Table of Contents
International Journal of Plant Genomics
Volume 2008, Article ID 362451, 6 pages
http://dx.doi.org/10.1155/2008/362451
Review Article

Genomics of Sorghum

Plant Genome Mapping Laboratory, Department of Crop and Soil Sciences, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA

Received 26 April 2007; Accepted 13 January 2008

Academic Editor: Yunbi Xu

Copyright © 2008 Andrew H. Paterson. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. A. E. Farrell, R. J. Plevin, B. T. Turner, A. D. Jones, M. O'Hare, and D. M. Kammen, “Ethanol can contribute to energy and environmental goals,” Science, vol. 311, no. 5760, 506 pages, 2006. View at Publisher · View at Google Scholar
  2. P. Wagoner, “Perennial grain development: past efforts and potential for the future,” Critical Reviews in Plant Sciences, vol. 9, no. 5, 381 pages, 1990. View at Google Scholar
  3. P. L. Scheinost, D. L. Lammer, X. Cai, T. D. Murray, and S. S. Jones, “Perennial wheat: the development of a sustainable cropping system for the U.S. Pacific Northwest,” American Journal of Alternative Agriculture, vol. 16, no. 4, 147 pages, 2001. View at Google Scholar
  4. A. H. Paterson, K. F. Schertz, Y.-R. Lin, S.-C. Liu, and Y.-L. Chang, “The weediness of wild plants: molecular analysis of genes influencing dispersal and persistence of johnsongrass, Sorghum halepense (L.) Pers,” Proceedings of the National Academy of Sciences of the United States of America, vol. 92, no. 13, 6127 pages, 1995. View at Publisher · View at Google Scholar
  5. F. Y. Hu, D. Y. Tao, E. Sacks et al., “Convergent evolution of perenniality in rice and sorghum,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 7, 4050 pages, 2003. View at Publisher · View at Google Scholar
  6. S. Kresovich, B. Barbazuk, J. A. Bedell et al., “Toward sequencing the Sorghum genome. A U.S. National Science Foundation-sponsored workshop report,” Plant Physiology, vol. 138, no. 4, 1898 pages, 2005. View at Publisher · View at Google Scholar
  7. L. G. Holm, D. L. Plucknett, J. V. Pancho, and J. P. Herberger, The World's Worst Weeds: Distribution and Biology, University Press of Hawaii, Honolulu, Hawaii, USA, 1977.
  8. B. S. Gaut, L. G. Clark, J. F. Wendel, and S. V. Muse, “Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae),” Molecular Biology and Evolution, vol. 14, no. 7, 769 pages, 1997. View at Google Scholar
  9. Z. Swigonová, J. Lai, J. Ma et al., “Close split of sorghum and maize genome progenitors,” Genome Research, vol. 14, no. 10, 1916 pages, 2004. View at Publisher · View at Google Scholar
  10. A. H. Paterson, J. E. Bowers, and B. A. Chapman, “Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 26, 9903 pages, 2004. View at Publisher · View at Google Scholar
  11. B. W. S. Sobral, D. P. V. Braga, E. S. LaHood, and P. Keim, “Phylogenetic analysis of chloroplast restriction enzyme site mutations in the Saccharinae griseb. subtribe of the Andropogoneae Dumort. tribe,” Theoretical and Applied Genetics, vol. 87, no. 7, 843 pages, 1994. View at Publisher · View at Google Scholar
  12. R. Ming, S.-C. Liu, Y.-R. Lin et al., “Detailed alignment of saccharum and sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes,” Genetics, vol. 150, no. 4, 1663 pages, 1998. View at Google Scholar
  13. J. M. J. de Wet, S. C. Gupta, J. R. Harlan, and C. O. Grassl, “Cytogenetics of introgression from Saccharum into Sorghum,” Crop Science, vol. 16, 568 pages, 1976. View at Google Scholar
  14. Z. Swigonová, J. Lai, J. Ma et al., “On the tetraploid origin of the maize genome,” Comparative and Functional Genomics, vol. 5, no. 3, 281 pages, 2004. View at Publisher · View at Google Scholar
  15. G.-W. Xu, C. W. Magill, K. F. Schertz, and G. E. Hart, “A RFLP linkage map of Sorghum bicolor (L.) Moench,” Theoretical and Applied Genetics, vol. 89, no. 2-3, 139 pages, 1994. View at Publisher · View at Google Scholar
