The Complete Sequence of 340 kb of DNA around the Rice Adh1–Adh2 Region Reveals Interrupted Colinearity with Maize Chromosome 4

A 2.3-centimorgan (cM) segment of rice chromosome 11 consisting of 340 kb of DNA sequence around the alcohol dehydrogenase Adh1 and Adh2 loci was completely sequenced, revealing the presence of 33 putative genes, including several apparently involved in disease resistance. Fourteen of the genes were confirmed by identifying the corresponding transcripts. Five genes, spanning 1.9 cM of the region, cross-hybridized with maize genomic DNA and were genetically mapped in maize, revealing a stretch of colinearity with maize chromosome 4. The Adh1 gene marked one significant interruption. This gene mapped to maize chromosome 1, indicating a possible translocation of Adh1 after the evolutionary divergence leading to maize and sorghum. Several other genes, most notably genes similar to known disease resistance genes, showed no cross-hybridization with maize genomic DNA, suggesting sequence divergence or absence of these sequences in maize, which is in contrast to several other well-conserved genes, including Adh1 and Adh2. These findings indicate that the use of rice as the model system for other cereals may sometimes be complicated by the presence of rapidly evolving gene families and microtranslocations. Seven retrotransposons and eight transposons were identified in this rice segment, including a Tc1/Mariner–like element, which is new to rice. In contrast to maize, retroelements are less frequent in rice. Only 14.4% of this genome segment consist of retroelements. Miniature inverted repeat transposable elements were found to be the most frequently occurring class of repetitive elements, accounting for 18.8% of the total repetitive DNA.

[1]  B. Gaut,et al.  Patterns of genetic diversification within the Adh gene family in the grasses (Poaceae). , 1999, Molecular biology and evolution.

[2]  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.

[3]  P. Rohani,et al.  Receptor-like Genes in the Major Resistance Locus of Lettuce Are Subject to Divergent Selection , 1998, Plant Cell.

[4]  Phillip SanMiguel,et al.  The paleontology of intergene retrotransposons of maize , 1998, Nature Genetics.

[5]  H. Hayashi,et al.  cDNA cloning and characterization of mouse nifS‐like protein, m‐Nfs1: mitochondrial localization of eukaryotic NifS‐like proteins , 1998, FEBS letters.

[6]  M. Nei,et al.  Positive Darwinian selection after gene duplication in primate ribonuclease genes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[7]  J. Bennetzen,et al.  Grass genomes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[8]  T. Sasaki,et al.  The rice genome project in Japan. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[9]  P. Piffanelli,et al.  Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana , 1998, Nature.

[10]  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.

[11]  S. Lin,et al.  A high-density rice genetic linkage map with 2275 markers using a single F2 population. , 1998, Genetics.

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

[13]  K. Tsunewaki,et al.  Presence of wheat retrotransposons in Gramineae species and the origin of wheat retrotransposon families. , 1997, Genes & genetic systems.

[14]  H. Zalkin,et al.  Role of NifS in maturation of glutamine phosphoribosylpyrophosphate amidotransferase , 1997, Journal of bacteriology.

[15]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[16]  M. Nei,et al.  Evolution by the birth-and-death process in multigene families of the vertebrate immune system. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[17]  D. Klessig,et al.  Signal perception and transduction in plant defense responses. , 1997, Genes & development.

[18]  N. Tolbert.  THE C2 OXIDATIVE PHOTOSYNTHETIC CARBON CYCLE. , 1997, Annual review of plant physiology and plant molecular biology.

[19]  Jonathan D. G. Jones,et al.  PLANT DISEASE RESISTANCE GENES. , 1997, Annual review of plant physiology and plant molecular biology.

[20]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[21]  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.

[22]  H R Garner,et al.  PRIMO: A primer design program that applies base quality statistics for automated large-scale DNA sequencing. , 1997, Genomics.

[23]  D. Hartl,et al.  Modern thoughts on an ancyent marinere: function, evolution, regulation. , 1997, Annual review of genetics.

[24]  S. Sideris,et al.  The cloned gene, Xa21, confers resistance to multiple Xanthomonas oryzae pv. oryzae isolates in transgenic plants. , 1996, Molecular plant-microbe interactions : MPMI.

[25]  J. Bennetzen,et al.  Nested Retrotransposons in the Intergenic Regions of the Maize Genome , 1996, Science.

[26]  Bruce A. Roe,et al.  DNA Isolation and Sequencing , 1996 .

[27]  R. Durbin,et al.  A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. , 1995, Gene.

[28]  S. Wessler,et al.  LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. , 1995, Current opinion in genetics & development.

[29]  Andrew H. Paterson,et al.  Convergent Domestication of Cereal Crops by Independent Mutations at Corresponding Genetic Loci , 1995, Science.

[30]  M. Yano,et al.  Rice-barley synteny and its application to saturation mapping of the barley Rpg1 region. , 1995, Nucleic acids research.

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

[32]  S. Chao,et al.  Relationship between chromosome 9 of maize and wheat homeologous group 7 chromosomes. , 1994, Genetics.

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

[34]  S. Tanksley,et al.  Comparative linkage maps of the rice and maize genomes. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[35]  L. Andersson,et al.  The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. , 1993, Nucleic acids research.

[36]  B. Hirel,et al.  Multiple functions of promoter sequences involved in organ-specific expression and ammonia regulation of a cytosolic soybean glutamine synthetase gene in transgenic Lotus corniculatus , 1993 .

[37]  J. Walker,et al.  Receptor-like protein kinase genes of Arabidopsis thaliana. , 1993, The Plant journal : for cell and molecular biology.

[38]  A S Olsen,et al.  Automated production of high density cosmid and YAC colony filters using a robotic workstation. , 1993, BioTechniques.

[39]  M. Grandbastien.  Retroelements in higher plants. , 1992, Trends in genetics : TIG.

[40]  D. Smyth,et al.  Plant retrotransposon from Lilium henryi is related to Ty3 of yeast and the gypsy group of Drosophila. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[41]  J. Weber,et al.  Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. , 1989, American journal of human genetics.

[42]  H. Saedler,et al.  Maize transposable elements. , 1989, Annual review of genetics.

[43]  M. Daly,et al.  MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. , 1987, Genomics.

[44]  H. Saedler,et al.  Molecular analysis of the En/Spm transposable element system of Zea mays , 1986, The EMBO journal.

[45]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[46]  I. Goto,et al.  Genetic studies on resistance of rice plant to blast fungus IV. Linkage analysis of four genes,Pi-a,Pi-k,Pi-z and Pi-i.:IV. Linkage Analysis of Four Genes, Pi - a , Pi - k , Pi - z and Pi - i , 1981 .

[47]  I. Goto.  Genetic Studies on Resistance of Rice Plant to Blast Fungus , 1978 .