Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice (Oryza sativa), plus the genomes of two wild relatives (O. rufipogon and O. punctata), to build a pan-genome inversion index of 1769 non-redundant inversions that span an average of ~29% of the O. sativa cv.

Nipponbare reference genome sequence. Using this index, we estimate an inversion rate of ~700 inversions per million years in Asian rice, which is 16 to 50 times higher than previously estimated for plants. Detailed analyses of these inversions show evidence of their effects on gene expression, recombination rate, and linkage disequilibrium. Our study uncovers the prevalence and scale of large inversions (≥100 bp) across the pan-genome of Asian rice and hints at their largely unexplored role in functional biology and crop performance.

In rice and the genus Oryza, inversion studies have been limited to small and mid-size inversions (10 bp~500 Kb) as a consequence of the reliance on short-read data for their detection or larger inversions (100 bp~5.5 Mb) via single or a limited number of pairwise genome scans. For example, Wang et al. performed a genome scan of inversions in the O. sativa cv. Nipponbare genome (i.e., IRGSP RefSeq) using short-read resequencing data from 453 high-coverage genomes (>20×) from the 3K Rice Genome Project (3K-RGP), and detected 152 ± 62 inversions per genome with a size range of 127.1 ± 19.4 Kb.