The SELF PRUNING (SP) gene controls the regularity of the vegetative-reproductive switch along the compound shoot of tomato and thus conditions the 'determinate' (sp/sp) and 'indeterminate' (SP_) growth habits of the plant. SP is a developmental regulator which is homologous to CENTRORADIALIS (CEN) from Antirrhinum and TERMINAL FLOWER 1 (TFL1) and FLOWERING LOCUS T (FT) from Arabidopsis. Here we report that SP is a member of a gene family in tomato composed of at least six genes, none of which is represented in the tomato EST collection. Sequence analysis of the SP gene family revealed that its members share homology along their entire coding regions both among themselves and with the six members of the Arabidopsis family. Furthermore, members of the gene family in the two species display a common genomic organization (intron-exon pattern). In tomato, phylogenetically close homologues diverged considerably with respect to their organ expression patterns while SP2I and its closest homologue from Arabidopsis (MFT) exhibited constitutive expression. This research focusing on a plant of sympodial growth habit sets the stage for a functional analysis of this weakly expressed gene family which plays a key role in determining plant architecture.

Allelic variation in the CETS (CENTRORADIALIS, TERMINAL FLOWER 1, SELF PRUNING) gene family controls agronomically important traits in many crops. CETS genes encode phosphatidylethanolamine-binding proteins that have a central role in the timing of flowering as florigenic and anti-florigenic signals. The great expansion of CETS genes in many species suggests that the functions of this family go beyond flowering induction and repression. Here, we characterized the tomato SELF PRUNING 3C (SP3C) gene, and show that besides acting as a flowering repressor it also regulates seed germination and modulates root architecture. We show that loss of SP3C function in CRISPR/Cas9-generated mutant lines increases root length and reduces root side branching relative to the wild type. Higher SP3C expression in transgenic lines promotes the opposite effects in roots, represses seed germination, and also improves tolerance to water stress in seedlings. These discoveries provide new insights into the role of SP paralogs in agronomically relevant traits, and support future exploration of the involvement of CETS genes in abiotic stress responses.