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Three-dimensional (3D) phenotyping is important for studying plant structure and function. Light detection and ranging (LiDAR) has gained prominence in 3D plant phenotyping due to its ability to collect 3D point clouds. However, organ-level branch detection remains challenging due to small targets, sparse points, and low signal-to-noise ratios. In addition, extracting biologically relevant angle traits is difficult. In this study, we developed a stratified, clustered, and growing-based algorithm (SCAG) for soybean branch detection and branch angle calculation from LiDAR data, which is heuristic, open-source, and expandable. SCAG achieved high branch detection accuracy ( F-score = 0.77) and branch angle calculation accuracy ( r = 0.84) when evaluated on 152 diverse soybean varieties. Meanwhile, the SCAG outperformed 2 other classic algorithms, the support vector machine ( F-score = 0.53) and density-based methods ( F-score = 0.55). Moreover, after applying the SCAG to 405 soybean varieties over 2 consecutive years, we quantified various 3D traits, including canopy width, height, stem length, and average angle. After data filtering, we identified novel heritable and repeatable traits for evaluating soybean density tolerance potential, such as the ratio of average angle to height and the ratio of average angle to stem length, which showed greater potential than the well-known ratio of canopy width to height trait. Our work demonstrates remarkable advances in 3D phenotyping and plant architecture screening. The algorithm can be applied to other crops, such as maize and tomato. Our dataset, scripts, and software are public, which can further benefit the plant science community by enhancing plant architecture characterization and ideal variety selection., Competing Interests: Competing interests: The authors declare that they have no competing interests., (Copyright © 2024 Songyin Zhang et al.)

Allometric rules provide insights into the structure-function relationships across species and scales and are commonly used in ecology. The fields of agronomy, plant phenotyping and modeling also need simplifications such as allometric rules to reconcile data at different temporal and spatial levels (organs/canopy). This paper explores the variations in relationships for wheat regarding (i) the distribution of crop green area between leaves and stems, and (ii) the allocation of above-ground biomass between leaves and stems during the vegetative period, using a large dataset covering different years, countries, genotypes and management practices. Our results show that the relationship between leaf and stem area was linear, genotype-specific, and sensitive to radiation. The relationship between leaf and stem biomass depended on genotype and nitrogen fertilization. The mass per area, associating area and biomass for both leaf and stem, varied strongly by developmental stage and was significantly affected by environment and genotype. These allometric rules were evaluated with satisfactory performance, and their potential use is discussed with regard to current phenotyping techniques and plant/crop models. Our results enable the definition of models and minimum datasets required for characterizing diversity panels and making predictions in various G × E × M contexts., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Poor grain filling in inferior spikelets (IS), which is influenced by the remobilization of nonstructural carbohydrates (NSC) stored in the sheath and internode of rice plants, limits the expected high yield of large-panicle rice. NSC remobilization from the sheath to the panicle is regulated by the T6P/SnRK1 pathway. However, in large-panicle rice, it is unclear whether IS grain filling is related to the NSC remobilization mediated by T6P/SnRK1 signaling. In this study, two large-panicle cultivars-W1844 and CJ03-with distinct differences in IS grain filling were used to explore the physiological mechanism mediating IS development. Compared to W1844, CJ03 IS showed lower expression of the genes related to sucrose uploading, later sucrose peaking, and delayed starch accumulation. In the CJ03, low OsSUTs expression and NSC output, transport rate, and contribution rate were detected in the sheaths and internodes. These results suggest that poor NSC remobilization results in insufficient assimilate supply for the IS, and consequently, poor IS grain filling. Furthermore, poor NSC remobilization coincided with the increased T6P content and decreased SnRK1 activity during grain filling in CJ03 IS. The expression levels of genes related to T6P metabolism and those encoding the catalytic subunit of SnRK1 were consistent with the observed T6P content and SnRK1 activity in the sheaths and internodes. Therefore, IS grain filling is potentially affected by T6P/SnRK1 signaling-mediated NSC remobilization in large-panicle rice., (© 2024 Scandinavian Plant Physiology Society.)

