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Genomics of Fungal- and Oomycete-Soybean Interactions

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Genetics and Genomics of Soybean

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References

  • Abdelmajid, K.M., Meksem, K., Wood, A.J., and Lightfoot, D.A. (2007) Loci Underlying SDS and SCN Resistance Mapped in the ‘Essex’ by ‘Forrest’ Soybean Recombinant Inbred Lines. Reviews in Biology and Biotechnology 6, 2–10.

    Google Scholar 

  • Alexander, D., Goodman, R. M., Gut-Rella, M., Glascock, C., Weymann, K., Friedrich, L., Maddox, D., Ahl-Goy, P., Luntz, T., Ward, E., and Ryals, J. (1993) Increased tolerance to two oomycete pathogens in transgenic tobacco expressing pathogenesis-related protein 1a. Proc. Natl. Acad. Sci. USA 90, 7327–7331.

    Article  PubMed  CAS  Google Scholar 

  • Aoki, T., O’Donnell, K., Homma, Y., and Lattanzi, A.R. (2003) Sudden-death syndrome of soybean is caused by two morphologically and phylogenetically distinct species within the Fusarium solani species complex—F. virguliforme in North America and F. tucumaniae in South America. Mycologia 95, 660–684.

    Article  Google Scholar 

  • Arahana, V., Graef, G.L., Specht, J.E., Steadman, J.R., and Eskridge, K.M. (2001) Identification of QTL for Resistance to Sclerotinia sclerotiorum in Soybean. Crop Science 41, 180–188.

    CAS  Google Scholar 

  • Ashfield, T., Bocian, A., Held, D., Henk, A. D., Marek, L. F., Danesh, D., Penuela, S., Meksem, K., Lightfoot, D. A., Young, N. D., Shoemaker, R. C., and Innes, R. W. (2003) Genetic and physical localization of the soybean Rpg1-b disease resistance gene reveals a complex locus containing several tightly linked families of NBS-LRR genes. Mol Plant Microbe Interact 16, 817–826.

    Article  PubMed  CAS  Google Scholar 

  • Bachman, M.S., Tamulonis, J.P., Nickell, C.D., and Bent, A.F. (2001) Molecular Markers Linked to Brown Stem Rot Resistance Genes, Rbs1 and Rbs2, in Soybean. Crop Science 41,527–535.

    CAS  Google Scholar 

  • Bhattacharyya, M. K., Narayanan, N. N., Gao, H., Santra, D. K., Salimath, S. S., Kasuga, T., Liu, Y., Espinosa, B., Ellison, L., Marek, L., Shoemaker, R., Gijzen, M., and Buzzell, R. I. (2005) Identification of a large cluster of coiled coil-nucleotide binding site–leucine rich repeat-type genes from the Rps1 region containing Phytophthora resistance genes in soybean. Theor Appl Genet 111, 75–86.

    Article  PubMed  CAS  Google Scholar 

  • Bhattacharyya, M.K., Sandhu, D., Gao, H., MacMil, S., Wiley, G., Roe, B., and Cannon, S. (2007) Application of 454 Technology (Pyrosequencing) in Transcript Analyses of the Soybean-Phytophthora sojae Interaction. Plant and Animal Genomes XV Conference. San Diego, California. http://www.intl-pag.org/15/abstracts/PAG15_W22_160.html

    Google Scholar 

  • Bhattacharyya, M.K. and Saravanan, R.S. (2007) Phosphoproteomics Of The Soybean-Phytophthora sojae Interaction. Plant and Animal Genomes XV Conference. San Diego, California. http://www.intl-pag.org/15/abstracts/PAG15_W55_353.html

    Google Scholar 

  • Bolton, M. D., Thomma, B., and Nelson, B. D. (2006) Sclerotinia sclerotiorum (Lib.) de Bary: biology and molecular traits of a cosmopolitan pathogen. Molecular Plant Pathology 7,1–16.

    Article  CAS  PubMed  Google Scholar 

  • Bromfield, K. R. (1984) Soybean Rust. American Phytopathological Society, St. Paul, MN.

    Google Scholar 

  • Burnham, K. D., Dorrance, A. E., Francis, D. M., Fioritto, R. J., and St-Martin, S. K. (2003a) Rps8, A New Locus in Soybean for Resistance to Phytophthora sojae. Crop Sci. 43,101–105.

