At present, structural variants, and in particular, INVs, remain largely uncharacterized in plants despite their importance for local adaptation in a variety of species, with only a few studies exploring INVs polymorphisms at the population level. Hence, it remains unclear whether adaptive INVs can directly shape the genetic basis for diverse phenotypes in plants, especially in domesticated crops.

 

As one of the most important staple food crops worldwide, rice has been extensively studied with abundant genomic sequencing data for wild and cultivated species and subpopulations performing various ecological and agronomic traits. That makes it an ideal subject for assessing the INV landscape and its potential application in population genetics, e.g., gene mining, in a domesticated species, especially following the publication of high-quality genomic, transcriptomic, and phenotypic datasets for a pan-genome rice population in our previous study.