Genomics as the key to unlocking the polyploid potential of wheat

PolyMarker: A fast polyploid primer design pipeline: Fig. 1.

(2015) Ricardo H. Ramirez-Gonzalez et al.   BIOINFORMATICS

From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development

(2015) Takehiko Ogura et al.   CURRENT OPINION IN PLANT BIOLOGY

Arabidopsis EF-Tu receptor enhances bacterial disease resistance in transgenic wheat

(2015) Henk-jan Schoonbeek et al.   NEW PHYTOLOGIST

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

Strategic pre-breeding for wheat improvement

(2015) Graham Moore   Nature Plants

Progress in TILLING as a tool for functional genomics and improvement of crops

(2014) Liang Chen et al.   Journal of Integrative Plant Biology

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew

(2014) Yanpeng Wang et al.   NATURE BIOTECHNOLOGY

Genome editing in rice and wheat using the CRISPR/Cas system

(2014) Qiwei Shan et al.   Nature Protocols

Using next-generation sequencing to isolate mutant genes from forward genetic screens

(2014) Korbinian Schneeberger   NATURE REVIEWS GENETICS

Polyploidy: adaptation to the genomic environment

(2014) Jesse D. Hollister   NEW PHYTOLOGIST

Triticeae Resources in Ensembl Plants

(2014) Dan M. Bolser et al.   PLANT AND CELL PHYSIOLOGY

RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat

(2014) Ricardo H. Ramirez-Gonzalez et al.   PLANT BIOTECHNOLOGY JOURNAL

Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array

(2014) Shichen Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing

(2014) I. M. Henry et al.   PLANT CELL

Efficient Agrobacterium transformation of elite wheat germplasm without selection

(2014) Terese Richardson et al.   PLANT CELL TISSUE AND ORGAN CULTURE

Suppression among alleles encoding nucleotide-binding-leucine-rich repeat resistance proteins interferes with resistance in F1hybrid and allele-pyramided wheat plants

(2014) Daniel Stirnweis et al.   PLANT JOURNAL

Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A

(2014) Naser Poursarebani et al.   PLANT JOURNAL

The powdery mildew resistance genePm8derived from rye is suppressed by its wheat orthologPm3

(2014) Severine Hurni et al.   PLANT JOURNAL

The Shutdown of Celiac Disease-Related Gliadin Epitopes in Bread Wheat by RNAi Provides Flours with Increased Stability and Better Tolerance to Over-Mixing

(2014) Javier Gil-Humanes et al.   PLoS One

Evolution of physiological responses to salt stress in hexaploid wheat

(2014) C. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient hybridizations among the ancestral genomes of bread wheat

(2014) T. Marcussen et al.   SCIENCE

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

(2014) et al.   SCIENCE

Genome interplay in the grain transcriptome of hexaploid bread wheat

(2014) M. Pfeifer et al.   SCIENCE

Structural and functional partitioning of bread wheat chromosome 3B

(2014) F. Choulet et al.   SCIENCE

Establishing the A. E. Watkins landrace cultivar collection as a resource for systematic gene discovery in bread wheat

(2014) Luzie U. Wingen et al.   THEORETICAL AND APPLIED GENETICS

Strategies for transferring resistance into wheat: from wide crosses to GM cassettes

(2014) Brande B. H. Wulff et al.   Frontiers in Plant Science

Mapping-by-sequencing accelerates forward genetics in barley

(2014) Martin Mascher et al.   GENOME BIOLOGY

Natural Variations and Genome-Wide Association Studies in Crop Plants

(2013) Xuehui Huang et al.   Annual Review of Plant Biology

Comparative analysis of protein-protein interactions in the defense response of rice and wheat

(2013) Dario Cantu et al.   BMC GENOMICS

Rice epigenomics and epigenetics: challenges and opportunities

(2013) Xiangsong Chen et al.   CURRENT OPINION IN PLANT BIOLOGY

TaCPK2-A, a calcium-dependent protein kinase gene that is required for wheat powdery mildew resistance enhances bacterial blight resistance in transgenic rice

(2013) Shuaifeng Geng et al.   JOURNAL OF EXPERIMENTAL BOTANY

Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement

(2013) Kassa Semagn et al.   MOLECULAR BREEDING

A systematic genome-wide analysis of zebrafish protein-coding gene function

(2013) Ross N. W. Kettleborough et al.   NATURE

Draft genome of the wheat A-genome progenitor Triticum urartu

(2013) Hong-Qing Ling et al.   NATURE

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

(2013) Jizeng Jia et al.   NATURE

Targeted genome modification of crop plants using a CRISPR-Cas system

(2013) Qiwei Shan et al.   NATURE BIOTECHNOLOGY

Epigenetic modification contributes to the expression divergence of threeTaEXPA1homoeologs in hexaploid wheat (Triticum aestivum)

(2013) Zhaorong Hu et al.   NEW PHYTOLOGIST

Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations

(2013) Florian Jupe et al.   PLANT JOURNAL

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

(2013) Martin Mascher et al.   PLANT JOURNAL

RNA Interference Suppression of Genes in Glycosyl Transferase Families 43 and 47 in Wheat Starchy Endosperm Causes Large Decreases in Arabinoxylan Content

(2013) A. Lovegrove et al.   PLANT PHYSIOLOGY

Functional characterization of GPC-1 genes in hexaploid wheat

(2013) Raz Avni et al.   PLANTA

FISHIS: Fluorescence In Situ Hybridization in Suspension and Chromosome Flow Sorting Made Easy

