Periodic Reporting for period 3 - CAPITALISE (COMBINING APPROACHES FOR PHOTOSYNTHETIC IMPROVEMENT TO ALLOW INCREASED SUSTAINABILITY IN EUROPEAN AGRICULTURE)
Reporting period: 2023-04-01 to 2024-11-30
CAPITALISE will accelerate efforts to 2030 and beyond, aiming to deliver next generation future-proofed high-yielding crops to farmers to meet growing global food demands.
Learning from nature and using biotechnology driven conventional and novel plant breeding techniques, CAPITALISE aims to develop new crop varieties with improved photosynthetic efficiency via techniques such as marker assisted breeding and genomic prediction, provide scientific insights to help global advances in gene editing and bioengineering, increase understanding about how photosynthesis works and how breeders can exploit the mechanisms underlying why one genotype has a higher rate of photosynthesis than another. The project will use social science, stakeholder engagement and Plant Science Literacy training to inform and educate citizens and industry about crops for the future and integrate ethical, societal, environmental and economic issues relevant to CAPITALISE and wider crop breeding technologies into future strategies for crop improvement.
Learning from nature and using biotechnology driven conventional and novel plant breeding techniques, CAPITALISE aims to develop new crop varieties with improved photosynthetic efficiency via techniques such as marker assisted breeding and genomic prediction, provide scientific insights to help global advances in gene editing and bioengineering, increase understanding about how photosynthesis works and how breeders can exploit the mechanisms underlying why one genotype has a higher rate of photosynthesis than another. The project will use social science, stakeholder engagement and Plant Science Literacy training to inform and educate citizens and industry about crops for the future and integrate ethical, societal, environmental and economic issues relevant to CAPITALISE and wider crop breeding technologies into future strategies for crop improvement.
The project focuses on three crop species, maize, barley and tomato. For the refinement of the quantitative trait loci (QTL) and candidate genes, efforts focused on the genetic materials that could effectively support the identification of candidate genomic regions and genes capable of boosting the understanding and improvement of Most Valuable Players (MoVaP) traits. The project managed to identify and validate candidate genes or the description of molecular markers and loci relevant for photosynthetic efficiency. Trait expression data of MoVaPs was collected through the use of high-throughput automated plant phenotyping platforms operated in environmentally controlled plant cultivation facilities. 3 Tiers of phenotyping experiments resulted in phenotypic data sets for QTL analyses that yielded elaborate and highly valuable results. Data acquired in the Tier 2 and Tier 3 experiments was used to i) validate selected QTL ii) assess their stability under benign and challenging environmental conditions and iii) verify causal genes and epistatic relations. The delivery of new methods and new devices for high-throughput measurements was completed.
Population-wide phenotypic characterization of germplasm was undertaken to provide detailed characterization of photosynthetic trait variation at the developmental stage where yield is most strongly determined by photosynthesis. The results have already been used to generate several publications, which are in various stages of development and peer review. In parallel the potential of CRISPR Cas9 editing techniques was explored to generate increases in photosynthetic efficiency. Several examples of promoter editing were tested using promoter-reporter construct in a transient expression assay.
Work on Leaf Chlorophyll content highlights the multifaceted impacts of chlorophyll reduction on photosynthetic efficiency, thylakoid stability, and stress responses in pale green mutants across diverse plant species. These findings not only advance our understanding of photosystem dynamics but also underscore the developmental and environmental modulation of photosynthetic processes in response to altered chlorophyll composition. Development of a non-destructive instrument for assessing the chlorophyll a/b ratio was successfully finalized.
Phenotypic and genotypic data was used to: (1) develop and compare machine learning models for predicting diverse photosynthesis-related traits from hyperspectral reflectance (HSR) data; (2) parametrize genotype-specific medium-scale kinetic models for the Calvin-Benson cycle (CBC) and related processes using gas exchange data (3) develop, implement, and test a new framework, termed kinetic genomic prediction (kinetic GP), that makes use of genetic markers to predict photosynthesis-related traits for unseen genotypes in unseen conditions; (4) employ genetic markers to conduct the first flux genome-wide association studies (5) develop, implement, and test a new framework, termed dynamic GP, to predict the dynamics of traits in unseen lines;
Across the public acceptance studies, it was repeatedly shown that (i) initial associations play a dominant role in how consumers respond to new product (ii) specific products into which these new crops are embedded influences acceptance of the new crops; a (iii) that conventional breeding techniques remain favoured by the public with gene-editing techniques being considered better than classical Genetic modification (cis-genesis) but still less liked than conventional breeding.
In the environmental impact, economic viability studies extensive models were developed that could predict environmental impact including potential effects around (i) increased nutrient demand (ii) increased water demand (iii) increased pesticide demand and/or disease load. The modelling showed that a more comprehensive view on the use of photosynthesis boosted plants, extending the range of analysis beyond the plant to (at least) the field is needed.
Production of a Roadmap for photosynthesis was lead by CAPITALISE, working with 3 other EU funded photosynthesis projects, 77 stakeholders through in person workshops, and 70 breeder and grower stakeholders from online surveys. The Roadmap is focuses on the translation of plant science research for societal gain with a view to developing future proof crops. To compliment this and facilitate the use of research results at a local level, WP8 co-organised two expert led webinars on i) The Nagoya Protocol and Access and Benefit Sharing and ii) Intellectual Property. These were particularly aimed at plant research scientists.
