Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.
AAAS Promotion

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Science 23 October 1998:
Vol. 282. no. 5389, pp. 656 - 659
DOI: 10.1126/science.282.5389.656

Viewpoint

Plant Comparative Genetics after 10 Years

M. D. Gale, K. M. Devos

The past 10 years have seen the discovery of unexpected levels of conservation of gene content and gene orders over millions of years of evolution within grasses, crucifers, legumes, some trees, and Solanaceae crops. Within the grasses, which include the three 500-million-ton-plus-per-year crops (wheat, maize, and rice), and the crucifers, which include all the Brassica crops, colinearity looks good enough to do most map-based cloning only in the small genome model species, rice and Arabidopsis. Elsewhere, knowledge gained in a few major crops is being pooled and applied across the board. The extrapolation of information from the well-studied species to orphan crops, which include many tropical species, is providing a solid base for their improvement. Genome rearrangements are giving new insights into evolution. In fact, comparative genetics is the key that will unlock the secrets of crop plants with genomes larger than that of humans.

The authors are at the John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, Norfolk, UK.


Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Tie-dyed2 Functions with Tie-dyed1 to Promote Carbohydrate Export from Maize Leaves.
R. F. Baker and D. M. Braun (2008)
Plant Physiology 146, 1085-1097
   Abstract »    Full Text »    PDF »
Microarray Analysis of Replicate Populations Selected Against a Wing-Shape Correlation in Drosophila melanogaster.
K. E. Weber, R. J. Greenspan, D. R. Chicoine, K. Fiorentino, M. H. Thomas, and T. L. Knight (2008)
Genetics 178, 1093-1108
   Abstract »    Full Text »    PDF »
Architectural Evolution and its Implications for Domestication in Grasses.
A. Doust (2007)
Ann. Bot. 100, 941-950
   Abstract »    Full Text »    PDF »
Comparative Physical Mapping Between Oryza sativa (AA Genome Type) and O. punctata (BB Genome Type).
H. Kim, P. S. Miguel, W. Nelson, K. Collura, M. Wissotski, J. G. Walling, J. P. Kim, S. A. Jackson, C. Soderlund, and R. A. Wing (2007)
Genetics 176, 379-390
   Abstract »    Full Text »    PDF »
Analyses of Synteny Between Arabidopsis thaliana and Species in the Asteraceae Reveal a Complex Network of Small Syntenic Segments and Major Chromosomal Rearrangements.
L. Timms, R. Jimenez, M. Chase, D. Lavelle, L. McHale, A. Kozik, Z. Lai, A. Heesacker, S. Knapp, L. Rieseberg, et al. (2006)
Genetics 173, 2227-2235
   Abstract »    Full Text »    PDF »
Sequence-Level Analysis of the Diploidization Process in the Triplicated FLOWERING LOCUS C Region of Brassica rapa.
T.-J. Yang, J. S. Kim, S.-J. Kwon, K.-B. Lim, B.-S. Choi, J.-A Kim, M. Jin, J. Y. Park, M.-H. Lim, H.-I. Kim, et al. (2006)
PLANT CELL 18, 1339-1347
   Abstract »    Full Text »    PDF »
What Is the Role of Genome Duplication in the Evolution of Complexity and Diversity?.
K. D. Crow and G. P. Wagner (2006)
Mol. Biol. Evol. 23, 887-892
   Abstract »    Full Text »    PDF »
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis.
L. Ma, C. Chen, X. Liu, Y. Jiao, N. Su, L. Li, X. Wang, M. Cao, N. Sun, X. Zhang, et al. (2005)
Genome Res. 15, 1274-1283
   Abstract »    Full Text »    PDF »
Large-Scale Identification of Expressed Sequence Tags Involved in Rice and Rice Blast Fungus Interaction.
C. Jantasuriyarat, M. Gowda, K. Haller, J. Hatfield, G. Lu, E. Stahlberg, B. Zhou, H. Li, H. Kim, Y. Yu, et al. (2005)
Plant Physiology 138, 105-115
   Abstract »    Full Text »    PDF »
Comparative genome analyses of Arabidopsis spp.: Inferring chromosomal rearrangement events in the evolutionary history of A. thaliana.
K. Yogeeswaran, A. Frary, T. L. York, A. Amenta, A. H. Lesser, J. B. Nasrallah, S. D. Tanksley, and M. E. Nasrallah (2005)
