh S., Scoles G.J., Li C.D., Webster F.H.et al. A molecular marker map in 'Kanota' × 'Ogle' hexaploid oat (Avena spp.) enhanced by additional markers and a robust framework. Genome. 46:2003;28-47.
14. Sorrells M.E., La Rota M., Bermudez-Kandianis C.E., Greene R.A., Kantety R., Munkvold J.D., Miftahudin, Mahmoud A., Ma X., Gustafson P.J.et al. Comparative DNA sequence analysis of wheat and rice genomes. Genome Res. 13:2003;1818-1827.
15. Nasu S., Suzuki J., Ohta R., Hasegawa K., Yui R., Kitazawa N., Monna L., Minobe Y. Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Res. 9:2002;163-171 Among the first illustrations of a genome-wide SNP map in plants, including early quantification of rates and types of SNPs within Oryza, and demonstration of an uneven genomic landscape of SNP distribution.
16. Draye X., Lin Y.-R., Bowers J.E., Burow G.B., Morrell P.L., Peterson D.G., Presting G.G., Ren S.X., Wing R.A., Paterson A.H. Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the Sorghum genome as a foundation. Plant Physiol. 125:2001;1325-1341.
17. Coe E., Cone K., McMullen M., Chen S.S., Davis G., Gardiner J., Liscum E., Polacco M., Paterson A., Sanchez-Villeda H.et al. Access to the maize genome: an integrated physical and genetic map. Plant Physiol. 128:2002;9-12.
18. Feuillet C., Keller B. Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann. Bot. (Lond.). 89:2002;3-10 A succinct review of micro-colinearity and its exceptions in the grasses.
19. Bowers JE, Abbey C, Anderson S, Chang C, Draye X, Hoppe AH, Jessup R, Lemke C, Lennington J, Li Z et al.: A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics 2003, in press.
20. Bennett MD, Leitch IJ: Angiosperm DNA C-values database (release 4.0, Jan. 2003). http://www.rbgkew.org.uk/cval/homepage.html.
21. Bennetzen J.L. Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica. 115:2002;29-36.
22. Bowers J.E., Chapman B.A., Rong J.K., Paterson A.H. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature. 422:2003;433-438 An early application of 'phylogenomics', a merger of phylogenetic inference with structural genomic information that is expected to be of growing importance in the analysis and interpretation of genomic data.
23. ••].
24. ••] is distinguished in also being the largest rice chromosome.
25. The Rice Chromosome 10 Sequencing Consortium: In-depth view of structure, activity, and evolution of rice chromosome 10. Science 2003, 300:1566-1569.
26. •].
27. •], published simultaneously, comprise the first genomic shotgun sequence of a cereal, and shed light on the genomic diversity of cereals from dicot plants such as Arabidopsis, as well as non-plant taxa.
28. •].
29. Zhao Q., Zhang Y., Cheng Z.K., Chen M.S., Wang S.Y., Feng Q., Huang Y.C., Li Y., Tang Y.S., Zhou B.et al. A fine physical map of the rice chromosome 4. Genome Res. 12:2002;817-823.
30. •] and elsewhere for application of 'phylogenomics' to the analysis of plant chromosome evolution.
31. Gaut B.S. Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses. Genome Res. 11:2001;55-66.
32. Gaut B.S. Evolutionary dynamics of grass genomes. New Phytol. 154:2002;15-28 A 'Tansley review' (by invitation only), providing an excellent overview of existing knowledge, challenges, and opportunities associated with comparative genomics in the grasses.
33. Kishimoto N., Higo H., Abe K., Arai S., Saito A., Higo K. Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions. Theor. Appl. Genet. 88:1994;722-726.
34. Nagamura Y., Inoue T., Antonio B., Shimano T., Kajiya H., Shomura A., Lin S., Kuboki Y., Harushima Y., Kurata N.et al. Conservation of duplicated segments between rice chromosomes 11 and 12. Breed Sci. 45:1995;373-376.
35. Wang S.P., Liu K.D., Zhang Q.F. Segmental duplications are common in rice genome. Acta. Bot. Sin. 42:2000;1150-1155.
36. Eckhardt N. A sense of self: the role of DNA sequence elimination in allopolyploidization. Plant Cell. 13:2001;1699-1704.
37. Devos K.M., Beales J., Nagamura Y., Sasaki T. Arabidopsis - rice: will colinearity allow gene prediction across the eudicot-monocot divide? Genome Res. 9:1999;825-829.
38. Liu H., Sachidanandam R., Stein L. Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order. Genome Res. 11:2001;2020-2026.
39. Vandepoele K., Saeys Y., Simillion C., Raes J., Van de Peer Y. The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res. 12:2002;1792-1801.
40. Salse J., Piegu B., Cooke R., Delseny M. Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project. Nucleic Acids Res. 30:2002;2316-2328.
41. Song R., Llaca V., Messing J. Mosaic organization of orthologous sequences in grass genomes. Genome Res. 12:2002;1549-1555.
