Detection of Diurnal Variation of Tomato Transcriptome through the Molecular Timetable Method in a Sunlight-Type Plant Factory

Abstract

The timing of measurement during plant growth is important because many genes are expressed periodically and orchestrate physiological events. Their periodicity is generated by environmental fluctuations as external factors and the circadian clock as the internal factor. The circadian clock orchestrates physiological events such as photosynthesis or flowering and it enables enhanced growth and herbivory resistance. These characteristics have possible applications for agriculture. In this study, we demonstrated the diurnal variation of the transcriptome in tomato (Solanum lycopersicum) leaves through molecular timetable method in a sunlight-type plant factory. Molecular timetable methods have been developed to detect periodic genes and estimate individual internal body time from these expression profiles in mammals. We sampled tomato leaves every 2 h for 2 days and acquired time-course transcriptome data by RNA-Seq. Many genes were expressed periodically and these expressions were stable across the 1st and 2nd days of measurement. We selected 143 time-indicating genes whose expression indicated periodically, and estimated internal time in the plant from these expression profiles. The estimated internal time was generally the same as the external environment time; however, there was a difference of more than 1 h between the two for some sampling points. Furthermore, the stress-responsive genes also showed weakly periodic expression, implying that they were usually expressed periodically, regulated by light–dark cycles as an external factor or the circadian clock as the internal factor, and could be particularly expressed when the plant experiences some specific stress under agricultural situations. This study suggests that circadian clock mediate the optimization for fluctuating environments in the field and it has possibilities to enhance resistibility to stress and floral induction by controlling circadian clock through light supplement and temperature control.

Circadian Oscillation of the Lettuce Transcriptome under Constant Light and Light–Dark Conditions

“…We utilized the molecular timetable method ( Ueda et al, 2004 ; Higashi et al, 2016 ) to detect oscillating contigs for LL and LD conditions. This method can detect some genes with high amplitude and periodicity from the time-course transcriptome data.…”

“…We calculated the measurement noise for the expression profiles of common oscillating contigs, using a previous molecular timetable method ( Ueda et al, 2004 ; Higashi et al, 2016 ). We calculated the measurement noise from the standard deviation of the difference between a real and an estimated expression of all selected oscillating contigs.…”

Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane

“…Recent studies featuring experiments conducted in field conditions in Arabidopsis, rice and tomato highlight the differences in gene expression, circadian regulation and plant metabolism compared to experiments conducted inside growth chambers (Annunziata et al, 2017;Annunziata et al, 2018;Izawa et al, 2011b;Higashi et al, 2016;Shalit-Kaneh et al, 2018). Because AS has an impact on the regulation of gene expression, which impacts circadian regulation and plant metabolism, it is important to start investigating the dynamic adjustment of AS in response to a fluctuating environment.…”

Estimation of the Circadian Phase by Oscillatory Analysis of the Transcriptome in Plants

“…The TiGs were selected using the threshold of a 0.15, r 0.8. This threshold was also used in previous studies (Ueda et al, 2004;Higashi et al, 2016a). As a result, 173 A. thaliana genes, 885 lettuce genes, and 1,131 tomato genes were selected as TiGs.…”

“…On the other hand, based on global gene expression analysis through microarray analysis, about 20% of plant genes are under the control of the circadian clock (Li et al, 2017). Recently, for crop species such as rice, tomato and lettuce, the circadian rhythm of the transcriptome in the field and in the plant factory has been clarified (Nagano et al, 2012;Matsuzaki et al, 2015;Tanigaki et al, 2015;Higashi et al, 2016a;2016b).…”