DNA markers for variety identification in date palm (Phoenix dactylifera L.)

Summary

Simple sequence repeats (SSRs; microsatellites) are currently the favoured type of molecular marker for identifying plant germplasm. However, identifying polymorphic SSRs and then using them to distinguish closely-related varieties can be time-consuming. Polymorphic markers originating from particularly labile regions of the genome are likely to be easier to develop and also have the potential to identify markers that have higher polymorphic information contents. Genomic regions that vary in somaclonal “off-types” are a possible source of such labile regions of the genome. Thirty-seven primer pairs, developed from sequences that differed between normal and mantled somaclonal mutant oil palm (Elaeis guineensis Jacq.) plants, were used in polymerase chain reactions to screen DNA from 18 varieties of date palm (Phoenix dactylifera L.). From the resulting polymorphisms, three primer pairs were selected which, when used in combination, could identify each of the date palm varieties, unambiguously. The polymorphic bands were isolated, sequenced, and new internal primers were designed. However, all of the amplifications using these new primers yielded only monomorphic bands, indicating that the variation among these date palm varieties lay mainly at or near the original primer sites, and that the internal sequences were conserved.