identification of microsatellite molecular markers in saffron (.crocus sativus L) using RNA-Seq data

Saffron (Crocus sativus L.) is the most valuable spice in the world. Due to the lack of genomic information, saffron breeding has encountered many problems. To this end, generating and collecting genetic data using Next Generation Sequencing (NGS) techniques is crucial for saffron traditional and molecular breeding programs. Molecular markers, especially powerful co-dominance markers such as simple sequence repeats (SSRs) markers play an important role in breeding projects. In the present study for the first time, SSR markers related to genes associated with F. oxysporum disease of corms were identified following a RNA-Seq based transcriptomic approach. To this end, total RNA was extracted from mature corms and RNA-Seq was performed based on the Novaseq6000 platform. The De-novo assembly was performed with Trinity software and the MISA search tool was used to identify SSRs. Based on the results of this study, 357028 transcripts were identified. A total of 70060 transcripts were identified to contain SSR sequences. BLAST algorithm analysis revealed that the highest similarity between saffron SSRs was found with that of rice and Arabidopsis. Among the identified unigenes, 18846, 23988 and 10969 genes were identified in UNIPROT, Nr and GO databases, respectively, in which 10375 unigenes were common to all databases. Due to the high priority of saffron in Iran as a strategic crop plant, any genetic information, including mining SSRs, is of great importance in studying genetic diversity, constructing genetic maps, linkage and QTLs analysis in saffron future breeding programs.