  16. D. Bhattramakki, J. Dong, A. K. Chhabra, and G. E. Hart, “An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench,” Genome, vol. 43, no. 6, 988 pages, 2000. View at Publisher · View at Google Scholar
  17. P. E. Klein, R. R. Klein, S. W. Cartinhour et al., “A high-throughput AFLP-based method for constructing integrated genetic and physical maps: progress toward a sorghum genome map,” Genome Research, vol. 10, no. 6, 789 pages, 2000. View at Publisher · View at Google Scholar
  18. M. A. Menz, R. R. Klein, J. E. Mullet, J. A. Obert, N. C. Unruh, and P. E. Klein, “A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP®, RFLP and SSR markers,” Plant Molecular Biology, vol. 48, no. 5-6, 483 pages, 2002. View at Publisher · View at Google Scholar
  19. L. M. Chittenden, K. F. Schertz, Y.-R. Lin, R. A. Wing, and A. H. Paterson, “A detailed RFLP map of Sorghum bicolor X S.propinquum, suitable for high-density mapping, suggests ancestral duplication of Sorghum chromosomes or chromosomal segments,” Theoretical and Applied Genetics, vol. 87, no. 8, 925 pages, 1994. View at Publisher · View at Google Scholar
  20. J. E. Bowers, C. Abbey, S. Anderson 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, vol. 165, no. 1, 367 pages, 2003. View at Google Scholar
  21. F. A. Feltus, G. E. Hart, K. F. Schertz et al., “Genetic map alignment and QTL correspondence between inter- and intra-specific sorghum populations,” Theoretical and Applied Genetics, vol. 112, no. 7, 1295 pages, 2006. View at Publisher · View at Google Scholar
  22. J.-S. Kim, P. E. Klein, R. R. Klein, H. J. Price, J. E. Mullet, and D. M. Stelly, “Chromosome identification and nomenclature of Sorghum bicolor,” Genetics, vol. 169, no. 2, 1169 pages, 2005. View at Publisher · View at Google Scholar
  23. A. H. Paterson, Y.-R. Lin, Z. Li et al., “Convergent domestication of cereal crops by independent mutations at corresponding genetic loci,” Science, vol. 269, no. 5231, 1714 pages, 1995. View at Publisher · View at Google Scholar
  24. R. Whitkus, J. Doebley, and M. Lee, “Comparative genetic mapping of sorghum and maize,” Genetics, vol. 132, 1119 pages, 1992. View at Google Scholar
  25. P. Dufour, M. Deu, L. Grivet et al., “Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid,” Theoretical and Applied Genetics, vol. 94, no. 3-4, 409 pages, 1997. View at Publisher · View at Google Scholar
  26. R. W. Jessup, B. L. Burson, G. Burow et al., “Segmental allotetraploidy and allelic interactions in buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.) as revealed by genome mapping,” Genome, vol. 46, no. 2, 304 pages, 2003. View at Publisher · View at Google Scholar
  27. A. M. Missaoui, A. H. Paterson, and J. H. Bouton, “Investigation of genomic organization in switchgrass (Panicum virgatum L.) using DNA markers,” Theoretical and Applied Genetics, vol. 110, no. 8, 1372 pages, 2005. View at Publisher · View at Google Scholar
  28. C. M. Bethel, E. B. Sciara, J. C. Estill, J. E. Bowers, W. Hanna, and A. H. Paterson, “A framework linkage map of bermudagrass (Cynodon dactylon x transvaalensis) based on single-dose restriction fragments,” Theoretical and Applied Genetics, vol. 112, no. 4, 727 pages, 2006. View at Publisher · View at Google Scholar
  29. S.-S. Woo, J. Jiang, B. S. Gill, A. H. Paterson, and R. A. Wing, “Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor,” Nucleic Acids Research, vol. 22, no. 23, 4922 pages, 1994. View at Publisher · View at Google Scholar
  30. D. G. Peterson, S. R. Schulze, E. B. Sciara et al., “Integration of cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery,” Genome Research, vol. 12, no. 5, 795 pages, 2002. View at Publisher · View at Google Scholar
  31. K. Arumuganathan and E. Earle, “Estimation of nuclear DNA content of plants by flow cytometry,” Plant Molecular Biology Reporter, vol. 9, no. 3, 208 pages, 1991. View at Google Scholar
