Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny

Functional and Integrative Genomics

Volumn 4, Issue 2, 2004, Pages 102-117

  Singh, Nagendra K ^a   Raghuvanshi, Saurabh ^b   Srivastava, Subodh K ^a   Gaur, Anupama ^b   Pal, Ajit K ^a   Dalal, Vivek ^a   Singh, Archana ^a   Ghazi, Irfan A ^a   Bhargav, Ashutosh ^a   Yadav, Mahavir ^a   Dixit, Anupam ^a   Batra, Kamlesh ^a   Gaikwad, Kishor ^a   Sharma, Tilak R ^a   Mohanty, Amitabh ^b   Bharti, Arvind K ^b   Kapur, Anita ^b   Gupta, Vikrant ^b   Kumar, Dibyendu ^b   Vij, Shubha ^b   Vydianathan, Ravi ^b   Khurana, Parul ^b   Sharma, Sulabha ^b   McCombie, W Richard ^c   Messing, Joachim ^d   Wing, Rod ^e   Sasaki, Takuji ^f   Khurana, Paramjit ^b   Mohapatra, Trilochan ^a   Khurana, Jitendra P ^b   Tyagi, Akhilesh K ^b   more..

^a NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY   (India)

^b UNIVERSITY OF DELHI   (India)

^c Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^d RUTGERS UNIVERSITY   (United States)

^e UNIVERSITY OF ARIZONA   (United States)

^f NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

Author keywords

Plant genome; Rice; Synteny; Wheat

Indexed keywords

COMPLEMENTARY DNA; CONTIG;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME 11Q; CHROMOSOME ABERRATION; CHROMOSOME ANALYSIS; CHROMOSOME TRANSLOCATION; COMPUTER PROGRAM; DNA SEQUENCE; DNA TRANSPOSITION; EXPRESSED SEQUENCE TAG; GENE DUPLICATION; GENE LOCATION; GENE MAPPING; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CONSERVATION; HEXAPLOIDY; MOLECULAR CLONING; NONHUMAN; PLANT GENETICS; PRIORITY JOURNAL; RICE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SYNTENY; WHEAT; CHROMOSOME MAP; GENETIC MARKER; GENETICS; NUCLEOTIDE SEQUENCE;

TRITICUM AESTIVUM;

BASE SEQUENCE; CHROMOSOME MAPPING; CONSERVED SEQUENCE; GENETIC MARKERS; ORYZA SATIVA; SEQUENCE ANALYSIS, DNA; SYNTENY; TRITICUM;

EID: 3242799971     PISSN: 1438793X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10142-004-0109-y     Document Type: Article

References (26)

