Home LiteratureArticle Details
PMID: 16217598 Published · ppublish English Comparative Study Journal Article

How can we use genomics to improve cereals with rice as a reference genome?

Plant molecular biology ·Vol. 59 ·No. 1 ·2005-09-00 ·Pages 7-26

Xu Y, McCouch SR, Zhang Q

Abstract

Rice serves as a model crop for cereal genomics. The availability of complete genome sequences, together with various genomic resources available for both rice and Arabidopsis, have revolutionized our understanding of the genetic make-up of crop plants. Both macrocolinearity revealed by comparative mapping and microcolinearity revealed by sequence comparisons among the grasses indicate that sequencing and functional analysis of the rice genome will have a significant impact on other cereals in terms of both genomic studies and crop improvement. The availability of mutants, introgression libraries, and advanced transformation techniques make functional genomics in rice and other cereals more manageable than ever before. A wide array of genetic markers, including anchor markers for comparative mapping, SSRs and SNPs are widely used in genetic mapping, germplasm evaluation and marker assisted selection. An integrated database that combines genome information for rice and other cereals is key to the effective utilization of all genomics resources for cereal improvement. To maximize the potential of genomics for plant breeding, experiments must be further miniaturized and costs must be reduced. Many techniques, including targeted gene disruption or allele substitution, insertional mutagenesis, RNA interference and homologous recombination, need to be refined before they can be widely used in functional genomic analysis and plant breeding.

MeSH Terms
Chromosome Mapping Chromosomes, Plant Cloning, Molecular Edible Grain/genetics,growth & development Genes, Plant/genetics Genetic Markers Genome, Plant Genomics/methods Oryza/genetics,growth & development Plants, Genetically Modified Synteny
Chemicals
Genetic Markers
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Xu Yunbi
Department of Plant Breeding, Cornell University, Ithaca, NY 14853-1901, USA.
McCouch Susan R
Zhang Qifa
References (114)
114 references, click to expand
  1. Genome relationships: the grass model in current research.
    Plant Cell. 2000 May;12(5):637-46 PMID: 10810140
  2. Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross.
    Theor Appl Genet. 1996 Feb;92(2):230-44 PMID: 24166172
  3. Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation.
    Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1663-8 PMID: 9465073
  4. Mosaic organization of orthologous sequences in grass genomes.
    Genome Res. 2002 Oct;12(10):1549-55 PMID: 12368247
  5. Multiplexed genotyping with sequence-tagged molecular inversion probes.
    Nat Biotechnol. 2003 Jun;21(6):673-8 PMID: 12730666
  6. Plant genome evolution: lessons from comparative genomics at the DNA level.
    Plant Mol Biol. 2002 Jan;48(1-2):21-37 PMID: 11860210
  7. Seed banks and molecular maps: unlocking genetic potential from the wild.
    Science. 1997 Aug 22;277(5329):1063-6 PMID: 9262467
  8. Structure of linkage disequilibrium and phenotypic associations in the maize genome.
    Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11479-84 PMID: 11562485
  9. Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS.
    Plant Cell. 2000 Dec;12(12):2473-2484 PMID: 11148291
  10. High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics.
    Plant J. 2004 Aug;39(3):450-64 PMID: 15255873
  11. Marker-assisted introgression of quantitative trait loci.
    Genetics. 1997 Nov;147(3):1469-85 PMID: 9383086
  12. The wheat VRN2 gene is a flowering repressor down-regulated by vernalization.
    Science. 2004 Mar 12;303(5664):1640-4 PMID: 15016992
  13. Towards map-based cloning of the barley stem rust resistance genes Rpg1 and rpg4 using rice as an intergenomic cloning vehicle.
    Plant Mol Biol. 1997 Sep;35(1-2):187-95 PMID: 9291972
  14. Inferences on the genome structure of progenitor maize through comparative analysis of rice, maize and the domesticated panicoids.
    Genetics. 1999 Sep;153(1):453-73 PMID: 10471726
  15. Establishing an efficient Ac/Ds tagging system in rice: large-scale analysis of Ds flanking sequences.
    Plant J. 2004 Jan;37(2):301-14 PMID: 14690513
  16. Efficient gene targeting by homologous recombination in rice.
    Nat Biotechnol. 2002 Oct;20(10):1030-4 PMID: 12219079
  17. Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm.
    Theor Appl Genet. 2004 Aug;109(4):681-9 PMID: 15300382
  18. Generation of T-DNA tagging lines with a bidirectional gene trap vector and the establishment of an insertion-site database.
