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Transcriptome-based gene expression profiling of diploid radish (Raphanus sativus L.) and the corresponding autotetraploid

  • Wanwan Cheng
  • Mingjia Tang
  • Yang Xie
  • Liang Xu
  • Yan Wang
  • Xiaobo Luo
  • Lianxue Fan
  • Liwang LiuEmail author
Original Article

Abstract

Polyploidy is an important evolutionary factor in most land plant lineages which possess more than two complete sets of chromosomes. Radish (Raphanus sativus L.) is an economically annual/biennial root vegetable crop worldwide. However, the expression patterns of duplicated homologs involved in the autopolyploidization remains unclear. In present study, the autotetraploid radish plants (2n = 4x = 36) were produced with colchicine and exhibited an increase in the size of flowers, leaves, stomata and pollen grains. The differential gene expression (DGE) profiling was performed to investigate the differences in gene expression patterns between diploid and its corresponding autotetraploid by RNA-Sequencing (RNA-Seq). Totally, 483 up-regulated differentially expressed genes (DEGs) and 408 down-regulated DEGs were detected in diploid and autotetraploid radishes, which majorly involved in the pathways of hormones, photosynthesis and stress response. Moreover, the xyloglucan endotransglucosylase/hydrolase (XTH) and pectin methylesterases (PME) family members related to cell enlargement and cell wall construction were found to be enriched in GO enrichment analysis, of which XTH family members enriched in “apoplast” and “cell wall” terms, while PME family members enriched in “cell wall” term. Reverse-transcription quantitative PCR (RT-qPCR) analysis indicated that the expression profile of DEGs were consistent with results from the RNA-Seq analysis. The DEGs involved in cell wall construction and auxin metabolism were predicted to be associated with organs size increase of autotetraploid radishes in the present study. These results could provide valuable information for elucidating the molecular mechanism underlying polyploidization and facilitating further genetic improvements of important traits in radish breeding programs.

Keywords

Radish (Raphanus sativus L.) Autotetraploid Transcriptome sequencing DEGs Reverse-transcription quantitative PCR (RT-qPCR) 

Notes

Acknowledgements

This work was in part supported by grants from the National Key Technology R&D Program of China (Grant Nos. 2016YFD0100204-25), Key Technology R&D Program of Jiangsu Province (Grant No. BE2016379), the Jiangsu Agricultural Science and Technology Innovation Fund [CX(16)1012], the Jiangsu Agricultural Key Project [JATS(2018)285], and Pukou (Nanjing) Applied Technology R&D Project (N2016-08).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

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

Supplementary material

11033_2018_4549_MOESM1_ESM.jpg (606 kb)
Fig. S1 Classification of raw reads. (JPG 606 KB)
11033_2018_4549_MOESM2_ESM.doc (184 kb)
Supplementary material 2 (DOC 184 KB)

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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  • Wanwan Cheng
    • 1
  • Mingjia Tang
    • 1
  • Yang Xie
    • 1
  • Liang Xu
    • 1
  • Yan Wang
    • 1
  • Xiaobo Luo
    • 1
  • Lianxue Fan
    • 1
  • Liwang Liu
    • 1
    Email author
  1. 1.National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingPeople’s Republic of China

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