PIF7 is the master regulator of thermomorphogenesis in shade [RNA-seq]

The size and shape of plant organs are highly responsive to the local environmental conditions. The embryonic stem, or hypocotyl, of the plant is one such organ that displays impressive phenotypic plasticity, and its length is affected by both light and temperature. After sensing surrounding vegetation, hypocotyls of shade avoiding species elongate to outcompete neighbouring plants and secure access to sunlight. A similar elongation response occurs when the plants are grown in high ambient temperatures. Previous studies have shown that this response is mediated by a family of transcription factors called PHYTOCHROME-INTERACTING FACTORS (PIFs). However, it is poorly understood how environmental light and temperature interact to affect plants at the morphological and molecular levels. Here, we examine the genetic and molecular basis of the response to low R/FR under warm ambient temperatures. We found that low R/FR combined with warm temperature dominantly regulate by PIF7 and exhibit a synergistic effect on hypocotyl growth, greater than either stimulus alone. While the synergistic response was dependent on PIF7 and the plant hormone auxin, we demonstrate that additional, yet unknown key factor/s must be involved, likely working downstream of the phyB-PIF-auxin module. As shade responses are known to affect crop yield and fruit quality in many species, our findings will improve the predictions of how plants will respond to increased ambient temperatures when grown at high density, a condition in which mutual shading occurs. In addition, we point out key factors in this response that can potentially be modulated to minimize the negative effect on yield. Two biological replicates of wild-type seedlings grown in constant LED white light (~70µE) at 21°C in white light (WL) for three days and moved to 21°C WL supplement with Far-red (21FR; R/FR=0.6), 30°C in white light (30WL), 30°C WL supplement with Far-red (30FR; R/FR=0.6) or left at 21WL. Samples (whole seedlings) were collected after one, three, six, or 24 hours and sequenced to analyze the genes regulated by each condition.