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Targeted comparative genome analysis and qualitative mapping of a major partial-resistance gene to the soybean cyst nematode

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Abstract

A major partial-resistance locus to the soybean cyst nematode (Heterodera glycines Ichinohe; SCN) was identified on linkage group ‘G’ of soybean [Glycine max (L.) Merr.] using restriction fragment length polymorphisms (RFLPs). This locus explained 51.4% (LOD=10.35) of the total phenotypic variation in disease response in soybean Plant Introduction (PI) 209332, 52.7% (LOD=15.58) in PI 90763, 40.0% (LOD=10.50) in PI 88788, and 28.1% (LOD=6.94) in ‘Peking’. Initially, the region around this major resistance locus was poorly populated with DNA markers. To increase marker density in this genomic region, first random, and later targeted, comparative mapping with RFLPs from mungbean [Vigna radiata (L.) R. Wilcz.] and common bean (Phaseolus vulgaris L.) was performed, eventually leading to one RFLP marker every 2.6 centimorgans (cM). Even with this marker density, the inability to resolve SCN disease response into discrete Mendelian categories posed a major limitation to mapping. Thus, qualitative scoring of SCN disease response was carried out in an F5∶6 recombinant inbred population derived from ‘Evans’xPI 209332 using a 30% disease index cut-off for resistance. Using the computer program JoinMap, an integrated map of the region of interest was created, placing the SCN resistance locus 4.6 cM from RFLP marker B53 and 2.8 cM from Bng30. This study demonstrates how a combination of molecularmapping strategies, including comparative genome analysis, join mapping, and qualitative scoring of a quantitative trait, potentially provide the necessary tools for high-resolution mapping around a quantitative-trait locus.

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References

  • Arumuganathan K, Earle E (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218

    CAS  Google Scholar 

  • Anand SC, Brar GS (1983) Response of soybean lines to differently selected cultures of soybean cyst nematode Heterodera glycines Ichinohe. J Nematol 15:120–123

    Google Scholar 

  • Anand SC, Gallo KM (1984) Identification of additional soybean germ plasm with resistance to race 3 of the soybean cyst nematode. Plant Dis 68:593–595

    Google Scholar 

  • Anand SC, Wrather JA, Shumway CR (1985) Soybean genotypes with resistance to races of the soybean cyst nematode. Crop Sci 25:1073–1075

    Google Scholar 

  • Bonierbale MW, Plaisted RL, Tanskley SD (1988) RFLP maps based on common sets of clones reveal modes of chromosome evolution in potato and tomato. Genetics 120:1095–1103

    Google Scholar 

  • Boutin S, Ansari H, Concibido V, Denny R, Orf J, Young N (1992) RFLP analysis of cyst nematode resistance in soybeans. Soybean Genet Newslett 19:123–127

    Google Scholar 

  • Boutin S, Young N, Yu ZH, Shoemaker R, Vallejos CE (1995) Genome conservation among three legume genera detected with DNA markers. Genome 38:928–937

    CAS  Google Scholar 

  • Chase CD, Ortega VM, Vallejos CE (1990) DNA restriction fragment length polymorphisms correlate with isozyme diversity in Phaseolus vulgaris L. Theor Appl Genet 81:806–811

    Google Scholar 

  • Concibido VC (1995) Identification and characterization of SCN resistance genes using DNA markers. PhD thesis, University of Minnesota

  • Concibido VC, Denny RL, Boutin SR, Hautea R, Orf JH, Young ND (1994) DNA marker analysis of loci underlying resistance to soybean cyst nematode (Heterodera glycines Ichinohe). Crop Sci 34:240–246

    Google Scholar 

  • Concibido VC, Denny R, Lange D, Danesh D, Orf J, Young N (1995) The soybean cyst nematode resistance gene on linkage group ‘G’ is common among sources of resistance. Soybean Genet Newslett 22:269–272

    Google Scholar 

  • Danesh D, Aarons S, McGill GE, Young ND (1994) Genetic dissection of oligogenic resistance to bacterial wilt in tomato. Mol Plant-Microbe Interact 7:464–471

    Google Scholar 

  • Danesh D, Young N, Concibido V, Orf J (1995) Physical mapping of DNA markers near a major soybean cyst nematode resistance locus. Soybean Genet Newslett 22:273–277

    Google Scholar 

  • Dellaporta SL, Wood I, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 5:19–21

