ArticleBMC genomics2012
Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed, 88 citations in OpenAlex.
- Development of an open-pollinated genetic mapping framework to facilitate the identification of QTL in apples.The plant genome · 2026Article
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- Natural variation in MdNAC5 contributes to fruit firmness and ripening divergence in apple.Horticulture research · 2025Article
- First note of QTL mapping of low vigor traits using the updated F2 'Koroneiki' linkage map of olive.Frontiers in plant science · 2025Article
- Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls.BMC genomics · 2021Article
- Anchoring a genetic map of an interspecific backcross two family to the genome builds of Elaeis.Journal of genetics · 2021Article
- Maximising recombination across macadamia populations to generate linkage maps for genome anchoring.Scientific reports · 2020Article
- Spring Is Coming: Genetic Analyses of the Bud Break Date Locus Reveal Candidate Genes From the Cold Perception Pathway to Dormancy Release in Apple (Frontiers in plant science · 2019Article
- Apple whole genome sequences: recent advances and new prospects.Horticulture research · 2019Review
- A Genome-Wide Association Study of Apple Quality and Scab Resistance.The plant genome · 2018Article
- Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum.PloS one · 2018Article
- LinkImputeR: user-guided genotype calling and imputation for non-model organisms.BMC genomics · 2017Article
- Elucidation of the 'Honeycrisp' pedigree through haplotype analysis with a multi-family integrated SNP linkage map and a large apple (Horticulture research · 2017Article
- Predicting Flowering Behavior and Exploring Its Genetic Determinism in an Apple Multi-family Population Based on Statistical Indices and Simplified Phenotyping.Frontiers in plant science · 2017Article
- Genomic dissection of a 'Fuji' apple cultivar: re-sequencing, SNP marker development, definition of haplotypes, and QTL detection.Breeding science · 2016Article
- Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population.Journal of experimental botany · 2016Article
- A new three-locus model for rootstock-induced dwarfing in apple revealed by genetic mapping of root bark percentage.Journal of experimental botany · 2016Article
- Genomics-assisted breeding in fruit trees.Breeding science · 2016Review
- QTL analysis of soft scald in two apple populations.Horticulture research · 2016Article
- Variation in Host and Pathogen in theFrontiers in plant science · 2016Article
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Authors and funding
10 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNP-based linkage map of an apple rootstock progeny.
resultsOf the 7,867 Malus SNP markers on the array, 1,823 (23.2%) were heterozygous in one of the two parents of the progeny, 1,007 (12.8%) were heterozygous in both parental genotypes, whilst just 2.8% of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the 'Golden Delicious' genome sequence. A total of 311 markers (13.7% of all mapped markers) mapped to positions that conflicted with their predicted positions on the 'Golden Delicious' pseudo-chromosomes, indicating the presence of paralogous genomic regions or mis-assignments of genome sequence contigs during the assembly and anchoring of the genome sequence.
conclusionsWe incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been assigned erroneous positions on the 'Golden Delicious' reference sequence will assist in the continued improvement of the genome sequence assembly for that variety.
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