Advertisement

3 Biotech

, 8:311 | Cite as

Identification of miRNAs and their targets in regulating tuberous root development in radish using small RNA and degradome analyses

  • Chen Liu
  • Xianxian Liu
  • Wenling Xu
  • Weimin Fu
  • Fengde Wang
  • Jianwei Gao
  • Qiaoyun Li
  • Zhigang Zhang
  • Jingjuan LiEmail author
  • Shufen WangEmail author
Original Article

Abstract

High-throughput small RNA sequencing and degradome analysis were used in this study to thoroughly investigate the role of miRNA-mediated regulatory network in tuberous root development of radish. Samples from the early seedling stage (RE) and the cortex splitting stage (RL) were used for the construction of six small RNA libraries and one degradome library. A total of 518 known and 976 novel miRNAs were identified, of which, 338 known and 18 novel miRNAs were expressed in all six libraries, respectively. A total of 52 known and 57 novel miRNAs were identified to be significantly differentially expressed between RE and RL, and 195 mRNAs were verified to be the targets of 194 miRNAs by degradome sequencing. According to the degradome analysis, 11 differentially expressed miRNAs had miRNA-mRNA targets, and 13 targets were identified for these 11 miRNAs. Of the 13 miRNA-mRNA targets, 4 genes (RSG11079.t1, RSG11844.t1, RSG16775.t1, and RSG42419.t1) were involved in hormone-mediated signaling pathway, 2 gens (RSG11079.t1 and RSG16775.t1) were related to post-embryonic root development, and 1 gene (RSG23799.t1) was involved in anatomical structure morphogenesis, according to the GO function analysis for biological process. Target Genes participated in these processes are important candidates for further studies. This study provides valuable information for a better understanding of the molecular mechanisms involved in radish tuberous root formation and development.

Keywords

Raphanus sativus Tuberous root Cortex splitting microRNA Degradome 

Notes

Acknowledgements

This study was supported by the Youth Foundation of Shandong Academy of Agricultural Sciences (2016YQN22, 2016YQN23), the National Key Research and Development Program of China (2017YFD0101806, 2016YFD0100204-27), and the Modern Agricultural Industrial Technology System Funding of Shandong Province (SDAIT-05-01).

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest regarding the publication of this article.

Supplementary material

13205_2018_1330_MOESM1_ESM.xlsx (11 kb)
Supplementary Table S1: qRT-PCR primers for 11 differentially expressed miRNAs and six target genes (XLSX 11 KB)
13205_2018_1330_MOESM2_ESM.xlsx (11 kb)
Supplementary Table S2: Analysis of sRNA reads from six sRNA libraries (XLSX 11 KB)
13205_2018_1330_MOESM3_ESM.xlsx (33 kb)
Supplementary Table S3: Known miRNAs identified in the six small RNA libraries (XLSX 32 KB)
13205_2018_1330_MOESM4_ESM.xlsx (46 kb)
Supplementary Table S4: Novel miRNAs identified in the six small RNA libraries (XLSX 46 KB)
13205_2018_1330_MOESM5_ESM.xlsx (16 kb)
Supplementary Table S5: The differentially expressed miRNAs between RE and RL (XLSX 16 KB)
13205_2018_1330_MOESM6_ESM.xlsx (11 kb)
Supplementary Table S6: Classification of clean tags identified by degradome sequencing (XLSX 11 KB)
13205_2018_1330_MOESM7_ESM.xlsx (54 kb)
Supplementary Table S7: Targets of miRNAs identified by degradome analysis in radish (XLSX 54 KB)
13205_2018_1330_MOESM8_ESM.xlsx (12 kb)
Supplementary Table S8: Target mRNAs for differentially expressed miRNAs between RE and RL in radish (XLSX 12 KB)

