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Volumn 8, Issue 3, 2013, Pages

Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity

Author keywords

[No Author keywords available]

Indexed keywords

GLYCININ; HISTONE; PROLINE RICH PROTEIN; TRANSCRIPTOME;

EID: 84875042712     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0059270     Document Type: Article
Times cited : (121)

References (41)
  • 3
    • 84863853995 scopus 로고    scopus 로고
    • Large-scale sequencing of normalized full-length cDNA library of soybean seed at different developmental stages and analysis of the gene expression profiles based on ESTs
    • Sha AH, Li C, Yan XH, Shan ZH, Zhou XA, et al. (2012) Large-scale sequencing of normalized full-length cDNA library of soybean seed at different developmental stages and analysis of the gene expression profiles based on ESTs. Mol Biol Rep 39: 2867-2874.
    • (2012) Mol Biol Rep , vol.39 , pp. 2867-2874
    • Sha, A.H.1    Li, C.2    Yan, X.H.3    Shan, Z.H.4    Zhou, X.A.5
  • 4
    • 85102326196 scopus 로고    scopus 로고
    • Reproductive morphology
    • In: Boerma HR, Specht JE, editors, Madison WI: American Society of Agronomy
    • Carlson JB, Lersten NR (2004) Reproductive morphology. In: Boerma HR, Specht JE, editors. Soybeans: improvement, production, and uses. Madison WI: American Society of Agronomy. 59-95.
    • (2004) Soybeans: Improvement, production, and uses , pp. 59-95
    • Carlson, J.B.1    Lersten, N.R.2
  • 5
    • 0003634035 scopus 로고    scopus 로고
    • Special Report No. 53. Ames, IA: Iowa State University of Science and Technology Cooperative Extension Service
    • Ritchie SW, Hanway JJ, Thompson HE, Benson GO (1996) How a soybean plant develops. Special Report No. 53. Ames, IA: Iowa State University of Science and Technology Cooperative Extension Service.
    • (1996) How a soybean plant develops
    • Ritchie, S.W.1    Hanway, J.J.2    Thompson, H.E.3    Benson, G.O.4
  • 6
    • 0003032039 scopus 로고    scopus 로고
    • Reproductive development
    • In: Buchanan BB, Gruissem W, Jones RL, editors, Rockville MD: American Society of Plant Physiologists
    • Bewley JD, Hempel FD, McCormick S, Zambryski P (2000) Reproductive development. In: Buchanan BB, Gruissem W, Jones RL, editors. Biochemistry and molecular biology of plants. Rockville MD: American Society of Plant Physiologists. 988-1043.
    • (2000) Biochemistry and molecular biology of plants , pp. 988-1043
    • Bewley, J.D.1    Hempel, F.D.2    McCormick, S.3    Zambryski, P.4
  • 7
    • 77951169414 scopus 로고    scopus 로고
    • Flux of transcript patterns during soybean seed development
    • Jones SI, Gonzalez DO, Vodkin LO, (2010) Flux of transcript patterns during soybean seed development. BMC Genomics 11: 136.
    • (2010) BMC Genomics , vol.11 , pp. 136
    • Jones, S.I.1    Gonzalez, D.O.2    Vodkin, L.O.3
  • 8
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 10
    • 0037311919 scopus 로고    scopus 로고
    • TM4: a free, open-source system for microarray data management and analysis
    • Saeed AI, Sharov V, White J, Li J, Liang W, et al. (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34: 374-378.
    • (2003) Biotechniques , vol.34 , pp. 374-378
    • Saeed, A.I.1    Sharov, V.2    White, J.3    Li, J.4    Liang, W.5
  • 11
    • 0024720617 scopus 로고
    • Developmentally regulated expression of soybean proline-rich cell wall protein genes