    CAS  Google Scholar 

  • Burnham, K. D., Dorrance, A. E., VanToai, T. T., and St. Martin, S. K. (2003b) Quantitative Trait Loci for Partial Resistance to Phytophthora sojae in Soybean. Crop Science 43, 1610–1617

    CAS  Google Scholar 

  • Buzzell, R.I., Anderson, T.R., and Rennie, B.D. (1987) Harosoy Rps isolines. Soybean Genet. Newsl. 14, 79–81.

    Google Scholar 

  • Calla, B., Zhang, Y., Simmonds, D., and Clough, S.J. (Year) Genomic analysis of soybean resistance to Sclerotinia sclerotiorm [abstract]. ARS Sclerotinia Initiative Annual Meeting. Minneapolis (Bloomington), MN January 17–19, 2007. http://www.whitemoldresearch. com/files/012507.pdf

    Google Scholar 

  • Chatot, C., Malno, P., Droz, E., Schneider, M., Mtraux, J. P., and Bonnel, E. (2002) Transgenic potato plants expressing oxalate oxidase have increased resistance to oomycete and bacterial pathogens. Potato Research 45, 177–185,

    Article  Google Scholar 

  • Chen, X.R., Shen, G., Wang, Y.L., Zheng, X.B., and Wang, Y.C. (2007) Identifcation of Phytophthora sojae genes upregulated during the early stage of soybean infection. Federation of European Microbiological Societies 269, 280–288.

    CAS  Google Scholar 

  • Choi, I. Y., Hyten, D. L., Matukumalli, L. K., Song, Q., Chaky, J. M., Quigley, C. V., Chase, K., Lark, K. G., Reiter, R. S., Yoon, M. S., Hwang, E. Y., Yi, S. I., Young, N. D., Shoemaker, R. C., van Tassell, C. P., Specht, J. E., and Cregan, P. B. (2007) A Soybean Transcript Map: Gene Distribution, Haplotype and SNP Analysis. Genetics 176, 685–696.

    Article  PubMed  CAS  Google Scholar 

  • Cregan, P. (2007) Soybean Genetic Map. In: Stacey,G. (Ed.), Soybean Genomics. Springer, New York, pp. xxx–xxx.

    Google Scholar 

  • Day, P. (1974) Genetics of Host-Parasite Interaction. W.H. Freeman and Co., San Francisco.

    Google Scholar 

  • de Farias Neto, A. L., Hashmi, R., Schmidt, M., Carlson, S. R., Hartman, G. L., Li, S.X., Nelson, R. L., and Diers, B. W. (2006) Mapping and confirmation of a new sudden death syndrome resistance QTL on linkage group D2 from the soybean genotypes PI 567374 and ‘Ripley’. Molecular Breeding 20, 53–62.

    Article  CAS  Google Scholar 

  • Donaldson, P.A., Anderson, T., Lane, B.G., Davidson, A.L., and Simmonds, D.H. (2001) Soybean plants expressing an active oligomeric oxalate oxidase from the wheat gf-2.8 (germin) gene are resistant to the oxalate-secreting pathogen Sclerotina sclerotiorum. Physiol. Molec.Plant Pathol. 59, 297–307.

    Article  CAS  Google Scholar 

  • Dorrance, A. E., McClure, S. A., and St. Martin, S. K. (2003a) Effect of partial resistance on Phytophthora stem rot incidence and yield of soybean in Ohio. Plant Dis. 87, 308–312.

    Article  Google Scholar 

  • Dorrance, A. E. and Schmitthenner, A. F. (2000) New sources of resistance to Phytophthora sojae in the soybean plant introductions. Plant Disease 84, 1303–1308.

    Article  CAS  Google Scholar 

  • Dorrance, A.E., McClure, S.A., and DeSilva, A. (2003b) Pathogenic diversity of Phytophthora sojae in Ohio soybean fields. Plant Disease 87, 139–146.

    Article  Google Scholar 

  • Eathington, S. R., Nickell, C. D., and Gray, L. E. (1995) Inheritance of Brown Stem Rot Resistance in Soybean Cultivar BSR 101. J. Heredity 86, 55–60.

    Google Scholar 

  • Enkerli, K., Hahn, M. G., and Mims, C. W. (1997) Ultrastructure of compatible and incompatible interactions of soybean roots infected with the plant pathogenic oomycete Phytophthora sojae. Can. J. Bot. 75, 1494–1508.

    Google Scholar 

  • Förster, H., Tyler, B.M., and Coffey, M.D. (1994) Phytophthora sojae races have arisen by clonal evolution and by rare outcrosses. Mol. Plant-Microbe Interact. 7, 780–791.

