Rice as a model for cereal genomics

Current Opinion in Plant Biology

Volumn 2, Issue 2, 1999, Pages 86-89

  Goff, Stephen A ^a  

^a SYNGENTA BIOTECHNOLOGY INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE SEQUENCING; PLANT GENOME; RICE;

EMBRYOPHYTA;

EID: 0033118587     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5266(99)80018-1     Document Type: Article

References (38)

1. 1. Ahn S, Anderson JA, Sorrells ME, Tanksley SD: Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet 1993, 241:483-490.
2. 2. Havukkala IJ: Cereal genome analysis using rice as a model. Curr Opin Genet Dev 1996, 6:711-714.
3. 3. On the World Wide Web URL: http://www.ncbi.nlm.nih.gov/dbEST/ index.html
4. 4. Sasaki T: The rice genome project in Japan. Proc Natl Acad Sci USA 1998, 95:2027-2028.
5. 5. dbEST on World Wide Web URL: http://bioserver.myogji.ac.kr/rice.html
6. 6. Yamamoto K, Sasaki T: Large-scale EST sequencing in rice. Plant Mol Biol 1997, 35:135-144.
7. 7. Brookhaven National Lab Genome FTP server on World Wide Web URL: ftp://genome1.bio.bnl.gov/pub/maize/RiceProject.html
8. 8. Brookhaven National Lab Genome FTP server on World Wide Web URL: ftp://genome1.bio.bnl.gov/pub/maize/rice.html
9. 9. National Science Foundation on World Wide Web URL: http://www.nsf.gov/bio/pubs/awards/genome98.html
10. 10. Zhang HB, Wing RA: Physical mapping of the rice genome with BACs. Plant Mol Biol 1997, 35:115-127.
11. 11. Hong G: A rapid and accurate strategy for rice contig map construction by combination of fingerprinting and hybridization. Plant Mol Biol 1997, 35:129-133.
12. 12. Hong G, Qian Y, Yu S, Hu X, Zhu J, Tao W, Li W, Su C, Zhao H, Qiu L et al.: A 120 kilobase resolution contig map of the rice genome. DNA Sequence 1997, 7:319-335.
13. 13. Kurata N, Umehara Y, Tanoue H, Sasaki T: Physical mapping of the rice genome with YAC clones. Plant Mol Biol 1997, 35:101-113.
14. 14. Clemson University Genomics Institute on the World Wide Web URL: http://www.genome.clemson.edu/
15. 15. Vandeynze AE, Sorrells ME, Park WD, Ayres NM, Fu H, Cartinhour SW, Paul E, McCouch SR: Anchor probes for comparative mapping of grass genera. Theoret Appl Genet 1998, 97:356-369.
16. 16. Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A et al.: A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 1998, 148:479-494. This paper summarizes an extensive effort to increase the number of molecular markers available to rice breeders and researchers interested in comparative genomics. This collection of markers will be very valuable for gaining access to the genetic diversity in ancestral populations.
17. 17. Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SE et al.: Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 1994, 138:1251-1274.
18. 18. Ahn S, Tanksley SD: Comparative linkage maps of the rice and maize genomes. Proc Nat Acad Sci USA 1993, 90:7980-7984.
19. 19. Moore G, Foote T, Helentjaris T, Devos K, Kurata N, Gale M: Was there a single ancestral chromosome? Trends Genet 1995, 11:81-82.
20. 20. Moore G: Cereal genome evolution: pastoral pursuits with 'Lego' genomes. Curr Opin Genet Devel 1995, 5:717-724.
21. 21. Moore G, Aragon-Alcaide L, Roberts M, Reader S, Miller T, Foote T: Are rice chromosomes components of a holocentric chromosome ancestor? Plant Mol Biol 1997, 35:17-23.
22. 22. Van Deynze AE, Nelson JC, O'Donoughue LS, Ahn SN, Siripoonwiwat W, Harrington SE, Yglesias ES, Braga DP, McCouch SR, Sorrells ME: Comparative mapping in grasses. Oat relationships. Mol Gen Genet 1995, 249:349-356.
23. 23. Van Deynze AE, Nelson JC, Yglesias ES, Harrington SE, Braga DP, McCouch SR, Sorrells ME: Comparative mapping in grasses. Wheat relationships. Mol Gen Genet 1995, 248:744-754.
24. 24. Bennetzen JL, Freeling M: Grasses as a single genetic system: genome composition, colinearity and compatibility. Trends Genet 1993, 9:259-261.