    • Hong JC, Nagao RT, Key JL, (1989) Developmentally regulated expression of soybean proline-rich cell wall protein genes. Plant Cell 1: 937-943.
    • (1989) Plant Cell , vol.1 , pp. 937-943
    • Hong, J.C.1    Nagao, R.T.2    Key, J.L.3
  • 12
    • 0026175595 scopus 로고
    • A soybean cell wall protein is affected by seed color genotype
    • Lindstrom JT, Vodkin LO, (1991) A soybean cell wall protein is affected by seed color genotype. Plant Cell 3: 561-571.
    • (1991) Plant Cell , vol.3 , pp. 561-571
    • Lindstrom, J.T.1    Vodkin, L.O.2
  • 15
    • 0001084976 scopus 로고
    • Expression of storage-protein genes during soybean seed development
    • Meinke DW, Chen J, Beachy RN, (1981) Expression of storage-protein genes during soybean seed development. Planta 153: 130-139.
    • (1981) Planta , vol.153 , pp. 130-139
    • Meinke, D.W.1    Chen, J.2    Beachy, R.N.3
  • 18
    • 79957876295 scopus 로고    scopus 로고
    • Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis
    • Peng FY, Weselake RJ, (2011) Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis. BMC Genomics 12: 286.
    • (2011) BMC Genomics , vol.12 , pp. 286
    • Peng, F.Y.1    Weselake, R.J.2
  • 19
    • 0000491770 scopus 로고    scopus 로고
    • Specific soybean lipoxygenases localize to discrete subcellular compartments and their mRNAs are differentially regulated by source-sink status
    • Stephenson LC, Bunker TW, Dubbs WE, Grimes HD, (1998) Specific soybean lipoxygenases localize to discrete subcellular compartments and their mRNAs are differentially regulated by source-sink status. Plant Physiol 116: 923-933.
    • (1998) Plant Physiol , vol.116 , pp. 923-933
    • Stephenson, L.C.1    Bunker, T.W.2    Dubbs, W.E.3    Grimes, H.D.4
  • 21
    • 0037052578 scopus 로고    scopus 로고
    • Isolation of lipoxygenase isoforms from Glycine max embryo axes based on apparent cross-reactivity with anti-myosin antibodies
    • Islas-Flores I, Corrales-Villamar S, Bearer E, Raya JC, Villanueva MA, (2002) Isolation of lipoxygenase isoforms from Glycine max embryo axes based on apparent cross-reactivity with anti-myosin antibodies. Biochim Biophys Acta 1571: 64-70.
    • (2002) Biochim Biophys Acta , vol.1571 , pp. 64-70
    • Islas-Flores, I.1    Corrales-Villamar, S.2    Bearer, E.3    Raya, J.C.4    Villanueva, M.A.5
  • 22
    • 0019185338 scopus 로고
    • Polyadenylated RNA sequences which are reduced in concentration following auxin treatment of soybean hypocotyls
    • Baulcombe DC, Key JL, (1980) Polyadenylated RNA sequences which are reduced in concentration following auxin treatment of soybean hypocotyls. J Biol Chem 255: 8907-13.
    • (1980) J Biol Chem , vol.255 , pp. 8907-8913
    • Baulcombe, D.C.1    Key, J.L.2
  • 23
    • 0037507700 scopus 로고    scopus 로고
    • Clustering of microarray data reveals transcript patterns associated with somatic embryogenesis in soybean
    • Thibaud-Nissen F, Shealy RT, Khanna A, Vodkin LO, (2003) Clustering of microarray data reveals transcript patterns associated with somatic embryogenesis in soybean. Plant Physiol 132: 118-136.
    • (2003) Plant Physiol , vol.132 , pp. 118-136
    • Thibaud-Nissen, F.1    Shealy, R.T.2    Khanna, A.3    Vodkin, L.O.4
  • 24
    • 41449118753 scopus 로고    scopus 로고
    • Specific elements of the glyoxylate pathway play a significant role in the functional transition of the soybean cotyledon during seedling development
