Achievements
From the work developed by the new GREEN-IT team we highlight the following most significant contributions achieved in the period of 2013-2017:
SnRK1 AND NUTRIENT SIGNALING PATHWAYS
We are at the forefront of one of the most rapid growing fields in plant biology: growth and developmental regulation by nutrient signaling pathways. Evolutionarily conserved C and N 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 made important and pioneering contributions to this field by identifying several mechanisms that control SnRK1 function (e.g., activation by ABA - abscisic acid - stress hormone and repression by PP2C phosphatases, the SR45 splicing factor and SUMOylation). We also gained significant mechanistic insight into how SnRK1 regulates gene expression and metabolism via bZIP transcription factors, miRNAs and candidate substrates (metabolic enzymes and other regulators) identified in proteome-wide analyses. Benefiting from numerous international collaborations fostered by EU networks (EMBO, MSCA-ITNs, Plants4Life PhD program) and invitations to lecture in conferences/institutions across Europe and elsewhere, we are bridging SnRK1 signaling to other signaling pathways and to specific developmental processes of agronomic relevance.
PHOTOSYNTHESIS REGULATION & BIOMASS
A modest improvement in plant photosynthesis is now recognized as a potential contributor to substantial gains in biomass. We address this Global Challenge by identifying new regulatory processes of C4-photosynthesis at the transcript and post-translational (PTM) levels. Our work started in 2012, within an EU FP7 project (3to4) that aimed at building the fundamental knowledge to comprehensively describe C4-photosynthesis, including the as yet unknown control of cell-specific localization and activity of key photosynthetic enzymes. We made significant contributions (e.g., identified two cis-elements in the NADP-ME promoter and two new transcription factors -TFs) that may aid in implementing C4 metabolism in C3 plants. Importantly at the PTM level, we built a comprehensive catalog of new modifications (phosphorylation/acetylation) that affect key enzymes in C-fixation, establishing a new paradigm in the landscape of plant protein regulation. As major recognition of our work, we were invited to participate in the setup of an EU Flagship-like program: Photosynthesis 2.0.
SEXUAL REPRODUCTION IN HIGHER PLANTS
This topic is of particular importance to increase crop yields, overcoming hybridization barriers and selecting and fixing quality traits. The study of land plant evolution serves to uncover conserved key components of such developmental processes and also those specific to angiosperms and thus all major crops. As partner in the MSCA-ITN PLANTORIGINS, we have created the first comprehensive transcriptome atlas for the extant bryophyte Physcomitrella patens, leading to high profile publications and a widely used Physcomitrella eFP browser. Since 2015 we are coordinating the ERA-CAPS project “Evolution of Sexual Reproduction in Plants”, comprising six EU and one US partner with a total budget of 2.6M€ (www.evorepro.org). This consortium employs a phylogenetic network analysis approach, combining their large-scale RNA-Seq data sets from extant bryophytes over early angiosperms (Amborella) 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 in that it allows phylogenetic network analyses for any developmental phase and is thus highly versatile for plant biology in general. Most recently, we joined the MSCA EID-ITN MossTech, involving several SMEs using Physcomitrella as green cell factories (www.mosstech.eu).
CORK OAK GENOMICS
To tackle the threats compromising one of the largest economic sectors in Portugal, we have launched and led a national consortium (20 labs/12 funded projects) for high-throughput sequencing of the cork oak transcriptome. Five GREEN-IT labs have actively participated in the cork oak genome sequencing initiative, attracting 1,2M€, and identifying critical aspects of cork oak development, from cork differentiation to abiotic stress adaptation. We have profiled the expression of genes related to abiotic stress and acorn development and identified novel miRNAs specifically expressed in phellem (cork). Using a candidate gene approach in the model woody species poplar, we demonstrated the role of a SHR protein in phellem and periderm formation through the regulation of cytokinin metabolism, triggering parallel studies in cork oak. In a genome-wide association study, we discovered distinct DNA methylation profiles related to cork quality. We are now investigating the impact of combined drought and heat stresses in the biosynthesis of the main cork polymer, suberin. We have extended our international partnerships to increase the scope and impact of our research by collaborating with experts in relevant model plant systems (in order to underpin our fundamental science efforts), and we are also 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
Policy-makers, producers and consumers worldwide are increasingly concerned with food quality and environmental sustainability. We study the genetic architecture underlying phenotypic variation of complex nutritional and organoleptic quality traits in grain legumes and their interaction with biotic/abiotic stress resistance. By GWAS (genome-wide association studies), we identified QTLs (quantitative trait loci)/genes underlying nutritional and health beneficial compounds in common bean and grass pea, and analysed 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, thus ensuring maximum commercial exposure and impact of our research findings. An exciting network of international collaborations, supported by several EU projects (H2020, FP7, ERA-PG, ARIMNet) resulted in many joint high impact research publications and seminal reviews.
