Achievements
MECHANISMS AND CONTROL OF PLANT PESTS AND DISEASES
The UN estimates that 40% of annual crop loss is due to pests and diseases. To address this, Green-it has been focusing on how plants perceive and respond to biotic stress, particularly in the environment interactions between host and stressor.
As such, we developed efficient screening methods to identify biopesticides, natural antimicrobial agents, dsRNAs and organism-derived extracts with relevant activity. Key achievements include identifying and characterizing antifungal peptides, now being developed as biofungicides, chemicals targeting Pinewood nematode, nitrogen-fixing bacteria with antagonistic capacity towards oomycetes, and biological control agents for major crop diseases.
Furthermore, we are testing new sustainable, biodegradable materials for micro-/nano-encapsulation, as well as digital tools for early detection and risk prediction. To support plant breeding and improve agricultural productivity, we are also applying machine learning to crop traits from genetic data.
QUANTITATIVE GENOMICS FOR STRESS RESISTANCE BREEDING
For a sustainable agriculture it is vital that we prioritize varieties that are not only resistant, but that also minimize pesticide use. However, the effectiveness of the resistant varieties differs according to factors, such as pathogen evolution and the genetic basis of resistance.
At Green-it, partial disease resistances are one of our major focuses. To better understand them, we leverage natural plant variation and employ statistical genomic methods. Through genotyping and phenotyping, we successfully elucidated the genetic architecture of various resistance mechanisms against root and leaf pathogens, acting at different infection stages.
Furthermore, we have identified key genes involved in biotic-abiotic stress interactions in underutilized legume crops. Currently, Green-it researchers have been conducting participatory research with farmers and breeders to test the identified candidate resistance genes and associated alleles and ensure widespread commercial impact.
INTERPLAY BETWEEN CARBON METABOLISM REGULATION AND PLANT GROWTH
During photosynthesis plants assimilate CO2, producing sugars that allow the plant to grow. To maximize this growth and yield, photosynthesis efficiency needs to be improved. As such, the understanding of the regulation of C4 photosynthesis is key for crop improvement.
Green-it has contributed to unveiling the molecular mechanisms that regulate cell-specific gene expression of enzymes used in C4 photosynthesis, its regulation by light, as well as its evolution from C3 ancestral species. Notably, we identified the first ever described phosphorylation in the NADP malic enzyme, which finetunes its activity during the day.
In parallel, we have identified novel interactors of SnRK1, a conserved central regulator crucial for coping with depletion of C reserves, and demonstrated its role in regulating sucrose homeostasis and gene expression under favorable conditions. Additionally, we showed the critical role of source-sink dynamics for crop yield.
GAMETOPHYTE DEVELOPMENT AND SEXUAL REPRODUCTION IN LAND PLANTS
Research on the reproductive phase of plants is vital for increasing crop yields, mitigating climate change impacts and breeding improved varieties.
Green-it researchers demonstrated that Arabidopsis sperm cell transcriptomes can be studied at the single cell level, besides finding significant differences between the transcript isoforms in sperm cells and vegetative nuclei, with potential implications at the proteome level. Additionally, we found that loss of a specific epigenomic modification in the DNA in sperm cells facilitates gene transcription during spermatogenesis and pre-determines a chromatin state that predicts gene expression in the next generation.
We also uncovered the gene expression dynamics in developing pollen and established NOT1, the scaffold protein of the CCR4-NOT1 complex, as a crucial regulator of microgametogenesis.
Using our evo-devo model Physcomitrium patens, we characterized de novo centriole biogenesis during spermatogenesis structurally and molecularly for the first time. By integrating expression data from 13 plant species compiled in our EVOREPRO database (https://evorepro.sbs.ntu.edu.sg/), we could identify conserved transcriptional programmes underlying organogenesis and reproduction in land plants.
MICROBIOTA FUNCTION AND MANIPULATION TO RECOVER SOIL HEALTH
Enhancing soil health is key for sustainable agricultural production. Green-it is highly invested in this area, focusing on how to make soil more resilient to degradation and the effects of climate change.