Population-wide phenotypic characterization of germplasm was undertaken to provide detailed characterization of photosynthetic trait variation at the developmental stage where yield is most strongly determined by photosynthesis. The results have already been used to generate several publications, which are in various stages of development and peer review. In parallel the potential of CRISPR Cas9 editing techniques was explored to generate increases in photosynthetic efficiency. Several examples of promoter editing were tested using promoter-reporter construct in a transient expression assay.
Work on Leaf Chlorophyll content highlights the multifaceted impacts of chlorophyll reduction on photosynthetic efficiency, thylakoid stability, and stress responses in pale green mutants across diverse plant species. These findings not only advance our understanding of photosystem dynamics but also underscore the developmental and environmental modulation of photosynthetic processes in response to altered chlorophyll composition. Development of a non-destructive instrument for assessing the chlorophyll a/b ratio was successfully finalized.
Phenotypic and genotypic data was used to: (1) develop and compare machine learning models for predicting diverse photosynthesis-related traits from hyperspectral reflectance (HSR) data; (2) parametrize genotype-specific medium-scale kinetic models for the Calvin-Benson cycle (CBC) and related processes using gas exchange data (3) develop, implement, and test a new framework, termed kinetic genomic prediction (kinetic GP), that makes use of genetic markers to predict photosynthesis-related traits for unseen genotypes in unseen conditions; (4) employ genetic markers to conduct the first flux genome-wide association studies (5) develop, implement, and test a new framework, termed dynamic GP, to predict the dynamics of traits in unseen lines;
Across the public acceptance studies, it was repeatedly shown that (i) initial associations play a dominant role in how consumers respond to new product (ii) specific products into which these new crops are embedded influences acceptance of the new crops; a (iii) that conventional breeding techniques remain favoured by the public with gene-editing techniques being considered better than classical Genetic modification (cis-genesis) but still less liked than conventional breeding.
In the environmental impact, economic viability studies extensive models were developed that could predict environmental impact including potential effects around (i) increased nutrient demand (ii) increased water demand (iii) increased pesticide demand and/or disease load. The modelling showed that a more comprehensive view on the use of photosynthesis boosted plants, extending the range of analysis beyond the plant to (at least) the field is needed.
Production of a Roadmap for photosynthesis was lead by CAPITALISE, working with 3 other EU funded photosynthesis projects, 77 stakeholders through in person workshops, and 70 breeder and grower stakeholders from online surveys. The Roadmap is focuses on the translation of plant science research for societal gain with a view to developing future proof crops. To compliment this and facilitate the use of research results at a local level, WP8 co-organised two expert led webinars on i) The Nagoya Protocol and Access and Benefit Sharing and ii) Intellectual Property. These were particularly aimed at plant research scientists.
Key Exploitable Results (KERs) from CAPITALISE include:
• GERMPLASM - Well characterised germplasm for three model crops (barley, maize and tomato); QTLs, QTNs identified for key MoVaPs in these crops; Molecular markers developed for allelic variation.
• PHENOTYPED MATERIAL - Validated phenotypic data sets (Tier 1-3).
• PHENOTYPING TOOLS – High Throughput Phenotyping and portable field phenotyping devices, (chlorophyll and NRS spectroscopy metabolic finger printing). Partner PSI is already commercialising part of this toolkit.
• SELECTED STRATEGIES - Future strategies for exploitation of variation including: Identification of key physiological traits in constant/fluctuating light; Metabolic profiling/development of models; Novel genetic toolbox; Novel proof of concept germplasm.
• CHLOROPHYLL TUNING Methods for chlorophyll analysis. Refined crop specific sub traits for chlorophyll tuning. Proof of concept test results from selected low chlorophyll phenotypes.
• DESCRIPTOR LISTS The lists are available for the three crops under study. Field trials for 1 MoVaP are progressing.
• SOCIETAL IMPACT ANALYSIS: Assessment of societal acceptance. Initial early-stage studies of environmental impact and economic viability.
• MODELLING - Kinetic model for CBC. Approaches for mapping multiple traits. Mechanistic models with genomic data.
A Strategic Research Agenda has been developed based on Key Exploitable results and is publicly available. This provides a strategy for CAPITALISE to take the results of the project forwards.
• GERMPLASM - Well characterised germplasm for three model crops (barley, maize and tomato); QTLs, QTNs identified for key MoVaPs in these crops; Molecular markers developed for allelic variation.
• PHENOTYPED MATERIAL - Validated phenotypic data sets (Tier 1-3).
• PHENOTYPING TOOLS – High Throughput Phenotyping and portable field phenotyping devices, (chlorophyll and NRS spectroscopy metabolic finger printing). Partner PSI is already commercialising part of this toolkit.
• SELECTED STRATEGIES - Future strategies for exploitation of variation including: Identification of key physiological traits in constant/fluctuating light; Metabolic profiling/development of models; Novel genetic toolbox; Novel proof of concept germplasm.
• CHLOROPHYLL TUNING Methods for chlorophyll analysis. Refined crop specific sub traits for chlorophyll tuning. Proof of concept test results from selected low chlorophyll phenotypes.
• DESCRIPTOR LISTS The lists are available for the three crops under study. Field trials for 1 MoVaP are progressing.
• SOCIETAL IMPACT ANALYSIS: Assessment of societal acceptance. Initial early-stage studies of environmental impact and economic viability.
• MODELLING - Kinetic model for CBC. Approaches for mapping multiple traits. Mechanistic models with genomic data.
A Strategic Research Agenda has been developed based on Key Exploitable results and is publicly available. This provides a strategy for CAPITALISE to take the results of the project forwards.