Abstract
The root plays an important role during plant development and growth, i.e., the plant body maintenance, nutrient storage, absorption of water, oxygen and nutrient from the soil, and storage of water and carbohydrates, etc. The objective of this study was attempted to determine root-specific genes at the initial developmental stages of maize by using network-based transcriptome analysis. The raw data obtained using RNA-seq were filtered for quality control of the reads with the FASTQC tool, and the filtered reads were pre-proceed using the TRIMMOMATIC tool. The enriched BINs of the DEGs were detected using PageMan analysis with the ORA_FISHER statistical test, and genes were assigned to metabolic pathways by using the MapMan tool, which was also used for detecting transcription factors (TFs). For reconstruction of the co-expression network, we used the algorithm for the reconstruction of accurate cellular networks (ARACNE) in the R package, and then the reconstructed co-expression network was visualized using the Cytoscape tool. RNA-seq. was performed using maize shoots and roots at different developmental stages of root emergence (6–10 days after planting, VE) and 1 week after plant emergence (V2). A total of 1286 differentially expressed genes (DEGs) were detected in both tissues. Many DEGs involved in metabolic pathways exhibited altered mRNA levels between VE and V2. In addition, we observed gene expression changes for 113 transcription factors and found five enriched cis-regulatory elements in the 1-kb upstream regions of both DEGs. The network-based transcriptome analysis showed two modules as co-expressed gene clusters differentially expressed between the shoots and roots during plant development. The DEGs of one module exhibited gene expressional coherence in the maize root tips, suggesting that their functional relationships are associated with the initial developmental stage of the maize root. Finally, we confirmed reliable mRNA levels of the hub genes in the potential sub-network related to initial root development at the different developmental stages of VE, V2, and 2 weeks after plant emergence.
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References
Ariel F, Diet A, Verdenaud M, Gruber V, Frugier F, Chan R, Crespi M (2010) Environmental regulation of lateral root emergence in Medicago truncatula requires the HD-Zip I transcription factor HB1. Plant Cell 22:2171–2183
Baâtour O et al (2012) Effect of growth stages on phenolics content and antioxidant activities of shoots in sweet marjoram (Origanum majorana L.) varieties under salt stress. Afr J Biotechnol 11:16486–16493
Bailey TL, Machanick P (2012) Inferring direct DNA binding from ChIP-sEq. Nucleic Acids Res 40:e128
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
Cai HG et al (2012) Mapping QTLs for root system architecture of maize (Zea mays L.) in the field at different developmental stages. Theor Appl Genet 125:1313–1324
Chae K, Gonong BJ, Kim SC, Kieslich CA, Morikis D, Balasubramanian S, Lord EM (2010) A multifaceted study of stigma/style cysteine-rich adhesin (SCA)-like Arabidopsis lipid transfer proteins (LTPs) suggests diversified roles for these LTPs in plant growth and reproduction. J Exp Bot 61:4277–4290
Coneva V et al (2014) Metabolic and co-expression network-based analyses associated with nitrate response in rice. Bmc Genomics 15:1056
Fan K et al (2014) Molecular evolution and expansion analysis of the NAC transcription factor in Zea mays. PLoS ONE 9:e111837
Gautier L, Cope L, Bolstad BM, Irizarry RA (2004) affy—analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20:307–315
Guingo E, Hébert Y, Charcosset A (1998) Genetic analysis of root traits in maize. Agronomie 18:225–235
Guo DS et al (2015) The WRKY transcription factor WRKY71/EXB1 controls shoot branching by transcriptionally regulating RAX genes in Arabidopsis. Plant Cell 27:3112–3127
He XJ et al (2016) Comparative RNA-seq analysis reveals that regulatory network of maize root development controls the expression of genes in response to N stress. PLoS ONE 11:e0151697
Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57
Kim SG, Kim SY, Park CM (2007) A membrane-associated NAC transcription factor regulates salt-responsive flowering via FLOWERING LOCUS T in Arabidopsis. Planta 226:647–654
Lan P, Li WF, Lin WD, Santi S, Schmidt W (2013) Mapping gene activity of Arabidopsis root hairs. Genome Biol 14:R67
Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinform 9:559
Lin WD, Liao YY, Yang TJW, Pan CY, Buckhout TJ, Schmidt W (2011) Coexpression-based clustering of Arabidopsis root genes predicts functional modules in early phosphate deficiency signaling. Plant Physiol 155:1383–1402
Liu J, Li J, Chen F, Zhang F, Ren T, Zhuang Z, Mi G (2008) Mapping QTLs for root traits under different nitrate levels at the seedling stage in maize (Zea mays L.). Plant Soil 305:253–265
Loudet O, Gaudon V, Trubuil A, Daniel-Vedele F (2005) Quantitative trait loci controlling root growth and architecture in Arabidopsis thaliana confirmed by heterogeneous inbred family. Theor Appl Genet 110:742–753
Makkena S, Lamb RS (2013) The bHLH transcription factor SPATULA regulates root growth by controlling the size of the root meristem. Bmc Plant Biol 13:1
Mano Y, Muraki M, Fujimori M, Takamizo T, Kindiger B (2005) Identification of QTL controlling adventitious root formation during flooding conditions in teosinte (Zea mays ssp. huehuetenangensis) seedlings. Euphytica 142:33–42
