Molecular Breeding

, Volume 24, Issue 1, pp 63–76 | Cite as

Development of SNP markers and haplotype analysis of the candidate gene for rhg1, which confers resistance to soybean cyst nematode in soybean

  • Ying-Hui Li
  • Chen Zhang
  • Zhong-Shan Gao
  • Marinus Johannes Maria Smulders
  • Zulu Ma
  • Zhang-Xiong Liu
  • Hai-Yang Nan
  • Ru-Zhen Chang
  • Li-Juan Qiu


Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) is one of the most destructive pests in the cultivation of soybean (Glycine max (L.) Merr.) worldwide. Markers based on the SCN resistance gene will enable efficient marker-assisted selection (MAS). We sequenced the candidate gene rhg1 in six resistant and two susceptible soybean genotypes and identified 37 SNPs (single nucleotide polymorphisms) among the sequences, of which 11 were in the coding region. Seven of these 11 SNPs led to changes in the amino acid sequence of the gene. The amino acid sequence we obtained differs from the previously published one by a stretch of 26–27 amino acids. Six codominant allele-specific SNP markers based on agarose gel detection were developed and tested in 70 genotypes, among which occurred only nine different haplotypes. Two neutrality tests (Tajima’s D and Fu and Li’s F) were significant for the six SNP loci in the 70 genotypes, which is consistent with intensive directional selection. A strong LD pattern was detected among five SNPs except 2868T > C. Two SNPs (689C > A and 757C > T) formed one haplotype (689C-757C) that was perfectly associated with SCN resistance. The new allele-specific PCR markers located in the alleged sequence of the rhg1 candidate gene, combined with the microsatellite marker BACR-Satt309, will significantly improve the efficiency of MAS during the development of SCN-resistant cultivars.


Haplotype SCN SNP marker Soybean 



Agarose gel-based co-dominant allele-specific


Agarose gel-based dominant allele-specific


Linkage disequilibrium


Leucine-rich repeats


Marker-assisted breeding


Quantitative trait nucleotide


Receptor-like kinase


Sequence-tagged sites


Serine threonine kinase domain


Trans-membrane domain


Untranslated region



This research was supported by the State High-tech (863) (nos. 2006AA10A110, 2006AA10Z164, 2006AA10A111), the National Natural Science Foundation of China (nos. 30490251 and 30471096), the National Key Technologies R&D Program in the 11th Five-Year Plan (no. 2006BAD13B05), the State Key Basic Research and Development Plan of China (973) (no. 2004CB117203), and the Academy and Institute Foundation for Basic Scientific Research in Institute of Crop Science, Chinese Academy of Agricultural Sciences. We thank Dr Robert McIntosh for revision and suggestions on the manuscript. We greatly appreciate the revision and good suggestion from reviewers and editors.


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Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Ying-Hui Li
    • 1
  • Chen Zhang
    • 1
  • Zhong-Shan Gao
    • 2
  • Marinus Johannes Maria Smulders
    • 3
  • Zulu Ma
    • 1
    • 4
  • Zhang-Xiong Liu
    • 1
  • Hai-Yang Nan
    • 1
  • Ru-Zhen Chang
    • 1
  • Li-Juan Qiu
    • 1
  1. 1.The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm & Biotechnology (MOA), Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingPeople’s Republic of China
  2. 2.Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality ImprovementZhejiang UniversityHangzhouChina
  3. 3.Plant Research International, Wageningen URWageningenThe Netherlands
  4. 4.BengBu Medical CollegeBengbuPeople’s Republic of China

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