A new approach to improve the scoring of mononucleotide microsatellite loci

Premise of the study: Mononucleotide microsatellites markers are useful for detecting genetic variation among individuals; however, scoring can be error-prone. We developed a new approach to improve the accuracy of allele scoring. Methods and Results: A set of 14 mononucleotide microsatellite primers of the chloroplast were developed based on published Pinus spp. chloroplast genomes. Due to substantial scoring error for mononucleotide repeats ≥ 10 bp, we included part of the microsatellite in the reverse primer to reduce slippage and improve the scoring of these polymorphic markers. For markers 10-20 bp, the error rate in scoring with this method has a binomial 95% confidence interval of 0.7-2.1%. Conclusions: These new primers provide variable chloroplast markers in species of subsection Cembroides and other Pinus spp. with more accurate assignment of the alleles. This approach can be used to improve the allele scoring of mononucleotide or dinucleotide repeats from nuclear and chloroplast genomes.