Turning genome duplication into a plant breeding tool
Plants have an extraordinary ability to duplicate their entire genome, a process known as polyploidisation. This phenomenon has played a central role in plant evolution: all seed plants have experienced at least one round of whole-genome duplication. Polyploid plants often show enhanced traits compared to their diploid ancestors, including improved stress resilience and flexible reproductive strategies. These advantages have long attracted the attention of plant breeders, yet the underlying genetic and epigenetic mechanisms remain poorly understood.
Turning an evolutionary force into breeding strategy
The EU-funded POLYPLOID(opens in new window) project set out to study polyploidisation across a wide range of crop and model species. The goal was to translate evolutionary insights into practical breeding tools. In this context, the team combined interdisciplinary expertise in genomics, epigenomics, transcriptomics and phenotyping across different plants. “We followed a multi-species approach which enabled direct comparisons that would be impossible by a single lab,” states project coordinator Emidio Albertini.
How genome duplication reshapes plants
POLYPLOID investigated the impact of genome duplication on plant genetics and phenotype. Across various model species, the team observed structural genome changes, non-random gene loss or retention(opens in new window) and targeted epigenetic modifications shortly after polyploidisation. Transcriptome and methylation analyses(opens in new window) showed coordinated changes in gene expression affecting stress tolerance, cell-cycle regulation, reproductive development and cell wall architecture. In several species, the number of differentially expressed genes increased with ploidy level, highlighting genome duplication as a powerful driver of regulatory innovation. “We identified a set of ‘ploidy-sensitive’ genes whose expression consistently changes with genome doubling,” highlights Albertini. “These genes form a molecular signature of polyploidy.” The team also investigated how genome duplication contributes to apomixis(opens in new window), a form of asexual reproduction through seeds which allows plants to produce offspring without fertilisation. This reproductive strategy is frequently associated with polyploid genomes and is of great interest to breeders because it allows the introduction of traits across generations. By identifying candidate pathways and molecular markers linked to apomixis, the project laid the groundwork for breeding approaches that combine polyploidy with clonal seed production.
Overcoming the triploid block
A major barrier to exploiting polyploidy in breeding is the triploid block(opens in new window), a post-zygotic mechanism that prevents viable seed formation after crosses between plants of different ploidy levels. POLYPLOID addressed this challenge by analysing crosses between diploid and tetraploid individuals. Researchers focused on abnormal endosperm development, a common cause of seed abortion. Although the project has not yet fully overcome the triploid block, it has identified key pathways involved, including sugar and lipid metabolism and epigenetic gene silencing. Candidate genes emerging from Arabidopsis studies(opens in new window) are now being explored as potential levers to stabilise seed development.
Towards sustainable, resilient agriculture
The most significant achievement of POLYPLOID is the creation of an unprecedented, multi-layer dataset linking genome structure, gene regulation, reproduction and field performance. These insights will pave the way for polyploid-based breeding, offering crops with enhanced stress resilience, improved quality and reduced input requirements. “Polyploid-based breeding is likely to influence future European food systems by producing crops with customised quality traits,” concludes Albertini. As climate change intensifies pressures on European agriculture, POLYPLOID provides a blueprint for using genome duplication as a deliberate breeding strategy rather than a chance event.
