Evolution, development, and mechanisms of floral organ photosynthesis.
Lead Research Organisation:
University of Liverpool
Department Name: Functional and Comparative Genomics
Abstract
Food security and climate change are two of the most important challenges facing modern society. Increased crop productivity is required to provide enough food for an ever-growing population, however, this should not come at a cost of increased carbon emissions. Novel plants variants that can use less land, capture more carbon, and produce higher yields are needed.
Many research groups around the globe are working on improving photosynthesis to meet these challenges, which includes modifying enzymes and changing the anatomy of the leaf to capture more carbon. However, relatively few groups have focused on improving photosynthesis that occurs outside of the leaf, in stems, flowers and fruits. Many species heavily rely on non-leaf photosynthesis, however, there are many aspects of this process that we do not understand.
This project aims to understand more about non-leaf photosynthesis: How has nature used it to improve plant health? How is it programmed on a genetic level? How can we manipulate it to benefit nature and society? We will focus our efforts initially on the mustard plant family because they contain 'model' plants as well as important crops, such as oilseed rape. Model plants are plants that are well-characterized (e.g. have a sequenced genome) and whose genome we can modify with ease. This is important because understanding how a complex process such as non-leaf photosynthesis functions requires the availability of tractable systems to test specific hypotheses. This power of this approach has been demonstrated recently with the development of plants with shatter-resistant fruits in oilseed rape, which reduces harvesting losses significantly. These plants were generated by directly using knowledge acquired from model plants.
Here, we will employ a similar strategy. First, we will develop our understanding of non-leaf photosynthesis on genetic and physiological levels. Next, we will use this knowledge to make specific hypotheses on how to modify non-leaf photosynthesis to improve agriculturally important traits. We will test these hypotheses in both model and crop plants and develop improved varieties in a step-wise manner.
Although we will initially investigate species in the mustard plant family, this work will also be relevant to species in other plant families including wheat, barley, and tomato, whose flowers and fruits also perform photosynthesis. Therefore, this project marks the beginning of a long-term goal to understand the evolution of non-leaf photosynthesis and to develop strategies to modify it in important crop plants.
Many research groups around the globe are working on improving photosynthesis to meet these challenges, which includes modifying enzymes and changing the anatomy of the leaf to capture more carbon. However, relatively few groups have focused on improving photosynthesis that occurs outside of the leaf, in stems, flowers and fruits. Many species heavily rely on non-leaf photosynthesis, however, there are many aspects of this process that we do not understand.
This project aims to understand more about non-leaf photosynthesis: How has nature used it to improve plant health? How is it programmed on a genetic level? How can we manipulate it to benefit nature and society? We will focus our efforts initially on the mustard plant family because they contain 'model' plants as well as important crops, such as oilseed rape. Model plants are plants that are well-characterized (e.g. have a sequenced genome) and whose genome we can modify with ease. This is important because understanding how a complex process such as non-leaf photosynthesis functions requires the availability of tractable systems to test specific hypotheses. This power of this approach has been demonstrated recently with the development of plants with shatter-resistant fruits in oilseed rape, which reduces harvesting losses significantly. These plants were generated by directly using knowledge acquired from model plants.
Here, we will employ a similar strategy. First, we will develop our understanding of non-leaf photosynthesis on genetic and physiological levels. Next, we will use this knowledge to make specific hypotheses on how to modify non-leaf photosynthesis to improve agriculturally important traits. We will test these hypotheses in both model and crop plants and develop improved varieties in a step-wise manner.
Although we will initially investigate species in the mustard plant family, this work will also be relevant to species in other plant families including wheat, barley, and tomato, whose flowers and fruits also perform photosynthesis. Therefore, this project marks the beginning of a long-term goal to understand the evolution of non-leaf photosynthesis and to develop strategies to modify it in important crop plants.
Technical Summary
A large number of domestication genes encode transcription factors (TFs), with MADS-domain TFs being highly represented. Preliminary data supports the role of the MADS-TF AGAMOUS (AG) as a regulator of floral organ photosynthesis (FOP), which makes an important contribution to fruit quality, seed viability and/or abiotic resistance in a variety of species. Our lack of understanding of the phenotypic and genetic variation underlying FOP is impeding our ability to exploit it to improve crop performance. This proposal aims to rectify these issues with a series of targeted objectives.