Genome Res. 15, 505-515
   Abstract »    Full Text »    PDF »
The Genetic Basis for Inflorescence Variation Between Foxtail and Green Millet (Poaceae).
A. N. Doust, K. M. Devos, M. D. Gadberry, M. D. Gale, and E. A. Kellogg (2005)
Genetics 169, 1659-1672
   Abstract »    Full Text »    PDF »
The Role of Genomics Research in Improvement of "Orphan" Crops.
R. J. Nelson, R. L. Naylor, and M. M. Jahn (2004)
Crop Sci. 44, 1901-1904
   Full Text »    PDF »
The evolution of nuclear genome structure in seed plants.
E. A. Kellogg and J. L. Bennetzen (2004)
Am. J. Botany 91, 1709-1725
   Abstract »    Full Text »    PDF »
Construction and Evaluation of cDNA Libraries for Large-Scale Expressed Sequence Tag Sequencing in Wheat (Triticum aestivum L.).
D. Zhang, D. W. Choi, S. Wanamaker, R. D. Fenton, A. Chin, M. Malatrasi, Y. Turuspekov, H. Walia, E. D. Akhunov, P. Kianian, et al. (2004)
Genetics 168, 595-608
   Abstract »    Full Text »    PDF »
Close Split of Sorghum and Maize Genome Progenitors.
Z. Swigonova, J. Lai, J. Ma, W. Ramakrishna, V. Llaca, J. L. Bennetzen, and J. Messing (2004)
Genome Res. 14, 1916-1923
   Abstract »    Full Text »    PDF »
Gene Loss and Movement in the Maize Genome.
J. Lai, J. Ma, Z. Swigonova, W. Ramakrishna, E. Linton, V. Llaca, B. Tanyolac, Y.-J. Park, O-Y. Jeong, J. L. Bennetzen, et al. (2004)
Genome Res. 14, 1924-1931
   Abstract »    Full Text »    PDF »
Characterization of the Maize Endosperm Transcriptome and Its Comparison to the Rice Genome.
J. Lai, N. Dey, C.-S. Kim, A. K. Bharti, S. Rudd, K. F.X. Mayer, B. A. Larkins, P. Becraft, and J. Messing (2004)
Genome Res. 14, 1932-1937
   Abstract »    Full Text »    PDF »
Incongruent Patterns of Local and Global Genome Size Evolution in Cotton.
C. E. Grover, H. Kim, R. A. Wing, A. H. Paterson, and J. F. Wendel (2004)
Genome Res. 14, 1474-1482
   Abstract »    Full Text »    PDF »
A gene cluster for secondary metabolism in oat: Implications for the evolution of metabolic diversity in plants.
X. Qi, S. Bakht, M. Leggett, C. Maxwell, R. Melton, and A. Osbourn (2004)
PNAS 101, 8233-8238
   Abstract »    Full Text »    PDF »
Genomic Targeting and High-Resolution Mapping of the Tsn1 Gene in Wheat.
K. M. Haen, H. Lu, T. L. Friesen, and J. D. Faris (2004)
Crop Sci. 44, 951-962
   Abstract »    Full Text »    PDF »
Comparative Mapping and Rapid Karyotypic Evolution in the Genus Helianthus.
J. M. Burke, Z. Lai, M. Salmaso, T. Nakazato, S. Tang, A. Heesacker, S. J. Knapp, and L. H. Rieseberg (2004)
Genetics 167, 449-457
   Abstract »    Full Text »    PDF »
Comparative Population Genetics of the Panicoid Grasses: Sequence Polymorphism, Linkage Disequilibrium and Selection in a Diverse Sample of Sorghum bicolor.
M. T. Hamblin, S. E. Mitchell, G. M. White, J. Gallego, R. Kukatla, R. A. Wing, A. H. Paterson, and S. Kresovich (2004)
Genetics 167, 471-483
   Abstract »    Full Text »    PDF »
A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes.
K. Ilic, P. J. SanMiguel, and J. L. Bennetzen (2003)
PNAS 100, 12265-12270
   Abstract »    Full Text »    PDF »
The Nitrilase ZmNIT2 Converts Indole-3-Acetonitrile to Indole-3-Acetic Acid.
W. J. Park, V. Kriechbaumer, A. Muller, M. Piotrowski, R. B. Meeley, A. Gierl, and E. Glawischnig (2003)
Plant Physiology 133, 794-802
   Abstract »    Full Text »    PDF »
History of the ADP/ATP-Translocase-Encoding Gene, a Parasitism Gene Transferred from a Chlamydiales Ancestor to Plants 1 Billion Years Ago.
G. Greub and D. Raoult (2003)
Appl. Envir. Microbiol. 69, 5530-5535
   Abstract »    Full Text »    PDF »
Comparative analyses of genomic locations and race specificities of loci for quantitative resistance to Pyricularia grisea in rice and barley.
H. Chen, S. Wang, Y. Xing, C. Xu, P. M. Hayes, and Q. Zhang (2003)
PNAS 100, 2544-2549
   Abstract »    Full Text »    PDF »
