Photoperiod-dependent transcriptional modifications in key metabolic pathways in Coffea arabica.

Doâa Djerrab,Geneviève Conejero,Hervé Etienne,Célia Barrachina,Claudine Campa,Benoît Bertrand,Eveline Dechamp,Ronan Sulpice,Sophie Léran,Jean-Christophe Breitler

doi:10.1093/treephys/tpaa130

Abstract

Photoperiod length induces in temperate plants major changes in growth rates, morphology and metabolism with, for example, modifications in the partitioning of photosynthates to avoid starvation at the end of long nights. However, this has never been studied for a tropical perennial species adapted to grow in a natural photoperiod close to 12 h/12 h all year long.We grew Coffea arabica L., an understorey perennial evergreen tropical species in its natural 12 h/12 h and in a short 8 h/16 h photoperiod, and we investigated its responses at the physiological, metabolic and transcriptomic levels. The expression pattern of rhythmic genes, including core clock genes, was affected by changes in photoperiod. Overall, we identified 2859 rhythmic genes, of which 89% were also rhythmic in Arabidopsis thaliana L. Under short-days, plant growth was reduced, and leaves were thinner with lower chlorophyll content. In addition, secondary metabolism was also affected with chlorogenic acid and epicatechin levels decreasing, and in agreement, the genes involved in lignin synthesis were overexpressed and those involved in the flavanol pathway were underexpressed.Our results show that the 8 h/16 h photoperiod induces drastic changes in morphology, metabolites and gene expression, and the responses for gene expression are similar to those observed in the temperate annual A. thaliana species.Short photoperiod induces drastic changes in gene expression, metabolites and leaf structure, some of these responses being similar to those observed in A. thaliana.

Highlights

The circadian clock provides plants with the ability to anticipate and adapt to daily and seasonal environmental changes
To establish how the photoperiod influences the circadian clock and the metabolism of coffee plants, we focused on genes of the clock and of primary and secondary metabolism for which the sequences were verified against the C. arabica genome
The plant biomass, size and number of leaves were significantly lower for the plants grown under 8 h/16 h photoperiod than for plants grown under the 12 h/12 h photoperiod (Figure 1)

Summary

Introduction

The circadian clock provides plants with the ability to anticipate and adapt to daily and seasonal environmental changes. Many genes involved in the regulation of the primary metabolism such as CRY1, PHOT1 and PHOT2 are regulated by the circadian output pathway and show a peak in expression at different times of the day. The elucidation of the exact role of the circadian clock on primary metabolism and growth is still ongoing Such studies are difficult for numerous reasons, e.g., the importance of post-transcriptional and post-translational regulations of central clock genes and the notorious impossibility to quantify most core clock proteins. The extent to which photoperiod influences daily global transcription has been widely described in Arabidopsis in a large range of photoperiods (Flis et al 2016) In this species, the phasing of several important clock components is photoperiod-dependent. These plants naturally grow in photoperiods close to 12 h/12 h and do not face almost any seasonal changes in photoperiods

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