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. 2014 Feb 11;2(3):apps.1300072. doi: 10.3732/apps.1300072

Development of nuclear microsatellites for the Arcto-Tertiary tree Zelkova carpinifolia (Ulmaceae) using 454 pyrosequencing1

Elmira H Maharramova 2,3,5, Ludo A Muller 4, Nadja Korotkova 2,4, Thomas Borsch 2,4
PMCID: PMC4103100  PMID: 25202606

Abstract

Premise of the study: The current study aimed at developing nuclear microsatellite markers for the relict tree species Zelkova carpinifolia, which is threatened in its natural range in the South Caucasus.

Methods and Results: Pyrosequencing of an enriched microsatellite library on the Roche FLX platform using the 454 Titanium kit produced 86,058 sequence reads, most of which contained short tandem repeats. Eighty microsatellite loci identified using the software package QDD version 1 were selected and tested for proper PCR amplification. Of these, 13 allowed proper amplification and were shown to be polymorphic among a sample of 25 Z. carpinifolia specimens from various geographic origins.

Conclusions: The set of microsatellite markers will be suitable for the assessment of genetic diversity in Z. carpinifolia. They will allow for an examination of phylogeographic patterns as well as of population structure and gene flow within this species.

Keywords: conservation genetics, microsatellites, phylogeography, pyrosequencing, Ulmaceae, Zelkova carpinifolia


Zelkova carpinifolia (Pall.) K. Koch. (Ulmaceae) is a representative species of the Arcto-Tertiary relict flora (Wang et al., 2001; Milne and Abbot, 2002; Kozlowski et al., 2012). It occurs naturally in Hyrcan and Colchic forests in Iran, Azerbaijan, Georgia, and Turkey (Browicz and Zielinski, 1982; Denk and Grimm, 2005; Kvavadze and Connor, 2005; Akhani et al., 2010). Its valuable timber has led to uncontrolled logging, which has resulted in a general population decline. Therefore, Z. carpinifolia was listed under the International Union for Conservation of Nature (IUCN) category “Near Threatened” (Güner and Zielinski, 1998). To plan conservation strategies for Z. carpinifolia, investigation of its genetic diversity is of great importance (Kozlowski et al., 2012). The phylogeography of the species needs to be understood as there may be specific refugia within the range of the species that harbor relatively high genetic diversities and regionally adapted genotypes may occur.

The first studies of genetic diversity in Zelkova Spach employed inter-simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) markers (Fineschi et al., 2004). Primers targeting microsatellite loci in Z. serrata (Thunb.) Makino (Fukatsu et al., 2005) did not amplify well in Z. carpinifolia and revealed only limited polymorphism (unpublished data). The current study therefore aimed to develop polymorphic microsatellite markers for Z. carpinifolia using 454 pyrosequencing.

METHODS AND RESULTS

Plant material and DNA extraction

Zelkova carpinifolia samples were collected from six populations (10–20 individuals per population) in Azerbaijan and Iran (Appendix 1). Genomic DNA was extracted from silica gel–dried leaves using either the NucleoSpin Plant II kit (Macherey Nagel, Düren, Germany) following the manufacturer’s protocol or a three-fraction cetyltrimethylammonium bromide (CTAB) method (Borsch et al., 2003).

