Analysis of chrysanthemum genetic diversity by genotyping-by-sequencing
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RESEARCH REPORT
Analysis of chrysanthemum genetic diversity by genotyping‑by‑sequencing Toan Khac Nguyen1 · Suong Tuyet Thi Ha1 · Jin Hee Lim1 Received: 6 January 2020 / Revised: 9 July 2020 / Accepted: 20 July 2020 © Korean Society for Horticultural Science 2020
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-bysequencing (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. Keywords Chrysanthemum · Genetic diversity · Genetic structure · Genotyping-by-sequencing · SNP
1 Introduction Genotyping-by-sequencing (GBS) is a potent genomic method that produces high density and low cost genotypic data that is suitable for assessing genetic variation in organisms with very large genomes without the requirement for the reference genome, making it useful for nonmodel plants (Fu and Peterson 2011; Peterson et al. 2012, 2014). The study of plant genetic diversity can involve the GBS approach for single nucleotide polymorphism (SNP) marker discovery, the use of restricted enzyme (van Orsouw et al. 2007), and SNP scoring with or without a reference genome (Elshire et al. 2011). GBS combines high-throughput sequencing in marker discovery with minimal cost for analyzing genetic diversity (Poland and Rife 2012; Fu et al. 2014). It can be used to sequence complex plant genomes Communicated by Sung-Chur Sim. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13580-020-00274-2) contains supplementary material, which is available to authorized users. * Jin Hee Lim [email protected] 1
Department of Plant Biotechnology, Sejong University, Seoul 05006, Korea
without SNP discovery, and it allows the screening of numerous genome databases. GBS is a beneficial tool for studying genetic diversity, and the technology is commonly used, although there are a few drawbacks associated with GBS library constructions, such as missing data, fragment size, and low coverage sequencing (Chung et al. 2017). Chrysanthemum (Chrysanthemum sp.), of the Asteraceae family, is high-profit floricultural crop and is ranked second to rose in market trade. The cultivation of chrysanthemums began a long time ago; they were first cultivated in China for medicinal purposes. Chrysanthemum flowers are characterized by their petal color, shape, and type and
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