Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Jun 12;7(6):e11269.
doi: 10.1002/aps3.11269. eCollection 2019 Jun.

Development of EST-SSR markers in Saxifraga sinomontana (Saxifragaceae) and cross-amplification in three related species

Yan Li  1   2 , Liu-Kun Jia  1   2 , Fa-Qi Zhang  1   3 , Zhi-Hua Wang  1   2 , Shi-Long Chen  1 , Qing-Bo Gao  1   3
Affiliations

Development of EST-SSR markers in Saxifraga sinomontana (Saxifragaceae) and cross-amplification in three related species

Yan Li et al. Appl Plant Sci. .

Abstract

Premise: Saxifraga sinomontana (Saxifragaceae) is a widespread alpine species in the Qinghai-Tibetan Plateau and its flanking mountains. We developed a set of expressed sequence tag-simple sequence repeat (EST-SSR) markers to investigate the genetic diversity and evolutionary history of the species.

Methods and results: We initially designed 50 EST-SSR markers based on transcriptome data of S. sinomontana. Nineteen of 50 loci (38%) were successfully amplified, 13 of which were polymorphic. These were tested on 71 individuals from four populations. Three to 18 alleles per locus were detected, and the levels of observed and expected heterozygosity ranged from 0.2817 to 0.9155 and 0.2585 to 0.8495, respectively. In addition, cross-amplification was successful for all 13 loci in three congeneric species, S. tangutica, S. heleonastes, and S. congestiflora.

Conclusions: These EST-SSR markers will be useful for studying the genetic diversity of S. sinomontana and disentangling the phylogenetic relationships of related species.

Keywords: EST‐SSR markers; Saxifraga congestiflora; Saxifraga heleonastes; Saxifraga sinomontana; Saxifraga tangutica; transcriptome.

PubMed Disclaimer

References

    1. Bouck, A. , and Vision T.. 2007. The molecular ecologist's guide to expressed sequence tags. Molecular Ecology 16: 907–924. - PubMed
    1. Doyle, J. J. , and Doyle J. L.. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11–15.
    1. Ellis, J. R. , and Burke J. M.. 2007. EST‐SSRs as a resource for population genetic analyses. Heredity 99: 125–132. - PubMed
    1. Gao, Q. B. , Li Y. H., Gornall R. J., Zhang Z. X., Zhang F. Q., Xing R., Fu P. C., et al. 2015. Phylogeny and speciation in Saxifraga sect. Ciliatae (Saxifragaceae): Evidence from psbA‐trnH, trnL‐F and ITS sequences. Taxon 64: 703–713.
    1. Grabherr, M. G. , Haas B. J., Yassour M., Levin J. Z., Thompson D. A., Amit I., Adiconis X., et al. 2011. Full‐length transcriptome assembly from RNA‐Seq data without a reference genome. Nature Biotechnology 29: 644–652. - PMC - PubMed