Large-scale discovery of Simple Sequence Repeat markers in snake gourd (Trichosanthes cucumerina L) and their cross-species validation

Snake gourd (Trichosanthes cucumerina L) is a medicinally important vegetable crop belonging to the Cucurbitaceae family. India, being the center of origin of snake gourd, is endowed with a rich genetic diversity in this crop, hence offering a tremendous scope for genetic improvement. The lack of sufficient molecular markers in the crop is, however, a big limitation that curtails the endeavors undertaken for crop improvement. In this study, a total of 18,604 SSR (Simple Sequence Repeat) markers were developed in snake gourd (TcSSR) through low coverage sequencing. A total of 1.5 gigabases (Gb) of sequencing data was assembled de novo and thereafter used for genome-wide SSR mining. The markers were validated by mapping onto the published whole genome sequence (WGS) of snake gourd. More than 77% of the SSR markers were mapped on the genome, which confirms the accuracy of the sequencing data. A few markers were wet lab validated through polymerase chain reaction (PCR) amplification across three different snake gourd genotypes (T. cucumerina) and analysed for cross-species transferability. A total of 40 out of 56 markers tested were identified to be transferable across the five different Trichosanthes species (other than T. cucumerina), which reflected a high degree of genetic relatedness among the species. To the best of our knowledge, this is the first report on the large-scale discovery of SSR markers in snake gourd. The markers identified in this study would serve as valuable genomic resources for germplasm characterization in snake gourd and facilitate trait improvement efforts in various breeding programs.