PHENO.GEN - Approcci avanzati di fenomica e genomica per la valorizzazione dei genotipi tolleranti a stress abiotici di specie erbacee di interesse agrario
The PHENO.GEN project, coordinated by ALSIA (Agenzia Lucana di Sviluppo e di Innovazione in Agricoltura), is an ambitious initiative that aims to combine advanced plant phenotyping technologies and genomic sequencing technologies to develop genetic resources that improve crop tolerance to abiotic stresses such as salinity and water scarcity. The target crops include rice, durum wheat, tomato, and eggplant. The project involves a public-private consortium of six partners: ALSIA, Arca 2010 Società Cooperativa A R.L (ARCA 2010), IGA Technology Services (IGA-Tech), ISI Sementi Spa (ISI), Università degli Studi di Palermo (UNIPA), and Università degli Studi del Piemonte Orientale “Amedeo Avogadro” (UPO).
The project is structured into five work packages (WP), each focusing on specific aspects of research and development of genetic resources.
WP1: Identification of gene mutants involved in the response to abiotic stresses in tomatoes through the TILLING approach
The first work package focuses on identifying gene mutants involved in the response to abiotic stresses in tomatoes. Using the TILLING (Targeting Induced Local Lesions IN Genomes) approach, researchers identify specific mutations in genes of interest. The M3 families, derived from these mutations, are multiplied and studied morphologically in the field to assess their tolerance to abiotic stresses. This process involves the analysis of approximately 200 samples to select the most promising genetic variants for further studies and applications
WP2: Phenotypic and agronomic performance study of tomato and eggplant populations
The second work package focuses on the phenotypic and agronomic performance study of three tomato populations and one RIL (Recombinant Inbred Line) population of eggplant. These populations segregate for traits of tolerance to abiotic stresses and are evaluated under controlled conditions and in the field to determine their ability to withstand salinity and water scarcity. The data collected from around 300 samples are used to identify the most resilient genotypes and to better understand the genetic mechanisms underlying stress tolerance
WP3: Phenotypic characterization of rice germplasm
The third work package focuses on the phenotypic characterization of rice germplasm to improve tolerance to saline and water stresses. Researchers evaluate different rice varieties under stress conditions to identify those that show greater resilience. This work includes the analysis of morphological, physiological, and biochemical traits, as well as the use of advanced imaging technologies to monitor plant growth and development. Approximately 150 rice samples are analyzed to provide valuable information for the selection of rice varieties more tolerant to stresses
WP4: Phenotypic characterization of herbaceous crops using High Throughput (HTP) technologies
The fourth work package uses High Throughput (HTP) technologies for the phenotypic characterization of herbaceous crops, including cereals and vegetables, in response to water and saline stresses. HTP technologies, such as image analysis, allow for the collection of detailed data on a large number of plants quickly and efficiently. This approach enables the identification of genotypes more resilient to climate change and the development of new crop varieties that can thrive in challenging environmental conditions. Around 400 samples are analyzed using HTP technologies
WP5: Advanced genomic approaches for sequencing and transcriptomics of genes
The fifth work package, led by IGATech, focuses on applying advanced genomic approaches for sequencing and transcriptomics of genes in tomatoes, rice, and durum wheat. Using next-generation sequencing (NGS) technologies, researchers analyze the genome and transcriptome of these crops to identify genes involved in tolerance to abiotic stresses. These genomic data provide a solid foundation for developing molecular markers and marker-assisted selection, facilitating the genetic improvement of crops.
Activities will include:
- Whole genome sequencing of 1600 tomato TILLING lines
- Whole genome sequencing of 150 tomato recombinant inbred lines (RILs)
- Whole genome skim sequencing of 288 rice introgression lines (ILs)
- Whole genome sequencing of 190 wild rice varieties (Oryza rufipogon)
- Transcriptomics experiment on rice drought stress
- Microbiome analysis
- Transcriptomics experiment on durum wheat drought stress
- Whole genome sequencing of 48 durum wheat varieties.
In summary, the PHENO.GEN project aims to develop new genetic resources and tools to improve crop resilience to climate change, contributing to sustainability and food security. By combining advanced phenotyping and genomic sequencing technologies, the project provides an in-depth understanding of the genetic mechanisms underlying abiotic stress tolerance and promotes innovation in the agricultural sector.
Involved Partners
The project involves a network of high-level academic and industrial partners:
- ALSIA (Agenzia Lucana di Sviluppo e di Innovazione in Agricoltura): https://www.alsia.it/
- ISI Sementi SPA: isisementi.com
- Arca 2010 Società Cooperativa A R.L (ARCA 2010)
- Università degli Studi di Palermo (UNIPA) : https://www.unipa.it/
- Università degli Studi del Piemonte Orientale “Amedeo Avogadro” (UPO): https://www.uniupo.it
- IGA Technology Services srl: igatechnology.com
Expected Results
The PHENO.GEN project aims to achieve several key results that will significantly advance our understanding and capabilities in plant phenotyping and genomic sequencing. Here are the expected results for each work package:
WP1:
- Identification of gene mutants involved in the response to abiotic stresses in tomatoes through the TILLING approach
- Identification of specific gene mutations that confer tolerance to abiotic stresses in tomatoes.
- Development of a collection of M3 families with enhanced tolerance to salinity and water scarcity.
- Detailed morphological and genetic characterization of these families to identify the most promising variants for further research and breeding programs.
WP2:
- Phenotypic and agronomic performance study of tomato and eggplant populations
- Comprehensive phenotypic and agronomic data on three tomato populations and one RIL population of eggplant.
- Identification of genotypes with superior tolerance to abiotic stresses.
- Insights into the genetic mechanisms underlying stress tolerance, which will inform future breeding efforts.
WP3:
- Phenotypic characterization of rice germplasm
- Identification of rice varieties with enhanced tolerance to saline and water stresses.
- Detailed phenotypic, physiological, and biochemical profiles of these varieties.
- Development of a robust set of phenotypic markers that can be used in breeding programs to select for stress-tolerant rice varieties.
WP4:
- Phenotypic characterization of herbaceous crops using High Throughput (HTP) technologies
- High-throughput phenotypic data on a large number of cereal and vegetable samples.
- Identification of genotypes that are more resilient to climate change.
- Development of new crop varieties that can thrive in challenging environmental conditions.
WP5:
- Advanced genomic approaches for sequencing and transcriptomics of genes
- Comprehensive genomic and transcriptomic data on tomatoes, rice, and durum wheat.
- Identification of key genes involved in tolerance to abiotic stresses.
- Development of molecular markers and marker-assisted selection tools to facilitate the genetic improvement of these crops.
Overall, the PHENO.GEN project aims to develop new genetic resources and tools that will improve crop resilience to climate change, contributing to sustainability and food security. By combining advanced phenotyping and genomic sequencing technologies, the project will provide an in-depth understanding of the genetic mechanisms underlying abiotic stress tolerance and promote innovation in the agricultural sector.