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Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust
Laura-Jayne Gardiner1, Pauline Bansept-Basler2, Lisa Olohan1
1Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
Summary
Researchers mapped the Yr6 yellow stripe rust resistance locus in hexaploid wheat using advanced mapping-by-sequencing. This method refines gene mapping in complex polyploid genomes and aids in developing disease-resistant wheat varieties.
Area of Science:
- Plant genetics and genomics
- Crop science
- Bioinformatics
Background:
- Previous work established mapping-by-sequencing with synteny-based pseudochromosomes for gene mapping in wheat.
- This technique successfully mapped a flowering time locus in diploid wheat (Triticum monococcum L.).
Purpose of the Study:
- To adapt and apply mapping-by-sequencing combined with gene enrichment for precise locus identification in hexaploid wheat.
- To map the Yr6 locus conferring yellow stripe rust resistance.
- To demonstrate the utility of this approach in complex polyploid genomes.
Main Methods:
- Utilized a 110 MB NimbleGen capture probe set for enrichment and sequencing of a doubled haploid mapping population (Avalon x Cadenza).
- Employed mapping-by-synteny analysis using POPSEQ chromosomal pseudomolecules and newly developed genic sequence-based pseudochromosomes.
- Developed a bespoke bioinformatics pipeline for data analysis and SNP marker association.
Main Results:
- Successfully identified the Yr6 locus for yellow stripe rust resistance in hexaploid wheat.
- Defined a smaller genic region for the Yr6 locus compared to previous studies.
- Associated the Yr6 locus with a specific wheat sub-genome and increased SNP marker density.
- Demonstrated the effectiveness of mapping-by-sequencing in poorly defined polyploid genomes.
Conclusions:
- The developed mapping-by-sequencing approach is effective for high-resolution mapping in complex polyploid wheat genomes.
- This method facilitates comparative genome annotation and precise locus identification.
- The iPlant pipeline provides a user-friendly resource for phenotype mapping in crop improvement.
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