Plant Molecular Biology Reporter

, Volume 28, Issue 4, pp 646–653

Development of Juglans Regia SSR Markers by Data Mining of the EST Database

  • Rui Zhang
  • AnDan Zhu
  • XinJian Wang
  • Jun Yu
  • HongRong Zhang
  • JiangSheng Gao
  • YunJiang Cheng
  • XiuXin Deng
Article

DOI: 10.1007/s11105-010-0192-2

Cite this article as:
Zhang, R., Zhu, A., Wang, X. et al. Plant Mol Biol Rep (2010) 28: 646. doi:10.1007/s11105-010-0192-2
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Abstract

Walnut (Juglans regia), an economically important woody plant, is widely cultivated in temperate regions for its timber and nutritional fruits. Despite abundant studies in germplasm, systemic molecular evaluations of walnut are sparsely reported mainly due to the limited molecular markers available. Expressed sequence tags (EST) provide a valuable resource for developing simple sequence repeat (SSR) markers. In this study, a total of 5,025 walnut ESTs (covering 16.41 Mb) were retrieved from the National Center for Biotechnology Information database. The SSR motifs were then analyzed by the SSRHunter software. In total, 398 SSRs were obtained with an average frequency of 1/4.08 kb. Dinucleotide (di-) repeat motifs accounted for 69.85% of all SSRs, followed by trinucleotide (tri-) with a frequency of 27.64%, while low frequency (2.51%) of tetranucleotide (tetra-) to hexanucleotide (hexa-) was observed. Meanwhile, GCA and TC motifs were prevalent among di- and tri- loci, respectively. Subsequently, a total of 123 primer pairs were designed from the non-redundant SSR-containing unigenes with the selection threshold of SSR length set to 10 bp or more. To examine the efficiency of candidate markers, seven DNA pools were collected from geographically different accessions. Results demonstrated that 41 SSR primer sets could generate high polymorphic amplification products (33.3%), and these polymorphic loci were mainly located in the 3′-untranslated region. Annotation analysis revealed that only two of these 41 loci were located inside open reading frames of characterized proteins (E ≤ 1E−30).

Keywords

Juglans regia EST data mining SSR primer EST data analysis Primer design 

Supplementary material

11105_2010_192_MOESM1_ESM.doc (104 kb)
Supplemental Table 1Polymorphic EST-SSR primer pairs for Juglans regia (DOC 104 kb)

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Rui Zhang
    • 1
    • 2
    • 3
  • AnDan Zhu
    • 2
    • 3
  • XinJian Wang
    • 1
  • Jun Yu
    • 1
  • HongRong Zhang
    • 3
  • JiangSheng Gao
    • 1
  • YunJiang Cheng
    • 2
    • 3
  • XiuXin Deng
    • 2
    • 3
  1. 1.Biological Technology Research & Development CenterTarim UniversityAlaerPeople’s Republic of China
  2. 2.National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanPeople’s Republic of China
  3. 3.College of Horticulture and Forestry ScienceHuazhong Agricultural UniversityWuhanPeople’s Republic of China

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