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Characterization of 12 Polymorphic Microsatellite Markers in the Chinese Tree Shrew (Tupaia Belangeri Chinensis)

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Characterization of 12 Polymorphic Microsatellite Markers in the Chinese Tree Shrew (Tupaia Belangeri Chinensis) Zoological Research 34 (E2): E62−E68 doi: 10.3724/SP.J.1141.2013.E02E62 Characterization of 12 polymorphic microsatellite markers in the Chinese tree shrew (Tupaia belangeri chinensis) Xiao-Hong LIU1, 4, Yong-Gang YAO1, 2, 3,* 1. Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; 2. Kunming Primate Research Center, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China; 3. Tree Shrew Inbreeding Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; 4. University of the Chinese Academy of Sciences, Beijing 100049, China Abstract: The Chinese tree shrew (Tupaia belangeri chinensis) is a small experimental animal with a close affinity to primates. This species has long been proposed to be an alternative experimental animal to primates in biomedical research. Despite decades of study, there is no pure breed for this animal, and the overall genetic diversity of wild tree shrews remains largely unknown. In order to obtain a set of genetic markers for evaluating the genetic diversity of tree shrew wild populations and tracing the lineages in inbreeding populations, we developed 12 polymorphic microsatellite markers from the genomic DNA of the tree shrew. An analysis of a wild population of 117 individuals collected from the suburb of Kunming, China, showed that these loci exhibited a highly expected heterozygosity (0.616). These 12 microsatellites were sufficient for individual identification and parentage analysis. The microsatellite markers developed in this study will be of use in evaluating genetic diversity and lineage tracing for the tree shrew. Keywords: Chinese tree shrew; Microsatellite; Heterozygosity; Individual identification; Parentage testing The Chinese tree shrew (Tupaia belangeri chinensis) hepatocellular carcinoma, myopia, psychosocial stress is a squirrel-like animal. It belongs to the Family (Cao et al, 2003; McBrien & Norton, 1992; van Kampen Tupaiidae of Scandentia. Tree shrews have the highest et al, 2002; Yan et al, 1996a; Yan et al, 1996b) and brain-to-body mass ratio of known mammals (Peng et al, learning and memory (Wang et al, 2011), although there 1991). Because tree shrews share some characteristics are many problems awaiting further studies (Xu et al, with primates and insectivores, the exact phylogenetic 2013b) . Despite an increasing interest in using the tree position of the tree shrew has been debated (Arnason et shrew to establish animal models for medical and al, 2002; Janecka et al, 2007; Peng et al, 1991; Xu et al, biological research, most of the animals used were 2012; Xu et al, 2013a). Analyses of the mitochondrial captured from the wild and/or domesticated for a few DNA (mtDNA) genome have shown that the tree shrew months. There is no pure inbreeding strain with a clear has a closer affinity with Lagomorpha (Arnason et al, genetic background similar to that of a mouse or rat at 2002; Xu et al, 2012), while nuclear gene sequences the present time, which would largely influence the provide evidence for a close affinity to primates (Janecka stability and repeatability of experiments.1 et al, 2007; Killian et al, 2001; Lindblad-Toh et al, 2011). Tupaiidae contains four genera: Tupaia, Anathana, The tree shrew has long been proposed to be an alternative experimental animal to primates in Received: 18 November 2012; Accepted: 20 December 2012 biomedical research due to its characteristics such as Foundation items: This work was supported by the National 863 small body size, short reproductive cycle and life span, Project of China (2012AA021801) and grants from Chinese Academy and low-cost maintenance (Peng et al, 1991). This animal of Sciences (KSCX2-EW-R-11 and KSCX2-EW-J-23) and Yunnan has been used to create animal models for infection with Province (2009CI119) the hepatitis B and C viruses, the development of * Corresponding author, E-mail: [email protected] Science Press Volume 34 Issue E2 Characterization of 12 polymorphic microsatellite markers in the Chinese tree shrew (Tupaia belangeri chinensis) E63 Urogale, and Dendrogale (Helgen, 2005). Currently, a Microsatellite identification and amplification total of 15 species is recognized in Tupaia, which is Based on the genomic DNA sequences of the broadly distributed across South and Southeast Asia, northern tree shrew (Tupaia belangeri) provided by the including southern China, India, Philippines, Java, Ensembl database (ftp://ftp.ensembl.org/), 20 loci were Borneo, Sumatra and Bali (Olson et al, 2005; Peng et al, chosen with a core repeat unit of 4−6 nucleotides. Primer 1991). Chinese tree