Population structure, relatedness and ploidy levels in an apple gene bank revealed through genotyping-by-sequencing

Unravelling genetic diversity and cultivar parentage in the Danish apple gene bank collection

(2017) Bjarne Larsen et al.   Tree Genetics & Genomes

Elucidation of the ‘Honeycrisp’ pedigree through haplotype analysis with a multi-family integrated SNP linkage map and a large apple (Malus×domestica) pedigree-connected SNP data set

(2017) Nicholas P Howard et al.   Horticulture Research

Patterns of genomic and phenomic diversity in wine and table grapes

(2017) Zoë Migicovsky et al.   Horticulture Research

DNA-informed breeding of rosaceous crops: promises, progress and prospects

(2017) Cameron P Peace   Horticulture Research

Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

(2016) Jorge Urrestarazu et al.   BMC PLANT BIOLOGY

Development and validation of the Axiom®Apple480K SNP genotyping array

(2016) Luca Bianco et al.   PLANT JOURNAL

A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality

(2015) Rui Sun et al.   BMC GENOMICS

Polyploid and aneuploid detection in apple using a single nucleotide polymorphism array

(2015) David Chagné et al.   Tree Genetics & Genomes

LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms

(2015) Daniel Money et al.   G3-Genes Genomes Genetics

network: A Package for Managing Relational Data inR

(2015) Carter T. Butts   Journal of Statistical Software

Genomics: A potential panacea for the perennial problem

(2014) Kendra A. McClure et al.   AMERICAN JOURNAL OF BOTANY

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)

(2014) Luca Bianco et al.   PLoS One

Fast and Cost-Effective Genetic Mapping in Apple Using Next-Generation Sequencing

(2014) K. M. Gardner et al.   G3-Genes Genomes Genetics

Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties

(2013) Nivedita Singh et al.   PLoS One

Improving fruit and wine: what does genomics have to offer?

(2013) Sean Myles   TRENDS IN GENETICS

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

(2012) David Chagné et al.   PLoS One

Sequence-Based Genotyping for Marker Discovery and Co-Dominant Scoring in Germplasm and Populations

(2012) Hoa T. Truong et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

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

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

Genetic structure and domestication history of the grape

(2011) Sean Myles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) A. McKenna et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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