    Google Scholar 

  • DeScenzo RA, Wise RP, Mahadevappa M (1994) High-resolution mapping of the Hor1/Mla/Hor2 region on chromosome 5S in barley. Mol Plant-Microbe Interact 7:657–666

    Google Scholar 

  • Doebley J, Stec A (1991) Genetic analysis of the morphological differences between maize and teosinte. Genetics 129: 285–295

    CAS  PubMed  Google Scholar 

  • Fatokun CA, Menancio-Hautea DI, Danesh D, Young ND (1992) Evidence for orthologous seed-weight genes in cowpea and mungbean based on RFLP mapping. Genetics 132:841–846

    Google Scholar 

  • Feinberg AP, Vogelstein B (1983) A technique for radiolabeling DNA restriction fragments to high specific activity. Anal Biochem 132:9

    Google Scholar 

  • Ferreira AR, Clayton K, Webb DM, Keim P (1994) Multiple locus RFLP-designed bulk segregant analysis of a soybean cyst nematode resistance QTL. In: Heller SR, Gale MD, Miksche JP, Takayanagi K (eds) Plant genome III. Scherago International, San Diego, Calif., p 28

    Google Scholar 

  • Geiger HH, Heun M (1989) Genetics of quantitative resistance to fungal diseases. Annu Rev Phytopathol 27:317–341

    Google Scholar 

  • Golden AM, Epps JM, Riggs RD, Duclos LA, Fox JA, Bernard RL (1970) Terminology and identity of infraspecific forms of the soybean cyst nematode (Heterodera glycines). Plant Dis Rep 54:544–546

    Google Scholar 

  • Hartwig EE (1985) Breeding productive soybeans with resistance to soybean cyst nematode. In: Shibles RA (ed). World Soybean Res.Conf. III. Westview Press, Boulder, Colo., pp. 394–399

    Google Scholar 

  • Hauge BM, Hanley SM, Cartinhour S, Cherry JM, Goodman HM, Koorneef M, Stam P, Chang C, Kempin S, Medrano L, Meyerwitz EM (1993) An integrated genetic/RFLP map of the Arabidopsis thaliana genome. Plant Jour 3:745–754

    Google Scholar 

  • Helentjaris T (1993) Implications for conserved genomic structure among plant species. Proc Natl Acad Sci USA 90:353–363

    Google Scholar 

  • Islam MR, Shepherd KW (1991) Analyses of phenotypes of recombinants and revertants from test cross progenies involving genes at the L group, conferring resistance to rust in flax. Heriditas 114:125–129

    Google Scholar 

  • Keim P, Shoemaker RC, Palmer RG (1989) Restriction fragment length polymorphism diversity in soybean. Theor Appl Genet 77:786–792

    Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12: 172–175

    Google Scholar 

  • Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199

    CAS  PubMed  Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE (1987) Mapmaker: an interactive computer package for constructing genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    CAS  PubMed  Google Scholar 

  • Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, Spirey R, Wu T, Earle ED, Tanksley SD (1993) Map-based cloning of a protein kinase gene conferring resistance in tomato. Science 262: 1432–1435

    CAS  PubMed  Google Scholar 

  • Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA. 88:9828–9832

    CAS  PubMed  Google Scholar 

  • Menancio-Hautea D, Kumar L, Danesh D, Young ND (1993) A genome map for mungbean [Vigna radiata (L.) Wilczek] based on DNA genetic markers (2N=2X=22). In: O'Brien SJ (ed) Genetic maps: locus maps of complex genomes. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp 6.259–6.261

    Google Scholar 

  • Nodari RO, Tsai SM, Gilbertson RL, Gepts P (1993) Toward an integrated linkage map of common bean. 2. Development of an RFLP-based linkage map. Theor Appl Genet 85:513–520

    Google Scholar 

  • Paran I, Kesseli R, Michelmore R (1991) Identification of restriction fragment length polymorphism and random amplified polymorphic DNA markers linked to downey mildew resistance genes in lettuce, using near-isogenic lines. Genome 34:1021–1027

    Google Scholar 

  • Paterson AH, Lander ES, Hewitt JD, Paterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorpisms. Nature 335:721–726

    Article  CAS  PubMed  Google Scholar 

  • Paterson AH, DeVerna JW, Lanini B, Tanksley SD (1990) Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics 124:735–742

    Google Scholar 

  • Paterson A, Damon S, Hewitt JD, Zamir D, Rabinowitch HD, Lincoln SE, Lander ES, Tanksley SD (1991) Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics 127:181–197

