Abstract Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Utilizing 16 high-quality genomes that represent the subpopulation structure of Asian rice ( O. sativa ), plus the genomes of two close relatives ( O. rufipogon and O. punctata ), we built a pan-genome inversion index of 1,054 non-redundant inversions that span an average of ∼ 14% of the O. sativa cv. Nipponbare reference genome sequence. Using this index we estimated an inversion rate of 1,100 inversions per million years in Asian rice, which is 37 to 73 times higher than previously estimated for plants. Detailed analyses of these inversions showed evidence of their effects on gene regulation, recombination rate, linkage disequilibrium and agronomic trait performance. Our study uncovers the prevalence and scale of large inversions (≥ 100 kb) across the pan-genome of Asian rice, and hints at their largely unexplored role in functional biology and crop performance.

Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice (Oryza sativa)