Microsatellite marker development

Construction of the enriched microsatellite libraries was carried out according to the protocol of Glenn and Schable (2005) with modifications. Genomic DNA was digested in 25-μL reactions containing 1× NEBuffer 3.1, 0.1 mg/mL bovine serum albumin (BSA), 0.05 M NaCl, 20 U EcoRI, 10 U MseI restriction enzymes (New England Biolabs, Frankfurt, Germany), and 2.4 μg genomic DNA during a 2-h incubation at 37°C. Digested DNA was run on a 2% agarose gel, and 200–400-bp fragments were extracted using the Gel/PCR DNA Fragment Extraction Kit (Avegene, Zollikofen, Switzerland) following the manufacturer’s protocol. To prepare double-stranded adapters, forward (EcoRI: 5′-CTCGTAGACTGCGTACC, MseI: 5′-GACGATGAGTCCTGAG) and reverse (EcoRI: 5′-AATTGGTACGCAGTCTACGAG, MseI: 5′-TACTCAGGACTCATCGTC) adapters (Metabion, Martinsried, Germany) were mixed in equimolar amounts (10 μM), incubated at 95°C for 5 min, and allowed to slowly cool down to room temperature. Adapters were ligated to the restriction fragments in 40-μL reactions containing 0.8 μM of each of the double-stranded EcoRI and MseI adapters, 1× T4 DNA ligase buffer, and 600 U T4 DNA ligase (New England Biolabs). Reactions were performed at 16°C for 12 h and successful ligation was tested by PCR amplification in 50-μL reactions containing 4 μL of the adapter-ligated DNA, 1× Taq DNA polymerase buffer, 1× PCR enhancer solution, 150 μM of each dNTP, 2 U Taq DNA polymerase (PeqLab, Erlangen, Germany), 35 ng/μL BSA, 0.5 μM EcoRI primer (5′-CTCGTAGACTGCGTACCAATTC), and 0.5 μM MseI primer (5′-GACGATGAGTCCTGAGTAA) (Metabion) using the following temperature profile: 95°C for 2 min; 20 cycles of 95°C for 20 s, 60°C for 20 s, 72°C for 1.5 min; and 72°C for 10 min. Two mixtures of 3′-biotinylated oligonucleotides [1: (AG)12, (TG)12, (AAG)8, (AAT)12, (ACT)12 and 2: (ACAG)6, (ACCT)6, (ACTC)6, (ACTG)6] were used to generate two separate libraries of adapter-ligated genomic DNA enriched for repetitive motifs. Hybridization of biotinylated oligonucleotides and adapter-ligated genomic DNA, followed by the capturing of hybridized DNA on Dynabeads (Life Technologies, Darmstadt, Germany) and subsequent washing and resuspension, followed the protocol of Glenn and Schable (2005). Recovery PCR was performed with 2 μL of enriched DNA in the same reaction mixture and the temperature profile as described above, but with 25 cycles. The enrichment procedure was repeated and the second recovery PCR was carried out with an EcoRI oligonucleotide primer extended with a Roche 454 pyrosequencing adapter (5′-GCCTCCCTCGCGCCATCAG-3′) and a specimen-specific barcode sequence and an MseI oligonucleotide primer extended with a Roche 454 B sequencing adapter (5′-GCCTTGCCAGCCCGCTCAG-3′; Appendix 2). Two enrichment libraries were prepared for each of six Z. carpinifolia specimens (population ZE053_IR, Appendix 1). Enrichment libraries were purified using the Amplicon Library Preparation Protocol (Roche, Branford, Connecticut, USA) according to the manufacturer’s instructions. Lib-L Kits and the GS FLX Titanium Sequencing Kit XLR70 (Roche) were used for the library sequencing on the Roche GS FLX System. The resulting DNA sequences were analyzed using the R package SeqinR (Charif and Lobry, 2007). The 454 pyrosequencing yielded 86,058 total reads ranging from 40 to 577 bp with an average length of 138 bp.

