Transcriptome sequencing of wild-type and double mutants of florigen using SAM region of rice

Utilizing a temperate japonica rice germplasm koshihikari as the genetic background, we employed CRISPR-Cas9 gene-editing technology to introduce specific deletions in both Hd3a and RFT1, excising 45 bp / 6bp biallelic mutations and 18 bp from the first exon of each gene, respectively and confirmed non-flowering phenotypes around one year in growth chambers for only double mutants among F1 progenies. Through the crossing with the wild-type plants, we obtained F1 heterozygous lines where one of chromosomes harbored both tandemly aligned mutations of Hd3a and RFT1, while the other chromosome remained intact. Subsequent self-pollination of these F1 plants allowed to select seedlings of the double homozygous mutants for both genes. To investigate the different transcriptomic dynamics among the specific stages of floral induction, we designed time-course RNA-seq experiments. We here collected samples across four days (SD0, SD4, SD6, SD9), with six time-points per day (ZT-7, ZT-3, ZT1, ZT5, ZT9, ZT13), to capture a comprehensive transcriptional landscape of floral induction dynamics. At the same time, time-series sampling was also performed on the wild-type under long-day conditions at LD9 (42+9 days grown under the LD conditions) to confirm the floral transition state under the LD conditions