Comparative Genome Mapping of Sorghum and Maize

INVESTIGATIONS

Comparative Genome Mapping of Sorghum and Maize

R. Whitkus, J. Doebley and M. Lee
Department of Botany and Plant Sciences, University of California, Riverside, California 92521

Linkage relationships were determined among 85 maize low copy number nuclear DNA probes and seven isozyme loci in an F(2) population derived from a cross of Sorghum bicolor ssp. bicolor X S. bicolor ssp. arundinaceum. Thirteen linkage groups were defined, three more than the 10 chromosomes of sorghum. Use of maize DNA probes to produce the sorghum linkage map allowed us to make several inferences concerning processes involved in the evolutionary divergence of the maize and sorghum genomes. The results show that many linkage groups are conserved between these two genomes and that the amount of recombination in these conserved linkage groups is roughly equivalent in maize and sorghum. Estimates of the proportions of duplicated loci suggest that a larger proportion of the loci are duplicated in the maize genome than in the sorghum genome. This result concurs with a prior estimate that the nuclear DNA content of maize is three to four times greater than that of sorghum. The pattern of conserved linkages between maize and sorghum is such that most sorghum linkage groups are composed of loci that map to two maize chromosomes. This pattern is consistent with the hypothesized ancient polyploid origin of maize and sorghum. There are nine cases in which locus order within shared linkage groups is inverted in sorghum relative to maize. These may have arisen from either inversions or intrachromosomal translocations. We found no evidence for large interchromosomal translocations. Overall, the data suggest that the primary processes involved in divergence of the maize and sorghum genomes were duplications (either by polyploidy or segmental duplication) and inversions or intrachromosomal translocations.

This article has been cited by other articles:

T. Nakazato, M.-K. Jung, E. A. Housworth, L. H. Rieseberg, and G. J. Gastony
Genetic Map-Based Analysis of Genome Structure in the Homosporous Fern Ceratopteris richardii
Genetics, July 1, 2006; 173(3): 1585 - 1597.
[Abstract] [Full Text] [PDF]

L. H. Pratt, C. Liang, M. Shah, F. Sun, H. Wang, St. P. Reid, A. R. Gingle, A. H. Paterson, R. Wing, R. Dean, 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, October 1, 2005; 139(2): 869 - 884.
[Abstract] [Full Text] [PDF]

Sorghum Genomics Planning Workshop Participants
Toward Sequencing the Sorghum Genome. A U.S. National Science Foundation-Sponsored Workshop Report
Plant Physiology, August 1, 2005; 138(4): 1898 - 1902.
[Full Text] [PDF]

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, February 1, 2005; 169(2): 1169 - 1173.
[Abstract] [Full Text] [PDF]

H. J. PRICE, S. L. DILLON, G. HODNETT, W. L. ROONEY, L. ROSS, and J. S. JOHNSTON
Genome Evolution in the Genus Sorghum (Poaceae)
Ann. Bot., January 1, 2005; 95(1): 219 - 227.
[Abstract] [Full Text] [PDF]

J. D. Munkvold, R. A. Greene, C. E. Bermudez-Kandianis, C. M. La Rota, H. Edwards, S. F. Sorrells, T. Dake, D. Benscher, R. Kantety, A. M. Linkiewicz, et al.
Group 3 Chromosome Bin Maps of Wheat and Their Relationship to Rice Chromosome 1
Genetics, October 1, 2004; 168(2): 639 - 650.
[Abstract] [Full Text] [PDF]

H. W. Bass, J. E. Krawetz, G. R. OBrian, C. Zinselmeier, J. E. Habben, and R. S. Boston
Maize ribosome-inactivating proteins (RIPs) with distinct expression patterns have similar requirements for proenzyme activation
J. Exp. Bot., October 1, 2004; 55(406): 2219 - 2233.
[Abstract] [Full Text] [PDF]

J. E. Bowers, C. Abbey, S. Anderson, C. Chang, X. Draye, A. H. Hoppe, R. Jessup, C. Lemke, J. Lennington, Z. Li, 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, September 1, 2003; 165(1): 367 - 386.
[Abstract] [Full Text] [PDF]

D. T. Morishige, K. L. Childs, L. D. Moore, and J. E. Mullet
Targeted Analysis of Orthologous Phytochrome A Regions of the Sorghum, Maize, and Rice Genomes using Comparative Gene-Island Sequencing
Plant Physiology, December 1, 2002; 130(4): 1614 - 1625.
[Abstract] [Full Text] [PDF]

