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Genomics of Soybean Seed Development

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References

  • Allen, E., Zie. Z., Gustafson, A.M., Sung, G-H., Spatafora, J.W. and Carrington, J.C. (2004) Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat. Genet. 36, 1282–1290.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Baulcombe, D. (2004) RNA silencing in plants. Nature 431, 356–363.

    Article  PubMed  CAS  Google Scholar 

  • Becerra, C., Puigdomenech, P. and Vicient, C.M. (2006) Computational and experimental analysis identifies Arabidopsis genes specifically expressed during early seed development. BMC Genomics, 7, 38.

    Article  PubMed  CAS  Google Scholar 

  • Bewley, J.D., Hempel, F.D., McCormick, S. and Zambryski, P. (2000) Reproductive development. In: Biochemistry and Molecular Biology of Plants (Buchanan, B.B., Gruissem, W. and Jones, R.L., eds), pp. 988–1043. Rockville, MD: American Society of Plant Physiologists.

    Google Scholar 

  • Buzzell, R.I., Buttery, R.B. and MacTavish, D.C. (1987) Biochemical genetics of black pigmentation of soybean seed. J. Hered. 78, 53–54.

    Google Scholar 

  • Carter, T.E., Nelsone, R.L., Sneller, C.H. and Cru, Z. (2004) In J.R. Wilcox, H.R. Boerma, and J.E. Specht (ed.) Soybeans: Improvement, Production and Uses. Agronomy No. 16. 3rd edition. ASA, CSSA, SSSA, Madison, WI.

    Google Scholar 

  • Casson, S., Spencer, M., Walker, K. and Lindsey, K. (2005) Laser capture microdissection for the analysis of gene expression during embryogenesis of Arabidopsis. Plant Jour. 42, 111–123.

    Article  CAS  Google Scholar 

  • Chen, T.H.H,, Marowitch, J., and Thompson, B.G. (1987) Genotypic effects on somatic embryogenesis and plant regeneration from callus cultures of alfalfa. Plant Cell Tissue Organ Cult 8, 73–81.

    Article  Google Scholar 

  • Clough, S.J., Tuteja, J.H., Li, M., Marek, L.F., Shoemaker, R.C. and Vodkin, L.O. (2004). Features of a 103-kb gene-rich region in soybean include an inverted perfect repeat cluster of CHS genes comprising the I locus. Genome 47, 819–831.

    Article  PubMed  CAS  Google Scholar 

  • Cullis, C.A. (2004) Plant Genomics and Proteomics. Wiley-Liss, Hoboken, NJ.

    Google Scholar 

  • Duan, K., Luo, Y-H., Luo, D., Xu, Z-H. and Xue, H-W. (2005) New insights into the complex and coordinated transcriptional regulation networks underlying rice seed development through cDNA chip-based analysis. Plant Mol. Biol. 57, 785–804.

    Article  PubMed  CAS  Google Scholar 

  • Della Vedova, C.B., Lorbiecke, R., Kirsch, H., Schulte, M.B., Scheets, K., Borchert, L.M., Scheffler, B.E., Wienand, U., Cone, K.C. and Birchler, J.A. (2005) The dominant inhibitory chalcone synthase allele C2-Idf (Inhibitor diffuse) from Zea mays (L.) acts via an endogenous RNA silencing mechanism. Genet. 170, 1989–2002.

    Article  CAS  Google Scholar 

  • Dhaubhadel, S., Gijzen, M., Moy, P. and Farhangkhoee, M. (2007) Transcriptome analysis reveals a critical role of CHS7 and CHS8 genes for isoflavonoid synthesis in soybean seeds. Plant Physiol. 143, 326–338.

    Article  PubMed  CAS  Google Scholar 

  • Fasoula, D.A., Stephens, P.A., Nickell, C.D. and Vodkin, L.O. (1995) Cosegregation of purple-throat flower color with a DNA polymorphism in soybean. Crop Science 35, 1028–1031.

    CAS  Google Scholar 

  • Finer, J.J. (1988) Apical proliferation of embryonic tissue of soybean [Glycine max (L.) Merrill]. Plant Cell Rep 7, 238–241

    Article  Google Scholar 

  • Finer, J.J. and McMullen, M.D. (1991) Transformation of soybean via particle bombardment of embryogenic suspension culture tissue. In Vitro Cell Dev Biol 27: 175–182

    Google Scholar 

  • Fisher, R. L. and Goldberg, R.B. (1982) Structure and flanking regions of soybean seed protein genes. Cell 29, 651–660.

