Apple whole genome sequences: recent advances and new prospects

Cross-species hybridization and the origin of North African date palms

(2019) Jonathan M. Flowers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

I Want to (Bud) Break Free: The Potential Role of DAM and SVP-Like Genes in Regulating Dormancy Cycle in Temperate Fruit Trees

(2019) Vítor da Silveira Falavigna et al.   Frontiers in Plant Science

Efficient Targeted Mutagenesis in Apple and First Time Edition of Pear Using the CRISPR-Cas9 System

(2019) Aurélie Charrier et al.   Frontiers in Plant Science

Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation

(2019) Concetta Burgarella et al.   Frontiers in Plant Science

Genetic mapping of the European canker (Neonectria ditissima) resistance locus Rnd1 from Malus ‘Robusta 5’

(2019) Vincent G. M. Bus et al.   Tree Genetics & Genomes

Two large-effect QTLs, Ma and Ma3, determine genetic potential for acidity in apple fruit: breeding insights from a multi-family study

(2019) S. Verma et al.   Tree Genetics & Genomes

Genomic heritability estimates in sweet cherry reveal non-additive genetic variance is relevant for industry-prioritized traits

(2018) Julia Piaskowski et al.   BMC GENETICS

Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress

(2018) Haibo Wang et al.   BMC PLANT BIOLOGY

UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study

(2018) Peng Qi et al.   BMC PLANT BIOLOGY

Evolutionary diversification of galactinol synthases in Rosaceae: adaptive roles of galactinol and raffinose during apple bud dormancy

(2018) Vítor da Silveira Falavigna et al.   JOURNAL OF EXPERIMENTAL BOTANY

RNA-sequencing Analysis Identifies Genes Associated with Chilling-mediated Endodormancy Release in Apple

(2018) Takanori Takeuchi et al.   JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE

Identification of a leucine-rich repeat receptor-like serine/threonine-protein kinase as a candidate gene for Rvi12 (Vb)-based apple scab resistance

(2018) S. Padmarasu et al.   MOLECULAR BREEDING

The red bayberry genome and genetic basis of sex determination

(2018) Hui-Min Jia et al.   PLANT BIOTECHNOLOGY JOURNAL

Apple fruit acidity is genetically diversified by natural variations in three hierarchical epistatic genes: MdSAUR37 , MdPP2CH and MdALMTII

(2018) Dongjie Jia et al.   PLANT JOURNAL

Generation of advanced fire blight-resistant apple (Malus × domestica) selections of the fifth generation within 7 years of applying the early flowering approach

(2018) Ina Schlathölter et al.   PLANTA

Horticultural performance and elemental nutrient concentrations on ‘Fuji’ grafted on apple rootstocks under New York State climatic conditions

(2018) Gemma Reig et al.   SCIENTIA HORTICULTURAE

Multi-environment QTL analysis of plant and flower morphological traits in tetraploid rose

(2018) Peter M. Bourke et al.   THEORETICAL AND APPLIED GENETICS

The isolation of the IGT family genes in Malus × domestica and their expressions in four idiotype apple cultivars

(2018) Limin Wang et al.   Tree Genetics & Genomes

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

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

Effective Genomic Selection in a Narrow-Genepool Crop with Low-Density Markers: Asian Rapeseed as an Example

(2018) Christian R. Werner et al.   Plant Genome

Morphometrics Reveals Complex and Heritable Apple Leaf Shapes

(2018) Zoë Migicovsky et al.   Frontiers in Plant Science

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

(2018) Francois Laurens et al.   Horticulture Research

Attention sports fans! The far-reaching contributions of bud sport mutants to horticulture and plant biology

(2018) Toshi M. Foster et al.   Horticulture Research

Genome-wide analyses of genes encoding FK506-binding proteins reveal their involvement in abiotic stress responses in apple

(2018) Qinglong Dong et al.   BMC GENOMICS

Genome-Wide Analysis and Cloning of the Apple Stress-Associated Protein Gene Family Reveals MdSAP15, Which Confers Tolerance to Drought and Osmotic Stresses in Transgenic Arabidopsis

(2018) Qinglong Dong et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Genome-wide identification and expression analysis of brassinosteroid biosynthesis and metabolism genes regulating apple tree shoot and lateral root growth

