The genetic basis for synchronised time perception in populations of plants

In order to efficiently breed plants for climate change, it is critical to identify traits in seedlings that are effective predictors of agronomically important traits at maturity that could be used to screen lines. Our work shows that the response of circadian clock to changes in photoperiod in seedling Arabidopsis is predictive of bolting time and bolting-associated traits, including the degree of synchronization in bolting. Using the first ever Recombinant Inbred Lines (RILs) between African and European Arabidopsis lineages, we find distinct Quantitative Trait Loci (QTLs) associated both with the synchronicity of circadian responses to photoperiodic changes and with bolting-related traits. Two QTLs contain K-Homology Domain RNA binding proteins (KH17 and KH29) associated with splicing variants in the MADS AFFECTING FLOWERING2 and 3 (MAF2, MAF3) genes, including generating chimeric transcripts between these two adjacent genes containing the MADS-box of MAF2 and the K-box dimerisation domain of MAF3. Many of the variants in KH17 in Arabidopsis ecotypes are found within its prion-like domain and are associated with de-coupling the mean and synchronicity of flowering time. Therefore, we have identified novel potential mechanisms that link synchronised responses on a diurnal scale and a developmental scale. Overall design: RNA-seq of Tnz-1 and Ws-2 parental ecotypes and Recombinant Inbred Lines of these lines in 12-day old seedlings that were entrained in Short day (8hrs light/16hrs dark) at ZT10, either in the dark or after 2 hours of extended light.