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.

Publications

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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M011216/1 01/10/2015 30/09/2023
1799723 Studentship BB/M011216/1 01/10/2016 30/01/2021 Emma Mckechnie-Welsh
 
Description My research has focused on functionally characterising two subfamilies of the large IQ-67 domain gene family in Arabidopsis thaliana. Specific expression patterns in the shoot apical meristem, as well as regulation by transcription factors important for shoot organ development, highlighted these uncharacterised genes for function in shoot organ development.

Initially an observable phenotype in a quadruple mutant in subfamily 1a intrigues a function in restricting organ growth and controlling patterning, with the higher order mutant displaying enhanced stem thickness and shoot growth with a small percentage of plants displaying SAM phyllotaxis pattern defects. Synergistically, a dex inducible line of a subfamily 1a IQD member driven by an ectopic RPS5a driver results 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.

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%) and is still being investigated whether different growth conditions affect this. Due to the rarity of such a patterning phenotype where one stable pattern changes to another in a mutant, with literature indicating this may be due to complexity of elements feeding into the outcome, it may be IQD loss of function increases the frequency in which conditions arise to generate the altered pattern, however the spiral pattern is still more likely to occur as a multitude of other factors remain in place to control this. Change from one stable phyllotactic pattern to another equally stable pattern is very rare in mutants. It will be interesting to probe whether this observation could be due mainly to de-restriction of growth and larger meristems or also incorporate altered PIN orientation and auxin gradients, key players in organ patterning from the SAM.
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, especially if paired with fertiliser application derepression of growth is able to generate a favourable phyllotactic patterning change that facilitaes more organs forming. As well as this, a mutant with a stable phyllotactic pattern change could be a valuble tool to study changes in growth parameters such as meristem size and auxin patterning that combine to control patterning.
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 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