42. Yano M. Genetic and molecular dissection of naturally occurring variation. Curr. Opin. Plant Biol. 4:2001;130-135.
43. Thornsberry J.M., Goodman M.M., Doebley J., Kresovich S., Nielsen D., Buckler E.S. Dwarf8 polymorphisms associate with variation in flowering time. Nat. Genet. 28:2001;286-289.
44. Tenaillon M.I., Sawkins M.C., Anderson L.K., Stack S.M., Doebley J., Gaut B.S. Patterns of diversity and recombination along chromosome 1 of maize (Zea mays ssp mays L.). Genetics. 162:2002;1401-1413 An elegant integration of cytological, structural and population genomic data, yielding new insights into how allelic diversity is distributed across genomes.
45. Remington D.L., Thornsberry J.M., Matsuoka Y., Wilson L.M., Whitt S.R., Doeblay J., Kresovich S., Goodman M.M., Buckler E.S. Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc. Natl. Acad. Sci. U.S.A. 98:2001;11479-11484.
46. Goldberg R.B. From cot curves to genomics. How gene cloning established new concepts in plant biology. Plant Physiol. 125:2001;4-8.
47. Peterson D.G., Wessler S.R., Paterson A.H. Efficient capture of unique sequences from eukaryotic genomes. Trends Genet. 18:2002;547-550.
48. Peterson DG, Schulze SR, Sciara EB, Lee SA, Bowers JE, Nagel A, Tibbitts DC, Wessler SR, Paterson AH: Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. http://www.ncbi.nlm.nih.gov/entrez (2001).
49. Peterson D.G., Schulze S.R., Sciara E.B., Lee S.A., Bowers J.E., Nagel A., Jiang N., Tibbitts D.C., Wessler S.R., Paterson A.H. Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res. 12:2002;795-807 Merger of a classic approach with modern methods to 'fractionate' genomes based on the degree of repetition of DNA element families. Together with [47], this illustrates an alternative to 'genomic shotgun sequencing' that may permit us to economically access the sequence complexity (set of unique sequences) in large, highly-repetitive genomes.
50. Yuan Y.N., SanMiguel P.J., Bennetzen J.L. High-Cot sequence analysis of the maize genome. Plant J. 34:2003;249-255.
51. Rabinowicz P.D., McCombie W.R., Martienssen R.A. Gene enrichment in plant genomic shotgun libraries. Curr. Opin. Plant Biol. 6:2003;150-156.
52. Altshuler D., Pollara V.J., Cowles C.R., Van Etten W.J., Baldwin J., Linton L., Lander E.S. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature. 407:2000;513-516.
53. Jordan B., Charest A., Dowd J.F., Blumenstiel J.P., Yeh R.F., Osman A., Housman D.E., Landers J.E. Genome complexity reduction for SNP genotyping analysis. Proc. Natl. Acad. Sci. U.S.A. 99:2002;2942-2947 A promising reduced-representation method to rapidly identify sufficient populations of SNPs for genetic mapping of genomes for which a minimum of a priori information exists.
54. Goodman R.M., Naylor R., Tefera H., Nelson R., Falcon W. The rice genome and the minor grains. Science. 296:2002;1801.
55. Yuan Q.P., Quackenbush J., Sultana R., Pertea M., Salzberg S.L., Buell C.R. Rice bioinformatics. Analysis of rice sequence data and leveraging the data to other plant species. Plant Physiol. 125:2001;1166-1174.
56. Yamada T., Kishida T. Genetic analysis of forage grasses based on heterologous RFLP markers detected by rice cDNAs. Plant Breed. 122:2003;57-60.
57. Spielmeyer W., Ellis M.H., Chandler P.M. Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene. Proc. Natl. Acad. Sci. U.S.A. 99:2002;9043-9048.
58. Lukens L., Doebley J. Molecular evolution of the teosinte branched gene among maize and related grasses. Mol. Biol. Evol. 18:2001;627-638.
59. Paterson A.H., Bowers J.E., Burow M.D., Draye X., Elsik C.G., Jiang C.X., Katsar C.S., Lan T.H., Lin Y.R., Ming R.G.et al. Comparative genomics of plant chromosomes. Plant Cell. 12:2000;1523-1539.
60. Paterson A.H., Lin Y.R., Li Z.K., Schertz K.F., Doebley J.F., Pinson S.R.M., Liu S.C., Stansel J.W., Irvine J.E. Convergent domestication of cereal crops by independent mutations at corresponding genetic-loci. Science. 269:1995;1714-1718.
61. Mitra R., Bhatia C.R. Repeated and non-repeated nucleotide sequences in polyploid wheat species. Heredity. 31:1973;251-262.
62. Smith D.B., Flavell R.B. Nucleotide sequence organisation in the rye genome. Biochim. Biophys. Acta. 474:1977;82-97.
63. Wimpee C.F., Rawson J.R.Y. Characterization of the nuclear genome of pearl-millet. Biochim. Biophys. Acta. 562:1979;192-206.
64. Hake S., Walbot V. The genome of Zea-Mays, its organization and homology to related grasses. Chromosoma. 79:1980;251-270.
65. Gupta V.S., Gadre S.R., Ranjekar P.K. Novel DNA-sequence organization in rice genome. Biochim. Biophys. Acta. 656:1981;147-154.