References

  1. Addo-Quaye C, Miller W, Axtell MJ (2009) CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics 25:130–131.  https://doi.org/10.1093/bioinformatics/btn604 CrossRefPubMedGoogle Scholar
  2. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106.  https://doi.org/10.1186/gb-2010-11-10-r106 CrossRefPubMedPubMedCentralGoogle Scholar
  3. Barillari J et al (2008) Kaiware daikon (Raphanus sativus L.) extract: a naturally multipotent chemopreventive agent. J Agric Food Chem 56:7823–7830.  https://doi.org/10.1021/jf8011213 CrossRefPubMedGoogle Scholar
  4. Bhogale S, Mahajan AS, Natarajan B, Rajabhoj M, Thulasiram HV, Banerjee AK (2014) MicroRNA156: a potential graft-transmissible microRNA that modulates plant architecture and tuberization in Solanum tuberosum ssp. andigena. Plant Physiol 164:1011–1027.  https://doi.org/10.1104/pp.113.230714 CrossRefPubMedGoogle Scholar
  5. Eyles RP, Williams PH, Ohms SJ, Weiller GF, Ogilvie HA, Djordjevic MA, Imin N (2013) microRNA profiling of root tissues and root forming explant cultures in Medicago truncatula. Planta 238:91–105.  https://doi.org/10.1007/s00425-013-1871-7 CrossRefPubMedGoogle Scholar
  6. Fan M, Liu Z, Zhou L, Lin T, Liu Y, Luo L (2010) Effects of plant growth regulators and saccharide on in vitro plant and tuberous root regeneration of Cassava (Manihot esculenta Crantz). J Plant Growth Regul 30:11–19.  https://doi.org/10.1007/s00344-010-9163-y CrossRefGoogle Scholar
  7. Griffiths-Jones S (2004) The microRNA registry. Nucleic Acids Res 32:D109–D111.  https://doi.org/10.1093/nar/gkh023 CrossRefPubMedPubMedCentralGoogle Scholar
  8. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34:D140–D144.  https://doi.org/10.1093/nar/gkj112 CrossRefPubMedGoogle Scholar
  9. Guo HS, Xie Q, Fei JF, Chua NH (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development. Plant Cell 17:1376–1386.  https://doi.org/10.1105/tpc.105.030841 CrossRefPubMedPubMedCentralGoogle Scholar
  10. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53.  https://doi.org/10.1146/annurev.arplant.57.032905.105218 CrossRefPubMedGoogle Scholar
  11. Khan GA, Declerck M, Sorin C, Hartmann C, Crespi M, Lelandais-Briere C (2011) MicroRNAs as regulators of root development and architecture. Plant Mol Biol 77:47–58.  https://doi.org/10.1007/s11103-011-9793-x CrossRefPubMedGoogle Scholar
  12. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39:D152–157  https://doi.org/10.1093/nar/gkq1027 CrossRefPubMedGoogle Scholar
  13. Kozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42:D68–D73.  https://doi.org/10.1093/nar/gkt1181 CrossRefPubMedGoogle Scholar
  14. Ku AT, Huang YS, Wang YS, Ma D, Yeh KW (2008) IbMADS1 (Ipomoea batatas MADS-box 1 gene) is involved in tuberous root initiation in sweet potato (Ipomoea batatas). Ann Bot 102:57–67.  https://doi.org/10.1093/aob/mcn067 CrossRefPubMedPubMedCentralGoogle Scholar
  15. Kuang P, Song D, Yuan Q, Yi R, Lv X, Liang H (2013) Separation and purification of sulforaphene from radish seeds using macroporous resin and preparative high-performance liquid chromatography. Food Chem 136:342–347.  https://doi.org/10.1016/j.foodchem.2012.08.082 CrossRefPubMedGoogle Scholar
  16. Lakhotia N et al (2014) Identification and characterization of miRNAome in root, stem, leaf and tuber developmental stages of potato (Solanum tuberosum L.) by high-throughput sequencing. BMC Plant Biol 14:6.  https://doi.org/10.1186/1471-2229-14-6 CrossRefPubMedPubMedCentralGoogle Scholar