Microsatellite screening

Screening for microsatellite loci and primer design was performed using QDD software version 1 (Meglécz et al., 2010), which identified 136 microsatellite loci containing di-, tri-, and tetranucleotide repeat motifs. A total of 80 microsatellite loci with 5–45 repeats, including three loci with tetranucleotide repeats, 17 loci with trinucleotide repeats, and 60 loci with dinucleotide repeats, were selected randomly, and oligonucleotide primer combinations with a GC content of 35–60% and melting temperature (Tm) ranging between 57°C and 60°C were tested for proper PCR amplification on genomic DNA extracted from three specimens (Table 1). A gradient PCR was carried out for each primer pair in a 25-μL reaction volume containing 20–40 ng DNA, 0.4 μM each of forward and reverse primer (Eurofins MWG Operon, Ebersberg, Germany), 1× TaqBuffer S, 1.5 mM MgCl2, 250 μM of each dNTP, and 0.75 U Hot Taq polymerase (PeqLab). The temperature profile was as follows: 96°C for 2 min, 54 ± 8°C for 30 s, 72°C for 30 s; followed by 34 cycles of 95°C for 30 s, 54 ± 8°C for 30 s, 72° for 30 s; and 72°C for 15 min. PCR performance was assessed by gel electrophoresis. Of the initial 80 loci tested, 40 primer pairs failed to amplify a product. The reactions with the other 40 primer pairs were repeated in 50-μL reaction volumes. PCR products were run on 1.5% agarose gel and extracted using the NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel) following the manufacturer’s protocol. PCR products were sequenced at Macrogen (Seoul, Korea) using standard Sanger sequencing to confirm locus-specificity of the oligonucleotide primers. Only the 20 primer pairs that specifically amplified the targeted microsatellite loci were retained for further analyses. Polymorphism assessment used genomic DNA extracted from 25 Z. carpinifolia specimens (five specimens per population; Appendix 1) and fluorescently labeled forward or reverse primers (Applied Biosystems, Warrington, United Kingdom), and the same reaction conditions as in the previous step. Two primer pairs did not amplify a product in all individuals and were excluded from further analysis. The rest of the PCR products were sent to Macrogen for fragment analysis.

Table 1.

Characteristics of 13 nuclear microsatellite loci for Zelkova carpinifolia.

Locus Primer sequences (5′–3′) Fluorescent label Repeat motif Ta (°C) Allele size range (bp) GenBank/ENA accession no.
ZMS_1 F: AAGGTTCATCCCATGAGCAC* 6-FAM (CTT)7 60 238–259 KF408341
R: GTCCAGTCCGGCATCTTTT
ZMS_2 F: CAAGCTGCCAATACTCCACA* VIC (AGA)7 60 181–213 KF408342
R: GGTTTGGTTTCTGCTTGGAA
ZMS_3 F: CCCAACAGCACTTGAAGCTA* 6-FAM (CA)8 60 136–138 KF408343
R: TTTGTGTAGTCTTTGGCCCC
ZMS_4 F: ACCGTTGGAAACAAAACTCG* NED (AG)9 52 105–131 KF408344
R: AGGGCAGTAGAGCTTGATCG
ZMS_5 F: TTTTGTTCGTTGTTGCATGTC* PET (GAA)6 60 99–114 KF408345
R: AGGCTTAGGTTGGGTGGTTT
ZMS_6 F: TTTGGTGCTTAGCATGTGGA* 6-FAM (CT)8 58 101–120 KF408346
R: TCTTTTGTTTGCGATAAGTCG
ZMS_7 F: TCTCTGTTATGATCACGTCTCCA NED (AC)9 60 120–128 KF408347
R: GAGCTAAACCCCATTTCAAATATAA*
ZMS_8 F: ACGAACAAGATCGACAGAGG* PET (TC)12 60 188–204 KF408348
R: ATTGGATGGCACACGTAATTC
ZMS_9 F: CAGGTGATTGGAATTGGAAAA* 6-FAM (AC)7 62 171–196 KF408350
R: CCTCACAGAGTACGAGGGATG
ZMS_10 F: CTGCGAGGGCAGTAGGTAAG* VIC (GA)8 62 175–189 KF408351
R: TCCTAGATCCTTTGATATCTTTCTCA
ZMS_11 F: AGTAGGCTTGGAAGCAAATGA VIC (GT)9 58 96–115 KF408352
R: TTGGAACTGCAATCGCTTT*
ZMS_12 F: CTTCCAATCATTCCGAGAGC* PET (CA)7 58 100–104 KF408353
R: TGACATCTCAAAGGTTGCCA
ZMS_13 F: AACAAAGAATCTTCATCCCC* NED (TG)9 58 110–116 KF408354
R: GCATTTGGTTTTACCTAAAGTTACAG
ZMS_14 F: GCGGTTGAGAGGAGAAAGAA 6-FAM (AGG)10 57 105 HG737351
R: ACCAAACCCATCAACCATTG*
ZMS_15 F: GCTCCTCTTCAGCCAAACAC* 6-FAM (AGG)12 60 128 HG737352
R: CTTCATCCTCGTTTGCATCA
ZMS_16 F: GCCGGTACTGATTCCTTCAA* 6-FAM (AAG)5 60 233 HG737353
R: GGACCATCTCACCAACATCC
ZMS_17 F: AGCCCGTGCTTTTGAATATG 6-FAM (GA)8 55 167 HG737354
R: GGATAAGGCTATTTTGGCCC*
ZMS_18 F: GCCACGTAAACAGAGTAAGGG* 6-FAM (TG)7 58 103 HG737355
R: GCATGTTGGTGCTTTGAGAA