We will use a combination of single cell transcriptomics, comparative transcriptomics, comparative protein localization experiments and comparative development/physiology to characterize the genotypic and phenotypic space of FOP in the fruits of the Brassicaceae. These systematic descriptions will provide an understanding of the variation that exists during the establishment of FOP and its activity. With this knowledge in hand, strategies to modify FOP will be developed and explored during this proposal and in the future. This work can be translated to understand FOP in other species, such as tomato and wheat, in which FOP is known to play an important role.
Additional benefits from this work includes an improved understanding of TF activity in plants. In particular, the evolution of gene regulatory networks will be explored through comparative protein localization experiments, of which there are few examples in plants. We will further explore the differentiation of floral organs and the establishment of cellular identity using state-of-the-art techniques, which will also help to further reveal how MADS-TFs modulate leaf identity to produce floral organs.
In sum, this proposal will provide specific strategies to modify FOP to improve crop performance, and provide detailed insights into the evolution of the mechanisms underlying FOP, floral organ development and gene regulatory networks.
We will use a combination of single cell transcriptomics, comparative transcriptomics, comparative protein localization experiments and comparative development/physiology to characterize the genotypic and phenotypic space of FOP in the fruits of the Brassicaceae. These systematic descriptions will provide an understanding of the variation that exists during the establishment of FOP and its activity. With this knowledge in hand, strategies to modify FOP will be developed and explored during this proposal and in the future. This work can be translated to understand FOP in other species, such as tomato and wheat, in which FOP is known to play an important role.
Additional benefits from this work includes an improved understanding of TF activity in plants. In particular, the evolution of gene regulatory networks will be explored through comparative protein localization experiments, of which there are few examples in plants. We will further explore the differentiation of floral organs and the establishment of cellular identity using state-of-the-art techniques, which will also help to further reveal how MADS-TFs modulate leaf identity to produce floral organs.
In sum, this proposal will provide specific strategies to modify FOP to improve crop performance, and provide detailed insights into the evolution of the mechanisms underlying FOP, floral organ development and gene regulatory networks.
Planned Impact
(1) Crop scientists. In principle, modifying floral organ photosynthesis can improve seed quality and/or improve water usage efficiency. Although there may be limited scope to realize these potentials during the project, by giving public talks, connecting on social media, and contributing to the Oilseed Genetic Improvement Network (OREGIN), communication of this work can promote the potential to use floral organ photosynthesis to improve crop performance.
(2) Agribusiness. The potential to increase seed oil content through floral organ photosynthesis will be thoroughly explored, and closer connections with seed oil companies will be made by proposing collaborative efforts. The broader potential to increase grain yield in wheat and barley will also be proposed to companies that have elite cultivars, in order to explore floral organ photosynthesis (e.g. in awns). To this end, I have made contact with the seed company KWS to explore the potential of this research to be applied to agribusiness.
(3) Policy makers. The increasing pressure to increase crop yields while reducing environmental impact is likely to lead to a drastic overhaul of agricultural practices. Policy makers are sure to explore every option to harmonize these goals. The potential of floral organ photosynthesis to contribute to solutions for these challenges will be highlighted through social media, and other press releases following paper publications.
(4) UK Science base. The technician and PDRA associated with the programme, and myself, will benefit through being trained in state-of-the-art genomic and transcriptomic techniques (FACS and single-cell sequencing), and techniques to measure photosynthetic activity. The technician will be provided with further training in standard molecular techniques (DNA extraction, PCR assays, cloning, plant transformation), as well as the essentials for cultivating Brassica plants. Furthermore, the technician will be provided with training at the University of Essex for measurements of photosynthetic activity in collaboration with Prof. Tracy Lawson. The PDRA will be trained in chromatin immunoprecipitation, gene expression analysis and genome-editing. Additional skills, applicable to alternative employment sectors, include independent management of small individual projects (e.g. management of plant growth for the technician, or a full experiment for the PDRA); the ability to formulate solutions for problems and effectively communicate them; and, developing the confidence to make decisions based on critical evaluation of given information. I will further benefit from an increased focus on floral organ photosynthesis and comparative approaches to develop my research profile. Moreover, all these techniques can be transferred into new collaboration projects widening the impact on the UK scientific community. These benefits will be realised during the timeframe of the project programme.
