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H2020

TomGEM Report Summary

Project ID: 679796
Funded under: H2020-EU.3.2.

Periodic Reporting for period 1 - 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: 2016-03-01 to 2017-08-31

Summary of the context and overall objectives of the project

Climate change calls for designing new strategies for growing crops under harsh conditions. The forecasted increase of the world population combined with the global changes in climate 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 high yields 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 and innovative breeding and management strategies to foster breeding of new tomato cultivars with improved yield under suboptimal temperature conditions. TomGEM also assesses the effect of high temperature on the nutrional and post-harvest behaviour of tomato fruit.

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

The objectives of the 1st period were:
- Exploration of tomato genetic resources from different geographical locations to assess yield trait tolerance/susceptibility to heat stress
- Generation of genetic material/methods allowing to map loci and chromosomic regions involved in heat tolerance/susceptibility
- Screening of a tomato mutant collection to assess floral meristem initiation and reproductive organ development under high temperatures and a genome-wide transcriptomic profiling of the flower-to-fruit transition
- Production of genetic material and molecular analysis to find markers associated with heat tolerance
- Agricultural operations incl. irrigation, fertilisation and pest management to fit plant cultivation in different locations and determination of optimal cultural practices for maintaining fruit yield
- Impact assessment of heat stress on fruit nutritional, sensory qualities and post-harvest behavior

Outcomes achieved in WP1 (Exploring diversified germplasm collections for yield stability at high temperature):
- Up to 658 genotypes grown in ES, IT, BG, AR in 2016
- All grown lines evaluated using a common set of control genotypes and core set of phenotypic descriptors and environmental parameters
- Seeds of top heat-tolerant genotypes exchanged between EU partners & grown across EU locations in 2017
- New database (PhenoTomGEM) developed and data from 1st year uploaded
Partners: JIC, INPT, RHUL, CSIC, UNINA, UBA, MVCRI, Alma-Seges, ENZA, FCValenciana, Rougline

Outcomes achieved in WP2 (Determinants of pollen fertility and stability under high temperature conditions):
- 2 promising QTLs and molecular markers associated with high temperature identified in RIL and IL populations, verification underway
- 2 strong candidate genes mapped in a region of tomato chromosome 4 defined as conferring pollen fertility and fruit set
- Analysis of pollen germination rate under normal and heat stress conditions
Partners: CSIC, INPT, RHUL, INRA, ENZA, FCValenciana, NTW

Outcomes achieved in WP3 (Genetic determinants and regulation of the fruit set process):
- Identification of pollination independent fruit set mutants under normal and heat stress conditions
- Genome-wide mapping of 3 histone marks and Cytosine methylation associated with fruit setting
- Integration of global transcriptomic profiling and epigenetic markers associated with fruit setting
- A transcriptomic pipeline and web tools for storing, processing, mining transcriptomic data created
- New and high quality de novo tomato genome assembly and annotation achieved
Partners: INPT, JIC, CSIC, UNINA, INRA, MVCRI

Outcomes achieved in WP4 (Genetic determinants and mechanisms of flower organ initiation):
- Screening of 614 Tomato EMS-mutant families at 29°C average temperature/day
- Identification of 33 mutants among which (i) 13 mutants produce germinating pollen under heat stress conditions, (ii) 12 mutants show parthenocarpic phenotypes, (iii) 2 mutants exhibit inflorescence alteration (iv) 6 mutants unable to produce flowers
Partners: INRA, INPT, UNINA, Rougeline

The following outcomes were achieved in WP5 (Breeding and management practices to increase yield at higher temperatures):
- 8 crosses between heat sensitive and heat tolerant parents generated, F1 hybrids and parents evaluated in Taiwan under hot, humid conditions, and, F4 seeds obtained by a SSD approach from three crosses
- A SSD F4 progeny from the control tolerant genotype JAG8810 obtained and evaluated under tunnel to start a genomic selection approach
- A preliminary list of more than 300 genes potentially involved in the heat stress response defined.
- An association mapping approach allowed detecting 29 markers potentially associated with 6 heat response-related traits.
Partners: UNINA, CSIC, AVRDC, MVCRI, Alma-Seges, FCValenciana

Outcomes achieved in WP6 (Impact of higher temperature on fruit quality traits and postharvest behaviour):
- 3 large-scale assessments of post-harvest properties

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)

While TomGEM is still in its first phase, a number of achievements were obtained incl. 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 setting was established and the first genome-wide epigenetic map was constructed. A number of candidate genes potentially involved in fruit initiation were selected. This builds a solid ground towards the characterisation of genes and QTLs controlling yield stability and to the design of new breeding strategies to capture these loci in the cultivated tomato varieties. Once the trait confirmed, these selected genotypes will be subjected to genetic, physiological and molecular investigation in order to precisely identify chromosomic regions and loci involved in yield stability upon heat stress. Their yield stability and quality performances under high temperature will be fixed, they will be grown following different management practices depending on their suitability for use as fresh market or processing varieties. New tomato varieties are expected to sustain increased diversity thus allowing higher adaptability to particular environments incl. changing climate. The outcome of TomGEM will be used in multiple ways and will ultimately feed into different user communities including 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.

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