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 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' , Plant Journal, 87 (4) , pp. 403-419.

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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
Schools: Schools > School of Environment and Life Sciences > Ecosystems and Environment Research Centre
Journal or Publication Title: Plant Journal
Publisher: Wiley
ISSN: 0960-7412
Related URLs:
Funders: Biotechnology and Biosciences Sciences Research Council (BBSRC)
Depositing User: RC Brenchley
Date Deposited: 02 Jun 2016 10:37
Last Modified: 15 Feb 2022 20:51

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