Development and characterization of SSR markers in Himalayan species Betula utilis

Abstract

Betula utilis D. Don. is an important species of alpine Himalaya and forms the major treeline component of western Himalaya. The different populations of B. utilis are declining and are under high risk. In the present study, novel expressed sequence tag–simple sequence repeat (EST–SSR) primers were developed from expressed sequence tag (EST) data of different Betula species. Of the 10,796 designed primers, the percentages of di-, tri-, tetra-, penta-, and hexa-repeats were 36%, 35%, 15%, 5.5% and 7.7%, respectively. For validation, 50 primers were synthesized randomly and were characterized in 20 different B. utilis accessions from north-western Himalaya. Of these, 45 primers amplified fragments in a range of 1–6. The 24 polymorphic primers produced 111 fragments in aggregate with 4.6 fragments on average. Polymorphism information content (PIC) ranged from 0.288 in marker BUMS-24 to 0.497 in BUMS-3 and BUMS-7, with an average of 0.447 among polymorphic markers. Dendrogram based on Jaccard’s similarity coefficient and UPGMA method showed that newly developed SSR markers distinguished twenty accessions of B. utilis into two groups. As no SSR markers were available in this species, the newly developed markers will foster molecular genetics research and conservation efforts for this species.