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


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.


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



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)


  1. 1.
    Doyle JJ, Flagel LE, Paterson AH, Rapp RA, Soltis DE, Soltis PS, Wendel JF (2008) Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet 42:443–461CrossRefGoogle Scholar
  2. 2.
    Wolfe KH (2001) Yesterday’s polyploids and the mystery of diploidization. Nat Rev Genet 2:333–341CrossRefGoogle Scholar
  3. 3.
    Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH et al (2009) Polyploidy and angiosperm diversification. Am J Bot 96:336–348CrossRefGoogle Scholar
  4. 4.
    Otto SP, Whitton J (2000) Polyploid incidence and evolution. Annu Rev Genet 34:401–437CrossRefGoogle Scholar
  5. 5.
    Ng DWK, Zhang C, Miller M, Shen Z, Briggs SP, Chen ZJ (2012) Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors. Heredity 108:419–430CrossRefGoogle Scholar
  6. 6.
    Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42:225–249CrossRefGoogle Scholar
  7. 7.
    Yu Z, Haberer G, Matthes M, Rattei T, Mayer KFX, Gierl A, Torres-Ruiz RA (2010) Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana. Proc Natl Acad Sci USA 107:17809–17814CrossRefGoogle Scholar
  8. 8.
    Zhang J, Liu Y, Xia EH, Yao QY, Liu XD, Gao LZ (2015) Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression. Proc Natl Acad Sci USA 112:7022–7029CrossRefGoogle Scholar
  9. 9.
    Soltis PS, Soltis DE (2000) The role of genetic and genomic attributes in the success of polyploids. Proc Natl Acad Sci USA 97:7051–7057CrossRefGoogle Scholar
  10. 10.
    Robins JG, Luth D, Campbell TA, Bauchan GR, He C, Viands DR, Hansen JL, Brummer EC (2007) Genetic mapping of biomass production in tetraploid alfalfa. Crop Sci 47:1–10CrossRefGoogle Scholar
  11. 11.
    Shahid MQ, Liu G, Li JQ, Naeem M, Liu XD (2011) Heterosis and gene action study of agronomic traits in diploid and autotetraploid rice. Acta Agr Scand B–Soil Plant Sci 61:23–32Google Scholar
  12. 12.
    Wu JW, Hu CY, Shahid MQ, Guo HB, Zeng YX, Liu XD, Lu YG (2013) Analysis on genetic diversification and heterosis in autotetraploid rice. Springer Plus 2:439CrossRefGoogle Scholar
  13. 13.
    Yang PM, Huang QC, Qin GY, Zhao SP, Zhou JG (2014) Different drought-stress responses in photosynthesis and reactive oxygen metabolism between autotetraploid and diploid rice. Photosynthetica 52(2):193–202CrossRefGoogle Scholar
  14. 14.
    Wu JW, Shahid MQ, Chen L, Chen ZX, Wang L, Liu XD, Lu YG (2015)  Polyploidy enhances F1 pollen sterility loci interactions that increase meiosis abnormalities and pollen sterility in autotetraploid rice. Plant Physiol 169:2700–2717PubMedPubMedCentralGoogle Scholar
  15. 15.
    Comai L (2005) The advantages and disadvantages of being polyploid. Nat Rev Genet 6:836–846CrossRefGoogle Scholar
  16. 16.
    Lee HS, Chen ZJ (2001) Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc Natl Acad Sci USA 98:6753–6758CrossRefGoogle Scholar
  17. 17.
    Wang J, Tian L, Madlung A et al (2004) Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167:1961–1973CrossRefGoogle Scholar
  18. 18.
    Guo M, Davis D, Birchler JA (1996) Dosage effects on gene expression in a maize ploidy series. Genetics 142: 1349–1355PubMedPubMedCentralGoogle Scholar
  19. 19.
