Molecular genetic and taxonomical relationship among selected Setaria species using inter simple sequence repeat (ISSR’s) and microsatellite (SSRs) markers

Foxtail millet is small diploid ( 2n = 2x = 18), one of the oldest domesticated, self-compatible, C 4 Panicoid cereal grains in Eurasia. Change in climatic conditions, ecological degradation, overexploitaion, and commercial cultivation has led to the genetic loss of landraces as well wild relatives of cultivated crops. Established genetic relations among the species are prerequisites for their future breeding programs to improve cultivars. Therefore, there is an urgent need to conserve plant genetic resources for sustainable agriculture. Keeping in view, we collected seven different species of Setaria that include S. italica , S. viridis , S. sphacelata , S. pumila , S. glauca , S. verticillata , and S. intermedia from Andhra Pradesh, India . The specimens were examined for species identification and taxonomically described. In the present study, the trait “awn” was used as a key taxonomic character for the differentiation of two species viz ., S. verticillata and S. intermedia. Earlier S. intermedia was merged in S. verticillata . We observed tremendous variation in phenotypic traits among weedy, wild, landrace, and cultivars of Setaria germplasm, indicating potential genotypic variation. To confirm the genetic variation, the selected Setaria sps were genotyped through ISSR and SSR genetic markers. The average number of amplicons amplified for ISSR and SSR markers was 3.75 and 2.45 alleles per locus, respectively. The Polymorphic information content and Shannon information index (I) for ISSR and SSR markers had an average value of 0.34, 0.34, and 0.46, 0.58, respectively. Gene flow among seven Setaria species was relatively high (Nm > − 1.0). Two-way cluster analysis separated 12 accessions into two significant clusters using combined marker systems and agreed with Principal coordinate analysis. An Analysis of molecular variance confirms that a substantial genetic variation among seven Setaria species. Morphological cluster analysis was almost similar to molecular cluster analysis.