ArticlePloS one2014
Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh).
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers.
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Who cites it
110 citing papers in PubMed, 272 citations in OpenAlex.
- Candidate genes with antagonistic roles in stomatal development are associated with population-wide variation in apple.Horticulture research · 2026Article
- Development of an open-pollinated genetic mapping framework to facilitate the identification of QTL in apples.The plant genome · 2026Article
- Article
- Identifying the contributions of progenitor Malus species to cultivated apple (M. domestica) using 20K SNP array data.BMC genomics · 2026Article
- QTL mapping and genomic prediction of resistance to apple blotch (Molecular breeding : new strategies in plant improvement · 2026Article
- Detection and Utilisation of KASPar SNP Marker Assays for Early Blight Resistance in Tomato.Current microbiology · 2026Article
- The FORGENIUS Genomic Resources: New Genotyping Tools and Genomic Data for 23 Forest Tree Species and Their Genetic Conservation Units.Molecular ecology resources · 2026Article
- Haplotype-phased 'Ottawa 3' genome unravels differential reaction of apple rootstock roots to mixed viral infection.The Plant journal : for cell and molecular biology · 2026Article
- Haplotype-resolved chromosome-level genome assemblies of nineteen apple (Malus domestica Borkh.) cultivars.Scientific data · 2026Article
- A bittersweet symphony: genetic insights into cider apple fruit quality.G3 (Bethesda, Md.) · 2026Article
- AxioSAFE: an accessible, semi-automatic filtering tool for the curation of genotyping datasets.Bioinformatics advances · 2026Article
- Microbial signaling and pest control in a medicinal plant: insights into insect, fungus, plant interactions.Frontiers in microbiology · 2026Review
- Integrative genomics for mango genetics and breeding.Horticulture research · 2026Article
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- The PeachSNP170K array facilitates insights into a large-scale population relatedness and genetic impacts on citrate content and flowering time.Communications biology · 2025Article
- Characterisation of the Gillenia S-locus provides insight into evolution of the nonself-recognition self-incompatibility system in apple.Scientific reports · 2025Article
- Integrative multi-environmental genomic prediction in apple.Horticulture research · 2025Article
- Evaluation of genomic and phenomic prediction for application in apple breeding.BMC plant biology · 2025Article
- Tracing the color: quantitative trait loci analysis reveals new insights into red-flesh pigmentation in apple (Horticulture research · 2024Article
50 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 7 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.