  17. Lelandais-Brière C, Naya LS, Calenge E, Frugier F, Hartmann F, Gouzy C, Crespi J M (2009) Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules. Plant Cell 21:2780–2796.  https://doi.org/10.1105/tpc.109.068130 CrossRefPubMedPubMedCentralGoogle Scholar
  18. Li J et al (1979) Cultivation of vegetables. Agricultural Press, BeijingGoogle Scholar
  19. Li J et al (2012) miRNA164-directed cleavage of ZmNAC1 confers lateral root development in maize (Zea mays L.). BMC Plant Biol 12:220CrossRefPubMedPubMedCentralGoogle Scholar
  20. Li J, Ding Q, Wang F, Zhang Y, Li H, Gao J (2015) Integrative analysis of mRNA and miRNA expression profiles of the tuberous root development at seedling stages in Turnips. Plos One 10:e0137983.  https://doi.org/10.1371/journal.pone.0137983 CrossRefPubMedPubMedCentralGoogle Scholar
  21. Liu X, Wang S, Shi Q (2008) Content changes of major nutrient components during root expansion of chinese Radish. Shandong Agric Sci 9:22–24Google Scholar
  22. Malhotra N, Sood H, Chauhan RS (2016) Transcriptome-wide mining suggests conglomerate of genes associated with tuberous root growth and development in Aconitum heterophyllum Wall. 3 Biotech 6:152.  https://doi.org/10.1007/s13205-016-0466-y CrossRefPubMedPubMedCentralGoogle Scholar
  23. Marin E et al (2010) miR390, Arabidopsis TAS3 tasiRNAs, and their AUXIN RESPONSE FACTOR targets define an autoregulatory network quantitatively regulating lateral root growth. Plant Cell 22:1104–1117.  https://doi.org/10.1105/tpc.109.072553 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Martin A, Adam H, Díaz-Mendoza M, Zurczak M, González-Schain N, Suárez-López P (2009) Graft-transmissible induction of potato tuberization by the microRNA miR172. Development 136:2873–2881CrossRefPubMedGoogle Scholar
  25. Mitsui Y et al (2015) The radish genome and comprehensive gene expression profile of tuberous root formation and development. Sci Rep 5:10835.  https://doi.org/10.1038/srep10835 CrossRefPubMedPubMedCentralGoogle Scholar
  26. Noh SA, Lee HS, Huh EJ, Huh GH, Paek KH, Shin JS, Bae JM (2010) SRD1 is involved in the auxin-mediated initial thickening growth of storage root by enhancing proliferation of metaxylem and cambium cells in sweetpotato (Ipomoea batatas). J Exp Bot 61:1337–1349.  https://doi.org/10.1093/jxb/erp399 CrossRefPubMedPubMedCentralGoogle Scholar
  27. Papi A et al (2008) Cytotoxic and antioxidant activity of 4-methylthio-3-butenyl isothiocyanate from Raphanus sativus L. (Kaiware Daikon) sprouts. J Agric Food Chem 56:875–883.  https://doi.org/10.1021/jf073123c CrossRefPubMedGoogle Scholar
  28. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140.  https://doi.org/10.1093/bioinformatics/btp616 CrossRefPubMedPubMedCentralGoogle Scholar
  29. Wang L, He Q (2005) Chinese radish. Science and Technology Literature Press, BeijingGoogle Scholar
  30. Wang J, Wang L, Mao Y, Cai W, Xue H, Chen X (2005) Control of root cap formation by microRNA targeted auxin response factors in Arabidopsis. Plant Cell 17:2204–2216.  https://doi.org/10.1105/tpc.105.033076 CrossRefPubMedPubMedCentralGoogle Scholar
