Transcriptome profiling of soybean root tips
Farzad Haerizadeh A , Mohan B. Singh A and Prem L. Bhalla A B
+ Author Affiliations
- Author Affiliations
A Plant Molecular Biology and Biotechnology Laboratory, Australian Research Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, The University of Melbourne, Parkville, Vic. 3010, Australia.
B Corresponding author. Email: premlb@unimelb.edu.au
Functional Plant Biology 38(6) 451-461 https://doi.org/10.1071/FP10230
Submitted: 26 November 2010 Accepted: 30 March 2011 Published: 3 June 2011
Abstract
Soybean (Glycine max L.), a major legume crop, is important to human nutrition and is a source of animal feed. Similar to many legumes, a key feature of the soybean is its symbiotic association with soil bacteria that fix atmospheric nitrogen. However, knowledge of the gene expression of its root system, particularly the root meristematic region, is limited. Here, we have addressed this by investigating the gene expression profile of the soybean root tip, using soybean Affymetrix chips containing 37 500 probe sets (Affymetrix Inc.) and have compared this expression profile with that of the nonmeristematic tissue. We identified a total of 5012 upregulated and 4136 downregulated genes in the soybean root tip. Among the upregulated genes, 559 showed strong preferential expression in the root tip, indicating that they are likely to be associated with root apical meristem specificity and root tip function. Genes involved in membrane transport, defence signalling and metabolism were upregulated in the soybean root tip. Further, our data provide a resource of novel target genes for further studies involving root development and biology, and will possibly have a positive impact on future crop breeding.
Additional keywords: gene expression, Glycine max, legume, root cap, root apical meristem.
References
Aida M, Beis D, Heidstra R, Willemsen V, Blilou I, Galinha C, Nussaume L, Noh Y-S, Amasino R, Scheres B (2004) The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche. Cell 119, 109–120.| The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXotlyqu7o%3D&md5=994ccfc28671a5a468e35609e9788174CAS | 15454085PubMed |
Benková E, Michniewicz M, Sauer M, Teichmann T, Seifertová D, Jürgens G, Friml J (2003) Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell 115, 591–602.
| Local, efflux-dependent auxin gradients as a common module for plant organ formation.Crossref | GoogleScholarGoogle Scholar | 14651850PubMed |
Bhalla PL, Singh MB (2006) Molecular control of stem cell maintenance in shoot apical meristem. Plant Cell Reports 25, 249–256.
| Molecular control of stem cell maintenance in shoot apical meristem.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28Xis1Olu70%3D&md5=7d1610e7a37b4842d009416394b87782CAS | 16315035PubMed |
Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (Oxford, England) 19, 185–193.
| A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3sXitlCnsL4%3D&md5=bdab9aaac97c24c50a1494b6d56f8db4CAS | 12538238PubMed |
Gao MJ, Parkin I, Lydiate D, Hannoufa A (2004) An auxin-responsive SCARECROW-like transcriptional activator interacts with histone deacetylase. Plant Molecular Biology 55, 417–431.
| An auxin-responsive SCARECROW-like transcriptional activator interacts with histone deacetylase.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXhsFWhtQ%3D%3D&md5=16be1171f16ab0769139fd6e6b05f6e6CAS | 15604690PubMed |
Groot EP, Doyle JA, Nichol SA, Rost TL (2004) Phylogenetic distribution and evolution of root apical meristem organization in dicotyledonous angiosperms. International Journal of Plant Sciences 165, 97–105.
| Phylogenetic distribution and evolution of root apical meristem organization in dicotyledonous angiosperms.Crossref | GoogleScholarGoogle Scholar |
Gunawardena U, Rodriguez M, Straney D, Romeo JT, VanEtten D, Hawes MC (2005) Tissue-specific localization of pea root infection by Nectria haematococcia. Mechanisms and consequences. Plant Physiology 137, 1363–1374.
| Tissue-specific localization of pea root infection by Nectria haematococcia. Mechanisms and consequences.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXjslaqu78%3D&md5=db9113f20596e4b27740b2a8e944ddf0CAS | 15778461PubMed |
Haerizadeh F, Wong CE, Singh MB, Bhalla PL (2009a) Genome-wide analysis of gene expression in soybean shoot apical meristem. Plant Molecular Biology 69, 711–727.
