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iTRAQ-based analysis of developmental dynamics in the soybean leaf proteome reveals pathways associated with leaf photosynthetic rate

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Abstract

Photosynthetic rate which acts as a vital limiting factor largely affects the potential of soybean production, especially during the senescence phase. However, the physiological and molecular mechanisms that underlying the change of photosynthetic rate during the developmental process of soybean leaves remain unclear. In this study, we compared the protein dynamics during the developmental process of leaves between the soybean cultivar Hobbit and the high-photosynthetic rate cultivar JD 17 using the iTRAQ (isobaric tags for relative and absolute quantification) method. A total number of 1269 proteins were detected in the leaves of these two cultivars at three different developmental stages. These proteins were classified into nine expression patterns depending on the expression levels at different developmental stages, and the proteins in each pattern were also further classified into three large groups and 20 small groups depending on the protein functions. Only 3.05–6.53 % of the detected proteins presented a differential expression pattern between these two cultivars. Enrichment factor analysis indicated that proteins involved in photosynthesis composed an important category. The expressions of photosynthesis-related proteins were also further confirmed by western blotting. Together, our results suggested that the reduction in photosynthetic rate as well as chloroplast activity and composition during the developmental process was a highly regulated and complex process which involved a serial of proteins that function as potential candidates to be targeted by biotechnological approaches for the improvement of photosynthetic rate and production.

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Acknowledgments

This study was supported by the Natural science fund for distinguished young scholars of Hebei Province (C2014301035), National Natural Science Foundation of China (31100880), the Key Project of the Natural Science Foundation of Hebei Province (C2012301020), the Key Research Foundation for Excellent Returned Overseas Chinese (C2011006001), and China Scholarship Council Program (201208130236).

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Authors and Affiliations

  1. National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean Ministry of Agriculture, Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050031, People’s Republic of China

    Jun Qin, Fengmin Wang & Mengchen Zhang

  2. Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, People’s Republic of China

    Jin Xu

  3. National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, People’s Republic of China

    Jianan Zhang

  4. Geochemical Environmental Research Group, Texas A&M University, 833 Graham Road, College Station, TX, 77845, USA

    Duan Liu

  5. Beijing Protein Innovation, B-8, Beijing Airport Industrial Zone, Beijing, 101318, People’s Republic of China

    Changcheng Yin & Hao Chen

  6. Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA

    Pengyin Chen

  7. Department of Horticulture, University of Arkansas, Fayetteville, AR, 72701, USA

    Jun Qin & Jinbing Ma

  8. Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA

    Bo Zhang

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  1. Jun Qin
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  2. Jianan Zhang
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  3. Duan Liu
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  4. Changcheng Yin
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  5. Fengmin Wang
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  7. Hao Chen
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  8. Jinbing Ma
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  9. Bo Zhang
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  10. Jin Xu
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  11. Mengchen Zhang
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Correspondence to Jin Xu or Mengchen Zhang.

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Communicated by K. Chong.

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438_2016_1202_MOESM1_ESM.pptx

Supplemental Fig 1A Cluster analysis of the proteins detected in JD 17 and Hobbit, the proteins were classified based on similarity of expression patter at three contiguous developmental stages 1B Nine clusters were identified by K-means clustering The pink lines indicate representative protein expression trends; x- and y-axes represent weeks after post-germination and normalized expression value, respectively, 1C Functional categorisation of the proteins that were detected in each cluster (PPTX 816 kb)

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Qin, J., Zhang, J., Liu, D. et al. iTRAQ-based analysis of developmental dynamics in the soybean leaf proteome reveals pathways associated with leaf photosynthetic rate. Mol Genet Genomics 291, 1595–1605 (2016). https://doi.org/10.1007/s00438-016-1202-3

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  • DOI: https://doi.org/10.1007/s00438-016-1202-3

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