Functional analysis of novel genes implicated in the control of plant growth
Lead Research Organisation:
University of East Anglia
Department Name: Graduate Office
Abstract
How genes shape plants and animals is one of the most important questions in Biology. In plants, the ability to genetically control the size and shape of organs (such as leaves, flowers, and stem) is also important to improve crop productivity.
Our lab has been been studying how regulatory genes shape floral organs and the stem in the model plant Arabidopsis. We found that different genes that control growth of different organs converge on the regulation of a common set of genes, which are likely to function as a general toolbox for plant organ growth. This set of genes implicated in growth of different organs includes a novel class of genes called IQD. Although one member of this gene family has been found to control fruit shape in tomato, the exact molecular and cellular functions of the proteins encoded by IQD genes are not known.
Our lab has been been studying how regulatory genes shape floral organs and the stem in the model plant Arabidopsis. We found that different genes that control growth of different organs converge on the regulation of a common set of genes, which are likely to function as a general toolbox for plant organ growth. This set of genes implicated in growth of different organs includes a novel class of genes called IQD. Although one member of this gene family has been found to control fruit shape in tomato, the exact molecular and cellular functions of the proteins encoded by IQD genes are not known.
People |
ORCID iD |
| Robert Sablowski (Primary Supervisor) | |
| Emma Mckechnie-Welsh (Student) |
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M011216/1 | 01/10/2015 | 31/03/2024 | |||
| 1799723 | Studentship | BB/M011216/1 | 01/10/2016 | 30/01/2021 | Emma Mckechnie-Welsh |
| Description | My research has focused on functionally characterising one subfamilies of the large IQ-67 domain gene family in Arabidopsis thaliana for role in regulating plant growth. This research was directed by specific expression patterns in the shoot apical meristem, as well as regulation by transcription factors important for shoot organ development and ties to phytohormones key in regulating plant growth such as auxin and giberellin. Suspected redundancy of function in the six genes classified to subfamily 1a first needed to be over come to establish their role in plant growth. A phenotype in a quadruple mutant in subfamily 1a intrigued a function in restricting organ growth and controlling organ patterning, with the higher order mutant displaying enhanced stem thickness and shoot growth with a small percentage of plants displaying phyllotaxis pattern defects. Synergistically, a dex inducible line of a subfamily 1a IQD member driven by an ectopic RPS5a driver resulted in severe dwarfing of plant growth. Proposed regulation by RGA through ChIP-seq data and these results indicate potential for 1a IQDs to possess restrictive growth function downstream of DELLAs however extensive biochemical and genetic analysis showed both RGA and IQD proteins were able to restrict plant growth independent of one another. Both appeared to interfere with the essential cellular mechanisms for growth, cell division. Establishment of the full sextuple knockout in subfamily 1a enhanced the stem thickness phenotype and rosettes appear bulkier with leaves less curled than WT Col-0 Arabidopsis. Leave shape is also altered with more serrated edges, enhanced in SD growth conditions vs long day or constant light. In identification of the sextuple an organ pairing phyllotactic patterning phenotype occurred where rosette transitioned from spiral pattern to bijugate and organ pairing extended to decussate side branching pattern and pairing in flowers. The reproducibility of this organ pairing phenotype however in offspring of the two parent plants has been low (around 10%). I investigated whether the impact was due to increased meristem size but disregarded this hypothesis based on results. The mechanism to establish leaf serrations as well as organ patterning involves PIN1 auxin efflux transporters and auxin gradients. Due to increased leaf margin complexity impact on auxin gradient establishment was investigated in the leaf and confirmed loss of IQD protein function led to less ordered PIN1 proteins during leaf serration outgrowth. Alteration to auxin transport in the shoot could also account for disturbance to patterning, with low frequency of occurrence due to contribution of many other genes in maintaining auxin distribution. Auxin is also strongly linked to cell proliferation and could be a means the gene family regulate number of cell divisions, contributing to organ size control. The impact on size in shoot organs appeared directional. Stem and leaf height was not altered but width increased. The orientation of cell divisions was investigated in early stem growth and it was apparent instead of highly ordered transverse divisions in the central stem which extend growth upwards a less organised pattern occurred. This would indeed contribute more to radial growth of the stem. IQD proteins are associated with microtubules (MAPs) for which roles in cell division plane orientation are well established. Therefore, research has tied 1a IQD proteins to regulate of both shoot organ size and shape through interplay with auxin transport and microtubule behaviour. This research is being extended to finish off two publications and seeks to interlink IQD proteins as a mechanosensing element in plant growth. |
