Advances in cereal genomics and applications in crop breeding.

Recent advances in cereal genomics have made it possible to analyse the architecture of cereal genomes and their expressed components, leading to an increase in our knowledge of the genes that are linked to key agronomically important traits. These studies have used molecular genetic mapping of quantitative trait loci (QTL) of several complex traits that are important in breeding. The identification and molecular cloning of genes underlying QTLs offers the possibility to examine the naturally occurring allelic variation for respective complex traits. Novel alleles, identified by functional genomics or haplotype analysis, can enrich the genetic basis of cultivated crops to improve productivity. Advances made in cereal genomics research in recent years thus offer the opportunities to enhance the prediction of phenotypes from genotypes for cereal breeding.

[1]  T. Sang,et al.  Rice Domestication by Reducing Shattering , 2007 .

[2]  A. Graner,et al.  Sequence analysis and gene identification in a set of mapped RFLP markers in barley (Hordeum vulgare). , 1999, Genome.

[3]  Edward S. Buckler,et al.  Dwarf8 polymorphisms associate with variation in flowering time , 2001, Nature Genetics.

[4]  Heiko Schoof,et al.  PlantMarkers—a database of predicted molecular markers from plants , 2004, Nucleic Acids Res..

[5]  J. Ellis,et al.  Molecular Characterization of the Maize Rp1-D Rust Resistance Haplotype and Its Mutants , 1999, Plant Cell.

[6]  Zhikang Li,et al.  Pyramiding three bacterial blight resistance genes (xa5, xa13 and Xa21) using marker-assisted selection into indica rice cultivar PR106 , 2001, Theoretical and Applied Genetics.

[7]  S. Tanksley,et al.  Saturated molecular map of the rice genome based on an interspecific backcross population. , 1994, Genetics.

[8]  W. Richard McCombie,et al.  Sorghum Genome Sequencing by Methylation Filtration , 2005, PLoS biology.

[9]  B. Keller,et al.  Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat. , 2004, The Plant journal : for cell and molecular biology.

[10]  K. Devos Updating the 'crop circle'. , 2005, Current opinion in plant biology.

[11]  D. Zilberman,et al.  Is marker-assisted selection cost-effective compared with conventional plant breeding methods? The case of quality protein Maize. , 2002 .

[12]  I. Leitch,et al.  Nuclear DNA Amounts in Angiosperms , 1995 .

[13]  Junhua Peng,et al.  Comparative DNA sequence analysis of wheat and rice genomes. , 2003, Genome research.

[14]  K. Edwards,et al.  Toward positional cloning of Vgt1, a QTL controlling the transition from the vegetative to the reproductive phase in maize , 2002, Plant Molecular Biology.

[15]  S. Jackson,et al.  The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. , 2005, Genome research.

[16]  Rod A Wing,et al.  A New Resource for Cereal Genomics: 22K Barley GeneChip Comes of Age1 , 2004, Plant Physiology.

[17]  A. Graner,et al.  Functional association between malting quality trait components and cDNA array based expression patterns in barley (Hordeum vulgare L.) , 2004, Molecular Breeding.

[18]  G. Wang,et al.  Genetic and physical mapping of Pi5(t), a locus associated with broad-spectrum resistance to rice blast , 2003, Molecular Genetics and Genomics.

[19]  B. Han,et al.  The Broad-Spectrum Blast Resistance Gene Pi9 Encodes a Nucleotide-Binding Site–Leucine-Rich Repeat Protein and Is a Member of a Multigene Family in Rice , 2006, Genetics.

[20]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

[21]  W. Powell,et al.  Introgression of quantitative trait loci (QTLs) determining stripe rust resistance in barley: an example of marker-assisted line development , 1998, Theoretical and Applied Genetics.

[22]  S. Henikoff,et al.  Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. , 2004, The Plant journal : for cell and molecular biology.

[23]  Nils Rostoks,et al.  The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Zhengwei Liang,et al.  Fine Mapping and Characterization of Quantitative Trait Loci Hd4 and Hd5 Controlling Heading Date in Rice. , 2003 .

[25]  A. Graner,et al.  The eukaryotic translation initiation factor 4E confers multiallelic recessive Bymovirus resistance in Hordeum vulgare (L.). , 2005, The Plant journal : for cell and molecular biology.

[26]  P. Langridge,et al.  The Ph2 pairing homoeologous locus of wheat (Triticum aestivum): identification of candidate meiotic genes using a comparative genetics approach. , 2003, The Plant journal : for cell and molecular biology.

[27]  E. Buckler,et al.  Structure of linkage disequilibrium in plants. , 2003, Annual review of plant biology.

[28]  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.

[29]  A. Paterson Leafing through the genomes of our major crop plants: strategies for capturing unique information , 2006, Nature Reviews Genetics.

