Theoretical and Experimental Plant Physiology

, Volume 28, Issue 1, pp 109–129 | Cite as

Reducing sampling bias in molecular studies of grapevine fruit ripening: transcriptomic assessment of the density sorting method

  • Pablo Carbonell-Bejerano
  • Virginia Rodríguez
  • Silvia Hernáiz
  • Carolina Royo
  • Silvia Dal Santo
  • Mario Pezzotti
  • José Miguel Martínez-Zapater


The interplay between environmental and genetic factors conditions the fruit ripening program in plants. Transcriptome analysis of grapevine fruits can help understanding these interactions to consciously cope with conditions leading to detrimental effects for viticultural purposes. However, considering the grapevine characteristic ripening asynchrony, which can be intensified by contrasting conditions, accurate grape sampling may be essential for molecular comparisons. In this study, berry density sorting according to floatability in NaCl solutions was transcriptomically assessed as a grape ripening staging strategy. The transcriptome was compared between three density classes collected near commercial maturity using grapevine whole-genome NimbleGen microarrays. Expression profiles clearly related with ripening progression were detected in a density series simultaneously collected from a vineyard of Albariño. By contrast, considerable differences were detected when the same density series was sampled on two different dates from the same vineyard of Tempranillo. Functional analysis indicated that environmental differences between both sampling moments determined most of these expression differences. Ripening degree-dependent responses to the environment were also detected. Finally, the effect of the sorting procedures on the grape transcriptome showed negligible when it was directly tested. Altogether, these findings evidence the convenience of homogenizing the developmental stage and the sampling time conditions for transcriptome comparisons. Berry density sorting proved useful to this end, although this method could be limited when berry sugar concentration increases through dehydration.


Grapevine Fruit ripening Ontogenetic sampling Density sorting Transcriptome–environment interaction Chronological sampling 



This work was carried out in the context of the CENIT-DEMETER Project, funded by the Spanish Centre for Technological and Industrial Development (CDTI) from the Spanish Ministry of Science and Innovation (MICINN). The authors express their gratitude to all entities participating in the CENIT-DEMETER Consortium, and especially to Bodegas Miguel Torres S. A., Bodegas Martín Códax, Bodegas Roda, and Bodegas Matarromera S. L. for their support and for providing the plants and the growing conditions. Collaboration between authors’ research groups was established in the context of COST (European Cooperation in Science and Technology) Action FA1106 “QualityFruit”. Part of the microarray hybridizations were carried out at the Genomics Unit of the National Centre for Biotechnology, CNB-CSIC, Madrid, Spain. We thank Anna Velazquez, Montse Torres-Viñals, Meritxell Salamero and Eudald Crivillés from Bodegas Miguel Torres S. A.; Miguel Tubío and Katia Álvarez from Bodegas Martín Códax; Lidia Martínez and Esperanza Tomás from Bodegas Roda S.A., and Gema Bravo from CNB-CSIC for their technical support. We also thank José Ramón Lissarrague, Lucia Rodríguez, Rosa Pedroso, Sara Sánchez-Elez and Patricia Sánchez De Miguel from Universidad Politécnica de Madrid for the field irrigation and the greenhouse cultivation setting.

Supplementary material

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Copyright information

© Brazilian Society of Plant Physiology 2016

Authors and Affiliations

  • Pablo Carbonell-Bejerano
    • 1
  • Virginia Rodríguez
    • 2
  • Silvia Hernáiz
    • 1
  • Carolina Royo
    • 1
  • Silvia Dal Santo
    • 3
  • Mario Pezzotti
    • 3
  • José Miguel Martínez-Zapater
    • 1
  1. 1.Instituto de Ciencias de la Vid y del Vino (ICVV)Consejo Superior de Investigaciones Científicas CSIC-Universidad de La Rioja-Gobierno de La RiojaLogroñoSpain
  2. 2.Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
  3. 3.Department of BiotechnologyUniversity of VeronaVeronaItaly

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