Abstract
Application of next-generation sequencing to very large genomes, such as chrysanthemum (Chrysanthemum sp.), faces challenges including repeated sequences, limited short-reads, and various contigs in massive fragments. Genotyping-by-sequencing (GBS) can overcome many of these drawbacks by high-multiplexing, and potential genotyping-sequencing approaches could have wide-ranging utilizations in chrysanthemum breeding. The study aimed to establish an approach for GBS application and to elucidate a phylogenomic structure in an individual with a large genome. We identified single nucleotide polymorphism (SNP) for SNP calling (279,189 markers) and SNP filtering (7758 markers) that will promote analysis of chrysanthemum population genetics. We conclude that GBS is the best approach for genotyping in chrysanthemum and can be applied in genetic breeding in various plants.
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Acknowledgements
This study was financed by the “Development of global-market strategic-type new cultivars in Chrysanthemum (PJ011750072020)” of the Rural Development Administration of Korea (RDA), South Korea.
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TKN carried out the experiments, organized data, wrote the manuscript. STTH revised the manuscript. JHL designed and superintended the Project.
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Communicated by Sung-Chur Sim.
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Nguyen, T.K., Ha, S.T.T. & Lim, J.H. Analysis of chrysanthemum genetic diversity by genotyping-by-sequencing. Hortic. Environ. Biotechnol. 61, 903–913 (2020). https://doi.org/10.1007/s13580-020-00274-2
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DOI: https://doi.org/10.1007/s13580-020-00274-2