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.

The inflorescence and spikelet structural units of rice significantly impact grain development. Among the grasses, the sterile lemma represents a unique spikelet organ exclusive to rice. As most studies on sterile lemma genes primarily focus on Asian cultivated rice (Oryza sativa L.), genes influencing the sterile lemma phenotype in African rice remain unreported. This study identified lsl3, a gene located on the short arm of chromosome 7 that controls the sterile lemma length in African rice. The key mutation of lsl3, leading to long sterile lemmas in African rice, was discovered and differed from that in Asian rice. The investigation of lsl3 not only provides a reference for the molecular evolution of cultivated rice in Africa but also offers new evidence supporting the parallel domestication of rice and the independent origin of Oryza glaberrima.

Panicle architecture is an agronomic determinant of crop yield and a target for cereal crop improvement. To investigate its molecular mechanisms in rice, we performed map-based cloning and characterization of OPEN PANICLE 1 (OP1), a gain-of-function allele of LIGULELESS 1 (LG1), controlling the spread-panicle phenotype. This allele results from a 48-bp deletion in the LG1 upstream region and promotes pulvinus development at the base of the primary branch. Increased OP1 expression and altered panicle phenotype in chimeric transgenic plants and upstream-region knockout mutants indicated that the deletion regulates spread-panicle architecture in the mutant spread panicle 1 (sp1). Knocking out BRASSINOSTEROID UPREGULATED1 (BU1) gene in the background of OP1 complementary plants resulted in compact panicles, suggesting OP1 may regulate inflorescence architecture via the brassinosteroid signaling pathway. We regard that manipulating the upstream regulatory region of OP1 or genes involved in BR signal pathway could be an efficient way to improve rice inflorescence architecture.