[30]  Kazuyuki Doi,et al.  Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. , 2004, Genes & development.

[31]  R. Koebner Marker Assisted Selection in the Cereals: The Dream and the Reality , 2004 .

[32]  B. Gill,et al.  Molecular Characterization of the Major Wheat Domestication Gene Q , 2006, Genetics.

[33]  Q. Qian,et al.  Cytokinin Oxidase Regulates Rice Grain Production , 2005, Science.

[34]  T. Schnurbusch,et al.  Dissection of quantitative and durable leaf rust resistance in Swiss winter wheat reveals a major resistance QTL in the Lr34 chromosomal region , 2004, Theoretical and Applied Genetics.

[35]  Li-li Chen,et al.  A Receptor Kinase-Like Protein Encoded by the Rice Disease Resistance Gene, Xa21 , 1995, Science.

[36]  W. Spielmeyer,et al.  Powdery mildew resistance and Lr34/Yr18 genes for durable resistance to leaf and stripe rust cosegregate at a locus on the short arm of chromosome 7D of wheat , 2005, Theoretical and Applied Genetics.

[37]  R. Tarchini,et al.  A Single Amino Acid Difference Distinguishes Resistant and Susceptible Alleles of the Rice Blast Resistance Gene Pi-ta , 2000, Plant Cell.

[38]  R. M. Goodman,et al.  Gene Transfer in Crop Improvement , 1987, Science.

[39]  I. Colas,et al.  Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat , 2006, Nature.

[40]  M. Sorrells,et al.  Association Mapping of Kernel Size and Milling Quality in Wheat (Triticum aestivum L.) Cultivars , 2006, Genetics.

[41]  M. Yano,et al.  Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the α subunit of protein kinase CK2 , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[42]  P. Langridge,et al.  Marker‐assisted backcross introgression of the Yd2 gene conferring resistance to barley yellow dwarf virus in barley , 2003 .

[43]  M. Wolter,et al.  The Barley Mlo Gene: A Novel Control Element of Plant Pathogen Resistance , 1997, Cell.

[44]  R. Naylor,et al.  Biotechnology in the developing world: a case for increased investments in orphan crops , 2004 .

[45]  Patrick Schweizer,et al.  Large-scale analysis of the barley transcriptome based on expressed sequence tags. , 2004, The Plant journal : for cell and molecular biology.

[46]  S. Salvi,et al.  QTLs and Genes for Tolerance to Abiotic Stress in Cereals , 2004 .

[47]  M. Yano,et al.  A rice spotted leaf gene, Spl7, encodes a heat stress transcription factor protein , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[48]  G. Toenniessen,et al.  Advances in plant biotechnology and its adoption in developing countries. , 2003, Current opinion in plant biology.

[49]  A. Aharoni,et al.  DNA microarrays for functional plant genomics , 2004, Plant Molecular Biology.

[50]  Thomas Lübberstedt,et al.  Functional markers in plants. , 2003, Trends in plant science.

[51]  R. Varshney,et al.  The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat , 2000, Euphytica.

[52]  Takuji Sasaki,et al.  The map-based sequence of the rice genome , 2005, Nature.

[53]  Steven G. Schroeder,et al.  Genetic, Physical, and Informatics Resources for Maize. On the Road to an Integrated Map1 , 2002, Plant Physiology.

[54]  B. Keller,et al.  Map-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[55]  E. Buckler,et al.  Genetic association mapping and genome organization of maize. , 2006, Current opinion in biotechnology.

[56]  M. Yano,et al.  The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. , 1999, The Plant journal : for cell and molecular biology.

[57]  S. Mccouch,et al.  The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. , 2004, Molecular plant-microbe interactions : MPMI.

[58]  R. Varshney,et al.  Molecular Maps in Cereals: Methodology and Progress , 2004 .

[59]  Andreas Graner,et al.  Genic microsatellite markers in plants: features and applications. , 2005, Trends in biotechnology.

[60]  Xinli Sun,et al.  Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein. , 2004, The Plant journal : for cell and molecular biology.

[61]  A. Thomson,et al.  The fast and the cheap: SNP and DArT-based whole genome profiling for crop improvement , 2005 .

[62]  D. Bartel,et al.  MicroRNAS and their regulatory roles in plants. , 2006, Annual review of plant biology.

[63]  R. Naylor,et al.  The Role of Genomics Research in Improvement of “Orphan” Crops , 2004 .

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

[65]  M. Morgante,et al.  Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. , 2004, Trends in genetics : TIG.

[66]  Y. Kohara,et al.  Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags. , 2003, The Plant journal : for cell and molecular biology.

[67]  李佩芳 International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. , 2005 .