Slow-controlled release fertilizers are experiencing a popularity in rice cultivation due to their effectiveness in yield and quality with low environmental costs. However, the underlying mechanism by which these fertilizers regulate grain quality remains inadequately understood. This study investigated the effects of five fertilizer management practices on rice yield and quality in a two-year field experiment: CK, conventional fertilization, and four applications of slow-controlled release fertilizer (UF, urea formaldehyde; SCU, sulfur-coated urea; PCU, polymer-coated urea; BBF, controlled-release bulk blending fertilizer). In 2020 and 2021, the yields of UF and SCU groups showed significant decreases when compared to conventional fertilization, accompanied by a decline in nutritional quality. Additionally, PCU group exhibited poorer cooking and eating qualities. However, BBF group achieved increases in both yield (10.8 t hm -2 and 11.0 t hm -2 ) and grain quality reaching the level of CK group. The adequate nitrogen supply in PCU group during the grain-filling stage led to a greater capacity for the accumulation of proteins and amino acids in the PCU group compared to starch accumulation. Intriguingly, BBF group showed better carbon-nitrogen metabolism than that of PCU group. The optimal nitrogen supply present in BBF group suitable boosted the synthesis of amino acids involved in the glycolysis/ tricarboxylic acid cycle, thereby effectively coordinating carbon-nitrogen metabolism. The application of the new slow-controlled release fertilizer, BBF, is advantageous in regulating the carbon flow in the carbon-nitrogen metabolism to enhance rice quality., (© 2024. The Author(s).)

Sucrose non-fermenting-1-related protein kinase 1 (SnRK1) and AMP-activated protein kinase (AMPK) are highly conserved. Compound 991 is an AMPK activator in mammals. However, whether 991 also activates SnRK1 remains unknown. The addition of 991 significantly increased SnRK1 activity in desalted extracts from germinating rice seeds in vitro. To determine whether 991 has biological activity, rice seeds were treated with different concentrations of 991. Germination was promoted at low concentrations but inhibited at high concentrations. The effects of 991 on germination were similar to those of OsSnRK1a overexpression. To explore whether 991 affects germination by specifically affecting SnRK1, germination of an snrk1a mutant and the wild type under 1 μM 991 treatment was compared. The snrk1a mutant was insensitive to 991. Phosphoproteomic analysis showed that the differential phosphopeptides induced by 991 and OsSnRK1a overexpression largely overlapped. Furthermore, SnRK1 might regulate rice germination in a dosage-dependent manner by regulating the phosphorylation of three phosphosites, namely S285-PIP2;4, S1013-SOS1, and S110-ABI5. These results indicate that 991 is a specific SnRK1 activator in rice. The promotion and inhibition of germination by 991 also occurred in wheat seeds. Thus, 991 is useful for exploring SnRK1 function and the chemical regulation of growth and development in crops., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Evaluating the impact of global warming on rice production and greenhouse gas (GHG) emissions is critical for ensuring food security and mitigating the consequences of climate change. Nonetheless, the impacts of warming on crop production, GHG emissions, and microbial mechanisms in the single-cropping rice systems remain unclear. Here, a two-year field experiment was conducted to explore the effects of warming (increased by 2.7-3.0 °C on average) in the rice growing season on crop production and functional microorganisms associated with GHG emissions. Results showed that warming resulted in significant reduction (p < 0.01) in the aboveground biomass and grain yield as well as in grain weight, the number of spikelets per panicle, and the seed-setting rate. However, it caused a significant increase (p < 0.01) in the number of panicles by 15.6 % and 34.9 %, respectively. Furthermore, warming significantly increased (p < 0.01) seasonal methane (CH 4 ) emissions but reduced nitrous oxide (N 2 O) emissions, particularly in 2022.The relative abundance of genes associated with CH 4 metabolism and nitrogen metabolism was increased by 40.7 % and 32.7 %, respectively, in response to warming. Moreover, warming had a positive impact on the abundance of genes related to CH 4 production and oxidation processes but did not affect the denitrification processes associated with N 2 O production. These results showed that warming decreased rice yield and biomass in the single cropping rice system but increased CH 4 emissions and global warming potential. Taken together, to address the increasing food demand of a growing population and mitigate the impacts of global warming, it is imperative to duce GHG emissions and enhance crop yields., Competing Interests: Declaration of competing interest We declare that we have no financial and personal relationships with other people or organizations that can inappropriately influence our work, there is no professional or other personal interest of any nature or kind in any product, service and/or company that could be construed as influencing the position presented in, or the review of, the manuscript entitled., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Key Message: Purine permease PUP11 is essential for rice seed development, regulates the seed setting rate, and influences the cytokinin content, sugar transport, and starch biosynthesis during grain development. The distribution of cytokinins in plant tissues determines plant growth and development and is regulated by several cytokinin transporters, including purine permease (PUP). Thirteen PUP genes have been identified within the rice genome; however, the functions of most of these genes remain poorly understood. We found that pup11 mutants showed extremely low seed setting rates and a unique filled seed distribution. Moreover, seed formation arrest in these mutants was associated with the disappearance of accumulated starch 10 days after flowering. PUP11 has two major transcripts with different expression patterns and subcellular locations, and further studies revealed that they have redundant positive roles in regulating the seed setting rate. We also found that type-A Response Regulator (RR) genes were upregulated in the developing grains of the pup11 mutant compared with those in the wild type. The results also showed that PUP11 altered the expression of several sucrose transporters and significantly upregulated certain starch biosynthesis genes. In summary, our results indicate that PUP11 influences the rice seed setting rate by regulating sucrose transport and starch accumulation during grain filling. This research provides new insights into the relationship between cytokinins and seed development, which may help improve cereal yield., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Nitrogen fertilization can mitigate the negative effects of high temperatures on rice. In this study, we simulated dynamic field temperature increases using a free-air temperature enhancement system. Changes in the physicochemical properties of starch were investigated under increasing nitrogen fertilization during the grain-filling stage. We observed that the application of nitrogen at elevated temperatures (ETN) did not change the chain length distribution compared with elevated temperatures (ET) alone; however, it did significantly increase the heights of the first and second amylose peaks. Specifically, ETN significantly decreased the height of fifth amylopectin and relative crystallinity, and the changes it introduced in the physicochemical properties of starch were greater than those of ET. Overall, these changes in starch properties may be associated with the ability of nitrogen to facilitate the maintenance of rice quality at high temperatures., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

