Tree Genetics & Genomes

, 14:30 | Cite as

A novel set of 223 EST-SSR markers in Casuarina L. ex Adans.: polymorphisms, cross-species transferability, and utility for commercial clone genotyping

  • Xiuyu Xu
  • Changpin Zhou
  • Yong Zhang
  • Weiqiang Zhang
  • Xianhua Gan
  • Huaxin Zhang
  • Yong Guo
  • Siming Gan
Original Article
  • 44 Downloads
Part of the following topical collections:
  1. Germplasm Diversity

Abstract

Simple sequence repeat (SSR) markers are very useful for genetic applications in plants, but SSR resource for the important tree genus Casuarina L. ex Adans. is still limited. In this study, we report a novel set of 223 SSR markers in Casuarina developed from expressed sequence tag (EST) resource of GenBank. The 223 EST-SSR markers were polymorphic among 10 unrelated individuals of C. equisetifolia L. Johnson, with the number of alleles per locus (Na), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic information content (PIC) averaging at 5.5, 0.72, 0.86, and 0.63, respectively. The rates of cross-species transferability ranged from 96.9% (C. glauca Sieber ex Sprengel) through 97.8% (C. cunninghamiana Miquel) to 99.1% (C. junghuhniana Miquel). Fifty-five C. equisetifolia clones widely planted in China were successfully genotyped with a subset of 20 EST-SSRs. These newly developed markers will have a great potential for genetic and breeding applications in Casuarina species and related taxa.

Keywords

Casuarina Expressed sequence tag (EST) Simple sequence repeat (SSR) Polymorphism Transferability Clone genotyping 

Notes

Acknowledgments

The authors would like to thank Hongxia Ji and Heyu Yang for technical assistance.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Data archiving statement

The primer sequences for the 223 EST-SSRs were deposited in Probe database of GenBank (http://www.ncbi.nlm.nih.gov/probe) with IDs Pr032826133–355. The allelic data of the 223 EST-SSRs against the 10 unrelated C. equisetifolia individuals and the 20 EST-SSRs against the 55 C. equisetifolia clones are available from the TreeGenes (http://treegenesdb.org) with accession no. TGDR074.

Supplementary material

11295_2018_1246_MOESM1_ESM.pdf (353 kb)
Online Resource 1 The sequence of forward and reverse primers and repeat motif for the 223 novel EST-SSR markers developed in Casuarina (PDF 353 kb)
11295_2018_1246_MOESM2_ESM.pdf (335 kb)
Online Resource 2 Functional annotations of the 223 novel EST-SSR markers developed in Casuarina (PDF 335 kb)
11295_2018_1246_MOESM3_ESM.pdf (749 kb)
Online Resource 3 Gene ontology (GO) classification of the SSR-containing ESTs into three categories, including cellular component (a), molecular function (b) and biological process (c) (PDF 748 kb)
11295_2018_1246_MOESM4_ESM.pdf (299 kb)
Online Resource 4 Polymorphisms and cross-species amplification for the 223 novel EST-SSR markers developed in Casuarina (PDF 298 kb)
11295_2018_1246_MOESM5_ESM.pdf (309 kb)
Online Resource 5 Nei’s genetic distance between the 55 commercial clones of C. equisetifolia (PDF 309 kb)
11295_2018_1246_MOESM6_ESM.pdf (294 kb)
Online Resource 6 Alleles of uniquely fingerprinted clonal genotypes of C. equisetifolia at a minimum of six EST-SSR markers (PDF 293 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Guangdong Key Laboratory of Forest Silviculture and UtilizationGuangdong Academy of ForestryGuangzhouChina
  2. 2.Research Center of State Forestry Administration on Saline and Alkali LandChinese Academy of ForestryBeijingChina
  3. 3.Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical ForestryChinese Academy of ForestryGuangzhouChina
  4. 4.Guangzhou Geneunion Biotechnological Company LtdGuangzhouChina

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