Asian rice, domesticated around 10,000 years ago, is a dietary staple for more than one third of the global population. Yet, intensive breeding for improved yield has reduced its genetic diversity – making modern varieties increasingly vulnerable to stressors like heat, drought, and salinity. In contrast, wild rice relatives have adapted to a wide range of environmental conditions providing untapped genetic material for rice crop improvement.
A landmark study, published in Nature Genetics on April 28, 2025, traced the evolutionary history of wild rice species, classified in the genus Oryza, defining their phylogenetic relationships and deciphering how their genomes have been shaped by 15 million years of evolutionary history. The research was led by Prof. Rod Wing, Director of the Arizona Genomics Institute (AGI), and his postdoctoral research associate, Alice Fornasiero, of the King Abdullah University of Science and Technology (KAUST) in Saudi Arabia, in collaboration with Wageningen University & Research in the Netherlands.
Thanks to the sequencing of both genomic DNA and RNA of 11 wild rice species (i.e. two diploids and nine tetraploids) using the PacBio Sequel II and IIe instruments, the team could successfully generate ultra-high quality genome assemblies and use accurate full-length transcripts for gene annotation. The analysis of this valuable and publicly available genomic resource allowed the construction of the Oryza pangenome – i.e. the genomic representation of the entire genus – and the description of a “core” portion remarkably stable and a “dispensable” portion mainly composed of transposable elements. Due to their ability to move and reshuffle the genome, these elements has played a crucial role in shaping the genetic diversity in these species.
The analysis of gene expression in Oryza coarctata, a species adapted to saline conditions of coastal regions, showed an unusual balance between its two subgenomes, with both contributing equally to gene activity. This equilibrium may help explain the resistance of O. coarctata to salty environments.
These findings build a genetic foundation that could help scientists breed more resilient rice varieties, or even domesticate wild species through approaches like neodomestication to generate climate-ready crops for a more sustainable agriculture.
Use of Sage technology at the Arizona Genomics Institute’s Service Center:
For the wild rice genome project described above, the genomes were sequenced in both CLR and CCS/HiFi modes. The WGS libraries were size selected with the BluePippin, using 0.75% agarose cassettes with marker U1 (for CLR libraries) or marker S1 (for CCS/HiFi libraries ).
For current projects at AGI, the team has switched from the BluePippin to the PippinHT for its size selection needs. AGI has been an early access test site for the PippinHT Range+T program mode (for improving accuracy of HMW size selection) and the soon-to-be-released PippinHT 0.75% agarose cassette internal standards (which increase sample capacity).