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

Volumn 165, Issue 1, 2003, Pages 367-386

  Bowers, John E ^a   Abbey, Colette ^b   Anderson, Sharon ^b   Chang, Charlene ^b   Draye, Xavier ^b   Hoppe, Alison H ^b   Jessup, Russell ^b   Lemke, Cornelia ^a   Lennington, Jennifer ^b   Li, Zhikang ^b   Lin, Yann Rong ^b   Liu, Sin Chieh ^b   Luo, Lijun ^b   Marler, Barry S ^a   Ming, Reiguang ^b   Mitchell, Sharon E ^c   Qiang, Dou ^b   Reischmann, Kim ^b   Schulze, Stefan R ^a   Skinner, D Neil ^a   Wang, Yue Wen ^b   Kresovich, Stephen ^c   Schertz, Keith F ^b   Paterson, Andrew H ^a,b   more..

^a UNIVERSITY OF GEORGIA   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c Cornell University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA;

ARTICLE; BIOMASS; CROP; DNA POLYMORPHISM; EVOLUTION; GENE LOCUS; GENE MAPPING; GENE REARRANGEMENT; GENETIC RECOMBINATION; GENOMICS; GRAIN; GRASS; MAIZE; NONHUMAN; PLANT; PRIORITY JOURNAL; RICE; SEQUENCE TAGGED SITE; SORGHUM;

CHROMOSOME MAPPING; EVOLUTION; GENES, DOMINANT; GENETIC MARKERS; GENOME, PLANT; HYBRIDIZATION, GENETIC; POACEAE; RECOMBINATION, GENETIC; SEQUENCE TAGGED SITES; SORGHUM;

ARABIDOPSIS; HORDEUM VULGARE SUBSP. VULGARE; ORYZA; PENNISETUM; PENNISETUM CILIARE; POACEAE; SACCHARUM; SACCHARUM HYBRID CULTIVAR; SECALE CEREALE; SORGHUM BICOLOR; SORGHUM PROPINQUUM; TRITICEAE; TRITICUM AESTIVUM; ZEA; ZEA MAYS;

EID: 12444347410     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (55)

