A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing of 240Eucalyptustree genomes across 12 species

A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array

(2014) Sandra Unterseer et al.   BMC GENOMICS

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array

(2014) Shichen Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

Design and Characterization of a 52K SNP Chip for Goats

(2014) Gwenola Tosser-Klopp et al.   PLoS One

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

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

Genotyping-by-Sequencing for Populus Population Genomics: An Assessment of Genome Sampling Patterns and Filtering Approaches

(2014) Martin P. Schilling et al.   PLoS One

High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination

(2013) Emilie Chancerel et al.   BMC BIOLOGY

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

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

Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping

(2013) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners

(2013) Nathalie Pavy et al.   Molecular Ecology Resources

A 34K SNP genotyping array forPopulus trichocarpa: Design, application to the study of natural populations and transferability to otherPopulusspecies

(2013) A. Geraldes et al.   Molecular Ecology Resources

Stability of quantitative trait loci for growth and wood properties across multiple pedigrees and environments inEucalyptus globulus

(2013) Jules S. Freeman et al.   NEW PHYTOLOGIST

On the importance of balancing selection in plants

(2013) Lynda F. Delph et al.   NEW PHYTOLOGIST

High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array

(2013) Wubishet A. Bekele et al.   PLANT BIOTECHNOLOGY JOURNAL

Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean

(2013) Qijian Song et al.   PLoS One

Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs

(2013) Joseph I. Hoffman et al.   PLoS One

Impacts of Population Structure and Analytical Models in Genome-Wide Association Studies of Complex Traits in Forest Trees: A Case Study in Eucalyptus globulus

(2013) Eduardo P. Cappa et al.   PLoS One

SNP calling by sequencing pooled samples

(2012) Emanuele Raineri et al.   BMC BIOINFORMATICS

A reference linkage map for Eucalyptus

(2012) Corey J Hudson et al.   BMC GENOMICS

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

(2012) Pablo Cingolani et al.   FLY

Consistent divergence times and allele sharing measured from cross-species application of SNP chips developed for three domestic species

(2012) J. M. Miller et al.   Molecular Ecology Resources

Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees

(2012) Marcos D. V. Resende et al.   NEW PHYTOLOGIST

Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple

(2012) David Chagné et al.   PLoS One

Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm

(2012) Ignazio Verde et al.   PLoS One

Identification of Novel Single Nucleotide Polymorphisms (SNPs) in Deer (Odocoileus spp.) Using the BovineSNP50 BeadChip

(2012) Gwilym D. Haynes et al.   PLoS One

Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence

(2012) Kimberly J. Felcher et al.   PLoS One

Genomic Characterization of DArT Markers Based on High-Density Linkage Analysis and Physical Mapping to the Eucalyptus Genome

(2012) César D. Petroli et al.   PLoS One

Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato

(2012) Sung-Chur Sim et al.   PLoS One

Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus

(2012) Dario Grattapaglia et al.   Tree Genetics & Genomes

Genotyping-by-Sequencing for Plant Breeding and Genetics

(2012) Jesse A. Poland et al.   Plant Genome

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

The development and characterization of a 60K SNP chip for chicken

(2011) Martien AM Groenen 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

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

(2011) Mark A DePristo et al.   NATURE GENETICS

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

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

Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation Ecotilling

(2011) Fabio Marroni et al.   PLANT JOURNAL

A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

(2011) Martin W. Ganal et al.   PLoS One

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

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

(2010) A. McKenna et al.   GENOME RESEARCH

Ascertainment Biases in SNP Chips Affect Measures of Population Divergence

(2010) A. Albrechtsen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

A high-density Diversity Arrays Technology (DArT) microarray for genome-wide genotyping in Eucalyptus

(2010) Carolina P Sansaloni et al.   Plant Methods

Genotyping systems for Eucalyptus based on tetra-, penta-, and hexanucleotide repeat EST microsatellites and their use for individual fingerprinting and assignment tests

(2010) Danielle Assis Faria et al.   Tree Genetics & Genomes

Quantification of rare allelic variants from pooled genomic DNA

(2009) Todd E Druley et al.   NATURE METHODS

Development and Characterization of a High Density SNP Genotyping Assay for Cattle

(2009) Lakshmi K. Matukumalli et al.   PLoS One

Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

(2009) Antonio M. Ramos et al.   PLoS One

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

(2008) Evandro Novaes et al.   BMC GENOMICS

A SNP transferability survey within the genus Vitis

(2008) Silvia Vezzulli et al.   BMC PLANT BIOLOGY

Eucalyptusapplied genomics: from gene sequences to breeding tools

(2008) Dario Grattapaglia et al.   NEW PHYTOLOGIST

Congruence between environmental parameters, morphology and genetic structure in Australia’s most widely distributed eucalypt, Eucalyptus camaldulensis

(2008) P. A. Butcher et al.   Tree Genetics & Genomes