메뉴 건너뛰기




Volumn 14, Issue 1, 2014, Pages

A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums

Author keywords

Functional genomics; Gene atlas; Gene expression; Microarray; Sorghum bicolor; Transcriptome

Indexed keywords

TRANSCRIPTOME;

EID: 84892686042     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-14-35     Document Type: Article
Times cited : (69)

References (47)
  • 2
    • 0003367283 scopus 로고
    • The origin and early cultivation of sorghums in Africa
    • Available electronically from
    • Mann J, Kimber C, Miller F. The origin and early cultivation of sorghums in Africa. Texas Agric Exp Station 1983, 1:128074. Available electronically from http://hdl.handle.net/1969.1/1280.
    • (1983) Texas Agric Exp Station , vol.1 , pp. 128074
    • Mann, J.1    Kimber, C.2    Miller, F.3
  • 3
    • 77951023470 scopus 로고    scopus 로고
    • Resource use efficiency and environmental performance of nine major biofuel crops, processed by first-generation conversion techniques
    • de Vries SC, van de Ven GW, van Ittersum MK, Giller KE. Resource use efficiency and environmental performance of nine major biofuel crops, processed by first-generation conversion techniques. Biomass and Bioenergy 2010, 34(5):588-601.
    • (2010) Biomass and Bioenergy , vol.34 , Issue.5 , pp. 588-601
    • de Vries, S.C.1    van de Ven, G.W.2    van Ittersum, M.K.3    Giller, K.E.4
  • 6
    • 80052259682 scopus 로고    scopus 로고
    • Genetic dissection of early-season cold tolerance in sorghum (Sorghum bicolor (L) Moench)
    • Burow G, Burke JJ, Xin Z, Franks CD. Genetic dissection of early-season cold tolerance in sorghum (Sorghum bicolor (L) Moench). Mol Breeding 2011, 28(3):391-402.
    • (2011) Mol Breeding , vol.28 , Issue.3 , pp. 391-402
    • Burow, G.1    Burke, J.J.2    Xin, Z.3    Franks, C.D.4
  • 8
    • 84875363989 scopus 로고    scopus 로고
    • Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L)
    • 10.1111/tpj.12104, 23289674
    • Zhang J-Y, Lee Y-C, Torres-Jerez I, Wang M, Yin Y, Chou W-C, He J, Shen H, Srivastava AC, Pennacchio C. Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L). Plant J 2013, 74(1):160-173. 10.1111/tpj.12104, 23289674.
    • (2013) Plant J , vol.74 , Issue.1 , pp. 160-173
    • Zhang, J.-Y.1    Lee, Y.-C.2    Torres-Jerez, I.3    Wang, M.4    Yin, Y.5    Chou, W.-C.6    He, J.7    Shen, H.8    Srivastava, A.C.9    Pennacchio, C.10
  • 9
    • 77953225899 scopus 로고    scopus 로고
    • Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses
    • 10.1186/gb-2010-11-2-r12, 2872872, 20128909
    • Swaminathan K, Alabady MS, Varala K, De Paoli E, Ho I, Rokhsar DS, Arumuganathan AK, Ming R, Green PJ, Meyers BC. Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses. Genome Biol 2010, 11(2):R12. 10.1186/gb-2010-11-2-r12, 2872872, 20128909.
    • (2010) Genome Biol , vol.11 , Issue.2
    • Swaminathan, K.1    Alabady, M.S.2    Varala, K.3    De Paoli, E.4    Ho, I.5    Rokhsar, D.S.6    Arumuganathan, A.K.7    Ming, R.8    Green, P.J.9    Meyers, B.C.10
  • 10
    • 37249034083 scopus 로고    scopus 로고
    • Coupling and coordination in gene expression processes: a systems biology view
    • 10.1038/nrg2223, 18071322
    • Komili S, Silver PA. Coupling and coordination in gene expression processes: a systems biology view. Nat Rev Genet 2008, 9(1):38-48. 10.1038/nrg2223, 18071322.
