Bioinformatic Resources for Soybean Genetic and Genomic Research

  • David Grant
  • Rex T. Nelson
  • Michelle A. Graham
  • Randy C. Shoemaker
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 2)


Quantitative Trait Locus Soybean Genome Soybean Cyst Nematode Bioinformatic Resource Molecular Linkage Group 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Abouelhoda, M.I., Kurtz, S. and Ohlebusch, E. (2004) Replacing suffix trees with enhanced suffix arrays. J. Discrete Algorithms 2, 53–86.CrossRefGoogle Scholar
  2. Ainsworth, E.A., Rogers A., Vodkin, L.O., Walter, A. and Schurr, U. (2006.) The effects of elevated CO2 on soybean gene expression: An analysis of growing and mature leaves. Plant Physiol. 142, 135–147.PubMedCrossRefGoogle Scholar
  3. Akkaya, M.S., Shoemaker, R.C., Specht, J.E., Bhagwat, A.A. and Cregan, P.B. (1995) Integration of simple sequence repeat DNA markers into a soybean linkage map. Crop Sci. 35, 1439–1445.Google Scholar
  4. Akkaya, M.S., Bhagwat, A.A. and Cregan, P.B. (1992) Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132, 1131–1139.PubMedGoogle Scholar
  5. Alkharouf, N.W., Klink, V.P., Chouikha, I.B., Beard, H.S., MacDonald, M.H., Meyer, S., Knap, H.T., Khan, R. and Matthews, B.F. (2006) Timecourse microarray analyses reveal global changes in gene expression of susceptible Glycine max (soybean) roots during infection by Heterodera glycines (soybean cyst nematode). Planta 224, 838–852.PubMedCrossRefGoogle Scholar
  6. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25, 3389–3402.PubMedCrossRefGoogle Scholar
  7. Apuya, N.R., Frazier, B.L., Keim, P., Roth, E.J. and Lark, K.G. (1998) Restriction fragment length polymorphisms as genetic markers in soybean, Glycine max (L.) Merrill. Theor. Appl. Genet. 75, 889–901.Google Scholar
  8. Apweiler, R., Bairoch, A., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Natale, D.A., O’Donovan, C., Redaschi, N. and Yeh, L.S. (2004) UniProt: the universal protein knowledgebase. Nucl. Acids Res. 32, D115–D119.PubMedCrossRefGoogle Scholar
  9. Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I.F., Soboleva, A., Tomashevsky, M. and Edgar, R. 2006. NCBI GEO: mining tens of millions of expression profiles—database and tools update. Nucl. Acids Res. 35, D760–D765.PubMedCrossRefGoogle Scholar
  10. Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich,V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L.L., Studholme, D.J., Yeats, C. and Eddy, S.R. (2004) The Pfam protein families database. Nucl. Acids Res. 32, D138–D141.PubMedCrossRefGoogle Scholar
  11. Berardini, T.Z., Mundodi, S., Reiser, R., Huala, E., Garcia-Hernandez, M., Zhang, P., Mueller, L.M., Yoon, J., Doyle, A., Lander, G., Moseyko, N., Yoo, D., Xu, I., Zoeckler, B., Montoya, M., Miller, N., Weems, D. and Rhee, S.Y. (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 135, 1–11.CrossRefGoogle Scholar
  12. Boguski, M.S., Lowe, T.M.J. and Tolstoshev, C.M. (1993) dbEST — database for “expressed sequence tags”. Nature Genetics 4, 332–333.PubMedCrossRefGoogle Scholar
  13. Bonaldo, M.F., Lennon, G. and Soares, M.B. (1996) Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res. 6, 791–806.PubMedCrossRefGoogle Scholar