We have characterized various soil microbiota and identified new relevant strains and microalga with beneficial effects on plant growth and stress mitigation. We have also explored the use of alternative resources for soil health improvement and biostimulation, as well as studied the role of soil in carbon sequestration.
Green-it researchers have looked into the exudate-mediated recruitment of beneficial microbiota, described the use of microbiota from extreme soils, defined the populations of extreme soil in the Iberian Peninsula, and explored non-conventional sources of microbiota. This area has sparked a lot of interest and attracted several collaborations with industry.
SnRK1 AND NUTRIENT SIGNALING PATHWAYS
Green-it researchers have been at the forefront of one of the most rapid growing fields in plant biology - growth and developmental regulation by nutrient signaling pathways.
Evolutionarily conserved carbon and nitrogen sensing pathways such as SnRK1 and TOR signaling are central components of the regulatory circuits that modulate plant growth in response to a changing environment. We have identified several mechanisms that control SnRK1 function, and also gained significant mechanistic insight into how SnRK1 regulates gene expression and metabolism.
PHOTOSYNTHESIS REGULATION & BIOMASS
Boosting plant photosynthesis can lead to substantial gains in biomass. As such, Green-it researchers have identified new regulatory processes of C4 photosynthesis at the transcript and post-translational levels. This work started in 2012, with the building of the fundamental knowledge to comprehensively describe C4 photosynthesis.
We made significant contributions that may aid in implementing C4 metabolism in C3 plants. Importantly at the post-translational modification level, we built a comprehensive catalog of new modifications that affect key enzymes in C-fixation, establishing a new paradigm in the landscape of plant protein regulation.
SEXUAL REPRODUCTION IN HIGHER PLANTS
The study of land plant evolution serves to uncover conserved key components of developmental processes, including those specific to angiosperms and thus all major crops. Sexual reproduction is of particular importance for increased crop yields, overcoming hybridization barriers and selecting and fixing quality traits.
Green-it researchers have contributed towards the first comprehensive transcriptome atlas for the extant bryophyte Physcomitrella patens, leading to the Physcomitrella eFP browser.
Green-it integrates a consortium that employs a phylogenetic network analysis approach, combining large-scale RNA-Seq data sets from extant bryophytes over early angiosperms to crops such as rice, tomato and maize, with the major objective of identifying missing key components involved in sexual reproduction. The resulting EVOREPRO database is unique, allowing phylogenetic network analyses for any developmental phase.
CORK OAK GENOMICS
Cork is one of the largest economic sectors in Portugal. To tackle the threats that compromise it, Green-it has launched and led a national consortium for high-throughput sequencing of cork oak transcriptome. Five of our labs have actively participated in the cork oak genome sequencing initiative, and identifying critical aspects of cork oak development, from cork differentiation to abiotic stress adaptation.
Green-it researchers have profiled the expression of genes related to abiotic stress and acorn development and identified novel miRNAs specifically expressed in phellem. Using a candidate gene approach in the model species poplar, we demonstrated the role of a SHR protein in phellem and periderm formation through the regulation of cytokinin metabolism, leading to similar studies in cork oak. Through a genome-wide association study, we were able to uncover distinct DNA methylation profiles related to cork quality. Currently, we are investigating the impact of combined drought and heat stresses in the biosynthesis of suberin.
Furthermore, we have been leading the development of data management and annotation tools for woody plants, as part of the European Infrastructure to manage life science data – ELIXIR.
QUANTITATIVE GENOMICS TOOLS FOR BREEDING
Policymakers, producers and consumers worldwide are increasingly concerned with food quality and environmental sustainability.
Green-it studies the genetic architecture underlying phenotypic variation of complex nutritional and organoleptic quality traits in grain legumes and their interaction with biotic/abiotic stress resistance.
Through genome-wide association studies, we were able to identify quantitative trait loci/genes underlying nutritional and health beneficial compounds in common bean and grass pea and analyzed genomic regions controlling fungal diseases and drought resistance. This uncovered gene interaction networks and allowed us to develop molecular selection tools for precision breeding. These tools are being tested through participatory breeding with national legume breeding/farming companies and processing industries.