    • (2008) Nat Rev Genet , vol.9 , Issue.1 , pp. 38-48
    • Komili, S.1    Silver, P.A.2
  • 11
    • 67650394369 scopus 로고    scopus 로고
    • Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing
    • 10.1186/1471-2164-10-264, 2707382, 19523228
    • Mane S, Evans C, Cooper K, Crasta O, Folkerts O, Hutchison S, Harkins T, Thierry-Mieg D, Thierry-Mieg J, Jensen R. Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing. BMC Genomics 2009, 10(1):264. 10.1186/1471-2164-10-264, 2707382, 19523228.
    • (2009) BMC Genomics , vol.10 , Issue.1 , pp. 264
    • Mane, S.1    Evans, C.2    Cooper, K.3    Crasta, O.4    Folkerts, O.5    Hutchison, S.6    Harkins, T.7    Thierry-Mieg, D.8    Thierry-Mieg, J.9    Jensen, R.10
  • 15
    • 64749094910 scopus 로고    scopus 로고
    • Genevestigator transcriptome meta-analysis and biomarker search using rice and barley gene expression databases
    • 10.1093/mp/ssn048, 19825587
    • Zimmermann P, Laule O, Schmitz J, Hruz T, Bleuler S, Gruissem W. Genevestigator transcriptome meta-analysis and biomarker search using rice and barley gene expression databases. Mol Plant 2008, 1(5):851-857. 10.1093/mp/ssn048, 19825587.
    • (2008) Mol Plant , vol.1 , Issue.5 , pp. 851-857
    • Zimmermann, P.1    Laule, O.2    Schmitz, J.3    Hruz, T.4    Bleuler, S.5    Gruissem, W.6
  • 16
    • 71049151525 scopus 로고    scopus 로고
    • Plant MetGenMAP: an integrative analysis system for plant systems biology
    • 10.1104/pp.109.145169, 2786002, 19819981
    • Joung J-G, Corbett AM, Fellman SM, Tieman DM, Klee HJ, Giovannoni JJ, Fei Z. Plant MetGenMAP: an integrative analysis system for plant systems biology. Plant Physiol 2009, 151(4):1758-1768. 10.1104/pp.109.145169, 2786002, 19819981.
    • (2009) Plant Physiol , vol.151 , Issue.4 , pp. 1758-1768
    • Joung, J.-G.1    Corbett, A.M.2    Fellman, S.M.3    Tieman, D.M.4    Klee, H.J.5    Giovannoni, J.J.6    Fei, Z.7
  • 19
  • 20
    • 24744440739 scopus 로고    scopus 로고
    • Transcriptional profiling of sorghum induced by methyl jasmonate, salicylic acid, and aminocyclopropane carboxylic acid reveals cooperative regulation and novel gene responses
    • 10.1104/pp.104.058206, 1104189, 15863699
    • Salzman RA, Brady JA, Finlayson SA, Buchanan CD, Summer EJ, Sun F, Klein PE, Klein RR, Pratt LH, Cordonnier-Pratt M-M. Transcriptional profiling of sorghum induced by methyl jasmonate, salicylic acid, and aminocyclopropane carboxylic acid reveals cooperative regulation and novel gene responses. Plant Physiol 2005, 138(1):352-368. 10.1104/pp.104.058206, 1104189, 15863699.
    • (2005) Plant Physiol , vol.138 , Issue.1 , pp. 352-368
    • Salzman, R.A.1    Brady, J.A.2    Finlayson, S.A.3    Buchanan, C.D.4    Summer, E.J.5    Sun, F.6    Klein, P.E.7    Klein, R.R.8    Pratt, L.H.9    Cordonnier-Pratt, M.-M.10
  • 21
    • 84872192136 scopus 로고    scopus 로고
    • Genetic variation and expression diversity between grain and sweet sorghum lines
    • 10.1186/1471-2164-14-18, 3616923, 23324212
    • Jiang S-Y, Ma Z, Vanitha J, Ramachandran S. Genetic variation and expression diversity between grain and sweet sorghum lines. BMC Genomics 2013, 14(1):18. 10.1186/1471-2164-14-18, 3616923, 23324212.
    • (2013) BMC Genomics , vol.14 , Issue.1 , pp. 18
    • Jiang, S.-Y.1    Ma, Z.2    Vanitha, J.3    Ramachandran, S.4
  • 22
    • 80054108670 scopus 로고    scopus 로고
    • Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid
    • 10.1186/1471-2164-12-514, 3219791, 22008187
    • Dugas DV, Monaco MK, Olson A, Klein RR, Kumari S, Ware D, Klein PE. Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid. BMC Genomics 2011, 12(1):514. 10.1186/1471-2164-12-514, 3219791, 22008187.
