Euphrasia nankotaizanensis is an endangered flowering plant distributed restrictedly on rocky slope of high mountain peaks in central and northern Taiwan. In order to undertake a conservation program, especially given impacts of the global warming, it is essential to evaluate its genetic diversity and population structure. We described nine novel microsatellite primer pairs in E. nankotaizanensis and also examined its relative E. transmorrisonensis. The number of alleles per locus ranged from 7 to 29. Expected (H E) and observed (H O) heterozygosities ranged from 0.83 to 0.98 and 0.00 to 0.95, respectively. Eight of the nine microsatellite loci displayed significant departures from Hardy-Weinberg expectations, likely due to the loss of habitats and the small population size. Significant linkage disequilibrium (LD) was detected in most loci. Cross-species amplification of microsatellites took place at five loci. These primers may provide a tool for understanding the demography and population structure of Euphrasia species in Taiwan.
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