SWATH-MS quantitative analysis of proteins in the rice inferior and superior spikelets during grain filling

Fu Yuan Zhu, Mo Xian Chen, Yu Wen Su, Xuezhong Xu, Neng Hui Ye, Yun Ying Cao, Sheng Lin, Tie Yuan Liu, Hao Xuan Li, Guan Qun Wang, Yu Jin, Yong Hai Gu, Wai Lung Chan, Clive Lo, Xinxiang Peng, Guohui Zhu*, Jianhua Zhang*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

15 Citations (Scopus)


Modern rice cultivars have large panicle but their yield potential is often not fully achieved due to poor grain-filling of late-flowering inferior spikelets (IS). Our earlier work suggested a broad transcriptional reprogramming during grain filling and showed a difference in gene expression between IS and earlier-flowering superior spikelets (SS). However, the links between the abundances of transcripts and their corresponding proteins are unclear. In this study, a SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) -based quantitative proteomic analysis has been applied to investigate SS and IS proteomes. A total of 304 proteins of widely differing functionality were observed to be differentially expressed between IS and SS. Detailed gene ontology analysis indicated that several biological processes including photosynthesis, protein metabolism, and energy metabolism are differentially regulated. Further correlation analysis revealed that abundances of most of the differentially expressed proteins are not correlated to the respective transcript levels, indicating that an extra layer of gene regulation which may exist during rice grain filling. Our findings raised an intriguing possibility that these candidate proteins may be crucial in determining the poor grain-filling of IS. Therefore, we hypothesize that the regulation of proteome changes not only occurs at the transcriptional, but also at the post-transcriptional level, during grain filling in rice.

Original languageEnglish
Article number1926
Number of pages11
JournalFrontiers in Plant Science
Publication statusPublished - 20 Dec 2016

Scopus Subject Areas

  • Plant Science

User-Defined Keywords

  • Grain filling
  • Post-transcriptional regulation
  • Proteomics
  • Rice
  • SWATH-MS analysis


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