(2018) Liwei Zheng et al.   JOURNAL OF PLANT PHYSIOLOGY

Towards map-based cloning of FB_Mfu10: identification of a receptor-like kinase candidate gene underlying the Malus fusca fire blight resistance locus on linkage group 10

(2018) Ofere Francis Emeriewen et al.   MOLECULAR BREEDING

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

(2018) Bjarne Larsen et al.   PLoS One

Detecting archaic introgression using an unadmixed outgroup

(2018) Laurits Skov et al.   PLoS Genetics

Multivariate GBLUP Improves Accuracy of Genomic Selection for Yield and Fruit Weight in Biparental Populations of Vaccinium macrocarpon Ait

(2018) Giovanny Covarrubias-Pazaran et al.   Frontiers in Plant Science

Overexpression of MhYTP2 enhances apple water-use efficiency by activating ABA and ethylene signaling

(2018) Changhai Liu et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

The EU Court of Justice extends the GMO Directive to gene-edited organisms

(2018) Daniela Ruffell   FEBS LETTERS

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

(2018) Sook Jung et al.   NUCLEIC ACIDS RESEARCH

Genome re-sequencing reveals the evolutionary history of peach fruit edibility

(2018) Yang Yu et al.   Nature Communications

Development of Wheat With Hypoimmunogenic Gluten Obstructed by the Gene Editing Policy in Europe

(2018) Aurélie Jouanin et al.   Frontiers in Plant Science

Prediction of genetic value for sweet cherry fruit maturity among environments using a 6K SNP array

(2018) Craig M. Hardner et al.   Horticulture Research

Overexpression of the RNA binding protein MhYTP1 in transgenic apple enhances drought tolerance and WUE by improving ABA level under drought condition

(2018) Tianli Guo et al.   PLANT SCIENCE

Deciphering the genetic control of fruit texture in apple by multiple family-based analysis and genome-wide association

(2017) Mario Di Guardo et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide association study unravels the genetic control of the apple volatilome and its interplay with fruit texture

(2017) Brian Farneti et al.   JOURNAL OF EXPERIMENTAL BOTANY

Frequency of a natural truncated allele of MdMLO19 in the germplasm of Malus domestica

(2017) Stefano Pessina et al.   MOLECULAR BREEDING

Epistatic fire blight resistance QTL alleles in the apple cultivar ‘Enterprise’ and selection X-6398 discovered and characterized through pedigree-informed analysis

(2017) Eric van de Weg et al.   MOLECULAR BREEDING

The draft genome of tropical fruit durian (Durio zibethinus)

(2017) Bin Tean Teh et al.   NATURE GENETICS

Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery

(2017) John M Hickey et al.   NATURE GENETICS

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

(2017) Nicolas Daccord et al.   NATURE GENETICS

Insertion of a solo LTR retrotransposon associates with spur mutations in ‘Red Delicious’ apple (Malus × domestica)

(2017) Mengxue Han et al.   PLANT CELL REPORTS

Apple fruit superficial scald resistance mediated by ethylene inhibition is associated with diverse metabolic processes

(2017) Nicola Busatto et al.   PLANT JOURNAL

The R2R3-MYB transcription factor MdMYB73 is involved in malate accumulation and vacuolar acidification in apple

(2017) Da-Gang Hu et al.   PLANT JOURNAL

Lipid droplet-associated gene expression and chromatin remodelling in LIPASE 5′-upstream region from beginning- to mid-endodormant bud in ‘Fuji’ apple

(2017) Takanori Saito et al.   PLANT MOLECULAR BIOLOGY

Functions of two Malus hupehensis (Pamp.) Rehd. YTP s ( MhYTP1 and MhYTP2 ) in biotic- and abiotic-stress responses

(2017) Na Wang et al.   PLANT SCIENCE

Mapping the sensory perception of apple using descriptive sensory evaluation in a genome wide association study

(2017) Beatrice Amyotte et al.   PLoS One

Effects of apple ( Malus × domestica ) rootstocks on scion performance and hormone concentration