| Genome-wide analysis of gene expression in soybean shoot apical meristem.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXis1artLs%3D&md5=45dcc6d8e7624d7389c19504a10ac52cCAS | 19115044PubMed |
Haerizadeh F, Wong CE, Bhalla PL, Gresshoff PM, Singh MB (2009b) Genomic expression profiling of mature soybean (Glycine max) pollen. BMC Plant Biology 9, 25
| Genomic expression profiling of mature soybean (Glycine max) pollen.Crossref | GoogleScholarGoogle Scholar | 19265555PubMed |
Hamamoto L, Hawes MC, Rost TL (2006) The production and release of living root cap border cells is a function of root apical meristem type in dicotyledonous angiosperm plants. Annals of Botany 97, 917–923.
| The production and release of living root cap border cells is a function of root apical meristem type in dicotyledonous angiosperm plants.Crossref | GoogleScholarGoogle Scholar | 16488922PubMed |
Hawes MC, Woo H, Wen F (2005) Root border cells: a delivery system for chemicals controlling plant health. Roots and Soil Management: Interactions Between Roots and Soil, Agronomy Monograph No. 48, 107–117.
Jasinski S, Piazza P, Craft J, Hay A, Woolley L, Rieu I, Phillips A, Hedden P, Tsiantis M (2005) KNOX action in Arabidopsis is mediated by coordinate regulation of cytokinin and gibberellin activities. Current Biology 15, 1560–1565.
| KNOX action in Arabidopsis is mediated by coordinate regulation of cytokinin and gibberellin activities.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXpslyitL8%3D&md5=be7227cad1d21c5b4e7233a2fbfbdf8fCAS | 16139211PubMed |
Jiang K, Zhang S, Lee S, Tsai G, Kim K, Huang H, Chilcott C, Zhu T, Feldman L (2006) Transcription profile analyses identify genes and pathways central to root cap functions in maize. Plant Molecular Biology 60, 343–363.
| Transcription profile analyses identify genes and pathways central to root cap functions in maize.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XitVamsr0%3D&md5=05994d6ade9e451e5fff23c998a1e830CAS | 16514559PubMed |
Kerk NM, Ceserani T, Tausta SL, Sussex IM, Nelson TM (2003) Laser capture microdissection of cells from plant tissues. Plant Physiology 132, 27–35.
| Laser capture microdissection of cells from plant tissues.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3sXktVGgsrs%3D&md5=d8b9941d69a4ba84315791186716aa9eCAS | 12746508PubMed |
Laskowski M, Grieneisen VA, Hofhuis H, TenHove CA, Hogeweg P, Marer AFM, Scheres B (2008) Root system architecture from coupling cell shape to auxin transport. PLoS Biology 6, e307
| Root system architecture from coupling cell shape to auxin transport.Crossref | GoogleScholarGoogle Scholar | 19090618PubMed |
Li J, Brader G, Palva ET (2004) The WRKY70 transcription factor: a node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense. The Plant Cell 16, 319–331.
| The WRKY70 transcription factor: a node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXhsFKisrY%3D&md5=fe80661380cebd140e129e1e776e188dCAS | 14742872PubMed |
Long J, Moan E, Medford J, Barton M (1996) Member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis. Nature 379, 66–69.
| Member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK28XivVKgsw%3D%3D&md5=f26de7a6d239f339ada35ca824621d47CAS | 8538741PubMed |
Maathuis FJ, Filatov V, Herzyk P, Krijger GC, Axelsen KB, Chen S, Green BJ, Li Y, Madagan KL, Sánchez-Fernández R, Forde BG, Palmgren MG, Rea PA, Williams LE, Sanders D, Amtmann A (2003) Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress. The Plant Journal 35, 675–692.
| Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3sXot1OqtbY%3D&md5=0f0fcfa10f144e2ec09518b3de09d621CAS | 12969422PubMed |
Mathesius U, Djordjevic MA, Oakes M, Goffard N, Haerizadeh F, Weiller GF, Singh MB, Bhalla PL (2011) Comparative proteomic profiles of the soybean (Glycine max) root apex and differentiated root zone. Proteomics 11, 1707–1719.
| Comparative proteomic profiles of the soybean (Glycine max) root apex and differentiated root zone.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXmslOhtrg%3D&md5=48c6103933627b6637b9b3867996229cCAS | 21438152PubMed |
Nagahashi G, Douds DD (2004) Isolated root caps, border cells, and mucilage from host roots stimulate hyphal branching of the arbuscular mycorrhizal fungus, Gigaspora gigantea. Mycological Research 108, 1079–1088.
