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

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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.

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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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  1. Department of Plant Breeding, Cornell University, Ithaca, NY, 14853-1901, USA

    Yunbi Xu & Susan R. McCouch

  2. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

    Qifa Zhang

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Xu, Y., McCouch, S.R. & Zhang, Q. How Can We Use Genomics to Improve Cereals with Rice as a Reference Genome?. Plant Mol Biol 59, 7–26 (2005). https://doi.org/10.1007/s11103-004-4681-2

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