Open Access
Translator Disclaimer
1 February 2014 Development and Characterization of EST-SSR Markers in Ostryopsis (Betulaceae)
Bing-Bing Liu, Bin Tian, Hui Ma, Zhi-Qiang Lu, Qiang Qiu, Kang-Shan Mao, Jian-Quan Liu
Author Affiliations +

Ostryopsis Decne. (Betulaceae) is a small genus endemic to China, consisting of only three recognized species: O. davidiana Decne., O. nobilis Balf. f. & W. W. Sm., and O. intermedia B. Tian & J. Q. Liu (Tian et al., 2010). Ostryopsis davidiana is mainly distributed in northern China, while O. nobilis and O. intermedia are limited to southwestern China. The northern vs. southwestern distributions of the three species in this genus suggest that Ostryopsis is a good model system to explore species divergence of plants in response to both habitat and temperature change across China. Until now, a total of 10 simple sequence repeat (SSR) markers have been developed for O. davidiana (Qiu et al., 2009). However, some of these markers could not be successfully amplified with the other two species. Furthermore, the development of expressed sequence tag (EST)–SSR markers is particularly attractive because they represent coding regions of the genome. EST-derived SSRs developed from one species can be easily amplified and used in closely related species (Wünsch, 2009). Here, we report 15 new polymorphic EST-SSR loci for Ostryopsis, which will facilitate the characterization of genetic diversity of each species in the genus and examination of gene flow and genetic divergence between the three species.

METHODS AND RESULTS

In this study, 20 or 30 individuals per species were collected for O. davidiana (Yijun, Shaanxi Province; Diebu, Gansu Province), O. nobilis (Tangdui, Yunnan Province; Jirenhe, Yunnan Province), and O. intermedia (Judian, Yunnan Province; Deqin, Yunnan Province) from their native distributions in China, and the voucher specimens were deposited in the herbarium of Lanzhou University (LZU), Lanzhou, China (Appendix 1). Genomic DNA was extracted using a cetyltrimethylammonium bromide (CTAB) procedure from leaves of each individual per species (Ghangal et al., 2009). The total RNA of O. davidiana and O. nobilis was also extracted using a CTAB procedure (Ghangal et al., 2009) and then the complementary DNA (cDNA) libraries were constructed and sequenced, respectively.

Approximately 4 µg of RNAs were purified using poly(dT)-conjugated beads (Life Technologies, Carlsbad, California, USA) to clear poly(A)-tagged mRNA. These RNAs were then broken into ∼200-bp fragments under divalent cations at 75°C. We synthesized the first strand of cDNA by the reverse transcriptase with random hexmer primers, and the second strand of cDNA by RNase H (Invitrogen, Ghent, Belgium) and DNA polymerase I (New England BioLabs, Ipswich, Massachusetts, USA). We sequenced the transcriptome on an Illumina (Solexa) Genome Analyzer II (Illumina Inc., San Diego, California, USA). After removing adapter sequences, we filtered and assembled two data sets of raw reads from O. davidiana and O. nobilis as described in Qiu et al. (2011). To identify orthologous genes between two species, their reads were mapped back against the assembled unigenes using Bowtie 2 (Langmead and Salzberg, 2012). We recalled single-nucleotide polymorphisms (SNPs) and indel calling with SAMtools (Li et al., 2009). We identified EST-SSRs using MISA ( http://pgrc.ipk-gatersleben.de/misa) based on the orthologous unigene sequences. Because the de novo assembly introduced multiple indels, we therefore removed the shared ones by two orthologous unigenes. We used only the indels with end-to-end alignment as candidate SSR regions for further primer design. The final analyses resulted in a total of 72 and 69 SSR indels according to the above reference unigenes from two species, respectively. We then designed the paired primers with Primer3 software (Rozen and Skaletsky, 2000). Primers were not retained when they targeted to the SNP region of the unigenes. In this way, we obtained a total of 38 primer pairs from both species.

Table 1.

Characteristics of 15 polymorphic EST-SSRs developed in Ostryopsis.

t01_01.gif

To evaluate polymorphisms of these primer pairs and their possible amplifications in the other species, we selected five individuals from each of the three species. PCR reactions were carried out in a 20-µL solution containing 20 ng of DNA template, 5 pmol of each primer, 100 µM each of dNTPs, 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5 mM MgCl2, and 0.2 U of Taq polymerase (Intron Biotechnology, Seongnam, South Korea). After a denaturing step of 5 min at 95°C, a touchdown amplification program was performed. This profile included a denaturing step of 45 s at 95°C and an extension step of 30 s at 72°C. The initial annealing step was 45 s at 60°C for one cycle, and subsequently the temperature was decreased by 0.7°C for every cycle to a final temperature of 53°C. This annealing temperature was employed for the last 30 cycles of the amplification, followed by one cycle of 72°C for 10 min. PCR products were assayed on 1.5% (w/v) agarose gels to test the utility of the primers. Finally, a total of 15 primer pairs were successfully amplified across all three species and all of them displayed clear polymorphisms (Table 1).

