Os03g0719800

PHYA encodes the phytochrome A protein which controls the deetiolation and flowering in Rice.

Annotated Information

Function

• phyA can mediate the R/FR-reversible LFR on the regulation of Lhcb gene expression in rice etiolated seedlings.

• phyA and phyB equally contribute to the perception of Rc for the coleoptile inhibition and that phyC has no effect on it.

• In rice, phyA suppresses flowering under LD conditions, and the effect does not depend on light quality. The role of phyA in flowering differs between Arabidopsis and rice, at least under LD conditions. phyA mutation alone does not affect the flowering time much, but in the phyB or phyC mutant background, phyA mutation makes a big contribution in determining the flowering time in LD conditions.

Mutation

• As shown in Figure 2A, dark-grown seedlings have long coleoptiles (white arrows) and first leaves (yellow arrows). The most striking feature is the remarkable elongation of second internodes (red arrows), which are hardly measurable in the light-grown seedlings. In principle, light represses the elongation of coleoptiles and first leaves and blocks the internode from elongating (Figures 2B and 2C), but phyA phyB under Rc (Figure 2B), and phyA phyC and phyA phyB double mutants grown under FRc (Figure 2C) showed the typical dark-grown phenotype characterized by the long coleoptiles (white arrows) and the elongated internode (red arrows).

Figure 2. Nine-Day-Old Seedlings of Wild-Type and Phytochrome Mutants Grown under Rc or FRc. Seedlings were grown in darkness (A) or under Rc (B) or FRc (C) for 9 d at 288C. The fluence rates of Rc and FRc are 15 mmol photons m-2 s-1. Two seedlings of Nipponbare (wild type) grown in dark are in (A). In (B) and (C), wild-type and single and double phytochrome mutants are aligned for comparison from left to right: wild type, phyA, phyB, phyC, phyA phyC, phyB phyC, and phyA phyB. White and yellow arrows indicate apexes of coleoptiles and first leaves, respectively. Red arrows indicate second nodes. All pictures are the samemagnitude. Bars ¼ 10 mm. .

• To quantify the differences, the researchers took comprehensive measurements of lengths on the seedlings under Rc and FRc, as well as darkness (Figure 3). Under Rc, the coleoptile elongation was severely inhibited in wild-type, phyA, phyC, and phyA phyC mutants. Coleoptiles of phyB and phyB phyC mutants were similarly longer than those of the wild type but were still greatly reduced in length compared with dark-grown seedlings, and no inhibition was observed in phyA phyB double mutants (Figure 3A, Rc). These results indicate that phyB plays a major role in coleoptile inhibition by Rc and that the role of phyA in coleoptile inhibition is also important, but visible only in the absence of phyB Under FRc, coleoptiles of phyA mutants were longer than those of the wild type but still shorter than those of dark-grown seedlings. The phyB mutation did not affect the coleoptile inhibition. The phyC single mutation also showed no effect, but phyA phyC double mutants had long coleoptiles, as long as those of dark-grown seedlings (Figure 3A, FRc). Therefore, when phyA is functional, phyC function is dispensable, but in the absence of phyA, phyC showed a limited effect by partially inhibiting the coleoptile (the difference between phyA and phyA phyC). No inhibition was detected in phyA phyB double mutants, probably due to a significant reduction in the phyC level of these mutants. First leaves of rice are incomplete and consist mostly of leaf sheaths and poorly developed tiny leaf blades. Thus, the lengths of first leaves represent mostly those of leaf sheaths. The growth of first leaves was also inhibited by Rc and FRc in basically the same manner as observed in coleoptiles (Figure 3B). The inhibitory effects of Rc and FRc appeared less drastic on first leaves than on coleoptiles. The second internodes of phyA phyB double mutants under Rc and those of phyA phyC and phyA phyB under FRc elongated as much as those of dark-grown seedlings. The other mutants had undetectable internodes when grown under FRc or Rc conditions except for the phyA mutants under FRc, which showed slight but measurable elongation (Figure 3C).

