Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species

作     者：Hantao Qin Guoqian Yang Jim Provan Jie Liu Lianming Gao 

作者机构：Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201 China University of Chinese Academy of SciencesBeijing100049China Germplasm Bank of Wild Species in Southwest ChinaKunming Institute of BotanyChinese Academy of SciencesKunming650201China Institute of BiologicalEnvironmental and Rural Sciences (IBERS)Aberystwyth UniversityPengiaisAberystwythSY23 3DAUK 

出 版 物：《Plant Diversity》 (植物多样性（英文版）)

年 卷 期：2017年第39卷第5期

页      面：294-299页

核心收录：

学科分类：0907[农学-林学] 08[工学] 0829[工学-林业工程] 09[农学] 

基　　金：funded by the National Natural Science Foundations of China (31370252, 41571059) the National Key Basic Research Program of China (2014CB954100) supported by the China Scholarship Council for one-year study at the Aberystwyth University,UK 

主　　题：MiddRAD-seq Endangered species Microsatellite Next-generation sequencing Taxus florinii 

摘      要：Microsatellites are highly polymorphic markers which have been used in a wide range of genetic *** recent years, various sources of next-generation sequencing data have been used to develop new microsatellite loci, but compared with the more common shotgun genomic sequencing or transcriptome data, the potential utility of RAD-seq data for microsatellite ascertainment is comparatively *** this study, we employed MiddRAD-seq data to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. Of 8,823,053 clean reads generated for ten individuals of a population, 94,851(~1%) contained microsatellite motifs. These corresponded to 2993 unique loci, of which 526(~18%) exhibited polymorphism. Of which, 237 were suitable for designing microsatellite primer pairs, and 128 loci were randomly selected for PCR validation and microsatellite screening. Out of the 128 primer pairs, 16 loci gave clear, reproducible patterns, and were then screened and characterized in 24 individuals from two populations. The total number of alleles per locus ranged from two to ten(mean=4.875), and within-population expected heterozygosity from zero to 0.789(mean = 0.530),indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.