    Hu G, Houston NL, Pathak D, Schmidt L, Thelen JJ, Wendel JF (2011) Genomically biased accumulation of seed storage proteins in allopolyploid cotton. Genetics 189:1103–1115CrossRefGoogle Scholar
  20. 20.
    Albertin W, Balliau T, Brabant P, Chèvre AM, Eber F, Malosse C, Thlellement H (2006) Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids. Genetics 173:1101–1113CrossRefGoogle Scholar
  21. 21.
    Cai D, Rodríguez F, Teng Y, Ané C, Bonierbale M, Mueller LA, Spooner DM (2012) Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota). BMC Evol Biol 12:70CrossRefGoogle Scholar
  22. 22.
    Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351CrossRefGoogle Scholar
  23. 23.
    Xie Y, Xu L, Wang Y, Fan L, Chen Y, Tang M, Luo X, Liu L (2018) Comparative proteomic analysis provides insight into a complex regulatory network of taproot formation in radish (Raphanus sativus L.). Horticult Res 5(1):51CrossRefGoogle Scholar
  24. 24.
    Wu JW, Shahid MQ, Guo HB, Yin W, Chen ZX, Wang L, Liu XD, Lu YG (2014) Comparative cytological and transcriptomic analysis of pollen development in autotetraploid and diploid rice. Plant Reprod 27:181–196CrossRefGoogle Scholar
  25. 25.
    Zhang X, Deng M, Fan G (2014) Differential transcriptome analysis between Paulownia fortunei and its synthesized autopolyploid. Int J Mol Sci 15:5079–5093CrossRefGoogle Scholar
  26. 26.
    Li Y, Fan G, Dong Y, Zhao Z, Deng M, Cao X, Xu E, Niu S (2014) Identification of genes related to the phenotypic variations of a synthesized Paulownia (Paulownia tomentosa × Paulownia fortunei) autotetraploid. Gene 553:75CrossRefGoogle Scholar
  27. 27.
    Saminathan T, Nimmakayala P, Manohar S et al (2014) Differential gene expression and alternative splicing between diploid and tetraploid watermelon. J Exp Bot 66:1369–1385CrossRefGoogle Scholar
  28. 28.
    Limera C, Wang K, Xu L, Wang Y, Zhu X, Feng H, Sha Y, Gong Y, Liu L (2016) Induction of autotetraploidy using colchicine and its identification in radish (Raphanus sativus L.). J Hortic Sci Biotech 91:63–70CrossRefGoogle Scholar
  29. 29.
    Xu L, Wang Y, Liu W et al (2015) De novo sequencing of root transcriptome reveals complex cadmium-responsive regulatory networks in radish (Raphanus sativus L.). Plant Sci 236:313–323CrossRefGoogle Scholar
  30. 30.
    Connett RJA, Hanke DE (1987) Changes in the pattern of phospholipid synthesis during the induction by cytokinin of cell division in soybean suspension cultures. Planta, 170(2):161–167CrossRefGoogle Scholar
  31. 31.
    Gao R, Wang H, Dong B et al (2016) Morphological, genome and gene expression changes in newly induced autopolyploid Chrysanthemum lavandulifolium (Fisch. ex Trautv.) Makino. Int J Mol Sci 17:1690CrossRefGoogle Scholar
  32. 32.
    Xu Y, Zhu X, Gong Y et al (2012) Evaluation of reference genes for gene expression studies in radish (Raphanus sativus L.) using quantitative real-time PCR. Biochem Biophl Res Co 424:398–403CrossRefGoogle Scholar
  33. 33.
    Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCt method. Methods 25:402–408CrossRefGoogle Scholar
  34. 34.
    Wang L, Feng Z, Wang X et al (2009) DEGseq: an R package for identifying differentially expressed genes from RNA-Seq data. Bioinformatics 26:136–138CrossRefGoogle Scholar
  35. 35.
    Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc B 57:289–300Google Scholar
  36. 36.
    Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323CrossRefGoogle Scholar
  37. 37.
    Young MD, Wakefield MJ, Smyth GK et al (2010) Gene ontology analysis for RNA-Seq: accounting for selection bias. Genome Biol 11:R14CrossRefGoogle Scholar
