Molecular Breeding

, 35:204 | Cite as

Large-scale development of expressed sequence tag-derived simple sequence repeat markers by deep transcriptome sequencing in garlic (Allium sativum L.)

  • Touming Liu
  • Liangbin Zeng
  • Siyuan Zhu
  • Xiaojun Chen
  • Qingming Tang
  • Shiyong Mei
  • Shouwei Tang


Garlic (Allium sativum L.) is an economically important crop and has significant value as a food, spice, and medicine. The lack of simple sequence repeat (SSR) markers is a major obstacle in genetic studies of garlic. In order to develop SSR markers on a large scale, we performed transcriptome analysis using Illumina pair-end sequencing. Approximately 69.7 million clean sequence reads were generated, and these reads were eventually assembled into 135,360 unigenes. Of these, 56,953 (42.1 %) unigenes were annotated for their function. Examination of SSR loci in these 135,360 ESTs identified 2446 SSRs. Because 940 of the loci were located on the end of the EST, only the residual 1506 SSRs were flanked by designing primer pairs complementary to regions, and these regions were designated as SSR markers. Within these markers, the trinucleotide repeat motif was the most abundant type (66.1 %), with the AGA/TCT and GAA/TTC motifs occurring most frequently. Using 200 randomly selected EST-SSRs, 194 markers were successfully amplified in garlic and 155–186 SSRs in five other Allium species. This suggests that the markers were good quality and had high cross-species transferability. The EST-SSRs developed in this study represent the first large-scale development of SSR markers for garlic. These SSRs could be used for the development of genetic and physical maps, quantitative trait loci mapping, genetic diversity studies, association mapping, and cultivar fingerprinting.


Garlic Transcriptome Illumina sequencing SSR marker Transferability 



We kindly thank the Novogene Bioinformatics Institute for its assistance in original data processing and related bioinformatics analysis. This work was supported by grants from The Agricultural Science and Technology Innovation Program (ASTIP) and National Modern Agro-industry Technology Research System.

Supplementary material

11032_2015_399_MOESM1_ESM.xls (370 kb)
Table S1 The primer sequences of 1506 garlic SSR markers (XLS 369 kb)
11032_2015_399_MOESM2_ESM.xls (39 kb)
Table S2 The summary of 200 SSRs amplification in 6 Allium species (XLS 39 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Touming Liu
    • 1
  • Liangbin Zeng
    • 1
  • Siyuan Zhu
    • 1
  • Xiaojun Chen
    • 1
  • Qingming Tang
    • 1
  • Shiyong Mei
    • 1
  • Shouwei Tang
    • 1
  1. 1.Institute of Bast Fiber Crops and Center of Southern Economic CropsChinese Academy of Agricultural SciencesChangshaChina

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