Note: ENA = European Nucleotide Archive; Ta = optimal annealing temperature.

*

Labeled primer.

Expected size.

Microsatellite marker data analysis

Electropherograms from the fragment analysis were analyzed using GeneMarker software version 1.95 (SoftGenetics, State College, Pennsylvania, USA). Analyzed amplification products with unscorable peaks were not considered to be useful in the studies of variability due to the possible misinterpretation of data. Thirteen primer pairs produced polymorphic and heterozygous loci (accession numbers KF408341–KF408348, KF408350–KF408354). The Excel Microsatellite Toolkit (Park, 2001) was used for the calculation of the number of alleles, observed (Ho) and expected (He) heterozygosities, and polymorphism information content (PIC) values. Allele sizes ranged from two to eight alleles per locus across 25 individuals from five different populations, with Ho and He varying between 0.12 and 0.84, and 0.25 and 0.81, respectively (Table 2).

Table 2.

Results of initial primer screening of specimens from five populations of Zelkova carpinifolia.

ZE001_AZ (N = 5) ZE007_AZ (N = 5) ZE013_AZ (N = 5) ZE017_AZ (N = 5) ZE021_AZ (N = 5) Total (N = 25)
Locus A Ho He A Ho He A Ho He A Ho He A Ho He A Ho He PIC
ZMS_1 2 0.60 0.4667 4 1.00 0.7778 2 0.80 0.5333 4 1.00 0.7111 4 0.60 0.6444 5 0.80 0.6294 0.5536
ZMS_2 3 1.00 0.7111 4 1.00 0.7333 4 0.60 0.5333 4 0.80 0.7333 3 0.80 0.6444 8 0.84 0.7053 0.6439
ZMS_3 2 1.00 0.5556 2 0.80 0.5333 2 0.80 0.5333 2 0.20 0.5556 2 0.20 0.4667 2 0.60 0.4971 0.3685
ZMS_4 3 0.80 0.6000 4 0.80 0.8000 4 0.80 0.8000 5 1.00 0.8444 5 0.40 0.8000 8 0.76 0.8188 0.7811
ZMS_5 3 0.40 0.3778 2 0.40 0.3556 1 0 0 1 0 0 3 0.60 0.5111 5 0.28 0.2596 0.2455
ZMS_6 2 0 0.3556 2 0 0.3556 3 0 0.6222 5 0.40 0.8667 5 0.20 0.8222 8 0.12 0.8049 0.7599
ZMS_7 3 1.00 0.6444 4 1.00 0.7778 4 0.60 0.6444 2 0.80 0.5333 3 0.80 0.6000 4 0.84 0.7094 0.6413
ZMS_8 5 1.00 0.8222 4 1.00 0.7333 4 1.00 0.7333 3 0.80 0.6000 4 0.20 0.6444 7 0.80 0.7861 0.7351
ZMS_9 3 0.40 0.6222 3 0 0.7111 4 0.60 0.7333 3 0.60 0.5111 3 0.20 0.5111 5 0.36 0.7127 0.6506
ZMS_10 2 0.20 0.5556 4 0.60 0.7333 3 0.40 0.6000 2 0.20 0.4667 4 0.80 0.7778 5 0.44 0.6588 0.6065
ZMS_11 1 0 0 3 0.40 0.7111 2 0 0.3556 5 0.40 0.8222 2 0 0.3556 6 0.16 0.5037 0.4526
ZMS_12 2 0.60 0.4667 2 0.40 0.3556 2 0.20 0.2000 2 0.20 0.2000 1 0 0 3 0.28 0.2539 0.2316
ZMS_13 3 0.60 0.6444 3 1.00 0.6444 2 0.80 0.5333 2 0.20 0.2000 2 0.20 0.2000 4 0.56 0.5102 0.4431

