Development of 36 novel polymorphic microsatellites for the critically endangered tree Pinus squamaia, by transcriptome database mining

Pinus squamaia X. W. Li is a critically endangered five-needle pine species, with only 35 wild individuals left. To understand its genetic variability, 506 novel microsatellite markers were developed by mining the transcriptome database of P. lambertiana. 196 loci were able to amplify a fragment of expected size in P. squamaia, of which 36 were polymorphic. The number of alleles of these 36 EST-SSRs in 16 individuals varied from 2 to 4, with an average of 2.2. The observed (Ho) and expected (He) heterozygosity values ranged from 0.000 to 1.000 (averaging 0.564) and 0.061 to 0.500 (averaging 0.356), respectively. Twenty-four loci showed significant departure from HWE after Bonferroni correction. This was the first report of candidate molecular markers on P. squamaia, which will facilitate future analyses of genetic diversity and population structure.