Waves of bovine genomic data have been produced as a result of the bovine
genome sequencing projects. In addition to the massive amounts of genomic sequence,
significant annotation including single nucleotide polymorphisms, sequence tagged sites
and haplotype blocks have been produced by the Bovine HapMap Project. Furthermore,
many agriculturally significant traits in cattle such as milk yield and carcass weight are
measured on a quantitative scale and have been genetically mapped as quantitative trait
loci (QTL). QTL data can be used to generate another form of bovine annotation linking
phenotype to genotype. However, it is impossible for humans to be able to analyze
genomic scale data without computer based tools. Bioinformatic tools have been shown
to greatly increase productivity and improve efficiency when dealing with large data
sets.
My dissertation presents an integrated, extensible database that houses SNPs,
STSs, haplotypes, and QTL. The database is presented to researchers through a
restructured, object oriented Bovine QTL Viewer that displays multiple levels of bovine annotation synergistically. Evaluation of use of the viewer was performed using a
survey based approach and measured quantitatively.
In addition, the QTL data from the database was used to analyze the frequency of
gene ontology (GO) annotations within QTL regions. QTL regions were divided into 8
trait based groups. GO terms were counted within each category of QTL and in non-
QTL regions of the genome. Top level GO term frequencies were generated from the
counts and these frequencies were compared between QTL and non-QTL portions of the
genome. Furthermore, specific sets of GO terms believed to be related to QTL
categories were also used to determine if QTL regions were enriched for genes annotated
with such GO terms. As a result, we determined that gene density varied significantly
across QTL regions and that many QTL categories showed GO term frequency
differences that could be related to the trait’s biology. Furthermore, our selected GO
term sets were shown to be significantly enriched in some QTL categories.
| Identifer | oai:union.ndltd.org:tamu.edu/oai:repository.tamu.edu:1969.1/ETD-TAMU-2969 |
| Date | 15 May 2009 |
| Creators | Salih, Hanni |
| Contributors | Adelson, David, Womack, James |
| Source Sets | Texas A and M University |
| Language | en_US |
| Detected Language | English |
| Type | Book, Thesis, Electronic Dissertation, text |
| Format | electronic, application/pdf, born digital |
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