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| Status |
Public on May 22, 2016 |
| Title |
Response of Tempranillo grapes to immersion in a concentrated NaCl solution |
| Organism |
Vitis vinifera |
| Experiment type |
Expression profiling by array
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| Summary |
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 assessed as a grape ripening staging strategy. Total sugar content was more correlated with berry density than with other non-invasive ripening parameters. 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 the berry sugar concentration is not determined by the ripening developmental program.
The potential berry transcriptional response to the high concentrated salt solutions used for berry density-sorting may involve a concern on the suitability of this method for transcriptomic studies. This possibility was directly tested by comparing the expression of berries immersed in a highly concentrated NaCl solution (170 g•L-1) during a relatively long time lapse (1 h) with that in berries kept at room air. This experiment was carried out using Tempranillo grapes at mid-véraison to standardize the ripening state by selecting berries with the same proportion of coloured skin surface (50%, corresponding to TSS of 9.9 ±0.3 ºBrix). Berries grown under watering (W) and no-watering (NW) conditions were analysed to test for possible irrigation-NaCl solution interactions affecting berry gene expression. No significant DEG was identified when the effect of the NaCl solution was analysed separately for berries collected from W or NW blocks (≥2-fold change and B-H adjusted P≤0.05 in 2-class limma). When W and NW samples were used together to analyse the effect of the NaCl immersion irrespectively of the irrigation treatment, 15 genes were detected with a B-H adjusted P≤0.05 and only 13 of these showed ≥2-fold change, confirming the slight effect. In summary, the effect of the NaCl immersion on the berry transcriptome is negligible and does not seem to interact with the transcriptomic response to other environmental cues.
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| Overall design |
Berries grown under watering (W) and no-watering (NW) conditions were analysed to test for possible irrigation-NaCl solution interactions affecting berry gene expression. Three independent W and NW vineyard blocks were successively sampled and submitted to the treatment. NaCl-treated berries (NaCl) were immersed in a highly concentrated NaCl solution (170 g•L-1) during a relatively long time lapse (1 h) simulating the density sorting procedure. Control berries (C) were kept at room air 1 h prior to sample freezing. This experiment was carried out using Tempranillo grapes at mid-véraison to standardize the ripening state by selecting berries with the same proportion of coloured skin surface (50%, corresponding to TSS of 9.9 ±0.3 ºBrix). RNA from five NaCl-treated and six control samples were finally hybridized to grapevine whole-genome NimbleGen microarrays.
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| Contributor(s) |
Carbonell-Bejerano P, Martínez-Zapater JM |
| Citation |
Carbonell-Bejerano P., Rodriguez V., Hernaiz S., Royo C., Dal Santo S., Pezzotti M., Martinez-Zapater J.M., 2016. Reducing sampling bias in molecular studies of grapevine fruit ripening: transcriptomic assessment of the density sorting method. Theoretical and Experimental Plant Physiology 28, 109-129. doi: http://dx.doi.org/10.1007/s40626-016-0059-5
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| Submission date |
Dec 14, 2015 |
| Last update date |
Aug 22, 2016 |
| Contact name |
Pablo Carbonell-Bejerano |
| E-mail(s) |
pablo.carbonell@icvv.es
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| Organization name |
CSIC
|
| Department |
Instituto de las Ciencias de la Vid y del Vino
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| Street address |
Madre de Dios, 51
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| City |
Logrono |
| State/province |
La Rioja |
| ZIP/Postal code |
26006 |
| Country |
Spain |
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| Platforms (1) |
| GPL17894 |
NimbleGen 090918 Vitus vinifera exp HX12 [090918_Vitus_exp; GENE_CALL_ID version] |
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| Samples (11)
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| GSM1971672 |
Tempranillo_pericarp_control_watering_block1_rep1 |
| GSM1971673 |
Tempranillo_pericarp_control_watering_block2_rep2 |
| GSM1971674 |
Tempranillo_pericarp_control_watering_block3_rep3 |
| GSM1971675 |
Tempranillo_pericarp_control_no-watering_block1_rep4 |
| GSM1971676 |
Tempranillo_pericarp_control_no-watering_block2_rep5 |
| GSM1971677 |
Tempranillo_pericarp_control_no-watering_block3_rep6 |
| GSM1971678 |
Tempranillo_pericarp_NaCl-immersion_watering_block1_rep1 |
| GSM1971679 |
Tempranillo_pericarp_NaCl-immersion_watering_block2_rep2 |
| GSM1971680 |
Tempranillo_pericarp_NaCl-immersion_watering_block3_rep3 |
| GSM1971681 |
Tempranillo_pericarp_NaCl-immersion_no-watering_block1_rep4 |
| GSM1971682 |
Tempranillo_pericarp_NaCl-immersion_no-watering_block3_rep5 |
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| This SubSeries is part of SuperSeries: |
| GSE76000 |
Reducing sampling bias in molecular studies of grapevine fruit ripening: transcriptomic assessment of the density sorting method |
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| Relations |
| BioProject |
PRJNA305928 |
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