Molecular Breeding

, 39:26 | Cite as

Characterization, validation, and cross-species transferability of newly developed EST-SSR markers and their application for genetic evaluation in crape myrtle (Lagerstroemia spp)

  • Yuanjun Ye
  • Lu Feng
  • Xiaohan Liang
  • Tingting Liu
  • Ming Cai
  • Tangren Cheng
  • Jia Wang
  • Qixiang Zhang
  • Huitang PanEmail author
Short Communication


Crape myrtle is an important ornamental woody plant, due to its long-lasting midsummer bloom and rich color. However, limited molecular markers on this species hinder the breeding and genetic studies. In this work, 8652 EST-SSRs were identified from L. indica transcriptome data. Di-nucleotide repeats (57.1%) were the most abundant type followed by tri-, tetra-, penta-, and hexa-nucleotide repeats, with the AG/CT motif occurring most frequently. Of the 1200 synthesized primer pairs, 761 EST-SSRs (63.4%) were successfully amplified and 245 EST-SSRs (20.4%) showed polymorphic. High cross-species transferabilities of these markers were observed except in L. speciosa (26.7%). The polymorphic information content (PIC) for each locus ranged from 0.210 to 0.813 with a mean of 0.589, suggesting a high level of informativeness. Using 30 polymorphic EST-SSRs, structure and cluster analyses roughly divided the 73 genotypes into three major groups with some admixtures. This work contributes to the better understanding of the genetic diversity and germplasm resources conservation in Lagerstroemia species. Thus, the newly developed EST-SSRs will provide a valuable tool for genetic analysis, linkage map construction, and marker-assisted selection breeding in crape myrtle.


Lagerstroemia Transcriptome EST-SSR markers Cross-transferability Genetic diversity 


Funding information

This work was financially supported by the National Natural Science Foundation of China (no. 31470695) and the 12th Five Years Key Programs for Science and Technology Development of China (no. 2013BAD01B07).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The authors declare that the experiments comply with the current laws of China.

