V. myrtillus L., V. vitis-idaea L. and V. uliginosum L. belong to the genus Vaccinium. These wild species are widely distributed and ecologically important within the Baltic countries but they have not been extensively studied using molecular markers. EST-SSR and cpSSR markers were used to investigate the population structure and genetic diversity of these species to obtain information useful for the development of in situ conservation strategies for these species.

Wild Vaccinium species populations are moderately genetically differentiated, with some populations more highly differentiated, but without higher order clustering of groups of populations, indicating that there are no dispersal barriers for these species within the Baltic countries. Genetic diversity of populations growing in protected areas, managed forests and intensively utilised public recreational areas is similar.

Vaccinium myrtillus samples were collected at 22 locations in Latvia, 9 locations in Lithuania and 7 locations in Estonia. Vaccinium vitis-idaea samples were collected at 20 locations in Latvia, 9 locations in Lithuania and 7 locations in Estonia. Vaccinium uliginosum samples were collected at 22 locations in Latvia, 8 locations in Lithuania and 5 locations in Estonia. For each species, eight accessions from different populations were tested with 25 EST-SSR markers (Boches et al. 2005), and 8 markers were determined to be suitable for bilberry analyses, 10 markers for lingonberries, and 8 markers for bog bilberries.

Six universal angiosperm primer pairs for chloroplast microsatellites – ccmp2, ccmp3, ccmp4, ccmp6, ccmp7, ccmp10 (Weising and Gardner 1999) were tested. In addition, six chloroplast microsatellite markers developed from V. macrocarpon (CP6, CP9, CP12, CP13, CP14 CP16), which were also reported to be transferable to other Vaccinium taxa and non-Vaccinium Ericaceae species (Schlautman et al. 2016), were tested in 16 accessions from different populations for each species. 192 bilberry accessions from 15 populations (four from Latvia, five from Estonia and six from Lithuania), 186 lingonberry accessions from 12 populations (six from Latvia, three from Estonia and three from Lithuania) were tested with marker CP6. 233 lingonberry accessions from 35 populations (19 from Latvia, seven from Estonia and nine from Lithuania) and 237 bog bilberry accessions from 21 populations (eight from Latvia, five from Estonia and eight from Lithuania) were tested with marker ccmp7.

All genotype files are uploaded in GenAlEx format with geographic coordinates for each population. V. mytillus and V. vitis-idaea samples are scored as diploid codominant markers. V. uliginosum samples include tetraploids, and are scored as binary data.

Chloroplast data files contain allele sizes in base pairs.