shrews (Tupaia belangeri) are pairs were designed using primer premier 5. PCR distributed across southwest China and are divided into amplification condition for each locus contained a pre- six subspecies according to geographical distribution and denaturation cycle at 94 ℃ for 5 min, followed by 30 morphological characteristics (Wang, 1987). cycles of denaturation at 94 ℃ for 30 s, annealing at Understanding the genetic diversity of the wild tree 55 ℃ for 30 s, and extension at 72 ℃ for 30 s, followed shrew population has critical importance for by a final extension cycle at 72 ℃ for 5 min. conservation and for a breeding program to establish Amplification was performed in a total volume of 20 μL, inbred lines. Recently, we evaluated the mtDNA genetic which contained 10×Taq polymerase reaction buffer diversity of the tree shrew inhabiting urban Kunming and (100 mmol/L Tris-HCl, pH 8.3; 500 mmol/L KCl; 15 observed a relatively high diversity (Chen et al, 2011). mmol/L MgCl2), 0.2 mmol/L dNTPs, 10 μmol/L of each Genetic markers from the nuclear genome are essential forward and reverse primer, 0.5 U Taq DNA polymerase for us to further validate this conclusion and to analyze (TaKaRa, Dalian, China), and 50 ng genomic DNA. PCR other behaviors of this animal, e.g., female-biased products were electrophoresed on 8% polyacrylamide dispersal and gene flow between different populations. gels to test successful and specific amplification. For Microsatellites are short tandem repeats (STR) in those loci with no amplification or with non-specific the genome and have been broadly used for evaluating bands, we optimized the reaction conditions by genetic diversity, population affinity, gene flow and increasing or decreasing the annealing temperature, or population microdifferentiation (Goldstein et al, 1999; adjusting the concentration of Mg2+ to achieve the best Schlöetterer & Pemberton, 1994; Waits et al, 2000), as efficiency and specificity. We validated the authentic well as individual identification and parentage tests (Behl sequencing of each amplified locus by TA-cloning et al, 2002; Butler, 2005). So far, there have been only sequencing. In brief, PCR product was ligated into PMD sporadic reports for characterizing microstatellites in the 19-T vector (TaKaRa, Dalian, China), followed by tree shrew (Munshi-South, 2008; Munshi-South & transforming DH5α competent cells (Tiangen, Beijing) Wilkinson, 2006; Srikwan et al, 2002). Amplification of according to the manufacturer’s instructions. We picked the Chinese tree shrew genomic DNA using up three to five plasmids with the right inserts for microsatellites developed from other species of sequencing. Scandentia revealed some problems, such as lack of After the pretest for primer pairs and the opti- polymorphism (He et al, 2009) and had non-specific mization for amplification, we labeled the forward amplification in our samples (data not shown). Therefore, primer of each locus by including 6-FAM (Carboxy- it is necessary to develop a set of species-specific fluorescein) at the 5' end of the primer. PCR microsatellite markers based on the available genome of amplification for each locus was performed using the the tree shrew. In this study, we successfully retrieved 12 above optimized conditions. PCR product was diluted polymorphic microsatellite markers from Chinese tree with double-distilled water to achieve a concentration of shrews and characterized them in a population of 117 1 ng/μL. We mixed 1 μL diluted PCR product with 0.1 individuals. Our results showed that this set of μL GenescanTM-500 LIZ® (Applied Biosystems) and Hi- microsatellite loci had sufficient data to measure DiTM Formamide (Applied Biosystems), and added population heterozygosity and individual discrimination. ddH2O to make a 10 μL volume of cocktail. The mixture was denatured at 95 ℃ for 5 min, then immediately MATERIALS AND METHODS chilled on ice. We loaded 1 μL of cocktail on an automated sequencer (ABI PRISM 3100, Applied Experimental animals Biosystems). Alleles were scored using program A total of 117 Chinese tree shrews inhabiting the Genemarker V1.5 (SoftGenetics LLC, State College, PA). suburb of Kunming, Yunnan Province, China, were collected and raised at the Experimental Animal Core Statistical analysis Facility of the Kunming Institute of Zoology, Chinese Allele frequencies, observed heterozygosity (Ho), Academy of Sciences. All sampling procedures were expected heterozygosity (He) and deviation from the approved by the Institute’s Institutional Animal Care and Hardy-Weinberg equilibrium (HWE) based on the Use Committee. Genomic DNA was extracted from the likelihood ratio test were calculated by POPgene 1.32 blood, ear and/or muscle tissues of each individual by (Yeh & Boyle, 1997). Polymorphism information content using the genomic DNA
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