  31. Wang W, Gong Y, Liu L, W Y, D. H ZJ, L. W (2007) Changes of sugar content and sucrose metabolizing enzyme activities during fleshy taproot development in radish (Raphanus sativus L.). Acta Hortic Sin 34:1313–1316Google Scholar
  32. Wang S et al (2012) Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish. Plant Cell Rep 31:1437–1447.  https://doi.org/10.1007/s00299-012-1259-3 CrossRefPubMedGoogle Scholar
  33. Wang R et al (2014a) Transcriptome-wide characterization of novel and heat-stress-responsive microRNAs in Radish (Raphanus sativus L.) Using Next-Generation Sequencing. Plant Mol Biol Report 33:867–880.  https://doi.org/10.1007/s11105-014-0786-1 CrossRefGoogle Scholar
  34. Wang Y et al (2014b) Identification of Radish (Raphanus sativus L.) miRNAs and their target genes to explore miRNA-mediated regulatory networks in Lead (Pb) stress responses by high-throughput sequencing and degradome analysis. Plant Mol Biol Report 33:358–376.  https://doi.org/10.1007/s11105-014-0752-y CrossRefGoogle Scholar
  35. Yang J, Liu X, Xu B, Zhao N, Yang X, Zhang M (2013) Identification of miRNAs and their targets using high-throughput sequencing and degradome analysis in cytoplasmic male-sterile and its maintainer fertile lines of Brassica juncea. BMC Genom 14:9.  https://doi.org/10.1186/1471-2164-14-9 CrossRefGoogle Scholar
  36. Yang Y, Zhang X, Su Y, Zou J, Wang Z, Xu L, Que Y (2017) miRNA alteration is an important mechanism in sugarcane response to low-temperature environment. BMC Genom 18:833.  https://doi.org/10.1186/s12864-017-4231-3 CrossRefGoogle Scholar
  37. Yin F et al (2015) Genome-wide identification and analysis of drought-responsive genes and microRNAs in tobacco. Int J Mol Sci 16:5714–5740.  https://doi.org/10.3390/ijms16035714 CrossRefPubMedGoogle Scholar
  38. Yu R et al (2015) Transcriptome profiling of root microRNAs reveals novel insights into taproot thickening in radish (Raphanus sativus L.). BMC Plant Biol 15:30.  https://doi.org/10.1186/s12870-015-0427-3 CrossRefPubMedPubMedCentralGoogle Scholar
  39. Zaki HEM, Takahata Y, Yokoi S (2012) Analysis of the morphological and anatomical characteristics of roots in three radish (Raphanus sativus) cultivars that differ in root shape. J Hortic Sci Biotechnol 87:172CrossRefGoogle Scholar
  40. Zhao C et al (2014a) Small RNA and degradome deep sequencing reveals Peanut microRNA roles in response to pathogen infection plant. Mol Biol Report 33:1013–1029.  https://doi.org/10.1007/s11105-014-0806-1 CrossRefGoogle Scholar
  41. Zhao X-Y et al (2014b) Investigating the MicroRNAomes of two developmental phases of Dendrocalamus latiflorus (Poaceae: Bambusoideae) inflorescences. Plant Mol Biol Report 33:1141–1155.  https://doi.org/10.1007/s11105-014-0808-z CrossRefGoogle Scholar
  42. Zhuang Y, Zhou XH, Liu J (2014) Conserved miRNAs and their response to salt stress in wild eggplant Solanum linnaeanum roots. Int J Mol Sci 15:839–849.  https://doi.org/10.3390/ijms15010839 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Chen Liu
    • 1
  • Xianxian Liu
    • 1
  • Wenling Xu
    • 1
  • Weimin Fu
    • 1
  • Fengde Wang
    • 1
  • Jianwei Gao
    • 1
  • Qiaoyun Li
    • 1
  • Zhigang Zhang
    • 1
  • Jingjuan Li
    • 1
    Email author
  • Shufen Wang
    • 1
    Email author
  1. 1.Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and FlowersShandong Academy of Agricultural SciencesJinanPeople’s Republic of China

Personalised recommendations