Periodic Reporting for period 2 - POLYPLOID (THE POLYPLOIDY PARADIGM AND ITS ROLE IN PLANT BREEDING)
Periodo di rendicontazione: 2023-10-01 al 2025-09-30
Plants can undergo spontaneous chromosome number duplication, or polyploidization, which is a major evolutionary trigger. While all seed plants have experienced at least one round of whole genome duplication in their history, it tends to be an isolated event within diploids. Plant breeders are aware of the potential of polyploidization for crop improvement. The present project focused on filling the knowledge gaps about non-model species regarding chromosomal changes, gene loss, gene expression, methylation and physiological changes, and ecological features. The project will encourage synergy between European and international expertise, aiming to facilitate plant breeding. The POLYPLOID Consortium involves nine partner institutions, six from 4 MS (Italy, Ireland, Spain, Netherlands) and three from TD (New Zealand, Argentina, and USA). It will have a sizable impact above and beyond those involved in the exchanges at different levels related to career prospects and the establishment of lasting research collaboration. This proposal aimed at strengthening and/or initiating partnerships between these groups, all focused on either model plants or crops, therefore facilitating interactions between fundamental and applied aspects of plant research. Therefore, POLYPLOID represents an attractive staff exchange platform for sharing knowledge and technical expertise and familiarizing with multicultural working environments. Enhancing the career prospects embraces the technical aspects of the research conducted and the capacity to design creative experiments, manage an interdisciplinary project in a multicultural environment, and acquire communication tools. This consolidates previous collaborations and generates opportunities for new ones within the Consortium. The action has succeeded in meeting the objectives posed for the second term of the project. Completed secondments allowed the follow-up of established research and the achievement of the common goals of participants. Some articles derived from the joint work were published or submitted to scientific journals.
From the start of the POLYPLOID project to its conclusion, significant progress has been made in understanding the mechanisms and practical applications of polyploidy in plant breeding. The consortium successfully carried out the research plan, promoting cross-sector collaboration, joint publications, and secondments.
The consortium produced high-quality multi-omics resources across various plant systems, including model and crop species such as Paspalum notatum, Eragrostis curvula, Helianthus annuus, Medicago sativa, Solanum species, and Arabidopsis. Using advanced sequencing and phenotyping platforms, the project assembled thirty reference genomes and generated extensive transcriptomic and epigenomic datasets. These datasets supported comparative studies of genome evolution, gene expression, methylation, and transposon mobilization in both natural and synthetic polyploids. Functional analyses identified specific genetic and epigenetic responses to polyploidization, especially pinpointing loci associated with reproductive mode, stress tolerance, and the triploid block, a major barrier in interploidy crosses that is crucial for seed viability. Artificial polyploid lines showing apomictic reproduction and improved agronomic traits (such as better lipid profiles in Paspalum and parthenogenesis in Helianthus) were created and are being registered to aid future breeding efforts.
Several peer-reviewed articles, data resources, and open-access databases have resulted from this work, with outputs actively shared through international conferences, workshops, and dedicated project communication channels. The project’s website, publications, and social media platforms provide ongoing access to genomic, transcriptomic, and marker data, effectively supporting knowledge transfer to the broader plant sciences, seed industry, and biotech stakeholders. Non-academic audiences are engaged through outreach events and collaborations, enhancing the project’s societal and sectoral impact. Artificially derived germplasm from the project is moving forward in registration and testing, with clear potential to improve animal feed quality and crop adaptation in real-world scenarios. The molecular markers and genomic resources already developed are empowering marker-assisted selection and breeding for stress tolerance and reproductive efficiency. By the end of the project, POLYPLOID has filled critical gaps in polyploidy research, providing a comprehensive resource of molecular data, analytical tools, and functional insights. The findings offer new breeding strategies, validated candidate genes, and usable germplasms and markers for industry, academia, and breeders. The collaborative and integrative approach has strengthened interdisciplinary connections and will continue to influence plant biotechnology and agricultural innovation beyond the project’s official conclusion. The final meeting was a moment for discusing the future researches as well as to have the ESR secondees to present the work they carried out during the secondments.
