Comparison of PCR marker methods for cereal identification

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Ko, HL & Henry, RJ 1996, 'Comparison of PCR marker methods for cereal identification', paper presented to the Plant Genome IV Conference, San Diego, California, USA, January.


Genotype identification in cereals is important as different varieties are suitable for different end-uses, e.g. malt vs. feed in barley, bread vs. pasta or noodles in wheat, aromatic vs. non-aromatic rice. Several PCR methods were compared for their suitability in providing DNA fingerprints for distinguishing cereal varieties from one another or to study the genetic diversity within a species. These included the use of RAPD-PCR using arbitrary primers and PCR using primers based on barley a-amylase genes and microsatellites. Reliable identification of cereal species is potentially useful for determination of the composition of admixtures or processed products. A simple method was developed for determining the presence or absence of the most important cereal species. This was achieved by designing species specific 'nested' primers from the intergenic 5S ribosomal RNA spacer region, consisting of 20-24 bp oligonucleotides. PCR using these primers in combination with one of the consensus 5S rRNA primers gave consistent banding profiles within a species using DNA samples extracted from a range of materials. Its application in processed foods is yet to be determined. Several methods for the preparation of DNA samples from leaves, embryos and flour (ground seeds) suitable for use in PCR were compared, with the aim of determining the simplest and fastest reliable method for use in routine sample analysis.