ArticleFrontiers in plant science2017
Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple.
Article in Frontiers in plant science, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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46 citing papers in PubMed, 104 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
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- QTL mapping and genomic prediction of resistance to apple blotch (Molecular breeding : new strategies in plant improvement · 2026Article
- Genome-wide association study reveals genomic regions associated withFrontiers in plant science · 2026Article
- Autosuppression of MdNAC18.1 endowed by a 61-bp promoter fragment duplication delays maturity date in apple.Plant biotechnology journal · 2025Article
- Evaluation of genomic and phenomic prediction for application in apple breeding.BMC plant biology · 2025Article
- Using near-infrared spectroscopy (NIRS) to predict budbreak of the following year.Quantitative plant biology · 2025Article
- A Pollen-Based Assisted Migration for Rapid Forest Adaptation.Global change biology · 2025Article
- An InDel variant in the promoter of the NAC transcription factor MdNAC18.1 plays a major role in apple fruit ripening.The Plant cell · 2024Article
- 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
- Flowering time: From physiology, through genetics to mechanism.Plant physiology · 2024Review
- Target enrichment sequencing coupled with GWAS identifiesFrontiers in plant science · 2024Article
- Comprehensive genetic diversity and genome-wide association studies revealed the genetic basis of avocado fruit quality traits.Frontiers in plant science · 2024Article
- Susceptibility Evaluation to Fire Blight and Genome-Wide Associations within a Collection of Asturian Apple Accessions.Plants (Basel, Switzerland) · 2023Article
- Marker-Assisted Selection in Breeding for Fruit Trait Improvement: A Review.International journal of molecular sciences · 2023Review
- Population Structure and Association Mapping for Agronomical and Biochemical Traits of a Large Spanish Apple Germplasm.Plants (Basel, Switzerland) · 2023Article
- Quantitative Traits of Interest in Apple Breeding and Their Implications for Selection.Plants (Basel, Switzerland) · 2023Article
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Authors and funding
30 authors at 11 institutions in 9 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.
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