Application of large-scale sequencing to marker discovery in plants

Genetic association studies in Eucalyptus pilularis Smith (blackbutt)

(2013) Timothy R. Sexton et al.   AUSTRALIAN FORESTRY

Gene expression in the developing aleurone and starchy endosperm of wheat

(2012) Susan A. Gillies 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

Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin

(2011) Luis Rodríguez-Moreno et al.   BMC GENOMICS

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

(2011) Shannon CK Straub 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

Defining the Transcriptome Assembly and Its Use for Genome Dynamics and Transcriptome Profiling Studies in Pigeonpea (Cajanus cajan L.)

(2011) A. Dubey et al.   DNA RESEARCH

The Complete Chloroplast Genome of 17 Individuals of Pest Species Jacobaea vulgaris: SNPs, Microsatellites and Barcoding Markers for Population and Phylogenetic Studies

(2011) L. Doorduin et al.   DNA RESEARCH

Variation in sorghum starch synthesis genes associated with differences in starch phenotype

(2011) Helen Hill et al.   FOOD CHEMISTRY

DNA sequencing methods contributing to new directions in cereal research

(2011) M.A. Edwards et al.   JOURNAL OF CEREAL SCIENCE

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Discovery of Genome-Wide DNA Polymorphisms in a Landrace Cultivar of Japonica Rice by Whole-Genome Sequencing

(2011) Yuko Arai-Kichise et al.   PLANT AND CELL PHYSIOLOGY

Discovery of polymorphisms in starch-related genes in rice germplasm by amplification of pooled DNA and deeply parallel sequencing†

(2011) Ardashir Kharabian-Masouleh et al.   PLANT BIOTECHNOLOGY JOURNAL

Origins and Recombination of the Bacterial-Sized Multichromosomal Mitochondrial Genome of Cucumber

(2011) A. J. Alverson et al.   PLANT CELL

Pectin Methylesterase Genes Influence Solid Wood Properties of Eucalyptus pilularis

(2011) T. R. Sexton et al.   PLANT PHYSIOLOGY

High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)

(2011) Yun-Jie Zhang et al.   PLoS One

Genome diversity in wild grasses under environmental stress

(2011) T. L. Fitzgerald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice

(2011) Daniel L. E. Waters et al.   Ecology and Evolution

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

(2011) Ziwen He et al.   PLoS Genetics

The Sugarcane Genome Challenge: Strategies for Sequencing a Highly Complex Genome

(2011) Glaucia Mendes Souza et al.   Tropical Plant Biology

High-throughput DNA sequencing - concepts and limitations

(2010) Martin Kircher et al.   BIOESSAYS

Discovery of global genomic re-organization based on comparison of two newly sequenced rice mitochondrial genomes with cytoplasmic male sterility-related genes

(2010) Sota Fujii et al.   BMC GENOMICS

SNP discovery by high-throughput sequencing in soybean

(2010) Xiaolei Wu et al.   BMC GENOMICS

Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms

(2010) Toshio Yamamoto et al.   BMC GENOMICS

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Cereal variety identification using MALDI-TOF mass spectrometry SNP genotyping

(2010) J.A. Pattemore et al.   JOURNAL OF CEREAL SCIENCE

Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines

(2010) J. B. WHITTALL et al.   MOLECULAR ECOLOGY

Application of single nucleotide polymorphisms to non-model species: a technical review

(2010) M. R. GARVIN et al.   Molecular Ecology Resources

Draft genome sequence of the oilseed species Ricinus communis

(2010) Agnes P Chan et al.   NATURE BIOTECHNOLOGY

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

(2010) Jinsheng Lai et al.   NATURE GENETICS

The genome of Theobroma cacao

(2010) Xavier Argout et al.   NATURE GENETICS

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

(2010) Jianbing Yan et al.   NATURE GENETICS

Assemblies: the good, the bad, the ugly

(2010) Ewan Birney   NATURE METHODS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research

(2010) A. Bräutigam et al.   PLANT BIOLOGY

Chloroplast genome sequences from total DNA for plant identification

(2010) Catherine J. Nock et al.   PLANT BIOTECHNOLOGY JOURNAL

Repeat subtraction-mediated sequence capture from a complex genome

(2010) Yan Fu et al.   PLANT JOURNAL

Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform

(2010) Robin A Atherton et al.   Plant Methods

Rapid Genomic Characterization of the Genus Vitis

(2010) Sean Myles et al.   PLoS One

Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome

(2010) M. Y. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

More genomic resources for less-studied crops

(2010) Rajeev K. Varshney et al.   TRENDS IN BIOTECHNOLOGY

Development of a Research Platform for Dissecting Phenotype–Genotype Associations in Rice (Oryza spp.)

(2010) Chih-Wei Tung et al.   Rice

Bioinformatics for Next Generation Sequencing Data

(2010) Alberto Magi et al.   Genes

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

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

(2009) Carsten Külheim et al.   BMC GENOMICS

Deep sequencing to reveal new variants in pooled DNA samples

(2009) Astrid A. Out et al.   HUMAN MUTATION

Capture of assay template by multiplex PCR of long amplicons for genotyping SNPs and InDels with MALDI-TOF mass spectrometry

(2009) Timothy R. Sexton et al.   MOLECULAR BREEDING

High-throughput SNP genotyping with the GoldenGate assay in maize

(2009) Jianbing Yan et al.   MOLECULAR BREEDING

Marker-assisted wheat breeding: present status and future possibilities

(2009) P. K. Gupta et al.   MOLECULAR BREEDING

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

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Quantification of rare allelic variants from pooled genomic DNA

(2009) Todd E Druley et al.   NATURE METHODS

Human genetic variation and its contribution to complex traits

(2009) Kelly A. Frazer et al.   NATURE REVIEWS GENETICS

Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing

(2009) Peter C. Bundock et al.   PLANT BIOTECHNOLOGY JOURNAL

New tools for single nucleotide polymorphism (SNP) discovery and analysis accelerating plant biotechnology

(2009) Robert Henry et al.   PLANT BIOTECHNOLOGY JOURNAL

A high-throughput assay for rapid and simultaneous analysis of perfect markers for important quality and agronomic traits in rice using multiplexed MALDI-TOF mass spectrometry

(2009) Ardashir K. Masouleh et al.   PLANT BIOTECHNOLOGY JOURNAL

Discovering genetic polymorphisms in next-generation sequencing data

(2009) Michael Imelfort et al.   PLANT BIOTECHNOLOGY JOURNAL

Plant genome sequencing: applications for crop improvement

(2009) David Edwards et al.   PLANT BIOTECHNOLOGY JOURNAL

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

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

(2008) Evandro Novaes et al.   BMC GENOMICS

Endonucleolytic mutation analysis by internal labeling (EMAIL)

(2008) Michael J. Cross et al.   ELECTROPHORESIS

Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes

(2008) K. E. Varley et al.   GENOME RESEARCH

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH