Research & Reviews: Journal of Crop Science and Technology Volume 1, Issue 1, April 2012, Pages 1-9 ___________________________________________________________________________ © STM Journals 2012. All Rights Reserved Page 1 Evaluation of the Yield, Quality and Integrity of Total RNA Extracted by Four Different Extraction Methods in Rice (Oryza sativa) Navin Srivastava, Spandan Chaudhary, Vinay Kumar*, Kalpesh Katudia, Kanak Vaidya, Manoj Kumar Vyas, Surendra K. Chikara* Genomics Centre, Xcelris Labs Limited, Old Premchandnagar, Bodakdev, Ahmedabad, Gujarat-380054, India *Authors for Correspondence E-mail: vinay.kumar@xcelrislabs.com, surendra.chikara@xcelrislabs.com, Tel: + 91-79-66197777. Fax: + 91-79-66309341. 1. INTRODUCTION Nowadays many researchers focus on understanding the stress responses which result from environmental alteration and lead to the induction of gene expression for protective stress conditions. The mechanisms that control and regulate cellular processes in living organisms are complex and involve several types of control, monitoring and activation/de-activation of genes. The genomics of abiotic stress response in plants has been extensively studied using a variety of molecular experimental methods and computational techniques. Advantages of next- generation sequencing (NGS) technology uses expression profiling to measure the changes, as a function of time, of almost all genes, as a result of the exposure to a variety of stress conditions. The large quantities of raw data produced by NGS technology enables global gene expression analysis in model and non- model organisms for identification of novel genes and gene-gene interaction in different metabolic pathways; therefore, it is essential to have high quality RNA from given frozen plant tissue. Isolation of high-quality total RNA is need of the day for obtaining intact mRNA and small RNA from plant tissue like leaf, stem and root. High throughput mRNA sequencing is required to study the alteration of gene expression in stressed response plants for comparative genomics. Small RNA molecules are a class of non-coding RNA gene and ABSTRACT The isolation of total intact RNA from plant tissues especially abiotic stressed plant samples is troublesome and challenging, because RNA in a stressed sample either rapidly degrades or is prone to degradation and the presence of high levels of phenolic compounds, polysaccharides, lipids, mucilage and some unidentified compounds could either bind and/or co-precipitate with RNA, making it unsuitable for downstream application. Four different methods, RNeasy plant mini kit-Qiagen, miRNA isolation kit-Invitrogen (combined protocol with RNA micro to midi kit-Invitrogen), TRIzol reagent (Invitrogen) based method and XcelGen Plant RNA isolation kit were used for high-quality RNA isolation from snap frozen leaf tissues of Oryza sativa. The yield and quality of RNA isolated by XcelGen kit was found efficient in comparison to other methods. Sample collection, transfer, storage, handling, grinding and quality control are all together critical steps for high-quality RNA isolation especially from plant tissues. Keywords: RNA isolation, rice (Oryza sativa), bioanalyzer, RIN number.