High-quality RNA is an important genetic study as it has minimal contaminants that can affect gene discovery including degraded RNAs, chemical, and biological residues. Hence, it is a prerequisite for genetic analysis using Next Generation Sequencing (NGS) for accurate and reliable data mining. Despite its importance, extracting high-quality RNA from different samples is often a challenge, as every tissue has a different biochemical composition, thus requiring different protocols. This paper reports protocols for the extraction of high-quality RNA from two type of pineapple tissues, which are thickly lignified hard tissue (tillers, inflorescence, flowers) and watery soft tissue (mature fruit, ripe fruit, and overripe fruit) via modified Kim and Hamada (2005) method. Total RNA was extracted in all six tissues, which showed two distinctive 25S and 18S band on agarose gel. The total RNA in this study was considered high-quality as the minimum concentration was 50 ng/μl, the absorbance ratio (A260:A280) was more than 1.8 and RNA integrity number (RIN) was greater than 7. The obtained results showed that the modified Kim and Hamada (2005) method was effective in extracting high-quality RNA from the challenging MD2 pineapple tissue, which is suitable for subsequent molecular analysis, including the highly sensitive NGS.

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