SSR mining of black cumin (Nigella sativa L.) transcriptome for molecular marker development

Black cumin (Nigella sativa L.) is of the crucial traditional plants and widely preffered for an array of diseases. However, N. sativa is not a widespread plant species and its distribution is limited to the Middle-East and Africa, in general. In comparison to the other plant species, the specific markers for the species have not been developed. So far, molecular characterizations of the germplasm were carried with general marker systems. In the present study, the transcriptome of the black cumin was searched for simple-sequence repeats (SSRs). Dinucleotide and trinucleotide repeats were the major repeat types which comprised 52.4% and 44.7% of total SSRs, respectively. TC/GA was the most frequent repeat motif (11.8%). A total of 4.779 SSR markers were developed. Functional annotation of 2.456 SSR markers was performed. For validation of the SSR markers, randomly selected 20 markers were tested in a subset population including nine N. sativa and one Nigella damascena genotypes. A total of 13 SSR makers produced clear amplification and generated 41 polymorphic fragments with a mean gene diversity of 0.25. Furthermore, Principal Coordinate Analyses (PCoA) and Markov chain Monte Carlo (MCMC) methods based on hierarchical clustering analysis revealed two clusters and moderate diversity with a mean value of 0.66 and 0.57 for interspecific and intraspecific populations, respectively. Up to our best knowledge, this is the first report of the development of SSR markers from black cumin transcriptome. These high-throughput crop-specific SSR markers might be valuable genomic sources for comprehensive genome analysis in black cumin.