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Genomic analysis of the rhg1 locus: candidate genes that underlie soybean resistance to the cyst nematode

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An ERRATUM to this article was published on 12 April 2011

Abstract

The rhg1 gene or genes lie at a recessive or co-dominant locus, necessary for resistance to all Hg types of the soybean (Glycine max (L.) Merr.) cyst nematode (Heterodera glycines I.). The aim here was to identify nucleotide changes within a candidate gene found at the rhg1 locus that were capable of altering resistance to Hg types 0 (race 3). A 1.5 ± 0.25 cM region of chromosome 18 (linkage group G) was shown to encompass rhg1 using recombination events from four near isogenic line populations and nine DNA markers. The DNA markers anchored two bacterial artificial chromosome (BAC) clones 21d9 and 73p6. A single receptor like kinase (RLK; leucine rich repeat-transmembrane-protein kinase) candidate resistance gene was amplified from both BACs using redundant primers. The DNA sequence showed nine alleles of the RLK at Rhg1 in the soybean germplasm. Markers designed to detect alleles showed perfect association between allele 1 and resistance to soybean cyst nematode Hg types 0 in three segregating populations, fifteen additional selected recombination events and twenty-two Plant Introductions. A quantitative trait nucleotide in the RLK at rhg1 was inferred that alters A47 to V47 in the context of H297 rather than N297. Contiguous DNA sequence of 315 kbp of chromosome 18 (about 2 cM) contained additional gene candidates that may modulate resistance to other Hg-types including a variant laccase, a hydrogen-sodium ion antiport and two proteins of unknown function. A molecular basis for recessive and co-dominant resistance that involves interactions among paralagous disease-resistance genes was inferred that would improve methods for developing new nematode-resistant soybean cultivars.

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Acknowledgments

This research was funded over the past 11 years in part by grants from the NSF 9872635, ISA 95-122-04; 98-122-02 and 02-127-03, and USB 2228-6228. The physical map was based upon work supported by the National Science Foundation under Grant No. 9872635. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation or USDA. The continued support of SIUC, College of Agriculture and Office of the Vice Chancellor for Research to MJI and DAL is appreciated. The authors thank Dr. Q Tao and Dr. H.B. Zhang for their assistance with fingerprinting. The authors thank Dr. P Gibson, O Myers and M Schmidt for their assistance with germplasm development and maintenance from 1991–2000. Thanks are due to Dr. Nevin Young and Dr. Paul Keim and their groups for assistance during the preliminary map development.

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Author notes

  1. E. Ruben

    Present address: National Center for Protein Structure Analysis, Gainesville, FL, 32611, USA

  2. A. Jamai

    Present address: Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA

  3. K. Triwitayakorn

    Present address: Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, Nakhon Pathom, 73170, Thailand

  4. V. N. Njiti

    Present address: Center for Plant Biotechnology and Genomics, Alcorn State University, Alcorn State, MS, 39096-7500, USA

  5. S. Yaegashi

    Present address: University of Tokyo, Tokyo, Japan

  6. P. Arelli

    Present address: USDA, Jackson, TN, 38305, USA

  7. K. Meksem

    Present address: Plants and Microbes Genomics and Genetics Laboratory, Southern Illinois University at Carbondale, Carbondale, IL, 62901, USA

  8. H. Ishihara

    Present address: Center for Biotechnology, Bioinformatics and Genome Research, Bielefeld University, Bielefeld, Germany

Authors and Affiliations

  1. Genomics Core Facility and Center of Excellence in Soybean Research, Teaching and Outreach, Department of Plant, Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL, 62901, USA

    E. Ruben, J. Afzal, V. N. Njiti, K. Triwitayakorn, M. J. Iqbal, S. Yaegashi, R. Bashir, S. Kazi, K. Meksem & D. A. Lightfoot

  2. The Institute for Genomic Research, Rockville, MD, 20850, USA

    C. D. Town

  3. Plants and Microbes Genomics and Genetics Laboratory, Southern Illinois University at Carbondale, Carbondale, IL, 62901, USA

    A. Jamai, H. Ishihara & K. Meksem

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  1. E. Ruben
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Correspondence to D. A. Lightfoot.

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Communicated by K. Shirasu.

An erratum to this article can be found online at http://dx.doi.org/10.1007/s00438-011-0606-3

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Ruben, E., Jamai, A., Afzal, J. et al. Genomic analysis of the rhg1 locus: candidate genes that underlie soybean resistance to the cyst nematode. Mol Genet Genomics 276, 503–516 (2006). https://doi.org/10.1007/s00438-006-0150-8

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