    Google Scholar 

  • Gao, H., Narayanan, N. N., Ellison, L., and Bhattacharyya, M. K. (2005) Two classes of highly similar coiled coil-nucleotide binding-leucine rich repeat genes isolated from the Rps1-k locus encode Phytophthora resistance in soybean. Mol Plant Microbe Interact 18,1035–1045.

    Article  PubMed  CAS  Google Scholar 

  • Gijzen, M., Forster, H., Coffey, M. D., and Tyler, B.M. (1996) Cosegregation of Avr4 and Avr6 in Phytophthora sojae. Can. J. Bot. 74, 800–802.

    Article  Google Scholar 

  • Glazebrook, J. (2005) Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annu Rev Phytopathol 43, 205–227.

    Article  PubMed  CAS  Google Scholar 

  • Gordon, Stuart G., St. Martin, Steven K., and Dorrance, Anne E. (2006) Rps8 Maps to a Resistance Gene Rich Region on Soybean Molecular Linkage Group F. Crop Science 46, 168–173.

    Article  CAS  Google Scholar 

  • Gore, M. A., Hayes, A. J., Jeong, S. C., Yue, Y. G., Buss, G. R., and Maroof, M.A.S. (2002) Mapping tightly linked genes controlling potyvirus infection at the Rsv1 and Rpv1 region in soybean. Genome 45, 592–599.

    Article  PubMed  CAS  Google Scholar 

  • Govers, F. and Gijzen, M. (2006) Phytophthora genomics: the plant destroyers’ genome decoded. Mol Plant Microbe Interact 19, 1295–1301.

    Article  PubMed  CAS  Google Scholar 

  • Graham, M.A., Marek, L.F., and Shoemaker, R.C. (2002) Organization, Expression and Evolution of a Disease Resistance Gene Cluster in Soybean. Genetics 162, 1961–1977.

    PubMed  CAS  Google Scholar 

  • Graham, T. L. (1995) Cellular biochemistry of phenylpropanoid responses of soybean to infection by Phytophthora sojae. In: Daniel and Purkayastha (Eds.), Handbook of Phytoalexin Metabolism and Action. Marcel Dekker, Inc., New York, pp. 85–116.

    Google Scholar 

  • Hartwig, E.E. (1986) Identification of a fourth major gene conferring resistance to soybean rust. Crop Sci. 26, 1135–1136.

    Google Scholar 

  • Hartwig, E.E. and Bromfield, K.R. (1983) Relationships among three genes conferring specific resistance to rust in soybeans. Crop Sci. 23, 237–239.

    Google Scholar 

  • Hyten, D. L., Hartman, G. L., Nelson, R. L., Frederick, R. D., Concibido, V. C., Narvel, J. M., and Cregan, P. B. (2007) Map Location of the Rpp1 Locus That Confers Resistance to Soybean Rust in Soybean. Crop Science 47, 837–840.

    CAS  Google Scholar 

  • Iqbal, M. J., Yaegashi, S., Ahsan, R., Shopinski, K. L., and Lightfoot, D. A. (2005) Root response to Fusarium solani f. sp. glycines: temporal accumulation of transcripts in partially resistant and susceptible soybean. Theor Appl Genet 110, 1429–1438.

    Article  PubMed  CAS  Google Scholar 

  • Iqbal, M. J., Yaegashi, S., Njiti, V. N., Ahsan, R., Cryder, K. L., and Lightfoot, D. A. (2002) Resistance locus pyramids alter transcript abundance in soybean roots inoculated with Fusarium solani f.sp. glycines. Mol Genet Genomics 268, 407–417.

    Article  PubMed  CAS  Google Scholar 

  • Iqbal, M.J., Meksem, K., Njiti, V.N., Kassem, M. A., and Lightfoot, D.A. (2001) Microsatellite markers identify three additional quantitative trait loci for resistance to soybean sudden-death syndrome (SDS) in Essex × Forrest RILs. Theor Appl Genet 102, 187–192.

    Article  CAS  Google Scholar 

  • Ithal, N., Recknor, J., Nettleton, D., Hearne, L., Maier, T., Baum, T. J., and Mitchum, M. G. (2007) Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean. Mol Plant Microbe Interact 20, 293–305.

    Article  PubMed  CAS  Google Scholar 

  • Jansen, R. C. and Nap, J.-P. (2001) Genetical genomics: The added value from segregation. Trends Genet. 17, 388–391.

