Plant Molecular Biology

, Volume 59, Issue 1, pp 7–26 | Cite as

How Can We Use Genomics to Improve Cereals with Rice as a Reference Genome?



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.


cereals functional genomics genome sequencing molecular markers plant breeding rice 



amplified fragment length polymorphism


bacterial artificial chromosome


conserved orthologous sequence


denaturing high-pressure liquid chromatography


expressed sequence tag


functional marker


marker assisted selection


open reading frame


quantitative trait locus or loci


random marker


RNA interference


serial analysis of gene expression


single nucleotide polymorphism


simple sequence repeat


targeting induced local lesions in genomes


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Copyright information

© Springer 2005

Authors and Affiliations

  1. 1.Department of Plant BreedingCornell UniversityIthacaUSA
  2. 2.National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina

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