A holistic multi-actor approach towards the design of new tomato varieties and management practices to improve yield and quality in the face of climate change

Project Information

TomGEM

Grant agreement ID: 679796

DOI

10.3030/679796

Project closed

EC signature date 8 February 2016

Start date 1 March 2016

End date 31 August 2020

Funded under

• SOCIETAL CHALLENGES - Food security, sustainable agriculture and forestry, marine, maritime and inland water research, and the bioeconomy

Total cost

€ 5 671 945,00

EU contribution

€ 4 993 506,25

Coordinated by

INSTITUT NATIONAL POLYTECHNIQUE DE TOULOUSE
France

Periodic Reporting for period 3 - TomGEM (A holistic multi-actor approach towards the design of new tomato varieties and management practices to improve yield and quality in the face of climate change)

Reporting period: 2019-03-01 to 2020-08-31

Summary of the context and overall objectives of the project

Climate change calls for designing new strategies for growing crops under harsh conditions and combined with the forecasted world demographic growth raises a major challenge for society to provide sufficient amounts of high nutritional and sensory quality food crops. TomGEM aims to design new strategies to maintain yields stability of fruit and vegetables produced at harsh temperature conditions, using the tomato as a reference fleshy fruit crop. TomGEM considers all developmental processes contributing to yield, including flower initiation, pollen fertility and fruit set and implements trans-disciplinary approaches to investigate the impact of high temperature on these traits. TomGEM applies a multi-actor approach involving tomato producers and breeders to provide new targets, innovative breeding and management strategies to foster breeding of new tomato cultivars with improved yield under suboptimal temperature conditions. TomGEM associates in a coordinated effort the basic investigation of the mechanisms of heat tolerance related to yield, the exploration of available genetic resources to select best genotypes and the search for optimal cultural practices adapted to heat. The project relies on the active collaboration between scientists, breeders and producers. The project also aims to assess the effect of high temperature on the nutrional and post-harvest behaviour of tomato fruit. Overall, the tailed multidisciplinary work plan in TomGEM applied to the heat tolerant tomato genotypes combined with the multilevel dissection of the key processes limiting tomato productivity under high temperatures lead to a better knowledge of complex plant-environment interactions. Maintaining yield crop stability in the face of climate change requires a better understanding of the genetic and physiological factors that impact yield trait at high temperature. This knowledge is anticipated to open new avenues to design innovative strategies for generating new genetic material displaying heat tolerance. The setup of optimal cultural practices is also required to better adapt to changing environmental conditions.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

A major achievement of TomGEM is to have gathered and made accessible a large collection of tomato germplasm from across the world corresponding to natural or induced variations. Over 2000 genotypes were screened in different locations using a common set of phenotypic descriptors and environmental parameters to evaluate their performance regarding heat stress. A set of heat tolerant tomato genotypes were identified following field and glasshouse tests at multiples locations including Spain, Italy, Bulgaria. Seeds of top heat-tolerant genotypes were exchanged between TomGEM partners to enable crossing as well as further physiological and molecular analyses. The data generated were made available online via the phenotyping PhenoTomGEM database created specifically for the need of TomGEM. Promising QTLs and molecular markers associated with high temperature were identified in different RIL and IL populations and candidate genes were identified for pollen fertility at high temperatures by integrating mapping and RNA-seq data. Mutant lines displaying pollination-independent fruit set under heat stress conditions were identified. Genome-wide mapping of histone marks and Cytosine methylation associated with fruit set was performed and integration of global transcriptomic profiling and epigenetic markers revealed the role of histone marks in genetic reprogramming associated with fruit set. Various management practices were tested on determinate and indeterminate genotypes grown in open field or under tunnel. The use of a biostimulant compounds and the whitening of leaves gave promising results. Large scale assessments of post-harvest properties of genotypes with natural variation for heat tolerance revealed a general trend of reduced quality but few genotypes have been identified that retain quality after being subjected to elevated temperature. Finally, new resources and tools have been generated in the framework of the project. A transcriptomic pipeline (TomExpress) gathering web tools for storing, processing, mining transcriptomic data was set up. An interactive phenotyping database gathering the outcome of the screening of all germplasm collections during the TomGEM project was created. A new high quality de novo tomato genome assembly and annotation was achieved allowing the building a new and updated version of TomExpress. A dissemination toolkit using the TomGEM corporate identity was continuously applied, a social media channel (Twitter: @TomGem_EU) and a project website (http://tomgem.eu/) were established and updated regularly with news information and peer-reviewed publications. Results were disseminated at scientific meetings, international conferences, trade and business fairs across different sectors and TomGEM engaged with civil society and young citizens. TomGEM reached out to a range of stakeholder groups such as the scientific community, industrial stakeholders including tomato breeders and growers, policy makers and the general public on national, European and international level (Europe, South America, Asia). However, the disseminations activities were greatly impacted the restrictions due to the Covid-19 pandemic.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

A number of achievements were obtained including selection of superior genotypes for yield stability under heat stress. Genetic markers and QTLs associated with heat tolerance were identified. The transcriptomic profiling of the fruit set was established and the first genome-wide epigenetic map associated with this developmental transition constructed. Candidate genes potentially involved in fruit initiation were selected providing suitable material for characterisation of genes and QTLs controlling yield stability and for design of new breeding strategies to capture these loci in the cultivated tomato varieties. The selected genotypes are now being subjected to further genetic, physiological and molecular investigation to validate their yield stability and the functional significance of the genes and loci underlying this trait. New tomato varieties are expected to sustain increased diversity thus allowing higher adaptability to particular environments. The outcome of TomGEM will be used in multiple ways and will ultimately feed into different user communities incl. researchers, breeders, tomato producers and consumers. The achievement of TomGEM in terms of knowledge and tools created will support productivity and stability of the agricultural sector in and outside Europe. One of the greatest satisfactions that came out of the project certainly is the high quality of the active collaboration between academic partners and private sector (breeders and producers). The success of these exchanges is illustrated by new collaborative projects between academic and private partner running as a continuation of the efforts initiated within the TomGEM framework.

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