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Molecular markers for diagnosis and genetic diversity studies in Orobanche

Detection of the presence and identification of the Orobanche species in a soil or crop seed lots is of great interest for growers and quarantine officers in order to prevent new infestations or spreading of the parasite. This is often difficult via traditional methods considering the minuscule seed size of the parasite. In a previous study we determined the differences among 28 species of the genera by sequencing cp DNA fragments. Specific primers can be designed from these sequences in order to obtain PCR amplification from a target parasite species, avoiding the fragment amplification from the host. Microsatellites have proven to be an extremely valuable tool for population genetic studies due to the high polymorphism shown and the relative ease of scoring. However, they have not been used yet in studies of the genus Orobanche. The major drawback of microsatellites is that they need to be isolated de novo from most species being examined for the first time. This is due to the fact that microsatellites are usually found in non-coding regions where the nucleotide substitution rate is higher than in coding region. Consequently, the strategy of designing "universal primers" matching conserved sequences is problematic. However the presence of highly conserved flanking regions across different species have been reported for some microsatellite loci.

Orobanche; parasite; molecular markers; diagnosis; quarantine

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