Isolation and Characterization of Microsatellite Markers for the Sable, Martes zibellina (Mammalia: Mustelidae)

Wanchao Zhu1, Qinguo Wei1, Shuyu Xue1, Huanxin Zhang2, Tianshu Lv1 and Honghai Zhang1,*

1College of Life Science, Qufu Normal University, Qufu, China

2College of Marine Life Sciences, Ocean University of China, Qingdao, China

Qinguo Wei and Wanchao Zhu contributed equally to this work.

ABSTRACT

The number of wild sables has declined dramatically in recent years due to the high value and increasing demand of their fur. In order to evaluate the genetic diversity and population structure for the conservation and management of sables (Martes zibellina), we developed six microsatellite markers using a method of fast isolation by AFLP of sequences containing repeats (FIASCO) from them in this study. The primers designed by Primer Premier 5.0 based on conservative regions were tested on 22 individuals. Our results demonstrated that the number of alleles per locus ranged from two to five and the mean number of alleles was 3.67. The observed and expected heterozygosities ranged from 0.227 to 0.545 and 0.201 to 0.630, respectively. The polymorphic information content value ranged from 0.181 to 0.573. Null allele frequency varied from -0.0548 to 0.0563. The sets of loci proved to correctly discriminate populations using Principal Coordinate analysis. These polymorphic markers will be useful tools for investigating genetic diversity and population structure of this species.

Article Information

Received 13 October 2016

Revised 12 December 2016

Accepted 24 February 2017

Available online 11 August 2017

Authors’ Contributions

WZ, HZ and OW conceived the study, designed the experiments. WZ, TL and SX performed the experiments. WZ analyzed the data and wrote the article.

Key words

Martes zibellina, Sable, FIASCO, Microsatellite, Genetic diversity.

DOI: http://dx.doi.org/10.17582/journal.pjz/2017.49.5.sc1

* Corresponding author: zhanghonghai67@126.com

0030-9923/2017/0005-1909 $ 9.00/0

Copyright 2017 Zoological Society of Pakistan

The geographic range of sable (Martes zibellina), extends in Russia (Siberia and the Far East), Kazakhstan, Mongolia, China, Korea and Japan (Geptner, 1967). There are four subspecies of sable (M. zibellina princeps, M. zibellina linkouensis, M. zibellina altaica and M. zibellina hamgyenensis) in China. They inhibit vast territories of the northeast and northwest China. Unfortunately, the demand for their highly valued fur has resulted in intense hunting, which led to a substantial population depression of the sable in China (Kashtanov et al., 2011). An assessment of their genetic diversity is necessary, since the genetic diversity is an important indicator for populations. It is all the more important since sable populations are evolving in response to environmental changes (Reed and Frankham, 2003). Several studies based on the cytochrome b (Cyt-b) gene or control region (D-loop) polymorphism data focused on sable have been carried out (Hosoda et al., 1999; Kurose et al., 1999; Murakami et al., 2004; Inoue et al., 2010). However, mtDNA as molecular marker has some unreliability because of molecular structure diversity, interspecific transfer and the nuclear copy (insert) of mtDNA (Ferris et al., 1983; Zullo et al., 1991; Niu et al., 2001). Therefore, some more reliable inherited molecular markers are necessary for studying the genetic diversity and population structure of sable.

Microsatellites, also known as simple sequence repeats (SSRs) or short tandem repeats (STRs), are highly polymorphic and codominant molecular markers that are based on simple repeated and frequent sequences common in eukaryotic genomes, which have proven to be an effective tool in genetic diversity and molecular ecology studies (Goldstein and Schlöterer, 1999). In the present study, we chose tetranucleotide repeat stretches that are less compound and easier to type to develop some reliable microsatellites for M. zibellina and test their validity using genetic analyze (Vandevliet et al., 2009).

Material and methods

Twenty two M. zibellina individuals, including specimens, bodies of natural death and road killing, were collected from two populations in Northeast China. Among them, 12 individuals of M. zibellina princeps were collected in Daxinganling (50°10′- 53°33′ N, 121°12′- 127°00′ E), and other 10 individuals (M. zibellina linkouensis) were collected in Xiaoxinganling (48°52′-49°11′ N, 126°45′-127°25′ E). All the muscle tissues were stored at -80°C. Total genomic DNA was extracted using DNeasy® Blood & Tissue Kit (QIAGEN GmbH) following the manufacturer’s guidelines. All DNAs showed qualified after the detection of 1% agarose gel electrophoresis.