  14. Cregan, P.B., Jarvik, T., Bush, A.L., Shoemaker, R.C., Lark, K.G., Kahler, A.L., Kaya, N., VanToai, T.T., Lohnes, D.G., Chung, J. and Specht, J.E. (1999) An integrated genetic linkage map of the soybean genome. Crop Sci. 39, 1464–1490.Google Scholar
  15. Durbin, R., Thierry-Mieg, J. (1994) The AceDB genome database. In Computational Methods in Genome Research (ed. S. Suhai), pp. 7821–7825. Plenum Press, New York.Google Scholar
  16. Edgar, R., Domrachev, M., and Lash, A.E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucl. Acids Res. 30, 207–210.PubMedCrossRefGoogle Scholar
  17. Gonzales, M.D., Archuleta, E., Farmer, A., Gajendran, K. Grant, D., Shoemaker, R., Beavis, W.D. and Waugh M.E. (2005) The Legume Information System (LIS): an integrated information resource for comparative legume biology. Nucl. Acids Res. 33, D660–D665.Google Scholar
  18. Huang, X. and Madan, A. (1999) CAP3: a DNA sequence assemblyprogram. Genome Res. 9, 868–877.Google Scholar
  19. Hymowitz, T. and Singh, R.J. (1987) Taxomony and speciation. In Soybeans: Improvement, production, and uses (ed. RJ Wilcox), pp. 23–48. ASA, CSSA, SSSA, Madison, Wisconsin.Google Scholar
  20. Hyten, D.L., Pantalone, V.R., Sams, C.E., Saxton, A.M., Landau-Ellis, D., Stefaniak, T.R. and Schmidt, M.E. (2004) Seed quality QTL in a prominent soybean population. Theor. Appl. Genet. 109, 552–561.PubMedCrossRefGoogle Scholar
  21. Hyten, D.L., Song, Q., Zhu, Y., Choi, I.Y., Nelson, R.L., Costa, J.M., Specht, J.E., Shoemaker, R.C. and Cregan, P.B. (2006) Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. USA 103, 16666–16671.PubMedCrossRefGoogle Scholar
  22. 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.CrossRefGoogle Scholar
  23. Kalyanaraman, A., Aluru, S., Kothari, S. and Brendel, V. (2003) Efficient clustering of large EST data sets on parallel computers. Nucl. Acids Res. 31, 2963–2974.PubMedCrossRefGoogle Scholar
  24. Keim, P., Diers, B.W., Olson, T.C. and Shoemaker, R.C. (1990) RFLP mapping in soybean: association between marker loci and variation in quantitative traits. Genetics 126, 735–742.PubMedGoogle Scholar
  25. Kopisch-Obuch, F.J., McBroom, R.L. and Diers, B.W. (2005) Association between soybean cyst nematode resistance loci and yield in soybean. Crop Sci. 45, 956–965.CrossRefGoogle Scholar
  26. Moy, P., Qutob, D., Chapman, B.P., Atkinson, I., Gijzen, M. (2004) Patterns of gene expression upon infection of soybean plants by Phytophthora sojae. Mol. Plant-Microbe Interact. 17, 1051–1062.PubMedCrossRefGoogle Scholar
  27. Nelson, R.T., Grant, D. and Shoemaker, R.C. (2005) ESTminer: a suite of programs for gene and allele identification. Bioinformatics 21, 691–693.PubMedCrossRefGoogle Scholar
  28. O’Rourke, J.A., Graham, M.A., Vodkin, L.O., Gonzales, D.O., Cianzio, S.R. and Shoemaker, R.C. (2007) Recovering from iron deficiency chlorosis in near isogenic soybeans: a microarray study. Plant Physiology and Biochemistry: in press.Google Scholar
  29. Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2005) NCBI Reference sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucl. Acids Res. 33, D501–D504.PubMedCrossRefGoogle Scholar