1. ANNEN, F., J. L. CHANG, A. H. PATERSON and J. L. STOCKHAUS, 1998 Characterization of 14 different putative protein kinase cDNA clones of the C-4 plant Sorghum bicolor. Mol. Gen. Genet. 259: 115-122.
2. ARUMUGANATHAN, K., and E. EARLE, 1991 Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9: 208-218.
3. ASHBURNER, M., C. A. BALL, J. A. BLAKE, D. BOTSTEIN, H. BUTLER et al., 2000 Gene ontology: tool for the unification of biology. Nat. Genet. 25: 25-29.
4. BENNETZEN, J. L., 2000 Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 12: 1021-1029.
5. CAI, W., J. RENEKER, C. CHOW, M. VAISHNAV and A. BRADLEY, 1998 An anchored framework BAC map of mouse chromosome 11 assembled using multiplex oligonucleotide hybridization. Genomics 54: 387-397.
6. BOIVIN, K., M. DEU, J. F. RAMI, G. TROUCHE and P. L. HAMON, 1999 Towards a saturated sorghum map using RFLP and AFLP markers. Theor. Appl. Genet. 98: 320-328.
7. CHITTENDEN, L. M., K. F. SCHERTZ, Y. R. LIN, R. A. WING and A. H. PATERSON, 1994 A detailed RFLP map of Sorghum bicolor X S. propinquum, suitable for high-density mapping, suggests ancestral duplication of sorghum chromosomes or chromosomal segments. Theor. Appl. Genet. 87: 925-933.
8. DAVIS, G. L., M. D. MCMULLEN, C. BAYSDORFER, T. MUSKET, D. GRANT et al., 1999 A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map. Genetics 152: 1137-1172.
9. DEWET, J. M. J., S. C. GUPTA, J. R. HARLAN and C. O. GRASSL, 1976 Cytogenetics of introgression from Saccharum into Sorghum. Crop Science 16: 568-572.
10. DRAYE, X., Y.-R. LIN, X. Y. QIAN, J. E. BOWERS, G. B. BUROW et al., 2001 Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the Sorghum genome as a foundation. Plant Physiol. 125: 1325-1341.
11. DUFOUR, P., L. GRIVET, A. DHONT, M. DEU, G. TROUCHE et al., 1996 Comparative genetic mapping between duplicated segments on maize chromosomes 3 and 8 and homoeologous regions in sorghum and sugarcane. Theor. Appl. Genet. 92: 1024-1030.
12. DUFOUR, P., M. DEU, L. GRIVET, A. DHONT, F. PAULET et al., 1997 Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid. Theor. Appl. Genet. 94: 409-418.
13. DVORAK, J., M. C. LUO and Z. L. YANG, 1998 Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing Aegilops species. Genetics 148: 423-434.
14. FAS, 2001 World sugar situation. U.S. Department of Agriculture, Foreign Agricultural Service (http://www.fas.usda.gov/htp/sugar/ 2001/nov/sugsit.htm).
15. 2 population. Genetics 134: 917-930.
16. GAUT, B. S., 2001 Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses. Genome Res. 11: 55-66.
17. GAUT, B. S., and J. F. DOEBLEY, 1997 DNA sequence evidence for the segmental allotetraploid origin of Maize. Proc. Natl. Acad. Sci. USA 94: 6809-6814.
18. GOFF, S. A., D. RICKE, T. H. LAN, G. PRESTING, R. L. WANG et al., 2002 A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 296: 92-100.
19. HAMBLIN, M. T., and C. F. AQUADRO, 1999 DNA sequence variation and the recombinational landscape in Drosophila pseudoobscura: a study of the second chromosome. Genetics 153: 859-869.
20. HAUSSMANN, B. I. G., D. E. HESS, N. SEETHARAMA, H. G. WELZ and H. H. GEIGER, 2002 Construction of a combined sorghum linkage map from two recombinant inbred populations using AFLP, SSR, RFLP, and RAPD markers, and comparison with other sorghum maps. Theor. Appl. Genet. 105: 629-637.
21. KATSAR, C. S., A. H. PATERSON, G. L. TEETES and G. C. PETERSON, 2002 Molecular analysis of Sorghum resistance to the greenbug (Homoptera: Aphididae). J. Econ. Entomol. 95: 448-457.
22. KISHIMOTO, N., H. HIGO, K. ABE, S. ARAI, A. SAITO et al., 1994 Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions. Theor. Appl. Genet. 88: 722-726.
23. KOSAMBI, D., 1944 The estimation of map distance from recombination values. Ann. Eugen. 12: 172-175.
24. LANDER, E., J. ABRAHAMSON, A. BARLOW, M. DALY, S. LINCOLN et al., 1987 Mapmaker: a computer package for constructing genetic-linkage maps. Genomics 1: 174-181.
25. LIN, Y., K. SCHERTZ and A. PATERSON, 1995 Comparative analysis of QTLs affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population. Genetics 141: 391-411.
26. LIN, Y., L. ZHU, S. REN, J. YANG, K. SCHERTZ et al., 1999 A Sorghum propinquum BAC library, suitable for cloning genes associated with loss-of-function mutations during crop domestication. Mol. Breed. 5: 511-520.
27. LINDER, H. P., 1987 The evolutionary history of the Poales/Restionales - a hypothesis. Kew Bull. 42: 297-318.
28. MCWHORTER, C. G., 1971 Introduction and spread of Johnsongrass in United States. Weed Sci. 19: 496.
29. MENZ, M. A., R. R. KLEIN, J. E. MULLET, J. A. OBERT, N. C. UNRUH et al., 2002 A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP (R), RFLP and SSR markers. Plant Mol. Biol. 48: 483-499.