  38. 38.
    Song XM, Huang ZN, Duan WK, Ren J, Liu TK, Li Y, Hou XL (2014) Genome-wide analysis of the bHlH transcription factor family in Chinese cabbage (Brassica rapa ssp. pekinensis). Mol Genet Genomics 289:77–91CrossRefGoogle Scholar
  39. 39.
    Nakashima K, Takasaki H, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2012) NAC transcription factors in plant abiotic stress responses. BBA-Gene Regul Mec 1819:97–103Google Scholar
  40. 40.
    Licausi F, Ohmetakagi M, Perata P (2013) APETALA2/Ethylene responsive factor (AP2/ERF) transcription factors: mediators of stress responses and developmental programs. New Phytol 199:639–649CrossRefGoogle Scholar
  41. 41.
    Sattler MC, Carvalho CR, Clarindo WR (2016) The polyploidy and its key role in plant breeding. Planta 243: 281–296CrossRefGoogle Scholar
  42. 42.
    Dar TH, Raina SN, Goel S (2017) Cytogenetic and molecular evidences revealing genomic changes after autopolyploidization: a case study of synthetic autotetraploid Phlox drummondii Hook. Physiol Mol Biol Pla 23:641–650CrossRefGoogle Scholar
  43. 43.
    Cosgrove DJ (2005) Growth of the plant cell wall. Nat Rev Mol Cell Biol 6:850–861CrossRefGoogle Scholar
  44. 44.
    Yokoyama R, Nishitani K (2001) A comprehensive expression analysis of all members of a gene family encoding cell-wall enzymes allowed us to predict cis-regulatory regions involved in cell-wall construction in specific organs of Arabidopsis. Plant Cell Physiol 42:1025–1033CrossRefGoogle Scholar
  45. 45.
    Rose JKC, Braam J, Fry SC, Nishitani K (2002) The XTH family of enzymes involved in xyloglucan endotransglucosylation and endohydrolysis: current perspectives and a new unifying nomenclature. Plant Cell Physiol 43:1421–1435CrossRefGoogle Scholar
  46. 46.
    Catalá C, Rose JKC, York WS, Albersheim P, Darvill AG, Bennett AB (2001) Characterization of a tomato xyloglucan endotransglycosylase gene that is down-regulated by auxin in etiolated hypocotyls. Plant Physiol 127:1180–1192CrossRefGoogle Scholar
  47. 47.
    Whitney SEC, Gothard MGE, Mitchell JT, Gidley MJ (1999) Roles of cellulose and xyloglucan in determining the mechanical properties of primary plant cell walls. Plant Physiol 121:657–664CrossRefGoogle Scholar
  48. 48.
    Li X, Yu E, Fan C, Zhang C, Fu T, Zhou Y (2012) Developmental, cytological and transcriptional analysis of autotetraploid Arabidopsis. Planta 236:579–596CrossRefGoogle Scholar
  49. 49.
    Moghe GD, Shiu SH (2014) The causes and molecular consequences of polyploidy in flowering plants. Ann NY Acad Sci 1320:16CrossRefGoogle Scholar
  50. 50.
    Zhao M, Zhang B, Lisch D, Ma J (2017) Patterns and consequences of subgenome differentiation provide insights into the nature of paleopolyploidy in plants. Plant Cell 29:2974–2994CrossRefGoogle Scholar
  51. 51.
    Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178CrossRefGoogle Scholar
  52. 52.
    Li Z, Defoort J, Tasdighian S, Maere S, De Peer YV, Smet RD (2016) Gene duplicability of core genes is highly consistent across all angiosperms. Plant Cell 28:326–344CrossRefGoogle Scholar
  53. 53.
    Smet RD, Sabaghian E, Li Z, Saeys Y, De Peer YV (2017) Coordinated functional divergence of genes after genome duplication in Arabidopsis thaliana. Plant Cell 29:2786–2800CrossRefGoogle Scholar

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

Personalised recommendations