| Isolated root caps, border cells, and mucilage from host roots stimulate hyphal branching of the arbuscular mycorrhizal fungus, Gigaspora gigantea.Crossref | GoogleScholarGoogle Scholar | 15506019PubMed |
Nawy T, Lee JY, Colinas J, Wang JY, Thongrod SC, Malamy JE, Birnbaum K, Benfey PN (2005) Transcriptional profile of the Arabidopsis root quiescent center. The Plant Cell 17, 1908–1925.
| Transcriptional profile of the Arabidopsis root quiescent center.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXnt1yjt7Y%3D&md5=e6b82281c19aa92d994090b6ecce1173CAS | 15937229PubMed |
Niemira BA, Safir GR, Hawes MC (1996) Arbuscular mycorrhizal colonization and border cell production: a possible correlation. Phytopathology 86, 563–568.
Palmgren MG (2001) Plant plasma membrane H+ -ATPases: powerhouses for nutrient uptake. Annual Review of Plant Physiology and Plant Molecular Biology 52, 817–845.
| Plant plasma membrane H+ -ATPases: powerhouses for nutrient uptake.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3MXkslWgtrs%3D&md5=90c129e3b1991d0f58c97963376668aaCAS | 11337417PubMed |
Rossignol P, Stevens R, Perennes C, Jasinski S, Cella R, Tremousaygue D, Bergounioux C (2002) AtE2F-a and AtDP-a, members of the E2F family of transcription factors, induce Arabidopsis leaf cells to re-enter S phase. Molecular Genetics and Genomics 266, 995–1003.
| AtE2F-a and AtDP-a, members of the E2F family of transcription factors, induce Arabidopsis leaf cells to re-enter S phase.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD38XjtlWhtL8%3D&md5=69f68aa115ff63e27598c8188c4c3362CAS | 11862494PubMed |
Rothstein SJ (2007) Returning to our roots: making plant biology research relevant to future challenges in agriculture. The Plant Cell 19, 2695–2699.
| Returning to our roots: making plant biology research relevant to future challenges in agriculture.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXhtlWiu7fE&md5=cb2b9eb1b94d302857181ca2802daac0CAS | 17873097PubMed |
Sabatini S, Heidstra R, Wildwater M, Scheres B (2003) SCARECROW is involved in positioning the stem cell niche in the Arabidopsis root meristem. Genes & Development 17, 354–358.
| SCARECROW is involved in positioning the stem cell niche in the Arabidopsis root meristem.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3sXhtF2mtLg%3D&md5=0d9c64d1de414cf76772932624bf9b1aCAS | 12569126PubMed |
Sakamoto T, Kamiya N, Ueguchi-Tanaka M, Iwahori S, Matsuoka M (2001) KNOX homeodomain protein directly suppresses the expression of a gibberellin biosynthetic gene in the tobacco shoot apical meristem. Genes & Development 15, 581–590.
| KNOX homeodomain protein directly suppresses the expression of a gibberellin biosynthetic gene in the tobacco shoot apical meristem.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3MXhvVChs7o%3D&md5=ef46f88d26ae9a19e86522a3ea7efcd6CAS | 11238378PubMed |
Schubert D, Clarenz O, Goodrich J (2005) Epigenetic control of plant development by Polycomb-group proteins. Current Opinion in Plant Biology 8, 553–561.
| Epigenetic control of plant development by Polycomb-group proteins.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXosVahtrs%3D&md5=e1e540bd20cc9bf7c98e477682332584CAS | 16043386PubMed |
Singh MB, Bhalla PL (2006) Plant stem cells find their own niche. Trends in Plant Science 11, 241–246.
| Plant stem cells find their own niche.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28Xks1Oktr8%3D&md5=70d0b7c06f68fc768c76803c3976ce55CAS | 16616580PubMed |
Smyth G (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3, Article 3
| Linear models and empirical Bayes methods for assessing differential expression in microarray experiments.Crossref | GoogleScholarGoogle Scholar |
Stahl Y, Simon R (2005) Plant stem cell niches. The International Journal of Developmental Biology 49, 479–489.
