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SSAP method was used to study the genetic diversity of 22  Linum  species from sections  Linum ,  Adenolinum, Dasylinum, Stellerolinum , and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposons  FL9  and  FL11 . Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism of  Fl1a, Fl1b , and  Cassandra  insertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation of  Linum  species. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sections  Dasylinum, Stellerolinum, Adenolinum , and  Linum . All species of sect.  Adenolinum  clustered apart from species of sect.  Linum . The data confirmed the accuracy of the separation in these sections. Members of section  Linum  are not as closely related as members of other sections, so taxonomic revision of this section is desirable.  L. usitatissimum  accessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization of  Cassandra  retrotransposon in  Linum  species was determined.

Retrotransposon-Based Molecular Markers for Analysis of Genetic Diversity within the GenusLinum