As a rosette plant, Arabidopsis thaliana forms leaves near to the ground, which causes the plant to be vulnerable to shading by neighbours. One mechanism to avoid such shading is the regulation of leaf inclination, such that leaves can be raised to more vertical orientations to prevent neighbouring leaves from overtopping them. Throughout Arabidopsis rosette development, rosette leaves move to more vertical orientations when shaded by neighbouring leaves, exposed to low light levels or placed in the dark. After darkinduced reorientation of leaves, returning them to white light causes the leaves to reorient to more horizontal inclinations. These light-dependent leaf movements are more robust than, and distinct from, the diurnal movements of rosette leaves. However, the movements are gated by the circadian clock. The light-dependent leaf orientation response is mediated primarily through phytochromes A, B and E, with the orientation varying with the ratio of red light to far-red light, consistent with other shade-avoidance responses. However, even plants lacking these phytochromes were able to alter leaf inclination in response to white light, suggesting a role for other photoreceptors. In particular, we found significant changes in leaf inclination for plants exposed to green light. This green light response may be caused, in part, by light-dependent regulation of abscisic acid (ABA) biosynthesis.

(J.L.M., R.P.H.)The interaction of tropisms is important in determining the final growth form of the plant body. In roots, gravitropism is the predominant tropistic response, but phototropism also plays a role in the oriented growth of roots in flowering plants. In blue or white light, roots exhibit negative phototropism that is mediated by the phototropin family of photoreceptors. In contrast, red light induces a positive phototropism in Arabidopsis roots. Because this red-light-induced response is weak relative to both gravitropism and negative phototropism, we used a novel device to study phototropism without the complications of a counteracting gravitational stimulus. This device is based on a computer-controlled system using real-time image analysis of root growth and a feedback-regulated rotatable stage. Our data show that this system is useful to study root phototropism in response to red light, because in wild-type roots, the maximal curvature detected with this apparatus is 30°to 40°, compared with 5°to 10°without the feedback system. In positive root phototropism, sensing of red light occurs in the root itself and is not dependent on shoot-derived signals resulting from light perception. Phytochrome (Phy)A and phyB were severely impaired in red-light-induced phototropism, whereas the phyD and phyE mutants were normal in this response. Thus, PHYA and PHYB play a key role in mediating red-light-dependent positive phototropism in roots. Although phytochrome has been shown to mediate phototropism in some lower plant groups, this is one of the few reports indicating a phytochrome-dependent phototropism in flowering plants.Plants have evolved selective and sensitive mechanisms to deal with the constant sensory input they receive from the environment. In roots, gravity is the most critical signal for growth and development, and, thus, gravitropism has been well-characterized in this organ (Sack, 1991;Kiss, 2000). However, it has become increasingly clear that gravitropism interacts with a number of other tropistic responses including phototropism, thigmotropism, and hydrotropism in determining the final growth form of the primary root and the entire root system (Hangarter, 1997;Correll and Kiss, 2002).Phototropism in roots was extensively reviewed in a classical paper by Hubert and Funke (1937) but has received increased attention since the report by Okada and Shimura (1992), who isolated mutants in root phototropism that were later shown to be deficient in the blue-light receptor PHOT1 (Briggs and Christie, 2002). Roots are typically negatively phototropic in response to white and blue light (Okada and Shimura, 1992;Vitha et al., 2000) and use the same photoreceptors that are involved in phototropism in stems and stem-like organs (Sakai et al., 2000). Furthermore, similar to root gravisensing (Blancaflor et al., 1998), sensing of blue light for phototropism occurs in the root cap .We have recently identified a red-light-induced positive phototropism in primary roots of Arabidopsis ). This tropistic response ...

Highlight textThis research is the first to examine the genetics of drought adaptive traits in Brassica napus and is supportive of an inherent trade-off between resource investment in reproduction and root development.

Although Arabidopsis is an important system for studying root physiology, the localized growth patterns of its roots have not been well defined, particularly during tropic responses. In order to characterize growth rate profiles along the apex of primary roots of Arabidopsis thaliana (L.) Heynh (ecotype Columbia) we applied small charcoal particles to the root surface and analyzed their displacement during growth using an automated video digitizer system with custom software for tracking the markers. When growing vertically, the maximum elongation rate occurred 481 +/- 50 microns back from the extreme tip of the root (tip of root cap), and the elongation zone extended back to 912 +/- 137 microns. The distal elongation zone (DEZ) has previously been described as the apical region of the elongation zone in which the relative elemental growth rate (REGR) is < or = 30% of the peak rate in the central elongation zone. By this definition, our data indicate that the basal limit of the DEZ was located 248 +/- 30 microns from the root tip. However, after gravistimulation, the growth patterns of the root changed. Within the first hour of graviresponse, the basal limit of the DEZ and the position of peak REGR shifted apically on the upper flank of the root. This was due to a combination of increased growth in the DEZ and growth inhibition in the central elongation zone. On the lower flank, the basal limit of the DEZ shifted basipetally as the REGR decreased. These factors set up the gradient of growth rate across the root, which drives curvature.