    Plant Mol Biol. 2004 Mar;54(4):489-502 PMID: 15316285
  19. Gramene: development and integration of trait and gene ontologies for rice.
    Comp Funct Genomics. 2002;3(2):132-6 PMID: 18628886
  20. The hidden duplication past of Arabidopsis thaliana.
    Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13627-32 PMID: 12374856
  21. Rice mutant resources for gene discovery.
    Plant Mol Biol. 2004 Feb;54(3):325-34 PMID: 15284490
  22. tA single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta.
    Plant Cell. 2000 Nov;12(11):2033-46 PMID: 11090207
  23. An introduction to the China Rice Functional Genomics Program.
    Comp Funct Genomics. 2002;3(2):161-3 PMID: 18628891
  24. Rapid reorganization of resistance gene homologues in cereal genomes.
    Proc Natl Acad Sci U S A. 1998 Jan 6;95(1):370-5 PMID: 9419382
  25. Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of bread wheat.
    Genetics. 2003 Jun;164(2):655-64 PMID: 12807786
  26. The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis.
    Curr Opin Plant Biol. 2003 Apr;6(2):128-33 PMID: 12667868
  27. A rice semi-dwarf gene, Tan-Ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase.
    Plant Mol Biol. 2004 Mar;54(4):533-47 PMID: 15316288
  28. Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon.
    Theor Appl Genet. 2003 Nov;107(8):1419-32 PMID: 14513215
  29. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).
    Science. 2002 Apr 5;296(5565):92-100 PMID: 11935018
  30. Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon.
    Genetics. 1998 Oct;150(2):899-909 PMID: 9755218
  31. Development of enhancer trap lines for functional analysis of the rice genome.
    Plant J. 2003 Aug;35(3):418-27 PMID: 12887592
  32. The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice.
    Genome Res. 2002 Nov;12(11):1792-801 PMID: 12421767
  33. Intraspecific violation of genetic colinearity and its implications in maize.
    Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9573-8 PMID: 12060715
  34. Genomics and synteny.
    Plant Physiol. 2001 Jan;125(1):152-5 PMID: 11154321
  35. Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson.
    Theor Appl Genet. 2003 Aug;107(3):479-93 PMID: 12736777
  36. Advances in cereal gene transfer.
    Curr Opin Plant Biol. 1998 Apr;1(2):161-5 PMID: 10066572
  37. Applications of single nucleotide polymorphisms in crop genetics.
    Curr Opin Plant Biol. 2002 Apr;5(2):94-100 PMID: 11856602
  38. Linkage disequilibrium mapping of molecular polymorphisms at the scabrous locus associated with naturally occurring variation in bristle number in Drosophila melanogaster.
    Genet Res. 1999 Dec;74(3):303-11 PMID: 10689806
  39. Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and Am genomes of wheat.
    Plant Cell. 2003 May;15(5):1186-97 PMID: 12724543
  40. The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4.
    Plant Cell. 2000 Mar;12(3):381-91 PMID: 10715324
  41. Control of tillering in rice.
    Nature. 2003 Apr 10;422(6932):618-21 PMID: 12687001
  42. Sequence and analysis of rice chromosome 4.
    Nature. 2002 Nov 21;420(6913):316-20 PMID: 12447439
  43. BRITTLE CULM1, which encodes a COBRA-like protein, affects the mechanical properties of rice plants.
    Plant Cell. 2003 Sep;15(9):2020-31 PMID: 12953108
  44. Simultaneous improvement for four quality traits of Zhenshan 97, an elite parent of hybrid rice, by molecular marker-assisted selection.
    Theor Appl Genet. 2003 Jan;106(2):326-31 PMID: 12582859
  45. Efficient discovery of DNA polymorphisms in natural populations by Ecotilling.
    Plant J. 2004 Mar;37(5):778-86 PMID: 14871304
  46. Comparative genetics in the grasses.
    Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):1971-4 PMID: 9482816
  47. A draft sequence of the rice genome (Oryza sativa L. ssp. indica).
    Science. 2002 Apr 5;296(5565):79-92 PMID: 11935017
  48. Single-nucleotide mutations for plant functional genomics.
    Annu Rev Plant Biol. 2003;54:375-401 PMID: 14502996
  49. Identification of the fertility restoration locus, Rfo, in radish, as a member of the pentatricopeptide-repeat protein family.
    EMBO Rep. 2003 Jun;4(6):588-94 PMID: 12740605
  50. Tandemly duplicated Safener-induced glutathione S-transferase genes from Triticum tauschii contribute to genome- and organ-specific expression in hexaploid wheat.
    Plant Physiol. 2002 Sep;130(1):362-73 PMID: 12226515
  51. Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants.
    Plant Cell. 2002 Jul;14(7):1457-67 PMID: 12119367
  52. Arabidopsis map-based cloning in the post-genome era.
    Plant Physiol. 2002 Jun;129(2):440-50 PMID: 12068090
  53. 'Green revolution' genes encode mutant gibberellin response modulators.