25. 25. Chen M, SanMiguel P, Bennetzen JL: Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 1998, 148:435-443. This paper further describes the microcolinearity or sequence level synteny of sorghum. The data presented in this paper provide further evidence that the rice genome can act as a model for other cereal genomes at a sequence level. The results suggest that several other regions of the genomes of cereals should be examined and compared on a sequence level. Provided that a similar level of conservation of sequence is found in other parts of various cereal genomes, comparative genomics studies may be approached by a variety of available molecular techniques.
26. 26. Chen M, SanMiguel P, de Oliveira AC, Woo SS, Zhang H, Wing RA, Bennetzen JL: Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc Nat Acad Sci USA 1997, 94:3431-3435. This paper describes the sequence level synteny of rice with maize and sorghum. As in the above paper, selected regions of the genomes of various cereals were found to be conserved, whereas non-coding regions were more divergent. The data presented in this and the above paper bring the comparison of cereal genomes down to a sequence based level, and suggest many additional experiments as well as possible approaches in comparative genomics.
27. 27. Avramova Z, Tikhonov A, Chen M, Bennetzen JL: Matrix attachment regions and structural colinearity in the genomes of two grass species. Nucleic Acids Res 1998, 26:761-767.
28. 28. Leister D, Kurth J, Laurie DA, Yano M, Sasaki T, Devos K, Graner A, Schulze-Lefert P: Rapid reorganization of resistance gene homologues in cereal genomes. Proc Natl Acad Sci USA 1998, 95:370-375. The data presented in this paper demonstrate that not all the regions of the genomes of cereals will be conserved in the coding regions. There is a rapid reorganization of genes involved in responses to disease pressure. Such rapid rearrangements will probably also occur in other genes under strong selective pressure. Regions of cereal genomes with such rearrangements may be of particular interest for comparative genomic studies.
29. 29. Kilian A, Kudrna DA, Kleinhofs A, Yano M, Kurata N, Steffenson B, Sasaki T: Rice-barley synteny and its application to saturation mapping of the barley Rpg1 region. Nucleic Acids Res 1995, 23:2729-2733.
30. 30. Kilian A, Chen J, Han F, Steffenson B, Kleinhofs A: Towards map-based cloning of the barley stem rust resistance genes Rpg1 and rpg4 using rice as an intergenomic cloning vehicle. Plant Mol Biol 1997, 35:187-195.
31. 31. Xiao JH, Li JM, Grandillo S, Ahn SN, Yuan LP, Tanksley SD, McCouch SR: Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. Genetics 1998, 150:899-909. This paper presents data of broad interest supporting the application of molecular breeding approaches toward crop improvement. Through the use of molecular marker technology, these researchers have shown that phenotypically poor wild relatives of commercial plant varieties carry genes that can have a strong impact on yield enhancement.
32. 32. Han F, Kleinhofs A, Ullrich SE, Kilian A, Yano M, Sasaki T: Synteny with rice - analysis of barley malting quality QTLs and RPG4 chromosomal regions. Genome 1998, 41:373-380.
33. 33. Zwick MS, Islam-Faridi MN, Czeschin DG, Wing RA, Hart GE, Stelly DM, Price HJ: Physical mapping of the liguless linkage group in Sorghum bicolor using rice RFLP-selected sorghum BACs. Genetics 1998, 148:1983-1992.
34. 34. Christou P, Ford TL, Kofron M: Production of transgenic rice (Oryza sativa L.) plants from agronomically important Indica and Japonica varieties via electric discharge particle acceleration of exogenous DNA into immature zygotic embryos. Bio-Technology 1991, 9:957-962.
35. 35. Chen L, Marmey P, Taylor NJ, Brizard JP, Espinosa C, D'Cruz P, Huet H, Zhang S, de Kochko A, Beachy RN, Fauquet CM: Expression and inheritance of multiple transgenes in rice plants. Nat Biotechnol 1998, 16:1060-1064.
36. 36. Laurie Kramers mapview on World Wide Web URL: http:// gdbwww.gdb.org/gdb/MapviewReleaseNotes.html
37. 37. Integrated Rice Genome Explorer on World Wide Web URL: http://www.staff.or.jp/INE.html
38. 38. The Genome Database on World Wide Web URL: http://gdbwww.gdb.org/