Manoli A, Sturaro A, Trevisan S, Quaggiotti S, Nonis A (2012) Evaluation of candidate reference genes for qPCR in maize. J Plant Physiol 169:807–815
Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A (2006) ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinform 7:S7
O’Keeffe K (2009) Maize growth & development. NSW Department of Primary Industries, State of New South Wales
Pace J, Gardner C, Romay C, Ganapathysubramanian B, Lubberstedt T (2015) Genome-wide association analysis of seedling root development in maize (Zea mays L.). BMC Genomics 16:47
Peng H et al (2015) Transcriptomic changes during maize roots development responsive to Cadmium (Cd) pollution using comparative RNAseq-based approach. Biochem Biophys Res Commun 464:1040–1047
Raun AL, Borum J, Sand-Jensen K (2010) Influence of sediment organic enrichment and water alkalinity on growth of aquatic isoetid and elodeid plants. Freshwater Biol 55:1891–1904
Ravid U, Ikan R, Sachs RM (1975) Structures related to jasmonic acid and their effect on lettuce seedling growth. J Agr Food Chem 23:835–838
Russell RS (1978) Plant root systems: their function and interaction with the soil. Soil Sci 125:272
Ryan PR, Kochian LV (1993) Interaction between aluminum toxicity and calcium uptake at the root apex in near-isogenic lines of wheat (Triticum aestivum L.) differing in aluminum tolerance. Plant Physiol 102:975–982
Sack FD (1991) Plant gravity sensing. Int Rev Cytol 127:193–252
Salazar-Henao JE, Lin WD, Schmidt W (2016) Discriminative gene co-expression network analysis uncovers novel modules involved in the formation of phosphate deficiency-induced root hairs in Arabidopsis. Sci Rep 6:26820
Schiefelbein JW, Benfey PN (1991) The development of plant roots: new approaches to underground problems. Plant Cell 3:1147–1154
Sekhon RS, Lin HN, Childs KL, Hansey CN, Buell CR, de Leon N, Kaeppler SM (2011) Genome-wide atlas of transcription during maize development. Plant J 66:553–563
Shannon P et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504
Staswick PE, Su W, Howell SH (1992) Methyl jasmonate inhibition of root growth and induction of a leaf protein are decreased in an Arabidopsis thaliana mutant. Proc Natl Acad Sci USA 89:6837–6840
Thimm O et al (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37:914–939
Tomic S, Gabdoulline RR, Kojic-Prodic B, Wade RC (1998) Classification of auxin related compounds based on similarity of their interaction fields: extension to a new set of compounds. Internet J Chem 1:26
Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25:1105–1111
Trapnell C et al (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578
Usadel B et al (2006) PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinform 7:535
Wei KF, Zhong XJ (2014) Non-specific lipid transfer proteins in maize. BMC Plant Biol 14:281
Wei HR, Yordanov YS, Georgieva T, Li X, Busov V (2013) Nitrogen deprivation promotes Populus root growth through global transcriptome reprogramming and activation of hierarchical genetic networks. New Phytol 200:483–497
Yilmaz A, Nishiyama MY, Fuentes BG, Souza GM, Janies D, Gray J, Grotewold E (2009) GRASSIUS: a platform for comparative regulatory genomics across the grasses. Plant Physiol 149:171–180
Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 136:2621–2632
Zou ZW, Ishida M, Li F, Kakizaki T, Suzuki S, Kitashiba H, Nishio T (2013) QTL analysis using SNP markers developed by next-generation sequencing for identification of candidate genes controlling 4-methylthio-3-butenyl glucosinolate contents in roots of radish, Raphanus sativus L. PLoS ONE 8:e53541
Acknowledgements
This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (Grant No. NRF-2015R1D1A4A01015702) as well as a grant from the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry (IPET) through Golden Seed Project, funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA) (213009-05-2-SB710), and the “Cooperative Research Program for Agriculture Science & Technology Development” (Project No. PJ012649022018) of Rural Development Administration, Republic of Korea.
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Supplementary Fig. 1. Quality of RNA-seq data used in this study
. (a) Box plot of FPKM values for all the genes after the normalization processing of raw data. (b) Hierarchical clustering of both samples, including the genes detected using RNA-seq. (PPTX 258 KB)
Supplementary Fig. 2. WGCNA analysis of DEGs
. (a) A scale-free topology for the power adjacency function parameter. The left panel shows the scale-free fit index (y-axis) as a function of the soft-thresholding power (x-axis). The right panel displays the scale-free topology plot with a power adjacency function parameter of 5. (b) Hierarchical clustering of both modules. (PPTX 185 KB)
Supplementary Fig. 3. Expression patters of 3 potential hub genes retrieved from MaizeGDB
(http://maizegdb.org/). Color represents the different transcript levels of gene in different maize tissues. (PPTX 1583 KB)
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Hwang, SG., Kim, KH., Lee, BM. et al. Transcriptome analysis for identifying possible gene regulations during maize root emergence and formation at the initial growth stage. Genes Genom 40, 755–766 (2018). https://doi.org/10.1007/s13258-018-0687-z
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DOI: https://doi.org/10.1007/s13258-018-0687-z