(3)INESC TEC - CRIIS
Agriculture faces the global challenge of producing more (in quantity and quality) with fewer resources, which must be aligned with the sustainable use of natural resources and the mitigation of climate scenarios. The significant gains in agricultural productivity resulting from the "green revolution" established after the Second World War were based on a model of intensive agriculture that is currently insufficient to develop sustainable food systems. This agricultural model was supported by several technological innovations, such as highly productive varieties, phytopharmaceuticals, fertilisers and mechanised systems that are no longer adjusted to the dramatic loss of soil fertility (e.g., erosion, salinisation), the need to preserve biodiversity and the escalating energy costs. Moreover, this model of agriculture was developed in a context of relative climate stability that is not suitable for climate scenarios in the 21st century.
In this model of productivist agriculture, agronomic decisions are based on simplified and standardised diagnoses that do not consider either the plant's physiology or its causality with the environmental context, that is, this agronomic process is not focused on the plant's performance (genotype) or its interaction with the environment (phenotype). This agronomic approach is, therefore, dissociated from the structured knowledge produced in technological laboratories (biotechnology and instrumentation) and is limited in assimilating the scientific and technological developments that have taken place in recent years within the scope of omics disciplines - genomics, transcriptomics, metabolomics and phenomics (Fig. 1).
Omics tools like systems biology and bioinformatics are currently available and allow the development of very thorough computer simulations of this omics cascade (fluxomics) and the respective production of in-silico models to connect the information between the genotype and the phenotype. These omic tools, combined with high-dimensional, high-throughput sensors, support the transfer of information to measure the plant's response at the cellular and metabolic level in the field, in a non-invasive way, thus enhancing the transition to a molecular precision agronomic model.
In this context, phenotyping has been developing the concept of genotype-phenotype mapping associated with genotype-environment-agronomic practices (GEP) interactions, which are an opportunity to promote advanced agronomic models based on omics disciplines.
Phenotyping consists of analysing a set of quantitative or qualitative characteristics of the phenotype of plants (e.g., dimensions, colour, and composition) and relating them to the performance of a genotype in certain environments (e.g., climate, soils) - which, in the agronomic case, includes cultural practices. Traditionally, phenotyping techniques focused on easily measurable plant characteristics, which farmers used to improve their production system since ancient times. Recently, plant sensing allowed to quickly and accurately obtain data related to the phenotypic characteristics of plants, including the most complex ones, such as molecules related to plant metabolism and physiology – pheno-metabolome (Fig. 1). These sensors can be mounted on different platforms and carry out "large-scale" mapping of the phenotypic characteristics of plants in their environmental context.
However, it is consensual that despite the clear advances in precision, speed and costs of the techniques applied to plant genomics in recent years, namely in DNA sequencing by "Next-Generation Sequencing -NGS", phenotyping techniques have not been developed at the same pace, currently being a "phenotyping bottleneck" so that agriculture, like medicine or the pharmaceutical industry, can also benefit from the major advances in omics disciplines (Fig.1).
In the last decade, the convergence between omics disciplines has benefited from initiatives - developed in various areas of the globe - of plant phenotyping structures with advanced technology, excellent human resources, great international interaction, and comfortable financial endowments. The "European Plant Phenotyping Network – EPPN" stands out the effective liaison with similar plant phenotyping structures mapped in various parts of the globe. In this context, in 2016, the European Union, through the "European Strategy Forum for Research Infrastructures (ESFRI), identified plant phenotyping as a priority area of research and, in 2018, outlined in its roadmap the strategic role of the plant phenotyping infrastructures in Europe for the next 20 years. In this roadmap, the European Infrastructure for Plant Phenotyping – EMPHASIS stands out, which Portugal recently joined with INESC TEC as a partner.
However, the worldwide panorama of plant phenotyping is still heterogeneous. It presents limitations for farm implementation, namely the multidirectional translation of model species for crops and the integration of these data at different scales, with low-cost field applications that also consider perennial woody crops.
INESC TEC has been developing robots with omics capabilities, performing high-throughput, high-dimensional digital phenotyping, integrating the various omics disciplines in the agronomic process of different crops (including arboreal shrubs). The robot "Metbots" is an example that uses smart-photonics based on low-cost, point-of-measurement devices to measure, process and map critical parameters of plant metabolism related to its physiology, in a non-destructive manner. Also under development, the "Omicbots" robot is another example capable of combining metabolic monitoring with bioinformatics and systems biology tools for precision physiological crop diagnosis (Fig. 1).
These robots are equipped with sensors based on photonics and artificial intelligence to determine a myriad of molecules of cellular metabolism or phenometabolome (e.g., chlorophylls, pheophytins, anthocyanins, carotenoids, phytohormones) produced by plants in response to biotic or abiotic stresses. These are the basis of the plant's physiological diagnosis operationalised in agronomic decisions (e.g., fertilisation, irrigation of diseases, selection of varieties adapted to micro-zoning). These smart sensors allow for the metabolic screening of each plant in different environmental conditions (soil, climate), and using systems biology techniques, bioinformatics and in-silico models incorporated in the "OmicBots". This system will allow to understand which enzymes are active and which genes are being activated or silenced in each situation and understand the plant mechanism, allowing a very precise actuation in the agronomic process.
The integration of these omics, photonics and agronomic technologies is operationalised through virtual biological digital-twin models for real-time and in situ transfer of information between the laboratories and the agronomic process.
This molecular precision agriculture approach promoted by INESC TEC opens a new frontier to study and implement adaptation mechanisms, treatments and advanced agronomic interventions: i) more precise management of resources and production factors, namely water and nutrients, allowing to produce more with fewer resources, ii) early detection of diseases, even in the asymptomatic phase, allowing localised treatment before dissemination occurs and, even, support in the development of phytopharmaceuticals with greater agronomic and environmental efficiency and less impact on non-target species, iii) act thoroughly in the frequent situations of combined stresses (e.g., water stress associated with heat stress, light stress), since the plant metabolism changes accordingly, even if the phenotype is not and iv ) to know the phenotypic plasticity of the plant when exposed to a set of environmental conditions (cultural practices included) as a tool for mitigating climate change. Genetic improvement is a time-consuming process, so we can take advantage of the phenotypic plasticity of plants (as long as it is known) to mitigate the unpredictable effects of climate scenarios.
The omics disciplines and tools envisage the development of a new Era of precise and causal agronomic action to support sustainable food systems. This requires advances in biotechnology and instrumentation flowing bidirectionally between the laboratory and the field. Basic science and technology are available, but the knowledge has yet to be applied. The technologies and scientific advances in this INESC TEC's research line received several prizes and awards and have recently been considered high-impact research for developing advanced models of precision agriculture.