(2017) J. Lordan et al.   SCIENTIA HORTICULTURAE

Genomic Selection in Plant Breeding: Methods, Models, and Perspectives

(2017) José Crossa et al.   TRENDS IN PLANT SCIENCE

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

(2017) Naibin Duan et al.   Nature Communications

Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts

(2017) Jean-Tristan Brandenburg et al.   PLoS Genetics

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

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

Transcriptomic Response of Resistant (PI613981–Malus sieversii) and Susceptible (“Royal Gala”) Genotypes of Apple to Blue Mold (Penicillium expansum) Infection

(2017) Ana-Rosa Ballester et al.   Frontiers in Plant Science

Combining Genome-Wide Information with a Functional Structural Plant Model to Simulate 1-Year-Old Apple Tree Architecture

(2017) Vincent Migault 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

A Conserved Carbon Starvation Response Underlies Bud Dormancy in Woody and Herbaceous Species

(2017) Carlos Tarancón et al.   Frontiers in Plant Science

Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops

(2017) Lunwen Qian 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

Apple dwarfing rootstocks exhibit an imbalance in carbohydrate allocation and reduced cell growth and metabolism

(2017) Toshi M Foster et al.   Horticulture Research

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

(2017) Cameron P Peace   Horticulture Research

Genotyping-by-sequencing markers facilitate the identification of quantitative trait loci controlling resistance to Penicillium expansum in Malus sieversii

(2017) John L. Norelli et al.   PLoS One

Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map

(2017) Amidou N’Diaye et al.   PLoS One

Chilling Affects Phytohormone and Post-Embryonic Development Pathways during Bud Break and Fruit Set in Apple (Malus domestica Borkh.)

(2017) Gulshan Kumar et al.   Scientific Reports

Genotype Imputation with Millions of Reference Samples

(2016) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits

(2016) I. M. MacLeod et al.   BMC GENOMICS

Cell wall dynamics during apple development and storage involves hemicellulose modifications and related expressed genes

(2016) Emmanuelle Dheilly et al.   BMC PLANT BIOLOGY

Analysis of transcripts differentially expressed between fruited and deflowered ‘Gala’ adult trees: a contribution to biennial bearing understanding in apple

(2016) B. Guitton et al.   BMC PLANT BIOLOGY

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

Genomics-assisted breeding in fruit trees

(2016) Hiroyoshi Iwata et al.   BREEDING SCIENCE

Crop-to-wild gene flow and its fitness consequences for a wild fruit tree: Towards a comprehensive conservation strategy of the wild apple in Europe

(2016) Alice Feurtey et al.   Evolutionary Applications

Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population

(2016) Alix Allard et al.   JOURNAL OF EXPERIMENTAL BOTANY

Expression of a putative dioxygenase gene adjacent to an insertion mutation is involved in the short internodes of columnar apples (Malus × domestica)

(2016) Kazuma Okada et al.   JOURNAL OF PLANT RESEARCH

PediHaplotyper: software for consistent assignment of marker haplotypes in pedigrees

(2016) Roeland E. Voorrips et al.   MOLECULAR BREEDING

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

InterPro in 2017—beyond protein family and domain annotations

(2016) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

An optimized TRV-based virus-induced gene silencing protocol for Malus crabapple

(2016) Jie Zhang et al.   PLANT CELL TISSUE AND ORGAN CULTURE

Interference with ethylene perception at receptor level sheds light on auxin and transcriptional circuits associated with the climacteric ripening of apple fruit (Malus x domesticaBorkh.)

(2016) Alice Tadiello et al.   PLANT JOURNAL

Different flowering response to various fruit loads in apple cultivars correlates with degree of transcript reaccumulation of a TFL1-encoding gene

(2016) Amnon Haberman et al.   PLANT JOURNAL

Development and validation of the Axiom®Apple480K SNP genotyping array

(2016) Luca Bianco et al.   PLANT JOURNAL

Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers

(2016) Ludivine Lassois et al.   PLANT MOLECULAR BIOLOGY REPORTER

Structural genomics and transcriptional characterization of the Dormancy-Associated MADS-box genes during bud dormancy progression in apple

(2016) Diogo Denardi Porto et al.   Tree Genetics & Genomes

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

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

Development of SNP-based assays for disease resistance and fruit quality traits in apple (Malus × domestica Borkh.) and validation in breeding pilot studies

(2016) Isabelle O. Baumgartner et al.   Tree Genetics & Genomes

Genome-wide association study of 12 agronomic traits in peach

(2016) Ke Cao et al.   Nature Communications

Genome to Phenome Mapping in Apple Using Historical Data

(2016) Zoë Migicovsky et al.   Plant Genome

Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence

(2016) Camille Roux et al.   PLOS BIOLOGY

Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)

(2016) Xuewei Li et al.   GigaScience

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

(2016) Erica A Di Pierro et al.   Horticulture Research

Chilling-Mediated DNA Methylation Changes during Dormancy and Its Release Reveal the Importance of Epigenetic Regulation during Winter Dormancy in Apple (Malus x domestica Borkh.)

