title: Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat.
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 110 MB 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.
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
authors.forename: Laura-Jayne
authors.initials: LJ
authors.lastname: Gardiner
authors.affiliation: Syngenta, Ferme de Moyencourt, 78910, Orgerus, France.
authors.forename: Pauline
authors.initials: P
authors.lastname: Bansept-Basler
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
authors.forename: Lisa
authors.initials: L
authors.lastname: Olohan
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
authors.forename: Ryan
authors.initials: R
authors.lastname: Joynson
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
authors.forename: Rachel
authors.initials: R
authors.lastname: Brenchley
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
authors.forename: Neil
authors.initials: N
authors.lastname: Hall
authors.affiliation: School of Agriculture, Policy and Development, University of Reading, PO Box 237, Whiteknights, Reading, RG6 6AR, UK.
authors.forename: Donal M
authors.initials: DM
authors.lastname: O'Sullivan
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK. Anthony.hall@liverpool.ac.uk.
authors.forename: Anthony
authors.initials: A
authors.lastname: Hall
mesh_terms: D001487:Basidiomycota / Q000502:physiology*; D058431:Brachypodium / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D004171:Diploidy; D060467:Disease Resistance / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D010935:Plant Diseases / Q000276:immunology* / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011123:Polyploidy; D017422:Sequence Analysis, DNA; D026801:Synteny; D014908:Triticum / Q000235:genetics* / Q000276:immunology / Q000382:microbiology
chemical_list: D005819:Genetic Markers
keywords: genomics; mapping-by-sequencing; next generation; target enrichment; wheat