Subsequently, we selected a total of 80 individuals from the three species to evaluate the potential value of these markers for estimating genetic diversity of each species. Fluorescence-based SSR genotyping was performed using a modified method of Hayden et al. (2008). Briefly, the forward primers of the 15 EST-SSRs were labeled with 6-FAM, VIC, or NED fluorescent tags (Applied Biosystems, Foster City, California, USA). The PCR reactions were carried out separately for each microsatellite as described above. Amplification products for which size and color did not overlap were pooled together for simultaneous detection of the amplified alleles.

Table 2.

Genetic diversity statistics for each sampled population of the three Ostryopsis species based on 15 pairs of EST-SSR primers.a

t02_01.gif

To characterize each EST-SSR marker, we calculated three genetic diversity statistics using POPGENE version 1.31 (Yeh et al., 1999): number of alleles per locus, observed heterozygosity, and expected heterozygosity (Table 2). We found that the number of alleles ranged from one to nine, with an average of 3.8 alleles per locus. The expected heterozygosity and observed heterozygosity ranged from 0 to 0.829 and 0 to 1, respectively, with their respective mean values as 0.483 and 0.416 (Table 2).

CONCLUSIONS

We developed 15 polymorphic EST-SSR markers for Ostryopsis from two cDNA libraries. The polymorphisms of these markers were further evaluated with 80 individuals representing the three species. These newly developed EST-SSRs have a high degree of universality between species and will be useful for studying the genetic diversity of each species and genetic divergence between the three species.

LITERATURE CITED

1.

R. Ghangal , S. Raghuvanshi , and P. C. Sharma . 2009. Isolation of good quality RNA from a medicinal plant seabuckthorn, rich in secondary metabolites. Plant Physiology and Biochemistry 47: 1113–1115. Google Scholar

2.

M. J. Hayden , T. M. Nguyen , A. Waterman , G. L. McMichael , and K. J. Chalmers . 2008. Application of multiplex-ready PCR for fluorescence-based SSR genotyping in barley and wheat. Molecular Breeding 21: 271–281. Google Scholar

3.

B. Langmead , and S. Salzberg . 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9: 357–359. Google Scholar

4.

H. Li , B. Handsaker , A. Wysoker , T. Fennell , J. Ruan , N. Homer , G. Marth , et al. (1000 Genome Project Data Processing Subgroup). 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England) 25: 2078–2079. Google Scholar

5.

Q. Qiu , B. Tian , H. Y. Wen , G. L. Wu , and Y. J. Wang . 2009. Isolation and characterization of microsatellite loci in Ostryopsis davidiana (Betulaceae). Conservation Genetics 10: 751–753. Google Scholar

6.

Q. Qiu , T. Ma , Q. J. Hu , B. B. Liu , Y. X. Wu , H. H. Zhou , Q. Wang , et al. 2011. Genome-scale transcriptome analysis of the desert poplar, Populus euphratica. Tree Physiology 31: 452–461. Google Scholar

7.

S. Rozen , and H. Skaletsky . 2000. Primer3 on the WWW for general users and for biologist programmers. In S. Misener and S. A. Krawetz [eds.], Methods in molecular biology, vol. 132: Bioinformatics methods and protocols, 365–386. Humana Press, Totowa, New Jersey, USA. Google Scholar

8.

B. Tian , T. L. Liu , and J. Q. Liu . 2010. Ostryopsis intermedia, a new species of Betulaceae from Yunnan, China. Botanical Studies (Taipei, Taiwan) 51: 257–262. Google Scholar

9.

A. Wünsch 2009. Cross-transferable polymorphic SSR loci in Prunus species. Scientia Horticulturae 120: 348–352. Google Scholar

10.

F. C. Yeh , R. C. Yang , and T. Boyle . 1999. POPGENE (version 1.31): Microsoft Windows–based freeware for population genetic analysis. Center for International Forestry Research, University of Alberta, Edmonton, Alberta, Canada. Google Scholar

Appendices

Appendix 1.

Locality information for the sampled populations of the Ostryopsis species used in this study. All voucher specimens are deposited at the herbarium of Lanzhou University (LZU), Lanzhou, China.

tA01_01.gif

Notes

[1] This study is supported by the National High Technology Research and Development Program of China (863 Program, no. 2013AA100605), Research Fund for the Doctoral Program of Higher Education of China (grant no. 20100211110008), and the Fundamental Research Funds for the Central Universities (lzujbky-2009-k05).

Bing-Bing Liu, Bin Tian, Hui Ma, Zhi-Qiang Lu, Qiang Qiu, Kang-Shan Mao, and Jian-Quan Liu "Development and Characterization of EST-SSR Markers in Ostryopsis (Betulaceae)," Applications in Plant Sciences 2(2), (1 February 2014). https://doi.org/10.3732/apps.1300062
Received: 26 July 2013; Accepted: 1 November 2013; Published: 1 February 2014
JOURNAL ARTICLE
PAGES


Share
SHARE
KEYWORDS
Betulaceae
EST-SSR marker
next-generation sequencing technology
ortholog genes
Ostryopsis.
RIGHTS & PERMISSIONS
Get copyright permission
Back to Top