Development of genomic simple sequence repeat (gSSR) markers in cumin and their application in diversity analyses and cross-transferability

Cumin (Cuminum cyminum L.), an industrially important seed spices, has diverse usage in food and pharma industries. Therefore, documentation and characterization of cumin germplasm is essential for its genetic improvement. However, reliable co-dominant marker system especially simple sequence repeat (SSR) is not available in cumin. To develop SSR markers in cumin, DNA survey sequencing was performed on Illumina Miseq next-generation sequencing (NGS) platform. A total of 8086 sequences were detected having microsatellite repeat sequences. A set of 6421 primer pairs (including 1278 mononucleotide) were generated from genomic sequences of cumin, in which di- and tri-nucleotides repeat were more common. For marker validation, 25 primer pairs were randomly selected and amplified in 30 cumin genotypes and five other species of family Apiaceae namely, dill seed, parsley, celery, fennel and ajwain. From 23 markers, a total of 79 alleles were identified with the mean of 3.43 alleles per marker with polymorphism information content (PIC) ranged from 0.03 to 0.70. The average gene diversity and heterozygosity was 0.44 and 0.53, respectively. With a mean dissimilarity coefficients of 0.398, five clusters were identified through neighbour-joining analysis. The highest genetic distance was observed between GC-1/GP-39 and GC-3/GP-39, while the lowest level was found between GP-47 and CE-2. Of 23 primers, 21 (91.30%) exhibited cross-amplification in at least one of the species of Apiaceae.