The adverse impact of climate change on crop production continues to increase, necessitating the development of suitable strategies to mitigate these effects and improve food security. Several studies have revealed how global warming negatively impacts the grain-filling stage of rice and that this effect could be mitigated by nitrogen; however, the impact of nitrogen application on rice canopy and rhizosphere microbial communities remains unclear. We conducted a study using an open-field warming system. Results showed that warming influenced rice canopy by decreasing aboveground biomass and harvest index, whereas nitrogen application had positive effect on rice production under warming conditions by increasing the plant nitrogen content, biomass, harvest index and soil fertilities. Moreover, soil ammonium nitrogen (NH 4 + -N) and nitrate nitrogen (NO 3 - -N) contents were significantly decreased under warming, which were higher after nitrogen application. Notably, warming and nitrogen fertilizer caused 19 % (P < 0.01) and 7 % (P < 0.05) variations, respectively, in the β diversity of the microbial community, respectively. The impact of warming was significant on NH 4 + -N-related microorganisms; however, this impact was weakened by nitrogen application for microbes in the rhizosphere. This study demonstrated that enhanced nitrogen fertilizer can alleviate the adverse impact of warming by weakening its effects on rhizosphere microbes, improving soil fertility, promoting rice nitrogen uptake, and increasing the aboveground biomass and harvest index. These findings provide an important theoretical basis for developing practical, responsive cultivation strategies., Competing Interests: Declaration of competing interest We declare that we have no financial and personal relationships with other people or organizations that can inappropriately influence our work, there is no professional or other personal interest of any nature or kind in any product, service and/or company that could be construed as influencing the position presented in, or the review of, the manuscript entitled., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Accurate assessment of crop biochemical profiles plays a crucial role in diagnosing their physiological status. The conventional destructive methods, although reliable, demand extensive laboratory work for measuring various traits. On the other hand, nondestructive techniques, while efficient and adaptable, often suffer from reduced precision due to the intricate interplay of the field environment and canopy structure. Striking a delicate balance between efficiency and accuracy, we have developed the Bio-Master phenotyping system. This system is capable of simultaneously measuring four vital biochemical components of the canopy profile: dry matter, water, chlorophyll, and nitrogen content. Bio-Master initiates the process by addressing structural influences, through segmenting the fresh plant and then further chopping the segment into uniform small pieces. Subsequently, the system quantifies hyperspectral reflectance and fresh weight over the sample within a controlled dark chamber, utilizing an independent light source. The final step involves employing an embedded estimation model to provide synchronous estimates for the four biochemical components of the measured sample. In this study, we established a comprehensive training dataset encompassing a wide range of rice varieties, nitrogen levels, and growth stages. Gaussian process regression model was used to estimate biochemical contents utilizing reflectance data obtained by Bio-Master. Leave-one-out validation revealed the model's capacity to accurately estimate these contents at both leaf and plant scales. With Bio-Master, measuring a single rice plant takes approximately only 5 min, yielding around 10 values for each of the four biochemical components across the vertical profile. Furthermore, the Bio-Master system allows for immediate measurements near the field, mitigating potential alterations in plant status during transportation and processing. As a result, our measurements are more likely to faithfully represent in situ values. To summarize, the Bio-Master phenotyping system offers an efficient tool for comprehensive crop biochemical profiling. It harnesses the benefits of remote sensing techniques, providing significantly greater efficiency than conventional destructive methods while maintaining superior accuracy when compared to nondestructive approaches., Competing Interests: Competing interests: The authors declare that they have no competing interests., (Copyright © 2023 Ruowen Liu et al.)

