GSE116423
Chromosomal deletions drove parallel domestication of plant architecture in Asian and African rice
Improving the yield by modifying plant architecture is key to progressive crop domestication. Here, we show that a 110-kb deletion on the short arm of chromosome 7 promotes the critical transition from semi-prostrate growth and low yield in wild rice (Oryza rufipogon), to erect growth and high yield in Asian cultivated rice (O. sativa). The microdeletion harbors a tandem repeat of seven putative Cys2-His2 zinc-finger genes. Three of these genes regulate the plant architecture in O. rufipogon and are closely linked to the previously identified PROSTRATE GROWTH 1 (PROG1) gene. Therefore, we refer to this locus as RICE PLANT ARCHITECTURE DOMESTICATION (RPAD). Furthermore, a similar but independent 113-kb deletion was detected at the RPAD locus in African cultivated rice. These results indicate that the deletions, coupled with the loss of a tandem repeat of zinc-finger genes, drove the parallel domestication of plant architecture in Asian and African rice. Overall design: Total RNA was isolated from tiller bases of the CP-PROG1, CP-ZnF5, CP-ZnF7, CP-ZnF8 transgenic lines and the control plants at 50 days after sowing, in triplicate, using Illumina system Hiseq2500.For transcriptome analysis, total RNAs of ten tissues from DXCWR,eight tissues from IRGC104165 and eight tissues from W1411 were isolated respectively, using TRIzol (Invitrogen, USA) according to the instructions.