In accordance with the FIASCO protocol (Zane et al., 2002), we constructed a partial genomic library and used 5’-biotinylated (AAAC)8 oligonucleptide probe for enrichment selection from it. Isolated DNA was digested by MseI and ligated to double strand AFLP linkers (MseI F: 5’-TACTCAGGACTCAT-3’ and MseI R: 5’-GACGATGAGTCCTGAG-3’). The hybrids strands were captured with Dynabeads® M-280 Streptavidin (Invitrogen) and were amplified to recover the dsDNA. The enriched fragments were ligated into pMD18-T simple cloning vector (TaKaRa) and transferred into Trans1-T1 chemically competent cells (TransGen Biotech). Recombinants were screened by PCR with three primers: vector primers (M13F and M13R) and (AAAC)8 oligonucleotide. Then, the PCR products of clones were examined by 1% agarose gel electrophoresis, and lanes showing multiple bands were considered as positive clones. The positive clones were sequenced by Sangon Biotech (Shanghai) with ABI3730XL Genetic Analyser (Applied Biosystems, Carlsbad, CA, USA).

A total of 196 positive clones were identified from 432 plasmids. Then 100 selected positive clones were sequenced and 79% of them had tandem repeats.

Thirty specific-primers were designed based on conserved regions using the software Primer Premier 5.0 (Lalitha, 2000) and eight primers were successfully yielded clear bands. PCRs were performed in a 25-µl reaction volume containing 7.5 µl 2×Easy Taq PCR Supermix (TransGen Biotech), 100–200 ng genomic DNA and 2.0 pM of each primer pair (forward primer fluorescently labeled with FAM, HEX). PCR-amplifications were carried out in an Applied Biosystems (ABI) 9700 thermal cycler under the following conditions: a first denaturation at 95°C for 5 min, 35 cycles at 95°C for 30 s, 30 s at the annealing temperature (Table I), and 72°C for 30 s, followed by a last cycle at 72°C for 10 min, and a hold step at 4°C. PCR products were analysed on an ABI 3500 genetic analyser (Applied Biosystems) with a LIZ600 size standard, and the allele sizes were estimated using the software GeneMapper (version 5.0, ABI).

The detection of potential scoring errors (e.g. stutter bands, large allele dropout and null alleles) for the data was analysed using Micro-Checker 2.2.1 (van Oosterhout et al., 2004). The number of alleles (NA), observed heterozygosities (HO), expected heterozygosities (HE) and Principal Coordinate analysis (PCoA) were estimated using GenAlEx 6.5 (Peakall and Smouse, 2012). Linkage disequilibrium (LD) between pairs of microsatellite loci and deviations from the Hardy-Weinberg equilibrium (HWE) were calculated by GENEPOP v4.2 (Rousset, 2008). Cervus 3.0 was used to assess the polymorphism information content (PIC) and the frequency of null alleles (Kalinowski et al., 2007). Inbreeding coefficients (Fis) were determined by FSTAT v2.9.3.2 (Goudet, 1995).

Table I.- Characterization for six microsatellite loci isolated from Martes zibellina.

Table II.- Genetic diversity over all loci for the two populations of Martes zibellina.

Although a high proportion of sequences contained repeats, the majority of them was unusable for primer design for several reasons such as the higher or lower annealing temperature (Zhi et al., 2014). Thirty primer pairs were designed, of which eight successfully yielded clear bands. Futhermore, only six markers yielded polymorphic amplification products in the test for polymorphisms across 22 individuals from two natural populations of M. zibellina. DNA sequences of the six microsatellites were deposited into Genbank (accessions KX712105- KX712110).

NA per locus varied from two to five, with an average of 3.67 (Table I), which showed a lower level than previous study (Kashtanov et al., 2011). At the species level, HO and HE ranged from 0.227 to 0.545 and from 0.201 to 0.630, with an average of 0.447 and 0.453, respectively (Table I).

None of these loci were found to deviate from the HWE (Table I), and significant LD was detected between the locus Mzf49 and Mzf56 after Bonferroni correction (p<0.05), which indicated significant allelic association between the two markers. The PIC value ranged from 0.181 to 0.573. Locus Mzf58 showed low polymorphism (PIC<0.25) and Mzf61 showed high polymorphism (PIC>0.5), while the rest were moderately polymorphic (0.25<PIC<0.5). The frequency of null alleles varied from -0.0548 to 0.0563 and none of these loci showed evidence of null alleles. None of the loci showed evidence for large allele dropout or stutter bands. Genetic diversity parameters in each population are presented in Table II. Numbers of effective alleles (NE) were all less than 3, and ranged from 1.180 to 2.824 in the two populations. The locus Mzf61 showed the highest inbreeding coefficient (Fis=0.267) in Daxinganling population. Furthermore, using the 6 microsatellites, PCoA permitted the discrimination of the populations of Daxinganling and Xiaoxinganling, although any overlap was observed. It suggested that the sets of loci proved to correctly discriminate populations (Fig. 1).