This study aimed to investigate the effect of static magnetic field (SMF, 0-10 mT) on the quality of rice dumplings subjected to 7, 14, 21, and 28 freeze-thaw cycles. The underlying mechanism was explored by monitoring changes in water phase transition, water distribution, and structural and physicochemical properties of rice flour. Results suggested that SMF enables the formation of small ice crystals by accelerating freezing rate, shortening phase transition time, and increasing bound water content, which attributes to reducing the mechanical damage on starch granules and thus improves the quality of frozen rice dumpling. After 7-28 freeze-thaw cycles, SMF treatment increased the whiteness by 0.08-1.58, reduced the cracking ratio by 1.67 %-8.34 %, decreased the water loss ratio by 0-0.75 %, and significantly improved the texture of cooked rice dumplings. This study confirmed the feasibility of SMF in improving the quality of rice dumpling, which contributes to expanding the applications of magnetic freezer in the preservation of starch-based foods., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Background: The intensified global warming during grain filling deteriorated rice quality, in particular increasing the frequency of chalky grains which markedly impact market value. The formation of rice quality is a complex process influenced by multiple genes, proteins and physiological metabolic processes. Proteins responsive to stimulus can adjust the ability of plants to respond to unfavorable environments, which may be an important protein involved in the regulation of quality formation under elevated temperature. However, relatively few studies have hindered our further understanding of rice quality formation under elevated temperature., Results: We conducted the actual field elevated temperature experiment and performed proteomic analysis of rice grains at the early stage of grain filling. Starting with the response to stimulus in GO annotation, 22 key proteins responsive to stimulus were identified in the regulation of grain filling and response to elevated temperature. Among the proteins responsive to stimulus, during grain filling, an increased abundance of signal transduction and other stress response proteins, a decreased abundance of reactive oxygen species-related proteins, and an increased accumulation of storage substance metabolism proteins consistently contributed to grain filling. However, the abundance of probable indole-3-acetic acid-amido synthetase GH3.4, probable indole-3-acetic acid-amido synthetase GH3.8 and CBL-interacting protein kinase 9 belonged to signal transduction were inhibited under elevated temperature. In the reactive oxygen species-related protein, elevated temperature increased the accumulation of cationic peroxidase SPC4 and persulfide dioxygenase ETHE1 homolog to maintain normal physiological homeostasis. The increased abundance of alpha-amylase isozyme 3E and seed allergy protein RA5 was related to the storage substance metabolism, which regulated starch and protein accumulation under elevated temperature., Conclusion: Auxin synthesis and calcium signal associated with signal transduction, other stress responses, protein transport and modification, and reactive oxygen species-related proteins may be key proteins responsive to stimulus in response to elevated temperature. Alpha-amylase isozyme 3E and seed allergy protein RA5 may be the key proteins to regulate grain storage substance accumulation and further influence quality under elevated temperature. This study enriched the regulatory factors involved in the response to elevated temperature and provided a new idea for a better understanding of grain response to temperature., (© 2023. The Author(s).)

Auxin plays an essential role in modulating leaf development. However, its role in leaf development in rice (Oryza sativa L.) remains largely unknown. In this study, we found that PINOID (OsPID) and two Sister-of-PIN1s, termed PIN-FORMED1c (OsPIN1c) and OsPIN1d, are necessary for rice leaf development. The ospin1c ospin1d null mutant lines presented severe defects in leaf morphogenesis, including drooping and semi-drooping blades, an abnormally thickened sheath and lamina joint, and fused leaves with absent ligules and auricles. Loss-of-function ospid mutants displayed generally similar leaf morphology but lacked leaf fusion. Interestingly, misshaped leaf genesis displayed a preference for being ipsilateral. In addition, OsPIN1c and OsPID were commonly localized in the initiating leaf primordia. Furthermore, accompanied by the more severe organ morphogenesis in the ospin1c ospin1d ospid triple mutant, RNA sequencing analysis revealed that many genes essential for leaf development have an altered expression level. Together, this study furthers our understanding of the role auxin transport plays during leaf development in monocot rice., (© The Author(s) 2023. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The redistribution of nonstructural carbohydrates (NSCs) in rice (Oryza sativa) sheaths contributes greatly to grain filling. Sucrose nonfermenting-1-related protein kinase 1 (SnRK1) regulates sheath-to-panicle transport of NSCs during rice grain filling; however, it is unknown whether elevated activity of SnRK1 in sheaths improves NSC transport and grain filling. Expression of OsSnRK1a is mainly responsible for regulating SnRK1 activity in rice sheaths. Analysis of transgenic rice plants containing the OsSnRK1a promoter::GUS construct indicated that OsSnRK1a is widely expressed in rice. Notably, OsSnRK1a is highly expressed in mesophyll cells of sheaths. Therefore, a green tissue promoter specifically expressed in sheaths and leaf parenchyma cells and phloem tissue was used to over-express OsSnRK1a in japonica rice. The transgenic lines exhibited increased SnRK1a expression and SnRK1 activity in sheaths. The NSC and starch in the transgenic lines and WT all showed accumulation before heading and during the early-filling stage, and declining at the peak filling stage. But the starch and NSC content in transgenic lines was lower than that of WT. Moreover, the transgenic lines showed lower sucrose contents and higher sucrose efflux rates. The accelerated sheath NSC transport improved grain filling, and stimulated panicle development in transgenic lines. SnRK1a expression and SnRK1 activity were also increased in the leaves of transgenic lines, which improved leaf photosynthetic activity and contributed to optimal grain filling and panicle development. These results verify the promotion of high SnRK1 activity in sheath NSC transport, and also provide a new approach to improving sheath NSC transport and rice yield., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Masson SAS. All rights reserved.)