The consortium produced high-quality multi-omics resources across various plant systems, including model and crop species such as Paspalum notatum, Eragrostis curvula, Helianthus annuus, Medicago sativa, Solanum species, and Arabidopsis. Using advanced sequencing and phenotyping platforms, the project assembled thirty reference genomes and generated extensive transcriptomic and epigenomic datasets. These datasets supported comparative studies of genome evolution, gene expression, methylation, and transposon mobilization in both natural and synthetic polyploids. Functional analyses identified specific genetic and epigenetic responses to polyploidization, especially pinpointing loci associated with reproductive mode, stress tolerance, and the triploid block, a major barrier in interploidy crosses that is crucial for seed viability. Artificial polyploid lines showing apomictic reproduction and improved agronomic traits (such as better lipid profiles in Paspalum and parthenogenesis in Helianthus) were created and are being registered to aid future breeding efforts.
Several peer-reviewed articles, data resources, and open-access databases have resulted from this work, with outputs actively shared through international conferences, workshops, and dedicated project communication channels. The project’s website, publications, and social media platforms provide ongoing access to genomic, transcriptomic, and marker data, effectively supporting knowledge transfer to the broader plant sciences, seed industry, and biotech stakeholders. Non-academic audiences are engaged through outreach events and collaborations, enhancing the project’s societal and sectoral impact. Artificially derived germplasm from the project is moving forward in registration and testing, with clear potential to improve animal feed quality and crop adaptation in real-world scenarios. The molecular markers and genomic resources already developed are empowering marker-assisted selection and breeding for stress tolerance and reproductive efficiency. By the end of the project, POLYPLOID has filled critical gaps in polyploidy research, providing a comprehensive resource of molecular data, analytical tools, and functional insights. The findings offer new breeding strategies, validated candidate genes, and usable germplasms and markers for industry, academia, and breeders. The collaborative and integrative approach has strengthened interdisciplinary connections and will continue to influence plant biotechnology and agricultural innovation beyond the project’s official conclusion. The final meeting was a moment for discusing the future researches as well as to have the ESR secondees to present the work they carried out during the secondments.
This project has achieved significant progress in understanding polyploidy at the molecular level, exceeding the current advances in plant evolutionary genetics and breeding. Using multidisciplinary approaches that combine genomics, epigenomics, transcriptomics, and phenomics across various polyploid crops (Paspalum, Eragrostis, Medicago, Solanum) and model species (Arabidopsis, Hieracium, Taraxacum), the consortium has created unique datasets and molecular tools. These offer a comprehensive view of how genomes react to polyploidization. Notably, more than 30 genomic and transcriptomic databases have been developed, aiding in the identification of key genes and molecular pathways involved in traits related to polyploidy, stress tolerance, and reproductive modes like apomixis. The research also reveals structural rearrangements and epigenetic changes that occur during genome doubling.
By correlating phenotypic, genomic, and epigenetic data, the project has uncovered mechanisms behind the triploid block and parent-of-origin effects in seeds, and identified epigenetic markers closely linked to important traits such as stress resistance, forage quality, and lipid makeup. Artificial polyploid lines with enhanced traits are being registered and shared, connecting fundamental findings to real-world impacts in crop development and biotechnology. The combination of remote sensing phenotyping and advanced molecular techniques has created a robust toolkit for breeders and researchers, improving their ability to select better genotypes more effectively.
Expected results by the end of the project include a comprehensive catalog of candidate genes for key traits, new molecular markers and breeding schemes, advanced protocols for genomic and epigenomic analysis, and the transfer of validated resources to breeding programs and industrial partners. Socioeconomic impacts are expected to manifest as improved agricultural productivity, enhanced product quality (e.g. milk and meat nutritional value), stress-resilient crops for climate adaptation, and more sustainable land management. Broader societal implications include empowering the seed and plant biotechnology.
By correlating phenotypic, genomic, and epigenetic data, the project has uncovered mechanisms behind the triploid block and parent-of-origin effects in seeds, and identified epigenetic markers closely linked to important traits such as stress resistance, forage quality, and lipid makeup. Artificial polyploid lines with enhanced traits are being registered and shared, connecting fundamental findings to real-world impacts in crop development and biotechnology. The combination of remote sensing phenotyping and advanced molecular techniques has created a robust toolkit for breeders and researchers, improving their ability to select better genotypes more effectively.
Expected results by the end of the project include a comprehensive catalog of candidate genes for key traits, new molecular markers and breeding schemes, advanced protocols for genomic and epigenomic analysis, and the transfer of validated resources to breeding programs and industrial partners. Socioeconomic impacts are expected to manifest as improved agricultural productivity, enhanced product quality (e.g. milk and meat nutritional value), stress-resilient crops for climate adaptation, and more sustainable land management. Broader societal implications include empowering the seed and plant biotechnology.