Functional Divergence of a Syntenic Invertase Gene Family in Tomato, Potato, and Arabidopsis.
E. Fridman and D. Zamir (2003)
Plant Physiology 131, 603-609
   Abstract »    Full Text »    PDF »
The Automatic Detection of Homologous Regions (ADHoRe) and Its Application to Microcolinearity Between Arabidopsis and Rice.
K. Vandepoele, Y. Saeys, C. Simillion, J. Raes, and Y. Van de Peer (2002)
Genome Res. 12, 1792-1801
   Abstract »    Full Text »    PDF »
Inflorescence diversification in the panicoid "bristle grass" clade (Paniceae, Poaceae): evidence from molecular phylogenies and developmental morphology.
A. N. Doust and E. A. Kellogg (2002)
Am. J. Botany 89, 1203-1222
   Abstract »    Full Text »    PDF »
Beyond the Arabidopsis Genome: Opportunities for Comparative Genomics.
A. E. Hall, A. Fiebig, and D. Preuss (2002)
Plant Physiology 129, 1439-1447
   Full Text »    PDF »
Exceptional haplotype variation in maize.
J. L. Bennetzen and W. Ramakrishna (2002)
PNAS 99, 9093-9095
   Full Text »    PDF »
Chromosomal Elements Evolve at Different Rates in the Drosophila Genome.
J. Gonzalez, J. M. Ranz, and A. Ruiz (2002)
Genetics 161, 1137-1154
   Abstract »    Full Text »    PDF »
Comparative Mapping of the Barley Ppd-H1 Photoperiod Response Gene Region, Which Lies Close to a Junction Between Two Rice Linkage Segments.
R. P. Dunford, M. Yano, N. Kurata, T. Sasaki, G. Huestis, T. Rocheford, and D. A. Laurie (2002)
Genetics 161, 825-834
   Abstract »    Full Text »    PDF »
What is Finished, and Why Does it Matter.
E. Mardis, J. McPherson, R. Martienssen, R. K. Wilson, and W. R. McCombie (2002)
Genome Res. 12, 669-671
   Full Text »    PDF »
A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica).
J. Yu, S. Hu, J. Wang, G. K.-S. Wong, S. Li, B. Liu, Y. Deng, L. Dai, Y. Zhou, X. Zhang, et al. (2002)
Science 296, 79-92
   Abstract »    Full Text »    PDF »
A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica).
S. A. Goff, D. Ricke, T.-H. Lan, G. Presting, R. Wang, M. Dunn, J. Glazebrook, A. Sessions, P. Oeller, H. Varma, et al. (2002)
Science 296, 92-100
   Abstract »    Full Text »    PDF »
An Integrated Physical and Genetic Map of the Rice Genome.
M. Chen, G. Presting, W. B. Barbazuk, J. L. Goicoechea, B. Blackmon, G. Fang, H. Kim, D. Frisch, Y. Yu, S. Sun, et al. (2002)
PLANT CELL 14, 537-545
   Abstract »    Full Text »    PDF »
Leaf shape and anatomy as indicators of phase change in the grasses: comparison of maize, rice, and bluegrass.
A. W. Sylvester, V. Parker-Clark, and G. A. Murray (2001)
Am. J. Botany 88, 2157-2167
   Abstract »    Full Text »    PDF »
Evolution of Gene Order in the Genomes of Two Related Yeast Species.
G. Fischer, C. Neuveglise, P. Durrens, C. Gaillardin, and B. Dujon (2001)
Genome Res. 11, 2009-2019
   Abstract »    Full Text »    PDF »
Comparative Genomics Between Rice and Arabidopsis Shows Scant Collinearity in Gene Order.
H. Liu, R. Sachidanandam, and L. Stein (2001)
Genome Res. 11, 2020-2026
   Abstract »    Full Text »    PDF »
Host Plant Resistance Genes for Fusarium Head Blight: Mapping and Manipulation with Molecular Markers.
F.L. Kolb, G-H. Bai, G.J. Muehlbauer, J.A. Anderson, K.P. Smith, and G. Fedak (2001)
Crop Sci. 41, 611-619
   Abstract »    Full Text »    PDF »
Genomic and genetic relationships among species of Leymus (Poaceae: Triticeae) inferred from 18S-26S ribosomal genes.
K. Anamthawat-Jónsson and S. K. Bödvarsdóttir (2001)
Am. J. Botany 88, 553-559
   Abstract »    Full Text »
Arabidopsis and Brassica Comparative Genomics: Sequence, Structure and Gene Content in the ABI1-Rps2-Ck1 Chromosomal Segment and Related Regions.
C. F. Quiros, F. Grellet, J. Sadowski, T. Suzuki, G. Li, and T. Wroblewski (2001)
Genetics 157, 1321-1330
   Abstract »    Full Text »
Toward Integration of Comparative Genetic, Physical, Diversity, and Cytomolecular Maps for Grasses and Grains, Using the Sorghum Genome as a Foundation.