Poor grain-filling initiation in inferior spikelets severely impedes rice yield improvement, while photo-assimilates from source leaves can greatly stimulate the initiation of inferior grain-filling (sink). To investigate the underlying mechanism of source-sink interaction, a two-year field experiment was conducted in 2019 and 2020 using two large-panicle rice cultivars (CJ03 and W1844). The treatments included intact panicles and partial spikelet removal. These two cultivars showed no significant difference in the number of spikelets per panicle. However, after removing spikelet, W1844 showed higher promotion on 1000-grain weight and seed-setting rate than CJ03, particularly for inferior spikelets. The reason was that the better sink activity of W1844 led to a more effective initiation of inferior grain-filling compared to CJ03. The inferior grain weight of CJ03 and W1844 did not show a significant increase until 8 days poster anthesis (DPA), which follows a similar pattern to the accumulation of photo-assimilates in leaves. After removing spikelets, the source leaves of W1844 exhibited lower photosynthetic inhibition compared to CJ03, as well as stronger metabolism and transport of photo-assimilates. Although T6P levels remained constant in both cultivars under same conditions, the source leaves of W1844 showed notable downregulation of SnRK1 activity and upregulation of phytohormones (such as abscisic acid, cytokinins, and auxin) after removing spikelets. Hence, the high sink strength of inferior spikelets plays a role in triggering the enhancement of source strength in rice leaves, thereby fulfilling grain-filling initiation demands., (© 2023. Springer Science+Business Media, LLC, part of Springer Nature.)

Rice glutelin is sensitive to temperature and nitrogen, however, the regulatory mechanism of glutelin response to temperature and nitrogen is unclear. In this study, we conducted the open field warming experiment by the Free-air temperature enhancement facility and application of nitrogen during grain filling. In three-year field warming experiments, glutelin relative content was significantly increased under elevated temperature and application of nitrogen. Temperature and nitrogen and their interaction increased the glutelin accumulation rate in the early and middle grain filling stages (10-25d after flowering), but decreased the glutelin accumulation rate in the middle and late grain filling stages (25-45d after flowering). Elevated temperature promoted pro-glutelin levels whereas application of nitrogen under warming increased the amount of α-glutelin. At the transcriptional level, the expression levels of the glutelin-encoding genes and protein disulphide isomerase-like enzyme (PDIL1-1), glutelin precursor accumulation 4 (GPA4), glutelin precursor mutant 6 (GPA2), glutelin precursor accumulation 3 (GPA3) and vacuolar processing enzyme (OsVPE1) of glutelin folding, transport and accumulation-related genes were up-regulated by nitrogen under natural temperature as early as 5d after flowering. However, elevated temperature up-regulated glutelin-encoding genes before 20d after flowering, and the expression of endoplasmic reticulum chaperone (OsBip1), OsPDIL1-1, small GTPase gene (GPA1), GPA2-GPA4 and OsVPE1 were significantly increased post 20d after flowering under warming. In addition, the increase in glutelin content worsened grain quality, particularly chalkiness and eating quality. Overall, the results were helpful to understand glutelin accumulation and provide a theoretical basis for further study the relationship between rice quality and glutelin under global warming., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Masson SAS. All rights reserved.)

