Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

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

(2020) Hélène Muranty et al.   BMC PLANT BIOLOGY

Dynamics of ascorbic acid content in apple (Malus x domestica) during fruit development and storage

(2020) Eline Lemmens et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Genetic Status of the Swedish Central collection of heirloom apple cultivars

(2020) Jonas Skytte af Sätra et al.   SCIENTIA HORTICULTURAE

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

Genetics of zonal leaf chlorosis and genetic linkage to a major gene regulating skin anthocyanin production (MdMYB1) in the apple (Malus × domestica) cultivar Honeycrisp

(2019) Nicholas P. Howard et al.   PLoS One

Elucidating the genetic background of the early-flowering transgenic genetic stock T1190 with a high-density SNP array

(2019) Feixiong Luo et al.   MOLECULAR BREEDING

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

Evaluation of genotype quality parameters for SowPro90, a new genotyping array for swine1

(2019) Hiruni R Wijesena et al.   JOURNAL OF ANIMAL SCIENCE

High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow

(2019) Stijn Vanderzande et al.   PLoS One

A new genomic tool for walnut (Juglans regia L.): development and validation of the high-density Axiom™ J. regia 700K SNP genotyping array

(2018) Annarita Marrano et al.   PLANT BIOTECHNOLOGY JOURNAL

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

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

Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

(2017) Awais Rasheed et al.   Molecular Plant

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

(2017) Nicolas Daccord et al.   NATURE GENETICS

Development and evaluation of high-density Axiom® CicerSNP  Array for high-resolution genetic mapping and breeding applications in chickpea

(2017) Manish Roorkiwal et al.   PLANT BIOTECHNOLOGY JOURNAL

Genetic diversity, population structure, and linkage disequilibrium of elite and local apple accessions from Belgium using the IRSC array

(2017) Stijn Vanderzande et al.   Tree Genetics & Genomes

Two QTL characterized for soft scald and soggy breakdown in apple (Malus × domestica) through pedigree-based analysis of a large population of interconnected families

(2017) Nicholas P. Howard et al.   Tree Genetics & Genomes

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

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

Predicting Flowering Behavior and Exploring Its Genetic Determinism in an Apple Multi-family Population Based on Statistical Indices and Simplified Phenotyping

(2017) Jean-Baptiste Durand et al.   Frontiers in Plant Science

Development and Evaluation of a Barley 50k iSelect SNP Array

(2017) Micha M. Bayer 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

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

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

New resources for genetic studies inPopulus nigra: genome-wide SNP discovery and development of a 12k Infinium array

(2016) P. Faivre-Rampant et al.   Molecular Ecology Resources

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

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

ASSIsT: an automatic SNP scoring tool for in- and outbreeding species

(2015) Mario Di Guardo et al.   BIOINFORMATICS

Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa

(2015) Nahla V Bassil et al.   BMC GENOMICS

A major QTL controlling apple skin russeting maps on the linkage group 12 of ‘Renetta Grigia di Torriana’

(2015) Luigi Falginella et al.   BMC PLANT BIOLOGY

QTLs detected for individual sugars and soluble solids content in apple

(2015) Yingzhu Guan et al.   MOLECULAR BREEDING

Development, validation and genetic analysis of a large soybean SNP genotyping array

(2015) Yun-Gyeong Lee et al.   PLANT JOURNAL

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

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

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

(2015) Hélène Muranty et al.   Horticulture Research

AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow

(2014) E. L. Nicolazzi et al.   BIOINFORMATICS

One-step reconstruction of multi-generation pedigree networks in apple (Malus × domestica Borkh.) and the parentage of Golden Delicious

(2014) Silvio Salvi et al.   MOLECULAR BREEDING

Development of an Alfalfa SNP Array and Its Use to Evaluate Patterns of Population Structure and Linkage Disequilibrium

(2014) Xuehui Li 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

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 consensus ‘Honeycrisp’ apple (Malus × domestica) genetic linkage map from three full-sib progeny populations

(2014) Matthew D. Clark et al.   Tree Genetics & Genomes

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

‘Schmidt's Antonovka’ is identical to ‘Common Antonovka’, an apple cultivar widely used in Russia in breeding for biotic and abiotic stresses

(2013) Anna Pikunova et al.   Tree Genetics & Genomes

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

Design of a Bovine Low-Density SNP Array Optimized for Imputation

(2012) Didier Boichard et al.   PLoS One

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

Technical Reproducibility of Genotyping SNP Arrays Used in Genome-Wide Association Studies

(2012) Huixiao Hong et al.   PLoS One

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

(2011) H. Li   BIOINFORMATICS

Next generation genome-wide association tool: Design and coverage of a high-throughput European-optimized SNP array

(2011) Thomas J. Hoffmann et al.   GENOMICS

A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

(2011) Martin W. Ganal et al.   PLoS One

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

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

Detection, Imputation, and Association Analysis of Small Deletions and Null Alleles on Oligonucleotide Arrays

(2008) Lude Franke et al.   AMERICAN JOURNAL OF HUMAN GENETICS

High-throughput genotyping with the GoldenGate assay in the complex genome of soybean

(2008) David L. Hyten et al.   THEORETICAL AND APPLIED GENETICS