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

Gardiner, L; Bansept-Basler, P; Olohan, L; Joynson, R; Brenchley, RC; Hall, N; O’Sullivan, DM; Hall, A

Abstract

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.

Citation

Gardiner, L., Bansept-Basler, P., Olohan, L., Joynson, R., Brenchley, R., Hall, N., …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. Plant Journal, 87(4), 403-419. https://doi.org/10.1111/tpj.13204

• Journal Article Type: Article
• Acceptance Date: Apr 26, 2016
• Online Publication Date: May 3, 2016
• Publication Date: Aug 1, 2016
• Deposit Date: Jun 2, 2016
• Publicly Available Date: May 4, 2017
• Journal: Plant Journal
• Print ISSN: 0960-7412
• Electronic ISSN: 1365-313X
• Publisher: Wiley
• Volume: 87
• Issue: 4
• Pages: 403-419
• DOI: https://doi.org/10.1111/tpj.13204
• Publisher URL: http://dx.doi.org/10.1111/tpj.13204
• Related Public URLs: http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-313X
• Additional Information: Funders : Biotechnology and Biosciences Sciences Research Council (BBSRC)