(2013) Debora Giorgi et al.   PLoS One

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

(2013) C. R. Cavanagh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Gene Sr33, an Ortholog of Barley Mla Genes, Encodes Resistance to Wheat Stem Rust Race Ug99

(2013) S. Periyannan et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Yield stability of hybrids versus lines in wheat, barley, and triticale

(2013) Jonathan Mühleisen et al.   THEORETICAL AND APPLIED GENETICS

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

(2013) Emma S. Mace et al.   Nature Communications

RNA-Guided Genome Editing for Target Gene Mutations in Wheat

(2013) Santosh Kumar Upadhyay et al.   G3-Genes Genomes Genetics

CerealsDB 2.0: an integrated resource for plant breeders and scientists

(2012) Paul A Wilkinson et al.   BMC BIOINFORMATICS

Development of high amylose wheat through TILLING

(2012) Ann J Slade et al.   BMC PLANT BIOLOGY

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

Paired-end sequencing of Fosmid libraries by Illumina

(2012) L. J. S. Williams et al.   GENOME RESEARCH

Genomic asymmetry in allopolyploid plants: wheat as a model

(2012) M. Feldman et al.   JOURNAL OF EXPERIMENTAL BOTANY

Flow cytometric chromosome sorting in plants: The next generation

(2012) Jan Vrána et al.   METHODS

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

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

(2012) Rachel Brenchley et al.   NATURE

Big data in small places

(2012) Daniel MacLean et al.   NATURE BIOTECHNOLOGY

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

Maize HapMap2 identifies extant variation from a genome in flux

(2012) Jer-Ming Chia et al.   NATURE GENETICS

Down-regulation of Glucan, Water-Dikinase activity in wheat endosperm increases vegetative biomass and yield

(2012) Jean-Philippe Ral et al.   PLANT BIOTECHNOLOGY JOURNAL

Targeted re-sequencing of the allohexaploid wheat exome

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

TILLINGin extremis

(2012) Trevor L. Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivumL.)

(2012) Alexandra M. Allen et al.   PLANT BIOTECHNOLOGY JOURNAL

Genotype-specific SNP map based on whole chromosome 3B sequence information from wheat cultivars Arina and Forno

(2012) Margarita Shatalina et al.   PLANT BIOTECHNOLOGY JOURNAL

Divergent functions of orthologous NAC transcription factors in wheat and rice

(2012) Assaf Distelfeld et al.   PLANT MOLECULAR BIOLOGY

Comparative Analysis of Syntenic Genes in Grass Genomes Reveals Accelerated Rates of Gene Structure and Coding Sequence Evolution in Polyploid Wheat

(2012) E. D. Akhunov et al.   PLANT PHYSIOLOGY

Epigenetics and crop improvement

(2012) Nathan M. Springer   TRENDS IN GENETICS

Genotyping-by-Sequencing for Plant Breeding and Genetics

(2012) Jesse A. Poland et al.   Plant Genome

Transgenerational epigenetic inheritance in plants

(2011) Marie-Theres Hauser et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Reconstruction of the Synthetic W7984 × Opata M85 wheat reference population

(2011) Mark E. Sorrells et al.   GENOME

Ploidy influences rarity and invasiveness in plants

(2011) Maharaj K. Pandit et al.   JOURNAL OF ECOLOGY

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.)

(2011) Alexandra M. Allen et al.   PLANT BIOTECHNOLOGY JOURNAL

Discovery of Rare Mutations in Populations: TILLING by Sequencing

(2011) H. Tsai et al.   PLANT PHYSIOLOGY

Genetic dissection of the biotic stress response using a genome-scale gene network for rice

(2011) I. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat

(2011) Z. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

Transgenerational Adaptation of Arabidopsis to Stress Requires DNA Methylation and the Function of Dicer-Like Proteins

(2010) Alex Boyko et al.   PLoS One

A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheat

(2009) Cristobal Uauy et al.   BMC PLANT BIOLOGY

Adaptive epigenetic memory of ancestral temperature regime in Arabidopsis thalianaThis paper is one of a selection of papers published in a Special Issue from the National Research Council of Canada – Plant Biotechnology Institute.

(2009) C. A. Whittle et al.   Botany

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

(2009) Korbinian Schneeberger et al.   NATURE METHODS

TriFLDB: A Database of Clustered Full-Length Coding Sequences from Triticeae with Applications to Comparative Grass Genomics

(2009) K. Mochida et al.   PLANT PHYSIOLOGY

Angiosperm genome comparisons reveal early polyploidy in the monocot lineage

(2009) H. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Energy use efficiency is characterized by an epigenetic component that can be directed through artificial selection to increase yield

(2009) M. Hauben et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors

(2009) J. Boch et al.   SCIENCE

A Simple Cipher Governs DNA Recognition by TAL Effectors

(2009) M. J. Moscou et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Detailed Recombination Studies Along Chromosome 3B Provide New Insights on Crossover Distribution in Wheat (Triticum aestivum L.)

(2008) C. Saintenac et al.   GENETICS

TILLMore, a resource for the discovery of chemically induced mutants in barley

(2008) Valentina Talamè et al.   PLANT BIOTECHNOLOGY JOURNAL

TaASY1 promotes homologous chromosome interactions and is affected by deletion ofPh1

(2008) Scott A. Boden et al.   PLANT JOURNAL

A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B

(2008) E. Paux et al.   SCIENCE

Adaptive evolution in invasive species

(2008) Peter J. Prentis et al.   TRENDS IN PLANT SCIENCE