M. S. Georgiady, R. W. Whitkus, and E. M. Lord
Genetic Analysis of Traits Distinguishing Outcrossing and Self-Pollinating Forms of Currant Tomato, Lycopersicon pimpinellifolium (Jusl.) Mill.
Genetics, May 1, 2002; 161(1): 333 - 344.
[Abstract] [Full Text] [PDF]

M. N. Islam-Faridi, K. L. Childs, P. E. Klein, G. Hodnett, M. A. Menz, R. R. Klein, W. L. Rooney, J. E. Mullet, D. M. Stelly, and H. J. Price
A Molecular Cytogenetic Map of Sorghum Chromosome 1: Fluorescence in Situ Hybridization Analysis With Mapped Bacterial Artificial Chromosomes
Genetics, May 1, 2002; 161(1): 345 - 353.
[Abstract] [Full Text] [PDF]

H. Ozkan, A. A. Levy, and M. Feldman
Allopolyploidy-Induced Rapid Genome Evolution in the Wheat (Aegilops-Triticum) Group
PLANT CELL, August 1, 2001; 13(8): 1735 - 1747.
[Abstract] [Full Text] [PDF]

X. Draye, Y.-R. Lin, X.-y. Qian, J. E. Bowers, G. B. Burow, P. L. Morrell, D. G. Peterson, G. G. Presting, S.-x. Ren, R. A. Wing, et al.
Toward Integration of Comparative Genetic, Physical, Diversity, and Cytomolecular Maps for Grasses and Grains, Using the Sorghum Genome as a Foundation
Plant Physiology, March 1, 2001; 125(3): 1325 - 1341.
[Abstract] [Full Text]

J. M. Ranz, F. Casals, and A. Ruiz
How Malleable is the Eukaryotic Genome? Extreme Rate of Chromosomal Rearrangement in the Genus Drosophila
Genome Res., February 1, 2001; 11(2): 230 - 239.
[Abstract] [Full Text]

B. S. Gaut, M. Le Thierry d'Ennequin, A. S. Peek, and M. C. Sawkins
Maize as a model for the evolution of plant nuclear genomes
PNAS, June 20, 2000; 97(13): 7008 - 7015.
[Abstract] [Full Text] [PDF]

Y.-r. Lin, X. Draye, X. Qian, S. Ren, L.-h. Zhu, J. Tomkins, R. A. Wing, Z. Li, and A. H. Paterson
Locus-specific contig assembly in highly-duplicated genomes, using the BAC-RF method
Nucleic Acids Res., April 1, 2000; 28(7): e23 - e23.
[Abstract] [Full Text] [PDF]

M. Frisch, M. Bohn, and A. E. Melchinger
Comparison of Selection Strategies for Marker-Assisted Backcrossing of a Gene
Crop Sci., September 1, 1999; 39(5): 1295 - 1301.
[Abstract] [Full Text]

G. L. Davis, M. D. McMullen, C. Baysdorfer, T. Musket, D. Grant, M. Staebell, G. Xu, M. Polacco, L. Koster, S. Melia-Hancock, et al.
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, July 1, 1999; 152(3): 1137 - 1172.
[Abstract] [Full Text]

L. H. Rieseberg, J. Whitton, and K. Gardner
Hybrid Zones and the Genetic Architecture of a Barrier to Gene Flow Between Two Sunflower Species
Genetics, June 1, 1999; 152(2): 713 - 727.
[Abstract] [Full Text]

R. Whitkus
Genetics of Adaptive Radiation in Hawaiian and Cook Islands Species of Tetramolopium (Asteraceae). II. Genetic Linkage Map and Its Implications for Interspecific Breeding Barriers
Genetics, November 1, 1998; 150(3): 1209 - 1216.
[Abstract] [Full Text]

U. Lagercrantz
Comparative Mapping Between Arabidopsis thaliana and Brassica nigra Indicates That Brassica Genomes Have Evolved Through Extensive Genome Replication Accompanied by Chromosome Fusions and Frequent Rearrangements
Genetics, November 1, 1998; 150(3): 1217 - 1228.
[Abstract] [Full Text]

L. Maloisel and J.-L. Rossignol
Suppression of crossing-over by DNA methylation in Ascobolus
Genes & Dev., May 1, 1998; 12(9): 1381 - 1389.
[Abstract] [Full Text]

M. S. Zwick, M. N. Islam-Faridi, D. G. C. Jr., R. A. Wing, G. E. Hart, D. M. Stelly, and H. J. Price
Physical Mapping of the liguleless Linkage Group in Sorghum bicolor Using Rice RFLP-Selected Sorghum BACs
Genetics, April 1, 1998; 148(4): 1983 - 1992.
[Abstract] [Full Text] [PDF]

J. Messing and V. Llaca
Importance of anchor genomes for any plant genome project
PNAS, March 3, 1998; 95(5): 2017 - 2020.
[Abstract] [Full Text] [PDF]

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
PNAS, February 17, 1998; 95(4): 1686 - 1691.
[Abstract] [Full Text] [PDF]

Sequence Organization and Conservation in sh2/a1-Homologous Regions of Sorghum and Rice
Genetics, January 1, 1998; 148(1): 435 - 444.