  30. Quackenbush, J., Cho, J., Lee, D., Liang, F., Holt, I., Karamycheva, S., Parvizi, B., Pertea, G., Sultana, R. and White, J. (2001) The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucl. Acids Res. 29: 159–164.PubMedCrossRefGoogle Scholar
  31. Rabinowicz, P.D., Schutz, K., Dedhia, N., Yordan, C., Parnell, L.D., Stein, L., McCombie, R.W. and Martienssen, R.A. (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nature Genetics 23, 305–308.PubMedCrossRefGoogle Scholar
  32. Rudd, S. (2003) Expressed sequence tags: alternative or complement to whole genome sequence? Trends Plant Sci. 8, 321–329.PubMedCrossRefGoogle Scholar
  33. Sandhu, D., Gao, H., 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.PubMedCrossRefGoogle Scholar
  34. Scheetz, T.E., Laffin, J.J., Berger, B., Holte, S., Baumes, S.A., Brown, R. II, Chang, S., Coco, J., Conklin, J., Crouch, K., Donohue, M., Doonan, G., Estes, C., Eyestone, M., Fishler, K., Gardineer, J., Guo, L., Johnson, B., Keppel, C., Kreger, R., Lebeck, M., Marcelin, R., Miljkovich, V., Perdue, M., Qui, L., Rehmann, J., Reiter, R.S., Rhoads, B., Schaefer, K., Smith, C., Sunjevaric, I., Trout, K., Wu, N., Birkett, C., Bischof. J., Gackle, B., Gavin, A., Grundstad, A.J., Mokrzycki, B., Moressi, C., O’Leary, B., Pedretti, K., Roberts, C., Robinson, N.L., Smith, M., Tack, D., Trivedi, N., Kucaba, T., Freeman, T., Lin, J.J., Bonaldo, M.F., Casavant T.L., Sheffields, V.C. and Soares, M.B. (2004) High-throughput gene discovery in the rat. Genome Res. 14, 733–741.Google Scholar
  35. Shen, L., Gong, J., Caldo, R.C., Nettleton, D., Cook, D., Wise, R.P. and Dickerson, J.A. (2005) BarleyBase — An expression profiling database for plant genomics. Nucl. Acids Res. 33, D614–D618.Google Scholar
  36. Shoemaker R.C. and Olson T.C. (1993) Molecular linkage map of soybean (Glycine max L). In Genetic maps: Locus maps of complex genomes (ed. SJ O’Brien), pp. 6–131. Cold Spring Harbor Laboratory Press, New York.Google Scholar
  37. Shoemaker, R., Keim, P., Vodkin, L., Retzel, E., Clifton, S.W., Waterson, R., Smoller, D., Coryell, V., Khanna, A., Erplding, J., Gai, X., Brendel, V., Raph-Schmidt, C., Shoop, E.G., Vielweber, C.V., Schimatz, 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.PubMedCrossRefGoogle Scholar
  38. 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. (2006a) 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. Nucl. Acids Res. 34, D758–D765.CrossRefGoogle Scholar
  39. Shultz, J.L., Yesudas, C., Yaegashi, S., Afzal, A.J., Kazi, S. and Lightfoot, D.A. (2006b) Three minimum tile paths from bacterial artificial chromosome libraries of the soybean (Glycine max cv. ‘Forrest’): tools for structural and functional genomics. Plant Methods. 2, 9.CrossRefGoogle Scholar
  40. Soares, M.B., Bonaldo, M.D.F., Jelene, P., Su, L., Lawton, L. and Efstratiadis, A. (1994) Construction and characterization of a normalized cDNA library. Proc. Natl. Acad. Sci. USA 91, 9228–9232.CrossRefGoogle Scholar
  41. Song, Q.J., Marek, L.F., Shoemaker, R.C., Lark, K.G., Concibido, V.C., Delannay, X., Spect, J.E. and Cregan, P.B. (2004) A new integrated genetic linkage map of the soybean. Theor. Appl. Genet. 109, 122–128.PubMedCrossRefGoogle Scholar
  42. Stam, P. (1993) Construction of integrated genetic linkage maps by means of a new computer package: Join Map. Plant Journal 3, 739–744.CrossRefGoogle Scholar
