Picea omorika (Panč.) Purk. is a relict and an endemic species found exclusively in the Balkan, within an area of ca. 10 000 km2. Marker-based genetic diversity data in this conifer are very limited and partially contradictory. Therefore, twelve nuclear markers (ten EST-SSRs and two genomic SSRs) were tested for cross-species amplification in P. omorika. Five EST-SSRs amplified successfully and a very high number of alleles per locus was found in 50 trees originating from two natural populations (7 to 18 alleles per locus), with a total of 61 alleles. Furthermore, a high number of private alleles were detected – 13 and 14 per population, respectively. Rare alleles, i.e., alleles whose frequency was lower than 0.05, were not observed. Markers were selectively neutral, no linkage disequilibrium was detected and the genotype frequencies fitted Hardy–Weinberg proportions. Expected heterozygosity per locus ranged from 0.64 to 0.91 in both populations, with an overall mean of 0.83. Considering the small remnant population sizes of P. omorika, these values are unexpectedly high and comparable to values in P. glauca (Moench) Voss., P. sitchensis (Bong.) Carr. and P. mariana (Mill.) B.S.P. detected with an identical set of markers in samples of similar sizes.
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