Standardization of an efficient protocol for isolation of RNA from Cuminum cyminum

Abstract

Cumin is one of the oldest seed species and second most popular after black pepper. Till date molecular work into cumin has been principally related to studying diversity based on phenotypic, biochemical and molecular aspects. Molecular aspects in cumin are restricted to DNA marker. But for more advanced study with profundity it is to bring forth the understanding related to transcriptome level studies. The prerequisite for such sophisticated strategy is high quality RNA. Here, we had attempted different RNA extraction procedures for fulfilling the basic preconditions for such studies. In this study we have used five different protocols to achieve high quality RNA from cumin. The RNA was isolated from root and shoot tissues using different extraction methods viz. Trizol method, CTAB Method, Quiagen RNAesy plant mini kit, QIAsymphony (Direct RNA extraction machine) and Phenol: choloroform method. Quality and quantity were assessed using Nanodrop [for quantity (ng/µL) at A260/280 and A260/230)], Qiaxcel [for RNA integrity score (RIS)] and 2% agarose gel electrophoresis (for intactness). RNA was converted into cDNA and visualized on agarose gel followed by real time PCR analysis to conform the quality of RNA. Eventually, the phenol chloroform extraction method was found to be most efficient for RNA extraction in terms of high yield and good quality.