Development of EST-derived SSR markers using next-generation sequencing to reveal the genetic diversity of 50 chrysanthemum cultivars |
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| Affiliation: | 1. Jiangsu Key Laboratory of Agriculture Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China;2. Institute of Atmospheric Physics, Chinese Academy of Sciences (IAP-CAS), Beijing, China;3. National Technical University of Athens (NTUA), Athens, Greece;4. Technological Educational Institute of West Macedonia, Kozani, Greece;1. Dipartimento di Chimica, Università di Bari “Aldo Moro”, Via Orabona 4, 70126 Bari, Italy;2. Institute of Sciences of Food Production (ISPA), National Research Council of Italy (CNR), Via G. Amendola 122/O, 70126 Bari, Italy;1. Department of Cytogenetics, Christian Medical College, Vellore 632004, India;2. Prof. B.V. Moses Center For Evidence Based Health Care & Health Policy, Christian Medical College, Vellore 632004, India;3. Glasgow Centre for Reproductive Medicine, The Fertility Partnership, Glasgow G51 4FD, United Kingdom;4. Department of Reproductive Medicine and Surgery, Christian Medical College, Vellore 632004, India;1. College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China;2. Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China;3. The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China;4. Plant & Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK;1. College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China;2. Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA |
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| Abstract: | Chrysanthemum plants are popular worldwide as cut flowers, potted, and in gardens. Several hundred cultivars have been commercialized, indicating that there is substantial genetic variations that can be manipulated under cultivations to produce a wide array of phenotypic variation. To study the genetic diversity of chrysanthemum cultivars in Korea, we first identified simple sequence repeats from chrysanthemum expressed sequence tags generated by FLX 454 sequencing. A total of 1109 ESTs out of 18,226 chrysanthemum ESTs were identified to carry SSRs. A total of 16 out of 46 primer pairs exhibited several polymorphisms among 50 chrysanthemum cultivars. The number of alleles per locus varied from 1 to 15, with an average of 6.25 alleles. The expected heterozygosity ranged from 0 to 0.8958, whereas polymorphism information content ranged from 0 to 0.8872. Based on polymorphisms using 16 SSR markers, a phylogenetic tree was generated revealing four groups within the 50 cultivars showing various levels of genetic diversity. The 16 polymorphic chrysanthemum SSR markers generated in this study would be useful for studies of the genetic conservation, diversity, and population structure of commercial chrysanthemum cultivars as well as closely related species. |
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| Keywords: | Genetic diversity Expressed sequence tag Microsatellite Marker Simple sequence repeat |
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