The potential of RAPD technology and its application in loblolly pine /
To evaluate the value of the extra work of converting RAPD markers to SCAR markers versus the problems associated with RAPD markers alone, nine RAPD markers, isolated from Loblolly pine endosperm DNA, were converted to SCAR markers in a comparison study of the two techniques. Most of RAPD markers c...
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| Format: | Thesis Book |
| Language: | English |
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[Place of publication not identified] :
[publisher not identified] ;
1995.
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| Subjects: | |
| Online Access: | http://proxy.library.tamu.edu/login?url=http://proquest.umi.com/pqdweb?did=742744621&sid=1&Fmt=2&clientId=2945&RQT=309&VName=PQD |
| Summary: | To evaluate the value of the extra work of converting RAPD markers to SCAR markers versus the problems associated with RAPD markers alone, nine RAPD markers, isolated from Loblolly pine endosperm DNA, were converted to SCAR markers in a comparison study of the two techniques. Most of RAPD markers comparison study of the two techniques. Most of RAPD markers (74%) were highly repetitive markers (> 30 copy) and only 11% were low copy number (< 10 copy) which closely represent the Loblolly pine genome. Only one marker gave exactly the same polymorphism in both techniques (11%), raising the question of RAPD fidelity. Southern hybridization revealed misscoring in RAPD markers. Part of RAPD misscoring was marker polymorphism misscoring where the RAPD marker was deceptively scored as a polymorphic marker (22%). The more frequent misscoring was band misscoring, e.g., absence and sequence misscoring. RAPD markers not only contained absence and sequence misscoring, but also expressed polymorphism patterns that were different from the corresponding SCAR- converted markers, in more than half the markers (56%). When SCAR-converted RAPD markers were constructed, amplification efficiency was improved, new polymorphism patterns appeared, sequence misscoring disappeared, and one marker lost its polymorphism (i 1 %). The repeatability factor for SCAR- converted RAPD markers was not better than the repeatability factor for RAPD markers, under the optimal conditions of RAPD PCR. The decrease in the repeatability factor of SCAR converted RAPD markers, after their conversion, might be due to preferential amplification conditions in the PCR reaction, e.g., the stringent conditions and the mismatching in the annealing duplex of the SCARs (further investigation is needed). No relationship was found between repeatability and any of the copy number categories, low medium, and high. On the other hand, SCAR's consistency seemed to be related with copy number, but further investigation is needed. The analysis of variance of amplified DNA amount in both RAPDs and SCARs showed significant differences in replication within markers in both techniques, which indicates the importance of replication for molecular biology analysis. One of the high copy number markers gave a strong homology with retrotransposon protein which agrees with the literature. |
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| Item Description: | Vita. "Major Subject: Genetics". |
| Physical Description: | xii, 143 leaves : illustrations ; 28 cm. Issued also on microfiche from University Microfilms Inc. |
| Bibliography: | Includes bibliographical references. |