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

Using the UK reference population Avalon × Cadenza as a platform to compare breeding strategies in elite Western European bread wheat

(2015) Juan Ma et al.   MOLECULAR BREEDING

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

(2015) Katherine W Jordan et al.   GENOME BIOLOGY

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

(2015) Jarrod A Chapman et al.   GENOME BIOLOGY

A Distorted Circadian Clock Causes Early Flowering and Temperature-Dependent Variation in Spike Development in theEps-3AmMutant of Einkorn Wheat

(2014) Piotr Gawroński et al.   GENETICS

Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species

(2014) Laura-Jayne Gardiner et al.   PLANT JOURNAL

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

An Eight-Parent Multiparent Advanced Generation Inter-Cross Population for Winter-Sown Wheat: Creation, Properties, and Validation

(2014) I. J. Mackay et al.   G3-Genes Genomes Genetics

Mapping-by-sequencing accelerates forward genetics in barley

(2014) Martin Mascher et al.   GENOME BIOLOGY

Wheat stripe (yellow) rust caused byPuccinia striiformisf. sp.tritici

(2013) Wanquan Chen et al.   MOLECULAR PLANT PATHOLOGY

Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers

(2013) Karl J V Nordström et al.   NATURE BIOTECHNOLOGY

Analysing complex Triticeae genomes – concepts and strategies

(2013) Manuel Spannagl et al.   Plant Methods

Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat

(2012) Martin Trick et al.   BMC PLANT BIOLOGY

CloudMap: A Cloud-Based Pipeline for Analysis of Mutant Genome Sequences

(2012) Gregory Minevich et al.   GENETICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Analysis of the bread wheat genome using whole-genome shotgun sequencing

(2012) Rachel Brenchley et al.   NATURE

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

MIPS PlantsDB: a database framework for comparative plant genome research

(2012) Thomas Nussbaumer et al.   NUCLEIC ACIDS RESEARCH

Targeted re-sequencing of the allohexaploid wheat exome

(2012) Mark O. Winfield et al.   PLANT BIOTECHNOLOGY JOURNAL

Fast Isogenic Mapping-by-Sequencing of Ethyl Methanesulfonate-Induced Mutant Bulks

(2012) B. Hartwig et al.   PLANT PHYSIOLOGY

Next-generation mapping of Arabidopsis genes

(2011) Ryan S. Austin et al.   PLANT JOURNAL

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

(2011) Stephen A. Goff et al.   Frontiers in Plant Science

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

(2010) Frédéric Choulet et al.   PLANT CELL

C. elegans Mutant Identification with a One-Step Whole-Genome-Sequencing and SNP Mapping Strategy

(2010) Maria Doitsidou et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

(2009) Korbinian Schneeberger et al.   NATURE METHODS

Evaluation of seedling and adult plant resistance in European wheat cultivars to Australian isolates of Puccinia striiformis f. sp. tritici

(2008) Amin K. Pathan et al.   EUPHYTICA

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Mapping a stripe rust resistance gene YrC591 in wheat variety C591 with SSR and AFLP markers

(2008) Y. Li et al.   THEORETICAL AND APPLIED GENETICS