    • Gonzalez DO, Vodkin LO, (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.
    • (2007) BMC Genomics , vol.8 , pp. 468
    • Gonzalez, D.O.1    Vodkin, L.O.2
  • 25
    • 0027140360 scopus 로고
    • Molecular responses to water deficit
    • Bray EB, (1993) Molecular responses to water deficit. Plant Physiol 103: 1035-1040.
    • (1993) Plant Physiol , vol.103 , pp. 1035-1040
    • Bray, E.B.1
  • 26
    • 0034007384 scopus 로고    scopus 로고
    • Highly hydrophilic proteins in prokaryotes and eukaryotes are common during conditions of water deficit
    • Garay-Arroyo A, Colmenero-Flores JM, Garciarrubio A, Covarrubias AA, (2000) Highly hydrophilic proteins in prokaryotes and eukaryotes are common during conditions of water deficit. J Biol Chem 275: 5668-5674.
    • (2000) J Biol Chem , vol.275 , pp. 5668-5674
    • Garay-Arroyo, A.1    Colmenero-Flores, J.M.2    Garciarrubio, A.3    Covarrubias, A.A.4
  • 27
    • 0034816095 scopus 로고    scopus 로고
    • The Arabidopsis TT2 gene encodes an R2R3 MYB domain protein that acts as a key determinant for proanthocyanidin accumulation in developing seed
    • Nesi N, Jond C, Debeaujon I, Caboche M, Lepiniec L, (2001) The Arabidopsis TT2 gene encodes an R2R3 MYB domain protein that acts as a key determinant for proanthocyanidin accumulation in developing seed. Plant Cell 13: 2099-2114.
    • (2001) Plant Cell , vol.13 , pp. 2099-2114
    • Nesi, N.1    Jond, C.2    Debeaujon, I.3    Caboche, M.4    Lepiniec, L.5
  • 28
    • 79960921597 scopus 로고    scopus 로고
    • TRANSPARENT TESTA1 interacts with R2R3-MYB factors and affects early and late steps of flavonoid biosynthesis in the endothelium of Arabidopsis thaliana seeds
    • Appelhagen I, Lu GH, Huep G, Schmelzer E, Weisshaar B, et al. (2011) TRANSPARENT TESTA1 interacts with R2R3-MYB factors and affects early and late steps of flavonoid biosynthesis in the endothelium of Arabidopsis thaliana seeds. Plant J 67: 406-419.
    • (2011) Plant J , vol.67 , pp. 406-419
    • Appelhagen, I.1    Lu, G.H.2    Huep, G.3    Schmelzer, E.4    Weisshaar, B.5
  • 29
    • 24944457267 scopus 로고    scopus 로고
    • Surge and destroy: the role of auxin in plant embryogenesis
    • Jenik PD, Barton MK, (2005) Surge and destroy: the role of auxin in plant embryogenesis. Development 132: 3577-85.
    • (2005) Development , vol.132 , pp. 3577-3585
    • Jenik, P.D.1    Barton, M.K.2
  • 30
    • 84864777559 scopus 로고    scopus 로고
    • Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing
    • Shamimuzzaman M, Vodkin L, (2012) Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing. BMC Genomics 13: 310.
    • (2012) BMC Genomics , vol.13 , pp. 310
    • Shamimuzzaman, M.1    Vodkin, L.2
  • 31
    • 72049114156 scopus 로고    scopus 로고
    • Endogenous, tissue-specific short interfering RNAs silence the chalcone synthase gene family in Glycine max seed coats
    • Tuteja JH, Zabala G, Varala K, Hudson M, Vodkin LO, (2009) Endogenous, tissue-specific short interfering RNAs silence the chalcone synthase gene family in Glycine max seed coats. Plant Cell 21: 3063-3077.
    • (2009) Plant Cell , vol.21 , pp. 3063-3077
    • Tuteja, J.H.1    Zabala, G.2    Varala, K.3    Hudson, M.4    Vodkin, L.O.5
  • 32
    • 84866791265 scopus 로고    scopus 로고
    • Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max