(2016) Gulshan Kumar et al.   PLoS One

On the Accuracy of Genomic Selection

(2016) Charles-Elie Rabier et al.   PLoS One

Comparative phylogenetic analysis and transcriptional profiling of MADS-box gene family identified DAM and FLC-like genes in apple (Malusx domestica)

(2016) Gulshan Kumar et al.   Scientific Reports

Efficient Genome Editing in Apple Using a CRISPR/Cas9 system

(2016) Chikako Nishitani et al.   Scientific Reports

Methyl jasmonate improves salinity resistance in German chamomile (Matricaria chamomilla L.) by increasing activity of antioxidant enzymes

(2015) F. Salimi et al.   ACTA PHYSIOLOGIAE PLANTARUM

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

Uncovering co-expression gene network modules regulating fruit acidity in diverse apples

(2015) Yang Bai et al.   BMC GENOMICS

The crop QTLome comes of age

(2015) Silvio Salvi et al.   CURRENT OPINION IN BIOTECHNOLOGY

Progress, challenges and the future of crop genomes

(2015) Todd P Michael et al.   CURRENT OPINION IN PLANT BIOLOGY

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

Comparative assessment of sugar and malic acid composition in cultivated and wild apples

(2015) Baiquan Ma et al.   FOOD CHEMISTRY

What are domestic apples worth? Hedonic responses and sensory information as drivers of willingness to pay

(2015) Laila Seppä et al.   FOOD QUALITY AND PREFERENCE

Multispectral airborne imagery in the field reveals genetic determinisms of morphological and transpiration traits of an apple tree hybrid population in response to water deficit

(2015) Nicolas Virlet et al.   JOURNAL OF EXPERIMENTAL BOTANY

Transcription profiling of the chilling requirement for bud break in apples: a putative role for FLC-like genes

(2015) Diogo Denardi Porto et al.   JOURNAL OF EXPERIMENTAL BOTANY

Transcriptome analysis of an apple (Malus×domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation

(2015) Islam El-Sharkawy et al.   JOURNAL OF EXPERIMENTAL BOTANY

Fine mapping of the Rvi5 (Vm) apple scab resistance locus in the ‘Murray’ apple genotype

(2015) Valentina Cova et al.   MOLECULAR BREEDING

High-resolution genetic and physical map of the Rvi1 (Vg) apple scab resistance locus

(2015) Valentina Cova et al.   MOLECULAR BREEDING

A co-expression gene network associated with developmental regulation of apple fruit acidity

(2015) Yang Bai et al.   MOLECULAR GENETICS AND GENOMICS

Scab resistance in ‘Geneva’ apple is conditioned by a resistance gene cluster with complex genetic control

(2015) Héloïse Bastiaanse et al.   MOLECULAR PLANT PATHOLOGY

Nonbrowning GM apple cleared for market

(2015) Emily Waltz   NATURE BIOTECHNOLOGY

Corrigendum

(2015)   NEW PHYTOLOGIST

MdSOS2L1 phosphorylates MdVHA-B1 to modulate malate accumulation in response to salinity in apple

(2015) Da-Gang Hu et al.   PLANT CELL REPORTS

Hormone and growth interactions of scions and size-controlling rootstocks of young apple trees

(2015) T. Tworkoski et al.   PLANT GROWTH REGULATION

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

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

Construction of a high density linkage map and its application in the identification of QTLs for soluble sugar and organic acid components in apple

(2015) Baiquan Ma et al.   Tree Genetics & Genomes

Homologs of the FB_MR5 fire blight resistance gene of Malus ×robusta 5 are present in other Malus wild species accessions

