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, Volume 32, Issue 6, pp 1609–1620 | Cite as

Whole-genome re-sequencing reveals molecular mechanisms of biomass changes in 11-year-old Bt transgenic poplar

  • Jin Zhang
  • Tian-Yi Zhan
  • Hui-Xia Jia
  • Li-Shuan Wu
  • Meng-Zhu Lu
  • Jian-Jun HuEmail author
Original Article
  • 123 Downloads

Abstract

Key message

Genome-wide insertions/deletions were identified in Bt transgenic poplar through whole-genome re-sequencing, revealing the molecular mechanisms underlying changes in the growth and wood characteristics of Bt transgenic poplar.

Abstract

Poplar is a fast-growing tree that relieves the wood demand in China. Previously, we found growth and wood characteristics differed in some lines of insect-resistant Bt transgenic poplar. Here, we selected five Bt transgenic lines (#12, #153, #172, #208 and #209), one untransformed control (CK2), one comparable control (CK3), and one native cultivar (JY, Populus × euramericana ‘Robusta’) in Xinjiang, China, for further study. Based on breast diameter, tree height, chemical content, and fibre morphology analyses, these transgenic lines showed fast growth and high-lignin and low-cellulose contents in the cell wall. In addition, genome-wide insertions/deletions (InDels) were compared between two transgenic lines (#12 and #153) and the untransformed control via whole-genome re-sequencing. GO enrichment and protein–protein interaction networks indicated the genes affected by differential InDels were related to programmed cell death and defence responses. This study provides new insight into the molecular mechanisms underlying changes in biomass characteristics in Bt transgenic poplar.

Keywords

Transgenic poplar Bt Wood characteristic Whole-genome re-sequencing InDels Protein–protein interaction network 

Abbreviations

ABA

Abscisic acid

ACC

Acetyl-CoA carboxylase

BP

Biological process

Bt

Bacillus thuringiensis

CAD

Cinnamyl alcohol dehydrogenase

CC

Cellular component

CDS

Coding sequences

GM

Genetically modified

GO

Gene ontolog

InDels

Insertion/deletion polymorphisms

LRR

Leucine-rich repeat

MF

Molecular function

MPK

Mitogen-activated protein kinase

NGS

Next-generation sequencing

OMT

O-Methyltransferase

PCD

Programmed cell death

PE

Pair-end

PPI

Protein–protein interaction

UTR

Untranslated regions

Notes

Acknowledgements

We thank Dr. Rongfeng Huang for the wood characteristics and chemical content measurement. The work was supported by the National Key Research and Development Program of China (2017YFD0600201) and the National Key Program on Transgenic Research (2018ZX08021001).

Author contribution

JH, JZ and ML conceived and designed the experiments. JZ, TZ, HJ and LW participated in the experiments. JZ and TZ performed data analysis and drafted the manuscript. JH provides reagents and analysis tools. All authors read and approved the final version of the manuscript.

Compliance with ethical standards

Conflict of interesr

The authors declare no competing financial interest.

Supplementary material

468_2018_1737_MOESM1_ESM.tif (1.3 mb)
Figure S1: Genotyping of twelve poplar accessions (TIF 1357 KB)
468_2018_1737_MOESM2_ESM.pdf (1.2 mb)
Figure S2: Whole-genome re-sequencing reads coverage on P. trichocarpa genome in three samples (PDF 1228 KB)
468_2018_1737_MOESM3_ESM.pdf (360 kb)
Figure S3: GO enrichment of genes affected by differential InDels in comparison “#12 vs. CK2” (PDF 359 KB)
468_2018_1737_MOESM4_ESM.pdf (323 kb)
Figure S4: GO enrichment of genes affected by differential InDels in comparison “#153 vs. CK2” (PDF 323 KB)
468_2018_1737_MOESM5_ESM.xlsx (18 kb)
Table S1: Enriched GO terms of genes affected by differential InDels in the four comparisons (XLSX 17 KB)
468_2018_1737_MOESM6_ESM.xlsx (40 kb)
Table S2: Functional annotation and link counts of genes in the PPI network (XLSX 39 KB)

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Copyright information

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

Authors and Affiliations

  • Jin Zhang
    • 1
  • Tian-Yi Zhan
    • 2
  • Hui-Xia Jia
    • 1
  • Li-Shuan Wu
    • 1
  • Meng-Zhu Lu
    • 1
  • Jian-Jun Hu
    • 1
    Email author
  1. 1.State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of ForestryChinese Academy of ForestryBeijingChina
  2. 2.College of Materials Science and EngineeringNanjing Forestry UniversityNanjingChina

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