Genes & Genomics

, Volume 39, Issue 1, pp 15–26 | Cite as

Transcriptome analysis reveals critical genes and key pathways involved in early phyllotaxy development in maize

  • Xiaojian Peng
  • Wenbo Chai
  • Yingquan Tan
  • Qing Dong
  • Haiyang Jiang
  • Beijiu Cheng
  • Yang Zhao
Research Article
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Abstract

Integrated networks of gene expression, hormonal signaling and metabolite sensing regulate phyllotaxy pattern development. In this study, we characterized differentially expressed genes (DEGs) between maize plants with alternate and opposite phyllotaxies. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that 2432 DEGs were involved in biological processes, molecular functions, cellular components and many pathways. Importantly, we identified 19 DEGs related to plant hormone signal transduction. Additionally, we identified four main alternative splicing types: skipped exons, retained introns, alternative 5′-splice sites, and alternative 3′-splice sites, which exhibited different characteristics in the alternate and opposite phyllotaxy libraries. The reliability of the sequencing data was verified through using quantitative real-time reverse transcription PCR analysis of the 19 genes: 15 were validated to play a role in phytohormone signal transduction pathways. Taken together, our data provide new insight into the mechanisms of phyllotaxy pattern development, and will increase our understanding of how relative changes in gene expression determine alternate/opposite phyllotaxy in maize.

Keywords

Zea mays Phyllotaxy Differential gene expression Alternative splicing Transcriptome 
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Notes

Acknowledgments

We thank members of the Key Laboratory of Crop Biology of Anhui province for their assistance in this study. This work was supported by the Natural Science Foundation of China (11075001, 31000871) and the Scientific and Technological Research Plan of Anhui (11010301026). We extend our thanks to the reviewers for their careful reading and helpful comments on this manuscript.

Compliance with ethical standards

Conflict of interest

Xiaojian Peng, Wenbo Chai, Yingquan Tan, Qing Dong, Haiyang Jiang, Beijiu Cheng and Yang Zhao declare that they have no conflict of interest.

Research involving human and animal rights

This article does not contain any studies with human subjects or animals performed by any of the authors.

Supplementary material

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Copyright information

© The Genetics Society of Korea and Springer-Science and Media 2016

Authors and Affiliations

  • Xiaojian Peng
    • 1
  • Wenbo Chai
    • 1
  • Yingquan Tan
    • 1
  • Qing Dong
    • 1
  • Haiyang Jiang
    • 1
  • Beijiu Cheng
    • 1
  • Yang Zhao
    • 1
  1. 1.Key Laboratory of Crop Biology of Anhui ProvinceAnhui Agricultural UniversityHefeiChina

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