    Article  Google Scholar 

  • Fire, A. Xu, S., Montgomery, S., Kostas, S., Driver, S.E. and Mello, C.C (1998) Potent and specific genetic interference by double stranded RNA in Caenorhabditis elegans. Nature 391, 806–811.

    Article  PubMed  CAS  Google Scholar 

  • Goldberg, R.B. (1988) Plants: novel developmental processes. Science 240, 1460–1467.

    Article  PubMed  CAS  Google Scholar 

  • Goldberg, R.B., Hoschek, G., Tam, S. H. Ditta, G.S. and Breidenbach, R.W. (1981a) Abundance, diversity, and regulation of mRNA sequence sets in soybean embryogenesis. Develop Biol 83, 201–217.

    Google Scholar 

  • Goldberg, R.B., Hoschek, G., Ditta, G.S., and Breidenbach, R.W. (1981b) Developmental regulation of cloned superabundant embryo mRNAs in soybean. Develop Biol 83, 218–231.

    Google Scholar 

  • Goldberg, R.B., Hoschek, G. and Vodkin, L.O. (1983) An insertion sequence blocks the expression of a soybean lectin gene. Cell 33, 465–475.

    Article  PubMed  CAS  Google Scholar 

  • Goldberg, R.G., Barker, S.J., and Perez-Grau, L. (1989) Regulation of gene expression during plant embryogenesis. Cell 56, 149–160

    Article  PubMed  CAS  Google Scholar 

  • Goldberg, R.B., Depaiva, G. and Yadegari, R. (1994) Plant embryogenesis - Zygote to seed. Science 266, 605–614

    Article  PubMed  CAS  Google Scholar 

  • Goldberg, R.B., Bui, A.Q., Le, B., Kawashima, R., Wang, X., Wagmaister, J, Fisher, R.L., and Harada, J.J. (2006) Using genomics to dissect seed development. 8th International Congress of Plant Molecular Biology, p. 69.

    Google Scholar 

  • Gonzalez, D.O. and Vodkin, L.O. (2006) Clustering analysis of transcript abundance in soybean cotyledons during germination and emergence. Plant and Animal Genome XIV, San Diego, CA, p. 295.

    Google Scholar 

  • Gonzalez, D.O. and Vodkin, L.O. (2007) Specific elements of the glyoxylate pathway play a significant role in the functional transition of the soybean cotyledon during seedling development. BMC Genomics 8, 468.

    Article  PubMed  Google Scholar 

  • Green P., 2001. Documentation for Phrap. http;//bozeman.mbt.washington.edu, Genome Center, University of Washington.

    Google Scholar 

  • Gupta, S., Gallavotti, A., Stryker, G.A., Schmidt, R.J. and Lal, S.K. (2005) A novel class of Helitron-related transposable elements in maize contain portions of multiple pseudogenes. Plant Mol. Biol. 57, 115–127.

    Article  PubMed  CAS  Google Scholar 

  • Hamilton, A.J. and Baulcombe D.C. (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286, 950–952.

    Article  PubMed  CAS  Google Scholar 

  • Hegstad, J.M., Tarter, J.A., Vodkin, L.O. and Nickell, C.D. (2000) Positioning the wp flower color locus on the soybean genome map. Crop Sci. 40, 534–537.

    CAS  Google Scholar 

  • Hills, M.J. (2004) Control of storage-product synthesis in seeds. Curr. Opin. Plant Biol. 7, 302–308.

    Article  PubMed  CAS  Google Scholar 

  • Huang X. and Madan A. (1999) CAP3: A DNA sequence assembly program. Genome Research 9, 868–877.

    Article  PubMed  CAS  Google Scholar 

  • Jiang, N., Bao, Z., Zhang, X., Eddy, S.R. and Wessler, S.R. (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431, 569–573.

    Article  PubMed  CAS  Google Scholar 

  • Johnson, E.O., Stephens, P.A., Fasoula, D.A., Nickell, C.D. and Vodkin, L.O. (1998) Instability of a novel multicolored flower trait in inbred and outcrossed soybean lines. J. Hered. 89, 508–515.