The study of gravitropism is hindered by the fact that as a root responds, the gravitational stimulus changes. Using a feedback system to connect a rotating stage platform to a video digitizer system, we were able to maintain a constant angle of gravistimulation to Arabidopsis roots for long time periods. The rate of curvature approximated the sine rule for angles of stimulation between 20°and 120°. For a given angle of stimulation, the rate of curvature also remained constant, with no observed diminishment of the response. Although previous reports of Arabidopsis root gravitropism suggest latent periods of approximately 30 min, using a smooth mechanical stage to reorient the root, we observed a mean time lag of approximately 10 min. This more rapid onset of curvature can, in part, be explained by reduced mechanical perturbation during the process of gravistimulation. This suggests that mechanical stimulation associated with rapid root re-orientation may confound investigations of early gravitropic events.Although the gravitropism of plant roots has been studied for well over 100 years, its mechanisms are still poorly understood. The use of Arabidopsis, with its plethora of mutants showing altered gravity response, promises to aid in the investigation of these mechanisms. Due to the small and fragile nature of the Arabidopsis root, characterizations of mutants are often performed with coarse temporal resolution, with the result that the initiation of the response is unobserved (Hobbie and Estelle, 1995; Kiss et al., 1996; Fukaki et al., 1997; Tian and Reed, 1999). Ishikawa and Evans (1997) and Mullen et al. (1998b) detailed the kinetics of gravitropic curvature in horizontally stimulated Arabidopsis roots. These studies revealed a time lag between 20 and 45 min before curvature was initiated in the distal elongation zone (DEZ). Yet interpretation of data for later time periods is complicated by the process of the graviresponse, which changes the stimulation angle at the root cap, the probable site of gravity perception (for review, see Sack, 1991). The response also creates a large difference in angle of orientation along the elongating region of the root and may involve adaptation to the gravity signal.Sachs (1882) proposed that the gravitropic response was proportional to the component of the gravity vector perpendicular to the root axis, leading to the "sine rule" approximation of the dependence of response on the stimulation angle. Although the rate of curvature has been found to be related to the sine of the stimulation angle for roots (Larsen, 1969;Perbal, 1974) and coleoptiles (Pickard, 1973; Iino et al., 1996), a simple sine dependence only held for angles of stimulation less than 90°, and the optimal angle of stimulation was in some cases greater than 90°. Further, a recent study of maize roots by Barlow et al. (1993) found no dependence of rate of curvature on stimulation angle, for angles between 20°and 90°, the range in which the sine rule approximation should be most valid.Since prior studies ...

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Interdisciplinary syntheses are needed to scale up discovery of the environmental drivers and molecular basis of adaptation in nature. Here we integrated novel approaches using whole genome sequences, satellite remote sensing, and transgenic experiments to study natural loss-of-function alleles associated with drought histories in wild Arabidopsis thaliana. The genes we identified exhibit population genetic signatures of parallel molecular evolution, selection for loss-of-function, and shared associations with flowering time phenotypes in directions consistent with longstanding adaptive hypotheses seven times more often than expected by chance. We then confirmed predicted phenotypes experimentally in transgenic knockout lines. These findings reveal the importance of drought timing to explain the evolution of alternative drought tolerance strategies and further challenge popular assumptions about the adaptive value of genetic loss-of-function in nature. These results also motivate improved species-wide sequencing efforts to better identify loss-of-function variants and inspire new opportunities for engineering climate resilience in crops.

Photometric analysis of chloroplast movements in various phytochrome (phy) mutants of Arabidopsis showed that phyA, B, and D are not required for chloroplast movements because blue light (BL)-dependent chloroplast migration still occurs in these mutants. However, mutants lacking phyA or phyB showed an enhanced response at fluence rates of BL above 10 mol m Ϫ2 s Ϫ1 . Overexpression of phyA or phyB resulted in an enhancement of the low-light response. Analysis of chloroplast movements within the range of BL intensities in which the transition between the low-and high-light responses occur (1.5-15 mol m Ϫ2 s Ϫ1 ) revealed a transient increase in light transmittance through leaves, indicative of the high-light response, followed by a decrease in transmittance to a value below that measured before the BL treatment, indicative of the low-light response. A biphasic response was not observed for phyABD leaves exposed to the same fluence rate of BL, suggesting that phys play a role in modulating the transition between the low-and high-light chloroplast movement responses of Arabidopsis.Plants have evolved a number of developmental and physiological mechanisms that allow them to adapt to changes in their environment. Many of these pathways are modulated in response to various environmental stimuli such as light, gravity, temperature, and nutrient availability (Hangarter, 1997). In the case of light, plants possess a variety of photoreceptor molecules that are sensitive to the quality, quantity, and direction of light within the environment. The known photoreceptors of Arabidopsis include the phytochromes (phys A, B, C, D, and E), which mainly function to detect red light (RL) and far-red light (FRL) and two distinct classes of blue light (BL) photoreceptors, the "photolyase-like" cryptochromes (cry1, cry2, and cry3) and the phototropins (phot1 and phot2; Somers et al., 1991; Ahmad and Cashmore, 1993;Dehesh et al., 1993;Reed et al., 1993Reed et al., , 1994Clack et al., 1994;Liscum and Briggs, 1995;Guo et al., 1998: Kleine et al., 2003. The crys regulate inhibition of stem elongation, photomorphogenesis, entrainment of the circadian clock, leaf expansion, and anthocyanin production (Ahmad et al., 1995;Somers et al., 1998;Toth et al., 2001;Wang et al., 2001;Mockler et al., 2003). The phots mediate such BL responses as early phase inhibition of hypocotyl elongation (phot1), phototropism, stomatal regulation, and chloroplast movements (Liscum and Briggs, 1995;Christie et al., 1998;Lasceve et al., 1999;Folta and Spalding, 2001a;Kagawa et al., 2001;Kinoshita et al., 2001;Sakai et al., 2001).Analysis of mutants lacking one or more of these photoreceptors has led to a better understanding of how plants respond to changes in their light environment. It has become increasingly clear that these photoreceptors often act redundantly, synergistically, and/or antagonistically in several different light-mediated pathways (Casal and Boccalandro, 1995; Ahmad and Cashmore, 1997; Ahmad et al., 1998;Mockler et al., 1999;. For example, the co...