Novel strategies for efficient selection of lines with synchronised development by using properties of the circadian clock

The circadian clock helps detect changes in day length, an indication of the season. In turn, this controls the timing of flowering and other developmental traits. However, we do not know the extent to which the circadian clock influences how well-synchronised plant development is. Much of our food waste comes from farmers disposing of vegetables and fruits that do not meet consumer-driven food standards (vegetable is too big/small; fruit is too ripe/not ripe enough, etc). If development was more synchronised, a higher proportion of plants would meet these standards at harvesttime, leading to improved yields. Synchronised flowering is also important for improving the efficiency of pollination.

In this proposal, we will investigate how the circadian clock coordinates the response to changes in day length, and how this influences the synchronicity of flowering time.

Additionally, we will pilot two strategies for utilising the associations between the circadian clock and synchronised development to improve the efficiency of plant selection (such as during breeding). First, we will build a statistical model to predict flowering time synchronicity, based on the gene expression of a marker gene for the circadian clock in seedlings. This will be used to pre-filter lines of plants, so that only the most promising lines will need to be grown to adulthood.

Secondly, we will identify genetic loci that are associated with properties of the circadian clock, response to photoperiod transition, and developmental synchrony. Genetic loci involved in all three processes will be good genetic markers for selection of synchronous lines of plants, because we will have an idea why these genetic loci might be associated with developmental synchrony.

Finally, we will develop new Arabidopsis lines that display synchronised flowering, which will be a valuable resource for future research on the genetic origins of synchronisation of developmental processes.

We will investigate how the circadian clock synchronises photoperiod-dependent developmental processes, using statistical modelling (Work plan 1) and QTL identification (WP2) in Arabidopsis. The model and QTLs will help us efficiently select new Arabidopsis lines that have synchronised flowering time (WP3).

Experiment: Our research will utilise three Recombinant Inbred Lines (RILs) in Arabidopsis that were generated from ecotypes from extreme latitudes that display variability in clock parameters and flowering time. These RILs all contain CCR2::LUC, a marker for the circadian clock. We will expose these RILs to various photoperiod transitions and measure (i) CCR2 expression over time and (ii) how well-synchronised the RILs are in terms of flowering (i.e. bolting) and hypocotyl elongation.

Analysis: We will utilise statistical techniques from the field of Functional Data Analysis to analyse complex features of the CCR2 gene expression time series (like transient 'wiggles' in expression after photoperiod transitions), rather than simple features like 'period', 'phase' and 'amplitude'. First, we will develop a statistical model to predict developmental synchrony traits (variability in flowering time, variability in hypocotyl elongation), using the gene expression pattern of CCR2 after different photoperiod transitions. Then, we will identify QTLs associated with developmental synchrony and CCR2 expression patterns that are predictive of developmental synchrony. We will develop a new statistical technique called dynamic-QTL which will help us identify QTLs that are associated with the more complex features of CCR2 expression time series.

Application: Finally, we will utilise the statistical models and QTLs to improve the efficiency of selection of lines of Arabidopsis with synchronised flowering time. This will provide us with a model system for future transcriptomic work about how changes in gene networks influence heterogeneity of flowering time.