  32. J. E. Bowers, M. A. Arias, R. Asher et al., “Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 37, 13206 pages, 2005. View at Publisher · View at Google Scholar
  33. L. H. Pratt, C. Liang, M. Shah et al., “Sorghum expressed sequence tags identify signature genes for drought, pathogenesis, and skotomorphogenesis from a milestone set of 16,801 unique transcripts,” Plant Physiology, vol. 139, no. 2, 869 pages, 2005. View at Publisher · View at Google Scholar
  34. J. A. Bedell, M. A. Budiman, A. Nunberg et al., “Sorghum genome sequencing by methylation filtration,” PLoS Biology, vol. 3, no. 1, e13 pages, 2005. View at Publisher · View at Google Scholar
  35. Y.-R. Lin, K. F. Schertz, and A. H. Paterson, “Comparative analysis of QTLs affecting plant height and maturity across the poaceae, in reference to an interspecific sorghum population,” Genetics, vol. 141, no. 1, 391 pages, 1995. View at Google Scholar
  36. P. E. Ulanch, K. L. Childs, P. W. Morgan, and J. E. Mullet, “Molecular markers linked to Ma(1) in sorghum,” Plant Physiology, vol. 111, 709 pages, 1996. View at Google Scholar
  37. R. R. Klein, P. E. Klein, A. K. Chhabra et al., “Molecular mapping of the rf1 gene for pollen fertility restoration in sorghum (Sorghum bicolor L.),” Theoretical and Applied Genetics, vol. 102, no. 8, 1206 pages, 2001. View at Publisher · View at Google Scholar
  38. L. Wen, H. V. Tang, W. Chen et al., “Development and mapping of AFLP markers linked to the sorghum fertility restorer gene rf4,” Theoretical and Applied Genetics, vol. 104, no. 4, 577 pages, 2002. View at Publisher · View at Google Scholar
  39. R. R. Klein, P. E. Klein, J. E. Mullet, P. Minx, W. L. Rooney, and K. F. Schertz, “Fertility restorer locus Rf1 of sorghum (Sorghum bicolor L.) encodes a pentatricopeptide repeat protein not present in the colinear region of rice chromosome 12,” Theoretical and Applied Genetics, vol. 111, no. 6, 994 pages, 2005. View at Publisher · View at Google Scholar
  40. C. S. Mutengwa, P. B. Tongoona, and I. Sithole-Niang, “Genetic studies and a search for molecular markers that are linked to Striga asiatica resistance in sorghum,” African Journal of Biotechnology, vol. 4, no. 12, 1355 pages, 2005. View at Google Scholar
  41. C. L. McIntyre, R. E. Casu, J. Drenth et al., “Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance,” Genome, vol. 48, no. 3, 391 pages, 2005. View at Publisher · View at Google Scholar
  42. C. L. McIntyre, S. M. Hermann, R. E. Casu et al., “Homologues of the maize rust resistance gene Rp1-D are genetically associated with a major rust resistance QTL in sorghum,” Theoretical and Applied Genetics, vol. 109, no. 4, 875 pages, 2004. View at Publisher · View at Google Scholar
  43. D. S. Multani, R. B. Meeley, A. H. Paterson, J. Gray, S. P. Briggs, and G. S. Johal, “Plant-pathogen microevolution: molecular basis for the origin of a fungal disease in maize,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 4, 1686 pages, 1998. View at Publisher · View at Google Scholar
  44. A. S. Totad, B. Fakrudin, and M. S. Kuruvinashetti, “Isolation and characterization of resistance gene analogs (RGAs) from sorghum (Sorghum bicolor L. Moench),” Euphytica, vol. 143, no. 1-2, 179 pages, 2005. View at Publisher · View at Google Scholar
  45. M. Singh, K. Chaudhary, H. R. Singal, C. W. Magill, and K. S. Boora, “Identification and characterization of RAPD and SCAR markers linked to anthracnose resistance gene in sorghum [Sorghum bicolor (L.) Moench],” Euphytica, vol. 149, no. 1-2, 179 pages, 2006. View at Publisher · View at Google Scholar
  46. M. L. Wang, R. Dean, J. Erpelding, and G. Pederson, “Molecular genetic evaluation of sorghum germplasm differing in response to fungal diseases: rust (Puccinia purpurea) and anthracnose (Collectotrichum graminicola),” Euphytica, vol. 148, no. 3, 319 pages, 2006. View at Publisher · View at Google Scholar
