Egyptian cotton plant tissues have high polyphenolic content, as soon as the cell wall breaks, these phenolic compounds break down rapidly to cause sudden shift in pH which allows irreversible binding of unprotected RNA molecules with contaminating materials in the media. This was considered to be the major cause for the difficulties raised in isolating RNA molecules. RNA contamination with unidentified materials surrounding the RNA media resulted in turning RNA pellet color to brown or yellow.

Successful attempts in this research for applying different standard procedures and its specific modifications led to identifying the difficulties in isolating and purifying RNA molecules from G. barbadense cotton leaves, flowers, seedlings and boll tissues. All experiments containing phenol or phenolic compounds in its procedure (phenol method, polysomal method, GT/cold method) did not succeed in isolating and/or purifying intact RNA molecules from G. barbadense var. Giza 45 and Giza 75. RNA isolation, using the presented CTAB method, from five varieties, three new hybrids, and different tissue organs of Egyptian cotton cultivars resulted in an RNA yield ranging from 73.3 ug - 159.0 ug RNA/g tissue with 260:280 ratio of about 2.00. RNA analysis, RNA formaldehyde gel electrophoretic and In-vitro translation analysis illustrated the integrity of the extracted RNA molecules.