Comparative DNA sequence analysis of wheat and rice genomes.

The use of DNA sequence-based comparative genomics for evolutionary studies and for transferring information from model species to crop species has revolutionized molecular genetics and crop improvement strategies. This study compared 4485 expressed sequence tags (ESTs) that were physically mapped in wheat chromosome bins, to the public rice genome sequence data from 2251 ordered BAC/PAC clones using BLAST. A rice genome view of homologous wheat genome locations based on comparative sequence analysis revealed numerous chromosomal rearrangements that will significantly complicate the use of rice as a model for cross-species transfer of information in nonconserved regions.

[1]  G. Moore.  CEREAL CHROMOSOME STRUCTURE, EVOLUTION, AND PAIRING. , 2000, Annual review of plant physiology and plant molecular biology.

[2]  J. Bennetzen,et al.  Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[3]  S. W. Cartinhour,et al.  Anchor probes for comparative mapping of grass genera , 1998, Theoretical and Applied Genetics.

[4]  Yoshiaki Nagamura,et al.  Conservation of Genome Structure Between Rice and Wheat , 1994, Bio/Technology.

[5]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[6]  J. Bennetzen,et al.  Colinearity and its exceptions in orthologous adh regions of maize and sorghum. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[7]  L. Qi,et al.  Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs , 2003, Functional & Integrative Genomics.

[8]  M. Sorrells.  The Evolution of Comparative Plant Genetics , 2000 .

[9]  Dubcovsky'and,et al.  Ribosomal RNA Multigene Loci : Nomads of the Triticeae Genomes , 2002 .

[10]  B. Gill,et al.  Identification and high-density mapping of gene-rich regions in chromosome group 1 of wheat. , 1996, Genetics.

[11]  G. Martin,et al.  Chromosome landing: a paradigm for map-based gene cloning in plants with large genomes. , 1995, Trends in genetics : TIG.

[12]  Yujun Zhang,et al.  Sequence and analysis of rice chromosome 4 , 2002, Nature.

[13]  K. Devos,et al.  Comparative genetics in the grasses. , 1998, Plant molecular biology.

[14]  B. Keller,et al.  Colinearity and gene density in grass genomes. , 2000, Trends in plant science.

[15]  S. Tanksley,et al.  Homoeologous relationships of rice, wheat and maize chromosomes , 1993, Molecular and General Genetics MGG.

[16]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica) , 2002, Science.

[17]  J. Bennetzen,et al.  Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5Am , 2002, Functional & Integrative Genomics.

[18]  J Dvorák,et al.  Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat. , 1995, Genome.

[19]  S. Tanksley,et al.  Development of a chromosomal arm map for wheat based on RFLP markers , 1992, Theoretical and Applied Genetics.

[20]  K. Devos,et al.  Comparative genetics in the grasses , 1997, Plant Molecular Biology.

[21]  Han,et al.  Sequence analysis of a rice BAC covering the syntenous barley Rpg1 region , 1999, Genome.

[22]  B. Gill,et al.  The colinearity of the Sh2/A1 orthologous region in rice, sorghum and maize is interrupted and accompanied by genome expansion in the triticeae. , 2002, Genetics.

[23]  G. Moore,et al.  Cereal Genome Evolution: Grasses, line up and form a circle , 1995, Current Biology.

[24]  R. Tarchini,et al.  The Complete Sequence of 340 kb of DNA around the Rice Adh1–Adh2 Region Reveals Interrupted Colinearity with Maize Chromosome 4 , 2000, Plant Cell.

[25]  D. Cyranoski,et al.  Commercial sector scores success with whole rice genome , 2001, Nature.

[26]  J. Bennetzen,et al.  Numerous small rearrangements of gene content, order and orientation differentiate grass genomes , 2002, Plant Molecular Biology.

[27]  T. Naranjo,et al.  Arm homoeology of wheat and rye chromosomes , 1987 .

[28]  M. Rebeiz,et al.  Compass of 47,787 cattle ESTs , 2000, Animal biotechnology.

[29]  M. Yano,et al.  Rapid reorganization of resistance gene homologues in cereal genomes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[30]  B. Gill,et al.  Identification and high-density mapping of gene-rich regions in chromosome group 5 of wheat. , 1996, Genetics.

[31]  Junhua Peng,et al.  The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. , 2003, Genome research.

[32]  L. Yan,et al.  Positional cloning of the wheat vernalization gene VRN1 , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[33]  S. Mccouch,et al.  Inferences on the genome structure of progenitor maize through comparative analysis of rice, maize and the domesticated panicoids. , 1999, Genetics.

[34]  Mark E. Sorrells,et al.  Comparative mapping in grasses. Oat relationships , 1995, Molecular and General Genetics MGG.

[35]  Brandon S. Gaut,et al.  Evolutionary dynamics of grass genomes , 2002 .

[36]  B. Gill,et al.  Physical characterization of the homoeologous group 5 chromosomes of wheat in terms of rice linkage blocks, and physical mapping of some important genes. , 2000, Genome.

[37]  M. Rebeiz,et al.  An ordered comparative map of the cattle and human genomes. , 2000, Genome research.

[38]  H. Fu,et al.  Intraspecific violation of genetic colinearity and its implications in maize , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[39]  B. Burr.  Mapping and Sequencing the Rice Genome , 2002, The Plant Cell Online.

[40]  Bikram S. Gill,et al.  The Deletion Stocks of Common Wheat , 1996 .

[41]  Jan Dvorak,et al.  Genetic map of diploid wheat, Triticum monococcum L., and its comparison with maps of Hordeum vulgare L. , 1996, Genetics.

[42]  Karri M. Haen,et al.  Saturation mapping of a gene-rich recombination hot spot region in wheat. , 2000, Genetics.

[43]  T. Sasaki,et al.  Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa) , 1998, Theoretical and Applied Genetics.

[44]  E. R. Sears.  The aneuploids of common wheat , 1954 .

[45]  D. Laurie,et al.  Conservation of fine-scale DNA marker order in the genomes of rice and the Triticeae. , 1995, Nucleic acids research.

[46]  B. Williams,et al.  An Integrated Physical and Genetic Map of the Rice Genome , 2002, The Plant Cell Online.

[47]  J. Bennetzen,et al.  Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. , 1997, Proceedings of the National Academy of Sciences of the United States of America.