Employing the natural genetic variation to improve nutritional properties and stress tolerance in vegetable crops

Project Information

NatGenCrop

Grant agreement ID: 101087091

DOI

10.3030/101087091

EC signature date 21 October 2022

Start date 1 January 2023

End date 31 December 2027

Funded under

• Widening participation and spreading excellence

Total cost

€ 2 432 500,00

EU contribution

€ 2 432 500,00

Coordinated by

TSENTAR PO RASTITELNA SISTEMNA BIOLOGIYA I BIOTEHNOGIYA
Bulgaria

Periodic Reporting for period 2 - NatGenCrop (Employing the natural genetic variation to improve nutritional properties and stress tolerance in vegetable crops)

Reporting period: 2024-04-01 to 2025-12-31

Summary of the context and overall objectives of the project

Yield and nutritional properties of vegetable crops are affected by unfavourable environmental conditions, such as drought, salinity, extreme temperatures, and pollutants. NatGenCrop aims at improving stress tolerance of major vegetable crops (tomato, pepper, legumes, lettuce) and design new strategies for maintaining higher yields and food quality even during unfavourable weather conditions. One of the major research directions is exploring the wide genetic and phenotypic variations of fleshy (tomato, pepper) and leafy (lettuce) vegetables to improve agronomical traits under abiotic stresses (e.g drought, salinity, and extreme temperatures). A suite of genetics and genomics approaches, such as GWAS in combination with QTL, will be employed to identify genes contributing to high yield and stress tolerance. In another research direction, the fruit metabolic compositions will be characterized in terms of flavour and healthy related compounds to assess the impact of abiotic stress on fruit quality. A wide range of plant phenotypic, and metabolic traits will be evaluated, followed by transcriptomic profiling in two genome-wide association (GWAS) panels and two backcrossed inbred lines (BILs) populations for both tomato and pepper. The identified genes will be subsequently validated by CRISPR-Cas9 editing technologies and field trials. To implement this ambitious work program, a new research department “Crop Quantitative Genetics” will be established in the Center of Plant Systems Biology and Biotechnology (CPSBB) in Plovdiv. The new research department will scale up the applied research on vegetable breeding in CPSBB and the region. Furthermore, the new CPSBB department will link with Bulgarian and international research organizations, companies, and farmer associations in the field of crop science, creating an ecosystem network that is highly attractive to talented researchers and brings the innovations to end users for the benefit of the society.

Overall Objective:

To exploit the vast natural genetic variation in vegetable crops, using quantitative genetics and systems biology approaches, in order to understand plant responses to abiotic stresses and achieve crops with enhanced resilience to stresses as well as improved nutritional properties.


Specific objectives:

• Objective 1: Establishment of a new research department “Crop Quantitative Genetics”. This department will be established within the structure of CPSBB, with the ERA Chairs holder acting as Department Head.
• Objective 2: Excellent research and innovation: Genetic, genomics, and phenotypic characterization of the vast collection of vegetable lines existing in CPSBB; GWAS analysis for identification of genes associated with traits of agronomical and human health significance (e.g. tomato and pepper fruit size, fruit shape, colour, metabolic composition, including antioxidants content, valuable secondary metabolites etc.).This will be done by the scientific staff of the new department, under the supervision of the ERA Chairs holder.
• Objective 3: Educating PhD students in the fields of plant systems biology and biotechnology.

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

At the beginning of the project, a dedicated website was created in order to serve as dissemination platform to the general public, partner organizations, universities, and breeding associations.

A new Department - Crop Quantitative Genetics, with the ERA Chairs holder, Dr. Saleh Alseekh, assigned as its Head, was established at CPSBB during 2023. This included setting up a separate laboratory, office spaces, growth facilities for the plants, and most importantly – recruiting the research team itself, which currently amounts to seven scientists.

Trials in both tomato and pepper, presented by 332 GWAS (152 tomato from 21 countries and 180 pepper from 6 Balkan countries) and 166 (56 tomato and 110 pepper) BIL lines in field and greenhouse conditions were carried out. The studied populations were extensively phenotyped (twice for the GWAS and once for the BIL populations) in order to select for lines that show prominent abiotic (drought in particular) and oxidative stress tolerance. These lines were subsequently linked with genotyping data to identify the putative genes candidates for further functional studies.

The ERA Chairs holder already successfully applied for an additional project to the Bulgarian National Science Fund in a call for fundamental research – “Metabolic diversity of botanical gardens in Bulgaria and Germany”.

Thousands of samples from both leaves and fruits of tomato and pepper were collected for metabolomics and ICP-MS analyses. The metabolomics analyses from the first experiments have already been completed.

GWAS analysis were already performed on both crops, identifying candidate genes related to fruit quality and yield as well as candidate genes associated with primary metabolites. The functional studies on some of the most promising genes in tomato has already started.

The project objectives, expected results and impact were communicated to various stakeholders in a number of various activities, with hundreds of thousands people reached. A dedicated project website has been launched and regularly udpated: https://natgencrop.com/. NatGenCrop team members already participated in several international conferneces to present their results.

Two early-stage researchers have already officially been enrolled in a PhD programme related to the project. One of the PhD students studies the response of the tomato and pepper populations to salt stress, while the other one focuses his efforts on biotic stress tolerance towads the pathogen Botrytis cinerea. Moreover, two other PhD candidates were selected and have joined the team to initiate their individual projects.

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)

The project is expected to identify new genes that regulate important agronomic traits, such as abiotic and biotic stress tolerance, fruit size, shape, and color, and fruit yield.
New cultivars with superior qualities in terms of yield and nutritional properties are expected to be introduced to the market.

Logo of the project in .png format