The 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

Genetic diversity, population structure, and linkage disequilibrium of elite and local apple accessions from Belgium using the IRSC array

Micheletti, D.;Troggio, M.;
2017-01-01

Abstract

The 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
Malus × domestica
SNP array
Parentage analysis
Tree architecture
Association study
Settore AGR/07 - GENETICA AGRARIA
2017
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
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