Development of novel polymorphic microsatellite markers by technology of next generation sequencing in western white pine
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The invasive fungal pathogen Cronartium ribicola has seriously damaged five-needle pines in North America. Genetic diversity assessment using DNA markers among natural populations will benefit conservation and restoration programs. This report presents characterization of the first set of microsatellite markers developed by analyzing a reference transcriptome de novo assembled from RNA-seq data and expressed sequence tags in western white pine (Pinus monticola). A total of 1,948 microsatellite loci were detected in 1,876 contigs. Forty-six loci were verified to be polymorphic, with allele number per locus ranging from 2 to 12. The mean observed and expected heterozygosity per locus was measured as 0.671 and 0.485, respectively. These microsatellite markers will be useful for characterizing genetic diversity and gene-flow among natural stands and population structure among seed families for conservation of this conifer species across western North America.
KeywordsExpressed sequence tag (EST) Microsatellites Next generation sequencing Pinus monticola
This research was supported, in part, by the Canadian Forest Service and the CFS–GRDI fund awarded to JJL. We thank L. Baerg at CFS for technical support on genomic DNA extraction.