1. Ahn S, Anderson JA, Sorrells ME, Tanksley SD (1993) Homoeologous relationships of rice, wheat, and maize chromosomes. Mol Gen Genet 241:483-490 1:CAS:528:DyaK2cXkt1yhuro%3D
2. Appels R, Francki M, Chibbar R (2003) Advances in cereal functional genomics. Funct Integr Genomics 3:1-24 1:CAS:528:DC%2BD3sXht1CktL8%3D
3. Bennetzen JL, Freeling M (1993) Grasses as a single genetic system: genome composition, colinearity and compatibility. Trends Genet 9:259-261 1:STN:280:ByyA1M3it1w%3D
4. Bennetzen JL, Ramakrishna W (2002) Numerous small rearrangements of gene content, order, and orientation differentiate grass genomes. Plant Mol Biol 48:821-827
5. Bowers JE, Chapman BE, Rong J, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433-537 10.1038/nature01521
6. Chen M, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S, Higingbottom S, Phimphilai J, Phimphilai D, Thurmond S, Gaudette B, Li P, Liu J, Hatfield J, Main D, Farrar K, Henderson C, Barnett L, Costa R, Williams B, Walser S, Atkins M, Hall C, Budiman MA, Tomkins JP, Luo M, Bancroft I, Salse J, Regad F, Mohapatra T, Singh NK, Tyagi AK, Soderlund C, Dean RA, Wing RA (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14:537-545 1:CAS:528:DC%2BD38XivVegt7o%3D
7. Deynze AE Van, Dubcovsky J, Gill KS, Nelson JC, Sorrells ME, Dvorak J, Gill BS, Lagudah ES, McCouch SR, Appels R (1995) Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat. Genome 38:45-59
8. Faris JD, Friebe B, Gill BS (2002) Wheat genomics: Exploring the polyploid model. Curr Genomics 3:577-591 1:CAS:528:DC%2BD38Xos1Gjsrc%3D
9. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95:1071-1974 10.1073/pnas.95.5.1971
10. 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 10.1139/gen-41-3-328
11. Gaut BS (2002) Evolutionary dynamics of grass genomes. New Phytol 154:15-28 10.1046/j.1469-8137.2002.00352.x
12. Han F, Kilian A, Chao 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 10.1139/ gen-42-6-1071
13. Heslop-Harrison JS (2000) Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell 12:617-635 10.1105/tpc.12.5.617
14. Islam AKMR, Shepherd KW (1992) Substituting ability of individual barley chromosomes for wheat chromosomes 1 substitutions involving barley chromosomes 1, 3 and 6. Plant Breed 109:141-150
15. Kihara H (1924) Cytologische und genetische Studien bei wichtigen Getreidearten mit besonderer Ruckischt auf das Verhalten der Chromosomen und die Sterilitat in den Bastarden. Mem Coll Sci Kyoto Imp Univ Ser B 1:1-200
16. Klein PE, Klein RR, Vrebalov J, Mullet JE (2003) Sequence-based alignment of sorghum chromosome 3 and rice chromosome 1 reveals extensive conservation of gene order and one major chromosomal rearrangement. Plant J 34:605-621 10.1046/j.1365-313X.2003.01751.x
17. Kurata N, Moore G, Nagamura Y, Foote T, Yano M, Minobe Y, Gale M (1994) Conservation of genome structure between rice and wheat. Bio/Technology 12:276-278
18. Ozkan H, Levy AA, Feldman M (2001) Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops - Triticum) group. Plant Cell 13:1735-1747 1:CAS:528:DC%2BD3MXmsFKiurg%3D
19. Paterson AH, Bowers JE, Burow MD, Draye X, Elsik CG, Jiang C-X, Katsar CS, Lan TH, Lin YR, Ming R, Wright RJ (2000) Comparative genomics of plant chromosomes. Plant Cell 12:1523-1539 1:CAS:528:DC%2BD3cXnsVylsbk%3D
20. Qi L, Echalier B, Friebe B, Gill BS (2003) Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs. Funct Integr Genomics 3:39-55 1:CAS:528:DC%2BD3sXht1CktLo%3D
21. Sakata K, Nagamura Y, Numa H, Antonio BA, Nagasaki H, Idonuma A, Watanabe W, Shimizu Y, Horiuchi I, Matsumoto T, Sasaki T, Higo K (2002) RiceGAAS: An automated annotation system and database for rice genome sequence. Nucleic Acids Res 30:98-102 10.1093/nar/30.1.98
22. Sears ER (1941) Chromosome pairing and fertility in hybrids and amphidiploids in the Triticinae. Mo Agric Exp Stn Res Bull 337:1-20
23. Song R, Llaca V, Messing J (2002) Mosaic organization of orthologous sequences in grass genomes. Genome Res 12:1549-1555 10.1101/gr.268302
24. Sorrells ME, Rota ML, Bermudez-Kandianis CE, Greene RA, Kantety R, Munkvold JD, Mahmoud MA, Ma X, Gustafson PJ, Qi LL, Echalier B, Gill BS, Matthews DE, Lazo GR, Chao S, Anderson OD, Edwards H, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorak J, Zhang D, Nguyen HT, Peng J, Lapitan NLV, Gonzalez-Hernandez JL, Anderson JA, Hossain K, Kalavacharla V, Kianian SF, Choi D-W, Close TJ, Dilbirligi M, Gill KS, Steber C, Walker-Simmons MK, McGuire PE, Qualset CO (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1818-1827 1:CAS:528:DC%2BD3sXmsVWqt7c%3D
25. Vandepoele K, Simillion C, Van de Peer Y (2003) Evidence that rice and other cereals are ancient aneuploids. Plant Cell 15:2192-2202 10.1105/ tpc.014019
26. Wicker T, Yahiaoui N, Guyot R, Schlagenhauf E, Liu Z-D, Dubcovsky J, Keller B (2003) Rapid genome divergence at orthologous low molecular weight glutelin loci of the A and A M genomes of wheat. Plant Cell 15:1186-1197 10.1105/tpc.011023