  47. Y. Z. Tao, D. R. Jordan, R. G. Henzell, and C. L. McIntyre, “Identification of genomic regions for rust resistance in sorghum,” Euphytica, vol. 103, no. 3, 287 pages, 1998. View at Publisher · View at Google Scholar
  48. C. S. Katsar, R. H. Paterson, G. L. Teetes, and G. C. Peterson, “Molecular analysis of sorghum resistance to the greenbug (Homoptera: Aphididae),” Journal of Economic Entomology, vol. 95, no. 2, 448 pages, 2002. View at Google Scholar
  49. H. Agrama, G. Widle, J. Reese, L. Campbell, and M. Tuinstra, “Genetic mapping of QTLs associated with greenbug resistance and tolerance in Sorghum bicolor,” Theoretical and Applied Genetics, vol. 104, no. 8, 1373 pages, 2002. View at Publisher · View at Google Scholar
  50. N. Nagaraj, J. C. Reese, M. R. Tuinstra et al., “Molecular mapping of sorghum genes expressing tolerance to damage by greenbug (Homoptera: Aphididae),” Journal of Economic Entomology, vol. 98, no. 2, 595 pages, 2005. View at Google Scholar
  51. Y. Z. Tao, A. Hardy, J. Drenth et al., “Identifications of two different mechanisms for sorghum midge resistance through QTL mapping,” Theoretical and Applied Genetics, vol. 107, no. 1, 116 pages, 2003. View at Publisher · View at Google Scholar
  52. B. I. G. Haussmann, D. E. Hess, G. O. Omanya et al., “Genomic regions influencing resistance to the parasitic weed Striga hermonthica in two recombinant inbred populations of sorghum,” Theoretical and Applied Genetics, vol. 109, no. 5, 1005 pages, 2004. View at Publisher · View at Google Scholar
  53. W. Xu, P. K. Subudhi, O. R. Crasta, D. T. Rosenow, J. E. Mullet, and H. T. Nguyen, “Molecular mapping of QTLs conferring stay-green in grain sorghum (Sorghum bicolor L. Moench),” Genome, vol. 43, no. 3, 461 pages, 2000. View at Publisher · View at Google Scholar
  54. P. K. Subudhi, D. T. Rosenow, and H. T. Nguyen, “Quantitative trait loci for the stay green trait in sorghum (Sorghum bicolor L. Moench): consistency across genetic backgrounds and environments,” Theoretical and Applied Genetics, vol. 101, no. 5-6, 733 pages, 2000. View at Publisher · View at Google Scholar
  55. O. R. Crasta, W. Xu, D. T. Rosenow, J. Mullet, and H. T. Nguyen, “Mapping of post flowering drought resistance traits in grain sorghum: association between QTLs influencing premature senescence and maturity,” Molecular and General Genetics, vol. 262, no. 3, 579 pages, 1999. View at Publisher · View at Google Scholar
  56. B. I. G. Haussmann, V. Mahalakshmi, B. V. S. Reddy, N. Seetharama, C. T. Hash, and H. H. Geiger, “QTL mapping of stay-green in two sorghum recombinant inbred populations,” Theoretical and Applied Genetics, vol. 106, no. 1, 133 pages, 2002. View at Publisher · View at Google Scholar
  57. F. Carrari, R. Benech-Arnold, R. Osuna-Fernandez et al., “Genetic mapping of the Sorghum bicolorvp1 gene and its relationship with preharvest sprouting resistance,” Genome, vol. 46, no. 2, 253 pages, 2003. View at Publisher · View at Google Scholar
  58. D. Lijavetzky, M. C. Martínez, F. Carrari, and H. E. Hopp, “QTL analysis and mapping of pre-harvest sprouting resistance in sorghum,” Euphytica, vol. 112, no. 2, 125 pages, 2000. View at Publisher · View at Google Scholar
  59. J. V. Magalhaes, D. F. Garvin, Y. Wang et al., “Comparative mapping of a major aluminum tolerance gene in sorghum and other species in the Poaceae,” Genetics, vol. 167, no. 4, 1905 pages, 2004. View at Publisher · View at Google Scholar
  60. S.-J. Park, Y. Huang, and P. Ayoubi, “Identification of expression profiles of sorghum genes in response to greenbug phloem-feeding using cDNA subtraction and microarray analysis,” Planta, vol. 223, no. 5, 932 pages, 2006. View at Publisher · View at Google Scholar