    Google Scholar 

  • Pereira MG, Lee M, Bramel-Cox P, Woodman W, Doebley J, Whitkus R (1994) Construction of an RFLP map in sorghum and comparative mapping in maize. Genome 37:236–243

    Google Scholar 

  • Phillips RL, Kim TS, Kaeppler SM, Parentoni SN, Shaver DL, Stucker RE, Openshaw SJ (1993) Genetic dissection of maturity using RFLPs. In: Proc 47th Annu Corn Sorghum Ind Res Conf. American Seed Trade Association, Chicago Ill. pp 135–150

  • Saiki RK, Gelfand DH, Stoffel S, Scharf S, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491

    CAS  PubMed  Google Scholar 

  • Schmitt DP, Shannon G (1992) Differentiating soybean to Heterodera glycines races. Crop Sci 32:275–277

    Google Scholar 

  • Shoemaker RC, Olson TC (1993) Molecular linkage map of soybean (Glycine max L. Merr.) In: O'Brien SJ (ed) Genetic maps: locus maps of complex genomes. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp 6.131–6.138

    Google Scholar 

  • Shoemaker RC, Specht JE (1995) Integration of the soybean molecular and classical genetic linkage groups. Crop Sci 35:436–446

    Google Scholar 

  • Song KM, Osborn TC, Williams PH (1990) Brassica taxonomy based on nuclear RFLPs. 3. Genome relationships in Brassica and related genera and the orgin of B. oleracea and B. rapa (syn. campestris). Theor Appl Genet 79:9

    Google Scholar 

  • Southern E (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503–517

    CAS  PubMed  Google Scholar 

  • Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant Jour 3:739–744

    Google Scholar 

  • Sudupak MA,Bennetzen JL, Hulbert SH (1993) Unequal exchange and meiotic instability of disease resistance genes in the Rp1 region of maize. Genetics 132:119–125

    Google Scholar 

  • Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205–233

    Article  CAS  PubMed  Google Scholar 

  • Tanksley SD, Bernatzky R, Lapitan NL, Prince JP (1988) Conservation of gene repertoire but not gene order in pepper and tomato. Proc Natl Acad Sci USA 85:6419–6423

    CAS  Google Scholar 

  • Tanksley SD, Ganal MW, Martin GB (1995) Chromosome landing: a paradigm for map-based gene cloning in plants with large genomes. Trends Genet 11 63–68

    Google Scholar 

  • Vallejos CE, Sakiyama NS, Chase CD (1992) A molecular markerbased linkage map of Phaseolus vulgaris L. Genetics 131:733–740

    Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    CAS  PubMed  Google Scholar 

  • Webb DE, Baltazar BM, Rao Arelli AO, Schupp J, Clayton K, Keim P, Beavis WD (1995) Genetic mapping of soybean cyst-nematode race-3 resistance loci in the soybean PI-437.654. Theor Appl Genet 91:74–581

    Google Scholar 

  • Weeden NF, Muehlbauer FJ, Ladizinsky G (1992) Extensive conservation of linkage relationships between pea and lentil genetic maps. J Hered 83:123–29

    Google Scholar 

  • Williams J, Kubelik A, Livak K, Rafalski J, Tingey S (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535

    CAS  PubMed  Google Scholar 

  • Young ND, Kumar L, Menancio-Hautea D, Danesh D, Talekar NS, Shanmugasundarum S, Kim DH (1992) RFLP mapping of a major bruchid resistance gene in mungbean (Vigna radiata L. Wilczek). Theor Appl Genet 84:839–844

    Google Scholar 

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Authors and Affiliations

  1. Department of Plant Pathology, 495 Borlaug Hall, University of Minnesota, 55108, St. Paul, MN, USA

    V. C. Concibido, N. D. Young, D. A. Lange, R. L. Denny & D. Danesh

  2. Department of Agronomy and Plant Genetics, 411 Borlaug Hall, University of Minnesota, 55108, St. Paul, MN, USA

    J. H. Orf

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  1. V. C. Concibido
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  2. N. D. Young
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  3. D. A. Lange
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  4. R. L. Denny
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  5. D. Danesh
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  6. J. H. Orf
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Communicated by G. Wenzel

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Concibido, V.C., Young, N.D., Lange, D.A. et al. Targeted comparative genome analysis and qualitative mapping of a major partial-resistance gene to the soybean cyst nematode. Theoret. Appl. Genetics 93, 234–241 (1996). https://doi.org/10.1007/BF00225751

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  • DOI: https://doi.org/10.1007/BF00225751

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