    Article  Google Scholar 

  • Jones, S. (2004) A global view of gene expression during soybean seed development using microarrays. Masters thesis. University of Illinois at Urbana-Champaign.

    Google Scholar 

  • Jones, S., Gonzalez, D.O. and Vodkin, L.O. (2006) global gene expression profiles of early soybean seed development using microarrays. Am. Soc. Plant Biologists, Boston, MA, p. 255.

    Google Scholar 

  • Kusaba, M., Miyahara, K., Iida, S., Fukuoka, H., Takano, T., Sassa, H., Nishimura, M. and Nishio, T. (2003). Low glutelin content1: a dominant mutation that suppresses the glutelin multigene family via RNA silencing in rice. Plant Cell 15, 1455–1467.

    Article  PubMed  CAS  Google Scholar 

  • Lal, S.K., Giroux, M.J., Brendel, V., Vallejos, E. and Hannah, L.C. (2003). The maize genome contains a Helitron Insertion. Plant Cell 15, 381–391.

    Article  PubMed  CAS  Google Scholar 

  • Le, B.H., Wagmaister, J.A., Kawashima, T., Bui, A.Q., Harada, J.J., and Goldberg, R.B. (2007) Using genomics to study legume seed development. Plant Physiol. 144, 562–574.

    Article  PubMed  CAS  Google Scholar 

  • Lindstrom, J.T. and Vodkin, L.O. (1991) A soybean cell wall protein is affected by seed color genotype. Plant Cell 3, 561–571.

    Article  PubMed  CAS  Google Scholar 

  • Matzke, M.A. and Matzke, A.J.M. (2004) Planting the seeds of a new paradigm. Plos Biol. 2, 582–585.

    Article  CAS  Google Scholar 

  • McConnell J. and Barton, M. (1998) Leaf polarity and meristem formation in Arabidopsis. Development 125, 2935–2942.

    PubMed  CAS  Google Scholar 

  • Meinke, D.W., Chen, J., and Beachy, R.N. (1981) Expression of storage protein genes during soybean seed development. Planta 153, 130–139.

    Article  CAS  Google Scholar 

  • Moise, J., Han, S., Gudynaite-Savitch, L., Johnson, D.A., and Miki, B.L. (2005) Seed coats: structure, development, composition, and biotechnology. In Vitro Cell. Dev. Biol. Plant 41, 620–644.

    Article  Google Scholar 

  • Napoli, C., Lemieux, C. and Jorgensen, R. (1990) Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2, 279–289.

    Article  PubMed  CAS  Google Scholar 

  • Nicholas C.D., Lindstrom J.T. and Vodkin, L.O. (1993) Variation in proline rich cell wall proteins in soybean lines with anthocyanin mutations. Plant Molecular Biol. 21: 145–156.

    Article  CAS  Google Scholar 

  • Nielsen, M.E., Lok, F. and Nielsen, H.B. (2006) Distinct developmental defense activations in barley embryos identified by transcriptome profiling. Plant Mol. Biol. 61, 589–601.

    Article  PubMed  CAS  Google Scholar 

  • Palmer, R.G. and Kilen, T.C. (1987) Qualitative Genetics. In Wilcox, J.R. (ed.), Soybean: Improvement, Production, and Uses, 2nd Edition, American Society of Agronomy, Madison, Wisconsin, pp.135–209.

    Google Scholar 

  • Palmer, R.G., Pfeiffer, T.W., Buss, G.R. and Kilen, T.C. (2004) Qualitative genetics. p. 137–233. In J.R. Wilcox, H.R. Boerma, and J.E. Specht (ed.) Soybeans: Improvement, Production and Uses. Agronomy No. 16. 3rd edition. ASA, CSSA, SSSA, Madison, WI.

    Google Scholar 

  • Percy, J. D., Philip R. and Vodkin, L.O. (1999) Defective seed coat mutations that affect the post-transcriptional abundance of soluble proline rich cell wall proteins. Plant Molecular Biol. 40, 603–613.

    Article  CAS  Google Scholar 

  • Rhodes, P.R. and Vodkin, L.O. (1985). Highly structured sequence homology between an insertion element and the gene in which it resides. Proc. Natl. Acad. Sci. 82, 493–497.

