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Optimized SDS-Based Protocol for High-Quality RNA Extraction from Musa spp.

Kishan Saha1, Onyinye C Ihearahu1, L H Stevenson Naitchede1

  • 1Department of Natural Sciences, Bowie State University, 14000 Jericho Park Road, Bowie, MD 20715, USA.

Methods and Protocols
|February 25, 2025
PubMed
Summary

This study presents a modified SDS-based method to efficiently extract high-quality RNA from banana (Musa spp.) tissues. The improved technique overcomes previous limitations, yielding more and better RNA for downstream applications like gene expression analysis.

Keywords:
CTABMusa spp.RNA extraction methodSDScDNA

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Area of Science:

  • Plant Molecular Biology
  • Biotechnology
  • Biochemistry

Background:

  • Banana (Musa spp.) tissues contain high levels of polyphenols and polysaccharides, hindering nucleic acid extraction.
  • Previous RNA extraction methods for Musa spp. often result in low yield and poor quality RNA.

Purpose of the Study:

  • To develop and validate a modified SDS-based RNA extraction method for Musa spp.
  • To improve RNA yield and quality from various banana tissues, including drought-stressed samples.
  • To ensure the extracted RNA is suitable for downstream molecular applications.

Main Methods:

  • Modification of the RNA extraction buffer composition, including SDS concentration and the addition of LiCl.
  • Inclusion of a heat incubation step during the extraction process.
  • Assessment of RNA quality and yield using gel electrophoresis, spectrophotometry (A260/280 and A260/230 ratios), and RNA Integrity Number (RNA IQ).

Main Results:

  • The modified method significantly increased RNA yield and quality across different Musa varieties and tissue types.
  • High-quality RNA was obtained, evidenced by clear ribosomal RNA bands, absence of genomic DNA contamination, and optimal A260/280 (1.83–2.25) and A260/230 ratios.
  • RNA extracted from drought-stressed plants showed high integrity (RNA IQ 7.8–9.9) and yield (2.92–6.30 µg/100 mg fresh weight).
  • Successfully applied in Polymerase Chain Reaction (PCR) and quantitative real-time PCR (qRT-PCR) for gene expression analysis.

Conclusions:

  • The modified SDS-based method is a reliable and efficient technique for extracting high-quality RNA from Musa spp.
  • This method surpasses the limitations of traditional RNA extraction procedures like Trizol, NucleoSpin, RNeasy, and CTAB for banana tissues.
  • The improved RNA extraction protocol facilitates accurate gene expression studies in banana.