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?

Article

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.

Keywords

cereals functional genomics genome sequencing molecular markers plant breeding rice 

Abbreviations

AFLP

amplified fragment length polymorphism

BAC

bacterial artificial chromosome

COS

conserved orthologous sequence

DHPLC

denaturing high-pressure liquid chromatography

EST

expressed sequence tag

FM

functional marker

MAS

marker assisted selection

ORF

open reading frame

QTL

quantitative trait locus or loci

RM

random marker

RNAi

RNA interference

SAGE

serial analysis of gene expression

SNP

single nucleotide polymorphism

SSR

simple sequence repeat

TILLING

targeting induced local lesions in genomes

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© 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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