Candidate genes and signatures of directional selection on fruit quality traits during apple domestication

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

(2020) Hélène Muranty et al.   BMC PLANT BIOLOGY

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

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

(2019) Liyi Zhang et al.   Nature Communications

Apple whole genome sequences: recent advances and new prospects

(2019) Cameron P. Peace et al.   Horticulture Research

Evolutionary Insights into the Nature of Plant Domestication

(2019) Michael D. Purugganan   CURRENT BIOLOGY

A Multifaceted Overview of Apple Tree Domestication

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

Using Living Germplasm Collections to Characterize, Improve, and Conserve Woody Perennials

(2019) Zoë Migicovsky et al.   CROP SCIENCE

A Ma10 gene encoding P-type ATPase is involved in fruit organic acid accumulation in apple

(2018) Baiquan Ma et al.   PLANT BIOTECHNOLOGY JOURNAL

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

(2017) Julio Rozas et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2017) Nicolas Daccord et al.   NATURE GENETICS

To what extent do wild apples in Kazakhstan retain their genetic integrity?

(2017) Madina Y. Omasheva et al.   Tree Genetics & Genomes

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

(2017) Naibin Duan et al.   Nature Communications

Characteristics of dihydroflavonol 4-reductase gene promoters from different leaf colored Malus crabapple cultivars

(2017) Ji Tian et al.   Horticulture Research

Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples

(2015) Amandine Cornille et al.   Evolutionary Applications

AmicroRNAallele that emerged prior to apple domestication may underlie fruit size evolution

(2015) Jia-Long Yao et al.   PLANT JOURNAL

Convergent Loss of Awn in Two Cultivated Rice Species Oryza sativa and Oryza glaberrima Is Caused by Mutations in Different Loci

(2015) Tomoyuki Furuta et al.   G3-Genes Genomes Genetics

A dual positional specific lipoxygenase functions in the generation of flavor compounds during climacteric ripening of apple

(2015) Doreen Schiller et al.   Horticulture Research

Fruit Quality Traits Have Played Critical Roles in Domestication of the Apple

(2015) M. Awais Khan et al.   Plant Genome

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

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Functional Traits Differ between Cereal Crop Progenitors and Other Wild Grasses Gathered in the Neolithic Fertile Crescent

(2014) Jennifer Cunniff et al.   PLoS One

Dynamics of total phenolic content in different apple tissues and genotypes: impacts and relevance for breeding programs

(2014) D.F. Holderbaum et al.   SCIENTIA HORTICULTURAE

A strategy for developing representative germplasm sets for systematic QTL validation, demonstrated for apple, peach, and sweet cherry

(2014) C. P. Peace et al.   Tree Genetics & Genomes

Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

(2014) Kevin Weitemier et al.   Applications in Plant Sciences

Did greater burial depth increase the seed size of domesticated legumes?

(2013) Thomas A. Kluyver et al.   JOURNAL OF EXPERIMENTAL BOTANY

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

A Multidisciplinary Approach Providing New Insight into Fruit Flesh Browning Physiology in Apple (Malus x domestica Borkh.)

(2013) Mario Di Guardo et al.   PLoS One

Identification of lipoxygenase (LOX) genes putatively involved in fruit flavour formation in apple (Malus × domestica)

(2013) Jörg Vogt et al.   Tree Genetics & Genomes

The domestication and evolutionary ecology of apples

(2013) Amandine Cornille et al.   TRENDS IN GENETICS

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Parallel domestication of the Shattering1 genes in cereals

(2012) Zhongwei Lin et al.   NATURE GENETICS

Identification of interspecific hybrids among domesticated apple and its wild relatives

(2012) Briana L. Gross et al.   Tree Genetics & Genomes

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Molecular cloning of three malic acid related genes MdPEPC, MdVHA-A, MdcyME and their expression analysis in apple fruits

(2009) Yu-Xin Yao et al.   SCIENTIA HORTICULTURAE

Molecular evidence for post-domestication selection in the Waxy gene of Chinese waxy maize

(2008) Longjiang Fan et al.   MOLECULAR BREEDING