In perennial Arabis alpina, CONSTANS and FLOWERING LOCUS T have common and distinct effects on flowering and inflorescence architecture.

Flowering of perennial Arabis alpina is differentially regulated on primary and axillary shoots. Although contributions of vernalization and ageing pathways have been analysed, those of photoperiodic flowering genes CONSTANS (CO), FLOWERING LOCUS T (FT), and TWIN-SISTER OF FT (TSF) remain unexplored. CRISPR-Cas9 mutations in AaCO and AaFT/TWIN SISTER OF FT-LIKE (TSFL) were recovered. Aaco and Aaft/tsfl mutants in pep1 background were scored for flowering time, inflorescence branching, and floral phenotypes under long (LD) or short days (SD) and after vernalization. RNA-seq data on primary and axillary branches were compared. AaCO activates AaFT/TSFL transcription in leaves, and Aaco and Aaft tsfl mutations delay flowering under LDs. Axillary branches flowered in Aaco mutants but not in Aaft tsfl mutants. Both lacked inflorescence branches and flowers on the primary shoot under LDs. However, Aaft tsfl mutants produced some flowers after vernalization, and Aaco a few in SDs. RNA-seq identified genes responsive to AaFT, TSFL, and AaCO on the primary shoot and in axillary branches. Therefore, AaCO-AaFT promote flowering of A. alpina under LDs, but with distinct roles in axillary branch flowering. Both genes are required for inflorescence branching and flower formation on the primary shoot. The complex role of the CO-FT module in inflorescence architecture may underlie the polycarpic, perennial life history of A. alpina.