    • (2011) BMC Genomics , vol.12 , Issue.1 , pp. 514
    • Dugas, D.V.1    Monaco, M.K.2    Olson, A.3    Klein, R.R.4    Kumari, S.5    Ware, D.6    Klein, P.E.7
  • 24
    • 79955875150 scopus 로고    scopus 로고
    • Genome-wide atlas of transcription during maize development
    • 10.1111/j.1365-313X.2011.04527.x, 21299659
    • Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, de Leon N, Kaeppler SM. Genome-wide atlas of transcription during maize development. Plant J 2011, 66(4):553-563. 10.1111/j.1365-313X.2011.04527.x, 21299659.
    • (2011) Plant J , vol.66 , Issue.4 , pp. 553-563
    • Sekhon, R.S.1    Lin, H.2    Childs, K.L.3    Hansey, C.N.4    Buell, C.R.5    de Leon, N.6    Kaeppler, S.M.7
  • 26
    • 59149095771 scopus 로고    scopus 로고
    • A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies
    • 10.1038/ng.282, 19122662
    • Jiao Y, Tausta SL, Gandotra N, Sun N, Liu T, Clay NK, Ceserani T, Chen M, Ma L, Holford M. A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet 2009, 41(2):258-263. 10.1038/ng.282, 19122662.
    • (2009) Nat Genet , vol.41 , Issue.2 , pp. 258-263
    • Jiao, Y.1    Tausta, S.L.2    Gandotra, N.3    Sun, N.4    Liu, T.5    Clay, N.K.6    Ceserani, T.7    Chen, M.8    Ma, L.9    Holford, M.10
  • 27
    • 77950104996 scopus 로고    scopus 로고
    • A dynamic gene expression atlas covering the entire life cycle of rice
    • 10.1111/j.1365-313X.2009.04100.x, 20003165
    • Wang L, Xie W, Chen Y, Tang W, Yang J, Ye R, Liu L, Lin Y, Xu C, Xiao J. A dynamic gene expression atlas covering the entire life cycle of rice. Plant J 2010, 61(5):752-766. 10.1111/j.1365-313X.2009.04100.x, 20003165.
    • (2010) Plant J , vol.61 , Issue.5 , pp. 752-766
    • Wang, L.1    Xie, W.2    Chen, Y.3    Tang, W.4    Yang, J.5    Ye, R.6    Liu, L.7    Lin, Y.8    Xu, C.9    Xiao, J.10
  • 29
    • 0005052243 scopus 로고    scopus 로고
    • Beltsville, Maryland: National Germplasm Resources Laboratory, USDA, ARS, National Genetic Resources Program
    • USDA, ARS, National Genetic Resources Program Germplasm Resources Information Network - (GRIN) 2014, Beltsville, Maryland: National Germplasm Resources Laboratory, USDA, ARS, National Genetic Resources Program.
    • (2014) Germplasm Resources Information Network - (GRIN)
  • 32
    • 84868676938 scopus 로고    scopus 로고
    • RNA-seq and microarray complement each other in transcriptome profiling
    • 10.1186/1471-2164-13-629, 3534599, 23153100
    • Kogenaru S, Yan Q, Guo Y, Wang N. RNA-seq and microarray complement each other in transcriptome profiling. BMC Genomics 2012, 13(1):629. 10.1186/1471-2164-13-629, 3534599, 23153100.
    • (2012) BMC Genomics , vol.13 , Issue.1 , pp. 629
    • Kogenaru, S.1    Yan, Q.2    Guo, Y.3    Wang, N.4
  • 33
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    • 10.1101/gr.079558.108, 2527709, 18550803
    • Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18(9):1509-1517. 10.1101/gr.079558.108, 2527709, 18550803.
    • (2008) Genome Res , vol.18 , Issue.9 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 34
    • 25444486426 scopus 로고    scopus 로고
    • Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR - how well do they correlate?
