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Theoretical and Applied Genetics

, Volume 132, Issue 8, pp 2181–2193 | Cite as

Comprehensive transcriptomics, proteomics, and metabolomics analyses of the mechanisms regulating tiller production in low-tillering wheat

  • Zhiqiang Wang
  • Haoran Shi
  • Shifan Yu
  • Wanlin Zhou
  • Jing Li
  • Shihang Liu
  • Mei Deng
  • Jian Ma
  • Yuming Wei
  • Youliang Zheng
  • Yaxi LiuEmail author
Original Article

Abstract

Key message

Tiller development in low-tillering wheat is related to several differentially expressed genes, proteins, and metabolites, as determined by an integrated omics approach combining transcriptome analysis, iTRAQ, and HPLC-MS on multiple NILs.

Abstract

Tillering is an important aspect of plant morphology that affects spike number, thereby contributing to the final crop yield. However, the mechanisms inhibiting tiller production in low-tillering wheat are poorly characterized. To investigate this aspect of wheat biology, two pairs of near-isogenic lines were developed, and an integrated omics approach combining transcriptome analysis, isobaric tags for relative and absolute quantification, and high-performance liquid chromatography-mass spectrometry were used to compare the free-tillering and low-tillering caused by an allele at Qltn.sicau-2D in wheat samples. Overall, 474 genes, 166 proteins, and 28 metabolites were identified as tillering-associated differentially expressed genes, proteins, and metabolites (DEGs, DEPs, and DEMs, respectively). Functional analysis indicated that the abundance of DEGs/DEPs/DEMs was related to lignin and cellulose metabolism, cell division, cell cycle processes, and glycerophospholipid metabolism; three transcription factor families, GRAS, GRF, and REV, might be related to the decrease in tillering in low-tillering wheat. These findings contribute to improve our understanding of the mechanisms responsible for the inhibition of tiller development in low-tillering wheat cultivars.

Notes

Acknowledgments

This study was supported by the National Key Research and Development Program of China (2016YFD0101004), the National Natural Science Foundation of China (31771794), the outstanding Youth Foundation of the Department of Science and Technology of Sichuan Province (2016JQ0040), the Key Technology Research and Development Program of the Department of Science and Technology of Sichuan Province (2016NZ0057), and the International Science & Technology Cooperation Program of the Bureau of Science and Technology of Chengdu China (No. 2015DFA306002015-GH0300008-HZ).

Author Contribution Statement

ZQW and HRS conducted data analysis and drafted the manuscript. SFY, WLZ, JL, and MD performed the phenotypic evaluation and field sampling and helped with data analysis. JM helped to draft the manuscript. YMW participated in the design of the study. YLZ helped to coordinate the study. YXL designed and coordinated this study and revised the manuscript. All authors have read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standard

The experiments comply with the ethical standards in the country in which they were performed.

Supplementary material

122_2019_3345_MOESM1_ESM.png (1014 kb)
Fig. S1. Schematic diagram of tillering node where tillering germinated (A); The different of tiller number between the free-tillering (B) and low-tillering (D) at Z16 stage; Schematic diagram of tillering buds was inhibited in low-tillering (C) (PNG 1014 kb)
122_2019_3345_MOESM2_ESM.png (36 kb)
Fig. S2. Upset plot of the number of polymorphism markers in free-tillering and low-tillering (PNG 35 kb)
122_2019_3345_MOESM3_ESM.png (166 kb)
Fig. S3. The distribution of polymorphic markers in free-tillering and low-tillering on chromosomes (PNG 165 kb)
122_2019_3345_MOESM4_ESM.pdf (1.3 mb)
Fig. S4. The average length of fragments for each samples (PDF 1365 kb)
122_2019_3345_MOESM5_ESM.png (15 kb)
Fig. S5. Heatmap of the biological replicates between NIL1A and NIL1B (A) (PNG 15 kb)
122_2019_3345_MOESM6_ESM.png (16 kb)
Fig. S5. Heatmap of the biological replicates between NIL7A and NIL7B (B) (PNG 15 kb)
122_2019_3345_MOESM7_ESM.png (33 kb)
Fig. S6. Distribution of genes identified in low-tiller and free-tiller (PNG 32 kb)
122_2019_3345_MOESM8_ESM.png (412 kb)
Fig. S7. Correlation of protein level change with corresponding transcript level change (PNG 411 kb)
122_2019_3345_MOESM9_ESM.pdf (860 kb)
Fig. S8. Score plots of PCA in tiller node of wheat in positive-ion mode and in negative-ion mode, between the NIL1A and NIL1B, between the NIL7A and NIL7B, between the NIL1A and NIL7B, between the NIL7A and NIL1B, between the NIL1B and NIL7B, between the NIL1A and NIL7A (PDF 860 kb)
122_2019_3345_MOESM10_ESM.pdf (877 kb)
Fig. S9. Score plots of OPLS-DA in tiller node of wheat in positive-ion mode and in negative-ion mode, between the NIL1A and NIL1B, between the NIL7A and NIL7B, between the NIL1A and NIL7B, between the NIL7A and NIL1B, between the NIL1B and NIL7B, between the NIL1A and NIL7A (PDF 876 kb)
122_2019_3345_MOESM11_ESM.xlsx (10 kb)
Table S1. The primers used in qRT-PCR for validation of DEGs (XLSX 9 kb)
122_2019_3345_MOESM12_ESM.xlsx (1.4 mb)
Table S2. The proteins identified by iTRAQ (XLSX 1445 kb)
122_2019_3345_MOESM13_ESM.xlsx (1.3 mb)
Table S3. The metabolites identified by HPLC-MS (XLSX 1316 kb)
122_2019_3345_MOESM14_ESM.xlsx (3.2 mb)
Table S4. The genotype of free-tillering and low-tillering by wheat 55 K SNP Array (XLSX 3322 kb)
122_2019_3345_MOESM15_ESM.xlsx (10 kb)
Table S5. Summary of RNA sequencing and mapping using the wheat genome (XLSX 9 kb)
122_2019_3345_MOESM16_ESM.xlsx (136 kb)
Table S6. The DEGs associated with tillering (XLSX 136 kb)
122_2019_3345_MOESM17_ESM.xlsx (20 kb)
Table S7. List of transcription factor were identified from the DEGs (XLSX 20 kb)
122_2019_3345_MOESM18_ESM.xlsx (56 kb)
Table S8. The DEPs associated with tillering (XLSX 56 kb)
122_2019_3345_MOESM19_ESM.xlsx (15 kb)
Table S9. The DEMs associated with tillering (XLSX 14 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Triticeae Research InstituteSichuan Agricultural UniversityWenjiang, ChengduChina

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