Next generation genomics tools for wheat improvement

Ramirez Gonzalez, Ricardo (2016) Next generation genomics tools for wheat improvement. Doctoral thesis, University of East Anglia.

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Abstract

In recent years the amount of genomic resources of wheat has increased
to the point where manual analysis is unfeasible. The aim of this PhD
was to develop bioinformatics tools that help answer biological questions
relevant to research and breeding by addressing the complexities
associated with the wheat genome. I took advantage of resources which
became publicly available as the analyses were carried out and I developed
new approaches, strategies and tools to help accelerate wheat
research. Chapter 1 reviews the genomic resources used for the thesis,
placing them in historic context with the work and analyses performed.
Chapter 2 describes the development of PolyMarker, a bioinformatics
pipeline to design genome-specific primers in a timely and effective manner.
Examples of different applications of PolyMarker are also included.
Chapter 3 describes the analysis of an F2 population to generate a genetic
map for Yr15, a gene that provides resistance to yellow rust. The SNP
calling was done from bulked segregating samples, sequenced with RNASeq
as a method of reduced representation. Chapter 4 describes expVIP,
a tool to integrate RNA-Seq experiments in a relational database. Data
from different studies can be visualised simultaneously, enabling comparisons
between them. Lastly, in Chapter 5 all the data types used for
the analysis on each of the previous chapters is integrated into a relational
database. The discussion further explores how genetic maps, SNP
markers, novel SNPs, gene annotations, gene assemblies and gene expression
can be used simultaneously in research and breeding programs. All
the tools and pipelines described in this thesis are open source and are
available on: https://github.com/homonecloco.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: Katie Miller
Date Deposited: 28 Mar 2017 15:12
Last Modified: 28 Mar 2017 15:12
URI: https://ueaeprints.uea.ac.uk/id/eprint/63098
DOI:

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