Genotyping single nucleotide polymorphisms in barley by tetra-primer ARMS-PCR.

Single nucleotide polymorphisms (SNPs) are the most abundant form of DNA polymorphism. These polymorphisms can be used in plants as simple genetic markers for many breeding applications, for population studies, and for germplasm fingerprinting. The great increase in the available DNA sequences in the databases has made it possible to identify SNPs by "database mining", and the single most important factor preventing their widespread use appears to be the genotyping cost. Many genotyping platforms rely on the use of sophisticated, automated equipment coupled to costly chemistry and detection systems. A simple and economical method involving a single PCR is reported here for barley SNP genotyping. Using the tetra-primer ARMS-PCR procedure, we have been able to assay unambiguously five SNPs in a set of 132 varieties of cultivated barley. The results show the reliability of this technique and its potential for use in low- to moderate-throughput situations; the association of agronomically important traits is discussed.

[1]  R. Henry.  Plant Genotyping: The DNA Fingerprinting of Plants , 2001 .

[2]  Brandon S. Gaut,et al.  Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.) , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Ridout,et al.  Use of AFLP in cereals research. , 1999, Trends in plant science.

[4]  E. Nevo,et al.  Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare) , 2002, Plant Molecular Biology.

[5]  W. Powell,et al.  Homology of AFLP products in three mapping populations of barley , 1997, Molecular and General Genetics MGG.

[6]  E. Southern.  Detection of specific sequences among DNA fragments separated by gel electrophoresis. , 1975, Journal of molecular biology.

[7]  D. Laurie,et al.  RFLP mapping of five major genes and eight quantitative trait loci controlling flowering time in a winter x spring barley (Hordeum vulgare L.) cross. , 1995, Genome.

[8]  A. Rafalski,et al.  High-throughput identification, database storage and analysis of SNPs in EST sequences. , 2001, Genome informatics. International Conference on Genome Informatics.

[9]  D. Delmer,et al.  A membrane-associated form of sucrose synthase and its potential role in synthesis of cellulose and callose in plants. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[10]  R K Varshney,et al.  Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). , 2004, Hereditas.

[11]  Mark Jung,et al.  SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines , 2002, BMC Genetics.

[12]  M. Ronaghi,et al.  A Sequencing Method Based on Real-Time Pyrophosphate , 1998, Science.

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

[14]  F. Salamini,et al.  SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes , 2001, Molecular Breeding.

[15]  S. Larson.  Plant Genotyping: The DNA Fingerprinting of Plants , 2002, Heredity.

[16]  G. Bryan,et al.  The potential of microsatellites for high throughput genetic diversity assessment in wheat and barley , 1998, Genetic Resources and Crop Evolution.

[17]  I. Day,et al.  An efficient procedure for genotyping single nucleotide polymorphisms. , 2001, Nucleic acids research.

[18]  A. Rafalski.  Applications of single nucleotide polymorphisms in crop genetics. , 2002, Current opinion in plant biology.

[19]  K. Mullis,et al.  Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. , 1988, Science.

[20]  P. Kwok,et al.  Reading bits of genetic information: methods for single-nucleotide polymorphism analysis. , 1998, Genome research.

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

[22]  R. J. Henry,et al.  Robust allele-specific polymerase chain reaction markers developed for single nucleotide polymorphisms in expressed barley sequences , 2005, Theoretical and Applied Genetics.