title: SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling.
abstract: 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.
authors.affiliation: College of Life Sciences, South China Agricultural UniversityGuangzhou, China; State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong KongHong Kong, Hong Kong; Shenzhen Research Institute, The Chinese University of Hong KongShenzhen, China.
authors.forename: Fu-Yuan
authors.initials: FY
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong Hong Kong, Hong Kong.
authors.forename: Mo-Xian
authors.initials: MX
authors.lastname: Chen
authors.affiliation: School of Pharmacy, Nanjing Medical University Nanjing, China.
authors.forename: Yu-Wen
authors.initials: YW
authors.lastname: Su
authors.affiliation: College of Life Sciences, South China Agricultural University Guangzhou, China.
authors.forename: Xuezhong
authors.initials: X
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong KongHong Kong, Hong Kong; Shenzhen Research Institute, The Chinese University of Hong KongShenzhen, China.
authors.forename: Neng-Hui
authors.initials: NH
authors.lastname: Ye
authors.affiliation: College of Life Sciences, Nantong University Nantong, China.
authors.forename: Yun-Ying
authors.initials: YY
authors.lastname: Cao
authors.affiliation: College of Life Sciences, Fujian Agriculture and Forestry University Fuzhou, China.
authors.forename: Sheng
authors.initials: S
authors.lastname: Lin
authors.affiliation: State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong Hong Kong, Hong Kong.
authors.forename: Tie-Yuan
authors.initials: TY
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong Hong Kong, Hong Kong.
authors.forename: Hao-Xuan
authors.initials: HX
authors.lastname: Li
authors.affiliation: State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong Hong Kong, Hong Kong.
authors.forename: Guan-Qun
authors.initials: GQ
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong Hong Kong, Hong Kong.
authors.forename: Yu
authors.initials: Y
authors.lastname: Jin
authors.affiliation: The Rice Research Institute, Guangdong Academy of Agricultural Sciences Guangzhou, China.
authors.forename: Yong-Hai
authors.initials: YH
authors.lastname: Gu
authors.affiliation: School of Biological Science, The University of Hong Kong Hong Kong, China.
authors.forename: Wai-Lung
authors.initials: WL
authors.lastname: Chan
authors.affiliation: School of Biological Science, The University of Hong Kong Hong Kong, China.
authors.forename: Clive
authors.initials: C
authors.lastname: Lo
authors.affiliation: College of Life Sciences, South China Agricultural University Guangzhou, China.
authors.forename: Xinxiang
authors.initials: X
authors.lastname: Peng
authors.affiliation: College of Life Sciences, South China Agricultural University Guangzhou, China.
authors.forename: Guohui
authors.initials: G
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong KongHong Kong, Hong Kong; Shenzhen Research Institute, The Chinese University of Hong KongShenzhen, China.
authors.forename: Jianhua
authors.initials: J
authors.lastname: Zhang
keywords: SWATH-MS analysis; grain filling; post-transcriptional regulation; proteomics; rice