Supplementary material

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  1. Bostein D, White RL, Sholnick M, David RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet 32:314–331Google Scholar
  2. Bouck A, Vision T (2007) The molecular ecologist’s guide to expressed sequence tags. Mol Ecol 16:907–924CrossRefGoogle Scholar
  3. Cai M, Meng R, Pan HT, Gao YK, Sun M, Song P, Wang XF, Zhang QX (2010) Isolation and characterization of microsatellite markers from Lagerstroemia caudata (Lythraceae) and cross-amplification in other related species. Conserv Genet Resour 2:89–91CrossRefGoogle Scholar
  4. Cai M, Pan HT, Wang XF, He D, Wang XY, Wang XJ, Zhang QX (2011) Development of novel microsatellites in Lagerstroemia indica and DNA fingerprinting in Chinese Lagerstroemia cultivars. Sci Hortic 131:88–94CrossRefGoogle Scholar
  5. Cheng YL, Yang Y, Wang ZY, Qi BY, Yin YL, Li HG (2015) Development and characterization of EST-SSR markers in Taxodium ‘zhongshansa’. Plant Mol Biol Rep 33:1804–1814CrossRefGoogle Scholar
  6. Deng TX, Pang CY, Lu XR, Zhu P, Duan AQ, Tan ZZ, Huang J, Li H, Chen MT, Liang XW (2016) De novo transcriptome assembly of the Chinese swamp buffalo by RNA sequencing and SSR marker discovery. PLoS One 11(1):e0147132CrossRefGoogle Scholar
  7. Furtado CX, Srisuko M (1969) A revision of Lagerstroemia (Lythraceae). Garden Bull 24:185–334Google Scholar
  8. Graham SA, Hall J, Sytsma K, Shi S (2005) Phylogenetic analysis of the Lythraceae based on four gene regions and morphology. Int J Plant Sci 166:995–1017CrossRefGoogle Scholar
  9. He D, Liu Y, Cai M, Pan HT, Zhang QX (2014) The first genetic linkage map of crape myrtle (Lagerstroemia) based on amplification fragment length polymorphisms and simple sequence repeats markers. Plant Breed 133:138–144CrossRefGoogle Scholar
  10. Jayakumar KS, Sajan JS, Aswati Nair R, Padmesh Pillai P, Deepu S, Padmaja R, Agarwal A, Pandurangan AG (2014) Corosolic acid content and SSR markers in Lagerstroemia speciosa (L.) Pers.: a comparative analysis among populations across the Southern Western Ghats of India. Phytochemistry 106:94–103CrossRefGoogle Scholar
  11. Knox GW (1992) University of Florida/IFAS Extension.
  12. Liu Y, He D, Cai M, Tang W, Li XY, Pan HT, Zhang QX (2013) Development of microsatellite markers for Lagerstroemia indica (Lythraceae) and related species. Appl Plant Sci 1:1200203CrossRefGoogle Scholar
  13. Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 11:180. CrossRefPubMedPubMedCentralGoogle Scholar
  14. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic sofware for teaching and research-an update. Bioinformatics 28:2537–2539CrossRefGoogle Scholar
  15. Pooler M, Dix RL (1999) ‘Chickasaw’, ‘Kiowa’, and ‘Pocomoke’ Lagerstroemia. HortScience 34:361–363CrossRefGoogle Scholar
  16. Pounders C, Rinehart T, Sakhanokho H (2007a) Evaluation of interspecific hybrids between Lagerstroemia indica and L. speciosa. HortScience 42:53–68Google Scholar
  17. Pounders C, Rinehart T, Edwards N, Knight P (2007b) An analysis of combining ability for height, leaf out, bloom data, and flower color for crapemyrtle. HortScience 42:1496–1499CrossRefGoogle Scholar
  18. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55CrossRefGoogle Scholar
  19. Wang XW, Dean D, Wadl PA, Hadziabdic D, Scheffler B, Rinehart T, Cabrera R, Trigiano R (2010) Development of microsatellite markers from crape myrtle (Lagerstroemia L.). HortScience 45:842–844CrossRefGoogle Scholar
  20. Wang XW, Wadl PA, Pounders C, Trigiano RN, Cabrera RI, Scheffler BE, Pooler M, Rinehart TA (2011) Evaluation of genetic diversity and pedigree within crapemyrtle cultivars using simple sequence repeat markers. J Am Soc Hort Sci 136:116–128CrossRefGoogle Scholar
  21. Wang XJ, Wang XF, Cai M, He D, Pan HT, Zhang QX (2012) In vitro chromosome doubling and tetraploid identification in Lagerstroemia indica. J Food Agric Environ 10:1364–1367Google Scholar
  22. Wang J, Dai XG, Chen YP, Yang Y, Zhang XZ, Li SH, Yin T (2015) Genomic sequencing using 454 pyrosequencing and development of an SSR primer database for Lagerstroemia indica L. Plant Omics J 8:17–23Google Scholar
  23. Wu J, Cai CF, Cheng FY, Cui HL, Zhou H (2014) Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences. Mol Breed 34:1853–1866CrossRefGoogle Scholar
  24. Xu CQ, Gao J, Du ZF, Li DK, Wang Z, Li YY, Pang XM (2016) Identification the genetic diversity, genetic structure and a core collection of Ziziphus jujuba Mill. var. jujuba accessions using microsatellite markers. Sci Rep 6:31503CrossRefGoogle Scholar
  25. Ye YJ, Liu Y, Cai M, He D, Shen JS, Ju YQ, Bian XM, Pan HT, Zhang QX (2015) Screening of molecular markers linked to dwarf trait in crape myrtle by bulked segregant analysis. Genet Mol Res 14:4369–4380CrossRefGoogle Scholar
  26. Ye YJ, Cai M, Ju YQ, Jiao Y, Feng L, Pan HT, Cheng TR, Zhang QX (2016) Identification and validation of SNP markers linked to dwarf traits using SLAF-Seq technology in Lagerstroemia. PLoS One 11:e0158970CrossRefGoogle Scholar
  27. Yeh FC, Yang RC, Boyle T (1999) POPGENE Version 1.32 Microsoft Windows-based freeware for population genetic analysis. University of Alberta and the Center for International Forestry ResearchGoogle Scholar
  28. You YN, Liu DC, Liu HB, Zheng XF, Diao Y, Huang XF, Hu ZL (2015) Development and characterisation of EST-SSR markers by transcriptome sequencing in taro (Colocasia esculenta (L.) Schoot). Mol Breed 35:134CrossRefGoogle Scholar
  29. Zhang ZY, Wang P, Li Y, Ma LL, Li LF, Yang RT, Ma YZ, Wang SA, Wang Q (2014) Global transcriptome analysis and identification of the flowering regulatory genes expressed in leaves of Lagerstroemia indica. DNA Cell Biol 33:680–688CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Yuanjun Ye
    • 1
  • Lu Feng
    • 1
  • Xiaohan Liang
    • 1
  • Tingting Liu
    • 1
  • Ming Cai
    • 1
  • Tangren Cheng
    • 1
  • Jia Wang
    • 1
  • Qixiang Zhang
    • 1
  • Huitang Pan
    • 1
    Email author
  1. 1.Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education and College of Landscape ArchitectureBeijing Forestry UniversityBeijingChina

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