(2015) Thomas Wöhner et al.   Tree Genetics & Genomes

Identification and genetic characterization of a quantitative trait locus for adventitious rooting from apple hardwood cuttings

(2015) Shigeki Moriya et al.   Tree Genetics & Genomes

Genomics and the Contrasting Dynamics of Annual and Perennial Domestication

(2015) Brandon S. Gaut et al.   TRENDS IN GENETICS

Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop

(2015) Khaled M. Hazzouri et al.   Nature Communications

Genome-Enabled Estimates of Additive and Nonadditive Genetic Variances and Prediction of Apple Phenotypes Across Environments

(2015) Satish Kumar et al.   G3-Genes Genomes Genetics

Genes Encoding Aluminum-Activated Malate Transporter II and their Association with Fruit Acidity in Apple

(2015) Baiquan Ma et al.   Plant Genome

Accuracy and responses of genomic selection on key traits in apple breeding

(2015) Hélène Muranty et al.   Horticulture Research

Genome-wide identification of vegetative phase transition-associated microRNAs and target predictions using degradome sequencing in Malus hupehensis

(2015) Libo Xing et al.   BMC GENOMICS

Characterization of the MLO gene family in Rosaceae and gene expression analysis in Malus domestica

(2014) Stefano Pessina et al.   BMC GENOMICS

Multiscale investigation of mealiness in apple: an atypical role for a pectin methylesterase during fruit maturation

(2014) Sandrine Mikol Segonne et al.   BMC PLANT BIOLOGY

Genome-wide identification of members in the YTH domain-containing RNA-binding protein family in apple and expression analysis of their responsiveness to senescence and abiotic stresses

(2014) Na Wang et al.   GENE

Breeding drought-tolerant maize hybrids for the US corn-belt: discovery to product

(2014) Mark Cooper et al.   JOURNAL OF EXPERIMENTAL BOTANY

Fine mapping of the gene Rvi18 (V25) for broad-spectrum resistance to apple scab, and development of a linked SSR marker suitable for marker-assisted breeding

(2014) Jose Miguel Soriano et al.   MOLECULAR BREEDING

Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing

(2014) Nathan R. Campbell et al.   Molecular Ecology Resources

Molecular basis of angiosperm tree architecture

(2014) Courtney A. Hollender et al.   NEW PHYTOLOGIST

Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control

(2014) Jean-Marc Celton et al.   NEW PHYTOLOGIST

The Draft Genome Sequence of European Pear (Pyrus communis L. ‘Bartlett’)

(2014) David Chagné et al.   PLoS One

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

An analysis of ash and isotopic carbon discrimination (Δ13C) methods to evaluate water use efficiency in apple

(2014) D. Michael Glenn   SCIENTIA HORTICULTURAE

Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple

(2014) M. C. A. M. Bink et al.   THEORETICAL AND APPLIED GENETICS

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

QTL mapping for brown rot (Monilinia fructigena) resistance in an intraspecific peach (Prunus persica L. Batsch) F1 progeny

(2014) Igor Pacheco et al.   Tree Genetics & Genomes

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

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

Breeding better cultivars, faster: applications of new technologies for the rapid deployment of superior horticultural tree crops

(2014) Steve van Nocker et al.   Horticulture Research

Novel genomic approaches unravel genetic architecture of complex traits in apple

(2013) Satish Kumar et al.   BMC GENOMICS

Plant genome sequencing — applications for crop improvement

(2013) Marie E Bolger et al.   CURRENT OPINION IN BIOTECHNOLOGY

The columnar mutation (“Co gene”) of apple (Malus × domestica) is associated with an integration of a Gypsy-like retrotransposon

(2013) Dominik Otto et al.   MOLECULAR BREEDING

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

Evidence for regulation of columnar habit in apple by a putative 2OG-Fe(II) oxygenase

(2013) Pieter J. Wolters et al.   NEW PHYTOLOGIST

The Genome Database for Rosaceae (GDR): year 10 update

(2013) Sook Jung et al.   NUCLEIC ACIDS RESEARCH

Reduced generation time of apple seedlings to within a year by means of a plant virus vector: a new plant-breeding technique with no transmission of genetic modification to the next generation

(2013) Noriko Yamagishi et al.   PLANT BIOTECHNOLOGY JOURNAL

The Fast-track breeding approach can be improved by heat-induced expression of the FLOWERING LOCUS T genes from poplar (Populus trichocarpa) in apple (Malus × domestica Borkh.)

