Transcriptome differences among Albariño densimetrically-sorted berries

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. Vitis vinifera cv. Albariño plants grafted on Millardet et de Grasset 420 A rootstock at Finca Pé Redondo (Meis, Galicia, Spain) were used. This experimental vineyard was planted in 2003, presents East-West oriented rows and belongs to Bodegas Martín Códax winery. Twelve samples were independently analysed: samples from the north and the south side of the rows were processed in separate for three W and three NW blocks. On each sample, 20-22 bunches were randomly and simultaneously harvested at maturity on 22/09/2010, each from a different plant and all the berries were densimetrically-sorted. Berries of the three density ranges 120-140, 140-160 and 160-180g NaCl•L-1 (corresponding to under-ripe, ripe, and pre-ripe ripening degrees, respectively) from each replicate were immediately rinsed in distilled H2O, dried, frozen in liquid nitrogen and kept at -80ºC until further analysis. Sampling started at 8:00 am (solar time) and time lapse from bunch collection to berry freezing ranged between 3-5 h. Water supplied to W blocks throughout the season was 204 mm (from 23/06/2010 to 26/09/2010). RNA from twelve under-ripe berry class, twelve ripe berry class, and eight over-ripe berry class samples was obtained and hybridized to grapevine whole-genome NimbleGen microarrays.