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Development of SSR Markers for Psammochloa villosa (Trin.) Bor (Poaceae), a Dominant Species in the Inner Mongolian Plateau

Liu Y.-P., Liang R.-F., Lv T., Ma Z.-L., Liu T., Liu F., Su X., Harris A.J.


We developed a set of SSR markers to investigate the genetic diversity and evolutionary history of Psammochloa villosa (Trin.) Bor, a dominant species of the Inner Mongolian Plateau and adjacent regions. We used sequenced transcriptomes of P. villosa to develop primer pairs for 97 SSR markers. Of these, we successfully amplified 46 (47 %) SSRs and found that eleven were polymorphic among individuals. We tested these eleven SSRs in 122 accessions of P. villosa representing ten populations, and determined that the number of alleles per locus ranged from one to seven, with an average of 2.727. The expected and observed heterozygosity per locus varied from 0 to 0.840 (mean: 0.471) and from 0 to 1.000 (mean: 0.679), respectively. The new SSR markers described in this study will be valuable for evaluating the population genetic structure and history of P. villosa throughout its range and may help to develop hypotheses for understanding the history of its divergence from its closest relatives in the genus Stipa L.

Key words: grass; Illumina; microsatellite marker; orthologous gene; transcriptome

Tsitologiya i Genetika 2021, vol. 55, no. 6, pp. 78-79

  1. Key Laboratory of Medicinal Animal and Plant Resources in the QinghaiTibetan Plateau, School of Life Sciences, Qinghai Normal University, Xining 810008, China
  2. Key Laboratory of Physical Geography and Environmental Process in Qinghai Province, Qinghai Normal University, Xining 810008, China
  3. Key Laboratory of Education Ministry of Earth Surface Processes and Ecological Conservation of the QinghaiTibet Plateau, Qinghai Normal University, Xining 810008, China
  4. Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China

E-mail: xusu8527972; aj.harris

Liu Y.-P., Liang R.-F., Lv T., Ma Z.-L., Liu T., Liu F., Su X., Harris A.J. Development of SSR Markers for Psammochloa villosa (Trin.) Bor (Poaceae), a Dominant Species in the Inner Mongolian Plateau, Tsitol Genet., 2021, vol. 55, no. 6, pp. 78-79.

In "Cytology and Genetics":
Yu-Ping Liu, Rui-Fang Liang, Ting Lv, Zi-Lan Ma, Tao Liu, Feng Liu, Xu Su & AJ Harris Development of SSR Markers for Psammochloa villosa (Trin.) Bor (Poaceae), a Dominant Species in the Inner Mongolian Plateau, Cytol Genet., 2021, vol. 55, no. 6, pp. 576582
DOI: 10.3103/S0095452721060086


1. Agarwal, M., Shrivastava, N., and Padh, H., Advances in molecular marker techniques and their applications in plant sciences, Plant Cell Rep., 2008, vol. 27, no. 4, pp. 617631.

2. Apweiler, R., Bairoch, A., Wu, C.H., et al., The UniProt Consortium. UniProt: the universal protein knowledgebase, Nucleic Acids Res., 2017, vol. 45, no. D1, pp. D158D169.

3. Ashburner, M., Ball, C. A., Blake, J. A., et al., Gene Ontology: tool for the unification of biology, The Gene Ontology Consortium, Nat. Genet., 2000, vol. 25, pp. 2529.

4. Dong, M. and Alaten, B., Clonal plasticity in response to rhizome severing and heterogeneous resource supply in the rhizomatous grass Psammochloa villosa in an Inner Mongolian dune, China, J. Plant Ecol., 1999, vol. 141, no. 1, pp. 5358.

5. Dong, M., Alaten, B., Xing, X.R., et al., Genet features and ramet population features in the rhizomatous grass species Psammochloa villosa, Chin. J. Plan. Ecol., 1999, vol. 23, no. 4, pp. 302310.

6. Esselman, E.J., Li, J.Q., Crawford, D.J., et al., Clonal diversity in the rare Calamagrostis porteri ssp. insperata (Poaceae): comparative results for allozymes and random applied polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers, Mol. Ecol., 1999, vol. 8, no. 3, pp. 443451.

7. Finn, R.D., Bateman, A., Clements, J., et al., Pfam: the protein families database, Nucleic Acids Res., 2014, vol. 42, no. D1, pp. D222D230.

8. Ghangal, R., Raghuvanshi, S., and Sharma, P.C., Isolation of good quality RNA from a medicinal plant sea buckthorn, rich in secondary metabolites, Plant Physiol. Biochem., 2009, vol. 47, no. 1112, pp. 11131115.

9. Gomes, S., Martins-Lopes, P., Lopes, J., et al., Assessing genetic diversity in Olea europaea L. using ISSR and SSR markers, Plant Mol. Biol. Rep., 2009, vol. 27, pp. 365373.

10. Haas, B.J., Papanicolaou, A., Yassour, et al., De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nat. Protoc. 2013. vol. 8, no. 8, pp. 14941512.

11. Hayden, M.J., Nguyen, T.M., Waterman, A., et al., Application of multiplex-ready PCR for fluorescence-based SSR genotyping in barley and wheat, Mol. Breeding, 2008, vol. 21, pp. 271281.

12. Huang, Z.Y., Dong, M., and Zhang, S.M., Strategies of seed germination on sand dune and seedling desiccation tolerance of Psammochloa villosa (Poaceae), Acta Ecol. Sin., 2005, vol. 25, no. 2, pp. 298303.

