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Soybean cyst nematode resistance in soybean is independent of the Rhg4 locus LRR-RLK gene

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Abstract

To test the function of candidate genes in soybean for resistance to the soybean cyst nematode (SCN), a large collection of EMS-mutants from the SCN-resistant soybean cultivar “Forrest” was developed for Targeting Induced Local Lesions IN Genomes (TILLING). Additionally, due to the complexity of the soybean genome, an integrated set of genomic and genetic analysis tools was employed to complement the TILLING approach. The efficiency of this integrated set of tools was tested using a candidate soybean gene for resistance to SCN, encoding a leucine-rich repeat receptor-like kinase (LRR-RLK) that was identified by map-based cloning at the Rhg4 locus. The Rhg4 locus is one of the major quantitative trait loci controlling soybean resistance against SCN race 3 (HG type 0) in cv. Forrest, but the gene(s) sequence for resistance remains to be determined. Using TILLING, a Forrest mutant containing a nonsense mutation in the LRR domain of the candidate resistance protein was identified and confirmed; however, the SCN-resistant phenotype of the mutant was not altered. Haplotyping and EcoTILLING of recombinant inbred lines along with complementation analysis corroborated the TILLING result and ruled out the possibility of functional redundancy by a second copy of the LRR-RLK gene identified in the soybean genome. This study validates the use of TILLING, in combination with an integrated set of genomic tools, as an efficient means of testing candidate genes for SCN resistance in soybean.

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Acknowledgments

We would like to thank Dr. David Sleper for bulking the soybean seed used in this project. Special thanks to Dr O. Myers and P. Gibson and the SIU breeding team for providing the original ExF RIL population. We are also grateful to Bob Heinz for assistance with SCN phenotyping and SCN culture maintenance during this project. Funding for this work was provided by the United Soybean Board project #0253, a grant from the Illinois-Missouri Biotechnology Alliance to Melissa G. Mitchum and Khalid Meksem, and grant #2006-03573 from the USDA-NRI Plant Genome Program to Khalid Meksem.

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Authors and Affiliations

  1. Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA

    Xiaohong Liu & Melissa G. Mitchum

  2. Plants and Microbes Genomics and Genetics Lab, Department of Plant Soil and Agricultural Systems, Southern Illinois University at Carbondale, Room 176, Carbondale, IL, 62901-4415, USA

    Shiming Liu, Aziz Jamai & Khalid Meksem

  3. Unité de Recherche en Génomique Végétale, UMR INRA-CNRS, Rue Gaston Crémieux, 91057, Evry Cedex, France

    Abdelhafid Bendahmane

  4. Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, 11451, Saudi Arabia

    Abdelhafid Bendahmane

  5. Center for Excellence, The Illinois Soybean Center, Southern Illinois University at Carbondale, Room 113, Forestry Bldg 66, 1231 Lincoln Drive, Carbondale, IL, 62901, USA

    David A. Lightfoot

Authors
  1. Xiaohong Liu
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  2. Shiming Liu
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  3. Aziz Jamai
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  4. Abdelhafid Bendahmane
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  5. David A. Lightfoot
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  6. Melissa G. Mitchum
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  7. Khalid Meksem
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Corresponding author

Correspondence to Khalid Meksem.

Additional information

Xiaohong Liu and Shiming Liu contributed equally to this work.

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Table S1

EcoTILLING of the EXF RILs population using the LRR-kinase sequences at each, the Rhg1 locus (Rhg1 allele) and the Rhg4 locus (Rhg4 allele) and the corresponding SCN phenotype of each line. RIL recombinant inbred line of EXF population, E allele from Essex, F allele from Forrest, R resistant, S susceptible (DOC 16 kb)

Fig. S1

(PPT 109 kb)

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Liu, X., Liu, S., Jamai, A. et al. Soybean cyst nematode resistance in soybean is independent of the Rhg4 locus LRR-RLK gene. Funct Integr Genomics 11, 539–549 (2011). https://doi.org/10.1007/s10142-011-0225-4

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