Transcriptome profiling reveals differentially expressed genes associated with flowering time in contrasting switchgrass genotypes

Switchgrass (Panicum virgatum L.) has become an important biofuel crop. The experiment was designed to identify differentially expressed genes (DEGs) for flowering time in switchgrass genotypes contrasting in heading and anthesis dates. Phytomers of early- (S041) and late-flowering (B901) parents and early- (7071) and late-flowering (7055) F-2 genotypes were collected on two sampling dates of vegetative stages, and transcriptome profiling was completed to identify DEGs involved in flowering time using RNA sequencing. Across two sampling dates, the comparison between S041 and B901 identified six upregulated (TOC1, FKF1, two PHYA, and two PFT1) and five downregulated flowering DEGs (FT, GASA, COP1, and two CHS) in S041, but one upregulated FT and one downregulated GASA in B901. When comparing two F-2 genotypes, three DEGs (PFT1 and two FT) were upregulated in 7071, and six DEGs (PRR7, PRR5, PHYB, TOC1, and two CKB4) were upregulated and one DEG (COP1) was downregulated in 7055 genotype. The upregulation of PRR5 and FKF1 and downregulation of GASA and COP1 were found in both early-flowering genotypes, whereas FKF1, PRR5, PRR7, and PHYB were upregulated and two GASA were downregulated in both late-flowering genotypes. Across both early-flowering genotypes, seven upregulated and 12 downregulated transcription factors (TFs) from nine families related to flowering were differentially expressed, whereas eight upregulated and 30 downregulated flowering related TFs from 16 families were differentially expressed across both late-flowering genotypes. The identification of key genes involved in the flowering pathways could facilitate the development of desirable flowering phenotypes of switchgrass.