13. Izzah, N.K., Lee, J., Jayakodi, M., et al., Transcriptome sequencing of two parental lines of cabbage (Brassica oleracea L. var. capitata L.) and construction of an EST-based genetic map, BMC Genomics, 2014, vol. 15, p. 149.

14. Kanehisa, M. and Goto, S., KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Res., 1999, vol. 27, no. 1, pp. 2934.

15. Kim, B.Y., Park, H.S., Kim, S., et al., Development of microsatellite markers for Viscum coloratum (Santalaceae) and their application to wild populations, Appl. Plant Sci., 2017, vol. 5, no. 1, p. 1600102.

16. Langmead, B. and Salzberg, S., Fast gapped-read alignment with Bowtie 2, Nat. Methods, 2012, vol. 9, pp. 357359.

17. Li, A. and Ge, S., Genetic variation and clonal diversity of Psammochloa villosa (Poaceae) detected by ISSR markers, Ann. Bot., 2001, vol. 87, no. 5, pp. 585590.

18. Liu, Y. X., Desert Flora of China, Beijing: Science Press, 1985, vol. 1, p. 34.

19. Liu, B.B., Tian, B., Ma, H., et al., Development and characterization of EST-SSR markers in Ostryopsis (Betulaceae), Appl. Plant Sci., 2014, vol. 2, p. 1300062.

20. Liu, J.T., Zhou, Y.L., Luo, C.X., et al., De novo transcriptome sequencing of desert herbaceous Achnatherum splendens (Achnatherum) seedlings and identification of salt tolerance genes, Gene, 2016, vol. 7, no. 4, p. 12.

21. Liu, Y.P., Su, X., Luo, W.C., et al., Development of SSR markers from transcriptomes for Orinus (Poaceae), an endemic of the QinghaiTibetan Plateau, Appl. Plant Sci., 2017, vol. 5, no. 7, p. 1700029.

22. Lu, S.L. and Kuo, P.C., Psammochloa Hitchc. In: Kuo, P.C., ed. Flora Republicae Popularis Sinicae, Beijing: Science Press, 1987, pp. 307309.

23. Lv, T., Liu, Y.P., Zhou, Y.H., et al., Germplasm collection and preliminary studies on genealogical differentiation of a desert speciesPsammochloa villosa, Acta Agrest. Sin., 2018, vol. 26, no. 3, pp. 733740.

24. Ma, Y.Q., Flora of Inner Mongolia, Hohhot: Inner Mongolia Peoples Publishing House, 1994, vol. 5, pp. 115152.

25. Rossetto, M., Jezierski, G., Hopper, S.D., et al., Conservation genetics and clonality in two critically endangered eucalypts from the highly endemic south-western Australian flora, Biol. Conserv., 1999, vol. 88, pp. 321331.

26. Rousset, F., GENEPOP007: A complete re-implementation of the GENEPOP software for Windows and Linux, Mol. Ecol. Resour., 2008, vol. 8, no. 1, pp. 103106.

27. Rozen, S. and Skaletsky, H., Primer3 on the WWW for general users and for biologist programmers, in Bioinformatics Methods and Protocols, Misener, S. and Krawetz, S.A., Eds., Methods in Molecular Biology, Totowa, New Jersey, USA: Humana Press, 2000, vol. 132, pp. 365386.

28. Serra, I.A., Procaccini, G., Intrieri, M.C., et al., Comparison of ISSR and SSR markers for analysis of genetic diversity in the seagrass Posidonia oceanica, Mar. Ecol. Prog. Ser., 2007, vol. 338, pp. 7179.

29. Simon, S.A., Zhai, J., Nandety, R.S., et al., Short-read sequencing technologies for transcriptional analyses, Annu. Rev. Plant Biol., 2009, vol. 60, no. 1, pp. 305333.

30. Tani, N., Tomaru, N., Tsumura, Y., et al., Genetic structure within a Japanese stone pine (Pinus pumila Regel) population on Mt. Aino-dake in Central Honshu, Japan, J. Plant Res., 1998, vol. 111, no. 1101, pp. 715.

31. Tatusov, R.L., Fedorova, N.D., Jackson, J.D., et al., The COG database: an updated version includes eukaryotes, BMC Bioinformatics, 2003, vol. 4, p. 41.

32. Wang, K.Q., Ge, S., and Dong M., Allozyme variance and clonal diversity in the rhizomatous grass Psammochloa villosa (Gramineae), Acta Bot. Sin., 1999, vol. 41, no. 5, pp. 534540.

33. Wheeler, D.L., Church, D.M., Federhen, S., et al., NCBI Resource Coordinators, Database resources of the National Center for Biotechnology Information, Nucleic Acids Res., 2014, vol. 42, no. D1, pp. D7D17.

34. Yang, J.B., Dong, Y.R., Wong, K.M., et al., Genetic structure and differentiation in Dendrocalamus sinicus (Poaceae: Bambusoideae) populations provide insight into evolutionary history and speciation of woody bamboos, Sci. Rep., 2018, vol. 8, pp. 16933.

35. Zhang, Z.S., Li, L.L., and Chen, W.L., Ptilagrostis contracta (Stipeae, Poaceae), a new species endemic to Qinghai-Tibet Plateau, PLoS One, 2017, vol. 12, no. 1, e0166603.

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