Key Message: SMC5/6 complex subunit OsMMS21 is involved in cell cycle and hormone signaling and required for stem cell proliferation during shoot and root development in rice. The structural maintenance of chromosome (SMC)5/6 complex is required for nucleolar integrity and DNA metabolism. Moreover, METHYL METHANESULFONATE SENSITIVITY GENE 21 (MMS21), a SUMO E3 ligase that is part of the SMC5/6 complex, is essential for the root stem cell niche and cell cycle transition in Arabidopsis. However, its specific role in rice remains unclear. Here, OsSMC5 and OsSMC6 single heterozygous mutants were generated using CRISPR/Cas9 technology to elucidate the function of SMC5/6 subunits, including OsSMC5, OsSMC6, and OsMMS21, in cell proliferation in rice. ossmc5/ + and ossmc6/ + heterozygous single mutants did not yield homozygous mutants in their progeny, indicating that OsSMC5 and OsSMC6 both play necessary roles during embryo formation. Loss of OsMMS21 caused severe defects in both the shoot and roots in rice. Transcriptome analysis showed a significant decrease in the expression of genes involved in auxin signaling in the roots of osmms21 mutants. Moreover, the expression levels of the cycB2-1 and MCM genes, which are involved the cell cycle, were significantly lower in the shoots of the mutants, indicating that OsMMS21 was involved in both hormone signaling pathways and the cell cycle. Overall, these findings indicate that the SUMO E3 ligase OsMMS21 is required for both shoot and root stem cell niches, improving the understanding of the function of the SMC5/6 complex in rice., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The green fraction (GF), which is the fraction of green vegetation in a given viewing direction, is closely related to the light interception ability of the crop canopy. Monitoring the dynamics of GF is therefore of great interest for breeders to identify genotypes with high radiation use efficiency. The accuracy of GF estimation depends heavily on the quality of the segmentation dataset and the accuracy of the image segmentation method. To enhance segmentation accuracy while reducing annotation costs, we developed a self-supervised strategy for deep learning semantic segmentation of rice and wheat field images with very contrasting field backgrounds. First, the Digital Plant Phenotyping Platform was used to generate large, perfectly labeled simulated field images for wheat and rice crops, considering diverse canopy structures and a wide range of environmental conditions (sim dataset). We then used the domain adaptation model cycle-consistent generative adversarial network (CycleGAN) to bridge the reality gap between the simulated and real images (real dataset), producing simulation-to-reality images (sim2real dataset). Finally, 3 different semantic segmentation models (U-Net, DeepLabV3+, and SegFormer) were trained using 3 datasets (real, sim, and sim2real datasets). The performance of the 9 training strategies was assessed using real images captured from various sites. The results showed that SegFormer trained using the sim2real dataset achieved the best segmentation performance for both rice and wheat crops (rice: Accuracy = 0.940, F1-score = 0.937; wheat: Accuracy = 0.952, F1-score = 0.935). Likewise, favorable GF estimation results were obtained using the above strategy (rice: R 2  = 0.967, RMSE = 0.048; wheat: R 2  = 0.984, RMSE = 0.028). Compared with SegFormer trained using a real dataset, the optimal strategy demonstrated greater superiority for wheat images than for rice images. This discrepancy can be partially attributed to the differences in the backgrounds of the rice and wheat fields. The uncertainty analysis indicated that our strategy could be disrupted by the inhomogeneity of pixel brightness and the presence of senescent elements in the images. In summary, our self-supervised strategy addresses the issues of high cost and uncertain annotation accuracy during dataset creation, ultimately enhancing GF estimation accuracy for rice and wheat field images. The best weights we trained in wheat and rice are available: https://github.com/PheniX-Lab/sim2real-seg., (Copyright © 2023 Yangmingrui Gao et al.)

Drug delivery via intra-articular (IA) injection has proved to be effective in osteoarthritis (OA) therapy, limited by the drug efficiency and short retention time of the drug delivery systems (DDSs). Herein, a series of modified cross-linked dextran (Sephadex, S0) was fabricated by respectively grafting with linear alkyl chains, branched alkyl chains or aromatic chain, and acted as DDSs after ibuprofen (Ibu) loading for OA therapy. This DDSs expressed sustained drug release, excellent anti-inflammatory and chondroprotective effects both in IL-1 β induced chondrocytes and OA joints. Specifically, the introduction of a longer hydrophobic chain, particularly an aromatic chain, distinctly improved the hydrophobicity of S0, increased Ibu loading efficiency, and further led to significantly improving OA therapeutic effects. Therefore, hydrophobic microspheres with greatly improved drug loading ratio and prolonged degradation rates show great potential to act as DDSs for OA therapy., Competing Interests: The authors declare that no potential conflicts of interest were disclosed., (© 2023 Published by Elsevier B.V. on behalf of Shenyang Pharmaceutical University.)