    Article  PubMed  CAS  Google Scholar 

  • Rhodes, P.R. and Vodkin, L.O. (1988). Organiztion of the Tgm family of transposable elements in soybean. Genet. 120, 597–604.

    CAS  Google Scholar 

  • Ritchie, S.W., Hanway, J.J., Thompson, H.E. and Benson, G.O. (1996) How a soybean plant develops. Spec. Rep. No. 53. Ames, IA: Iowa State Univ. of Science and Tech. Coop. Ext. Serv.

    Google Scholar 

  • Rosenberg, L.A. and Rinne, R.W. (1986) Moisture loss as a prerequisite for seedling growth in soybean seeds (Glycine max L. Merr.). J. Exp. Bot. 37, 1663–1674.

    Article  CAS  Google Scholar 

  • Santarem, E.R., Pelissier B. and Finer, J.J. (1997) Effect of explant orientation, pH, solidifying agent and wounding on initiation of soybean somatic embryos. In Vitro Cell Dev Biol 33, 13–19.

    CAS  Google Scholar 

  • Sawa, S., Watanabe, K., Goto, K., Kanaya, E., Morita, E.H. and Okada, K. (1999) FILAMENTOUS FLOWER, a meristem and organ identity gene of Arabidopsis, encodes a protein with a zinc finger and HMG-related domains. Genes Dev. 13, 1079–1088.

    Article  PubMed  CAS  Google Scholar 

  • Schmidt, J.S., Lindstrom, J.T. and Vodkin, L.O. (1994) Genetic length polymorphisms create size variation in proline rich proteins of the cell wall. Plant Journal 6: 177–186.

    Article  PubMed  CAS  Google Scholar 

  • Senda, M., Masuta, C., Ohnishi, S., Goto, K., Kasai, A., Sano, T., Hong, J-S. and MacFarlane, S. (2004) Patterning of virus-infected soybean seed coat is associated with suppression of endogenous silencing of chalcone synthase genes. Plant Cell 16, 807–818.

    Article  PubMed  CAS  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, EG., 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 

  • Shoemaker, R.C., Cregan, P.B. and Vodkin, L.O. (2004) Soybean Genomics. Pages 235–263 in Soybeans: Improvement, Production and Uses, 3rd edition, ASA monograph, J. Specht (ed). American Society of Agronomy, Madison, WI.

    Google Scholar 

  • Siegfried, K., Eshed, Y., Baum, S., Otsuga, D., Drews, G. and Bowman, J. (1999) Members of the YABBY gene family specify abaxial cell fate in Arabidopsis. Development 126, 4117–4128.

    PubMed  CAS  Google Scholar 

  • Spencer, M.W.B., Casson, S.A. and Lindsey, K. (2007) Transcriptional profiling of the Arabidopsis embryo. Plant Physiol. 143, 924–940.

    Article  PubMed  CAS  Google Scholar 

  • Stacey, G., Vodkin, L. O., Parrott, W. and Shoemaker, R.C. (2004) Draft plant for soybean Genomics. Plant Physiol. 135, 59–70.

    Article  PubMed  CAS  Google Scholar 

  • Stephens, P.A. and Nickell, C.D. (1992) Inheritance of pink flower color in soybean. Crop Sci. 32, 1131–1132.

    Google Scholar 

  • Stephens, P.A, Nickell, C.D. and Vodkin, L.O. (1993) Pink flower color associated with increased protein and seed size in soybean. Crop Sci. 33, 1135–1137.

    CAS  Google Scholar 

  • Stromvik, M.V., Thibaud-Nissen, F., and Vodkin, L.O. (2004) Mining soybean expressed sequence tag and microarray data. Ann Rev. Phytochemistry 38, 177–195.

    Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Toda, K., Yang, D., Yamanaka, N., Watanabe, S., Harada, K. and Takahashi, R. (2002) A single-base deletion in soybean flavonoid 3′-hydroxylase gene is associated with gray pubescence color. Plant Mol. Biol. 50, 187–196.

    Article  PubMed  CAS  Google Scholar 

  • Todd, J.J. and Vodkin, L.O. (1993) Pigmented soybean seed coats accumulate proanthocyanidins during development. Plant Physiol. 102, 663–670.

