Plant Molecular Biology Reporter

, Volume 34, Issue 6, pp 1204–1214 | Cite as

Genome-Wide Discovery of Tissue-Specific Genes in Maize

  • Feng Lin
  • Huabin Bao
  • Jun Yang
  • Yuhe Liu
  • Huixue Dai
  • Han Zhao
Original Paper


Analysis of spatial and temporal gene expression pattern is instrumental to elucidation of gene networks and molecular mechanisms of tissue development. It also holds great value to applied research by providing tissue-specific (TS) promoter candidates for transgenic studies. Here, we present a large-scale systematic discovery of tissue-specific genes in maize. Profiles of TS genes were generated from a maize transcriptome atlas, with 71, 539, 23, 352, 51, and 287 genes showing expression specificity in the root, leaf, cob, endosperm, silk, and anther. Functional annotations and enrichment analysis of these TS genes identified pathways overrepresented for each tissue. Tissue specificity was experimentally confirmed by RT-PCR, mRNA in situ hybridization, and transgenic expression of promoter-fluorescent proteins. Two significantly enriched binding motifs, CATTGYCG and KGGTATCA, were identified from the promoter analysis of the anther- and endosperm-specifically expressed genes. Further, co-expression analysis on a broader set of maize germplasms identified molecular networks of TS genes and revealed a number of novel transcripts including non-coding RNA expressing the same pattern with the TS genes from B73. Our global analysis of maize TS transcriptomes could shed light on the molecular mechanisms of tissue specificity and facilitate transgenic studies by providing a valuable resource of TS promoter candidates.


Maize Transcriptome analysis Tissue-specific expression Promoter Transgene 



This work was supported by a grant from Natural Science Foundation of Jiangsu Province, China (BK20141385), Natural Science Foundation of China (31271728), and Jiangsu Agriculture Science and Technology Innovation Fund [CX(14)5054].

Authors’ Contributions

H.Z. and F.L. conceived, designed, and conducted the experiments. H.B., H.X.D., and J.Y. helped in conducting the experiments. F.L. and H.B. analyzed the data and results. F.L., Y.H.L., and H.Z. wrote the manuscript. All authors read and approved the final manuscript.

Compliance with Ethical Standards

Competing Interests

The authors declare that they have no competing interests.

Supplementary material

11105_2016_1001_MOESM1_ESM.xlsx (83 kb)
Supplementary Table S1 The list of 1323 tissue-specific gene candidates with average FPKM detected in three RNA-seq datasets. (XLSX 82 kb)
11105_2016_1001_MOESM2_ESM.xlsx (23 kb)
Supplementary Table S2 Non-coding predictions of 389 unannotated TS transcripts with sequences. (XLSX 23 kb)
11105_2016_1001_MOESM3_ESM.xlsx (12 kb)
Supplementary Table S3 Functions enriched in each tissue analyzed by using SEA tool. (XLSX 11 kb)
11105_2016_1001_MOESM4_ESM.xlsx (20 kb)
Supplementary Table S4 Electronic northern analysis of predicted genes queried to EST libraries. (XLSX 19 kb)
11105_2016_1001_MOESM5_ESM.xlsx (18 kb)
Supplementary Table S5 The list of 270 genes clustered into six modules with co-expression in seed. (XLSX 18 kb)


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Feng Lin
    • 1
  • Huabin Bao
    • 1
    • 2
  • Jun Yang
    • 3
  • Yuhe Liu
    • 4
  • Huixue Dai
    • 5
  • Han Zhao
    • 1
  1. 1.Provincial Key Laboratory of Agrobiology, Institute of BiotechnologyJiangsu Academy of Agricultural SciencesNanjingChina
  2. 2.Nanjing Agricultural UniversityNanjingChina
  3. 3.National Key Laboratory of Plant Molecular GeneticsShanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghaiChina
  4. 4.Department of Crop SciencesUniversity of Illinois at Urbana-ChampaignUrbana-ChampaignUSA
  5. 5.Nanjing Institute of Vegetable SciencesNanjingChina

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