GSE118893
The transcriptomic response to a short day to long day shift in the reference legume Medicago truncatula
Photoperiod regulated flowering is a well understood developmental pathway in the intensively studied Brassicaceae species Arabidopsis thaliana and in the monocot rice, but less so in other angiosperm groups. One such group, the temperate legumes in the Fabaceae family which are important both agriculturally and ecologically, accelerate their flowering in response to long-day photoperiods (LD), but lack functional homologues of key regulatory genes present in A. thaliana such as CO. Curiously previous work in the reference legume Medicago truncatula has shown that floral activator MtFTa1, which is upregulated by LD and vernalisation, does not exhibit a peak in expression at dusk like its homologue in A. thaliana FLOWERING LOCUS T, instead MtFTa1 maintains a near constant pattern of expression. In addition legumes possess for other FT-like genes such as the MtFTb genes expressed in LD which may also act in the regulation of flowering time. This study utilises RNA-Seq to identify genes which may regulate or be co-expressed with these FT-like genes in Medicago truncatula. Following a shift from short-day photoperiods to inductive long-days genes which alter their pattern of expression are distinguished from those which just alter their magnitude of expression (and those that do neither). Specifically this study focuses on the first few hours of the day in the young leaves which coincides with the first diurnal peak of the FTb genes. It goes on to categorise these genes into groups with similar patterns of expression using c-means clustering. In the process this study identifies a number of potential candidate genes for future studies to consider. Overall design: Combines two similar experiments where plants were grown in short-day photoperiods and shifted to long-day photoperiods after 10 days. Triplicate RNA-seq libraries from both short-day and long-day leaf tissue were generated in experiment 1 at ZT0 and ZT4 at 13 days. In experiment 2 at ZT4 at 15 days.