Final Report Summary - ENCODE (Environmental Control of Development)
Plants show remarkable flexibility in their development, allowing them to adjust their form to suit the environmental conditions in which they are growing. For example, plants growing with a limited supply of the key nutrient, nitrate, typically suppress shoot branching but protect root growth, prioritizing nutrient foraging in the soil. The EnCoDe project used the model plant Arabidopsis to elucidate how this process is regulated and to understand its significance in natural populations.
Shoot branching is controlled by a network of interacting hormonal signals that move over long distances in the plant and regulate the activity of axillary buds, which can remain dormant or grow out to form branches. The hormones include strigolactones (SLs) and cytokinins (CKs), which are made throughout the plant and move upward from root to shoot. SLs typically inhibit shoot branching whereas CKs promote it. Both appear to act by two distinct mechanisms. First, they regulate the expression of the BRC1 gene in buds. BRC1 encodes a transcription factor that can inhibit branching. We have shown that BRC1 is neither necessary nor sufficient for bud inhibition, but rather tunes the activation potential of buds. Sustained bud activity appears to depend on the establishment of the export of a third hormone, auxin, from the bud into the main stem, where it joins the polar auxin transport stream down the plant to the roots. We have made significant progress in understanding the auxin transport system in the shoot and the ways in which both CKs and SLs tune its properties to regulate branching. Overall, our work provides evidence that auxin, cyctokinin and strigolactone act in a network of interlocking feedback loops to modulate shoot branching in response to nitrate availability. We have made extensive use of computational modelling of this network to understand its properties.
To explore the properties of the shoot branching regulatory system in natural populations, we investigated the ability of a large collection of natural accessions of Arabidopsis to adjust shoot branching levels in response to nitrate supply. We found that there is substantial variation in this response, associated with life history strategy. Many accessions respond in the way that we expected, being highly branched when nitrate is plentiful, but suppressing branching when it is scarce. In contrast, some lines produced a moderate number of branches regardless of nutrient supply. The non-responding lines typically produced more seed than the strongly responding lines when nitrate was limiting, but fewer seed when nitrate was abundant. The non-responding lines are very early flowering and therefore can be interpreted as following a rapid exit strategy to low nutrient conditions, which apparently comes at the expense of being able to exploit abundant nitrate. In contrast, the strongly responding lines flower later and adopt a nitrate foraging strategy. Interestingly, our results suggest that the nitrate foraging lines can switch to the rapid exit strategy, a phenomenon that is influenced by the season. We have made significant progress in understanding the genetic basis for all these behaviours. We have combined these results with our understanding of the hormonal network that regulates branching, and the models we have developed that capture its dynamic properties, providing an integrated understanding of the environmental control of shoot branching.
Shoot branching is controlled by a network of interacting hormonal signals that move over long distances in the plant and regulate the activity of axillary buds, which can remain dormant or grow out to form branches. The hormones include strigolactones (SLs) and cytokinins (CKs), which are made throughout the plant and move upward from root to shoot. SLs typically inhibit shoot branching whereas CKs promote it. Both appear to act by two distinct mechanisms. First, they regulate the expression of the BRC1 gene in buds. BRC1 encodes a transcription factor that can inhibit branching. We have shown that BRC1 is neither necessary nor sufficient for bud inhibition, but rather tunes the activation potential of buds. Sustained bud activity appears to depend on the establishment of the export of a third hormone, auxin, from the bud into the main stem, where it joins the polar auxin transport stream down the plant to the roots. We have made significant progress in understanding the auxin transport system in the shoot and the ways in which both CKs and SLs tune its properties to regulate branching. Overall, our work provides evidence that auxin, cyctokinin and strigolactone act in a network of interlocking feedback loops to modulate shoot branching in response to nitrate availability. We have made extensive use of computational modelling of this network to understand its properties.
To explore the properties of the shoot branching regulatory system in natural populations, we investigated the ability of a large collection of natural accessions of Arabidopsis to adjust shoot branching levels in response to nitrate supply. We found that there is substantial variation in this response, associated with life history strategy. Many accessions respond in the way that we expected, being highly branched when nitrate is plentiful, but suppressing branching when it is scarce. In contrast, some lines produced a moderate number of branches regardless of nutrient supply. The non-responding lines typically produced more seed than the strongly responding lines when nitrate was limiting, but fewer seed when nitrate was abundant. The non-responding lines are very early flowering and therefore can be interpreted as following a rapid exit strategy to low nutrient conditions, which apparently comes at the expense of being able to exploit abundant nitrate. In contrast, the strongly responding lines flower later and adopt a nitrate foraging strategy. Interestingly, our results suggest that the nitrate foraging lines can switch to the rapid exit strategy, a phenomenon that is influenced by the season. We have made significant progress in understanding the genetic basis for all these behaviours. We have combined these results with our understanding of the hormonal network that regulates branching, and the models we have developed that capture its dynamic properties, providing an integrated understanding of the environmental control of shoot branching.