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Genome-wide identification, characterization and expression analysis of novel long non-coding RNAs that mediate IBA-induced adventitious root formation in apple rootstocks

  • Yuan Meng
  • Libo Xing
  • Ke Li
  • Yanhong Wei
  • Hui Wang
  • Jiangping Mao
  • Feng Dong
  • Doudou Ma
  • Zhaoxiang Zhang
  • Mingyu Han
  • Caiping Zhao
  • Muhammad Mobeen Tahir
  • Dong ZhangEmail author
Original paper
  • 50 Downloads

Abstract

Adventitious roots (ARs) induced are essential for apple rootstock vegetative propagation, however, a transcriptomic analysis of long non-coding RNAs (lncRNAs) that mediate AR formation under exogenous indole-3-butyric acid (IBA) treated in the apple dwarf rootstock ‘M26’ (Malus pumila Mill.) rarely been explored. To explore this, we examined ‘M26’ stem cuttings treated with IBA (1 mg L−1) and control (without IBA treatment), where anatomical analysis showed IBA-treated stems began to develop AR primordia within third day and ARs occurred after 16 days, while the control had no ARs developed. An assessment of hormone content levels in basal stem cuttings showed that, after IBA treatment, indole-3-acetic acid, zeatin riboside, and jasmonic acid were increased at third day but subsequently decreased later, however gibberellin-3 was decreased at third day. The control and IBA-treated third day basal stem cuttings were sent for whole-genome, high-throughput RNA sequencing. The results showed a total of 855 reliable lncRNAs were identified as novel lncRNAs and 63 novel lncRNAs were defined as IBA-responsive lncRNAs. Fifteen IBA-responsive lncRNAs were predicted to be putative targets for 94 miRNAs and three IBA-responsive lncRNA (CUFF.16781, CUFF.2143 and CUFF.41325) was predicted to be the target mimic of mdm-miR156 and mdm-miR396. Functional annotations of these potential target genes suggest that they are involved in many different biological processes, including plant hormone and sucrose signaling, which suggests that IBA-responsive lncRNAs may participate in AR formation in apple rootstocks. This study sheds light on IBA-mediated AR formation in apple rootstock cuttings and provides a foundation for further research.

Keywords

Apple rootstock Adventitious root formation Indole-3-butyric acid (IBA) Long non-coding RNAs LncRNA–miRNA target mimic 

Notes

Acknowledgements

We are grateful to Beijing ORI-GENE company, Beijing, China for providing technical support.

Funding

This work was financially supported by Science and Technology Innovative Engineering Project in the Shaanxi province of China (2017NY0055, 2016KTZDNY01-10), Tang Scholar by Cyrus Tang Foundation and Northwest Agriculture and Forestry University, the China Apple Research System (CARS-27), the Yangling Subsidiary Center Project of the National Apple Improvement Center, Collaborative Innovation Center for Shaanxi Fruit Industry Development.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

10725_2018_470_MOESM1_ESM.tif (310 kb)
Figure S1. Pipeline for predicting novel lncRNAs. (TIF 309 KB)
10725_2018_470_MOESM2_ESM.tif (3.6 mb)
Figure S2. Sequencing result evaluation of lncRNAs. (A) The FPKM density distribution of lncRNAs. (B) The boxplot of FPKM distribution of lncRNAs. (C) The volcano plot to show differential lncRNAs. (D) The correlation between sequencing samples. M01, M02, and M03 respectively represent Control l1, Control 2, Control 3. M31, M32, and M33 respectively represent IBA 1, IBA 2, IBA 3. Control represents control samples and IBA represents IBA-treated samples. (TIF 3681 KB)
10725_2018_470_MOESM3_ESM.tif (14.8 mb)
Figure S3. Functional categorization of potential target genes of IBA-responsive lncRNAs based on the biological process of Gene Ontology. (TIF 15166 KB)
10725_2018_470_MOESM4_ESM.xlsx (15 kb)
Table S1. Primers used in this study. (XLSX 14 KB)
10725_2018_470_MOESM5_ESM.xlsx (145 kb)
Table S2. Details of IBA-responsive lncRNAs. (XLSX 144 KB)
10725_2018_470_MOESM6_ESM.xlsx (10 kb)
Table S3. IBA-responsive lncRNAs corresponding to miRNA precursors. (XLSX 10 KB)
10725_2018_470_MOESM7_ESM.xlsx (20 kb)
Table S4. IBA-responsive lncRNAs targeted by miRNAs. (XLSX 19 KB)
10725_2018_470_MOESM8_ESM.xlsx (11 kb)
Table S5. IBA-responsive lncRNAs predicated as miRNAs target-mimic. (XLSX 11 KB)
10725_2018_470_MOESM9_ESM.xlsx (419 kb)
Table S6. Potential target genes of IBA-responsive lncRNAs. (XLSX 419 KB)
10725_2018_470_MOESM10_ESM.xlsx (173 kb)
Table S7. Functional categorization of up-regulated IBA-responsive lncRNAs targets based on the biological process of Gene Ontology. (XLSX 173 KB)
10725_2018_470_MOESM11_ESM.xlsx (124 kb)
Table S8. Functional categorization of down-regulated IBA-responsive lncRNAs targets based on the biological process of Gene Ontology. (XLSX 124 KB)
10725_2018_470_MOESM12_ESM.xlsx (14 kb)
Table S9. The annotation of Gene Ontology terms of up-regulated IBA-responsive lncRNAs targets. (XLSX 13 KB)
10725_2018_470_MOESM13_ESM.xlsx (26 kb)
Table S10. The pathway that IBA-responsive lncRNAs may involve in base on Kyoto Encyclopedia of Genes and Genomes (KEGG). (XLSX 26 KB)
10725_2018_470_MOESM14_ESM.xlsx (11 kb)
Table S11. Details of RNA-seq data. (XLSX 10 KB)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Yuan Meng
    • 1
  • Libo Xing
    • 1
  • Ke Li
    • 1
  • Yanhong Wei
    • 1
  • Hui Wang
    • 1
  • Jiangping Mao
    • 1
  • Feng Dong
    • 1
  • Doudou Ma
    • 1
  • Zhaoxiang Zhang
    • 1
  • Mingyu Han
    • 1
  • Caiping Zhao
    • 1
  • Muhammad Mobeen Tahir
    • 1
  • Dong Zhang
    • 1
    Email author
  1. 1.Department of Horticulture CollegeNorthwest Agriculture & Forestry UniversityYanglingChina

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