| Summary: | <i>Liquidambar formosana</i> (Hamamelidaceae) is a relatively fast-growing deciduous tree of high ornamental value that is indigenous to China. However, few molecular markers are available for the species or its close relatives; this has hindered genomic and genetic studies. Here, we develop a series of transferable expressed sequence tag-simple sequence repeats (EST-SSRs) for genomic analysis of <i>L. formosana</i>. We downloaded the sequence of the <i>L. formosana</i> transcriptome from the National Center of Biotechnology Information Database and identified SSR loci in the Unigene library. We found 3284 EST-SSRs by mining 34,491 assembled unigenes. We synthesized 100 random primer pairs for validation of eight <i>L. formosana</i> individuals; of the 100 pairs, 32 were polymorphic. We successfully transferred 12 EST-SSR markers across three related <i>Liquidambar</i> species; the markers exhibited excellent cross-species transferability and will facilitate genetic studies and breeding of <i>Liquidambar</i>. A total of 72 clones of three <i>Liquidambar</i> species were uniquely divided into three main clusters; principal coordinate analysis (PCoA) supported this division. Additionally, a set of 20 SSR markers that did not exhibit nonspecific amplification were used to genotype more than 53 <i>L</i>. <i>formosana</i> trees. The mean number of alleles (Na) was 5.75 and the average polymorphism information content (PIC) was 0.578, which was higher than that of the natural <i>L. formosana</i> population (0.390). In other words, the genetic diversity of the plus <i>L</i>. <i>formosana</i> population increased, but excellent phenotypic features were maintained. The primers will be valuable for genomic mapping, germplasm characterization, gene tagging, and further genetic studies. Analyses of genetic diversity in <i>L</i>. <i>formosana</i> will provide a basis for efficient application of genetic materials and rational management of <i>L</i>. <i>formosana</i> breeding programs.
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