Proteomic profiling of rice embryos from a hybrid rice cultivar and its parental lines

Authors

  • Weiwei Wang,

    1. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    2. Graduate University of Chinese Academy of Sciences, Beijing, China
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  • Bo Meng,

    1. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    2. Graduate University of Chinese Academy of Sciences, Beijing, China
    3. Beijing Proteomics Institute, Beijing, China
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  • Xiaomeng Ge,

    1. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    2. Graduate University of Chinese Academy of Sciences, Beijing, China
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  • Shuhui Song,

    1. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    2. Graduate University of Chinese Academy of Sciences, Beijing, China
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  • Yue Yang,

    1. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    2. Graduate University of Chinese Academy of Sciences, Beijing, China
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  • Xiaomin Yu,

    1. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    2. Graduate University of Chinese Academy of Sciences, Beijing, China
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  • Liguo Wang,

    1. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    2. Graduate University of Chinese Academy of Sciences, Beijing, China
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  • Songnian Hu,

    1. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
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  • Siqi Liu,

    1. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    2. Beijing Proteomics Institute, Beijing, China
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  • Jun Yu Professor

    Corresponding author
    1. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    • Beijing Institute of Genomics, Chinese Academy of Sciences, No. 7 Beitucheng West Road, ChaoYang District, Beijing 100029, China Fax: +86-10-8299-5401
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Abstract

Elite rice hybrids, when compared to their parental lines, exhibit increased yield and other favorable agronomical traits, such as pathogen- and water-stress resistances, which are described as heterosis, and the molecular mechanism of heterosis remains to be elucidated. Since genomic sequences of the paternal (9311) and maternal lines (P64S) of a major rice hybrid variety LYP9 (Liang-You-Pei-Jiu) were acquired recently, we performed a proteomic study on mature embryos of this hybrid triad based on 2-DE and MALDI-TOF MS analyses, and identified 54 differentially expressed proteins involved in major biological processes including nutrient reservoir, response to stress, and metabolism. We observed that most of the storage proteins exhibit overdominance and stress-induced proteins display additivity. We compared proteomic results with transcriptomic data generated from the same embryo samples and found 28 candidate heterosis-associated genes shared by the two datasets. We further traced back to their genomic structures including protein-coding and regulatory regions and found that most of these genes have multiple copies in rice genomes as paralogous genes. Based on alignment of coding and regulation regions, we found that most of the differentially expressed genes at both protein and RNA levels are recent gene duplicates (paralogous genes) with relative little difference in protein-coding regions between orthologous genes (between genes of the two parental genomes) as compared to regulatory regions that harbor numerous indels and base substitutions.

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