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http://dx.doi.org/10.14578/jkfs.2016.105.2.186

Identification and Characterization of Polymorphic Microsatellite Loci using Next Generation Sequencing in Quercus variabilis  

Baek, Seung-Hoon (Division of Forest Genetic Resources, National Institute of Forest Science)
Lee, Jei-Wan (Division of Forest Genetic Resources, National Institute of Forest Science)
Hong, Kyung-Nak (Division of Forest Genetic Resources, National Institute of Forest Science)
Lee, Seok-Woo (Division of Forest Genetic Resources, National Institute of Forest Science)
Ahn, Ji-Young (Division of Forest Genetic Resources, National Institute of Forest Science)
Lee, Min-Woo (Division of Forest Genetic Resources, National Institute of Forest Science)
Publication Information
Journal of Korean Society of Forest Science / v.105, no.2, 2016 , pp. 186-192 More about this Journal
Abstract
This study was conducted to develop microsatellite markers in Quercus variabilis using next generation sequencing. A total of 305,771 reads (384 bp on average) were generated on a Roche GS-FLX system, yielding 117 Mbp of sequences. The de novo assembly resulted in 7,346 contigs. A total of 606 contigs (20.75%) including 911 microsatellite loci were derived from the 2,921 contigs longer than 500 bp. A total of 180 primer sets were designed from the 911 microsatellite loci and screened in eight Q. variabilis individual trees sampled from a natural stand to obtain polymorphic loci. As a result, a total of thirteen polymorphic microsatellite loci were selected and used for estimating population genetic parameters in the 54 individual trees. The mean number of effective alleles was 4.996 ranging from 2.439 to 7.515. The observed heterozygosity and the expected heterozygosity ranged between 0.731 and 1.000 with an average of 0.873 and from 0.590 to 0.867 with an average of 0.766, respectively. Null alleles were not detected in all loci. No significant linkage disequilibrium was detected after Bonferroni correction in all loci. In the near future, these novel polymorphic microsatellite markers will be used to study population and conservation genetics of Q. variabilis of Korea in more detail.
Keywords
Quercus variabilis; next generation sequencing; de novo assembly; microsatellite; SSR; genetic diversity;
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