30. MILLER, J. T., F. G. DONG, S. A. JACKSON, J. SONG and J. M. JIANG, 1998 Retrotransposon-related DNA sequences in the centromeres of grass chromosomes. Genetics 150: 1615-1623.
31. MING, R., S. LIU, Y. LIN, J. DASILVA, W. WILSON et al., 1998 Alignment of the Sorghum and Saccharum chromosomes: comparative genome organization and evolution of a polysomic polyploid genus and its diploid cousin. Genetics 150: 1663-1682.
32. MING, R., S. C. LIU, J. E. BOWERS, P. H. MOORE, J. E. IRVINE et al., 2002 Construction of a Saccharum consensus genetic map from two interspecific crosses. Crop Sci. 42: 570-583.
33. NAGAMURA, Y., T. INOUE, B. ANTONIO, T. SHIMANO, H. KAJIYA et al., 1995 Conservation of duplicated segments between rice chromosomes 11 and 12. Breed. Sci. 45: 373-376.
34. PATERSON, A., Y. LIN, Z. LI, K. SCHERTZ, J. DOEBLEY et al., 1995a Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269: 1714-1718.
35. PATERSON, A., K. SCHERTZ, Y. LIN, S. LIU and Y. CHANG, 1995b The weediness of wild plants: molecular analysis of genes influencing dispersal and persistence of johnsongrass, Sorghum halepense (L.) Pers. Proc. Natl. Acad. Sci. USA 92: 6127-6131.
36. PATERSON, A., J. BOWERS, M. BUROW, X. DRAYE, C. ELSIK et al., 2000 Comparative genomics of plant chromosomes. Plant Cell 12: 1523-1539.
37. PENG, Y., K. F. SCHERTZ, S. CARTINHOUR and G. E. HART, 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.
38. PEREIRA, M. G., M. LEE, P. BRAMEL-COX, W. WOODMAN, J. DOEBLEY et al., 1994 Construction of an RFLP map in sorghum and comparative mapping in maize. Genome 37: 236-243.
39. PETERSON, D. G., S. R. SCHULZE, E. B. SCIARA, S. A. LEE, J. E. BOWERS et al., 2002 Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res. 12: 795-807.
40. RAGAB, R. A., S. DRONAVALLI, M. A. S. MAROOF and Y. G. L. YU, 1994 Construction of a sorghum RFLP linkage map using sorghum and maize DNA probes. Genome 37: 590-594.
41. SCHLOSS, S. J., S. E. MITCHELL, G. M. WHITE, R. KUKUATALA, J. E. BOWERS et al., 2002 Characterization of RFLP probe sequences for gene discovery and SSR development in Sorghum bicolor (L.) Moench. Theor. Appl. Genet. 105: 912-920.
42. SHISHIDO, R., Y. SANO and K. FUKUI, 2000 Ribosomal DNAs: an exception to the conservation of gene order in rice genomes. Mol. Gen. Genet. 263: 586-591.
43. SINGH, R. J., H. H. KIM and T. HYMOWITZ, 2001 Distribution of rDNA loci in the genus Glycine Willd. Theor. Appl. Genet. 103: 212-218.
44. SMITH, C. W., and R. A. FREDERIKSEN, 2000 Sorghum: Origin, History, Technology and Production. John Wiley & Sons, New York.
45. SOBRAL, B. W. S., D. P. V. BRAGA, E. S. LAHOOD and P. KEIM, 1994 Phylogenetic analysis of chloroplast restriction enzyme site mutations in the Saccharinae Griseb subtribe of the Andropogoneae Dumort tribe. Theor. Appl. Genet. 87: 843-853.
46. SUBUDHI, P. K., and H. T. NGUYEN, 2000 Linkage group alignment of sorghum RFLP maps using a RIL mapping population. Genome 43: 240-249.
47. THOMASSON, J. R., 1987 Fossil grasses, 1820-1986 and beyond, pp. 159-167 in Grass Systematics and Evolution, edited by T. R. SODERSTROM, K. W. HILU, C. S. CAMPBELL and M. E. BARKWORTH. Smithsonian Institution Press, Washington, DC.
48. TIKHONOV, A. P., J. L. BENNETZEN and Z. V. AVRAMOVA, 2000 Structural domains and matrix attachment regions along colinear chromosomal segments of maize and sorghum. Plant Cell 12: 249-264.
49. WHITKUS, R., J. DOEBLEY and M. LEE, 1992 Comparative genome mapping of sorghum and maize. Genetics 132: 1119-1130.
50. WYRICH, R., U. DRESSEN, S. BROCKMANN, M. STREUBEL, C. CHANG et al., 1998 The molecular basis of C-4 photosynthesis in sorghum: isolation, characterization and RFLP mapping of mesophyll- and bundle-sheath-specific cDNAs obtained by differential screening. Plant Mol. Biol. 37: 319-335.
51. XU, G. W., C. W. MAGILL, K. F. SCHERTZ and G. E. HART, 1994 A RFLP linkage map of Sorghum bicolor (L) Moench. Theor. Appl. Genet. 89: 139-145.
52. YU, J., S. N. HU, J. WANG, G. K. S. WONG, S. G. LI et al., 2002 A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 296: 79-92.
53. ZAMIR, D., and S. TANKSLEY, 1988 Tomato genome is comprised largely of fast-evolving, low copy-number sequences. Mol. Gen. Genet. 213: 254-261.
54. ZDOBNOV, E. M., and R. APWEILER, 2001 InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848.
55. ZWICK, M. S., M. N. ISLAM-FARIDI, H. B. ZHANG, G. L. HODNETT, M. I. GOMEZ et al., 2000 Distribution and sequence analysis of the centromere-associated repetitive element CEN38 of Sorghum bicolor (Poaceae). Am. J. Bot. 87: 1757-1764.