Genomic consequences of apple improvement

Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

(2020) Hélène Muranty et al.   BMC PLANT BIOLOGY

Population genomic analysis of mango ( Mangifera indica ) suggests a complex history of domestication

(2019) Emily J. Warschefsky et al.   NEW PHYTOLOGIST

A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour

(2019) Liyi Zhang et al.   Nature Communications

A Multifaceted Overview of Apple Tree Domestication

(2019) Amandine Cornille et al.   TRENDS IN PLANT SCIENCE

Genome-wide association mapping of date palm fruit traits

(2019) Khaled M. Hazzouri et al.   Nature Communications

A Genome-Wide Association Study of Apple Quality and Scab Resistance

(2018) Kendra A. McClure et al.   Plant Genome

An integrated approach for increasing breeding efficiency in apple and peach in Europe

(2018) Francois Laurens et al.   Horticulture Research

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

(2018) Bjarne Larsen et al.   PLoS One

15 years of GDR: New data and functionality in the Genome Database for Rosaceae

(2018) Sook Jung et al.   NUCLEIC ACIDS RESEARCH

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

(2018) Michael J. Roach et al.   PLoS Genetics

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

(2017) Nicolas Daccord et al.   NATURE GENETICS

Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement

(2017) Naibin Duan et al.   Nature Communications

Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple

(2017) Jorge Urrestarazu et al.   Frontiers in Plant Science

Exploiting Wild Relatives for Genomics-assisted Breeding of Perennial Crops

(2017) Zoë Migicovsky et al.   Frontiers in Plant Science

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

Genomic ancestry estimation quantifies use of wild species in grape breeding

(2016) Zoë Migicovsky et al.   BMC GENOMICS

A functional genetic marker for apple red skin coloration across different environments

(2016) David Chagné et al.   Tree Genetics & Genomes

Genome to Phenome Mapping in Apple Using Historical Data

(2016) Zoë Migicovsky et al.   Plant Genome

Chloroplast heterogeneity and historical admixture within the genus Malus

(2015) G. M. Volk et al.   AMERICAN JOURNAL OF BOTANY

Cultivars as Consumer Brands: Trends in Protecting and Commercializing Apple Cultivars via Intellectual Property Rights

(2015) James J. Luby et al.   CROP SCIENCE

Genetic diversity in Malus ×domestica (Rosaceae) through time in response to domestication

(2014) Briana L. Gross et al.   AMERICAN JOURNAL OF BOTANY

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

(2014) Anil Raj et al.   GENETICS

selscan: An Efficient Multithreaded Program to Perform EHH-Based Scans for Positive Selection

(2014) Z. A. Szpiech et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular-level and trait-level differentiation between the cultivated apple (Malus× domestica Borkh.) and its main progenitor Malus sieversii

(2014) Satish Kumar et al.   Plant Genetic Resources-Characterization and Utilization

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

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

Genomics Assisted Ancestry Deconvolution in Grape

(2013) Jason Sawler et al.   PLoS One

The domestication and evolutionary ecology of apples

(2013) Amandine Cornille et al.   TRENDS IN GENETICS

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations

(2012) Vincent Segura et al.   NATURE GENETICS

New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties

(2012) Amandine Cornille et al.   PLoS Genetics

From forest to field: Perennial fruit crop domestication

(2011) Allison J. Miller et al.   AMERICAN JOURNAL OF BOTANY

Regulation of plant growth and metabolism by the TOR kinase

(2011) Thomas Dobrenel et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The variant call format and VCFtools

(2011) P. Danecek 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 of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A Genealogical Interpretation of Principal Components Analysis

(2009) Gil McVean   PLoS Genetics