Plant Genome Synthesis: The Next Frontier of Bioengineering for Future Agriculture

In this scientific note, Prof. Vahdati highlights the emerging field of plant genome synthesis and its implications for the future of crop improvement and horticultural breeding.

Over the past several decades, major advances in genome sequencing, gene editing, and synthetic biology have enabled increasingly precise study and modification of plant genomes. The field is now moving beyond genome editing toward genome synthesis- an emerging approach that could ultimately enable the design and construction of plants with combinations of pre-defined traits.

The authors of the 2025 article in Nature Reviews Bioengineering identify genome synthesis as one of the important emerging frontiers in plant biotechnology. Unlike conventional approaches that generally modify individual genes or relatively small genomic regions, genome synthesis aims to enable the design, construction, and assembly of much larger genomic segments and, potentially, the redesign of entire plant chromosomes. This could open new possibilities for crop improvement and the development of plants with combinations of traits that are difficult to achieve through conventional breeding.

The article emphasizes that plants offer several important advantages over animals for the development of genome synthesis technologies. The capacity of many plant species to regenerate an entire plant from a single cell, relatively fewer ethical constraints, and the remarkable flexibility of plant tissue culture systems make plants particularly suitable biological systems for advancing this technology.

From a horticultural perspective, the significance of genome synthesis could extend far beyond the improvement of individual traits. In the longer term, it may become possible to design fruit-tree genomes that combine resistance or tolerance to multiple stresses- including drought, salinity, heat, pests, and diseases- with improved fruit quality, extended shelf life, and enhanced nutritional value. Such an approach could help overcome some of the inherent limitations of conventional breeding, which often requires many generations of hybridization, selection, and evaluation and therefore may take decades in perennial fruit crops.

The authors, however, emphasize that the realization of this vision remains subject to major scientific and technical challenges. These include the synthesis and assembly of very large plant chromosomes, their successful introduction into cells, appropriate epigenetic reprogramming, maintenance of genome stability, and ensuring normal plant growth and physiological function. Nevertheless, rapid advances in DNA synthesis and assembly, genome editing, synthetic biology, tissue culture, and artificial intelligence are strengthening the prospects of overcoming at least some of these challenges.

For countries such as Iran, which face increasing water scarcity, climate change, and the urgent need to enhance agricultural productivity and resilience, investment in emerging biotechnologies- particularly advanced approaches to plant genome engineering and synthesis- could contribute to the development of a new generation of resilient and sustainable horticultural cultivars. Such technologies, however, should be pursued alongside conventional breeding, conservation of genetic resources, and advanced tissue culture and phenotyping platforms.

It can be argued that, just as genome sequencing fundamentally transformed biological sciences during the late twentieth century, genome synthesis may have the potential to reshape the future of plant breeding and agriculture by moving from the modification of existing genomes toward the rational design of new genomic architectures.

Lan, T., Chen, L.-G., Wang, Y., et al. (2025). Genome synthesis in plants. Nature Reviews Bioengineering, 3, 875–889. https://doi.org/10.1038/s44222-025-00326-1