ArticleBreeding science2016
Genomic dissection of a 'Fuji' apple cultivar: re-sequencing, SNP marker development, definition of haplotypes, and QTL detection.
Article in Breeding science, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 34 citations in OpenAlex.
- Haplotype bias detection using pedigree-based transmission simulation: traces of selection that occurred in apple breeding.Horticulture research · 2026Article
- Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study.Horticulture research · 2021Article
- Natural variations in a pectin acetylesterase gene, MdPAE10, contribute to prolonged apple fruit shelf life.The plant genome · 2021Article
- Review of the Impact of Apple Fruit Ripening, Texture and Chemical Contents on Genetically Determined Susceptibility to Storage Rots.Plants (Basel, Switzerland) · 2020Review
- Flavor and Texture Characteristics of 'Fuji' and Related Apple (Molecules (Basel, Switzerland) · 2020Review
- The use of a fertile doubled haploid apple line for QTL analysis of fruit traits.Breeding science · 2019Article
- Mapping Gene Markers for Apple Fruit Ring Rot Disease Resistance Using a Multi-omics Approach.G3 (Bethesda, Md.) · 2019Article
- Identifying Genome-Wide Sequence Variations and Candidate Genes Implicated in Self-Incompatibility by ResequencingInternational journal of molecular sciences · 2019Article
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Authors and funding
18 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
'Fuji' is one of the most popular and highly-produced apple cultivars worldwide, and has been frequently used in breeding programs. The development of genotypic markers for the preferable phenotypes of 'Fuji' is required. Here, we aimed to define the haplotypes of 'Fuji' and find associations between haplotypes and phenotypes of five traits (harvest day, fruit weight, acidity, degree of watercore, and flesh mealiness) by using 115 accessions related to 'Fuji'. Through the re-sequencing of 'Fuji' genome, total of 2,820,759 variants, including single nucleotide polymorphisms (SNPs) and insertions or deletions (indels) were detected between 'Fuji' and 'Golden Delicious' reference genome. We selected mapping-validated 1,014 SNPs, most of which were heterozygous in 'Fuji' and capable of distinguishing alleles inherited from the parents of 'Fuji' (i.e., 'Ralls Janet' and 'Delicious'). We used these SNPs to define the haplotypes of 'Fuji' and trace their inheritance in relatives, which were shown to have an average of 27% of 'Fuji' genome. Analysis of variance (ANOVA) based on 'Fuji' haplotypes identified one quantitative trait loci (QTL) each for harvest time, acidity, degree of watercore, and mealiness. A haplotype from 'Delicious' chr14 was considered to dominantly cause watercore, and one from 'Ralls Janet' chr1 was related to low-mealiness.
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