Genomic selection prediction models comparing sequence capture and SNP array genotyping methods

Genome-wide association of multiple complex traits in outbred mice by ultra-low-coverage sequencing

(2016) Jérôme Nicod et al.   NATURE GENETICS

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

(2015) Orzenil B. Silva-Junior et al.   NEW PHYTOLOGIST

Genotyping by sequencing for genomic prediction in a soybean breeding population

(2014) Diego Jarquín et al.   BMC GENOMICS

Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

(2014) Ana M. Pérez O’Brien et al.   Livestock Science

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

(2014) Wan-Ping Lee et al.   PLoS One

Development of genomics-based genotyping platforms and their applications in rice breeding

(2013) Haodong Chen et al.   CURRENT OPINION IN PLANT BIOLOGY

Whole-exome targeted sequencing of the uncharacterized pine genome

(2013) Leandro G. Neves et al.   PLANT JOURNAL

The advantages and limitations of trait analysis with GWAS: a review

(2013) Arthur Korte et al.   Plant Methods

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

Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity

(2013) Nicolas Heslot et al.   PLoS One

Genetic variation of wood chemical traits and association with underlying genes in Eucalyptus urophylla

(2013) M. Denis et al.   Tree Genetics & Genomes

Genomic Prediction in Maize Breeding Populations with Genotyping-by-Sequencing

(2013) José Crossa et al.   G3-Genes Genomes Genetics

Accelerating Improvement of Livestock with Genomic Selection

(2013) Theo Meuwissen et al.   Annual Review of Animal Biosciences

Accuracy of Genomic Selection Methods in a Standard Data Set of Loblolly Pine (Pinus taeda L.)

(2012) M. F. R. Resende et al.   GENETICS

Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels

(2012) M. Erbe et al.   JOURNAL OF DAIRY SCIENCE

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

Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing

(2012) Jesse Poland et al.   Plant Genome

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Imputation of Missing Genotypes From Sparse to High Density Using Long-Range Phasing

(2011) Hans D. Daetwyler et al.   GENETICS

Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness

(2011) B Mangin et al.   HEREDITY

Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments

(2011) M. F. R. Resende et al.   NEW PHYTOLOGIST

Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP

(2011) Jeffrey B. Endelman   Plant Genome

Accurate Prediction of Genetic Values for Complex Traits by Whole-Genome Resequencing

(2010) T. Meuwissen et al.   GENETICS

Ascertainment Biases in SNP Chips Affect Measures of Population Divergence

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

Uncovering the roles of rare variants in common disease through whole-genome sequencing

(2010) Elizabeth T. Cirulli et al.   NATURE REVIEWS GENETICS

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

(2010) Carolina P Sansaloni et al.   Plant Methods

Genomic selection in forest tree breeding

(2010) Dario Grattapaglia et al.   Tree Genetics & Genomes

Invited review: Genomic selection in dairy cattle: Progress and challenges

(2009) B.J. Hayes et al.   JOURNAL OF DAIRY SCIENCE

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

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Association Mapping: Critical Considerations Shift from Genotyping to Experimental Design

(2009) S. Myles et al.   PLANT CELL

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

(2009) et al.   SCIENCE

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

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

Eucalyptusapplied genomics: from gene sequences to breeding tools

(2008) Dario Grattapaglia et al.   NEW PHYTOLOGIST

Genetic parameters for growth, wood density and pulp yield in Eucalyptus globulus

(2008) João Costa e Silva et al.   Tree Genetics & Genomes