Opportunities and Limitations of Crop Phenotyping in Southern European Countries

Abstract

The Mediterranean climate is characterized by hot dry summers and frequent droughts. Mediterranean crops are frequently subjected to high evapotranspiration demands, soil water deficits, high temperatures, and photo-oxidative stress. These conditions will become more severe due to global warming which poses major challenges to the sustainability of the agricultural sector in Mediterranean countries. Selection of crop varieties adapted to future climatic conditions and more tolerant to extreme climatic events is urgently required. Plant phenotyping is a crucial approach to address these challenges. High-throughput plant phenotyping (HTPP) helps to monitor the performance of improved genotypes and is one of the most effective strategies to improve the sustainability of agricultural production. In spite of the remarkable progress in basic knowledge and technology of plant phenotyping, there are still several practical, financial, and political constraints to implement HTPP approaches in field and controlled conditions across the Mediterranean. The European panorama of phenotyping is heterogeneous and integration of phenotyping data across different scales and translation of "phytotron research" to the field, and from model species to crops, remain major challenges. Moreover, solutions specifically tailored to Mediterranean agriculture (e.g., crops and environmental stresses) are in high demand, as the region is vulnerable to climate change and to desertification processes. The specific phenotyping requirements of Mediterranean crops have not yet been fully identified. The high cost of HTPP infrastructures is a major limiting factor, though the limited availability of skilled personnel may also impair its implementation in Mediterranean countries. We propose that the lack of suitable phenotyping infrastructures is hindering the development of new Mediterranean agricultural varieties and will negatively affect future competitiveness of the agricultural sector. We provide an overview of the heterogeneous panorama of phenotyping within Mediterranean countries, describing the state of the art of agricultural production, breeding initiatives, and phenotyping capabilities in five countries: Italy, Greece, Portugal, Spain, and Turkey. We characterize some of the main impediments for development of plant phenotyping in those countries and identify strategies to overcome barriers and maximize the benefits of phenotyping and modeling approaches to Mediterranean agriculture and related sustainability.

Keywords: crop selection and performance; heat and water stress; high-throughput; phenotyping infrastructures; phenotyping technology.

Figure 1

Phenotyping at different scales and levels of plant biological organization: from the molecular level (A) until the plant (E) and ecosystem level (F). Arrows indicate the complementarity between different phenotyping levels and the need of integrating phenotyping outputs for improved practical application e.g., in crop selection and breeding. Different plant species were used as examples (Quercus suber L., Fontinalis antipyretica Hedw., Arabidopsis thaliana L., Oryza sativa L., and Vitis vinifera L.).

Figure 2

Data flow from trials to genetic analyses and dissemination considered within the EMPHASIS and ELIXIR which are two ESFRI infrastructures, dedicated to phenomics and data sharing and integration, respectively. ESFRI is the European Strategy Forum on Research Infrastructures, aiming at developing scientific integration of Europe and to strengthen its international outreach. The relation between data production/analysis and modeling will be promoted by the interaction of the academic/industrial communities focused on phenomics (e.g., EMPHASIS) as well on crop modeling (e.g., AgMIP project—Agricultural Model Intercomparison and Improvement Project, http://www.agmip.org/) (adapted from EMPHASIS, 2018).

Figure 3

The ALSIA greenhouse phenotyping facility (Basilicata, southern Italy) consisting of Scanalyzer 3D-systems which include conveyor belts (0.3 km and 500 cars) and image chambers: (A, B) the robot system for randomization of pots, consistent monitoring of pot weight, accurate application of water and imaging of plants; (C) phenotyping of tomato seedlings; and (D) phenotyping of root architecture.