Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat

Gardiner, L.-J., Bansept-Basler, P., Olohan, L., Joynson, R., Brenchley, R., Hall, N., O'Sullivan, D. M. ORCID: https://orcid.org/0000-0003-4889-056X and Hall, A. (2016) Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat. The Plant Journal, 87 (4). pp. 403-419. ISSN 0960-7412 doi: 10.1111/tpj.13204

Abstract/Summary

Previously we extended the utility of mapping-by-sequencing by combining it with sequence capture and mapping sequence data to pseudo-chromosomes that were organized using wheat-Brachypodium synteny. This, with a bespoke haplotyping algorithm, enabled us to map the flowering time locus in the diploid wheat Triticum monococcum L identifying a set of deleted genes (Gardiner et al., 2014). Here, we develop this combination of gene enrichment and sliding window mapping-by-synteny analysis to map the Yr6 locus for yellow stripe rust resistance in hexaploid wheat. A 110MB NimbleGen capture probe set was used to enrich and sequence a doubled-haploid mapping population of hexaploid wheat derived from an Avalon and Cadenza cross. The Yr6 locus was identified by mapping to the POPSEQ chromosomal pseudomolecules using a bespoke pipeline and algorithm (Chapman et al., 2015). Furthermore the same locus was identified using newly developed pseudo-chromosome sequences as a mapping reference that are based on the genic sequence used for sequence enrichment. The pseudo-chromosomes allow us to demonstrate the application of mapping-by-sequencing to even poorly defined polyploidy genomes where chromosomes are incomplete and sub-genome assemblies are collapsed. This analysis uniquely enabled us to: compare wheat genome annotations; identify the Yr6 locus - defining a smaller genic region than was previously possible; associate the interval with one wheat sub-genome and increase the density of SNP markers associated. Finally, we built the pipeline in iPlant, making it a user-friendly community resource for phenotype mapping.

Item Type	Article
URI	https://reading-clone.eprints-hosting.org/id/eprint/65830
Identification Number/DOI	10.1111/tpj.13204
Refereed	Yes
Divisions	Life Sciences > School of Agriculture, Policy and Development > Department of Crop Science
Publisher	Wiley-Blackwell
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