| Plant stem cell niches.Crossref | GoogleScholarGoogle Scholar | 16096958PubMed |
Stahl Y, Wink RH, Ingram GC, Simon R (2009) A signaling module controlling the stem cell niche in Arabidopsis root meristems. Current Biology 19, 909–914.
| A signaling module controlling the stem cell niche in Arabidopsis root meristems.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXntVGjurg%3D&md5=60b7ebdfdcd99869273cb1a73e75d5a9CAS | 19398337PubMed |
Swarup K, Benková E, Swarup R, Casimiro I, Péret B, et al (2008) The auxin influx carrier LAX3 promotes lateral root emergence. Nature Cell Biology 10, 946–954.
| The auxin influx carrier LAX3 promotes lateral root emergence.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXpt1SmtLY%3D&md5=39936e95f55eef306ff965f453d9f222CAS | 18622388PubMed |
Tromas A, Braun N, Muller P, Khodus T, Paponov IA, Palme K, Ljung K, Lee JY, Benfey P, Murray JA, Scheres B, Perrot-Rechenmann C (2009) The AUXIN BINDING PROTEIN 1 is required for differential auxin responses mediating root growth. PLoS One 4, e6648
| The AUXIN BINDING PROTEIN 1 is required for differential auxin responses mediating root growth.Crossref | GoogleScholarGoogle Scholar | 19777056PubMed |
Tsukagoshi H, Saijo T, Shibata D, Morikami A, Nakamura K (2005) Analysis of a sugar response mutant of Arabidopsis identified a novel B3 domain protein that functions as an active transcriptional repressor. Plant Physiology 138, 675–685.
| Analysis of a sugar response mutant of Arabidopsis identified a novel B3 domain protein that functions as an active transcriptional repressor.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXmtVaqu70%3D&md5=d8774a338a7c23196018862953eff6ffCAS | 15894743PubMed |
Volpe TA, Kidner C, Hall IM, Teng G, Grewal SIS, Martienssen RA (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833–1837.
| Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD38XmvFGgsr4%3D&md5=e557a2f8db11c2239a8d477028d42b3fCAS | 12193640PubMed |
Wildwater M, Campilho A, Perez-Perez JM, Heidstra R, Blilou I, Korthout H, Chatterjee J, Mariconti L, Gruissem W, Scheres B (2005) The RETINOBLASTOMA-RELATED gene regulates stem cell maintenance in Arabidopsis roots. Cell 123, 1337–1349.
| The RETINOBLASTOMA-RELATED gene regulates stem cell maintenance in Arabidopsis roots.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XktlWhsw%3D%3D&md5=121a3ae080f6034ecdf7d4c904751106CAS | 16377572PubMed |
Williams L, Fletcher JC (2005) Stem cell regulation in the Arabidopsis shoot apical meristem. Current Opinion in Plant Biology 8, 582–586.
| Stem cell regulation in the Arabidopsis shoot apical meristem.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXhtFers7jN&md5=c5942bd047501b199d347a40013916deCAS | 16183326PubMed |
Wong CE, Singh MB, Bhalla PL (2009) Molecular processes underlying floral transition in the soybean shoot apical meristem. The Plant Journal 57, 832–845.
| Molecular processes underlying floral transition in the soybean shoot apical meristem.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXjslSlsbo%3D&md5=d7d424acfb0ea8811e025d72f5cdbf43CAS | 18980639PubMed |
Zanetti ME, Chang IF, Gong F, Galbraith DW, Bailey-Serres J (2005) Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiology 138, 624–635.
| Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXmtVaqurY%3D&md5=8ac65efe2e3bd0cc9871e0d5b9a33fc4CAS | 15955926PubMed |
Zhang Z-L, Xie Z, Zou X, Casaretto J, Ho THD, Shen QJ (2004) A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Plant Physiology 134, 1500–1513.
| A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXjsFKms7c%3D&md5=ee98533a9138f0fa671d3c6208025500CAS | 15047897PubMed |
Zou X, Seemann JR, Neuman D, Shen QJ (2004) A WRKY gene from creosote bush encodes an activator of the abscisic acid signaling pathway. The Journal of Biological Chemistry 279, 55770–55779.
| A WRKY gene from creosote bush encodes an activator of the abscisic acid signaling pathway.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXhtFeis7fJ&md5=97910f5c3b22c8104b2a7891f3ce88abCAS | 15504732PubMed |
