title: PIFs as a novel target in soybean to modulate the shade avoidance syndrome
Creators: name: Van De Weyer, Rist
Publisher: name: The University of Edinburgh
Year: 2024
Subjects: subject: soybean
subject: shade avoidance syndrome
subject: dense cropping
subject: soil water loss
subject: red-light photoreceptors (phytochromes)
subject: Phytochrome Interacting Factors (PIFs)
subject: Arabidopsis
subject: PIF8 overexpression
subject: phyA-induced High Irradiance Response (HIR)

description: Soybean is one of the most widely grown and distributed crops worldwide. Until now, most research on Soybean has focused on cultivars from the USA, South America, and China which consistently underperform in new developing regions with a high demand for protein- and oil-rich Soybeans, such as West and Southeast Africa. A reoccurring problem in these regions are the high temperatures in combination with agricultural practices, such as dense cropping to reduce soil water loss, triggering the shade avoidance response in Soybean plants, causing an increase in lodging and reduced carbon allocation to yield. Current research in the Halliday lab has shown that downstream components of the red-light photoreceptors (phytochromes) called Phytochrome Interacting Factors (PIFs) are not only important signal transducers in light signalling, acting as strong modulators of growth, but also act as central hubs regulating a variety of responses to heat and drought. In this project, we will study these PIFs as potential targets in Soybean to improve plant architecture under high temperature and cropping density conditions. Internal data has shown that PIF7 is a major regulator of these shade avoidance response in the model plant Arabidopsis. We used in silico phylogenetic analysis to characterise the PIF family in Soybean and to identify any potential orthologues of PIF7. In the process, we identified another, hitherto understudied, potential candidate for gene manipulation called PIF8, which has a high sequence similarity and identity to PIF7 and is more prevalent amongst crop species, unlike the more well studied PIF7. This study aimed to characterise these PIFs using CRISPR/Cas9. We generated PIF8 knockouts in Arabidopsis and a PIF7 and double PIF8 knockout in African Soybean varieties. Our studies revealed that shade responsiveness is highly cultivar- dependent, with deep shade conditions triggering substantial changes in plant morphology, indicating a different shade response in non-rosette crops compared to Arabidopsis. We further constructed a library of level 0 parts in Mobius to facilitate the rapid assembly of complex L1 and L2 vectors for plant transformation. We then created multiple transgenic lines of Arabidopsis expressing both PIF7 and PIF8 with either a sfGFP or nanoluc-tag under native Arabidopsis PIF7 and PIF8 promoters. Both Soybean PIF7 and PIF8 successfully restored the pif7-1 phenotype in Arabidopsis, suggesting divergent evolutionary functions of these proteins in different plants. The nanoluc tag allowed us to map PIF7 and PIF8 ‘live’ expression and protein dynamics for the first time under diurnal conditions. Lastly, our investigation revealed a pronounced effect of PIF8 under shade in diurnal conditions, which was more potent in short-day (SD) than long-day (LD) conditions. PIF8 overexpression suppressed the phyA-induced High Irradiance Response (HIR). Surprisingly, PIF7 also inhibited phyA-induced HIR under deep shade conditions, revealing a novel function. We also observed that an unknown factor regulated by PIF7 and PIF8 is crucial for End-of-day Far-Red (EodFR)-induced hypocotyl elongation. Further research is needed to decipher how PIF7 and PIF8 are regulated by blue and UV light under shaded conditions. In conclusion, our study offers valuable insights into the role of PIF7 and PIF8 in modulating SAS in Soybean. The knowledge generated here could be leveraged to engineer improved crop architecture for dense planting conditions, enhance biotic and abiotic stress resistance, make crops more resilient to climate change, and ultimately bolster food security in Africa.