    Nature. 1999 Jul 15;400(6741):256-61 PMID: 10421366
  54. Positional cloning of rice semidwarfing gene, sd-1: rice "green revolution gene" encodes a mutant enzyme involved in gibberellin synthesis.
    DNA Res. 2002 Feb 28;9(1):11-7 PMID: 11939564
  55. Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2.
    Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7922-7 PMID: 11416158
  56. Gramene, a tool for grass genomics.
    Plant Physiol. 2002 Dec;130(4):1606-13 PMID: 12481044
  57. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science. 2003 Jul 18;301(5631):376-9 PMID: 12869764
  58. Plant bioinformatics: from genome to phenome.
    Trends Biotechnol. 2004 May;22(5):232-7 PMID: 15109809
  59. The genome sequence and structure of rice chromosome 1.
    Nature. 2002 Nov 21;420(6913):312-6 PMID: 12447438
  60. The distribution and copy number of copia-like retrotransposons in rice (Oryza sativa L.) and their implications in the organization and evolution of the rice genome.
    Proc Natl Acad Sci U S A. 1999 Jun 8;96(12):6824-8 PMID: 10359797
  61. Rapid recent growth and divergence of rice nuclear genomes.
    Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12404-10 PMID: 15240870
  62. Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein.
    Plant J. 2004 Feb;37(4):517-27 PMID: 14756760
  63. Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene.
    Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):9043-8 PMID: 12077303
  64. Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5A(m).
    Funct Integr Genomics. 2002 May;2(1-2):70-80 PMID: 12021852
  65. Sequence-based alignment of sorghum chromosome 3 and rice chromosome 1 reveals extensive conservation of gene order and one major chromosomal rearrangement.
    Plant J. 2003 Jun;34(5):605-21 PMID: 12787243
  66. Relationships of cereal crops and other grasses.
    Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2005-10 PMID: 9482825
  67. Rice as a model for comparative genomics of plants.
    Annu Rev Plant Biol. 2002;53:399-419 PMID: 12221982
  68. T-DNA insertional mutagenesis for functional genomics in rice.
    Plant J. 2000 Jun;22(6):561-70 PMID: 10886776
  69. Comparative linkage maps of the rice and maize genomes.
    Proc Natl Acad Sci U S A. 1993 Sep 1;90(17):7980-4 PMID: 8103599
  70. Development of genome-wide DNA polymorphism database for map-based cloning of rice genes.
    Plant Physiol. 2004 Jul;135(3):1198-205 PMID: 15266053
  71. Comparative analyses of genomic locations and race specificities of loci for quantitative resistance to Pyricularia grisea in rice and barley.
    Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2544-9 PMID: 12601171
  72. Comparative DNA sequence analysis of wheat and rice genomes.
    Genome Res. 2003 Aug;13(8):1818-27 PMID: 12902377
  73. Establishing gene function by mutagenesis in Arabidopsis thaliana.
    Plant J. 2004 Sep;39(5):682-96 PMID: 15315632
  74. A large rearrangement involving genes and low-copy DNA interrupts the microcollinearity between rice and barley at the Rph7 locus.
    Genetics. 2003 Jun;164(2):673-83 PMID: 12807788
  75. In-depth view of structure, activity, and evolution of rice chromosome 10.
    Science. 2003 Jun 6;300(5625):1566-9 PMID: 12791992
  76. Plant molecular diversity and applications to genomics.
    Curr Opin Plant Biol. 2002 Apr;5(2):107-11 PMID: 11856604
  77. Numerous small rearrangements of gene content, order and orientation differentiate grass genomes.
    Plant Mol Biol. 2002 Mar-Apr;48(5-6):821-7 PMID: 11999852
  78. New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome.
    Plant J. 2004 May;38(3):396-409 PMID: 15086801
  79. Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.).
    Genetics. 2003 Oct;165(2):759-69 PMID: 14573486
  80. Evidence for orthologous seed weight genes in cowpea and mung bean based on RFLP mapping.
    Genetics. 1992 Nov;132(3):841-6 PMID: 1361476
  81. Convergent domestication of cereal crops by independent mutations at corresponding genetic Loci.
    Science. 1995 Sep 22;269(5231):1714-8 PMID: 17821643
  82. QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice ( Oryza sativa) using microsatellite markers.
    Theor Appl Genet. 2002 May;104(6-7):1192-1203 PMID: 12582630
  83. The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases.
    Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9328-33 PMID: 12077318
  84. Plant genome modification by homologous recombination.
    Curr Opin Plant Biol. 2003 Apr;6(2):157-62 PMID: 12667873
  85. Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions.
    Plant Cell Physiol. 2002 Oct;43(10):1096-105 PMID: 12407188
  86. Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines.
