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      The use of 2D-electrophoresis and de novo sequencing to characterize inter- and intra-cultivar protein polymorphisms in an allopolyploid crop.

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          Abstract

          Polyploidy and allopolyploidy have played an important role in the evolution of many plants and crops. Several techniques exist to characterize allopolyploid varieties. Analyzing the consequences of genomic reorganization at the gDNA level is a prerequisite but a better insight into the consequences for the phenotype is also primordial. As such, protein polymorphism analysis is important in understanding plant and crop biodiversity and is a driving force behind crop improvement. Our strategy to analyze protein isoforms and to detect possible gene silencing or deletion in bananas was based on protein analysis. Bananas are a good representative of a complex allopolyploid and important crop. We combined two-dimensional electrophoresis (2DE) and 2D DIGE with de novo MS/MS sequence determination to characterize a range of triploid varieties. Via Principal Component Analysis (PCA) and hierarchical clustering we were able to blindly classify the different varieties according to their presumed genome constitution. We report for the first time the application of an automated approach for the derivatization of peptides for facilitated MS/MS de novo sequence determination. We conclude that the proteome does not always correspond to the presumed genome formulae and that proteomics is a powerful tool to characterize varieties. The observations at the protein level provide good indications for a more complex genome structure and genomic rearrangement in some banana varieties.

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          Author and article information

          Journal
          Phytochemistry
          Phytochemistry
          Elsevier BV
          1873-3700
          0031-9422
          Jul 2011
          : 72
          : 10
          Affiliations
          [1 ] K.U.Leuven, Department of Biosystems, Division of Crop Biotechnics, Leuven, Belgium. sebastien.carpentier@biw.kuleuven.be
          Article
          S0031-9422(10)00396-1
          10.1016/j.phytochem.2010.10.016
          21109271
          0ba9e85b-8f72-47fd-bf9f-7d195869ac11
          Copyright © 2010 Elsevier Ltd. All rights reserved.
          History

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