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EnglishThe identification of molecular markers associated with economic and quality traits will help improve breeding for new apple (Malus × domestica Borkh.) cultivars. Tools such as the 8K apple SNP array developed by the RosBREED consortium allow for high-throughput genotyping of SNP polymorphisms within collections. However, genetic characterization and the identification of population stratification and kinship within germplasm collections is a fundamental prerequisite for identifying robust marker–trait associations. In this study, a collection of apple germplasm originally developed for plant architectural studies and consisting of both non-commercial/local and elite accessions was genotyped using the 8K apple SNP array to identify cryptic relationships between accessions, to analyze population structure and to calculate the linkage disequilibrium (LD). A total of nine pairs of synonyms and several triploids accessions were identified within the 130 accessions genotyped. In addition, most of the known parent-child relations were confirmed, and several putative, previously unknown parent-child relations were identified among the local accessions. No clear subgroups could be identified although some separation between local and elite accessions was evident. The study of LD showed a rapid decay in our collection, indicating that a larger number of SNPs is necessary to perform whole genome association mapping. Finally, an association mapping effort for architectural traits was carried out on a small number of accessions to estimate the feasibility of this approach
Vanderzande, S.; Micheletti, D.; Troggio, M.; Davey, M.W.; Keulemans, J. (2017). Genetic diversity, population structure, and linkage disequilibrium of elite and local apple accessions from Belgium using the IRSC array. TREE GENETICS & GENOMES, 13: 125. doi: 10.1007/s11295-017-1206-0 handle: http://hdl.handle.net/10449/49290
| Citation: | Vanderzande, S.; Micheletti, D.; Troggio, M.; Davey, M.W.; Keulemans, J. (2017). Genetic diversity, population structure, and linkage disequilibrium of elite and local apple accessions from Belgium using the IRSC array. TREE GENETICS & GENOMES, 13: 125. doi: 10.1007/s11295-017-1206-0 handle: http://hdl.handle.net/10449/49290 | |
| Internal authors: | ||
| Organization unit: | CRI [2011-01 - today]: DEPARTMENT OF GENOMICS AND BIOLOGY OF FRUIT CROPS CRI [2016-02 - today]: UNIT OF COMPUTATIONAL BIOLOGY | |
| Authors: | Vanderzande, S.; Micheletti, D.; Troggio, M.; Davey, M.W.; Keulemans, J. | |
| Title: | Genetic diversity, population structure, and linkage disequilibrium of elite and local apple accessions from Belgium using the IRSC array | |
| Journal: | TREE GENETICS & GENOMES | |
| Issue Date: | 2017 | |
| Scientific Disciplinary Area: | Settore AGR/07 - GENETICA AGRARIA | |
| Keywords ENG: | Malus × domestica SNP array Parentage analysis Tree architecture Association study | |
| Language: | English | |
| IF: | With Impact Factor ISI | |
| Publication status: | Published | |
| Nature of content: | Articolo in rivista/Article | |
| Digital Object Identifier (DOI): | http://dx.doi.org/10.1007/s11295-017-1206-0 | |
| Other types of funding: | IWT (IWT LO-080510) | |
| Appears in Collections: | 01 - Journal article |
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