Development and characteristics of microsatellite markers for sugi (Cryptomeria japonica D. Don) derived from microsatellite-enriched libraries

Abstract

We have developed a series of microsatellite markers for C. japonica. First, DNA fragments including microsatellite sequences were isolated from two GA-enriched genomic libraries using magnetic beads. After eliminating redundant clones and clones in which the tandem repeats were located too close to the cloning site to allow primers to be constructed, the remaining sequences could be examined for their suitability for primer design. Primer sets were designed from each conserved sequence flanking the microsatellites. We found 1 479 unique sequences in the enriched genomic libraries, of which 962 contained a tandem repeat motif, and we have been able to design 196 primer pairs using these sequences to date. The potential of these primers to amplify single fragment, and the polymorphism of the sequences they amplify, were investigated using a panel of 28 plus trees selected from Cryptomeria plantations covering the wide distributional range of the species in Japan. Forty-two of the microsatellite markers displayed a polymorphic nature throughout this panel of 28 DNA samples. The polymorphic information coefficients (PICs) ranged from 0.156 to 0.919. There was a significant correlation, between the number of repeats and the size of the PICs, according to Kendall's τ rank correlation coefficient analyses.