(2013) Stephanie Wenzel et al.   PLANT CELL TISSUE AND ORGAN CULTURE

Evaluation of SNP Data from the Malus Infinium Array Identifies Challenges for Genetic Analysis of Complex Genomes of Polyploid Origin

(2013) Michela Troggio et al.   PLoS One

The domestication and evolutionary ecology of apples

(2013) Amandine Cornille et al.   TRENDS IN GENETICS

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases

(2013) Lacey-Anne Sanderson et al.   Database-The Journal of Biological Databases and Curation

Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus ‘Robusta 5’ accessions

(2012) Susan E Gardiner et al.   BMC GENETICS

Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple

(2012) Qiong Zhang et al.   BMC GENOMICS

Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array

(2012) Laima Antanaviciute et al.   BMC GENOMICS

QTL and candidate gene mapping for polyphenolic composition in apple fruit

(2012) David Chagné et al.   BMC PLANT BIOLOGY

Down-regulation of POLYGALACTURONASE1 alters firmness, tensile strength and water loss in apple (Malus x domestica) fruit

(2012) Ross G Atkinson et al.   BMC PLANT BIOLOGY

The transcriptomes of columnar and standard type apple trees (Malus x domestica) — A comparative study

(2012) Clemens Krost et al.   GENE

Whole-Genome Regression and Prediction Methods Applied to Plant and Animal Breeding

(2012) G. de los Campos et al.   GENETICS

Genetic and physical characterisation of the locus controlling columnar habit in apple (Malus × domestica Borkh.)

(2012) Paolo Baldi et al.   MOLECULAR BREEDING

A natural mutation-led truncation in one of the two aluminum-activated malate transporter-like genes at the Ma locus is associated with low fruit acidity in apple

(2012) Yang Bai et al.   MOLECULAR GENETICS AND GENOMICS

Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops

(2012) Rachel S. Meyer et al.   NEW PHYTOLOGIST

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Fine mapping ofCo, a gene controlling columnar growth habit located on apple (Malus×domesticaBorkh.) linkage group 10

(2012) Shigeki Moriya et al.   PLANT BREEDING

AppleSEPALLATA1/2-like genes control fruit flesh development and ripening

(2012) Hilary S. Ireland et al.   PLANT JOURNAL

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

(2012) David Chagné et al.   PLoS One

Genomic Selection for Fruit Quality Traits in Apple (Malus×domestica Borkh.)

(2012) Satish Kumar et al.   PLoS One

Apple, from genome to breeding

(2012) M. Troggio et al.   Tree Genetics & Genomes

Differences in acidity of apples are probably mainly caused by a malic acid transporter gene on LG16

(2012) Sabaz Ali Khan et al.   Tree Genetics & Genomes

A candidate gene for fire blight resistance in Malus × robusta 5 is coding for a CC–NBS–LRR

(2012) Johannes Fahrentrapp 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

Growth, biomass allocation, and water use efficiency of 31 apple cultivars grown under two water regimes

(2011) Binghua Liu et al.   AGROFORESTRY SYSTEMS

Apple skin patterning is associated with differential expression of MYB10

(2011) Adriana Telias et al.   BMC PLANT BIOLOGY

Genomic Selection in Plant Breeding: A Comparison of Models

(2011) Nicolas Heslot et al.   CROP SCIENCE

Genetic control of biennial bearing in apple

(2011) Baptiste Guitton et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genomic organisation of the Mal d 1 gene cluster on linkage group 16 in apple

(2011) Giulia Pagliarani et al.   MOLECULAR BREEDING

Genetic characterization of the Ma locus with pH and titratable acidity in apple

(2011) Kenong Xu et al.   MOLECULAR BREEDING

Identification of serine/threonine kinase and nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in the fire blight resistance quantitative trait locus of apple cultivar ‘Evereste’

(2011) GABRIELLA PARRAVICINI et al.   MOLECULAR PLANT PATHOLOGY

On the evolutionary history of the domesticated apple

(2011) Diego Micheletti et al.   NATURE GENETICS

Deciphering the genetic determinism of bud phenology in apple progenies: a new insight into chilling and heat requirement effects on flowering dates and positional candidate genes

