A near-complete genomic framework of wild Oryza species now provides insights into the evolution of the genus and offers new avenues for crop improvement and conservation efforts [1] .
The Oryza genus, containing related species of plants in the grass family, provides the world with one of the most important domesticated grain crops: rice. Oryza includes the Asian and African cultivated rice species (O. sativa and O. glaberrima), as well as 26 species of wild rice, which offer a rich, untapped source of genetic diversity for crop improvement.
This genomic resource, generated by a team of scientists including researchers from KAUST and Wageningen University in the Netherlands, is now publicly available and can be used for future neodomestication efforts: the generation of new rice varieties from wild relatives that possess natural resistance to abiotic and biotic stress, and are adapted to local climates.
"With climate change threatening global rice production, this was a critical moment to generate high-quality, chromosome-level reference genomes of the wild Oryza species. This resource is crucial to investigate evolutionary patterns in the genus and detect adaptive traits useful for crop improvement," says Alice Fornasiero, a postdoctoral researcher who worked under the supervision of Rod Wing at KAUST.
To boost an existing Oryza genome reference dataset previously developed by Wing, Fornasiero and co-workers generated new chromosome-level genome assemblies of eleven wild Oryza species. These included two diploids (genomes with two copies of each chromosome) and nine tetraploids (with four chromosome sets organized into two subgenomes). This resource enabled the researchers to explore the genome size and composition of the wild Oryza species in the context of 15 million years of evolution in the genus.
"We merged the information from all the sequenced genomes to build a pangenome (a representation of the entire genus) and found that it consists of a stable 'core' portion shared by all the species and a 'dispensable' portion, malleable in size and composition across the species" says Fornasiero. "Our analysis added new evidence of the phylogenetic relationships between the species and refined the classification for one of them."
The team also analyzed gene activity in O. coarctata, a species adapted to the saline conditions of coastal regions from Pakistan to Myanmar. They found that O. coarctata showed an unusual balance between its two subgenomes, with genes from one subgenome being expressed at higher levels over the other in a mosaic form. Taken together, the two subgenomes contribute equally to gene activity. This equilibrium may help explain the resistance of O. coarctata to salty environments, although additional work is needed to understand this mechanism, notes Fornasiero.
"Our extensive genomic resource will help scientists improve cultivated rice to meet global food security needs and tackle future agricultural and environmental challenges," says Wing. "Genome editing techniques, such as CRISPR/Cas9, allow the introduction of precise modifications in the sequences of key genes for domestication, such as the genes controlling seed dispersal, grain size, flowering time, and plant height. This approach allows us to generate novel crops exhibiting domesticated traits that preserve original adaptations to local climates."
The team will next focus on characterizing the genetic variation in wild Oryza populations to identify adaptive and resilience traits in specific local climates. In particular, they will examine wild rice species endemic to the American continent before extending this approach to other wild species of the genus.
Reference
- Fornasiero, A., Feng, T., Al-Bader, N., Alsantely, A., Mussurova, S., Hoang, N.V., Misra, G., Zhou, Y., Fabbian, L., Mohammed, N., Rivera Serna, L., Thimma, M., Llaca, V., Parakkal, P., Kudrna, D., Copetti, D., Rajasekar, S., Lee, S., Talag, J., Sobel-Sorenson, C., Carpentier, M-C., Panaud, O., McNally, K.L., Zhang, J., Zuccolo, A., Schranz, M.E., & Wing, R.A. Oryza genome evolution through a tetraploid lens. Nature Genetics 57, 1287–1297 (2025).| article