    PubMed  CAS  Google Scholar 

  • Todd, J.J. and Vodkin, L.O. (1996) Duplications that suppress and deletions that restore expression from a CHS multigene family. Plant Cell 8, 687–699.

    Article  PubMed  CAS  Google Scholar 

  • Tuteja, J.H., Clough, S.J., Chan, W.C. and Vodkin, L.O. (2004). Tissue-specific gene silencing mediated by a naturally occurring chalcone synthase gene cluster in Glycine max. Plant Cell 16, 819–835.

    Article  PubMed  CAS  Google Scholar 

  • Van der Krol, A.R., Mur, L.A., Beld, M., Mol, J.N.M and Stuitje, A.R. (1990) Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell 2, 291–299.

    Article  PubMed  Google Scholar 

  • Vodkin, L.O. (1981) Isolation and characterization of messenger RNAs for seed lectin and Kunitz trypsin inhibitor in soybean. Plant Physiology 68, 766–771.

    Article  PubMed  CAS  Google Scholar 

  • Vodkin, L.O., Rhodes, P.R. and Goldberg, R.B. (1983) A lectin gene insertion has the structural features of a transposable element. Cell, 34, 1023–1031.

    Article  PubMed  CAS  Google Scholar 

  • Vodkin, L.O., Khanna, A., Shealy, R., Clough, S.J., Gonzalez, D.O., Philip, P., Zabala, G., Thibaud-Nissen, F., Sidarous, M., Strömvik, 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, C.S., Todd, J.J. and Vodkin, L.O. (1994). Chalcone synthase mRNA and activity are reduced in yellow soybean seed coats with dominant I alleles. Plant Physiol. 105, 739–748.

    Article  PubMed  CAS  Google Scholar 

  • Walbot, V. (1999) Genes, genomes, genomics. What can plant biologists expect from the 1998 National Science Foundation Plant Genome Research Program. Plant Physiol. 119, 1151–1155.

    Article  PubMed  CAS  Google Scholar 

  • Wilcox, J.R. (1988) Performance and use of seed coat mutants in soybean. Crop Sci 28, 30–32.

    Google Scholar 

  • Wright M.S., Launis, K.L., Novitzky, R., Duesing, J.H. and Harms, C.T. (1991) A simple method for the recovery of multiple fertile plants from individual somatic embryos of soybean [Glycine max (L.) Merrill]. In Vitro Cell Dev Biol 27, 153–157.

    Article  Google Scholar 

  • Woodworth, C. M. (1921) Inheritance of cotyledon, seed-coat, hilum, and pubescence colors in soy-beans. Genet. 6, 487–553.

    CAS  Google Scholar 

  • Zabala, G.C. and Vodkin, L.O. (2003) Cloning of the pleiotropic T locus in soybean and two recessive alleles that differentially affect structure and expression of the encoded flavonoid 3′ hydroxylase. Genet. 163, 295–309.

    CAS  Google Scholar 

  • Zabala, G. and Vodkin, L.O. (2005) The wp mutation of Glycine max carries a gene-fragment-rich transposon of the CACTA superfamily. Plant Cell 17, 2619–2632.

    Article  PubMed  CAS  Google Scholar 

  • Zabala, G., Zou, J., Tuteja, J., Gonzalez, 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 Biology 6, 26.

    Article  PubMed  CAS  Google Scholar 

  • Zabala, G. and Vodkin, L.O. (2007a) A rearrangement resulting in small tandem repeats in the F3′5′ H gene of white flower genotypes is associated with the soybean W1 locus. Plant Genome 47, 113–124.

    Google Scholar 

  • Zabala, G. and Vodkin, L.O. (2007b) Novel exon combinations generated by alternative splicing of gene fragments mobilized by a CACTA transposon in Glycine max. BMC Plant Biology 7, 38.

    Google Scholar 

  • Zimmerman, J. L. (1993) Somatic embryogenesis: a model for early development in higher plants. Plant Cell 5, 1411–1423.

    Article  PubMed  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 down regulation of photosynthesis. Mol Plant Microbe Interact. 18, 1161–1174.

    Article  PubMed  CAS  Google Scholar 

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Vodkin, L., Jones, S., Gonzalez, D.O., Thibaud-Nissen, F., Zabala, G., Tuteja, J. (2008). Genomics of Soybean Seed Development. 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_11

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