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Societal Impact Statement: Rice farming is transitioning from transplanting rice seedlings towards the less labour-intensive and less water-demanding method of directly seeding rice. This, however, is accompanied by increased weed proliferation. To tackle this issue, this study seeks to identify how the crop itself can better suppress weeds, with a focus on light competition via shading. Using a rice diversity panel, traits were identified that contribute to enhanced shading capacity, and these traits were encapsulated into a single shading capacity metric. This was followed by the identification of the genetic loci underpinning variation in the core traits. The identified haplotypes can be used in breeding programmes to improve weed suppression by rice, thus contributing to sustainable agriculture. Summary: In modern rice farming, one of the major constraints is weed proliferation and the entailed ecological impact of herbicide application. This requires increased weed competitiveness in current rice varieties, achieved via enhanced shade casting to limit the growth of shade-sensitive weeds. To identify traits that increase rice shading capacity, we exhaustively phenotyped a rice diversity panel of 344 varieties at an early vegetative stage. A genome-wide association study (GWAS) revealed genetic loci underlying variation in canopy architecture traits linked with shading capacity. The screen shows considerable natural variation in shoot architecture for 13 examined traits, of which shading potential is mostly determined by projected shoot area, number of leaves, culm height and canopy solidity. The shading rank, a metric based on these core traits, identifies varieties with the highest shading potential. Five genetic loci were found to be associated with canopy architecture, shading potential and early vigour. Identification of traits contributing to shading capacity and underlying allelic variation will serve future genomic-assisted breeding programmes. Implementi

Plant organs move throughout the diurnal cycle, changing leaf and petiole positions to balance light capture, leaf temperature, and water loss under dynamic environmental conditions. Upward movement of the petiole, called hyponasty, is one of several traits of the shade avoidance syndrome (SAS). SAS traits are elicited upon perception of vegetation shade signals such as far-red light (FR) and improve light capture in dense vegetation. Monitoring plant movement at a high temporal resolution allows studying functionality and molecular regulation of hyponasty. However, high temporal resolution imaging solutions are often very expensive, making this unavailable to many researchers. Here, we present a modular and low-cost imaging set-up, based on small Raspberry Pi computers, that can track leaf movements and elongation growth with high temporal resolution. We also developed an open-source, semi-automated image analysis pipeline. Using this setup we followed responses to FR enrichment, light intensity, and their interactions. Tracking both elongation and the angle of the petiole, lamina, and entire leaf in Arabidopsis (Arabidopsis thaliana) revealed insight into R:FR sensitivities of leaf growth and movement dynamics and the interactions of R:FR with background light intensity. The detailed imaging options of this system allowed us to identify spatially separate bending points for petiole and lamina positioning of the leaf.

Rice is one of the most important crops for agricultural purposes. The space required for farming (i.e., rice) will likely increase to feed a growing world population. Research on plant growth responses, may contribute to understanding factors limiting potential yield. Plants absorb mostly red and blue light for photosynthesis and reflect green and far-red light. Therefore, neighbouring plants, especially in high density growth conditions, lower ambient R:FR ratios. This triggers a range of responses referred to as the shade avoidance syndrome (SAS), in shade-avoiding plants. The SAS is important as it may negatively impact yield and limit the density of crops grown in agriculture. In this report, we discuss an observed response of rice to low R:FR light conditions that is atypical of what generally is observed in the SAS. The research question was: why is the observed response of rice under low R:FR light conditions so distinctly different from the typical SAS? We have seen increased or decreased shoot biomass and number of tillers (branches) and leaves in rice grown in FR light in autumn or winter, respectively. As an extension to existing literature, our results suggest that FR light and light that can be used for photosynthesis together, determine the growth response of rice under low R:FR light conditions. Additionally, we found that, even though it has not been described in other literature, rice also shows a (typical) SAS. We concluded this after a light treatment that removes the effect of FR light on photosynthesis. Then, we also investigated how different genes of interest were expressed in rice that was grown under low R:FR light conditions. We grew rice and exposed it to FR light 5 days after sowing, and harvested three tissues (meristem, culm and leaves) separately at three different timepoints (19, 24 and 29 hours after FR light exposure). We used these samples to determine different expression patterns in low R:FR grown rice compared to control grown

Although plants are immobile, many of their organs are flexible to move in response to environmental cues. In dense vegetation, plants detect neighbors through far-red light perception with their leaf tip. They respond remotely, with asymmetrical growth between the abaxial and adaxial sides of the leafstalk, the petiole. This results in upward movement that brings the leaf blades into better lit zones of the canopy. The plant hormone auxin is required for this response, but it is not understood how non-differential leaf tip-derived auxin can remotely regulate movement. Here, we show that remote signaling of far-red light promotes auxin accumulation in the abaxial petiole. This local auxin accumulation is facilitated by reinforcing an intrinsic directionality of the auxin transport protein PIN3 on the petiole endodermis, as visualized with a PIN3-GFP line. Using an auxin biosensor, we show that auxin accumulates in all cell layers from endodermis to epidermis in the abaxial petiole, upon far-red light signaling in the remote leaf tip. In the petiole, auxin elicits a response to both auxin itself as well as a second growth promoter; gibberellin. We show that this dual regulation is necessary for hyponastic leaf movement in response to light. Our data indicate that gibberellin is required to permit cell growth, whereas differential auxin accumulation determines which cells can grow. Our results reveal how plants can spatially relay information about neighbor proximity from their sensory leaf tips to the petiole base, thus driving adaptive growth.

This dataset is an add-on for Gautrat et al., containing processed files for the mRNAseq data in tab delimited txt format. Here, you can obtain the raw counts file, the normalized CPM values, and the normalized logCPM values The RNA-seq raw data supporting the conclusions of this article have been deposited in ArrayExpress (Kolesnikov et al., 2015) at EMBL-EBI (www.ebi.ac.uk/arrayexpress), under accession numbers E-MTAB-13638. All relevant custom r scripts are available at https://github.com/aromanowski/shade_N_ck