Theoretical and Applied Genetics

, Volume 121, Issue 1, pp 1–8 | Cite as

Genome-wide identification of intron fragment insertion mutations and their potential use as SCAR molecular markers in the soybean

  • Yongjun Shu
  • Yong Li
  • Yanming Zhu
  • Zhenlei Zhu
  • Dekang Lv
  • Xi Bai
  • Hua Cai
  • Wei Ji
  • Dianjing Guo
Original Paper


Introns often have a high probability of mutation as a result of DNA insertions and deletions (indels). In this study, 503 introns with exon-derived insertions were identified using a comprehensive search of the soybean genome. Of the 375 pairs of PCR primer sets designed for the loci in question, 161 primer sets amplified length polymorphism among nine soybean varieties and were identified as soybean gene-intron-driven functional sequence characterized amplified region (SCAR) markers. These SCAR markers are distributed among all 20 of the soybean chromosomes, and they developed from numerous genes involved in various physiological and biochemical processes that influence important agronomic traits of the soybean. The development of these novel gene-driven functional SCAR markers was fast and cost effective, and their use will facilitate molecular-assisted breeding of the soybean.


Wild Soybean Soybean Genome Sequence Characterize Amplify Region Marker Soybean Cyst Nematode Soybean Variety 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The soybean genome sequence data were produced by the US Department of Energy Joint Genome Institute ( in collaboration with the user community, and we would thank to them. The project was supported by the National “863” Program (2006AA100104, 2008AA10Z153), the National Transgenic Research Project (2008ZX08004), the Key Research Plan of Heilongjiang Province (GA06B103), and the Innovation Research Group of NEAU (CXT004).

Supplementary material

122_2010_1285_MOESM1_ESM.xls (32 kb)
Supplementary material 1 (XLS 32 kb)
122_2010_1285_MOESM2_ESM.xls (14 kb)
Supplementary material 2 (XLS 13 kb)


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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Yongjun Shu
    • 1
  • Yong Li
    • 1
  • Yanming Zhu
    • 1
  • Zhenlei Zhu
    • 1
  • Dekang Lv
    • 1
  • Xi Bai
    • 1
  • Hua Cai
    • 1
  • Wei Ji
    • 1
  • Dianjing Guo
    • 2
  1. 1.College of Life ScienceNortheast Agricultural UniversityHarbinPeople’s Republic of China
  2. 2.State Key Laboratory of Agrobiotechnology, Department of BiologyThe Chinese University of Hong KongShatin, N.T.Hong Kong

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