NGS technologies for analyzing germplasm diversity in genebanks*

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

(2011) Philippa C Griffin et al.   BMC BIOLOGY

Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae)

(2011) Juan S Escobar et al.   BMC EVOLUTIONARY BIOLOGY

Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)

(2011) Shiaoman Chao et al.   BMC GENOMICS

Identification of factors required for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach

(2011) Michal Mokry 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

Exome-wide DNA capture and next generation sequencing in domestic and wild species

(2011) Ted Cosart et al.   BMC GENOMICS

High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

(2011) Dario Grattapaglia et al.   BMC PLANT BIOLOGY

Development of genome-wide SNP assays for rice

(2011) Susan R. McCouch et al.   BREEDING SCIENCE

Exploring plant transcriptomes using ultra high-throughput sequencing

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

From lab to field, new approaches to phenotyping root system architecture

(2011) Jinming Zhu et al.   CURRENT OPINION IN PLANT BIOLOGY

High-throughput approaches for plant epigenomic studies

(2011) Robert J Schmitz et al.   CURRENT OPINION IN PLANT BIOLOGY

Association studies for next-generation sequencing

(2011) L. Luo et al.   GENOME RESEARCH

Low-coverage sequencing: Implications for design of complex trait association studies

(2011) Y. Li et al.   GENOME RESEARCH

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

(2011) P. Andolfatto et al.   GENOME RESEARCH

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1

(2011) Luke Ramsay et al.   NATURE GENETICS

Genome-wide association study of leaf architecture in the maize nested association mapping population

(2011) Feng Tian et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

Epigenome-wide association studies for common human diseases

(2011) Vardhman K. Rakyan et al.   NATURE REVIEWS GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

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

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

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Analysis of >1000 single nucleotide polymorphisms in geographically matched samples of landrace and wild barley indicates secondary contact and chromosome-level differences in diversity around domestication genes

(2011) Joanne Russell et al.   NEW PHYTOLOGIST

Unlocking the Barley Genome by Chromosomal and Comparative Genomics

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

Genomic tools for the analysis of genetic diversity

(2011) J. Antoni Rafalski   Plant Genetic Resources-Characterization and Utilization

Genomics of plant genetic resources: past, present and future

(2011) Kyujung Van et al.   Plant Genetic Resources-Characterization and Utilization

Next-generation mapping of Arabidopsis genes

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

A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

(2011) Wenyu Zhang et al.   PLoS One

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

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

Linkage Mapping and Comparative Genomics Using Next-Generation RAD Sequencing of a Non-Model Organism

(2011) Simon W. Baxter et al.   PLoS One

Large Scale Library Generation for High Throughput Sequencing

(2011) Erik Borgström et al.   PLoS One

Genetic structure and domestication history of the grape

(2011) Sean Myles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death

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

Mixed model association scans of multi-environmental trial data reveal major loci controlling yield and yield related traits in Hordeum vulgare in Mediterranean environments

(2011) J. Comadran et al.   THEORETICAL AND APPLIED GENETICS

Agricultural biotechnology for crop improvement in a variable climate: hope or hype?

(2011) Rajeev K. Varshney et al.   TRENDS IN PLANT SCIENCE

Fast-forward genetics enabled by new sequencing technologies

(2011) Korbinian Schneeberger et al.   TRENDS IN PLANT SCIENCE

Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

(2011) Ziwen He et al.   PLoS Genetics

Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea

(2010) Chrystel Deulvot et al.   BMC GENOMICS

High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence

(2010) David L Hyten et al.   BMC GENOMICS

DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits

(2010) Grit Haseneyer et al.   BMC PLANT BIOLOGY

Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers

(2010) Charlotte J Allender et al.   BMC PLANT BIOLOGY

Genetic structure and ecogeographical adaptation in wild barley (Hordeum chilense Roemer et Schultes) as revealed by microsatellite markers

(2010) Almudena Castillo et al.   BMC PLANT BIOLOGY

Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing

(2010) Eva Hřibová et al.   BMC PLANT BIOLOGY

Using association mapping to dissect the genetic basis of complex traits in plants

(2010) D. Hall et al.   Briefings in Functional Genomics

Association genetics in crop improvement

(2010) J Antoni Rafalski   CURRENT OPINION IN PLANT BIOLOGY

More than taking the heat: crops and global change

(2010) Stephen P Long et al.   CURRENT OPINION IN PLANT BIOLOGY

Accessing genetic diversity for crop improvement

(2010) JC Glaszmann et al.   CURRENT OPINION IN PLANT BIOLOGY

Quality management for the collection of biological samples in multicentre studies

(2010) J. Peplies et al.   EUROPEAN JOURNAL OF EPIDEMIOLOGY

Trends in ex situ conservation of plant genetic resources: a review of global crop and regional conservation strategies

(2010) Colin Khoury et al.   GENETIC RESOURCES AND CROP EVOLUTION

SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napusThis 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) G. Durstewitz et al.   GENOME

Accurate detection and genotyping of SNPs utilizing population sequencing data

(2010) V. Bansal et al.   GENOME RESEARCH

Population genetic inference from genomic sequence variation

(2010) J. E. Pool et al.   GENOME RESEARCH

Optimization of de novo transcriptome assembly from next-generation sequencing data

