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Coombes, Benedict, Fellers, John P., Grewal, Surbhi, Rusholme-Pilcher, Rachel, Hubbart-Edwards, Stella, Yang, Cai-yun, Joynson, Ryan, King, Ian P., King, Julie and Hall, Anthony 
ORCID: https://orcid.org/0000-0002-1806-020X
(2023)
Whole-genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines.
Plant Biotechnology Journal, 21 (3).
pp. 482-496.
ISSN 1467-7644
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Abstract
Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheat's wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is constrained by poor genomic resolution and limited understanding of the genomic impact of introgression breeding programmes. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments, most of which occur within genes. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust. Our analysis has identified an abundance of structural disruption and homoeologous pairing across the introgression lines, likely caused by the suppressed Ph1 locus. mRNAseq analysis of six of these introgression lines revealed that novel introgressed genes are rarely expressed and those that directly replace a wheat orthologue have a tendency towards downregulation, with no discernible compensation in the expression of homoeologous copies. This study explores the genomic impact of introgression breeding and provides a schematic that can be followed to characterize introgression lines and identify segments and candidate genes underlying the phenotype. This will facilitate more effective utilization of introgression pre-breeding material in wheat breeding programmes.
| Item Type: | Article |
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| Additional Information: | Data availability statement: Sequencing data produced as part of this study, along with the Am. muticum assembly is available at: https://opendata.earlham.ac.uk/wheat/under_license/toronto/Hall_2021-10-08_wheatxmuticum. Am. muticum Illumina short-read sequencing reads available at: https://opendata.earlham.ac.uk/wheat/under_license/toronto/Grewal_et_al_2021-09-13_Amybylopyrum_muticum/. The Chinese Spring sequencing data used is available from ENA (study PRJNA393343; runs SRR5893651 and SRR5893652). The Paragon sequencing data used are available from ENA (study PRJEB35709; runs ERR3728451, ERR3760033, ERR3760405 and ERR3728448). Custom scripts used for introgression detection are available at: https://github.com/benedictcoombes/alien_detection. Funding Information: BBSRC Core Capability Grant BB/CCG1720/1 (AH, RJ, RR-P). BBSRC funded Norwich Research Park Biosciences Doctoral Training Partnership grant BB/M011216/1 (BC). BBSRC Designing Future Wheat grant BB/P016855/1 and its constituent work packages DFW WP4 Data Access and Analysis (AH, RJ, RR-P, JK, IPK, SG, SE, CY). BBSRC grant BB/J004596/1 as part of the Wheat Improvement Strategic Programme (WISP) (JK, IPK, SG, SE, CY). USDA-ARS CRIS 3020–21000-011-000-D (JF). We would like to acknowledge BBS/E/T/000PR9816 (NC1 - Supporting EI's ISPs and the UK Community with Genomics and Single Cell Analysis) for data generation and BB/CCG1720/1 for the physical HPC infrastructure and data centre delivered via the NBI Computing infrastructure for Science (CiS) group. |
| Uncontrolled Keywords: | breeding,genomics,introgression,resistance,wheat,wild relative,biotechnology,agronomy and crop science,plant science ,/dk/atira/pure/subjectarea/asjc/1300/1305 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 31 Oct 2024 14:30 |
| Last Modified: | 07 Nov 2024 00:55 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97382 |
| DOI: | 10.1111/pbi.13859 |
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