ArticleThe Plant journal : for cell and molecular biology2016
Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat.
Article in The Plant journal : for cell and molecular biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Advances in gene cloning and functional genomics approaches for wheat (Triticum aestivum L.) improvement.The plant genome · 2026Review
- Multiomic insights into sucrose accumulation in sugarcane.Plant molecular biology · 2025Article
- Genomics-driven discovery of superior alleles and genes for yellow rust resistance in wheat.Nature genetics · 2025Article
- Transcriptome Analysis Reveals Potential Mechanism in Storage Protein Trafficking within Developing Grains of Common Wheat.International journal of molecular sciences · 2022Article
- Whole-exome sequencing of selected bread wheat recombinant inbred lines as a useful resource for allele mining and bulked segregant analysis.Frontiers in genetics · 2022Article
- Genetic Analysis of Adult Plant Resistance to Stripe Rust in Common Wheat Cultivar "Pascal".Frontiers in plant science · 2022Article
- Delaying or delivering: identification of novel NAM-1 alleles that delay senescence to extend wheat grain fill duration.Journal of experimental botany · 2021Article
- A framework for gene mapping in wheat demonstrated using the Yr7 yellow rust resistance gene.PloS one · 2020Article
- Combining a New Exome Capture Panel With an Effective varBScore Algorithm Accelerates BSA-Based Gene Cloning in Wheat.Frontiers in plant science · 2020Article
- Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat.GigaScience · 2019Article
- Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat.The Plant journal : for cell and molecular biology · 2019Review
- Hidden variation in polyploid wheat drives local adaptation.Genome research · 2018Article
- Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study.Molecular genetics and genomics : MGG · 2018Article
- Mapping Late Leaf Spot Resistance in Peanut (Frontiers in plant science · 2018Article
- Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly.Nature biotechnology · 2017Article
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Authors and funding
8 authors.
Funding
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.
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