C. T. Guimaraes, G. R. Sills, and B. W. S. Sobral
Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize
PNAS, December 23, 1997; 94(26): 14261 - 14266.
[Abstract] [Full Text] [PDF]

B. S. Gaut and J. F. Doebley
DNA sequence evidence for the segmental allotetraploid origin of maize
PNAS, June 24, 1997; 94(13): 6809 - 6814.
[Abstract] [Full Text] [PDF]

				L. H. Pratt, C. Liang, M. Shah, F. Sun, H. Wang, St. P. Reid, A. R. Gingle, A. H. Paterson, R. Wing, R. Dean, 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, October 1, 2005; 139(2): 869 - 884. [Abstract] [Full Text] [PDF]

				Sorghum Genomics Planning Workshop Participants Toward Sequencing the Sorghum Genome. A U.S. National Science Foundation-Sponsored Workshop Report Plant Physiology, August 1, 2005; 138(4): 1898 - 1902. [Full Text] [PDF]

				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, February 1, 2005; 169(2): 1169 - 1173. [Abstract] [Full Text] [PDF]

				H. J. PRICE, S. L. DILLON, G. HODNETT, W. L. ROONEY, L. ROSS, and J. S. JOHNSTON Genome Evolution in the Genus Sorghum (Poaceae) Ann. Bot., January 1, 2005; 95(1): 219 - 227. [Abstract] [Full Text] [PDF]

				J. D. Munkvold, R. A. Greene, C. E. Bermudez-Kandianis, C. M. La Rota, H. Edwards, S. F. Sorrells, T. Dake, D. Benscher, R. Kantety, A. M. Linkiewicz, et al. Group 3 Chromosome Bin Maps of Wheat and Their Relationship to Rice Chromosome 1 Genetics, October 1, 2004; 168(2): 639 - 650. [Abstract] [Full Text] [PDF]

				H. W. Bass, J. E. Krawetz, G. R. OBrian, C. Zinselmeier, J. E. Habben, and R. S. Boston Maize ribosome-inactivating proteins (RIPs) with distinct expression patterns have similar requirements for proenzyme activation J. Exp. Bot., October 1, 2004; 55(406): 2219 - 2233. [Abstract] [Full Text] [PDF]

				J. E. Bowers, C. Abbey, S. Anderson, C. Chang, X. Draye, A. H. Hoppe, R. Jessup, C. Lemke, J. Lennington, Z. Li, 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, September 1, 2003; 165(1): 367 - 386. [Abstract] [Full Text] [PDF]

				D. T. Morishige, K. L. Childs, L. D. Moore, and J. E. Mullet Targeted Analysis of Orthologous Phytochrome A Regions of the Sorghum, Maize, and Rice Genomes using Comparative Gene-Island Sequencing Plant Physiology, December 1, 2002; 130(4): 1614 - 1625. [Abstract] [Full Text] [PDF]

				M. S. Georgiady, R. W. Whitkus, and E. M. Lord Genetic Analysis of Traits Distinguishing Outcrossing and Self-Pollinating Forms of Currant Tomato, Lycopersicon pimpinellifolium (Jusl.) Mill. Genetics, May 1, 2002; 161(1): 333 - 344. [Abstract] [Full Text] [PDF]

				M. N. Islam-Faridi, K. L. Childs, P. E. Klein, G. Hodnett, M. A. Menz, R. R. Klein, W. L. Rooney, J. E. Mullet, D. M. Stelly, and H. J. Price A Molecular Cytogenetic Map of Sorghum Chromosome 1: Fluorescence in Situ Hybridization Analysis With Mapped Bacterial Artificial Chromosomes Genetics, May 1, 2002; 161(1): 345 - 353. [Abstract] [Full Text] [PDF]

				H. Ozkan, A. A. Levy, and M. Feldman Allopolyploidy-Induced Rapid Genome Evolution in the Wheat (Aegilops-Triticum) Group PLANT CELL, August 1, 2001; 13(8): 1735 - 1747. [Abstract] [Full Text] [PDF]

