Department of Genetics

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Browsing Department of Genetics by browse.metadata.advisor "Bierman, Anandi"

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    Karyotyping and in silico characterisation of the chromosomes of Diuraphis noxia (Hemiptera: Aphididae)
    (Stellenbosch : Stellenbosch University, 2016-12) Steyn, Louis Johannes; Oberholster, Anna-Maria; Bierman, Anandi; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics.
    ENGLISH ABSTRACT: Diuraphis noxia Kurdjumov (Russian wheat aphid (RWA)), is an economically important agricultural pest that causes substantial losses in small grain production, particularly wheat and barley. Approaches that can be taken to manage this invasive pest include the cultivation of RWA resistant cultivars. The development of new RWA biotypes, virulent against previously classified resistant wheat cultivars presents, an additional problem to the goal of reducing crop losses. Therefore, studying the underlying molecular genetics of the RWA brings us closer to understanding wheat resistance to the RWA and ultimately battling this pest in small grain fields. The objectives of this study were: to study the sex (X) chromosome of the RWA by karyotyping and isolation using flow cytometry; to sequence the X chromosome; and then to map it against the reference genomes of the RWA and Acyrthosiphon pisum (pea aphid). Since aphids reproduce via parthenogenesis, mapping populations reliant on sexual recombination are not available, and therefore information about the locations of genes on chromosomes is completely lacking. To this end, reference mapping against the X chromosome of Drosophila melanogaster (fruit fly) was conducted to identify orthologous regions spanning the X chromosome of RWA. The results confirmed that the RWA karyotype consists of a diploid chromosome number of 10, with a large X chromosome pair and four autosomal chromosome pairs. Flow sorting yielded 2,047,296 X chromosomes and sequencing produced a total read count of 136,814,894 with a Q20 score of 96.32%. The X chromosome had a higher mapping percentage to the RWA genome (82.88%) compared to that of the pea aphid (51.3%). Interestingly, a high mapping coverage across the entire genome of both aphids was observed, suggesting that flow cytometry did not separate the X chromosome from the rest of the chromosomes of the RWA but allowed unintended chromosomes to contaminate the series. Mapping against the fruit fly X chromosome produced eight orthologous regions of which six was confirmed to be present in the RWA karyotype through in situ hybridization, while a protein BLAST of the fruit fly X chromosome against the RWA genome aided in determining approximately 67.42% of the length of the RWA X chromosome.