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Transcriptome analysis for identifying possible gene regulations during maize root emergence and formation at the initial growth stage

Genes & Genomics volume 40, pages 755–766 (2018)Cite this article

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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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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  1. Byung-Moo Lee and Jun-Cheol Moon equally contributed to this article.

Affiliations

  1. Plant Genomics Laboratory, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea

    Sun-Goo Hwang

  2. Department of Life Science, Dongguk University-Seoul, Seoul, 04620, Republic of Korea

    Kyung-Hee Kim & Byung-Moo Lee

  3. Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon, 24341, Republic of Korea

    Jun-Cheol Moon

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  1. Sun-Goo Hwang
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Correspondence to Byung-Moo Lee or Jun-Cheol Moon.

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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)

Supplementary Table 1. List of CEL files obtained from NCBI GEO

. (XLSX 24 KB)

Supplementary Table 2. Mapped reads by Illumina high-throughput sequencing

. (XLSX 11 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

Keywords

  • Maize
  • Root
  • Initial developmental stage
  • Differentially expressed genes
  • RNA-Seq