Tissue collection and RNA sequencing

For expression analysis, we collected 15 immature panicles each from at least 10 plants per accession, per stage, collected from 4 to 15 d after floral induction (i.e. transfer to short day conditions) for each biological replicate. For sample collection, leaves surrounding the young panicle were removed by hand and the reproductive tissue was cut with a sharp blade under a Stemi 508 (Zeiss, Germany) stereo microscope to identify developmental stage. The reproductive tissues were immediately frozen in liquid nitrogen, and total RNA including small RNA was extracted using the RNeasy Plant Mini kit with RLT and RWT buffers (Qiagen, Germany). DNase treatments were performed using the RNase-free DNase set (Qiagen, Germany). RNA integrity numbers of the extracted RNA, measured using a 2100 Bioanalyzer (Agilent, USA), were between 8.6 and 10. Stage specificity was validated with quantitative real-time RT-PCR (qPCR) using stage-specific marker genes (Supplementary Table S2); 400 ng of total RNA was used for each sample for RNAseq library preparation with the TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina, USA). After quantification with a 2100 Bioanalyzer, 125-base paired-end reads were generated on a HiSeq 2500 (Illumina) by the GeT platform (Toulouse, France).