[68]  R. B. Flavell,et al.  Genome size and the proportion of repeated nucleotide sequence DNA in plants , 1974, Biochemical Genetics.

[69]  N. Baisakh,et al.  Molecular Breeding for the Development of Blast and Bacterial Blight Resistance in Rice cv. IR50 , 2002 .

[70]  R. Varshney,et al.  Methodological Advancement in Molecular Markers to Delimit the Gene(s) for Crop Improvement , 2006 .

[71]  A. Paterson,et al.  Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation. , 2001, Plant physiology.

[72]  M. Ellis,et al.  Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[73]  S. Luan,et al.  A rice quantitative trait locus for salt tolerance encodes a sodium transporter , 2005, Nature Genetics.

[74]  B. Gill,et al.  Genomics for Cereal Improvement , 2004 .

[75]  P. Schulze-Lefert,et al.  A Novel Class of Eukaryotic Zinc-Binding Proteins Is Required for Disease Resistance Signaling in Barley and Development in C. elegans , 1999, Cell.

[76]  Nori Kurata,et al.  PLASTOCHRON1, a timekeeper of leaf initiation in rice, encodes cytochrome P450. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[77]  R. Varshney,et al.  Genomics-assisted breeding for crop improvement. , 2005, Trends in plant science.

[78]  P. Donnelly,et al.  Association mapping in structured populations. , 2000, American journal of human genetics.

[79]  M. Yano,et al.  Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[80]  P. Langridge,et al.  Molecular breeding of wheat and barley , 2005 .

[81]  W. Spielmeyer,et al.  Fine genetic mapping fails to dissociate durable stem rust resistance gene Sr2 from pseudo-black chaff in common wheat (Triticum aestivum L.) , 2006, Theoretical and Applied Genetics.

[82]  Takashi Araki,et al.  Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. , 2002, Plant & cell physiology.

[83]  M. Morgante,et al.  From plant genomics to breeding practice. , 2003, Current opinion in biotechnology.

[84]  D. Hoisington,et al.  Marker-assisted selection: new tools and strategies , 1998 .

[85]  M. Morgante,et al.  Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[86]  M. Yano,et al.  Rice gibberellin-insensitive dwarf mutant gene Dwarf 1 encodes the alpha-subunit of GTP-binding protein. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[87]  A. Jaime,et al.  Floriculture, ornamental and plant biotechnology : advances and topical issues , 2006 .

[88]  Bryan Frank,et al.  Independence and reproducibility across microarray platforms , 2005, Nature Methods.

[89]  Ashutosh Kumar Singh,et al.  Combining bacterial blight resistance and Basmati quality characteristics by phenotypic and molecular marker-assisted selection in rice , 2004, Molecular Breeding.

[90]  J. Bennetzen,et al.  The Wheat VRN2 Gene Is a Flowering Repressor Down-Regulated by Vernalization , 2004, Science.

[91]  Vikrant Gupta,et al.  Decoding the rice genome , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

[92]  Zhikang Li,et al.  Sequence Tagged Site Marker-Assisted Selection for Three Bacterial Blight Resistance Genes in Rice , 2000 .

[93]  Jian Jin,et al.  Development of Genome-Wide DNA Polymorphism Database for Map-Based Cloning of Rice Genes1[w] , 2004, Plant Physiology.

[94]  M. Yano,et al.  An SNP Caused Loss of Seed Shattering During Rice Domestication , 2006, Science.

[95]  Jun Wang,et al.  Genome-wide transcription analyses in rice using tiling microarrays , 2006, Nature Genetics.

[96]  B. Gill,et al.  Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of bread wheat. , 2003, Genetics.

[97]  A. Rafalski Applications of single nucleotide polymorphisms in crop genetics. , 2002, Current opinion in plant biology.

[98]  M. Yano,et al.  Hd1, a Major Photoperiod Sensitivity Quantitative Trait Locus in Rice, Is Closely Related to the Arabidopsis Flowering Time Gene CONSTANS , 2000, Plant Cell.

[99]  L. Mao,et al.  The Mla (powdery mildew) resistance cluster is associated with three NBS-LRR gene families and suppressed recombination within a 240-kb DNA interval on chromosome 5S (1HS) of barley. , 1999, Genetics.

[100]  F. V. van Eeuwijk,et al.  Linkage Disequilibrium Mapping of Yield and Yield Stability in Modern Spring Barley Cultivars , 2004, Genetics.

[101]  S. Fuerstenberg,et al.  A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING , 2005, Nature Biotechnology.

[102]  L. Eriksen,et al.  QTLs and Genes for Disease Resistance in Barley and Wheat , 2004 .

[103]  J. Anderson,et al.  Targeted molecular mapping of a major wheat QTL for Fusarium head blight resistance using wheat ESTs and synteny with rice. , 2003, Genome.