    Theor Appl Genet. 1996 Feb;92(2):191-203 PMID: 24166168
  87. Dwarf8 polymorphisms associate with variation in flowering time.
    Nat Genet. 2001 Jul;28(3):286-9 PMID: 11431702
  88. Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes.
    Plant Physiol. 2001 Mar;125(3):1342-53 PMID: 11244114
  89. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA.
    Plant J. 1994 Aug;6(2):271-82 PMID: 7920717
  90. Genome-wide intraspecific DNA-sequence variations in rice.
    Curr Opin Plant Biol. 2003 Apr;6(2):134-8 PMID: 12667869
  91. Cereal genome evolution. Grasses, line up and form a circle.
    Curr Biol. 1995 Jul 1;5(7):737-9 PMID: 7583118
  92. Positional cloning of the wheat vernalization gene VRN1.
    Proc Natl Acad Sci U S A. 2003 May 13;100(10):6263-8 PMID: 12730378
  93. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
    Nature. 2000 Dec 14;408(6814):796-815 PMID: 11130711
  94. A role of OsGA20ox1 , encoding an isoform of gibberellin 20-oxidase, for regulation of plant stature in rice.
    Plant Mol Biol. 2004 Jul;55(5):687-700 PMID: 15604710
  95. Tackling the plant proteome: practical approaches, hurdles and experimental tools.
    Plant J. 2004 Sep;39(5):715-33 PMID: 15315634
  96. A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21.
    Science. 1995 Dec 15;270(5243):1804-6 PMID: 8525370
  97. Zooming in on a quantitative trait for tomato yield using interspecific introgressions.
    Science. 2004 Sep 17;305(5691):1786-9 PMID: 15375271
  98. The radish Rfo restorer gene of Ogura cytoplasmic male sterility encodes a protein with multiple pentatricopeptide repeats.
    Plant J. 2003 Jul;35(2):262-72 PMID: 12848830
  99. Monitoring of gene expression profiles and isolation of candidate genes involved in pollination and fertilization in rice ( Oryza sativa L.) with a 10K cDNA microarray.
    Plant Mol Biol. 2004 Mar;54(4):471-87 PMID: 15316284
  100. Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop species.
    Plant Physiol. 2004 Jun;135(2):622-9 PMID: 15208410
  101. LineUp: statistical detection of chromosomal homology with application to plant comparative genomics.
    Genome Res. 2003 May;13(5):999-1010 PMID: 12695327
  102. Comparative analysis of QTLs affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population.
    Genetics. 1995 Sep;141(1):391-411 PMID: 8536986
  103. Restriction fragment length polymorphism maps and the concept of graphical genotypes.
    Theor Appl Genet. 1989 Jan;77(1):95-101 PMID: 24232480
  104. Evidence that rice and other cereals are ancient aneuploids.
    Plant Cell. 2003 Sep;15(9):2192-202 PMID: 12953120
  105. Maximizing the potential of functional genomics.
    Nat Rev Genet. 2004 Mar;5(3):190-201 PMID: 14970821
  106. High gene density is conserved at syntenic loci of small and large grass genomes.
    Proc Natl Acad Sci U S A. 1999 Jul 6;96(14):8265-70 PMID: 10393983
  107. Comparative mapping in grasses. Oat relationships.
    Mol Gen Genet. 1995 Nov 27;249(3):349-56 PMID: 7500960
  108. Re-evaluating the relevance of ancestral shared synteny as a tool for crop improvement.
    Curr Opin Plant Biol. 2004 Apr;7(2):126-31 PMID: 15003211
  109. Structural domains and matrix attachment regions along colinear chromosomal segments of maize and sorghum.
    Plant Cell. 2000 Feb;12(2):249-64 PMID: 10662861
  110. A bacterial artificial chromosome contig spanning the major domestication locus Q in wheat and identification of a candidate gene.
    Genetics. 2003 May;164(1):311-21 PMID: 12750342
  111. Comparative mapping of the barley Ppd-H1 photoperiod response gene region, which lies close to a junction between two rice linkage segments.
    Genetics. 2002 Jun;161(2):825-34 PMID: 12072477
  112. Targeting induced local lesions IN genomes (TILLING) for plant functional genomics.
    Plant Physiol. 2000 Jun;123(2):439-42 PMID: 10859174
  113. Functional markers in plants.
    Trends Plant Sci. 2003 Nov;8(11):554-60 PMID: 14607101
  114. The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes.
    Plant J. 1999 Jul;19(1):55-64 PMID: 10417726
Article Info
Journal
Plant molecular biology
Abbr.
Plant Mol Biol
ISSN
0167-4412
DOI
10.1007/s11103-004-4681-2
Published
2005-09-00
Pages
7-26
Language
English
Region
Netherlands
NLM ID
9106343
Subset
IM
External Links
PubMed source DOI: 10.1007/s11103-004-4681-2 View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2