Transcriptional and Post-transcriptional Mechanisms Limit Heading Date 1 (Hd1) Function to Adapt Rice to High Latitudes

Abstract

Rice flowering is controlled by changes in the photoperiod that promote the transition to the reproductive phase as days become shorter. Natural genetic variation for flowering time has been largely documented and has been instrumental to define the genetics of the photoperiodic pathway, as well as providing valuable material for artificial selection of varieties better adapted to local environments. We mined genetic variation in a collection of rice varieties highly adapted to European regions and isolated distinct variants of the long day repressor HEADING DATE 1 (Hd1) that perturb its expression or protein function. Specific variants allowed us to define novel features of the photoperiodic flowering pathway. We demonstrate that a histone fold domain scaffold formed by GRAIN YIELD, PLANT HEIGHT AND HEADING DATE 8 (Ghd8) and several NF-YC subunits can accommodate distinct proteins, including Hd1 and PSEUDO RESPONSE REGULATOR 37 (PRR37), and that the resulting OsNF-Y complex containing Hd1 can bind a specific sequence in the promoter of HEADING DATE 3A (Hd3a). Artificial selection has locally favored an Hd1 variant unable to assemble in such heterotrimeric complex. The causal polymorphism was defined as a single conserved lysine in the CCT domain of the Hd1 protein. Our results indicate how genetic variation can be stratified and explored at multiple levels, and how its description can contribute to the molecular understanding of basic developmental processes.

Antagonistic Transcription Factor Complexes Modulate the Floral Transition in Rice

“…This observation suggests the existence of a mechanism that downregulates their expression upon commitment to flowering and that could possibly depend on Ehd1, encoding a common upstream promoter of Hd3a and RFT1 expression (Goretti et al, 2017;Ogiso-Tanaka et al, 2013;Gómez-Ariza et al, 2015). Under our growing conditions, expression of the florigens reached a peak ;12 to 15 d after shifting plants from LD to SD (Galbiati et al, 2016).…”

CONSTANS Imparts DNA Sequence Specificity to the Histone Fold NF-YB/NF-YC Dimer

“…Our data (Figures 5 and 6) suggest that the CCT does contact the same acidic surface patch of the HFD dimer recognized by NF-YA A1. A variant in this basic CCT region of both Heading date 1 (Hd1; the rice CO homolog) and OsPRR37 (another rice CCT protein involved in flowering) also impairs HFD interactions (Goretti et al, 2017), further solidifying the idea that multiple CCTs can form NF-CO complexes.…”

“…Specifically, there is well established evidence that different NF-Y HFD subunits are involved in the regulation of timing of flowering in Arabidopsis (Wenkel et al, 2006;Chen et al, 2007;Cai et al, 2007;Kumimoto et al, 2008Kumimoto et al, , 2010Hackenberg et al, 2012;Hou et al, 2014;Cao et al, 2014), rice (Oryza sativa; Dai et al, 2012;Wei et al, 2010;Yan et al, 2011;Feng et al, 2014;Chen et al, 2014;Kim et al, 2016;Hwang et al, 2016;Goretti et al, 2017), wheat (Triticum aestivum; , and tomato (Solanum lycopersicum; Ben-Naim et al, 2006). Wenkel et al originally observed homology between the CCT domain and the conserved domain of NF-YA, suggesting that CO and NF-YA might both bind DNA with NF-YB/NF-YC HFD dimers (Wenkel et al, 2006).…”

“…A rice Hd1 variant with genetic adaptation to flowering in long-day conditions (Mediterranean cultivar) shows deletion of a lysine in the subunit interaction (A1 helix) portion. This protein is unable to associate with OsNF-YB/NF-YC dimers and to bind a conserved CORE element in the Hd3a (FT) promoter (Goretti et al, 2017).…”

Post‐transcriptional regulation of Ghd7 protein stability by phytochrome and OsGI in photoperiodic control of flowering in rice

“…Rice (Oryza sativa) is a typical SD plant whose flowering is promoted under SD conditions, but delayed under LD conditions (Yano et al, 2000). During rice domestication and genetic breeding, rice has dramatically expanded its cultivating areas through modulation of the flowering regulatory pathways (Goretti et al, 2017;Itoh et al, 2018).…”