Widespread inversions shape the genetic and phenotypic diversity in rice.

Genomic structural variations affected widely gene function and morphological traits in plants.Chromosomal inversions(INVs),as an important form of structural variation,can be large and extend to megabases in length[1],and form the genetic basis of local adaptation and ecotypic differentiation in sunflowers[2],Boechera stricta[3],monkeyflowers[4],mimetic butterflies[5]and ruffs[6],sex determination in nine-spined stickleback[7]and cancer and neurodevelopmental disease in human[8].At pre-sent,structural variants,and in particular,INVs,remain largely uncharacterized in plants despite their importance for local adap-tation in a variety of species[1],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.