Sweetpotato is arguably one of Earth’s top ten most important crops. It is relatively low maintenance, packed with essential vitamins and nutrients, and in addition to serving as an effective food crop, it has been suggested for use as a material for synthesizing plastics and as a replacement for corn as a source for bioethanol production. Sweetpotatoes are difficult to bring to seed, so most sweetpotato plants are grown from slips, which are cuttings from sweetpotato vines. This makes it very easy for sweetpotato viruses to spread from generation to generation. Currently, virus disease complexes, which are infections of two or more viruses with a synergistic interaction, pose the biggest threat to sweetpotato yields. It is therefore crucial to have a better understanding of different sweetpotato genotypes. Sweetpotato genotypes tend to be very similar, since crossing and outbreeding strategies are all but impossible to carry out on sweetpotatoes, as different genotypes tend to be very similar. Transcriptome profiling could prove to be an extremely useful method for understanding the causes of phenotypic differences in genotypes. This project details the construction of the transcriptome profiles of three phenotypically different genotypes. Illumina sequencing was carried out on the 2500HiSeq platform and the resulting reads were aligned to the sweetpotato genome constructed by the Max Planck Institute. Bioinformatics software was used to carry out alignment and analysis. The analysis techniques were used to calculate and normalize gene expression, make fold change comparisons, convert this data to log 2-fold change, determine which genes had the greatest expression differences, group these genes into functional groups, and perform other analyses.
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|Advisor:||Kalavacharla, Venu (Kal)|
|Commitee:||Barczewski, Richard, Alvarez, Marikis, Manoharan, Muthusamy|
|School:||Delaware State University|
|School Location:||United States -- Delaware|
|Source:||MAI 81/3(E), Masters Abstracts International|
|Subjects:||Plant sciences, Agriculture, Molecular biology|
|Keywords:||Bioinformatics, Hexaploid, Illumina, Ipomoea batatas, RNA Sequencing, Transcriptome|
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