The molecular basis of somaclonal variation is not precisely known, but both genetic and epigenetic mechanisms have been proposed. The available evidence points toward the existence of labile portions of the genome that can be modulated when the cells undergo the stress of tissue culture. Therefore, the hypothesis that there are identifiable and predictable DNA markers for the early diagnosis of somaclonal variation has been tested. Representational difference analysis was used to isolate unique fragments of DNA (difference products) between visible culture‐induced off‐type and normal banana plants. Markers generated from six difference products differentiated between some of the off‐type and normal pairs. The genomic region around one of these difference products has been extensively characterized and has a high degree of polymorphism, with variation in up to 10% of the nucleotides sequenced in the region. This same region has been shown to vary in other pairs of off‐type and normal banana plants derived from tissue culture as well as in plants propagated commercially in vitro. The data are consistent with the hypothesis that there is at least one particularly labile portion of the genome that is especially susceptible to the stress imposed during tissue culture and that is associated with higher rearrangement and mutation rates than other portions of the genome. Consequently, the regions that are reported here have the potential to be used as early detection tools for identifying somaclonal variants.
DNA-based markers have revolutionized the whole process of generating genetic maps, as well as parentage analysis, association mapping, marker assisted selection and the genetic fingerprinting of cultivars and associated population analysis. Modern molecular techniques have been developed to meet the demands of the agriculture and horticulture industries. A major bottleneck in the application of molecular techniques to the identification and improvement of plants is the development of the appropriate molecular markers for every species. The most popular source of markers is the simple sequence repeats (SSRs) found in all eukaryotic genomes. However, since the primers to characterize the polymorphic state of the SSRs are generally species specific they need to be identified for each species individually. We have developed a novel strategy that combines a sampling strategy, SSR enrichment and next generation sequencing to simultaneously isolate SSRs and identify those that are polymorphic within the germplasm of interest (patent pending). This strategy facilitates the identification of a useful set of polymorphic SSRs for all plant species independent of the availability of any other molecular information.
SummarySimple 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.
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