    Article  PubMed  CAS  Google Scholar 

  • Jayaraman, D., Shultz, J., Ali, S., Yuan, J., and Lightfoot, D.A. (2007) The Fusarium virguliforme Genome Database (FVGD): A Tool For Integrated Pathogen Biology. Plant & Animal Genomes XV Conference. San Diego, California. http://www.intl-pag.org/15/abstracts/PAG15_C01_944.html

    Google Scholar 

  • Jiang, R. H., Tyler, B. M., and Govers, F. (2006) Comparative analysis of Phytophthora genes encoding secreted proteins reveals conserved synteny and lineage-specific gene duplications and deletions. Mol Plant Microbe Interact 19, 1311–1321.

    Article  PubMed  CAS  Google Scholar 

  • Kanazin, V., Marek, L. F., and Shoemaker, R. C. (1996) Resistance gene analogs are conserved and clustered in soybean. Proc. Nat. Acad. Sci. USA 93, 11746–11750.

    Article  PubMed  CAS  Google Scholar 

  • Kim, H. S. and Diers, B. W. (2000) Inheritance of Partial Resistance to Sclerotinia Stem Rot in Soybean. Crop Science 40, 55–61.

    Google Scholar 

  • Klos, K.L.E., Paz, M.M., Marek, L.Fredrick, Cregan, P.B., and Shoemaker, R.C. (2000) Mo-lecular Markers Useful for Detecting Resistance to Brown Stem Rot in Soybean. Crop Science 40, 1445–1452.

    CAS  Google Scholar 

  • Kuchler, F., Duffy, M., Shrum, R. D., and Dowler, W. M. (1984) Potential economic consequences of the entry of an exotic fungal pest: the case of soybean rust. Phytopathology 74,916–920.

    Google Scholar 

  • Levine, A., Tenhaken, R., Dixon, R., and Lamb, C. (1994) H2O2 from the oxidative burst orchestrates the plant hypersensitive disease resistance response. Cell 79, 583–593.

    Article  PubMed  CAS  Google Scholar 

  • Li, M., Zou, J.J., Li, S.X., Vodkin, L., and Clough, S.J. (2004a) Microarray analysis of sudden death syndrome in soybeans. Plant & Animal Genomes XII Conference. San Diego, California. http://www.intl-pag.org/12/abstracts/P7a_PAG12_809.html

    Google Scholar 

  • Li, S., Liu, L., Hernandez, A.G., Hartman, G.L., Domier, L.L., and Schweitzer, P.A. (2004b) Generation and Analysis of Expressed Sequence Tags of Fusarium solani f. sp. glycines during Infection of Soybean. Plant & Animal Genomes XII Conference. San Diego, California. http://www.intl-pag.org/12/abstracts/P01_PAG12_72.html

    Google Scholar 

  • Lohnes, D. G. and Schmitthenner, A. F. (1997) Position of the Phytophthora resistance gene Rps7 on the soybean molecular map. Crop Science 37, 555–556.

    CAS  Google Scholar 

  • Lozovaya, V. V., Lygin, A. V., Li, S., Hartman, G. L., and Widholm, J. M. (2004) Biochemical Response of Soybean Roots to Fusarium solani f. sp. glycines Infection. Crop Science 44, 819–826.

    CAS  Google Scholar 

  • MacGregor, T., Bhattacharyya, M., Tyler, B. M., Bhat, R., Schmitthenner, A. F., and Gijzen, M. (2002) Genetic and physical mapping of Avr1a in Phytophthora sojae. Genetics 949–959.

    Google Scholar 

  • May, K.J., Whisson, S.C., Zwart, R.S., Searle, I.R., Irwin, J.A.G., Maclean, D.J., Carroll, B.J., and Drenth, A. (2002) Inheritance and mapping of eleven avirulence genes in Phytophthora sojae. Fungal Genet. Biol. 37, 1–12.

    Article  PubMed  CAS  Google Scholar 

  • Mian, M.A.R., Wang, T., Phillips, D.V., Alvernaz, J., and Boerma, H.R. (1999) Molecular Mapping of the Rcs3 Gene for Resistance to Frogeye Leaf Spot in Soybean. Crop Science 39,1687–1691.

    CAS  Google Scholar 

  • Mideros, S., Nita, M., and Dorrance, A. E. (2007) Characterization of components of partial resistance, Rps2, and root resistance to Phytophthora sojae in soybean. Phytopathology in press.

    Google Scholar 

  • Miles, M.R., Frederick, R.D., and Hartman, G.L. (2003) Soybean Rust: Is the U.S. Soybean Crop At Risk? APSNet feature. American Phytopathological Society. http://www.apsnet. org/online/feature/rust/.

