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Proteomic profiling of foxtail millet hybrid Zhangzagu10 and its parent lines using iTRAQ-based technique

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Abstract

Heterosis had been increasingly applied in crop production for nearly a century, but the molecular basis of it was poorly understood especially in foxtail millet (Setaria italica). Zhangzagu10 which derived from two-line hybrid breeding system has the characters of ultra-high yield, good stability and extensive disease and lodging resistance. To gain a better understanding of the molecular basis of S.italica heterosis, the isobaric tags for relative and absolute quantification based quantitative proteomic analyses was performed between S.italica hybrid Zhangzagu10 and it parents (male parent Zhangzagu10fu and female parent A2). A total of 4015 proteins were detected, among which 610/276 differentially expressed proteins (DEPs) between Zhangzagu10 and the female/male parent, respectively. The cluster analysis showed that the DEPs expression profiles of Zhangzagu10 were closer to those of the male parent. GO functional classification divided the DEPs into three functional categories (Cellular component, Biological process and Molecular function) and 26 subfamilies, among which three subfamilies had 100% difference between Zhangzagu10 and its parents. KEGG metabolic pathway exhibited significant enrichment of DEPs in Metabolic pathways, Carbon fixation in photosynthetic organisms and Photosynthesis. qRT-PCR verification confirmed the differential expression data and revealed that the expression level of 3 selected genes (such as peroxidase 5-like,G-type lectin S-receptor-like serine/threonine-protein kinase SD2-5,two-on-two hemoglobin-3, etc.) was higher in Zhangzagu10 than that in its male parent. The expression level of 7 selected genes (such as peroxidase 64-like, cysteine-rich receptor-like protein kinase 45, indole-3-acetaldehyde oxidase, etc.) was higher in Zhangzagu10 than that in its male parent, but significantly lower than that in A2. Thus, A2 can potentially optimise the agricultural qualities of Zhangzagu10. Taken together, we hope that this study provides valuable information for the further utilisation and study on the molecular mechanisms of heterosis in hybrid millet.

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Abbreviations

DEPs:

Differentially expressed proteins

S. italica :

Setaria italica

iTRAQ:

Isobaric tags for relative and absolute quantification

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

qRT-PCR:

Quantitative real-time polymerase chain reaction

MS:

Mass spectrometry

PVPP:

Polyvinylpolypyrrolidone

TCA:

Trichloroacetic acid

PMSF:

Phenylmethanesulfonyl fluoride

HEPES:

4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid

EDTA:

Ethylene diamine tetraacetic acid

DTT:

Dithiothreitol

IAM:

Iodoacetamide

TEAB:

Tetraethylammonium bicarbonate

SDS:

Sodium dodecyl sulphate

HPLC:

High performance liquid chromatography

ACN:

Acetonitrile

DEPC:

Diethy pyrocarbonate

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Acknowledgements

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the iProX partner repository with the dataset identifier PXD017131. (Ma et al. 2019). This research was funded by Major national science and technology projects (2014ZX0800909B), Selection and training of talents of higher discipline plan of Hebei Province (BR2-234), Hebei Province Natural Science Fund (C2018405042); Key R & D projects of Hebei Province (19226420D); Hebei Province Science and Technology Support Program under grant number 13226326; Major Projects Foundation of Hebei North University (ZD201407) and Major Projects Foundation of Hebei North University (ZD201305).

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Author notes

  1. Qiaoyun Weng, Xiaoqing Song and Yan Zhao have equally contributed to this work.

Authors and Affiliations

  1. College of Agriculture and Forestry, Hebei North University, Zhangjiakou, 075000, China

    Qiaoyun Weng & Yinghui Liu

  2. Basic Medical College, Hebei North University, Zhangjiakou, 075000, China

    Xiaoqing Song

  3. Millet Research Institute, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhang, China

    Yan Zhao

  4. Millet Research Institute, Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou, China

    Jincheng Yuan

  5. Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China

    Zhiping Dong

  6. Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou, China

    Zhihai Zhao

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  1. Qiaoyun Weng
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  2. Xiaoqing Song
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  3. Yan Zhao
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Correspondence to Yinghui Liu.

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Weng, Q., Song, X., Zhao, Y. et al. Proteomic profiling of foxtail millet hybrid Zhangzagu10 and its parent lines using iTRAQ-based technique. J. Plant Biochem. Biotechnol. 29, 439–449 (2020). https://doi.org/10.1007/s13562-020-00551-2

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