Dataset Information

Spatial Variability of Grape Berry Maturation Program at the Molecular Level

ABSTRACT: The application of sensors in viticulture is a fast and efficient method to monitor grapevine vegetative, yield, and quality parameters and determine spatial intra-vineyard variability. Molecular analysis at the gene expression level can further contribute to the understanding of the observed variability by elucidating how pathways contributing to different grape quality traits behave in zones diverging on any of these parameters. The intra-vineyard variability of a Cabernet Sauvignon vineyard was evaluated through a Normalized Difference Vegetation Index (NDVI) map calculated from a multispectral image and detailed ground-truthing (e.g., vegetative, yield, and berry ripening compositional parameters). The relationships between NDVI and ground measurements were explored by correlation analysis. Moreover, berries were investigated by microarray gene expression analysis performed at five time points from fruit set to full ripening. Comparison between the transcriptomes of samples taken from locations with the highest and lowest NDVI values identified 968 differentially expressed genes. Spatial variability maps of the expression level of key berry ripening genes showed consistent patterns aligned with the vineyard vigor map. These insights indicate that berries from different vigor zones present distinct molecular maturation programs and suggest that transcriptome analysis may be a valuable tool for the management of vineyard variability.

ORGANISM(S): Vitis vinifera

PROVIDER: GSE254304 | GEO | 2024/02/27

REPOSITORIES: GEO

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Project description: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.

Project description:Noble rot results from atypical infections of ripe grape berries by Botrytis cinerea. Unlike bunch rot, noble rot promotes favorable changes in grape berries and accumulation of secondary metabolites that enhance wine grape quality. Noble rot-infected berries of SÃ©millon, a white-skinned variety, were collected over three years from a commercial vineyard at the same time fruit were harvested for botrytized wine production. Transcriptomic and metabolomic data were integrated to identify pathways associated with distinct stages of noble rot. Botrytis induced the expression of known key regulators of pathways in secondary metabolism associated with berry ripening. The activation by Botrytis during noble rot of metabolic pathways associated with berry ripening was further supported by comparisons with transcriptomes of red-skinned varieties at vÃ©raison. A prominent and common outcome of noble rot and berry ripening was the enhancement of the phenylpropanoid metabolism. Induced synthesis of stilbenes, flavonoids, and anthocyanins was supported by both transcriptional and metabolite analyses. Enzyme assays and targeted gene expression analyses of samples from the three distinct years confirmed that the activation of central and peripheral phenylpropanoid pathways is a consistent hallmark of noble rot. Finally, we show that the impact of noble rot on grape metabolism is still detectable in botrytized wines. These results demonstrate that despite the late stage of terminal senescence of a plant organ, a biotic stress can cause a major reprogramming of plant metabolism leading, in case of noble rot, to the synthesis of important metabolites for grape berry flavor and aroma. The experimental design consists of 4 treatments, berries at 3 distinct stages of noble rot and berries without apparent symptoms of infection. From each treatment a total of 4 biological replicates were sequenced with RNAseq, each replicate corresponded to independent pools of 10-15 berries harvested from adjacent grapevines.

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