    Google Scholar 

  • Mithofer, Axel, Muller, Bernd, Wanner, Gerhard, and Eichacker, Lutz A. (2002) Identification of defence-related cell wall proteins in Phytophthora sojae-infected soybean roots by ESI-MS/MS. Molecular Plant Pathology 3, 163–166.

    Article  CAS  PubMed  Google Scholar 

  • Monteros, Maria J., Missaoui, Ali M., Phillips, Daniel V., Walker, David R., and Boerma, H. Roger (2007) Mapping and Confirmation of the ‘Hyuuga’ Red-Brown Lesion Resistance Gene for Asian Soybean Rust. Crop Science 47, 829–836.

    CAS  Google Scholar 

  • Moy, P., Qutob, D., Chapman, B. P., Atkinson, I., and Gijzen, M. (2004) Patterns of gene expression upon infection of soybean plants by Phytophthora sojae. Mol Plant Microbe Interact 17,1051–1062.

    Article  PubMed  CAS  Google Scholar 

  • Narayanan, N.N., Tasma, M., Grant, D., Shoemaker, R., and Bhattacharyya, M. K. (2004) Early Gene Expression in Soybean Hypocotyls Following Infection With Phytopthora sojae. Plant and Animal Genomes XII Conference. San Diego, California. http://www.intl-pag.org/pag/12/abstracts/P7a_PAG12_811.html

    Google Scholar 

  • Panthee, D. R., Yuan, J. S., Wright, D. L., Marois, J. J., Mailhot, D., and Jr., C. N. Stewart (2007) Gene expression analysis in soybean in response to the causal agent of Asian soybean rust (Phakopsora pachyrhizi Sydow) in an early growth stage. Funct Integr Genomics DOI 10.1007/s10142-10007-10045-10148.

    Google Scholar 

  • Polzin, K.M., Lohnes, D. G., Nickell, C. D., and Shoemaker, R. C. (1994) Integration of Rps2, Rmd, and Rj2 Into Linkage Group J of the Soybean Molecular Map. J. Heredity 85, 300–303.

    CAS  Google Scholar 

  • Posada-Buitrago, M. L. and Frederick, R. D. (2005) Expressed sequence tag analysis of the soybean rust pathogen Phakopsora pachyrhizi. Fungal Genet Biol 42, 949–962.

    PubMed  CAS  Google Scholar 

  • Quackenbush, J. (2007) Soybean Gene Index. http://compbio.dfci.harvard. edu/tgi/cgi-bin/tgi/gimain.pl?gudb=soybean

    Google Scholar 

  • Qutob, D., Hraber, P., Sobral, B., and Gijzen, M. (2000) Comparative Analysis of Expressed Sequences in Phytophthora Sojae. Plant Phys. 123, 243–253.

    Article  CAS  Google Scholar 

  • Qutob, D., Kamoun, S., and Gijzen, M. (2002) Expression of a Phytophthora sojae necrosis-inducing protein occurs during transition from biotrophy to necrotrophy. Plant J 32, 361–373.

    Article  PubMed  CAS  Google Scholar 

  • Rea, G., Metoui, O., Infantino, A., Federico, R., and Angelini, R. (2002) Copper amine oxidase expression in defense responses to wounding and Ascochyta rabiei invasion. Plant Physiol 128, 865–875.

    Article  PubMed  CAS  Google Scholar 

  • Rokhsar, D. (2007) Sequencing the soybean genome. In: Stacey (Eds.), Soybean Genomics. Springer, New York, pp. xxx–xxx.

    Google Scholar 

  • Rollins, J., Cuomo, C., Kodira, C., Mauceli, E., DeCaprio, D., Galagan, J., Birren, B., Dickman, M., and Kohn, L. (2007) Moving Beyond An Assembled Genome With Sclerotinia sclerotiorum. Plant & Animal Genomes XV Conference. San Diego, California. http://www.intl-pag.org/15/abstracts/PAG15_W23_165.html

    Google Scholar 

  • Roy, K.W., Rupe, J. C., Hershman, D. E., and Abney, T. S. (1997) Sudden Death Syndrome of Soybean. Plant Disease 81, 1100–1111.

    Article  Google Scholar 

  • Saksirirat, W. and Hoppe, H. H. (1991) Teliospore germination of soybean rust fungus (Phakopsora pachyrhizi Syd.). J. Phytopathol. 132, 339–342.

    Article  Google Scholar 

  • Sandhu, D., Gao, H.Y., Cianzio, S., and Bhattacharyya, M.K. (2004) Deletion of a Disease Resistance Nucleotide-Binding-Site Leucine-Rich-Repeat-like Sequence Is Associated With the Loss of the Phytophthora Resistance Gene Rps4 in Soybean. Genetics 168, 2157–2167.

