Circadian oscillatory transcriptional programs in grapevine ripening fruits

Carbonell-Bejerano et al. BMC Plant Biology 2014, 14:78 http://www.biomedcentral.com/1471-2229/14/78 RESEARCH ARTICLE Open Access Circadian oscillatory transcriptional programs in grapevine ripening fruits Pablo Carbonell-Bejerano1*, Virginia Rodríguez2, Carolina Royo1, Silvia Hernáiz1, Luis Carlos Moro-González3, Montserrat Torres-Viñals4 and José Miguel Martínez-Zapater1 Abstract Background: Temperature and solar radiation influence Vitis vinifera L. berry ripening. Both environmental conditions fluctuate cyclically on a daily period basis and the strength of this fluctuation affects grape ripening too. Additionally, a molecular circadian clock regulates daily cyclic expression in a large proportion of the plant transcriptome modulating multiple developmental processes in diverse plant organs and developmental phases. Circadian cycling of fruit transcriptomes has not been characterized in detail despite their putative relevance in the final composition of the fruit. Thus, in this study, gene expression throughout 24 h periods in pre-ripe berries of Tempranillo and Verdejo grapevine cultivars was followed to determine whether different ripening transcriptional programs are activated during certain times of day in different grape tissues and genotypes. Results: Microarray analyses identified oscillatory transcriptional profiles following circadian variations in the photocycle and the thermocycle. A higher number of expression oscillating transcripts were detected in samples carrying exocarp tissue including biotic stress-responsive transcripts activated around dawn. Thermotolerance-like responses and regulation of circadian clock-related genes were observed in all studied samples. Indeed, homologs of core clock genes were identified in the grapevine genome and, among them, VvREVEILLE1 (VvRVE1), showed a consistent circadian expression rhythm in every grape berry tissue analysed. Light signalling components and terpenoid biosynthetic transcripts were specifically induced during the daytime in Verdejo, a cultivar bearing white-skinned and aromatic berries, whereas transcripts involved in phenylpropanoid biosynthesis were more prominently regulated in Tempranillo, a cultivar bearing black-skinned berries. Conclusions: The transcriptome of ripening fruits varies in response to daily environmental changes, which might partially be under the control of circadian clock components. Certain cultivar and berry tissue features could rely on specific circadian oscillatory expression profiles. These findings may help to a better understanding of the progress of berry ripening in short term time scales. Keywords: Circadian, Fruit ripening, Gene expression, Grapevine, Light, Microarray, Phenylpropanoid, Temperature, Terpene, Vitis vinifera Background The grapevine fruit is a characteristic berry consisting of an external skin surrounding a fleshy pulp that encloses seeds. Grape biochemical composition is crucial for the different uses of grapes such as winemaking, production of juice and liqueur, fresh consumption or elaboration of raisins, and the final composition is mostly achieved * Correspondence: 1 Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, Madre de Dios 51, 26006 Logroño, Spain Full list of author information is available at the end of the article during the ripening phase [1]. Grape ripening is triggered once the seeds have developed and radically changes fruit features from frugivore-repulsive to -attractive. This shift comprises sugar accumulation in the vacuoles of mesocarp cells accompanied by organic acid metabolisation and titratable acidity reduction [2]. Mechanisms to protect seeds from biotic and abiotic stress sources are also activated, mainly in the berry skin [3]. Phenolic compounds are accumulated, including phytoalexins, damaging lightabsorbing compounds and animal-attractive anthocyanin pigments [4]. Changes in terpenoid composition result in © 2014 Carbonell-Bejerano et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Carbonell-Bejerano et al. BMC Plant Biology 2014, 14:78 http://www.biomedcentral.com/1471-2229/14/78 attractive aromatic profiles, while other compounds of the same family accumulate to accomplish protective functions [5,6]. Although grapevine ripening is regulated by an intrinsic program that is partially triggered by hormonal signals [7], the process is also strongly modulated by external factors that influence the final berry composition and its commercial quality. Temperature is a major factor altering grape ripening with high temperatures hastening organic acid metabolisation and inhibiting anthocyanin accumulation [8,9]. Irradiation intensity and quality perceived in the berry skin produces changes in secondary metabolism. Light promotes flavonols and terpenoids accumulation with some effects being more specifically related with ultraviolet radiation, which is also able to enhance stilbenoids accumulation [6,10-13]. Moreover, temperature and light conditions cyclically fluctuate under field environments due to the Earth's rotation and, in fact, the strength of their daily oscillation has been shown to affect grape ripening. For instance, reduction in temperature fluctuation intensity hastens berry ripening and alters flavonoid partitioning [14] and high temperatures applied during night-times are also able to reduce anthocyanin accumulation [15]. In contrast, light pulses applied during the night-time enhance anthocyanin accumulation [16]. These effects of environmental variation on grape ripening rely, at least in part, on changes at the level of gene expression [17-21]. Thus, it can be hypothesised that daily oscillations in factors such as temperature, light or humidity could influence grape ripening progression and consequently on its final composition by means of conditioning circadian fluctuations on the grape transcriptome. An internal molecular clock is another daily cycling element modulating plant physiology. Core clock components are transcription factors that reciprocally regulate their expression resulting in characteristic circadian expression profiles. Altogether, they determine daily rhythms of expression in a great proportion of plant transcriptomes [22-24]. In addition, the circadian clock integrates inputs from fluctuating conditions like light and temperature, which allows for plants to discriminate daily and seasonal changes [25,26]. In this way, the circadian clock togeth (...truncated)