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Effective identification of soybean candidate genes involved in resistance to soybean cyst nematode via direct whole genome re-sequencing of two segregating mutants

Abstract

Key message

Three soybean candidate genes involved in resistance to soybean cyst nematode race 4 were identified via direct whole genome re-sequencing of two segregating mutants.

Abstract

The genes conferring resistance to soybean cyst nematode (SCN) race 4 (Hg type 1.2.3.5.7) in soybean (Glycine max L. Merr.) remains unknown. Next generation sequencing-based methods identify a wide range of targets, it is difficult to identify genes underlying traits. Use of the MutMap and QTL-seq methods to identify trait candidate genes needs backcrossing and is very time-consuming. Here we report a simple method to effectively identify candidate genes involved in resistance to SCN race 4. Two ethane methylsulfonate mutagenized mutants of soybean ‘PI 437654’, whose SCN race 4-infection phenotype altered, were selected. Six relevant whole genomes were re-sequenced, and then calling of genomic variants (SNPs and InDels) was conducted and compared to ‘Williams 82’. The comparison eliminated many genomic variants from the mutant lines that overlapped two non-phenotypic but mutant progeny plants, wild-type PI 437654 and ‘Zhonghuang 13’. Finally, only 27 mutations were found among 10 genes. Of these 10 genes, 3 genes, Glyma.09g054000, Glyma.16g065700 and Glyma.18g192200 were overlapped between two phenotypic mutant progeny plants. Therefore, the three genes may be the candidate genes involved in resistance of PI 437654 to soybean cyst nematode race 4. This method simplifies the effective identification of candidate genes.

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Acknowledgements

This work was financially supported by the Innovation Program and Youth Elite Program of Chinese Academy of Agricultural Sciences and the Special Fund for Agro-scientific Research in the Public Interest of China (201503114). We thank the staff at OE Biotech, China, for sequencing and analyzing the original sequencing data.

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Correspondence to Shiming Liu.

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Liu, S., Ge, F., Huang, W. et al. Effective identification of soybean candidate genes involved in resistance to soybean cyst nematode via direct whole genome re-sequencing of two segregating mutants. Theor Appl Genet 132, 2677–2687 (2019). https://doi.org/10.1007/s00122-019-03381-6

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Keywords

  • Soybean
  • Soybean cyst nematode
  • Chemically mutagenized mutants
  • Whole genome re-sequencing
  • Resistant candidate genes