    • 10.1186/1471-2164-6-59, 1142514, 15854232
    • Dallas PB, Gottardo NG, Firth MJ, Beesley AH, Hoffmann K, Terry PA, Freitas JR, Boag JM, Cummings AJ, Kees UR. Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR - how well do they correlate?. BMC Genomics 2005, 6(1):59. 10.1186/1471-2164-6-59, 1142514, 15854232.
    • (2005) BMC Genomics , vol.6 , Issue.1 , pp. 59
    • Dallas, P.B.1    Gottardo, N.G.2    Firth, M.J.3    Beesley, A.H.4    Hoffmann, K.5    Terry, P.A.6    Freitas, J.R.7    Boag, J.M.8    Cummings, A.J.9    Kees, U.R.10
  • 35
    • 33845624887 scopus 로고    scopus 로고
    • Microarray validation: factors influencing correlation between oligonucleotide microarrays and real-time PCR
    • 10.1251/bpo126, 1779618, 17242735
    • Morey JS, Ryan JC, Van Dolah FM. Microarray validation: factors influencing correlation between oligonucleotide microarrays and real-time PCR. Biol Proced Online 2006, 8(1):175-193. 10.1251/bpo126, 1779618, 17242735.
    • (2006) Biol Proced Online , vol.8 , Issue.1 , pp. 175-193
    • Morey, J.S.1    Ryan, J.C.2    Van Dolah, F.M.3
  • 36
    • 76749138441 scopus 로고    scopus 로고
    • The bHLH transcription factor SPATULA controls final leaf size in Arabidopsis thaliana
    • 10.1093/pcp/pcp184, 20040585
    • Ichihashi Y, Horiguchi G, Gleissberg S, Tsukaya H. The bHLH transcription factor SPATULA controls final leaf size in Arabidopsis thaliana. Plant Cell Physiol 2010, 51(2):252-261. 10.1093/pcp/pcp184, 20040585.
    • (2010) Plant Cell Physiol , vol.51 , Issue.2 , pp. 252-261
    • Ichihashi, Y.1    Horiguchi, G.2    Gleissberg, S.3    Tsukaya, H.4
  • 37
    • 1142269617 scopus 로고    scopus 로고
    • Characterization in maize of ZmTIP2-3, a root-specific tonoplast intrinsic protein exhibiting aquaporin activity
    • 10.1093/jxb/052, 14673023
    • Lopez F, Bousser A, Sissoéff I, Hoarau J, Mahé A. Characterization in maize of ZmTIP2-3, a root-specific tonoplast intrinsic protein exhibiting aquaporin activity. J Exp Bot 2004, 55(396):539-541. 10.1093/jxb/052, 14673023.
    • (2004) J Exp Bot , vol.55 , Issue.396 , pp. 539-541
    • Lopez, F.1    Bousser, A.2    Sissoéff, I.3    Hoarau, J.4    Mahé, A.5
  • 38
    • 84861529088 scopus 로고    scopus 로고
    • Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel research
    • 10.1111/j.1365-313X.2012.04938.x, 22324449
    • Meyer E, Logan TL, Juenger TE. Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel research. Plant J 2012, 70(5):879-890. 10.1111/j.1365-313X.2012.04938.x, 22324449.
    • (2012) Plant J , vol.70 , Issue.5 , pp. 879-890
    • Meyer, E.1    Logan, T.L.2    Juenger, T.E.3
  • 39
    • 77954299992 scopus 로고    scopus 로고
    • AgriGO: a GO analysis toolkit for the agricultural community
    • 2896167, 20435677
    • Du Z, Zhou X, Ling Y, Zhang Z, Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 2010, 38(suppl 2):W64-W70. 2896167, 20435677.
    • (2010) Nucleic Acids Res , vol.38 , Issue.SUPPL. 2
    • Du, Z.1    Zhou, X.2    Ling, Y.3    Zhang, Z.4    Su, Z.5
  • 40
    • 84857443387 scopus 로고    scopus 로고
    • Stem sugar accumulation in sweet sorghum - activity and expression of sucrose metabolizing enzymes and sucrose transporters
    • 10.1016/j.jplph.2012.01.005, 22325624
    • Qazi HA, Paranjpe S, Bhargava S. Stem sugar accumulation in sweet sorghum - activity and expression of sucrose metabolizing enzymes and sucrose transporters. J Plant Physiol 2012, 169(6):605-613. 10.1016/j.jplph.2012.01.005, 22325624.
