Survey sequencing and in-silico development and validation of genomic SSR markers in Indian dill seed

Abstract

Indian dill seed (Anethum sowa Roxb. ex Fleming) is an important member of family Apiaceae. It is a significant seed spice having many medicinal properties. But, this aromatic herb is still orphan from breeding and crop improvement perspective as no serious attention has been given by breeders. To swift the breeding program, molecular markers play the main role. But due to the paucity of markers, breeding is slower in dill seed. Therefore, an attempt was made to develop the genomic SSR markers in dill seed through next-generation sequencing. A total of 2119.51 Mbp of raw data were generated on the Miseq NGS platform during survey sequencing. In 2,25,956 contigs created by Spades assembler, a total 48,951 repeat motifs were identified. A set of 20,294 primer pairs (dimer to hexamer repeats) were produced. Among detected repeat motifs, 48.89% was mononucleotides. Of 12 primers, 10 (83%) primers could be successfully amplified in dill seed and produced 11 amplicons. During cross-genera amplification of markers, 9 out of 10 primers could be successfully amplified in related genera. Developed markers can also be used to initiate the molecular breeding program, association mapping and to assess the evolutionary relationship among seed spices. Keywords: Anethum, Seed spices, SSR, Transferability