In conclusion, microsatellite DNA is an effective molecular marker for studying the genetic diversity of sables. The FIASCO protocol is fast and simple, and its utility is better than traditional enrichment methods. The six microsatellite markers show polymorphism in the two populations, which is helpful for the research and conservation of M. zibellina in the future.

Ferris, S.D., Sage, R.D., Huang, C.M., Nielsen, J.T., Ritte, U. and Wilson, A.C., 1983. Proc. natl. Acad. Sci. U.S.A., 80: 2290-2294. https://doi.org/10.1073/pnas.80.8.2290

Geptner, V.G., 1967. Sable, in Mlekopitayushchie Sovetskogo Soyuza: Khishchnye (Mammals of the Soviet Union: Carnivores), Vol. 2, Nauka, Moscow, pp. 507–533.

Goldstein, D. and Schlöterer, C., 1999. Microsatellites: evolution and applications. Oxford University Press, Oxford.

Goudet, J., 1995. J. Hered., 86: 485-486. https://doi.org/10.1093/oxfordjournals.jhered.a111627

Hosoda, T., Suzuki, H., Iwata, M.A., Hayashida, M., Watanabe, S., Tatara, M. and Tsuchiya, K., 1999. Mammal Study, 24: 25–33. https://doi.org/10.3106/mammalstudy.24.25

Inoue, T., Murakami, T., Abramov, A.V. and Masuda, R., 2010. Mammal Study, 35: 145-155. https://doi.org/10.3106/041.035.0301

Kashtanov, S.N., Afanasiev, K.I., Potapov, S.G. and Lazebny, O.E., 2011. Genetika, 47: 1622-1628.

Kurose, N., Masuda, R., Siriaroonrat, B. and Yoshida, M.C., 1999. Zool. Sci., 16: 693-700. https://doi.org/10.2108/zsj.16.693

Kalinowski, S.T., Taper, M.L. and Marshall, T.C., 2007. Mol. Ecol., 16: 1099-1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x

Lalitha, S., 2000. Biotech. Softw. Int. Rep., 1: 270. https://doi.org/10.1089/152791600459894

Murakami, T., Asano, M. and Ohtaishi, N., 2004. Japan. J. Vet. Res., 51: 135-142.

Niu, Y., Li, M., Wei, F. and Feng Z., 2001. Hereditas, 23: 593-598.

Peakall, R. and Smouse, P.E., 2012. Bioinformatics, 28: 2537-2539. https://doi.org/10.1093/bioinformatics/bts460

Reed, D.H. and Frankham, R., 2003. Conserv. Biol., 17: 230-237. https://doi.org/10.1046/j.1523-1739.2003.01236.x

Rousset, F., 2008. Mol. Ecol. Resour., 8: 103-106. https://doi.org/10.1111/j.1471-8286.2007.01931.x

Vandevliet, M.S., Diekann, O.E., Serrsao, E.T.A. and Beja, P., 2009. Mol. Ecol. Resour., 9: 425-428. https://doi.org/10.1111/j.1755-0998.2008.02436.x

van Oosterhout, C., Hutchinson, W.F., Wills, DM. and Shipley, P., 2004. Mol. Ecol. Notes, 4: 535-538. https://doi.org/10.1111/j.1471-8286.2004.00684.x

Zullo, S., Sieu, L.C., Slightom, J.L., Hadler, H.I. and Eisenstadt, J.M., 1991. J. mol. Biol., 221: 1223-1235. https://doi.org/10.1016/0022-2836(91)80123-C

Zane, L., Bargelloni, L. and Patarnello, T., 2002. Mol. Ecol., 11: 1-16. https://doi.org/10.1046/j.0962-1083.2001.01418.x

Zhi, Y.B., Ding, L., Wang, Y., Hu, L., Hua, Y., Zhao, K., He, J., Yang, C. and Zhang, B., 2014. Conserv. Genet. Resour., 6: 297-299. https://doi.org/10.1007/s12686-013-0135-y