(2) Agribusiness. The potential to increase seed oil content through floral organ photosynthesis will be thoroughly explored, and closer connections with seed oil companies will be made by proposing collaborative efforts. The broader potential to increase grain yield in wheat and barley will also be proposed to companies that have elite cultivars, in order to explore floral organ photosynthesis (e.g. in awns). To this end, I have made contact with the seed company KWS to explore the potential of this research to be applied to agribusiness.
(3) Policy makers. The increasing pressure to increase crop yields while reducing environmental impact is likely to lead to a drastic overhaul of agricultural practices. Policy makers are sure to explore every option to harmonize these goals. The potential of floral organ photosynthesis to contribute to solutions for these challenges will be highlighted through social media, and other press releases following paper publications.
(4) UK Science base. The technician and PDRA associated with the programme, and myself, will benefit through being trained in state-of-the-art genomic and transcriptomic techniques (FACS and single-cell sequencing), and techniques to measure photosynthetic activity. The technician will be provided with further training in standard molecular techniques (DNA extraction, PCR assays, cloning, plant transformation), as well as the essentials for cultivating Brassica plants. Furthermore, the technician will be provided with training at the University of Essex for measurements of photosynthetic activity in collaboration with Prof. Tracy Lawson. The PDRA will be trained in chromatin immunoprecipitation, gene expression analysis and genome-editing. Additional skills, applicable to alternative employment sectors, include independent management of small individual projects (e.g. management of plant growth for the technician, or a full experiment for the PDRA); the ability to formulate solutions for problems and effectively communicate them; and, developing the confidence to make decisions based on critical evaluation of given information. I will further benefit from an increased focus on floral organ photosynthesis and comparative approaches to develop my research profile. Moreover, all these techniques can be transferred into new collaboration projects widening the impact on the UK scientific community. These benefits will be realised during the timeframe of the project programme.
People |
ORCID iD |
Diarmuid Seosamh O'Maoileidigh (Principal Investigator / Fellow) |
Publications
Brazel A
(2023)
AGAMOUS mediates timing of guard cell formation during gynoecium development
in PLOS Genetics
Fattorini R
(2022)
Cis -regulatory variation expands the colour palette of the Brassicaceae
in Journal of Experimental Botany
Sang Q
(2022)
MicroRNA172 controls inflorescence meristem size through regulation of APETALA2 in Arabidopsis.
in The New phytologist
Description | We have identified a genetic mechanism for how fruit photosynthesis is established. As this mechanism is likely conserved, which we are investigating, this will lead to strategies to improve crop performance by increasing yield and/or water usage efficiency. |
Exploitation Route | Targets that we have identified and are validating can be translated to elite cultivars. |
Sectors | Agriculture, Food and Drink |
Description | BBSRC Doctoral Training Partnership between Newcastle, Liverpool and Durham |
Amount | £96,000 (GBP) |
Organisation | University of Liverpool |
Sector | Academic/University |
Country | United Kingdom |
Start | 10/2022 |
End | 09/2026 |
Description | BBSRC Doctoral Training Partnership between Newcastle, Liverpool and Durham |
Amount | £96,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 10/2020 |
End | 09/2024 |
Description | SUMOcode: deciphering how SUMOylation enables plants to adapt to their environment |
Amount | £3,647,367 (GBP) |
Funding ID | BB/V003534/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2020 |
End | 09/2025 |
Description | UK GenSoc Summer Studentship |
Amount | £3,125 (GBP) |
Organisation | University of Liverpool |
Sector | Academic/University |
Country | United Kingdom |
Start | 07/2021 |
End | 08/2021 |
Title | AP1pro:AP1-GR ap1-1 cal-1 ag-10 / shp1-1 shp2-1 plants |
Description | The AP1-GR ap1 cal phenotype facilitates the collection of synchronous flowers. By adding the ag-10 and shp1 shp2, we can assess the redundant and independent activities of these genes throughout flower development. |
Type Of Material | Technology assay or reagent |
Year Produced | 2020 |
Provided To Others? | No |
