Ambient temperature influenced co-expression network of major developmental, circadian, and photoreceptor genes in bread wheat

The developmental process of bread wheat comprises of two major phases: the generative development of the apices from double ridge to terminal spikelet formation, followed by the intensive stem elongation. The two phases differ significantly in terms of the most influential environmental stimuli; ambient temperature above the vernalization threshold exert a more pronounced influence on the molecular-genetic regulation of intensive stem elongation. We assume that dynamic interactions among circadian rhythms, photoreceptors, and key developmental genes play a critical role in shaping the genotypic responses. For this purpose, we chose three, well characterised winter bread wheat varieties with different genetic backgrounds and developmental patterns, in which we studied the daily expression of main developmental (VRN1, VRN2, VRN3, PPD1), circadian (CCA1, PRR95, TOC1, LUX, ELF3, GI, CO1) and photoreceptor (PHYA, PHYB, PHYC, CRY1, CRY2) genes using generic primers and determined their possible relationship under three environments (18 °C vernalized/unvernalized and 25 °C vernalized in the phytotron). The correlation-based network analyses underlined the strong probability of several gene interactions. The positive relationship between VRN1 and VRN3 existed in all treatments confirming that the close relationship between these two genes is essential for the flowering regulation. The vernalized VRN2 showed an explicit diurnal activity in late heading cultivars, which became most expressive at 18 °C. In vernalized plants at 18 °C, PPD1 expression was significantly increased in all three cultivars, becoming more pronounced in late heading cultivars. We found a significant negative association between CCA1 and TOC1, in addition a significant negative association between CCA1 and LUX and a significant positive correlation between TOC1 and LUX was observed, irrespective to the environment. The close temperature-independent relationship between these major circadian genes may also illustrate their fundamental role in the floral regulatory system. Another strong positive correlation was observed between GI vs LUX and PHYC vs ELF3, independently of the environment. Our results, obtained by studying gene expression patterns within the complexity of whole-genome backgrounds, provide complementary information to the knowledge derived from studies using mutant and/or near-isogenic lines. They demonstrate the environmentally driven genetic plasticity present in varieties in response to diverse environmental cues, which may represent an important factor in ecological adaptation and a key element in improving resilience to climate change.