Development of Microsatellite Markers Using Next-Generation Sequencing and Genetic Characterization in Three Natural Monument Populations of Koelreuteria paniculata (Goldenrain Tree)

This study was conducted to develop microsatellite markers in Koelreuteria paniculata using next-generation sequencing. A total of 71,114,562 reads of 20x coverage for the K paniculata genome were generated and assembled to 141,924 contigs of a minimum of 500 bp long. One hundred seventy-nine of the 79,633 contigs containing microsatellite regions were used for primer design. Fourteen primer sets were selected as polymorphic markers by applying them to three K paniculata populations, designated as natural monuments in Korea. Somewhat low levels of genetic diversity were observed. The grand means of the number of alleles, observed heterozygosity, and expected heterozygosity were 2.7, 0.493, and 0.407, respectively. Analysis of molecular variance indicated a high level of genetic differentiation among populations. Distinct patterns of three populations were identified in the principal coordinate analysis and Bayesian structure analysis. The probability of identity of these markers was estimated to be quite low, suggesting that these markers have the robust potential power to distinguish genetically different individuals. K. paniculata has a high economic value as an ornamental tree, and a honey tree. The novel microsatellite markers developed in this study will be useful for future breeding programs and genetic studies aimed at developing conservation plans.