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Open AccessArticle

Development and Characterization of Simple Sequence Repeat Markers for, and Genetic Diversity Analysis of Liquidambar formosana

1
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education; Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
2
College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
3
Henan Longyuan Flowers & Trees Co., Ltd., Yanling 461200, China
*
Authors to whom correspondence should be addressed.
Forests 2020, 11(2), 203; https://doi.org/10.3390/f11020203
Received: 29 November 2019 / Revised: 2 January 2020 / Accepted: 24 January 2020 / Published: 12 February 2020
(This article belongs to the Section Forest Ecophysiology and Biology)
Liquidambar formosana (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 L. formosana. We downloaded the sequence of the L. formosana 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 L. formosana individuals; of the 100 pairs, 32 were polymorphic. We successfully transferred 12 EST-SSR markers across three related Liquidambar species; the markers exhibited excellent cross-species transferability and will facilitate genetic studies and breeding of Liquidambar. A total of 72 clones of three Liquidambar 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 L. formosana 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 L. formosana population (0.390). In other words, the genetic diversity of the plus L. formosana 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 L. formosana will provide a basis for efficient application of genetic materials and rational management of L. formosana breeding programs.
Keywords: EST-SSR markers; Liquidambar formosana; plus trees; transcriptome; cross-amplification; genetic diversity EST-SSR markers; Liquidambar formosana; plus trees; transcriptome; cross-amplification; genetic diversity
MDPI and ACS Style

Chen, S.; Dong, M.; Zhang, Y.; Qi, S.; Liu, X.; Zhang, J.; Zhao, J. Development and Characterization of Simple Sequence Repeat Markers for, and Genetic Diversity Analysis of Liquidambar formosana. Forests 2020, 11, 203.

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