Integration of transcriptomic and proteomic analyses reveals several levels of metabolic regulation in the excess starch and early senescent leaf mutant lses1 in rice.

BACKGROUND: The normal metabolism of transitory starch in leaves plays an important role in ensuring photosynthesis, delaying senescence and maintaining high yield in crops. OsCKI1 (casein kinase I1) plays crucial regulatory roles in multiple important physiological processes, including root development, hormonal signaling and low temperature-treatment adaptive growth in rice; however, its potential role in regulating temporary starch metabolism or premature leaf senescence remains unclear. To reveal the molecular regulatory mechanism of OsCKI1 in rice leaves, physiological, transcriptomic and proteomic analyses of leaves of osckI1 allele mutant lses1 (leaf starch excess and senescence 1) and its wild-type varieties (WT) were performed. RESULTS: Phenotypic identification and physiological measurements showed that the lses1 mutant exhibited starch excess in the leaves and an obvious leaf tip withering phenotype as well as high ROS and MDA contents, low chlorophyll content and protective enzyme activities compared to WT. The correlation analyses between protein and mRNA abundance are weak or limited. However, the changes of several important genes related to carbohydrate metabolism and apoptosis at the mRNA and protein levels were consistent. The protein-protein interaction (PPI) network might play accessory roles in promoting premature senescence of lses1 leaves. Comprehensive transcriptomic and proteomic analysis indicated that multiple key genes/proteins related to starch and sugar metabolism, apoptosis and ABA signaling exhibited significant differential expression. Abnormal increase in temporary starch was highly correlated with the expression of starch biosynthesis-related genes, which might be the main factor that causes premature leaf senescence and changes in multiple metabolic levels in leaves of lses1. In addition, four proteins associated with ABA accumulation and signaling, and three CKI potential target proteins related to starch biosynthesis were up-regulated in the lses1 mutant, suggesting that LSES1 may affect temporary starch accumulation and premature leaf senescence through phosphorylation crosstalk ABA signaling and starch anabolic pathways. CONCLUSION: The current study established the high correlation between the changes in physiological characteristics and mRNA and protein expression profiles in lses1 leaves, and emphasized the positive effect of excessive starch on accelerating premature leaf senescence. The expression patterns of genes/proteins related to starch biosynthesis and ABA signaling were analyzed via transcriptomes and proteomes, which provided a novel direction and research basis for the subsequent exploration of the regulation mechanism of temporary starch and apoptosis via LSES1/OsCKI1 in rice.

Compressive spectral imaging using variable number of measurements.

The compressive spectral imaging method always cuts down on the number of images for obtaining the spectral data cube of a scene. Our method cuts down on the number of sensors on the imaging plane, so as to fit some practical constraints, (e.g., size, weight, battery capacity, memory space, transmission bandwidth). Moreover, only a few of sensors on the imaging plane are needed, while more prior knowledge about the object in the scene has been achieved. The proposed method is based on the concept of coded dispersion, by which many pixels of spectral data are caught by one pixel on the imaging plane. Its measurement matrix is modified so that the number of measurements can be variable under different circumstances to save the transmission bandwidth. We demonstrate the validity of the proposed method, that with prior knowledge of scenes available, it offers a way to acquire spectral images using a variable number of measurements.

High-resolution spectral imaging based on coded dispersion.

Since the energy of the incident light is constant, the spatial and spectral resolution can hardly be improved without scarifying the other with the spectral imaging method of a pushbroom scanner. Thus, a new spectral imaging method is proposed to obtain a high-resolution (HR) spectral image with a low-resolution detector array. The method, namely coded dispersion, by which compressive measurement is achieved, improves light collection efficiency, and then a high-quality reconstructed HR spectral image is obtained with fewer sensors. The simulation result shows that with prior knowledge of scenes available, the proposed method also offers a new way to acquire an HR spectral image while the density of detector array is constrained by battery, capacity, transmission bandwidth, and cost.

Panicle-Cloud: An Open and AI-Powered Cloud Computing Platform for Quantifying Rice Panicles from Drone-Collected Imagery to Enable the Classification of Yield Production in Rice.

Rice (Oryza sativa) is an essential stable food for many rice consumption nations in the world and, thus, the importance to improve its yield production under global climate changes. To evaluate different rice varieties' yield performance, key yield-related traits such as panicle number per unit area (PNpM2) are key indicators, which have attracted much attention by many plant research groups. Nevertheless, it is still challenging to conduct large-scale screening of rice panicles to quantify the PNpM2 trait due to complex field conditions, a large variation of rice cultivars, and their panicle morphological features. Here, we present Panicle-Cloud, an open and artificial intelligence (AI)-powered cloud computing platform that is capable of quantifying rice panicles from drone-collected imagery. To facilitate the development of AI-powered detection models, we first established an open diverse rice panicle detection dataset that was annotated by a group of rice specialists; then, we integrated several state-of-the-art deep learning models (including a preferred model called Panicle-AI) into the Panicle-Cloud platform, so that nonexpert users could select a pretrained model to detect rice panicles from their own aerial images. We trialed the AI models with images collected at different attitudes and growth stages, through which the right timing and preferred image resolutions for phenotyping rice panicles in the field were identified. Then, we applied the platform in a 2-season rice breeding trial to valid its biological relevance and classified yield production using the platform-derived PNpM2 trait from hundreds of rice varieties. Through correlation analysis between computational analysis and manual scoring, we found that the platform could quantify the PNpM2 trait reliably, based on which yield production was classified with high accuracy. Hence, we trust that our work demonstrates a valuable advance in phenotyping the PNpM2 trait in rice, which provides a useful toolkit to enable rice breeders to screen and select desired rice varieties under field conditions.