| Exploitation Route | IQDs are a gene family conserved from the evolution of land plants and are present in all crop species. The family displays a diverse array of cellular localisation patterns including cortical microtubule and plasma membrane association, as well as a conserved calmodulin binding domain.These lines can be used to investigate function of IQDs in shoot development involving cortical microtubule arrays and the role of calcium signalling in modulating their function. Understanding how IQDs are functioning in shoot growth may enable modulation of their function for enhanced yield of crop plants. The work in Arabidopsis can direct research in crop species such as tomato and cucurbit family where similar organ shape and leaf shape phenotypes are observed which could lead eventually to important agronomic impact. |
| Sectors | Agriculture, Food and Drink |
| Description | Establishment of IQD high order mutants |
| Organisation | Leibniz Association |
| Department | Leibniz Institute of Plant Biochemistry |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Additional CRISPR mutation for IQD24 in subfamily 1a in the goal of establishing higher order mutant and subsequent crosses to try obtain the sextuple 1a knockout line for investigation of shoot developmental defects. Both our research groups hope to better functionally characterise IQDs' role in plant development and believe redundancy in function is a key aspect as to why any such function remains undiscovered. |
| Collaborator Contribution | Multiple materials including single, double and triple T-DNA mutant lines in IQD subfamily 1a and promoter GFP:GUS lines for investigation of IQD expression in this subfamily. |
| Impact | A shoot growth phenotype has been identified in a higher order quadruple mutant and further devlopmental defects may be uncovered by the full sextuple subfamily 1a knockout which can advance characterisation of the gene family's role in plant growth. This research may help in understanding of factors contributing to crop yeild with future impact being ability to modulate and enhance yield in an array of crop species. |
| Start Year | 2017 |
| Description | Ivestigation of IQD subfamily 1c |
| Organisation | Wageningen University & Research |
| Department | WU Agrotechnology & Food Sciences |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | I have imaged the lines in the shoot apical meristem, providing novel information of expression patterns in the shoot apex vs the root apex. I also have used these lines to validated specific regulation of these IQD members in the boundary regions of the shoot apical meristem by replumless by crossing them to the transcription factor mutant, providing valuable data that I would not obtain from qPCR of the shoot apex. These lines continue to help further characterisation of this gene family in multiple tissues and developmental stages. |
| Collaborator Contribution | Provision of seed lines stably expressing translational and transcriptional GFP/YFP fusions for two IQD members our research group was interested in studying for roles in shoot development and images/ findings of the expression of these lines in the root. |
| Impact | data collected from materials shared in this collaborations have helped validate the likely importance of IQDs in this subfamily specifically in early shoot development as well as validating the regulation by transcription factors important in shoot development processes such as stem elongation and phylotaxy, for which IQDs functional role can now be further probed. |
| Start Year | 2017 |
| Description | Interview for Radio 4 programme Farming Today |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Interview on Radio 4 Farming Today on 22/8/17. The interview centred on our publication on how a gene that has been widely used to increase crop yields by reducing plant height could actually have a hidden cost by limiting the number of flowers that can be produced, and how this hidden cost could be removed to maximise the benefits on plant yield. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Norwich and cambridge Science festivals |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Topics approached were synthetic biology where children could build different circuits switching light bulbs on/off with different switches and combine different elements to create plants that can do out of the ordinary things to highlight potential use of plants in biology/technology. One stand highlighted natural products found in plants and their uses such as dyes and scents & another introduced DNA and mechanism (ribosome complex with mRNA) reading of genes to control different outputs. The activities and discussion were targeted to excite/interest children from age range 6-15 with different information provided depending on those visiting the work station. As well as this parents and teacher gained insight into way to engage children with science. |
| Year(s) Of Engagement Activity | 2017,2018 |
| URL | https://www.openplant.org/blog/2018/4/3/cambridge-science-festival-march-2018 |
| Description | Plant science outreach with children |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | I designed 2 primary school lesson plans based on my research area, plant growth and development, for the SAW trust and implemented the science part of the lesson as well as engaging with the second part of the day where children created poetry and art inspired by the science. The aim of the projects were to demonstrate the creativity science involved and spark interest in plant science as a subject before the children went on to secondary school where science can have a reputation as a hard, unrewarding and less fun subject than the arts. These lesson plans will eventually be published alongside others run by SAW workshop days, which school teachers can access to replicate the experience in their own schools. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.openplant.org/blog/plant-science-saw-projects-at-tunstead-primary-school |