    • Zabala G, Campos E, Varala KK, Bloomfield S, Jones SI, et al. (2012) Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max. BMC Plant Biol 12: 177.
    • (2012) BMC Plant Biol , vol.12 , pp. 177
    • Zabala, G.1    Campos, E.2    Varala, K.K.3    Bloomfield, S.4    Jones, S.I.5
  • 33
    • 57749110646 scopus 로고    scopus 로고
    • The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance
    • Li WX, Oono Y, Zhu J, He XJ, Wu JM, et al. (2008) The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. Plant Cell 20: 2238-2251.
    • (2008) Plant Cell , vol.20 , pp. 2238-2251
    • Li, W.X.1    Oono, Y.2    Zhu, J.3    He, X.J.4    Wu, J.M.5
  • 34
    • 79960144673 scopus 로고    scopus 로고
    • Functions and application of the AP2/ERF transcription factor family in crop improvement
    • Xu ZS, Chen M, Li LC, Ma YZ, (2011) Functions and application of the AP2/ERF transcription factor family in crop improvement. J Integr Plant Biol 53: 570-585.
    • (2011) J Integr Plant Biol , vol.53 , pp. 570-585
    • Xu, Z.S.1    Chen, M.2    Li, L.C.3    Ma, Y.Z.4
  • 35
    • 77956175784 scopus 로고    scopus 로고
    • AP2/EREBP transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde signaling
    • Dietz KJ, Vogel MO, Viehhauser A, (2010) AP2/EREBP transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde signaling. Protoplasma 245: 3-14.
    • (2010) Protoplasma , vol.245 , pp. 3-14
    • Dietz, K.J.1    Vogel, M.O.2    Viehhauser, A.3
  • 36
    • 13744249762 scopus 로고    scopus 로고
    • NAC transcription factors: structurally distinct, functionally diverse
    • Olsen AN, Ernst HA, Leggio L, Skriver K, (2005) NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci 10: 79-87.
    • (2005) Trends Plant Sci , vol.10 , pp. 79-87
    • Olsen, A.N.1    Ernst, H.A.2    Leggio, L.3    Skriver, K.4
  • 37
    • 80052005755 scopus 로고    scopus 로고
    • Genome-wide survey and expression analysis of the plant-specific NAC transcription factor family in soybean during development and dehydration stress
    • Le DT, Nishiyama R, Watanabe Y, Mochida K, Yamaguchi-Shinozaki K, et al. (2011) Genome-wide survey and expression analysis of the plant-specific NAC transcription factor family in soybean during development and dehydration stress. DNA Res 18: 263-276.
    • (2011) DNA Res , vol.18 , pp. 263-276
    • Le, D.T.1    Nishiyama, R.2    Watanabe, Y.3    Mochida, K.4    Yamaguchi-Shinozaki, K.5
  • 39
    • 81255129648 scopus 로고    scopus 로고
    • Transcript profiling reveals expression differences in wild-type and glabrous soybean lines
    • Hunt M, Kaur N, Strömvik M, Vodkin L, (2011) Transcript profiling reveals expression differences in wild-type and glabrous soybean lines. BMC Plant Biol 11: 145.
    • (2011) BMC Plant Biol , vol.11 , pp. 145
    • Hunt, M.1    Kaur, N.2    Strömvik, M.3    Vodkin, L.4
  • 40
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W, (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106.
    • (2010) Genome Biol , vol.11
    • Anders, S.1    Huber, W.2
  • 41
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: open software development for computational biology and bioinformatics
    • Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
    • (2004) Genome Biol , vol.5
    • Gentleman, R.C.1    Carey, V.J.2    Bates, D.M.3    Bolstad, B.4    Dettling, M.5


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