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

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Abstract

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.

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Abbreviations

ACAS:

Agarose gel-based co-dominant allele-specific

ADAS:

Agarose gel-based dominant allele-specific

LD:

Linkage disequilibrium

LRR:

Leucine-rich repeats

MAS:

Marker-assisted breeding

QTNs:

Quantitative trait nucleotide

RLK:

Receptor-like kinase

STSs:

Sequence-tagged sites

STYKc:

Serine threonine kinase domain

TM:

Trans-membrane domain

UTR:

Untranslated region

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Acknowledgments

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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Authors and Affiliations

  1. The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm & Biotechnology (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, People’s Republic of China

    Ying-Hui Li, Chen Zhang, Zulu Ma, Zhang-Xiong Liu, Hai-Yang Nan, Ru-Zhen Chang & Li-Juan Qiu

  2. Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, 310029, Hangzhou, China

    Zhong-Shan Gao

  3. Plant Research International, Wageningen UR, P.O. Box 16, 6700AA, Wageningen, The Netherlands

    Marinus Johannes Maria Smulders

  4. BengBu Medical College, 233000, Bengbu, People’s Republic of China

    Zulu Ma

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  1. Ying-Hui Li
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  2. Chen Zhang
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  9. Li-Juan Qiu
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Correspondence to Li-Juan Qiu.

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Li, YH., Zhang, C., Gao, ZS. et al. Development of SNP markers and haplotype analysis of the candidate gene for rhg1, which confers resistance to soybean cyst nematode in soybean. Mol Breeding 24, 63–76 (2009). https://doi.org/10.1007/s11032-009-9272-0

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