Accessing complex crop genomes with next-generation sequencing

Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum ; Fabaceae), a crop species without a reference genome

(2012) Sarwar Azam et al.   AMERICAN JOURNAL OF BOTANY

Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology

(2012) Xiaojun Nie et al.   AMERICAN JOURNAL OF BOTANY

Next-generation sequencing applications for wheat crop improvement

(2012) Paul J. Berkman et al.   AMERICAN JOURNAL OF BOTANY

Targeted re-sequencing of the allohexaploid wheat exome

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

Second-generation sequencing for gene discovery in the Brassicaceae

(2012) Alice Hayward et al.   PLANT BIOTECHNOLOGY JOURNAL

A tailed PCR procedure for cost-effective, two-order multiplex sequencing of candidate genes in polyploid plants

(2012) Mahmood Gholami et al.   PLANT BIOTECHNOLOGY JOURNAL

Identification and characterization of candidateRlm4blackleg resistance genes inBrassica napususing next-generation sequencing

(2012) Reece Tollenaere et al.   PLANT BIOTECHNOLOGY JOURNAL

Bread matters: a national initiative to profile the genetic diversity of Australian wheat

(2012) David Edwards et al.   PLANT BIOTECHNOLOGY JOURNAL

Enrichment of genomic DNA for polymorphism detection in a non-model highly polyploid crop plant

(2012) Peter C. Bundock et al.   PLANT BIOTECHNOLOGY JOURNAL

Single nucleotide polymorphism discovery from wheat next-generation sequence data

(2012) Kaitao Lai et al.   PLANT BIOTECHNOLOGY JOURNAL

Potential to improve oilseed rape and canola breeding in the genomics era

(2012) Rod J. Snowdon et al.   PLANT BREEDING

A knockout mutation in the lignin biosynthesis gene CCR1 explains a major QTL for acid detergent lignin content in Brassica napus seeds

(2012) Liezhao Liu et al.   THEORETICAL AND APPLIED GENETICS

Genetic and physical mapping of flowering time loci in canola (Brassica napus L.)

(2012) Harsh Raman et al.   THEORETICAL AND APPLIED GENETICS

Genomic Databases for Crop Improvement

(2012) Kaitao Lai et al.   Agronomy-Basel

Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa

(2011) Jun Wang et al.   BMC GENOMICS

Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

(2011) Frank M You et al.   BMC GENOMICS

Exploring plant transcriptomes using ultra high-throughput sequencing

(2011) L. Wang et al.   Briefings in Functional Genomics

Genomic selection in plant breeding: from theory to practice

(2011) J.-L. Jannink et al.   Briefings in Functional Genomics

Bioinformatics tools and databases for analysis of next-generation sequence data

(2011) H. C. Lee et al.   Briefings in Functional Genomics

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Sequencing for the cream of the crop

(2011) Jer-Ming Chia et al.   NATURE BIOTECHNOLOGY

Linkage illuminates a complex genome

(2011) John K McKay et al.   NATURE BIOTECHNOLOGY

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Genomic advances will herald new insights into the Brassica: Leptosphaeria maculans pathosystem

(2011) A. Hayward et al.   PLANT BIOLOGY

Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS

(2011) Paul J. Berkman et al.   PLANT BIOTECHNOLOGY JOURNAL

Unlocking the Barley Genome by Chromosomal and Comparative Genomics

(2011) Klaus F.X. Mayer et al.   PLANT CELL

Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content

(2011) Pilar Hernandez et al.   PLANT JOURNAL

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne

(2011) W. F. Pfender et al.   THEORETICAL AND APPLIED GENETICS

Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome

(2011) Cyrille Saintenac et al.   GENOME BIOLOGY

Development of Chromosome-Specific BAC Resources for Genomics of Bread Wheat

(2010) J. Šafář et al.   CYTOGENETIC AND GENOME RESEARCH

Future tools for association mapping in crop plantsThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

(2010) Chris Duran et al.   GENOME

Digital transcriptome profiling from attomole-level RNA samples

(2010) F. Ozsolak et al.   GENOME RESEARCH

An association transcriptomics approach to the prediction of hybrid performance

(2010) David Stokes et al.   MOLECULAR BREEDING

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

The first meiosis of resynthesized Brassica napus, a genome blender

(2010) E. Szadkowski et al.   NEW PHYTOLOGIST

A Genetic Framework for Grain Size and Shape Variation in Wheat

(2010) Vasilis C. Gegas et al.   PLANT CELL

Repeat subtraction-mediated sequence capture from a complex genome

(2010) Yan Fu et al.   PLANT JOURNAL

Targeted identification of genomic regions using TAGdb

(2010) Daniel J Marshall et al.   Plant Methods

Genome sequence data: management, storage, and visualization

(2009) Jacqueline Batley et al.   BIOTECHNIQUES

De novo sequencing of plant genomes using second-generation technologies

(2009) M. Imelfort et al.   BRIEFINGS IN BIOINFORMATICS

Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation

(2009) Chris Duran et al.   Current Bioinformatics

Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat

(2009) Humphrey Wanjugi et al.   GENOME

Invited review: Genomic selection in dairy cattle: Progress and challenges

(2009) B.J. Hayes et al.   JOURNAL OF DAIRY SCIENCE

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Homoeologous recombination in allopolyploids: the polyploid ratchet

(2009) Robert T. Gaeta et al.   NEW PHYTOLOGIST

Single nucleotide polymorphism discovery in barley using autoSNPdb

(2009) Chris Duran et al.   PLANT BIOTECHNOLOGY JOURNAL

Discovering genetic polymorphisms in next-generation sequencing data

(2009) Michael Imelfort et al.   PLANT BIOTECHNOLOGY JOURNAL

Single nucleotide polymorphism (SNP) discovery in the polyploidBrassica napususing Solexa transcriptome sequencing

(2009) Martin Trick et al.   PLANT BIOTECHNOLOGY JOURNAL

Gene Content and Virtual Gene Order of Barley Chromosome 1H

(2009) K. F.X. Mayer et al.   PLANT PHYSIOLOGY

Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae

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

Genetic Properties of the Maize Nested Association Mapping Population

(2009) M. D. McMullen et al.   SCIENCE

A First-Generation Haplotype Map of Maize

(2009) M. A. Gore et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Next-generation sequencing technologies and their implications for crop genetics and breeding

(2009) Rajeev K. Varshney et al.   TRENDS IN BIOTECHNOLOGY

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

(2009) Nathan M. Springer et al.   PLoS Genetics

Genetic Design and Statistical Power of Nested Association Mapping in Maize

(2008) Jianming Yu et al.   GENETICS

Next-generation genetics in plants

(2008) Magnus Nordborg et al.   NATURE

AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants

(2008) C. Duran et al.   NUCLEIC ACIDS RESEARCH

Editorial

(2008) Keith Edwards   PLANT BIOTECHNOLOGY JOURNAL

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

(2008) E. Paux et al.   SCIENCE

Genomic Plasticity and the Diversity of Polyploid Plants

(2008) A. R. Leitch et al.   SCIENCE