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Grewal, Surbhi, Coombes, Benedict, Joynson, Ryan, Hall, Anthony 
ORCID: https://orcid.org/0000-0002-1806-020X, Fellers, John, Yang, Cai-yun, Scholefield, Duncan, Ashling, Stephen, Isaac, Peter, King, Ian P. and King, Julie
(2022)
Chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines.
Plant Genome, 15 (1).
ISSN 1940-3372
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Abstract
Many wild-relative species are being used in prebreeding programs to increase the genetic diversity of wheat (Triticum aestivum L.). Genotyping tools such as single nucleotide polymorphism (SNP)-based arrays and molecular markers have been widely used to characterize wheat–wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP-based Kompetitive allele-specific polymerase chain reaction (KASP) markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome- and polymerase chain reaction (PCR)-amplicon-based sequencing of the wild species. But chromosome-specific KASP assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum (Boiss.) Eig and development of a de novo SNP discovery pipeline that generated ∼38,000 SNPs in unique wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as diagnostic for Am. muticum in a wheat background. Together with assays validated in previous studies, 498 well distributed chromosome-specific markers were used to recharacterize previously genotyped wheat–Am. muticum doubled haploid (DH) introgression lines. The chromosome-specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines.
| Item Type: | Article |
|---|---|
| Additional Information: | Data Availability Statement: Raw reads data for Am. muticum have been made available through the Sequence Read Archive via Project PRJNA783544 and through the Grassroots data repository hosted by the Earlham Institute and funded by DFW programe (https://opendata.earlham.ac.uk/wheat/under_license/toronto/Grewal_et_al_2021-09-13_Amybylopyrum_muticum/). The latter also hosts the raw and filtered vcf files generated in this study. The code and custom scripts for the entire pipeline is available via https://github.com/Surbhigrewal/chromosome-specific_KASPs. All DH lines used in this study are available through the Germplasm Resource Unit at the John Innes Centre. The genotyping data are available from the corresponding author on reasonable request. Funding Information: This research was funded by the Biotechnology and Biological Sciences Research Council (Grant No. BB/J004596/1 and BB/P016855/1) as part of the Wheat Improvement Strategic Programme (WISP) and Designing Future Wheat (DFW) Programme, respectively. |
| Uncontrolled Keywords: | genetics,agronomy and crop science,plant science ,/dk/atira/pure/subjectarea/asjc/1300/1311 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 29 Oct 2024 15:30 |
| Last Modified: | 31 Oct 2024 14:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97348 |
| DOI: | 10.1002/tpg2.20193 |
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