Figure 3. Lengths of Different Tissues of the Nine-Day-Old Seedlings Represented in Figure 2. Coleoptile lengths (A), lengths of first leaves (B), and lengths of second internodes (C) of 9-d-old seedlings are shown for wild-type and phytochrome mutants grown in the dark (black bars) or under Rc (gray bars) or FRc (white bars) as in Figure 2. The means 6 SE were obtained from 20 to ;50 seedlings. .

• Another significant phenotypical difference was observed in leaf blade angles of second leaves under Bc and Wc (Figures 5A and 5B). We took pictures of seedlings and measured the declination angles of second leaf blades. Bc increased leaf blade declination, and the effects were different among wild-type and phytochrome mutants (Figure 5A). As shown in Figure 5C, declination angles of phyA mutants were the same as those of the wild type, and phyC and phyA phyC mutants showed a slightly greater declination than the wild type. The declination angles were much greater in phyB and phyB phyC mutants and greatest in phyA phyB double mutants (almost at a right angle). These results

indicate that phyB and phyC are involved in different ways in the second leaf declination upon perceiving Bc. The phyA also makes a significant contribution to the second leaf declination by Bc, but the strong effect of the phyA mutation is revealed only in the absence of phyB. Under Wc, phyB, phyB phyC, and phyA phyB seedlings showed the same declination angles as in the Bc, but wild-type and phyA, phyC, and phyA phyC mutants did not. These observations suggest that phyB seems to function antagonistically to blue light receptors (maybe cryptochromes) on the leaf blade declination.

Figure 5. Second Leaf Blade Declination Induced by Bc and Wc. (A) and (B) Seedlings were grown under Bc (A) or Wc (B) for 9 d at 288C. The fluence rates of Bc and Wc are 15 and 40 mmol photons m-2 s-1, respectively. Wild-type and single and double phytochrome mutants are aligned for comparison from left to right: wild type, phyA, phyB, phyC, phyA phyC, phyB phyC, and phyA phyB. Yellow arrows indicate lamina joints of second leaves. The two pictures are the same magnitude, and scale bars at left sides are 10 mm. (C) Declination angles are measured from the pictures and shown for wild-type and phytochrome mutants grown under Bc (shaded bars) or Wc (open bars). The means6 SE were obtained from 20 to;50 seedlings. .

• As in lane2, phyA mutants showed a clear R/FR reversibility but lost the induction of Lhcb genes by a FRp.

Figure 6. Induction of Lhcb Gene Expression by R and/or FR Pulses in Etiolated Rice Seedlings. .

• To verify this hypothesis, the researchers determined the expression levels of Lhcb and RbcS genes in the seedlings of wild-type and phytochrome single and double mutants grown in darkness or under FRc or Rc(Figure 7).

Figure 7. Induction of Lhcb and RbcS Genes by FRc or Rc in Wild-Type and Phytochrome Mutant Seedlings. .

• The researchers examined flowering times of phytochrome mutants under natural daylength (in the paddy field) and short-day (SD) conditions (in the growth chamber). Because daylengths during this cultivation were >13 h, our natural daylength condition was considered equivalent to LD conditions. The phyA mutation delays, the phyB accelerates, and the phyC has no effect on the flowering, but the double mutations caused different responses.

Figure 8. Comparison of Flowering Times between Wild-Type and phyB Mutants under Natural Daylengths and SD Conditions. (A) and (B) Nipponbare (WT) and phytochrome single (phyA, phyB, and phyC) and double (phyA phyC, phyB phyC, and phyA phyB) mutants were grown in the paddy field (A) or in a growth chamber set as SD (10L/ 14D; [B], open bars) or LD (14L/10D; [B], shaded bars), and their flowering times were measured (natural daylength). (C) Wild-type (open bars) and phyB mutants (hatched bars) were grown in a growth chamber set as SD (normal, 10L/14D; severe, 8L/16D) or SD (10L/14D) plus EDO-FR conditions. The means 6 SE obtained from 20 plants are displayed. .

Expression

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Evolution

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Labs working on this gene

• Department of Plant Physiology, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
• Hitachi Central Research Laboratory, Hatoyama, Saitama 350-0395, Japan
• Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
• Institute of Radiation Breeding, National Institute of Agrobiological Sciences, Hitachi-ohmiya, Ibaraki 319-2293, Japan