Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels

Extreme-phenotype genome-wide association study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel

(2015) Jinliang Yang et al.   PLANT JOURNAL

Characterisation of betalain biosynthesis in Parakeelya flowers identifies the key biosynthetic gene DOD as belonging to an expanded LigB gene family that is conserved in betalain-producing species

(2015) Hsiao-Hang Chung et al.   Frontiers in Plant Science

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A Genome-Wide Scan for Evidence of Selection in a Maize Population Under Long-Term Artificial Selection for Ear Number

(2014) T. M. Beissinger et al.   GENETICS

The beet Y locus encodes an anthocyanin MYB-like protein that activates the betalain red pigment pathway

(2014) Gregory J Hatlestad et al.   NATURE GENETICS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Harvesting the Promising Fruits of Genomics: Applying Genome Sequencing Technologies to Crop Breeding

(2014) Rajeev K. Varshney et al.   PLOS BIOLOGY

Plant genome sequencing — applications for crop improvement

(2013) Marie E Bolger et al.   CURRENT OPINION IN BIOTECHNOLOGY

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

(2013) Juliane C. Dohm et al.   NATURE

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

The beet R locus encodes a new cytochrome P450 required for red betalain production

(2012) Gregory J Hatlestad et al.   NATURE GENETICS

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

(2012) B. Hartwig et al.   PLANT PHYSIOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Next-generation mapping of Arabidopsis genes

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

Bulk Segregant Analysis Using Single Nucleotide Polymorphism Microarrays

(2011) Anthony Becker et al.   PLoS One

Fast-forward genetics enabled by new sequencing technologies

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

The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing

(2011) Paul M. Magwene et al.   PLoS Computational Biology

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

(2010) A. McKenna et al.   GENOME RESEARCH

Identification of a Spontaneous Frame Shift Mutation in a Nonreference Arabidopsis Accession Using Whole Genome Sequencing

(2010) R. A. E. Laitinen et al.   PLANT PHYSIOLOGY

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

Identification of EMS-Induced Mutations in Drosophila melanogaster by Whole-Genome Sequencing

(2009) J. P. Blumenstiel et al.   GENETICS

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

(2009) Korbinian Schneeberger et al.   NATURE METHODS

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

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