Key Message: The transcription elongation factor SPT4/SPT5 complex is essential for rice vegetative and reproductive growth and that OsSPT5-1, with its interactor APO2, is involved in multiple phytohormone pathways. The SPT4/SPT5 complex is a transcription elongation factor that regulates the processivity of transcription elongation. However, our understanding of the role of SPT4/SPT5 complex in developmental regulation remains limited. Here, we identified three SPT4/SPT5 genes (OsSPT4, OsSPT5-1, and OsSPT5-2) in rice, and investigated their roles in vegetative and reproductive growth. These genes are highly conserved with their orthologs in other species. OsSPT4 and OsSPT5-1 are widely expressed in various tissues. By contrast, OsSPT5-2 is expressed at a relatively low level, which could cause osspt5-2 null mutants have no phenotypes. Loss-of-function mutants of OsSPT4 and OsSPT5-1 could not be obtained; their heterozygotes showed severe reproductive growth defects. An incomplete mutant line (osspt5-1#12) displayed gibberellin-related dwarfed defects and a weak root system at an early vegetative phase, and a short life cycle in different planting environments. Furthermore, OsSPT5-1 interacts with the transcription factor ABERRANT PANICLE ORGANIZATION 2 (APO2) and plays a similar role in regulating the growth of rice shoots. RNA sequencing analysis verified that OsSPT5-1 is involved in multiple phytohormone pathways, including gibberellin, auxin, and cytokinin. Therefore, the SPT4/SPT5 complex is essential for both vegetative and reproductive growth in rice., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Detailed observation of the phenotypic changes in rice panicle substantially helps us to understand the yield formation. In recent studies, phenotyping of rice panicles during the heading-flowering stage still lacks comprehensive analysis, especially of panicle development under different nitrogen treatments. In this work, we proposed a pipeline to automatically acquire the detailed panicle traits based on time-series images by using the YOLO v5, ResNet50, and DeepSORT models. Combined with field observation data, the proposed method was used to test whether it has an ability to identify subtle differences in panicle developments under different nitrogen treatments. The result shows that panicle counting throughout the heading-flowering stage achieved high accuracy ( R 2 = 0.96 and RMSE = 1.73), and heading date was estimated with an absolute error of 0.25 days. In addition, by identical panicle tracking based on the time-series images, we analyzed detailed flowering phenotypic changes of a single panicle, such as flowering duration and individual panicle flowering time. For rice population, with an increase in the nitrogen application: panicle number increased, heading date changed little, but the duration was slightly extended; cumulative flowering panicle number increased, rice flowering initiation date arrived earlier while the ending date was later; thus, the flowering duration became longer. For a single panicle, identical panicle tracking revealed that higher nitrogen application led to earlier flowering initiation date, significantly longer flowering days, and significantly longer total duration from vigorous flowering beginning to the end (total DBE). However, the vigorous flowering beginning time showed no significant differences and there was a slight decrease in daily DBE., (Copyright © 2023 Qinyang Zhou et al.)

Seed dormancy and germination are regulated by endogenous gene expression as well as hormonal and environmental conditions, such as salinity, which greatly inhibits seed germination. MOTHER OF FT AND TFL1 (MFT), which encodes a phosphatidylethanolamine-binding protein, is a key regulator of seed germination in Arabidopsis thaliana. There are two orthologous genes of AtMFT in rice (Oryza sativa), namely, OsMFT1 and OsMFT2. However, the functions of these two genes in regulating rice seed germination under salt stress remain unknown. In this study, we found that seeds of loss-of-function osmft1 mutants germinated faster than wild-type (WT) seeds under salt stress, but this was not the case for loss-of-function osmft2 mutants. Overexpression of OsMFT1 (OsMFT1OE) or OsMFT2 increased the sensitivity to salt stress during seed germination. Transcriptome comparisons of osmft1 vs WT in the absence and presence of salt stress yielded several differentially expressed genes, which were associated with salt stress, plant hormone metabolism and signaling pathways, such as B-BOX ZINC FINGER 6, O. sativa bZIP PROTEIN 8 and GIBBERELLIN (GA) 20-oxidase 1. In addition, the sensitivity of OsMFT1OE seeds to GA and osmft1 seeds to abscisic acid (ABA) during seed germination increased under salt stress. Overall, our results indicate that ABA and GA metabolism and their signaling pathways are regulated by OsMFT1, modulating seed germination in rice under salt stress., (© The Author(s) 2023. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The impact of habitual physical activity on vagal-cardiac function and baroreflex sensitivity in elderly women is poorly characterized. This study compared vagal-cardiac modulation and carotid baroreflex (CBR) function in eight physically active (67.6 ± 1.9 years; peak O 2 uptake 29.1 ± 2.5 mL/min/kg) versus eight sedentary (67.3 ± 1.8 years; peak O 2 uptake 18.6 ± 0.9 mL/min/kg) elderly women. Heart rate (HR) variabilities and maximal changes of HR and mean arterial pressure (MAP) elicited by 5-s pressure pulses between +40 and -80 mmHg applied to the carotid sinus were measured at rest and during carotid baroreceptor unloading effected by -15 mmHg lower-body negative pressure (LBNP). HR variability was greater in active than sedentary women in both low (0.998 ± 0.286 versus 0.255 ± 0.063 bpm 2 ; P  = 0.036) and high (0.895 ± 0.301 versus 0.156 ± 0.045 bpm 2 ; P  = 0.044) frequency domains. CBR-HR gains (bpm/mmHg) were greater (fitness factor P  < 0.001) in active versus sedentary women at rest (-0.146 ± 0.014 versus -0.088 ± 0.011) and during LBNP (-0.105 ± 0.014 versus -0.065 ± 0.008). CBR-MAP gains (mmHg/mmHg) tended to be greater (fitness factor P  = 0.077) in active versus sedentary women at rest (-0.132 ± 0.013 versus -0.110 ± 0.011) and during LBNP (-0.129 ± 0.015 versus -0.113 ± 0.013). However, LBNP did not potentiate CBR-MAP gains in either sedentary or active women (LBNP factor P  = 0.94), and it depressed CBR-HR gains in both groups (LBNP factor P  = 0.003). CBR-HR gains in the sedentary women did not differ (sex factor P  = 0.65) from gains reported in age-matched sedentary men, although CBR-MAP gains tended to be greater (sex factor P  = 0.109) in the men. Thus, tonic vagal modulation indicated by HR variability and dynamic vagal responses assessed by CBR-HR gain were augmented in physically active women. Enhanced vagal-cardiac function may protect against senescence-associated cardiac electrical and hemodynamic instability in elderly women.

