Vol. 10, Issue 6 (2021)

Author(s):
Abhay Kumar and VK Sharma

Abstract:
Completely sequenced rice genome provides scope for designing candidate gene specific microsatellite markers for their effective utilization in genetic analysis and breeding programs. An effort was made to develop novel microsatellite markers from candidate genes related to fragrance in aromatic rice, which can be utilized for fragrance specific molecular characterization and biological individuation of the aromatic rice germplasm. Aroma specific gene sequences were retrieved from the rice genome database available in the public domain. From a total of 11 genes/QTLs sequences, 47 microsatellites (simple sequence repeats) were detected with the BatchPrimer3 v1.0 web application. Altogether thirty-eight simple sequence repeats (SSRs) specific primer pairs were designed and tested by commonly used SSR reaction condition using 18 landraces and improved varieties of aromatic rice genomic DNA as templates. Analysis of amplification profiles revealed that all primer pairs generated recognizable amplification patterns. These SSR primers could be utilized for molecular characterization, identification and genetic divergence analysis in relation to fragrance of landraces and improved varieties of aromatic rice.