Impact | A better understanding of the activities of these genes in photosynthesis will help to provide strategies to improve crop performance. |
Title | Arabidopsis AGAMOUS-Venus plasmids |
Description | Cloned full-length AGAMOUS and fused final exon to Venus fluorescent coding region. Have transformed ag-12 plants with this plasmid to assess ability to restore phenotype. |
Type Of Material | Biological samples |
Year Produced | 2021 |
Provided To Others? | No |
Impact | The resulting transgenic plants will be essential for comparative ChIP-Seq and will provide a better understanding of AGAMOUS expression as the Venus fluorescent protein is more easily visualized than GFP, which has been previously used. Furthermore, the promoter in this version is longer than in previously cloned versions. |
Title | Arabidopsis MUTE-Venus plasmids |
Description | Cloned full-length MUTE and fused final exon to Venus fluorescent coding region. Have transformed mute-2 plants with this plasmid to assess ability to restore phenotype. 4 different versions of the plasmid prepared with modifications in important binding sites. |
Type Of Material | Biological samples |
Year Produced | 2021 |
Provided To Others? | No |
Impact | These plasmids will provide a better understanding of how MUTE is regulated during plant development and the mechanism by which it is regulated by AGAMOUS. |
Title | At1g56100 promoter plasmids |
Description | A putative silique-specific promoter has been cloned and used to express Venus and SCRM-amiRNA (to disrupt stomatal formation). Plants have been transformed with this plasmid. |
Type Of Material | Biological samples |
Year Produced | 2022 |
Provided To Others? | No |
Impact | This plasmid will help to determine the requirement for stomata on the silique of Arabidopsis plants. |
Title | Cardamine hirsuta AG Venus plasmids |
Description | Cloned full-length AGAMOUS and fused final exon to Venus fluorescent coding region. Have transformed Chag-1 plants with this plasmid to assess ability to restore phenotype. |
Type Of Material | Biological samples |
Year Produced | 2021 |
Provided To Others? | No |
Impact | The resulting transgenic plants will be essential for comparative ChIP-Seq and will provide a first look at AGAMOUS expression in Cardamine. |
Title | Cardamine hirsuta GOLDEN-LIKE CRISPR plasmid |
Description | sgRNAs targeting GLK1 and GLK2 in Cardamine hirsuta have been cloned into a plasmid that also contains the Cas9 coding region driven by and egg-cell promoter. |
Type Of Material | Biological samples |
Year Produced | 2022 |
Provided To Others? | No |
Impact | This plasmid will be used to mutate GLK1 and GLK2 in Cardamine for comparative studies between Arabidopsis and Cardamine. |
Title | ChAG-amiRNA plants |
Description | A Cardamine hirsuta plants with a DEX-inducible version of an AG-amiRNA, which knocks down AGAMOUS function, has been generated and validated. This line resulted in complete but inducible knockdown of AG activity so that the plants resemble Chag-1 mutants. |
Type Of Material | Technology assay or reagent |
Year Produced | 2022 |
Provided To Others? | No |
Impact | This line will be used to perform comparative phenotypic, physiological, and comparative studies between Arabidopsis and Cardamine. |
Title | GLK2 promoter bashing plasmids |
Description | We have dissected the promoter of GLK2 in A. thaliana and have transformed plants with different version to understand which fragments drive GLK2 expression in siliques. |
Type Of Material | Biological samples |
Year Produced | 2022 |
Provided To Others? | No |
Impact | A key reagent to understand how photosynthesis is established in siliques. |
Title | GOLDEN-LIKE2 genomic plasmids |
Description | Generated a full length clone of GLK2, fused to Venus, and 4 different versions with modified promoters (6 plasmids in total). They have been transformed into Arabidopsis glk1 glk2 plants to assess their ability to restore GLK2 function. |
Type Of Material | Biological samples |
Year Produced | 2022 |
Provided To Others? | No |
Impact | These plasmids will help to identify the cis elements required for tissue-specific expression of GLK2. This is an important regulator of chloroplast biogenesis and will be a centre-piece of future research. |
Title | Triple mutant ag-10 shp1-1 shp2-1 |
Description | Assessment of the redundancy between AGAMOUS and the SHATTERPROOF genes has been difficult due to the severity of ag-1 mutants. However, the milder ag-10 mutant facilitates this assessment and we are using it for phenotypic and molecular characterization to assess how these genes contribute to photosynthesis in the flower. Additional understand of how flower and fruit development is controlled will also be garnered using this mutant. |
