Development of 36 novel polymorphic microsatellites for the critically endangered tree Pinus squamaia , by transcriptome
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MICROSATELLITE LETTERS
Development of 36 novel polymorphic microsatellites for the critically endangered tree Pinus squamaia, by transcriptome database mining Jian-Feng Mao • Bin-Bin Cui • Zhi-Yong Zhang Hui Liu • Ying-Yue Li
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Received: 30 July 2014 / Accepted: 19 August 2014 / Published online: 2 September 2014 Ó Springer Science+Business Media Dordrecht 2014
Abstract Pinus squamaia X. W. Li is a critically endangered five-needle pine species, with only 35 wild individuals left. To understand its genetic variability, 506 novel microsatellite markers were developed by mining the transcriptome database of P. lambertiana. 196 loci were able to amplify a fragment of expected size in P. squamaia, of which 36 were polymorphic. The number of alleles of these 36 EST-SSRs in 16 individuals varied from 2 to 4, with an average of 2.2. The observed (Ho) and expected (He) heterozygosity values ranged from 0.000 to 1.000 (averaging 0.564) and 0.061 to 0.500 (averaging 0.356), respectively. Twenty-four loci showed significant departure from HWE after Bonferroni correction. This was the first report of candidate molecular markers on P. squamaia, which will facilitate future analyses of genetic diversity and population structure.
Electronic supplementary material The online version of this article (doi:10.1007/s12686-014-0300-y) contains supplementary material, which is available to authorized users. J.-F. Mao H. Liu Y.-Y. Li (&) National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Qinghua East Road No. 35, Beijing 100083, People’s Republic of China e-mail: [email protected] B.-B. Cui Department of Biology and Chemistry, Baoding University, Baoding 071000, Hebei, People’s Republic of China Z.-Y. Zhang National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, People’s Republic of China
Keywords Microstallites Pinus squamaia Pinus lambertiana Transcriptome Expressed sequence tag (EST) Pinus squamaia X. W. Li is endemic to Qiaojia County, China, with small population of only 35 wild individuals. Field observation suggested that P. squamaia has suffered large population decline due to overexploitation during recent decades. Given its narrow geographic distribution range and small population size, it has been listed as the critically endangered species by The International Union for the Conservation of Nature (IUCN) in 2012. Multiple artificial breeding and ex situ conservation programs have been implemented since the 1990s, but the genetic information of the population has been poorly investigated except Zhang and Li (2003). To better inform seed sourcing strategies for restoration, it is necessary to investigate the genetic diversity and population structure of P. squamaia using informative molecular marker such as microsatellite (Simple Sequence Repeats; SSR). Herein we report the development of efficient SSR markers from the transcriptome resources of P. lamberti
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