ArticleHorticulture research2021
Genomic consequences of apple improvement.
Article in Horticulture research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Population Genomics of Almond (Prunus dulcis) Reveals Region-Specific Selection and a Complex History of Domestication.Molecular ecology · 2026Article
- Development of an open-pollinated genetic mapping framework to facilitate the identification of QTL in apples.The plant genome · 2026Article
- Identifying the contributions of progenitor Malus species to cultivated apple (M. domestica) using 20K SNP array data.BMC genomics · 2026Article
- Population and pangenome analyses uncover the evolutionary dynamics of the peroxidase gene family in barley.BMC genomics · 2026Article
- Changes in Environmental Conditions Differentially Affect the Bacterial Microbiome Communities in Different Apple Fruit Tissues.Environmental microbiology reports · 2025Article
- Cytometric and genetic analysis of Slovenian local apple genotypes.BMC plant biology · 2025Article
- Genomic resources for crop wild relatives are critical for perennial fruit breeding and conservation.American journal of botany · 2025Review
- Towards Stewardship of Wild Species and Their Domesticated Counterparts: A Case Study in Northern Wild Rice (Ecology and evolution · 2025Article
- Article
- Exploring phenotypic diversity and stability of key traits for apple breeding in northeastern Spanish germplasm.Frontiers in plant science · 2025Article
- Parental Reconstruction from a Half-Sib Population of Stoneless JujubePlants (Basel, Switzerland) · 2024Article
- Pomological and Molecular Characterization of Apple Cultivars in the German Fruit Genebank.Plants (Basel, Switzerland) · 2024Article
- Tracing the color: quantitative trait loci analysis reveals new insights into red-flesh pigmentation in apple (Horticulture research · 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
- The genetic basis of apple shape and size unraveled by digital phenotyping.G3 (Bethesda, Md.) · 2024Article
- Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding.Plants (Basel, Switzerland) · 2024Review
- Genomic analysis of fruit size and shape traits in apple: unveiling candidate genes through GWAS analysis.Horticulture research · 2024Article
- An efficient screening system of disease-resistant genes from wild apple, Malus sieversii in response to Valsa mali pathogenic fungus.Plant methods · 2023Article
- Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits.Annual review of genetics · 2023Review
- Genetic diversity, population structure, and genome-wide association analysis of ginkgo cultivars.Horticulture research · 2023Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The apple (Malus domestica) is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years. Here, we genetically characterise over 1000 apple accessions from the United States Department of Agriculture (USDA) germplasm collection using over 30,000 single-nucleotide polymorphisms (SNPs). We confirm the close genetic relationship between modern apple cultivars and their primary progenitor species, Malus sieversii from Central Asia, and find that cider apples derive more of their ancestry from the European crabapple, Malus sylvestris, than do dessert apples. We determine that most of the USDA collection is a large complex pedigree: over half of the collection is interconnected by a series of first-degree relationships. In addition, 15% of the accessions have a first-degree relationship with one of the top 8 cultivars produced in the USA. With the exception of 'Honeycrisp', the top 8 cultivars are interconnected to each other via pedigree relationships. The cultivars 'Golden Delicious' and 'Red Delicious' were found to have over 60 first-degree relatives, consistent with their repeated use by apple breeders. We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased firmness. Our results suggest that Americans are eating apples largely from a single family tree and that the apple's future improvement will benefit from increased exploitation of its tremendous natural genetic diversity.
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