A Deletion in the PHYD Gene of the Arabidopsis Wassilewskija Ecotype Defines a Role for Phytochrome D in Red/Far-Red Light Sensing

Abstract

The PHYD gene of the Wassilewskija (Ws) ecotype of Arabidopsis contains a 14-bp deletion (the phyD-1 mutation) beginning at amino acid 29 of the reading frame, resulting in translation termination at a nonsense codon 138 nucleotides downstream of the deletion end point. Immunoblot analyses showed that Ws lacks phyD but contains normal levels of phyA, phyB, and phyC. By backcrossing into the Ws and Landsberg erecta genetic backgrounds, we constructed sibling pairs of PHYD+ and phyD-1 lines and of phyB- PHYD+ and phyB- phyD- lines. Hypocotyl lengths after growth under white or red light increased sequentially in strains that were B+D+, B+D-, B-D+, and B-D-. In the Ws genetic background, an increase in petiole length, a reduction in cotyledon area and in anthocyanin accumulation in seedling stems, a diminished effect of an end-of-day pulse of far-red light on hypocotyl elongation, and a decrease in the number of rosette leaves at the onset of flowering were also seen sequentially in these lines. Thus, phyD, which is approximately 80% identical in amino acid sequence to phyB, acts in conjunction with phyB in regulating many shade avoidance responses. The existence of the apparently naturally occurring phyD-1 mutation indicates that phyD is not essential in some natural environments.

Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes

“…Perhaps consistent with this is the fact that null mutants of these loci in Arabidopsis were not easily identified in genetic screens and the phenotypes of the monogenic mutants are not readily apparent (Aukerman et al, 1997;Devlin et al, 1998;Franklin et al, 2003;Monte et al, 2003). However, PHYC, D, and E have been retained much longer than the expected half-life of duplicate genes of ;3 to 7 million years (Lynch and Conery, 2000).…”

“…Several plant species have two copies of PHYB (or P), including P. trichocarpa, maize, and members of Pinaceae, Solanaceae, Fabaceae, and Piperaceae. In Arabidopsis, phyB is the principal mediator of R-mediated development and shade avoidance, whereas phyD appears to play a minor role in shade avoidance; phyD-1 is a naturally occurring mutant, suggesting that phyD is dispensable in some environments (Aukerman et al, 1997). However, a recent study showing that the phyD null but not phyAphyB lost the ability to adjust the chlorophyll a/b ratio in response to canopy shading (Boonman et al, 2009) suggests that in shade avoidance, phyD but not phyB controls this response.…”

Combinatorial interaction of light‐responsive elements plays a critical role in determining the response characteristics of light‐regulated promoters in Arabidopsis

“…By analyzing the hypocotyl elongation under continous light conditions, a high-irradiance light response, it has been determined that PhyA is responsible for perceiving far-red light, whereas PhyB plays a primary role in perceiving red light (Quail et al, 1995). Recently, it has been shown that PhyD plays a minor role in mediating leaf expansion and stem elongation in conjunction with PhyB (Aukerman et al, 1997). Cry1 is a well defined blue-light receptor, mutations in which (hy4 mutants) cause a decrease in sensitivity to high-irradiance blue lightmediated inhibition of hypocotyl elongation (Ahmad and Cashmore, 1993;Lin et al, 1995).…”

Microarray-based rapid cloning of an ion accumulation deletion mutant in Arabidopsis thaliana

“…MABS analysis was performed by backcrossing the FN1148 mutant once to the same ecotype (Col-0) from which it originated to circumvent natural variation in ion accumulation between different ecotypes (see Introduction). Backcrossing into the parental ecotype also circumvented problems that could result from naturally occurring genomic deletion polymorphisms between two different ecotypes (12). F 2 mutants with Na ϩ overaccumulation phenotypes were identified by ICP, and a DNA pool was extracted from five of these individual F 2 mutant plants.…”