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, decoding the genetic architecture and diversity of rice. Published online in Nature on April 16, this study offers a powerful resource for breeding and agricultural innovation, while shedding new light on the evolutionary and domestication history of rice. 

Asian cultivated rice (Oryza sativa) is a staple food for billions of people. In the face of climate change and rapid global population growth, boosting the yield of O. sativa, as well as its disease and pest resistance, is a pressing priority. Equally important, however, is unlocking the genetic potential of its wild progenitor, Oryza rufipogon, which has adapted over thousands of years to diverse environments.

In this study, the researchers sequenced 145 rice genomes—including 129 wild accessions and 16 cultivated varieties—selected for their geographic and genetic diversity. Primarily using advanced PacBio high-fidelity (HiFi) sequencing technology and computational methods, they created the highest resolution “pangenome” to date, capturing the full genetic landscape of wild rice and uncovering hidden variations crucial for crop improvement.

Their analysis revealed 3.87 billion base pairs of novel genetic sequences absent from the single acknowledged reference genome (O. sativa ssp. japonica cv. Nipponbare), as well as 69,531 genes collectively spanning the pangenome. Remarkably, nearly 20% of these genes exist only in wild rice, with many linked to traits such as disease resistance and environmental adaptation. These genes represent a “genetic goldmine” for developing modern rice varieties capable of withstanding pests, disease, and climate challenges.

Using these high-quality genome sequences, the researchers also performed haplotype analysis of early key domestication genes in various groups of Asian cultivated rice. Their results confirmed that all domestication loci originated from the japonica ancestor Or-IIIa—providing strong support for the long-debated hypothesis of a single initial domestication event for all Asian rice varieties. 

The researchers also discovered extensive gene flow among cultivated rice groups in South Asia, leading to the classification of a newly identified subpopulation, intro-indica, and development of a comprehensive map of rice evolution and domestication.

In examining the genetic divergence between indica and japonica—the two main subspecies of O. sativa—the researchers identified over 850,000 single-nucleotide polymorphisms and 13,000 presence–absence variations between them. These differences mainly originated from divergence between their ancestor lineages and a larger genetic bottleneck in japonica, creating new opportunities for combining beneficial genes from different rice subspecies.

This near-saturated pangenome dataset, enriched with valuable wild genetic resources, provides a powerful foundation for agricultural research and plant breeding. Scientists can mine beneficial alleles, trace the origin of key genes, and deepen understanding of rice environmental adaptation and phenotypic plasticity. The study offers a roadmap for developing rice varieties that can withstand climate extremes, require fewer resources, and produce higher yields. Nature editors also commended this study for its importance to future food security in Research Briefing.