Structural genomic variation in African cultivated rice contributed to shorter awns

African cultivated rice ( Oryza glaberrima ) was domesticated from its wild progenitor, Oryza barthii . The transition from long-awn to short-awn or awnless glumes was an important evolutionary event during domestication. A QTL analysis of 331 recombinant inbred lines (RILs) using 194 InDel markers identified five quantitative trait loci (QTL) associated with awn length. Locus qObAwn5 made the highest contribution in regulating awn length and was fine-mapped to a 260-kb genomic interval. RNA-seq and RT-qPCR analyses, combined with CRISPR/Cas9-mediated knockout that disruption of gene G12 caused a significant reduction in awn length indicating that G12 was ObAwn5 . Genomic analysis revealed a large structural variation (SV) between W1411 and IRGC104165 within this region, characterized by an inversion and two large deletions. Population genomic analyses revealed that all the cultivated African accessions exhibit a domestication-like (Dom-like) pattern, whereas non-cultivated accessions consisted of two distinct types: W1050-like and W1411-like. The W1411-like type was exclusively found in the AA genome of African wild rice. This discovery of ObAwn5 newly substantiates the independent origin of African cultivated rice.