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Polymorphisms of soybean isoflavone synthase and flavanone 3-hydroxylase genes are associated with soybean mosaic virus resistance

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Abstract

Soybean mosaic disease, caused by soybean mosaic virus (SMV), is one of the most devastating diseases that limit soybean production throughout the world. Soybean isoflavone synthase (IFS) and flavanone 3-hydroxylase (F3H) genes catalyze the production of isoflavones and flavonoids, the increase of which is correlated with increased disease resistance. We have cloned, sequenced, and analyzed the IFS1, IFS2 and F3H genomic regions from 33 Chinese soybean accessions including 16 Glycine soja and 17 Glycine max. High nucleotide diversity and low extent of linkage disequilibrium (LD) in these three genes provided sufficient genetic resolution for association mapping. As a result, a set of single nucleotide polymorphisms (SNPs) with significant (P < 0.05) association to SMV strain SC-3 and SC-7 resistance were discovered in these genes. Among them, the SNP haplotype ‘TCACAACGA-TACA’ in IFS1 gene was found to be extremely significantly (P < 0.01) associated with SMV SC-3 resistance. After 7 days of SC-3 inoculation, the expression level of IFS1 gene in the two SC-3 resistance accessions that have this significant site continued to increased and reach to 30–160 folds high, while in the SC-3 susceptible accession which does not carry the significant site the expression level decreased to near zero. These polymorphisms were corresponding to the trait variance and thus can be considered as the candidate sites for functional molecular markers for future SMV resistance breeding.

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Acknowledgments

We thank Drs. Zhiwu Zhang and Ed Buckler of Cornell University for their advice on association analysis and help on TASSEL software. We also thank two anonymous reviewers for their critical comments and helpful discussions. This work was funded in part by National 973 Project (No. 2004CB117206), National 863 Projects (No. 2006AA10Z1C1, No. 2006AA10A111), and National Natural Science Foundation of China (No. 30771362).

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Authors and Affiliations

  1. National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China

    Hao Cheng, Hua Yang, Dan Zhang, Junyi Gai & Deyue Yu

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  1. Hao Cheng
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  2. Hua Yang
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  3. Dan Zhang
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  4. Junyi Gai
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  5. Deyue Yu
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Correspondence to Deyue Yu.

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The authors Hao Cheng and Hua Yang contributed equally to this paper.

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Cheng, H., Yang, H., Zhang, D. et al. Polymorphisms of soybean isoflavone synthase and flavanone 3-hydroxylase genes are associated with soybean mosaic virus resistance. Mol Breeding 25, 13–24 (2010). https://doi.org/10.1007/s11032-009-9305-8

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