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. (2001)
Plant Physiology 125, 1325-1341
   Abstract »    Full Text »
How Malleable is the Eukaryotic Genome? Extreme Rate of Chromosomal Rearrangement in the Genus Drosophila.
J. M. Ranz, F. Casals, and A. Ruiz (2001)
Genome Res. 11, 230-239
   Abstract »    Full Text »
Prevalence of small inversions in yeast gene order evolution.
C. Seoighe, N. Federspiel, T. Jones, N. Hansen, V. Bivolarovic, R. Surzycki, R. Tamse, C. Komp, L. Huizar, R. W. Davis, et al. (2000)
PNAS
   Abstract »    Full Text »
Comparative Fluorescence in Situ Hybridization Mapping of a 431-kb Arabidopsis thaliana Bacterial Artificial Chromosome Contig Reveals the Role of Chromosomal Duplications in the Expansion of the Brassica rapa Genome.
S. A. Jackson, Z. Cheng, M. L. Wang, H. M. Goodman, and J. Jiang (2000)
Genetics 156, 833-838
   Abstract »    Full Text »
Comparative Genomics of Plant Chromosomes.
A. H. Paterson, J. E. Bowers, M. D. Burow, X. Draye, C. G. Elsik, C.-X. Jiang, C. S. Katsar, T.-H. Lan, Y.-R. Lin, R. Ming, et al. (2000)
PLANT CELL 12, 1523-1540
   Abstract »    Full Text »
Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny.
H.-M. Ku, T. Vision, J. Liu, and S. D. Tanksley (2000)
PNAS
   Abstract »    Full Text »
Rice Transposable Elements: A Survey of 73,000 Sequence-Tagged-Connectors.
L. Mao, T. C. Wood, Y. Yu, M. A. Budiman, J. Tomkins, S.-s. Woo, M. Sasinowski, G. Presting, D. Frisch, S. Goff, et al. (2000)
Genome Res. 10, 982-990
   Abstract »    Full Text »
Comparative Sequence Analysis of Plant Nuclear Genomes: Microcolinearity and Its Many Exceptions.
J. L. Bennetzen (2000)
PLANT CELL 12, 1021-1030
   Abstract »    Full Text »
Extensive Duplication and Reshuffling in the Arabidopsis Genome.
G. Blanc, A. Barakat, R. Guyot, R. Cooke, and M. Delseny (2000)
PLANT CELL 12, 1093-1102
   Abstract »    Full Text »
Transposons and genome evolution in plants.
N. Fedoroff (2000)
PNAS 97, 7002-7007
   Abstract »    Full Text »    PDF »
Genome Relationships: The Grass Model in Current Research.
K. M. Devos and M. D. Gale (2000)
PLANT CELL 12, 637-646
   Abstract »    Full Text »
Synergy of Empirical Breeding, Marker-Assisted Selection, and Genomics to Increase Crop Yield Potential.
C. W. Stuber, M. Polacco, and M.L. Senior (1999)
Crop Sci. 39, 1571-1583
   Abstract »    Full Text »
Plant Functional Genomics.
C. Somerville and S. Somerville (1999)
Science 285, 380-383
   Abstract »    Full Text »
Genome Mapping in Capsicum and the Evolution of Genome Structure in the Solanaceae.
K. D. Livingstone, V. K. Lackney, J. R. Blauth, R. van Wijk, and M. K. Jahn (1999)
Genetics 152, 1183-1202
   Abstract »    Full Text »
Inaugural Article: Comparative organization of cattle chromosome 5 revealed by comparative mapping by annotation and sequence similarity and radiation hybrid mapping.
A. Ozawa, M. R. Band, J. H. Larson, J. Donovan, C. A. Green, J. E. Womack, and H. A. Lewin (2000)
PNAS 97, 4150-4155
   Abstract »    Full Text »    PDF »
Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny.
H.-M. Ku, T. Vision, J. Liu, and S. D. Tanksley (2000)
PNAS 97, 9121-9126
   Abstract »    Full Text »    PDF »
Prevalence of small inversions in yeast gene order evolution.
C. Seoighe, N. Federspiel, T. Jones, N. Hansen, V. Bivolarovic, R. Surzycki, R. Tamse, C. Komp, L. Huizar, R. W. Davis, et al. (2000)
PNAS 97, 14433-14437
   Abstract »    Full Text »    PDF »
Conservation of Microstructure between a Sequenced Region of the Genome of Rice and Multiple Segments of the Genome of Arabidopsis thaliana.
K. Mayer, G. Murphy, R. Tarchini, R. Wambutt, G. Volckaert, T. Pohl, A. Dusterhoft, W. Stiekema, K.-D. Entian, N. Terryn, et al. (2001)
Genome Res. 11, 1167-1174
   Abstract »    Full Text »    PDF »



ADVERTISEMENT
Click Me!

ADVERTISEMENT
Click Me!

To Advertise     Find Products