Assessing The Effectiveness of RAPD and ISSR Markers on The Genetic Variation of MD2 Pineapple (Ananas comosus var MD2) Clones

Fifi Hafizzah, Pendi (2021) Assessing The Effectiveness of RAPD and ISSR Markers on The Genetic Variation of MD2 Pineapple (Ananas comosus var MD2) Clones. Masters thesis, Universiti Malaysia Sarawak (UNIMAS).

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Abstract

The cultivation practice of pineapple plant through tissue culture method has led to numerous abnormalities such as dwarfism, small fruit and small crown which are not suitable for commercialisation. Morphological description as early intervention has resulted in the loss of energy, time and money since the indicator relies upon morphology changes posed by the individual plant. Despite enormous research studies on DNA based molecular markers to detect genetic variation among plants, there were no study has been done on genetic fidelity study among micropropagated MD2 pineapple plants using DNA based molecular markers. Thus, this study aimed to assess genetic variation among clonally raised MD2 pineapple plants using Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) molecular markers. A total of 22 genomic DNA amplified using six RAPD and six anchored ISSR markers. RAPD markers generated a total of 120 bands with 93% polymorphism percentage whereas the ISSR markers generated a total of 93 bands with 73% polymorphism percentage. Evaluation through resolving power (Rp), polymorphism information content (PIC) and marker index (MI) showed RAPD markers (Rp=7.08; PIC=0.34; MI=1.72)are more informative compared to ISSR markers (Rp=4.17; PIC=0.32; MI=1.00). Clustering analyses using Principal Component Analysis (PCA) and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) resulted in the indefinite clustering patterns while the dendrograms revealed the inability of the markers to correlate the plant morphology with their genetic structure. AMOVA analysis found high genetic variation within groups of pineapple with variation percentage >70% and Phi statistic estimated wide genetic variation among the studied genotypes. In general, the RAPD and ISSR markers revealed that the plant's morphology did not evitably correlate to its genetic structure. The results obtained are closely related with the genome coverage and the loci number detected by the molecular markers. This study may form the basis for MD2 breeding program and exploring other molecular markers that can potentially corresponds to the phenotypic polymorphisms.

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