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5 January 2017 Development of Microsatellite Markers for Viscum coloratum (Santalaceae) and Their Application to Wild Populations
Bo-Yun Kim, Han-Sol Park, Soonok Kim, Young-Dong Kim
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Mistletoes have been proposed to be a keystone resource influencing biodiversity in forest ecosystems globally (Cooney and Watson, 2008). The Korean mistletoe, Viscum coloratum (Kom.) Nakai (Santalaceae), is distributed in many countries, including Korea, Japan, China, and Russia (Qiu and Gilbert, 2003). Viscum L. species have lectins that are known for their potential therapeutic, immunomodulatory, and anticancer properties (Lavastre et al., 2002; Lyu and Park, 2007). According to previous studies, V. coloratum possesses similar cytotoxic and immunological activities as seen in European mistletoe, V. album L. (Lee et al., 2009; Lyu and Park, 2010). Such uses have led to a great demand for these plants, resulting in the large-scale harvesting of wild populations of V. coloratum. The increasing demand has raised concerns about its status as a potentially threatened species. Recently, the environmental management of mistletoes for conservation has become an international focus. For example, the International Union for Conservation of Nature (IUCN) has listed 19 species of mistletoe on the official IUCN Red List of Threatened Species (International Union for Conservation of Nature, 2006). For this reason, the genetic diversity and population structure of V. coloratum should be immediately investigated for resource conservation. Despite the ecological and medical importance of V. coloratum, no studies have evaluated the genetic diversity in wild populations of this species.

Expressed sequence tags–simple sequence repeats (EST-SSRs) have proven valuable for their cross-transferability, facilitating studies of population genetic diversity in many plant species (Dikshit et al., 2015; Zhou et al., 2016). In this study, 19 polymorphic microsatellite loci for V. coloratum were developed based on EST data obtained from Illumina paired-end sequencing. The usefulness of these markers was assessed for 60 individuals representing three populations of V. coloratum in Korea, Japan, and China. Cross-species amplification was tested using 20 individuals of V. album, a close relative of V. coloratum.

METHODS AND RESULTS

We collected 60 individuals of V. coloratum from natural populations from three countries (Korea, Japan, and China), and the voucher specimens representing each population were deposited in the Herbarium of the National Institute of Biological Resources (KB) and the Herbarium of Hallym University (HHU), Republic of Korea (Appendix 1). To test cross-species amplification, we collected 20 individuals of V. album from a single population in Japan (Appendix 1). Whole genomic DNA was extracted from silica gel-dried leaf tissue using the DNeasy Plant Mini Kit (QIAGEN, Valencia, California, USA). DNA concentrations were estimated using the NanoDrop 2000c (Thermo Fisher Scientific, Waltham, Massachusetts, USA), and samples were stored at -20°C.

For RNA library construction, total RNA was extracted from the leaf of a single individual plant collected from Korea (voucher no. : GEIBGR0000298682; Appendix 1). Total RNA quality and quantity were verified using the NanoDrop 2000c (Thermo Fisher Scientific) and Bioanalyzer 2100 (Agilent Technologies, Santa Clara, California, USA). We constructed Illumina-compatible transcriptome libraries using a TruSeq RNA Library Preparation Kit version 2 (Illumina, San Diego, California, USA), according to the manufacturer's instructions. In brief, mRNA was purified from total RNA by poly A selection, and was then chemically fragmented and converted into single-stranded cDNA with random hexamer-primed reverse transcription. A second cDNA strand was generated to create double-stranded cDNA for TruSeq library construction. The short double-stranded cDNA fragments were then connected using sequencing adapters. Finally, RNA libraries were built by PCR amplification. The RNA libraries were quantified using real-time PCR (qPCR), according to the qPCR Quantification Protocol Guide (Illumina), and qualified using an Agilent 2200 Bioanalyzer.

Paired-end 150-bp sequencing of V. coloratum was conducted on the Illumina HiSeq 2000 platform. All sequence information has been deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (Bioproject no. SRP092226). Adapter/quality trimming was performed using Trimmomatic 0.32 (Bolger et al., 2014) with the following parameters: seed mismatch of 2, palindrome clip threshold of 30, simple clip threshold of 10, a minimum adapter length of 2, headcrop of 7, leading and trailing quality of 3, sliding window size of 4 with an average quality of 20 and a minimum sequence length of 50 bases. After trimming, there were 39,226,078 reads for a total length of 6,216,400,383 bp. The de novo transcriptome assembly of these reads was performed using the short-read assembling program Trinity (Haas et al., 2013) with default settings: seqType fq, min contig length 200, group pair distance 500, path reinforcement distance 75, min kmer cov 1, SS lib type FR.