  61. C. D. Buchanan, S. Lim, R. A. Salzman et al., “Sorghum bicolor's transcriptome response to dehydration, high salinity and ABA,” Plant Molecular Biology, vol. 58, no. 5, 699 pages, 2005. View at Publisher · View at Google Scholar
  62. R. A. Salzman, J. A. Brady, S. A. Finlayson et al., “Transcriptional profiling of sorghum induced by methyl jasmonate, salicylic acid, and aminocyclopropane carboxylic acid reveals cooperative regulation and novel gene responses,” Plant Physiology, vol. 138, no. 1, 352 pages, 2005. View at Publisher · View at Google Scholar
  63. M. T. Hamblin, M. G. Salas Fernandez, A. M. Casa, S. E. Mitchell, A. H. Paterson, and S. Kresovich, “Equilibrium processes cannot explain high levels of short- and medium-range linkage disequilibrium in the domesticated grass Sorghum bicolor,” Genetics, vol. 171, no. 3, 1247 pages, 2005. View at Publisher · View at Google Scholar
  64. S. J. Schloss, S. E. Mitchell, G. M. White et al., “Characterization of RFLP probe sequences for gene discovery and SSR development in Sorghum bicolor (L.) Moench,” Theoretical and Applied Genetics, vol. 105, no. 6-7, 912 pages, 2002. View at Publisher · View at Google Scholar
  65. M. T. Hamblin, S. E. Mitchell, G. M. White et al., “Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor,” Genetics, vol. 167, no. 1, 471 pages, 2004. View at Publisher · View at Google Scholar
  66. A. M. Casa, S. E. Mitchell, M. T. Hamblin et al., “Diversity and selection in sorghum: simultaneous analyses using simple sequence repeats,” Theoretical and Applied Genetics, vol. 111, no. 1, 23 pages, 2005. View at Publisher · View at Google Scholar
  67. A. R. Gingle, Y. Huang, H. Yang, J. Bowers, S. Kresovich, and A. H. Paterson, “CGGC: an integrated web resource for sorghum,” submitted to Plant Physiology.
  68. Z. Xin, M. Wang, N. Barkley Jr et al., “Development of a tilling population for sorghum functional genomics,” in Proceedings of the 15th International Plant & Animal Genome Conference, San Diego, Calif, USA, January 2007.
  69. S. Chopra, V. Brendel, J. Zhang, J. D. Axtell, and T. Peterson, “Molecular characterization of a mutable pigmentation phenotype and isolation of the first active transposable element from Sorghum bicolor,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 26, 15330 pages, 1999. View at Publisher · View at Google Scholar
  70. H. J. Price, S. L. Dillon, G. Hodnett, W. L. Rooney, L. Ross, and J. S. Johnston, “Genome evolution in the genus Sorghum (Poaceae),” Annals of Botany, vol. 95, no. 1, 219 pages, 2005. View at Publisher · View at Google Scholar
  71. R. Spangler, B. Zaitchik, E. Russo, and E. Kellogg, “Andropogoneae evolution and generic limits in Sorghum (Poaceae) using ndhF sequences,” Systematic Botany, vol. 24, no. 2, 267 pages, 1999. View at Publisher · View at Google Scholar
  72. Z. Swigoňová, J. Lai, J. Ma et al., “Close split of sorghum and maize genome progenitors,” Genome Research, vol. 14, no. 10, 1916 pages, 2004. View at Publisher · View at Google Scholar
  73. S. M. Al-Janabi, R. J. Honeycutt, M. McClelland, and B. W. S. Sobral, “A genetic linkage map of Saccharum spontaneum L. ‘SES 208’,” Genetics, vol. 134, no. 4, 1249 pages, 1993. View at Google Scholar
  74. L. Grivet, A. D'Hont, D. Roques, P. Feldmann, C. Lanaud, and J. C. Glaszmann, “RFLP mapping in cultivated sugarcane (Saccharum spp.): genome organization in a highly polyploid and aneuploid interspecific hybrid,” Genetics, vol. 142, no. 3, 987 pages, 1996. View at Google Scholar
  75. A. H. Paterson, B. A. Chapman, J. C. Kissinger, J. E. Bowers, F. A. Feltus, and J. C. Estill, “Convergent retention or loss of gene/domain families following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces, and Tetraodon,” Trends in Genetics, vol. 22, no. 11, 597 pages, 2006. View at Publisher · View at Google Scholar