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Background  Flowering time is an important trait for productivity in legumes, which include many food and fodder plants.  Medicago truncatula  (Medicago) is a model temperate legume used to study flowering time pathways. Like  Arabidopsis thaliana  (Arabidopsis), its flowering is promoted by extended periods of cold (vernalization, V), followed by warm long day (LD) photoperiods. However, Arabidopsis flowering-time genes such as the  FLOWERING LOCUS C  ( FLC )/  MADS AFFECTING FLOWERING  ( MAF ) clade are missing and  CONSTANS-LIKE  ( CO-LIKE ) genes do not appear to have a role in Medicago or  Pisum sativum  (pea). Another photoperiodic regulator, the red/far red photoreceptor PHYTOCHROME A (PHYA), promotes Arabidopsis flowering by stabilizing the CO protein in LD. Interestingly, despite the absence of CO-LIKE function in pea, PsPHYA plays a key role in promoting LD photoperiodic flowering and plant architecture. Medicago has one homolog of  PHYA ,  MtPHYA,  but its function is not known.    Results  Genetic analysis of two  MtPHYA Tnt1  insertion mutant alleles indicates that  MtPHYA  has an important role in promoting Medicago flowering and primary stem elongation in VLD and LD and in perception of far-red wavelengths in seedlings.  MtPHYA  positively regulates the expression of  MtE1-like  ( MtE1L ), a homologue of an important legume-specific flowering time gene,  E1  in soybean and other Medicago LD-regulated flowering-time gene homologues, including the three  FLOWERING LOCUS T-LIKE  ( FT-LIKE)  genes,  MtFTa1, MtFTb1  and  MtFTb2  and the two  FRUITFULL-LIKE  ( FUL-LIKE ) genes  MtFULa  and  MtFULb. MtPHYA  also modulates the expression of the circadian clock genes,  GIGANTEA  ( GI)  and  TIMING OF CAB EXPRESSION 1a (TOC1a) . Genetic analyses indicate that  Mtphya-1 Mte1l  double mutants flowered at the same time as the single mutants. However,  Mtphya-1 Mtfta1  double mutants had a weak additive effect in delaying flowering and in reduction of primary axis lengths beyond what was conferred by either of the single mutants.    Conclusion   MtPHYA  has an important role in LD photoperiodic control of flowering, plant architecture and seedling de-etiolation under far-red wavelengths in Medicago. It promotes the expression of LD-induced flowering time genes and modulates clock-related genes. In addition to  MtFTa1, MtPHYA  likely regulates other targets during LD floral induction in Medicago.

Medicago PHYA promotes flowering, primary stem elongation and expression of flowering time genes in long days