    • (2012) J Plant Physiol , vol.169 , Issue.6 , pp. 605-613
    • Qazi, H.A.1    Paranjpe, S.2    Bhargava, S.3
  • 41
    • 84882427325 scopus 로고    scopus 로고
    • Loss of function of cinnamyl alcohol dehydrogenase 1 leads to unconventional lignin and a temperature-sensitive growth defect in Medicago truncatula
    • 10.1073/pnas.1312234110, 3746925, 23901113
    • Zhao Q, Tobimatsu Y, Zhou R, Pattathil S, Gallego-Giraldo L, Fu C, Jackson LA, Hahn MG, Kim H, Chen F. Loss of function of cinnamyl alcohol dehydrogenase 1 leads to unconventional lignin and a temperature-sensitive growth defect in Medicago truncatula. Proc Natl Acad Sci USA 2013, 110(33):13660-13665. 10.1073/pnas.1312234110, 3746925, 23901113.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.33 , pp. 13660-13665
    • Zhao, Q.1    Tobimatsu, Y.2    Zhou, R.3    Pattathil, S.4    Gallego-Giraldo, L.5    Fu, C.6    Jackson, L.A.7    Hahn, M.G.8    Kim, H.9    Chen, F.10
  • 42
    • 84861528759 scopus 로고    scopus 로고
    • Brown midrib2 (Bmr2) encodes the major 4 coumarate: coenzyme A ligase involved in lignin biosynthesis in sorghum (Sorghum bicolor (L.) Moench)
    • 10.1111/j.1365-313X.2012.04933.x, 22313236
    • Saballos A, Sattler SE, Sanchez E, Foster TP, Xin Z, Kang C, Pedersen JF, Vermerris W. Brown midrib2 (Bmr2) encodes the major 4 coumarate: coenzyme A ligase involved in lignin biosynthesis in sorghum (Sorghum bicolor (L.) Moench). Plant J 2012, 70(5):818-830. 10.1111/j.1365-313X.2012.04933.x, 22313236.
    • (2012) Plant J , vol.70 , Issue.5 , pp. 818-830
    • Saballos, A.1    Sattler, S.E.2    Sanchez, E.3    Foster, T.P.4    Xin, Z.5    Kang, C.6    Pedersen, J.F.7    Vermerris, W.8
  • 44
    • 84893428105 scopus 로고    scopus 로고
    • Modifying lignin to improve bioenergy feedstocks: strengthening the barrier against pathogens?
    • 3617363, 23577013
    • Sattler SE, Funnell-Harris DL. Modifying lignin to improve bioenergy feedstocks: strengthening the barrier against pathogens?. Front Plant Sci 2013, 4:70. 3617363, 23577013.
    • (2013) Front Plant Sci , vol.4 , pp. 70
    • Sattler, S.E.1    Funnell-Harris, D.L.2
  • 45
    • 0001779714 scopus 로고
    • Growth stages of sorghum [Sorghum bicolor (L.) Moench]
    • Vanderlip R, Reeves H. Growth stages of sorghum [Sorghum bicolor (L.) Moench]. Agronomy J 1972, 64(1):13-16.
    • (1972) Agronomy J , vol.64 , Issue.1 , pp. 13-16
    • Vanderlip, R.1    Reeves, H.2
  • 46
    • 84855891546 scopus 로고    scopus 로고
    • Processing of materials derived from sweet sorghum for biobased products
    • Whitfield MB, Chinn MS, Veal MW. Processing of materials derived from sweet sorghum for biobased products. Ind Crops Products 2012, 37(1):362-375.
    • (2012) Ind Crops Products , vol.37 , Issue.1 , pp. 362-375
    • Whitfield, M.B.1    Chinn, M.S.2    Veal, M.W.3
  • 47
    • 0035710746 scopus 로고    scopus 로고
    • Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method
    • 10.1006/meth.2001.1262, 11846609
    • Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25(4):402-408. 10.1006/meth.2001.1262, 11846609.
    • (2001) Methods , vol.25 , Issue.4 , pp. 402-408
    • Livak, K.J.1    Schmittgen, T.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.