Type Of Material | Technology assay or reagent |
Year Produced | 2020 |
Provided To Others? | No |
Impact | The shp1-1 shp2-1 double mutant does not shatter and this trait is useful to reduce seed loss in an agricultural setting. These genes may also play a role in photosynthesis, which can improve seed quality. Assessment of this and the triple ag-10 shp1 shp2 mutants will provide clarity and may serve as a useful model produce more efficient crop plants (e.g. oilseed rape) in the future through breeding programmes and/or genome editing. |
Title | ag-10 cia2-1 |
Description | A double mutant between an essential chlorophyll regulator and the weak ag-10 mutant. ag-10 has higher levels of cia2 and ag-10 produces more chlorophyll. This mutant will clarify whether CIA2 is required for higher levels of chlorophyll in ag-10 and what effect the absence of cia2 will have on the ag-10 phenotype. |
Type Of Material | Technology assay or reagent |
Year Produced | 2020 |
Provided To Others? | No |
Impact | A better understanding of how chlorophyll levels are regulated in fruits will improve photosynthesis, which will improve seed yield and have an impact on strategies for improving crop performance. |
Title | ag-10 epf1-1 |
Description | A double mutant between a stomatal spacing gene and the weak ag-10 mutant. ag-10 mutants have very high transcript levels of EPF1 and we ask what the effect of removing these high EPF1 levels are on the phenotype of ag-10. |
Type Of Material | Technology assay or reagent |
Year Produced | 2020 |
Provided To Others? | No |
Impact | A better understanding of how stomatal differentiation occurs on fruits can improve photosynthesis, which will improve yield and have applications for crops. |
Title | ag-10 shp1-1 shp2-1 glk1 glk2 plants |
Description | Crossed glk1 glk2 mutants into ag10 shp1-1 shp2-1 plants to generate a quintuple mutant. Plants are being resolved for different combinations of these genotypes. |
Type Of Material | Technology assay or reagent |
Year Produced | 2022 |
Provided To Others? | No |
Impact | These lines will be used to understand how AG and SHP proteins modify chlorophyll accumulation in the absence of GLK activity and vice versa. |
Title | ag-10 shp1-1 shp2-1 gynoecium RNA |
Description | Manually dissected the stage 9-13 gynoecia from flowers of ag-10, shp1 shp2, ag-10 shp1 shp2, and L-er and extracted total RNA. Have submitted these samples for RNA-sequencing and am awaiting results. |
Type Of Material | Biological samples |
Year Produced | 2020 |
Provided To Others? | No |
Impact | How these genes control flower development and photosynthesis is important to understand so that we can generate additional strategies to improve crop performance. |
Title | ful-1 ag-10 |
Description | Crossed ful-1 and ag-10 mutants. |
Type Of Material | Technology assay or reagent |
Year Produced | 2022 |
Provided To Others? | No |
Impact | This mutant will be used to understand if presence of ag-10 can promote the formation of stomata on ful-1 valves, which normally lack stomata. |
Title | ag-10, shp1-1 shp2-1, ag-10 shp1-1 shp2-1, L-er pistils RNA-Seq |
Description | Harvested pre-anthesis pistils from ag-10, shp1-1 shp2-1, ag-10 shp1-1 shp2-1, L-er genotypes, extracted total RNA, DNaseI-treated, and performed high-throughput sequencing of 5 independent biological replicates. Data has been analyzed and reveals how AG and SHP control photosynthetic establishment. |
Type Of Material | Database/Collection of data |
Year Produced | 2022 |
Provided To Others? | No |
Impact | These data will provide an insight into how these genes control differentiation in the Arabidopsis pistil. |
Description | Control of stomatal development by MADS proteins |
Organisation | Friedrich Schiller University Jena (FSU) |
Department | Imre Kertész Kolleg Jena |
Country | Germany |
Sector | Academic/University |
PI Contribution | I developed the collaboration and topic for experimentation. I have generated data that can be extended upon through this collaboration. |
Collaborator Contribution | My collaborator Florian Rumpler has expertise, reagents, and equipment suitable for testing interactions between MADS proteins and DNA complexes. He has tested specific interactions and we anticipate these experiments being included for publication along with results obtained by my research team. |
Impact | None yet but submission for publication aimed for this year. |
Start Year | 2022 |