A study led by Prof. HAN Bin's team at the Center for Excellence in Molecular Plant Sciences of the Chinese Academy of Sciences has constructed an unprecedented pangenome map of wild and cultivated rice, and decoded the genetic architecture and diversity of rice. This study, published online in Nature on April 16, provides a powerful resource for breeding and agricultural innovation, and offers new insights into the evolutionary and domestication history of rice.
Facing both climate change and a rapidly growing global human population, Asian cultivated rice (Oryza sativa), a staple food for billions worldwide, urgently needs to sustainably boost its resistance to pests and diseases and yield. While domesticated rice has been extensively studied, its wild progenitor, Oryza rufipogon-shaped by thousands of years adaptation to diverse environments-has largely remained underexplored, leaving critical gaps in understanding the full genetic potential of wild rice.
In this study, researchers obtained 145 geographically and genetically diverse rice genomes, including 129 wild accessions and 16 cultivated varieties. Mainly using advanced PacBio high-fidelity (HiFi) sequencing technology and computational methods, they created the highest resolution "pangenome" to date that captures the full genetic landscape of wild rice and reveals hidden variations critical for crop improvement.
Researchers uncovered 3.87 billion base pairs of novel genetic sequences absent from the single acknowledged reference genome (O. sativa ssp. japonica cv. Nipponbare), along with 69,531 genes collectively spanning the pangenome. Nearly 20% of these genes exist only in wild rice, many linked to disease resistance and environmental adaptation. These genes represent a 'genetic goldmine' that could help develop modern rice varieties capable of withstanding pests, diseases, and the challenges of a changing climate.
Using high-quality genome sequences, researchers conducted haplotype analysis of early key domestication genes in various groups of Asian cultivated rice, and proved that all domestication loci are derived from the japonica ancestor Or-IIIa. This finding strongly supports the hypothesis that all Asian cultivated rice groups underwent a single initial domestication event, providing crucial evidence for a long-standing scientific debate. In addition, researchers identified extensive gene flow among cultivated rice groups in South Asia, leading to the classification of a newly identified subpopulation, intro-indica, and the successful mapping a comprehensive roadmap of rice evolution and domestication.
Moreover, researchers explored the genetic divergence between indica and japonica, the two main subspecies. They identified over 850,000 single-nucleotide polymorphisms and 13,000 presence-absence variations between them. The findings suggested that these variations mainly originated from the divergence of their respective ancestors and the existence of a larger genetic bottleneck in japonica, which opens up new opportunities to combine beneficial genes from different rice subspecies.
The near-saturated pangenome dataset, integrating valuable wild genetic resources, provides a powerful foundation for agricultural researchers and plant breeders. Scientists can mine favorable alleles, trace the origin of key genes and enhance understanding of rice environmental adaptation and phenotypic plasticity. The study offers a roadmap to develop rice varieties that can withstand climate extremes, require fewer resources, and produce higher yields. Nature's editors commended this study for its importance to future food security in Research Briefing.