    Article  PubMed  CAS  Google Scholar 

  • Sandhu, D., Schallock, K. G., Rivera-Velez, N., Lundeen, P., Cianzio, S., and Bhattacharyya, M. K. (2005) Soybean Phytophthora resistance gene Rps8 maps closely to the Rps3 region. J Heredity 96, 536–541.

    Article  CAS  Google Scholar 

  • Schmitthenner, A.F. (1985) Problems and progress in controlling Phytophthora root rot of soybean. Plant Dis. 69, 362–368.

    Article  Google Scholar 

  • Schmitthenner, A.F. (1989) Phytophthora rot. In: Sinclair and Backman (Eds.), Compendium of Soybean Diseases, 3rd Ed. APS Press, St. Paul, MN, pp. 35–38.

    Google Scholar 

  • Schmitthenner, A.F., Hobe, M., and Bhat, R.G. (1994) Phytophthora sojae races in Ohio over a 10-year interval. Plant Disease 78, 269–276.

    Google Scholar 

  • Sexton, A. C., Cozijnsen, A. J., Keniry, A., Jewell, E., Love, C. G., Batley, J., Edwards, D., and Howlett, B. J. (2006) Comparison of transcription of multiple genes at three developmental stages of the plant pathogen Sclerotinia sclerotiorum. FEMS Microbiol Lett 258, 150–160.

    Article  PubMed  CAS  Google Scholar 

  • Shan, W., Cao, M., Leung, D., and Tyler, B.M. (2004) The Avr1b Locus of Phytophthora sojae Encodes an Elicitor and A Regulator Required for Avirulence on Soybean Plants Carrying Resistance Gene Rps1b. Mol. Plant Microbe Interact 17, 394–403.

    Article  PubMed  CAS  Google Scholar 

  • Shoemaker, R. (2007) Elucidating soybean genome structure. In: Stacey, G. (Ed.), Soybean Genomics. Springer, New York, pp. xxx–xxx.

    Google Scholar 

  • Shoemaker, R., Keim, P., Vodkin, L., Retzel, E., Clifton, S. W., Waterston, R., Smoller, D., Coryell, V., Khanna, A., Erpelding, J., Gai, X., Brendel, V., Raph-Schmidt, C., Shoop, E. G.,Vielweber, C. J., Schmatz, M., Pape, D., Bowers, Y., Theising, B., Martin, J., Dante, M., Wylie, T., and Granger, C. (2002) A compilation of soybean ESTs: generation and analysis. Genome 45, 329–338.

    Article  PubMed  Google Scholar 

  • Shultz, J. L., Kazi, S., Bashir, R., Afzal, J. A., and Lightfoot, D. A. (2007) The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor Appl Genet 114, 1081–1090.

    Article  PubMed  CAS  Google Scholar 

  • Shultz, J. L., Kurunam, D., Shopinski, K., Iqbal, M. J., Kazi, S., Zobrist, K., Bashir, R., Yaegashi, S., Lavu, N., Afzal, A. J., Yesudas, C. R., Kassem, M. A., Wu, C., Zhang, H. B., Town, C. D., Meksem, K., and Lightfoot, D. A. (2006) The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max. Nucleic Acids Res 34, D758–765.

    Article  PubMed  CAS  Google Scholar 

  • Song, Q. J., Marek, L. F., Shoemaker, R. C., Lark, K. G., Concibido, V. C., Delannay, X., Specht, J. E., and Cregan, P. B. (2004) A new integrated genetic linkage map of the soybean. Theor Appl Genet 109, 122–128.

    Article  PubMed  CAS  Google Scholar 

  • Tamulonis, J. P., Luzzi, B. M., Hussey, R. S., Parrott, W. A., and Boerma, H. R. (1997) RFLP Mapping of Resistance to Southern Root-Knot Nematode in Soybean. Crop Science 37,1903–1909.

    CAS  Google Scholar 

  • Thomas, R., Fang, X., Ranathunge, K., Anderson, T. R., Peterson, C. A., and Bernards, M. A. (2007) Soybean Root Suberin: Anatomical Distribution, Chemical Composition, and Relationship to Partial Resistance to Phytophthora sojae. Plant Physiol 144, 299–311.

    Article  PubMed  CAS  Google Scholar 

  • Tian, A. G., Wang, J., Cui, P., Han, Y. J., Xu, H., Cong, L. J., Huang, X. G., Wang, X. L., Jiao, Y. Z., Wang, B. J., Wang, Y. J., Zhang, J. S., and Chen, S. Y. (2004) Characterization of soybean genomic features by analysis of its expressed sequence tags. Theor Appl Genet 108,903–913.