(2011) J-M. Celton et al.   NEW PHYTOLOGIST

Application of a high-speed breeding technology to apple (Malus × domestica) based on transgenic early flowering plants and marker-assisted selection

(2011) Henryk Flachowsky et al.   NEW PHYTOLOGIST

High temperature reduces apple fruit colour via modulation of the anthocyanin regulatory complex

(2011) KUI LIN-WANG et al.   PLANT CELL AND ENVIRONMENT

Isolation of flowering genes and seasonal changes in their transcript levels related to flower induction and initiation in apple (Malus domestica)

(2011) C. Hattasch et al.   TREE PHYSIOLOGY

Tripal: a construction toolkit for online genome databases

(2011) S. P. Ficklin et al.   Database-The Journal of Biological Databases and Curation

MiRNA Control of Vegetative Phase Change in Trees

(2011) Jia-Wei Wang et al.   PLoS Genetics

Impact of reduced marker set estimation of genomic relationship matrices on genomic selection for feed efficiency in Angus cattle

(2010) Megan M Rolf et al.   BMC GENETICS

Developmental changes of carbohydrates, organic acids, amino acids, and phenolic compounds in ‘Honeycrisp’ apple flesh

(2010) Yanzi Zhang et al.   FOOD CHEMISTRY

Isolation and characterization of an apple cytosolic malate dehydrogenase gene reveal its function in malate synthesis

(2010) Yu-Xin Yao et al.   JOURNAL OF PLANT PHYSIOLOGY

Genotyping of pedigreed apple breeding material with a genome-covering set of SSRs: trueness-to-type of cultivars and their parentages

(2010) K. M. Evans et al.   MOLECULAR BREEDING

TheRvi15(Vr2) Apple Scab Resistance Locus Contains Three TIR-NBS-LRR Genes

(2010) Paolo Galli et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

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

(2010) Riccardo Velasco et al.   NATURE GENETICS

Molecular Characterization of FLOWERING LOCUS T-Like Genes of Apple (Malus × domestica Borkh.)

(2010) Nobuhiro Kotoda et al.   PLANT AND CELL PHYSIOLOGY

Estimating Effects and Making Predictions from Genome-Wide Marker Data

(2010) Michael E. Goddard et al.   STATISTICAL SCIENCE

QTL analysis and candidate gene mapping for skin and flesh color in sweet cherry fruit (Prunus avium L.)

(2010) Suneth S. Sooriyapathirana et al.   Tree Genetics & Genomes

Identification of a major QTL for time of initial vegetative budbreak in apple (Malus x domestica Borkh.)

(2010) Maria M. van Dyk et al.   Tree Genetics & Genomes

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Two distinct major QTL for resistance to fire blight co-localize on linkage group 12 in apple genotypes ‘Evereste’ and Malus floribunda clone 821

(2009) C.-E. Durel et al.   GENOME

Gibberellin as a factor in floral regulatory networks

(2009) E. Mutasa-Gottgens et al.   JOURNAL OF EXPERIMENTAL BOTANY

Multiple Repeats of a Promoter Segment Causes Transcription Factor Autoregulation in Red Apples

(2009) R. V. Espley et al.   PLANT CELL

Association Mapping: Critical Considerations Shift from Genotyping to Experimental Design

(2009) S. Myles et al.   PLANT CELL

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

Regulation of floral initiation in horticultural trees

(2008) J. D. Wilkie et al.   JOURNAL OF EXPERIMENTAL BOTANY

Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species

(2008) Ksenija Gasic et al.   MOLECULAR BREEDING

The ethylene receptors: Complex perception for a simple gas

(2008) Brad M. Binder   PLANT SCIENCE

Differences in fruit colour development, anthocyanin content, fruit quality and consumer acceptability of eight ‘Gala’ apple strains

(2008) I. Iglesias et al.   SCIENTIA HORTICULTURAE

Identification and stability of QTLs for fruit quality traits in apple

(2008) Katrien Kenis et al.   Tree Genetics & Genomes

Dissecting apple tree architecture into genetic, ontogenetic and environmental effects: QTL mapping

(2008) Vincent Segura et al.   Tree Genetics & Genomes