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

• Published in: Tree genetics & genomes 2017-12, Vol.13 (6), p.1-16, Article 125
• Main Authors: Vanderzande, Stijn, Micheletti, Diego, Troggio, Michela, Davey, Mark W., Keulemans, Johan
• Format: Article
• Language: English
• Subjects: Apples; Biomedical and Life Sciences; Biotechnology; Collection; Consortia; Cultivars; Decay; Forestry; Fruits; Gene mapping; Genetic diversity; Genotyping; Germplasm; Life Sciences; Linkage disequilibrium; Malus domestica; Mapping; Original Article; Parent-child relations; Plant breeding; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Polymorphism; Population genetics; Population structure; Single-nucleotide polymorphism; Stratification; Subgroups; Tree Biology
• ISSN: 1614-2942; 1614-2950
• DOI: 10.1007/s11295-017-1206-0

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.