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing

(2010) J. K. Teer et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

(2010) R. A. Swanson-Wagner et al.   GENOME RESEARCH

Development of wild barley-derived DArT markers and their integration into a barley consensus map

(2010) B. P. Alsop et al.   MOLECULAR BREEDING

Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana

(2010) Marco Todesco et al.   NATURE

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

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

(2010) Susanna Atwell et al.   NATURE

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Genome-wide patterns of genetic variation among elite maize inbred lines

(2010) Jinsheng Lai et al.   NATURE GENETICS

Rare genetic variation at Zea mays crtRB1 increases β-carotene in maize grain

(2010) Jianbing Yan et al.   NATURE GENETICS

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

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

(2010) Xuehui Huang et al.   NATURE GENETICS

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Computational solutions to large-scale data management and analysis

(2010) Eric E. Schadt et al.   NATURE REVIEWS GENETICS

Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana

(2010) Joy Bergelson et al.   NATURE REVIEWS GENETICS

Annotating non-coding regions of the genome

(2010) Roger P. Alexander et al.   NATURE REVIEWS GENETICS

Genome-wide association studies in diverse populations

(2010) Noah A. Rosenberg et al.   NATURE REVIEWS GENETICS

Genotype imputation for genome-wide association studies

(2010) Jonathan Marchini et al.   NATURE REVIEWS GENETICS

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Rapid Genomic Characterization of the Genus Vitis

(2010) Sean Myles et al.   PLoS One

Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome

(2010) Keyan Zhao et al.   PLoS One

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Breeding Technologies to Increase Crop Production in a Changing World

(2010) M. Tester et al.   SCIENCE

Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding

(2010) Jafar A. Mammadov et al.   THEORETICAL AND APPLIED GENETICS

Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data

(2010) M. Moragues et al.   THEORETICAL AND APPLIED GENETICS

Crop genome sequencing: lessons and rationales

(2010) Catherine Feuillet et al.   TRENDS IN PLANT SCIENCE

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454

(2010) Niall J Lennon et al.   GENOME BIOLOGY

Comparative SNP diversity among four Eucalyptus species for genes from secondary metabolite biosynthetic pathways

(2009) Carsten Külheim et al.   BMC GENOMICS

Development and implementation of high-throughput SNP genotyping in barley

(2009) Timothy J Close et al.   BMC GENOMICS

DNA changes tell us about rice domestication

(2009) Takeshi Izawa et al.   CURRENT OPINION IN PLANT BIOLOGY

The emergence of whole genome association scans in barley

(2009) Robbie Waugh et al.   CURRENT OPINION IN PLANT BIOLOGY

SNP identification in crop plants

(2009) Martin W Ganal et al.   CURRENT OPINION IN PLANT BIOLOGY

Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond

(2009) Ryan Lister et al.   CURRENT OPINION IN PLANT BIOLOGY

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

Finding the fifth base: Genome-wide sequencing of cytosine methylation

(2009) R. Lister et al.   GENOME RESEARCH

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.)

(2009) J A Labate et al.   HEREDITY

Genetic diversity in a crop metapopulation

(2009) J van Heerwaarden et al.   HEREDITY

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Targeted sequencing with microfluidics

(2009) Ewen F Kirkness   NATURE BIOTECHNOLOGY

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Natural variation at the DEP1 locus enhances grain yield in rice

(2009) Xianzhong Huang et al.   NATURE GENETICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

The genetics of quantitative traits: challenges and prospects

(2009) Trudy F. C. Mackay et al.   NATURE REVIEWS GENETICS

Population structure and phenotypic variation of a spring barley world collection set up for association studies

(2009) G. Haseneyer et al.   PLANT BREEDING

A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley

(2009) Thomas Wicker et al.   PLANT JOURNAL

Genes and Mutations Underlying Domestication Transitions in Grasses

(2009) T. Sang   PLANT PHYSIOLOGY

Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers

(2009) Jianbing Yan et al.   PLoS One

Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10

(2009) F. Tian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput, high-accuracy array-based resequencing

(2009) J. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unlocking wheat genetic resources for the molecular identification of previously undescribed functional alleles at the Pm3 resistance locus

(2009) N. K. Bhullar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The origin and evolution of fragrance in rice (Oryza sativa L.)

(2009) M. J. Kovach 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

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

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

Enrichment of sequencing targets from the human genome by solution hybridization

(2009) Ryan Tewhey et al.   GENOME BIOLOGY

The 1001 Genomes Project for Arabidopsis thaliana

(2009) Detlef Weigel et al.   GENOME BIOLOGY

Methods and implementation of a central biosample and data management in a three-centre clinical study

(2008) Aniela Angelow et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Leveraging natural diversity: back through the bottleneck

(2008) MJ Kovach et al.   CURRENT OPINION IN PLANT BIOLOGY

Population-Based Resequencing Reveals That the Flowering Time Adaptation of Cultivated Barley Originated East of the Fertile Crescent

(2008) H. Jones et al.   MOLECULAR BIOLOGY AND EVOLUTION

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Genetic approaches to crop improvement: responding to environmental and population changes

(2008) Shin Takeda et al.   NATURE REVIEWS GENETICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds

(2008) W. M. Muir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) E. Paux et al.   SCIENCE

Association mapping reveals gene action and interactions in the determination of flowering time in barley

(2008) Silke Stracke et al.   THEORETICAL AND APPLIED GENETICS