    Article  PubMed  Google Scholar 

  • Tipping, A. J. and McPherson, M. J. (1995) Cloning and molecular analysis of the pea seedling copper amine oxidase. J Biol Chem 270, 16939–16946.

    Article  PubMed  CAS  Google Scholar 

  • Tooley, P.W. and Grau, C.R. (1982) Identification and Quantitative Characterization of Rate-Reducing Resistance to Phytophthora megasperma f.sp. glycinea in Soybean Seedlings. Phytopathology 72, 727–733.

    Google Scholar 

  • Tooley, P.W. and Grau, C.R. (1984) Field characterization of rate-reducing resistance to Phytophthora megasperma f.sp. glycinea in soybean. Phytopathology 74, 1201–1208.

    Google Scholar 

  • Torto, T. A., Li, S., Styer, A., Huitema, E., Testa, A., Gow, N. A., van West, P., and Kamoun, S. (2003) EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen Phytophthora. Genome Res 13, 1675–1685.

    Article  PubMed  CAS  Google Scholar 

  • Torto-Alalibo, T., Tripathy, S., Smith, B. M., Arredondo, F., Zhou, L., Li, H., Qutob, D., Gijzen, M., Mao, C., Sobral, B.W.S., Waugh, M.E., Mitchell, T. K., Dean, R.A., and Tyler, B.M. (2007) Expressed sequence tags from Phytophthora sojae reveal genes specific to development and infection. Mol. Plant-Microbe Interact. in press.

    Google Scholar 

  • Tyler, B. M., Tripathy, S., Zhang, X., Dehal, P., Jiang, R.H.Y., Aerts, A., Arredondo, F., Baxter, L., Bensasson, D., Beynon, J. L., Damasceno, C. M. B., Dickerman, A., Dorrance, A. E., Dou, D., Dubchak, I., Garbelotto, M., Gijzen, M., Gordon, S., Govers, F., Grunwald, N., Huang, W., Ivors, K., Jones, R. W., Kamoun, S., Krampis, K., Lamour, K., Lee, M.-K., McDonald, W. H., Medina, M., Meijer, H.J.G., Nordberg, E., Maclean, D. J., Ospina-Giraldo, M. D., Morris, P., Phuntumart, V., Putnam, N., Rash, S., Rose, J.K.C., Sakihama, Y., Salamov, A., A.Savidor, Scheuring, C., Smith, B., Sobral, B.W. S., Terry, A., Torto-Alalibo, T., Win, J., Xu, Z., Zhang, H., Grigoriev, I., Rokhsar, D., and Boore, J.L. (2006) Phytophthora Genome Sequences Uncover Evolutionary Origins And Mechanisms Of Pathogenesis. Science 313, 1261–1266.

    Article  PubMed  CAS  Google Scholar 

  • Tyler, B.M., Jiang, R. H.Y., Zhou, L., Tripathy, S., Dou, D., Torto-Alalibo, T., Li, H., Mao, Y., Liu, B., Vega-Sanchez, M., Mideros, S.X., Hanlon, R., Smith, B.M., Krampis, K., Ye, K., Martin, S. St, Dorrance, A.E., Hoeschele, I., and Maroof, M.A.S. (2007) Functional genomics and bioinformatics of the Phytophthora sojae-soybean interaction. In: Gustafson, Stacey, and Taylor (Eds.), The Genomics of Disease. Kluwer Academic/Plenum Publisher, New York, pp. in press.

    Google Scholar 

  • van de Mortel, M., Recknor, J.C., Graham, M.A., Nettleton, D., Dittman, J.D., Nelson, R.T., Godoy, C.V., Abdelnoor, R.V., Almeida, M.R., Baum, T.J., and Whitham, S.A. (2007) Distinct biphasic mRNA changes in response to Asian soybean rust infection. Molec Plant Microbe Interact in press.

    Google Scholar 

  • Van Etten, H. D., Sandrock, R. W., Wasman, C. C., Soby, S. D., McCluskey, K., and Wang, P. (1995) Detoxification of phytoanticipins and phytoalexins by phytopathogenic fungi. Can. J. Bot. 73, S518–S525.

    Google Scholar 

  • Vega-Sánchez, M.E., Redinbaugh, M.G., Costanzo, S., and Dorrance, A.E. (2005) Spatial and temporal expression analysis of defense-related genes in soybean cultivars with different levels of partial resistance to Phytophthora sojae. Physiological and Molecular Plant Pathology 66, 175–182.

