Pcr-based multiplex DNA fingerprinting techniques for the analysis of conifer genomes

Abstract

We utilised fingerprinting techniques such as amplified restriction fragment polymorphism (AFLP) and selective amplification of microsatellite polymorphic loci (SAMPL) in order to identify molecular markers in the conifer species Norway spruce (Picea abies K). A total of 366 polymorphic AFLP and 20 polymorphic SAMPL bands were scored, with an average of 12.6 polymorphic bands obtained per primer combination. Of the bands, 94% segregated in a Mendelian fashion, and 14% of the AFLP bands behaved as codominant markers. Norway spruce, as well as other conifers, has a very large genome (1.5–2.5 × 10¹⁰ bp) which is thought to be largely composed of repetitive sequences of different origin, either organised in tandem or interspersed in the genome. The high complexity of these genomes has so far hindered the efficient use of multiplexed fingerprinting techniques for their analysis. The use of the methylation-sensitive restriction enzyme PstI as 6 bp cutter allows a reduction in pattern complexity as compared to EcoRI. We thus demonstrated that high-throughput PCR-based multiplex fingerprinting techniques such as AFLP and SAMPL, when opportunely modified, can be effectively applied also to these species and be useful for mapping purposes.