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Premise of the study:   Metasequoia glyptostroboides  is an endangered relict conifer species endemic to China. In this study, expressed sequence tag–simple sequence repeat (EST‐SSR) markers were developed using transcriptome mining for future genetic and functional studies.    Methods and Results:  We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty‐three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively.    Conclusions:  These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species.

Development of 23 novel polymorphic EST‐SSR markers for the endangered relict conifer Metasequoia glyptostroboides