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Advancing genomics to enable anticipatory breeding of resistance in Brassica crops to diseases of global importance
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Crowther, William (2021) Advancing genomics to enable anticipatory breeding of resistance in Brassica crops to diseases of global importance. PhD thesis, University of Warwick.
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Official URL: http://webcat.warwick.ac.uk/record=b3717997~S15
Abstract
White rust (WR) (caused by the oomycete Albugo candida) inflicts significant yield decline in brassica crops across the world. It is a particular problem in countries like India, where resource poor farmers cultivating oilseed mustard (Brassica juncea) suffer between 30-60% yield losses per year. Breeding for host resistance is the most effective and environmentally friendly way of protecting brassica crops from WR. Rapid evolution of the pathogen highlights the need to efficiently map multiple resistance genes for combined integration into cultivars. Here we present novel methods for achieving this, with an emphasis on directly mapping from undeveloped genebank populations.
In this work, the application of Whole Genome Resequencing (WGS) and Bulked Segregant Analysis (BSA) proved to be highly effective for rapidly mapping sixteen major effect white rust resistance (WRR) QTLs across five geographically diverse Brassica rapa genebank populations, including a landrace and a wild species. This includes a QTL mapped on chromosome 6, containing a WRR allele that provides resistance to Donskaja-virulent UK race 2 isolate AcBjDC. WGS for all QTLs has been scrutinised, allowing identification of various polymorphic candidate WRR genes.
WRR was also explored in the Brassica oleracea EBH527 x A12DH mapping population, where a previously fine-mapped ACA2 locus contains a recessive race non-specific resistance. A CRISPR-Cas9 knockout of the primary candidate (a GDSL Lipase) yielded no alteration to susceptibility and WGS of the two parents has since been used to identify other potentially causal mutations within the region. WGS-BSA was also applied here to map a dominant resistance locus in tight-linkage to ACA2 from segregating recombinant line EH177.
Finally, Oxford Nanopore Technology long-read sequencing was used to produce high-quality genome assemblies for race 2 isolates AcBj12 and AcBjDC, augmented with Illumina reads. The AcBj12_ONT assembly provided a 30 % improvement in contiguity relative to previous efforts using PacBio data. Comparative genomics that included Donskaja-virulent isolate Ac2v was used to document allelic variation in “CCG” class effectors that provides a platform for future identification of the Avr elicitor. Collectively, methods presented here enhance rapid identification of loci and candidate genes for the benefit of global brassica production.
Item Type: | Thesis (PhD) | ||||
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Subjects: | Q Science > QK Botany S Agriculture > SB Plant culture |
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Library of Congress Subject Headings (LCSH): | Brassica -- Genetics, Brassica -- Genome mapping, Brassica -- Disease and pest resistance, Albugo candida, Plant genome mapping, Crop improvement | ||||
Official Date: | February 2021 | ||||
Dates: |
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Institution: | University of Warwick | ||||
Theses Department: | School of Life Sciences | ||||
Thesis Type: | PhD | ||||
Publication Status: | Unpublished | ||||
Supervisor(s)/Advisor: | Holub, E. B. ; Allender, Charlotte J. | ||||
Sponsors: | Biotechnology and Biological Sciences Research Council (Great Britain) ; Midlands Integrative Biosciences Training Partnership | ||||
Format of File: | |||||
Extent: | xvi, 168 leaves : illustrations (some colour) | ||||
Language: | eng |
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