Cloning and mapping of variety-specific rice genomic DNA sequences: amplified fragment length polymorphisms (AFLP) from silver-stained polyacrylamide gels.

An efficient technique for cloning DNA from silver-stained denaturing polyacrylamide gels was developed to allow the isolation of specific bands obtained from selective restriction fragment amplification (SRFA). This method proved as reliable as cloning radioactively labelled SRFA bands from the same gels. Rice DNA was used as a template, both with and without [32P]dCTP, using the same PCR profiles. Amplified products were separated using denaturing polyacryamide gel electrophoresis and visualized either by silver staining of gels or by autoradiography of 32P-labelled products. We cloned specific polymorphic SRFA bands directly from the denaturing polyacrylamide gels with one round of PCR amplification and confirmed that the sequences of the bands from silver-stained gels were identical to the corresponding 32P-labelled bands. The bands that were chosen represented amplified fragment length polymorphisms (AFLPs) between japonica and indica rice varieties. We studied the ability of two cloned AFLP bands to serve as heritable genetic markers by mapping them as RFLPs in an interspecific rice population and found that they represented single-copy DNA at unique loci in the rice genome.

[1]  A. Paterson,et al.  Preparation of megabase‐size DNA from plant nuclei , 1995 .

[2]  P. Vos,et al.  AFLP: a new technique for DNA fingerprinting. , 1995, Nucleic acids research.

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

[4]  S. Lin,et al.  A 300 kilobase interval genetic map of rice including 883 expressed sequences , 1994, Nature Genetics.

[5]  D. Labuda,et al.  Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. , 1994, Genomics.

[6]  L. M. Callahan,et al.  Isolation and cloning of DNA amplification products from silver-stained polyacrylamide gels. , 1994, BioTechniques.

[7]  A. Pardee,et al.  Distribution and cloning of eukaryotic mRNAs by means of differential display: refinements and optimization. , 1993, Nucleic acids research.

[8]  B J Bassam,et al.  Fast and sensitive silver staining of DNA in polyacrylamide gels. , 1991, Analytical biochemistry.

[9]  K. Livak,et al.  DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. , 1990, Nucleic acids research.

[10]  Christopher Southan,et al.  Purification to apparent homogeneity and partial amino acid sequence of rat liver O6-alkylguanine-DNA-alkyltransferase , 1990, Nucleic Acids Res..

[11]  J. Welsh,et al.  Fingerprinting genomes using PCR with arbitrary primers. , 1990, Nucleic acids research.

[12]  S. Tanksley,et al.  Restriction fragment length polymorphism in Oryza sativa L. , 1989 .

[13]  M. Daly,et al.  MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. , 1987, Genomics.

[14]  K. Mullis,et al.  Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. , 1986, Cold Spring Harbor symposia on quantitative biology.

[15]  A. Feinberg,et al.  A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. , 1983, Analytical biochemistry.

[16]  C. Merril,et al.  Silver staining of DNA in polyacrylamide gels: Linearity and effect of fragment size , 1982 .