    Article  CAS  Google Scholar 

  • Vodkin, L. O., Khanna, A., Shealy, R., Clough, S. J., Gonzalez, D. O., Philip, R., Zabala, G., Thibaud-Nissen, F., Sidarous, M., Stromvik, M. V., Shoop, E., Schmidt, C., Retzel, E., Erpelding, J., Shoemaker, R. C., Rodriguez-Huete, A. M., Polacco, J. C., Coryell, V., Keim, P., Gong, G., Liu, L., Pardinas, J., and Schweitzer, P. (2004) Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant. BMC Genomics 5, 73.

    Article  PubMed  Google Scholar 

  • Wang, Z., Wang, Y., Chen, X., Shen, G., Zhang, Z., and Zheng, X. (2006) Differential screening reveals genes differentially expressed in low- and high-virulence near-isogenic Phytophthora sojae lines. Fungal Genet Biol 43, 826–839.

    Article  PubMed  CAS  Google Scholar 

  • Whisson, S. C., Basnayake, S., Maclean, D. J., Irwin, J. A., and Drenth, A. (2004) Phytophthora sojae avirulence genes Avr4 and Avr6 are located in a 24kb, recombination-rich region of genomic DNA. Fungal Genet Biol 41, 62–74.

    Article  PubMed  CAS  Google Scholar 

  • Whisson, S.C., Drenth, A., Maclean, D.J., and Irwin, J.A.G. (1995) Phytophthora sojae avirulence genes, RAPD and RFLP markers used to construct a detailed genetic linkage map. Mol. Plant-Microbe Interact. 8, 988–995.

    PubMed  CAS  Google Scholar 

  • Wrather, J.A., Anderson, T.R., Arsyad, D.M., Tan, Y., Ploper, L.D., Porta-Puglia, A., Ram, H.H., and Yorinori, J.T. (2001a) Soybean disease loss estimates for the top ten soybean-producing countries in 1998. Canada J. Plant Pathol. 23, 115–121.

    Google Scholar 

  • Wrather, J.A., Koenning, S.R., and Anderson, T.R. (2003) Effect of Diseases on Soybean Yields in the United States and Ontario (1999 to 2002). Online. Plant Health Progress March 25, doi:10.1094/PHP-2003-0325-1001-RV.

    Google Scholar 

  • Wrather, J.A., and Koenning, S.R. (2006). Estimates of disease effects on soybean yields in the United States 2003 to 2005. J. Nematology 38, 173–180.

    Google Scholar 

  • Wrather, J.A., Stienstra, W.C., and Koenning, S.R. (2001b) Soybean disease loss estimates for the United States from 1996 to 1998. Can. J. Plant Pathol. 23, 122–131.

    Google Scholar 

  • Yeh, C. C., Tschanz, A. T., and Sinclair, J. B. (1981) Induced teliospore formation by Phakopsora pachyrhizi on soybeans and other hosts. Phytopathology 71, 1111–1112.

    Google Scholar 

  • Yoder, O. C. and Turgeon, B. G. (1996) Molecular-genetic evaluation of fungal molecules for roles in pathogenesis in plants. Journal of Genetics 75, 425–440.

    Article  CAS  Google Scholar 

  • Yoder, O.C. and Turgeon, B. Gillian (2001) Fungal genomics and pathogenicity. Current Opinion in Plant Biology 4, 315–321.

    Article  PubMed  CAS  Google Scholar 

  • Yu, Y. G., Buss, G. R., and Maroof, S. M. A. (1996) Isolation of a superfamily of candidate disease-resistance genes in soybean based on a conserved nucleotide-binding site. Proc. Nat. Aca. Sci. USA 93, 11751–11756.

    Article  CAS  Google Scholar 

  • Zou, J., Rodriguez-Zas, S., Aldea, M., Li, M., Zhu, J., Gonzalez, D. O., Vodkin, L. O., DeLucia, E., and Clough, S. J. (2005) Expression profiling soybean response to Pseudomonas syringae reveals new defense-related genes and rapid HR-specific down-regulation of photosynthesis. Mol Plant Microbe Interact 18, 1161–1174.

    Article  PubMed  CAS  Google Scholar 

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Tyler, B.M. (2008). Genomics of Fungal- and Oomycete-Soybean Interactions. In: Stacey, G. (eds) Genetics and Genomics of Soybean. Plant Genetics and Genomics: Crops and Models, vol 2. Springer, New York, NY. https://doi.org/10.1007/978-0-387-72299-3_14

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