The isolation and identification of molecular markers linked to sugar production in pineapple (Ananas comosus var. comosus)

• Main Author: Thien, Yong Nam
• Format: Thesis
• Language: English; English
• Published: 2006
• Subjects: QK900-989 Plant ecology
• Online Access: https://eprints.ums.edu.my/id/eprint/38642/1/24%20PAGES.pdf; https://eprints.ums.edu.my/id/eprint/38642/2/FULLTEXT.pdf; https://eprints.ums.edu.my/id/eprint/38642/

Most pineapple (Ananas comosus var. comosus, Family: Bromelieceae) varieties produced fruits with low sugar content quality which affects the agronomical and breeding potential of pineapple. Thus, a better knowledge of the genetic and molecular basis underlying fruit quality would benefit pineapple breeding programmes. Isolation and identification are the essential steps for the development of molecular markers to be used in marker assisted selection for plant breeding programmes. Hence, two analyses, the Bulked Line Analysis (BLA) and the Differential Gene Expression Analysis were employed in this study. Genomic DNA (leaf) and total RNA (fruit tissue) were isolated and grouped into two groups "Acid" (<11 % Brix) and "Acidless" (>17% Brix) prior to polymerase chain reaction (PCR) and reverse transcriptionpolymerase chain reaction (RT-PCR). In the DNA study, the Random Amplified Polymorphic DNA (RAPD) assay and the Direct Amplified Length Polymorphisms (DALP) assay were used in conjunction with Bulked Line Analysis to identify sugar-content linked markers in pineapple. The experiments showed no polymorphism was observed between the "Acid" and "Acidless" groups of pineapples. This showed that both the RAPD and the DALP methods were unable to differentiate the desired characteristic within clonally propagated individuals. However with the limited number of primers used, it was difficult to conclude that DNA based markers are not suitable in this particular investigation. In the RNA study, newly synthesized double stranded cDNAs were subjected to PCR using three different sets of primers from Amplified Differential Gene Expression (ADGE), Differential Gene Expression Based Annealing Control Primer analysis (DEG-ACP) and specific markers linked to sugar content from peach and tomato. Differential gene expression analysis indicated five markers linked to the sugar content in pineapple. Three of the markers (M1, M3 and M4) were from ADGE, marker HK1 was from specific primer linked to sugar content and one marker (TYN4) was from DEG. A comparison of the differential expression between the cDNA from the "Acid" and "Acidless" groups of pineapple revealed differences in markers M1, M3, M4, and the markers HK1 and TYN4. These markers can be used in marker assisted selection (MAS) to aid in identifying Quantitative Trait Loci since the majority of quantitative traits in crop plants are controlled by polygenes. Selection of quantitative trait loci for crop improvement such as sweetness in pineapple, will result in significant reduction in the time taken for reducing the productivity of low sugar content pineapples and increasing the productivity of high sugar content pineapples.