Is Transcriptomic Regulation of Berry Development More Important at Night than During the Day?

Diurnal changes in gene expression occur in all living organisms and have been studied on model plants such as Arabidopsis thaliana. To our knowledge the impact of the nycthemeral cycle on the genetic program of fleshly fruit development has been hitherto overlooked. In order to circumvent environmental changes throughout fruit development, young and ripening berries were sampled simultaneously on continuously flowering microvines acclimated to controlled circadian light and temperature changes. Gene expression profiles along fruit development were monitored during both day and night with whole genome microarrays (Nimblegen® vitis 12x), yielding a total number of 9273 developmentally modulated probesets. All day-detected transcripts were modulated at night, whereas 1843 genes were night-specific. Very similar developmental patterns of gene expression were observed using independent hierarchical clustering of day and night data, whereas functional categories of allocated transcripts varied according to time of day. Many transcripts within pathways, known to be up-regulated during ripening, in particular those linked to secondary metabolism exhibited a clearer developmental regulation at night than during the day. Functional enrichment analysis also indicated that diurnally modulated genes considerably varied during fruit development, with a shift from cellular organization and photosynthesis in green berries to secondary metabolism and stress-related genes in ripening berries. These results reveal critical changes in gene expression during night development that differ from daytime development, which have not been observed in other transcriptomic studies on fruit development thus far.

所有活生物体均存在基因表达的昼夜节律变化，该现象已在拟南芥（Arabidopsis thaliana）等模式植物中得到深入研究。据我们所知，此前尚未有研究关注昼夜周期对肉质果实发育遗传程序的影响。为规避果实发育过程中的环境波动，研究人员在适应了可控昼夜光温变化的连续开花微型葡萄藤上，同时采集幼果与成熟浆果样本。本研究采用全基因组微阵列（Nimblegen® vitis 12x），监测了昼夜条件下果实发育全程的基因表达谱，共获得9273个受发育调控的探针集。所有日间检测到的转录本均在夜间发生表达调控，另有1843个基因为夜间特异性表达基因。对日间与夜间数据集分别进行独立分层聚类分析，得到的基因表达发育模式高度相似，但被归类的转录本的功能分类却随采样时段存在显著差异。诸多已知在果实成熟过程中上调的通路转录本——尤其是与次生代谢相关的转录本——在夜间表现出比日间更为显著的发育调控特征。功能富集分析同样显示，受昼夜调控的基因在果实发育全程存在显著动态变化：从绿果阶段的细胞组织与光合作用相关基因，逐渐转变为成熟浆果阶段的次生代谢与胁迫相关基因。本研究结果揭示了此前果实发育转录组研究中未被发现的关键差异：夜间发育过程中的基因表达变化模式与日间显著不同。