Theoretical and Experimental Plant Physiology

, Volume 28, Issue 1, pp 109–129

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
Article

DOI: 10.1007/s40626-016-0059-5

Cite this article as:
Carbonell-Bejerano, P., Rodríguez, V., Hernáiz, S. et al. Theor. Exp. Plant Physiol. (2016) 28: 109. doi:10.1007/s40626-016-0059-5

Abstract

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.

Keywords

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

Supplementary material

40626_2016_59_MOESM1_ESM.xls (351 kb)
Supplementary material 1 (XLS 351 kb)
40626_2016_59_MOESM2_ESM.xls (82 kb)
Supplementary material 2 (XLS 82 kb)
40626_2016_59_MOESM3_ESM.xls (657 kb)
Supplementary material 3 (XLS 657 kb)
40626_2016_59_MOESM4_ESM.pdf (141 kb)
Supplementary material 4 (PDF 140 kb)

Funding information

Funder NameGrant NumberFunding Note
Spanish Centre for Technological and Industrial Development (CDTI) from the Spanish Ministry of Science and Innovation (MICINN)
  • CENIT-DEMETER

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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