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Report

Teaser, summary, work performed and final results

Periodic Reporting for period 2 - 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)

Teaser

Summary

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. Finally, TomGEM also assesses the effect of high temperature on the nutritional and post-harvest behaviour of tomato fruit.

Work performed

The following results were achieved during the 2nd reporting period of TomGEM:

Outcomes WP1:
-10-30 heat tolerant tomato genotypes identified following field and glasshouse tests in 2017 and 2018 at multiples locations in ES, IT, BG and AR
-Seeds of top heat-tolerant genotypes exchanged between TomGEM partners to enable crossing as well as further physiological and molecular analyses
-Data from 2017 and 2018 experiments uploaded and made available online via the PhenoTomGEM database
Partners: JIC, INPT, RHUL, CSIC, UNINA, UBA, MVCRI, Alma-Seges, ENZA, FCValenciana, Rougline

Outcomes WP2:
-Development of fast screening methods to evaluate heat resistant pollen
-Promising QTLs and molecular markers associated with high temperature identified in different RIL and IL populations, validation underway
-Identification of candidate genes for pollen fertility at high temperatures by comparing mapping and RNA-seq analysis
-A candidate gene identified in tomato chromosome 4 conferring gamete advantage for pollen fertility and fruit set
-TILLNG and CRISPR approaches for functional validation of a candidate gene conferring viable pollen at high temperature
Partners: CSIC, INPT, RHUL, INRA, ENZA, FCValenciana, NTW

Outcomes WP3:
-Identification of pollination independent fruit set mutants under normal and heat stress conditions
-Genome-wide mapping of histone marks and Cytosine methylation associated with fruit setting
-Integration of global transcriptomic profiling and epigenetic markers associated with fruit setting
-Setup of TomExpress a transcriptomic pipeline and web tools for storing, processing, mining transcriptomic data create
-Setup of an interactive phenotyping database gathering the outcome of the screening of all germplasm collection during the TomGEM project
-New and high quality de novo tomato genome assembly and annotation achieved that allowed building a new and updated version of TomExpress
Partners: INPT, JIC, CSIC, UNINA, INRA, MVCRI

Outcomes WP4:
-Mapping by sequencing of 2 mutant loci to pinpoint the causal mutation for pollen heat resistance
-RNA-seq analysis on flower buds of commercial cultivars before and after induction of heat stress. A total of 175 candidates genes were identified.
Partners: INRA, INPT, UNINA, Rougeline

Outcomes WP5:
-Five RILs populations have been developed from different sources of tolerant and susceptible tomato lines, and are being used for mapping purposes
-3 F5 RILs from Taiwan and 1F4 RIL from Italy were evaluated for yield and fruit quality traits under high temperatures
-A catalogue of approximately 300 genes/TFs potentially involved in the heat stress response was defined
-10 candidate genes were located in chromosomal regions carrying QTLs or molecular markers associated to yield-related traits under high temperatures
-17 F1 hybrids deriving from different cross combinations were evaluated under high temperatures, in some cases combined with reduced water regime, and seven combinations were identified as best performing
-Various management practices were tested on determinate and indeterminate genotypes, grown in open field or under tunnel and the use of a biostimulant compound and the whitening of leaves gave the best results in terms of yield-related traits
Partners: UNINA, CSIC, AVRDC, MVCRI, Alma-Seges, FCValenciana, Enza Zaden

Outcomes WP6:
-3 large-scale assessments of post-harvest properties
-Collection/processing of genotypes with natural variation for heat tolerance (30 genotypes under heat). The general trend of reduced quality with heat has been observed but genotypes have been identified that retain quality after being subjected to elevated temperature. The biological mechanisms contributing to adaption to heat have been at least partially elucidated.
-Mapping of a gene conferring tolerance to blossom end rot at high temperatures
-Candidate genes identified based on changes in expression and a knock out strategy using CRISPR/Cas9 technology applied for 6 genes i

Final results

While TomGEM is entering its last phase, 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 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 provides suitable material for 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. The selected genotypes are now being subjected to genetic, physiological and molecular investigation in order to validate their yield stability and the functional significance of the genes and loci underlying this trait. Their yield stability and quality performances under high temperature are being investigated. , the selected genotypes are grown following different management practices depending on their suitability for fresh market or processing varieties. 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 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.