Exploring wild relative introgressions in wheat and their impact on genomic methodology

Coombes, Benedict (2024) Exploring wild relative introgressions in wheat and their impact on genomic methodology. Doctoral thesis, University of East Anglia.

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Deploying novel genetic variation, such as wild relative introgressions, into wheat breeding programmes could help to satisfy the global demands of wheat despite a rising population and a changing climate. Sequencing data, which has become much cheaper and more accessible over time, can play an important role by being used to identify and characterise introgressions in wheat that confer beneficial traits and can be deployed into breeding programmes. This thesis offers insights into wheat introgressions in the context of sequencing data, exploring how sequencing data can be used to detect and characterise introgressions and also how introgressions can interfere with the accurate processing of sequencing data in common genomic analyses.

First, I used whole-genome sequencing data to characterise a set of hexaploidy wheat/Ambylopyrum muticum introgression lines to a high resolution, identifying introgressions and other structural changes in the lines. I then combined the sequencing data with rust resistance phenotype data to demonstrate how the region of introgressed genes underlying the phenotype can be identified and candidate genes proposed.

I then present findings on an important heat tolerance phenotype identified in wheat that is driven by three marker trait associations that together increase yield by over 50% under heat stress conditions. Using sequencing data, I discovered that one of these is driven by an Aegilops tauschii introgression. I then searched for candidate genes in multiple Ae. tauschii genomes, exposing the limits of relying on a single reference genome.

Finally, I found that the abundant introgressions across wheat accessions cause inaccurate RNA-seq read alignment that compromises research findings by leading to the underestimation of gene expression and the expression balance categories of triads being incorrectly assigned. To address this, I proposed a solution in which transcripts from multiple wheat cultivars are integrated into a pantranscriptome reference to use for RNAseq read alignment.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: Nicola Veasy
Date Deposited: 29 May 2024 11:05
Last Modified: 29 May 2024 11:05
URI: https://ueaeprints.uea.ac.uk/id/eprint/95328


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