Note: A = number of alleles; He = expected heterozygosity (Nei’s unbiased gene diversity); Ho = observed heterozygosity; N = sample size; PIC = polymorphism information content.

CONCLUSIONS

In the current study, we used 454 pyrosequencing to obtain sequence reads for microsatellite primer development in Z. carpinifolia. After thorough evaluation, we present 13 primer pairs for amplifying polymorphic microsatellite loci in Z. carpinifolia. These 13 loci are proposed to be used for the microsatellite screening of naturally distributed Z. carpinifolia populations, but they may also cross-amplify in closely related species. Analysis of the obtained allele frequencies and knowledge of the individual genotypes will help us to understand the population structure and relationships between and within different populations of Zelkova species.

Appendix

Appendix 1.

Locations and voucher information for populations of Zelkova carpinifolia used in this study. Vouchers are deposited at the herbarium of the Botanischer Garten und Botanisches Museum Berlin-Dahlem (B), Berlin, Germany.

Population Locality Geographic coordinates Collection no.
ZE001_AZ Zuvand Mtn., Lerik, Azerbaijan 38°43′33″N, 48°25′53″E EM01
ZE007_AZ Azfilial, Lankaran, Azerbaijan 38°40.938′N, 48°47.222′E EM13
ZE013_AZ Tezekend, Lankaran, Azerbaijan 38°39.091′N, 48°48.284′E EM20
ZE017_AZ Zungulesh, Astara, Azerbaijan 38°27.175′N, 48°47.575′E EM28
ZE021_AZ Khanbulan, Lankaran, Azerbaijan 38°39.809′N, 48°46.649′E EM33
ZE053_IR* Gorgan, Golestan, Iran 36°43′35″N, 54°34′49″E
*

Used for construction of the genomic library.

Appendix 2.

EcoRI-A and MseI-B primers used for PCR recovery of the enriched DNA library.

Primer name Primer sequence (5′–3′)a
EcoRI_A001 CCA TCT CAT CCC TGC GTG TCT CCG ACT CAG ACG AGT GCG TCT CGT AGA CTG CGT ACC AAT TC
EcoRI_A002 CCA TCT CAT CCC TGC GTG TCT CCG ACT CAG ACG CTC GAC ACT CGT AGA CTG CGT ACC AAT TC
EcoRI_A003 CCA TCT CAT CCC TGC GTG TCT CCG ACT CAG AGA CGC ACT CCT CGT AGA CTG CGT ACC AAT TC
EcoRI_A004 CCA TCT CAT CCC TGC GTG TCT CCG ACT CAG AGC ACT GTA GCT CGT AGA CTG CGT ACC AAT TC
EcoRI_A005 CCA TCT CAT CCC TGC GTG TCT CCG ACT CAG ATC AGA CAC GCT CGT AGA CTG CGT ACC AAT TC
EcoRI_A006 CCA TCT CAT CCC TGC GTG TCT CCG ACT CAG ATA TCG CGA GCT CGT AGA CTG CGT ACC AAT TC
MseI_B CCT ATC CCC TGT GTG CCT TGG CAG TCT CAG GAC GAT GAG TCC TGA GTA A
a

Specimen-specific barcodes (tags) are shown in bold.

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