ArticlePloS one2012
Genome-wide SNP detection, validation, and development of an 8K SNP array for apple.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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Who cites it
117 citing papers in PubMed, 294 citations in OpenAlex.
- Article
- Fine-mapping, candidate gene identification, and marker development for the apple scab resistance gene Rvi2.Journal of experimental botany · 2026Article
- Mapping and identification of QTLs for low light tolerance traits in grapevine.BMC plant biology · 2025Article
- The PeachSNP170K array facilitates insights into a large-scale population relatedness and genetic impacts on citrate content and flowering time.Communications biology · 2025Article
- Natural variation in MdNAC5 contributes to fruit firmness and ripening divergence in apple.Horticulture research · 2025Article
- Why we thrive beneath a northern sky - genomic signals of selection in apple for adaptation to northern Sweden.Heredity · 2024Article
- Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems: application to apple fruit quality traits.Horticulture research · 2024Article
- Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives.Plants (Basel, Switzerland) · 2024Article
- Transcriptome Analysis of White- and Red-Fleshed Apple Fruits Uncovered Novel Genes Related to the Regulation of Anthocyanin Biosynthesis.International journal of molecular sciences · 2024Article
- Phenotyping, genetics, and "-omics" approaches to unravel and introgress enhanced resistance against apple scab (Horticulture research · 2024Article
- Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences.Database : the journal of biological databases and curation · 2023Review
- Genomewide selection for fruit quality traits in apple: breeding insights gained from prediction and postdiction.Horticulture research · 2023Article
- Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit.Plant biotechnology journal · 2023Article
- Molecular characterization of intergeneric hybrids betweenHorticulture research · 2023Article
- Deducing genotypes for loci of interest from SNP array data via haplotype sharing, demonstrated for apple and cherry.PloS one · 2023Article
- A high-density integrated map for grapevine based on three mapping populations genotyped by the Vitis18K SNP chip.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Applications of Genomic Tools in Plant Breeding: Crop Biofortification.International journal of molecular sciences · 2022Review
- A DNA test for high incidence of soft scald and soggy breakdown postharvest disorders inMolecular breeding : new strategies in plant improvement · 2021Article
- Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls.BMC genomics · 2021Article
- Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study.Horticulture research · 2021Article
57 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
20 authors at 12 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of 'Golden Delicious', SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple.
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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.