				X. Draye, Y.-R. Lin, X.-y. Qian, J. E. Bowers, G. B. Burow, P. L. Morrell, D. G. Peterson, G. G. Presting, S.-x. Ren, R. A. Wing, et al. Toward Integration of Comparative Genetic, Physical, Diversity, and Cytomolecular Maps for Grasses and Grains, Using the Sorghum Genome as a Foundation Plant Physiology, March 1, 2001; 125(3): 1325 - 1341. [Abstract] [Full Text]

				J. M. Ranz, F. Casals, and A. Ruiz How Malleable is the Eukaryotic Genome? Extreme Rate of Chromosomal Rearrangement in the Genus Drosophila Genome Res., February 1, 2001; 11(2): 230 - 239. [Abstract] [Full Text]

				B. S. Gaut, M. Le Thierry d'Ennequin, A. S. Peek, and M. C. Sawkins Maize as a model for the evolution of plant nuclear genomes PNAS, June 20, 2000; 97(13): 7008 - 7015. [Abstract] [Full Text] [PDF]

				Y.-r. Lin, X. Draye, X. Qian, S. Ren, L.-h. Zhu, J. Tomkins, R. A. Wing, Z. Li, and A. H. Paterson Locus-specific contig assembly in highly-duplicated genomes, using the BAC-RF method Nucleic Acids Res., April 1, 2000; 28(7): e23 - e23. [Abstract] [Full Text] [PDF]

				M. Frisch, M. Bohn, and A. E. Melchinger Comparison of Selection Strategies for Marker-Assisted Backcrossing of a Gene Crop Sci., September 1, 1999; 39(5): 1295 - 1301. [Abstract] [Full Text]

				G. L. Davis, M. D. McMullen, C. Baysdorfer, T. Musket, D. Grant, M. Staebell, G. Xu, M. Polacco, L. Koster, S. Melia-Hancock, et al. 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, July 1, 1999; 152(3): 1137 - 1172. [Abstract] [Full Text]

				L. H. Rieseberg, J. Whitton, and K. Gardner Hybrid Zones and the Genetic Architecture of a Barrier to Gene Flow Between Two Sunflower Species Genetics, June 1, 1999; 152(2): 713 - 727. [Abstract] [Full Text]

				R. Whitkus Genetics of Adaptive Radiation in Hawaiian and Cook Islands Species of Tetramolopium (Asteraceae). II. Genetic Linkage Map and Its Implications for Interspecific Breeding Barriers Genetics, November 1, 1998; 150(3): 1209 - 1216. [Abstract] [Full Text]

				U. Lagercrantz Comparative Mapping Between Arabidopsis thaliana and Brassica nigra Indicates That Brassica Genomes Have Evolved Through Extensive Genome Replication Accompanied by Chromosome Fusions and Frequent Rearrangements Genetics, November 1, 1998; 150(3): 1217 - 1228. [Abstract] [Full Text]

				L. Maloisel and J.-L. Rossignol Suppression of crossing-over by DNA methylation in Ascobolus Genes & Dev., May 1, 1998; 12(9): 1381 - 1389. [Abstract] [Full Text]

				M. S. Zwick, M. N. Islam-Faridi, D. G. C. Jr., R. A. Wing, G. E. Hart, D. M. Stelly, and H. J. Price Physical Mapping of the liguleless Linkage Group in Sorghum bicolor Using Rice RFLP-Selected Sorghum BACs Genetics, April 1, 1998; 148(4): 1983 - 1992. [Abstract] [Full Text] [PDF]

				J. Messing and V. Llaca Importance of anchor genomes for any plant genome project PNAS, March 3, 1998; 95(5): 2017 - 2020. [Abstract] [Full Text] [PDF]

				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 PNAS, February 17, 1998; 95(4): 1686 - 1691. [Abstract] [Full Text] [PDF]

				Sequence Organization and Conservation in sh2/a1-Homologous Regions of Sorghum and Rice Genetics, January 1, 1998; 148(1): 435 - 444.

				C. T. Guimaraes, G. R. Sills, and B. W. S. Sobral Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize PNAS, December 23, 1997; 94(26): 14261 - 14266. [Abstract] [Full Text] [PDF]

				B. S. Gaut and J. F. Doebley DNA sequence evidence for the segmental allotetraploid origin of maize PNAS, June 24, 1997; 94(13): 6809 - 6814. [Abstract] [Full Text] [PDF]