Table 1.

Characteristics of the 19 microsatellite loci developed for Viscum coloratum in this study.

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Microsatellites were detected using the Perl script MIcroSAtellite (MISA) identification tool (Thiel et al., 2003) with thresholds of 10 repeat units for mononucleotides, six for dinucleotides, and five for tri-, tetra-, penta-, and hexanucleotides. MISA identified 15,562 microsatellite sequences, of which 124 loci were selected for further testing (based on the above criteria) in 60 individuals of V. coloratum from three countries (Appendix 1). Primers were designed using Primer3 (Rozen and Skaletsky, 1999) to flank the microsatellite-rich regions with a minimum of six repeats.

PCRs were performed in a total volume of 25 µL containing 10× Ex Taq buffer (TaKaRa Bio Inc., Otsu, Shiga, Japan) 2.5 µL, 2.5 mM dNTPs 2 µL, 0.01 µM forward primers, 0.01 µM reverse primers, 5 units TaKaRa Ex Taq (TaKaRa Bio Inc.) 0.1 µL, 5–10 ng template DNA, and distilled water up to the final volume. Reactions were performed in a Gene Amp PCR System 9700 thermo-cycler (Applied Biosystems, Carlsbad, California, USA) programmed with an initial denaturation step at 98°C for 5 min; followed by 30 cycles of denaturation at 95°C for 1 min, annealing at 55°C for 1 min, and extension at 72°C for 1.5 min; and a final extension step at 72°C for 10 min. Fluorescently labeled PCR products were analyzed using an ABI 3730XL sequencer with the GeneScan 500 LIZ Size Standard (Applied Biosystems). The resulting microsatellite profiles were examined using GeneMapper 3.7 (Applied Biosystems), and peaks were scored manually by visual inspection. Population genetic parameters, including number of alleles per locus, observed heterozygosity, and expected heterozygosity, were estimated using GeneAlEx 6.5 (Peakall and Smouse, 2012). Deviation from Hardy–Weinberg equilibrium was estimated with GENEPOP 4.0 (Rousset, 2008).

Of the 124 microsatellite primer pairs screened, 19 yielded polymorphic SSR loci in V. coloratum (Table 1), with the number of alleles ranging from two to six per locus. Through the prescreening of 60 different individuals from three countries, these markers exhibited favorable stability and high degrees of polymorphism, with an average of 3.26 per marker. The observed and expected heterozygosity ranged from 0.033 to 0.833 and 0.032 to 0.672, respectively (Table 2). Thirteen loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction (P < 0.05) within the populations. Additional tests of cross-amplification in V. album were successful across all 19 markers (Table 3).

Table 2.

Genetic diversity in three Viscum coloratum populationsa based on the 19 newly developed polymorphic microsatellite markers.

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CONCLUSIONS

In this study, we developed 19 novel polymorphic microsatellite markers for the medicinal plant V. coloratum. The results of cross-species amplification testing indicate that these markers can also be applicable for the genetic investigation of the related species V. album. These markers will be useful for estimating the genetic structure and diversity among and within populations of these species, and will further help in the development of effective strategies for their conservation.

Table 3.

Genetic properties of a single population of 20 individuals of Viscum albuma for the 19 microsatellite loci developed for this study.

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ACKNOWLEDGMENTS

This research was supported by the grant “The Genetic and Genomic Evaluation of Indigenous Biological Resources” (NIBR201403202), funded by the National Institute of Biological Resources, Republic of Korea.

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Appendices

Appendix 1.

Locality and voucher information for Viscum coloratum and V. album populations sampled in this study. Voucher specimens were deposited in the Herbarium of the National Institute of Biological Resources (KB) and the Herbarium of Hallym University (HHU), Republic of Korea.

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Bo-Yun Kim, Han-Sol Park, Soonok Kim, and Young-Dong Kim "Development of Microsatellite Markers for Viscum coloratum (Santalaceae) and Their Application to Wild Populations," Applications in Plant Sciences 5(1), (5 January 2017). https://doi.org/10.3732/apps.1600102
Received: 27 August 2016; Accepted: 1 November 2016; Published: 5 January 2017
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