Genome-wide identification of SNPs and copy number variation in common bean (Phaseolus vulgaris L.) using genotyping-by-sequencing (GBS)

Optimization of genotyping by sequencing (GBS) data in common bean (Phaseolus vulgaris L.)

(2016) Stephan Schröder et al.   MOLECULAR BREEDING

A high density GBS map of bread wheat and its application for dissecting complex disease resistance traits

(2015) Huihui Li et al.   BMC GENOMICS

Association mapping of QTLs for sclerotinia stem rot resistance in a collection of soybean plant introductions using a genotyping by sequencing (GBS) approach

(2015) Elmer Iquira et al.   BMC PLANT BIOLOGY

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

(2015) O. A. Ali et al.   GENETICS

A System for Dosage-Based Functional Genomics in Poplar

(2015) Isabelle M. Henry et al.   PLANT CELL

Genotyping-by-Sequencing Enabled Mapping and Marker Development for the Potyvirus Resistance Allele in Common Bean

(2015) John P. Hart et al.   Plant Genome

Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms

(2014) Maja P Greminger et al.   BMC GENOMICS

An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley

(2014) Hui Liu et al.   BMC GENOMICS

Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL-hotspot” region for drought tolerance in chickpea

(2014) Deepa Jaganathan et al.   MOLECULAR GENETICS AND GENOMICS

A reference genome for common bean and genome-wide analysis of dual domestications

(2014) Jeremy Schmutz et al.   NATURE GENETICS

TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline

(2014) Jeffrey C. Glaubitz et al.   PLoS One

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

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

Marker Density and Read Depth for Genotyping Populations Using Genotyping-by-Sequencing

(2013) T. M. Beissinger et al.   GENETICS

Genome-wide single nucleotide polymorphism and Insertion-Deletion discovery through next-generation sequencing of reduced representation libraries in common bean

(2013) Xiaolu Zou et al.   MOLECULAR BREEDING

Genotyping-by-Sequencing (GBS): A Novel, Efficient and Cost-Effective Genotyping Method for Cattle Using Next-Generation Sequencing

(2013) Marcos De Donato et al.   PLoS One

Copy number polymorphism in plant genomes

(2013) Agnieszka Żmieńko et al.   THEORETICAL AND APPLIED GENETICS

ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data

(2012) Christopher R Cabanski et al.   BMC BIOINFORMATICS

Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing

(2012) Jennifer Monson-Miller et al.   BMC GENOMICS

Current state-of-art of sequencing technologies for plant genomics research

(2012) M. Thudi et al.   Briefings in Functional Genomics

A beginners guide to SNP calling from high-throughput DNA-sequencing data

(2012) André Altmann et al.   HUMAN GENETICS

Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes

(2012) Elena Bitocchi et al.   NEW PHYTOLOGIST

Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes

(2012) L. K. McHale et al.   PLANT PHYSIOLOGY

Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean

(2012) D. E. Cook et al.   SCIENCE

Genetic and epigenetic regulation of stress responses in natural plant populations

(2011) Clícia Grativol et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

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

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

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

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

Genetic diversity and selection of genotypes to enhance Zn and Fe content in common bean

(2010) Z I Talukder et al.   CANADIAN JOURNAL OF PLANT SCIENCE

Copy Number Variation Shapes Genome Diversity in Arabidopsis Over Immediate Family Generational Scales

(2010) Seth DeBolt   Genome Biology and Evolution

Adaptation genomics: the next generation

(2010) Jessica Stapley et al.   TRENDS IN ECOLOGY & EVOLUTION

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery

(2009) Stéphane Deschamps et al.   MOLECULAR BREEDING

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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