  43. Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A. and Lewis, S. (2002) The generic genome browser: a building block for a model organism system database. Genome Res. 12, 1599–610.PubMedCrossRefGoogle Scholar
  44. Thibaud-Nissen, F., Shealy, R.T., Khanna, A. and Vodkin, L.O. (2003) Clustering of microarray data reveals transcript patterns associated with somatic embryogenesis in soybean. Plant Physiol 132, 118–136.PubMedCrossRefGoogle Scholar
  45. Vodkin, L.O., Khanna, A., Shealy, R., Clough, S.J., Gonzalez, D.O., Philip, R., Zabala, G., Thibaud-Nissen, F., Sidarous, M., Strömvik, M.V., Shoop, E., Schmidt, C., Retzel, E., Erpelding, E., Shoemaker, R.C., Rodriguez-Huete, A.M., Polacco, J.C., Coryell, V., Keim, P., Gong, G., Lui, 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.PubMedCrossRefGoogle Scholar
  46. Wheeler, D.L., Church, D.M., Federhen, S., Lash, A.E., Madden, T.L., Pontius, J.U., Schuler, G.D., Schriml, L.M., Sequeira, E., Tatusova, T.A. and Wagner, L. (2003) Database resources of the National Center for Biotechnology. Nucl. Acids Res. 31, 28–33.CrossRefGoogle Scholar
  47. Whitelaw, C.A., Barbazuk, W.B., Pertea, G., Chan, A.P., Cheung, F., Lee, Y., Zheng, L., van Heeringen, S., Karamycheva, S., Bennetzen, J.L., SanMiguel, P., Lakey, N., Bedell, J., Yuan, Y., Budiman, M.A., Resnick, A., Van Aken, S., Utterback, T., Riedmuller, S., Williams, M., Feldblyum, T., Schubert, K., Beachy, R., Fraser, C.M. and Quackenbush, J. (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302, 2118–2120.PubMedCrossRefGoogle Scholar
  48. Woodworth, C.M. (1921) Inheritance of cotyledon, seed-coat, hilum, and pubescence colors in soybeans. Genetics 6, 487–555.PubMedGoogle Scholar
  49. Wosik, E. (2006) Oligonucleotide Arrays-Detailed Information. Connexions, March 31, 2006. Scholar
  50. Wu, C.C., Nimmakayala, P., Santos, F.A., Springman, R., Scheuring, C., Meksem, K., Lightfoot, D.A. and Zhang, H.B. (2004) Construction and characterization of a soybean bacterial artificial chromosome library and use of multiple complementary libraries for genome physical mapping. Theor. Appl. Genet. 109, 1041–1050.PubMedCrossRefGoogle Scholar
  51. Zabala, G., Zou, J.,Tuteja, J., Gonzales, D.O., Clough, S.J. and Vodkin, L.O. (2006) Transcriptome changes in the phenylpropanoid pathway of Glycine max in response to Pseudomonas syringae infection. BMC Plant Biol 6, 26.PubMedCrossRefGoogle Scholar
  52. Zhang, Z., Schwartz, S., Wagner, L. and Miller, W. (2000), “A greedy algorithm for aligning DNA sequences”, J. Comput. Biol. 7, 203–214.PubMedCrossRefGoogle Scholar
  53. Zhu, Y.L., Song, Q.J., Hyten, D.L., Van Tassell, C.P., Matukumalli, L.K., Grimm, D.R., Hyatt, S.M., Fickus, E.W., Young, N.D. and Cregan, P.B. (2003) Single-nucleotide polymorphisms in soybean. Genetics 163 1123–1134.PubMedGoogle Scholar
  54. 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 downregulation of photosynthesis. Mol Plant-Microbe Interact 18, 1161–1174.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • David Grant
    • 1
  • Rex T. Nelson
  • Michelle A. Graham
  • Randy C. Shoemaker
  1. 1.USDA-ARS CICGRU, Department of AgronomyIowa State UniversityAmesUSA

Personalised recommendations