Genetic analysis of Ximenia Americana under natural conditions
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Date
2015
Authors
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Journal ISSN
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Publisher
University of Namibia
Abstract
Cross-species hybridization approaches have been used for genetic analysis of species that do not have complete genome arrays available. The study used the cross-species DNA-DNA hybridization approach to characterize Ximenia americana biological processes. Preliminary micro-array studies done in the Department of Chemistry and Biochemistry at the University of Namibia has created X. americana DNA-DNA hybridization to a well-known Arabidopsis thaliana genechip (ATH1). A. thaliana probe-pairs that hybridised to the X. americana genomic DNA on the basis of the perfect-match (PM) probe signal were selected and analysed using a cel file parser script to generate a new high density probe mask files. These files effectively represent the first ever X. americana DNA-DNA hybridisation data. This study conducted gene ontology analysis of X. americana/A. thaliana hybridisation data. Such gene ontology analysis demonstrated that abiotic stress response genes are over-represented in relative
comparison to model species A. thaliana under natural conditions. This observation was independently confirmed with PCR amplification of the following orthologous genes using X. americana genomic DNA: AT4G15910.1, SAD2, HXK1, ACC and ERF/AP2. Given the lack of genomic sequence information in X. americana background, primers for genomic amplification was design using A. thaliana genomic sequence information. Primers where designed to yield 100 bp genomic PCR product. Each of the selected genes was successfully amplified hence giving evidence of homology within primer binding sites. Nonetheless, the genomic amplification of these key abiotic factors in X. americana confirms the type of responses that supports the adaptation of X. americana under natural conditions that are stress related (heat and drought stress). Although transcript levels of this important abiotic response factors could not be measured in absolute or relative terms, the study demonstrated inherent presence of such genes at the
genomic level of X. americana. Further studies will be required to demonstrate that
some sort of modification of any of these or other abiotic response factors within the
genome of X. americana provides the key basis for its adaptation to the relatively dry and hot climatic conditions.
Description
A thesis submitted in partial fulfilment of the requirements for the Degree of Master of Science
Keywords
Genetic analysis, Ximenia Americana, Gene ontology, Cross-species hybridization