In dense canopy, a reduction in red to far-red (R/FR) light ratio triggers shade avoidance responses (SARs) in Arabidopsis thaliana, a shade avoiding plant. Two red/far-red (R/FR) light photoreceptors, PHYB and PHYA, were reported to be key negative regulators of the SARs. PHYB represses the SARs under normal light conditions; however, the role of PHYA in the SARs remains elusive. We set up two shade conditions: Shade and strong Shade (s-Shade) with different R/FR ratios (0.7 and 0.1), which allowed us to observe phenotypes dominated by PHYB-and PHYA-mediated pathway, respectively. By comparing the hypocotyl growth under these two conditions with time, we found PHYA was predominantly activated in the s-Shade after prolonged shade treatment. We further showed that under s-Shade, PHYA inhibits hypocotyl elongation partially through repressing the brassinosteroid (BR) pathway. COP1 and PIF4,5 act downstream of PHYA. After prolonged shade treatment, the nuclear localization of COP1 was reduced, while the PIF4 protein level was much lower in the s-Shade than that in Shade. Both changes occurred in a PHYA-dependent manner. We propose that under deep canopy, the R/FR ratio is extremely low, which promotes the nuclear accumulation of PHYA. Activated PHYA reduces COP1 nuclear speckle, which may lead to changes of downstream targets, such as PIF4,5 and HY5. Together, these proteins regulate the BR pathway through modulating BES1/BZR1 and the expression of BR biosynthesis and BR target genes.

Application of sequence-related amplified polymorphism (SRAP) markers to unravel variations and relationships with biological and morphological traits has been reported in a variety of plant species, and their potential for breeding has also been highlighted. (1) Assess the diversity level of a Cunninghamia lanceolata (Chinese fir) genetic panel based on phenotypic traits and SRAP markers, (2) identify SRAP loci linked to juvenile wood basic density (JWBD) and growth traits, and (3) address the overlap of the trait-associated SRAP markers during the juvenile and mature stages of this species. A total of 227 Chinese fir genotypes were subjected to phenotype, SRAP genotyping, and marker-trait association analyses. A total of 564 unambiguous SRAP bands and 558 polymorphic loci were identified from the genotypes. The overall percentage of polymorphic bands, polymorphism information content, Nei's gene diversity, and Shannon's Information Index were 98.9%, 0.2576, 0.3196 and 0.4838, respectively. An analysis of molecular variance further demonstrated that the genotypes varied significantly at SRAP polymorphisms (p < 0.01). A wide genetic distance span from 0.0531 to 0.9097 was also observed; most (94.9%) fell within the range of 0.3000-0.6999. An association analysis based on general linear model (GLM) and mixed linear model (MLM) unraveled 21, 26, 25, and 19 marker-trait associations for JWBD, height (H), diameter at breast height (DBH, 1.3 m) and stem volume (V), respectively. These marker-trait associations corresponded to 64 different SRAP markers; 46 of these were linked to only one trait, while the other 18 markers appeared to be associated with more than one trait but limited to growth traits. Overall, the SRAP markers represented R 2 (percentage of the phenotypic variation explained by marker) values of 1.7-9.2% for the GLM and 1.7-5.6% for the MLM. Strikingly, the significant trait-associated marker list seemed to be rather different from that of the previous study performed on mature traits (WBD, H, DBH and V), except for overlap of two markers. This study demonstrated an association of SRAP markers with JWBD and growth traits in Chinese fir. The results further our understanding of the genetic basis of the Chinese fir WBD and growth traits at the juvenile stage.