Enhancing the photosynthetic rate is one of the effective ways to increase rice yield, given that photosynthesis is the basis of crop productivity. At the leaf level, crops' photosynthetic rate is mainly determined by photosynthetic functional traits including the maximum carboxylation rate ( V cmax ) and stomatal conductance (gs). Accurate quantification of these functional traits is important to simulate and predict the growth status of rice. In recent studies, the emerging sun-induced chlorophyll fluorescence (SIF) provides us an unprecedented opportunity to estimate crops' photosynthetic traits, owing to its direct and mechanistic links to photosynthesis. Therefore, in this study, we proposed a practical semimechanistic model to estimate the seasonal V cmax and gs time-series based on SIF. We firstly generated the coupling relationship between the open ratio of photosystem II (qL) and photosynthetically active radiation (PAR), then estimate the electron transport rate (ETR) based on the proposed mechanistic relationship between SIF and ETR. Finally, V cmax and gs were estimated by linking to ETR based on the principle of evolutionary optimality and the photosynthetic pathway. Validation with field observations showed that our proposed model can estimate V cmax and gs with high accuracy ( R 2 > 0.8). Compared to simple linear regression model, the proposed model could increase the accuracy of V cmax estimates by >40%. Therefore, the proposed method effectively enhanced the estimation accuracy of crops' functional traits, which sheds new light on developing high-throughput monitoring techniques to estimate plant functional traits, and also can improve our understating of crops' physiological response to climate change., (Copyright © 2023 Hao Ding et al.)

The number of leaves at a given time is important to characterize plant growth and development. In this work, we developed a high-throughput method to count the number of leaves by detecting leaf tips in RGB images. The digital plant phenotyping platform was used to simulate a large and diverse dataset of RGB images and corresponding leaf tip labels of wheat plants at seedling stages (150,000 images with over 2 million labels). The realism of the images was then improved using domain adaptation methods before training deep learning models. The results demonstrate the efficiency of the proposed method evaluated on a diverse test dataset, collecting measurements from 5 countries obtained under different environments, growth stages, and lighting conditions with different cameras (450 images with over 2,162 labels). Among the 6 combinations of deep learning models and domain adaptation techniques, the Faster-RCNN model with cycle-consistent generative adversarial network adaptation technique provided the best performance ( R 2 = 0.94, root mean square error = 8.7). Complementary studies show that it is essential to simulate images with sufficient realism (background, leaf texture, and lighting conditions) before applying domain adaptation techniques. Furthermore, the spatial resolution should be better than 0.6 mm per pixel to identify leaf tips. The method is claimed to be self-supervised since no manual labeling is required for model training. The self-supervised phenotyping approach developed here offers great potential for addressing a wide range of plant phenotyping problems. The trained networks are available at https://github.com/YinglunLi/Wheat-leaf-tip-detection.

There is a need to comprehensively evaluate the rice quality of different rice varieties under different nitrogen treatments. Therefore, in this study, we used twenty-one hybrid indica rice varieties and twenty-three inbred japonica rice varieties with three nitrogen fertilizer levels to investigate differences in rice qualities. As compared with hybrid indica rice, inbred japonica rice had lower coefficient of variation values for grain shape, mild rice percentage, and head rice percentage, but relatively higher coefficient of variation values for chalkiness traits, appearance, and taste value of cooked rice. A principal component analysis and membership function method were used to comprehensively evaluate the qualities of rice. The overall eating quality value by sensory evaluation and head rice percentage explained 61.3% and 67.9% of the variations in comprehensive quality of hybrid indica rice and inbred japonica rice across different nitrogen levels, respectively. We also found that rice comprehensive quality was better under low nitrogen levels for hybrid indica rice, while for inbred japonica rice, properly increasing nitrogen application could improve the comprehensive quality.

Glucose-6-phosphate dehydrogenase (G6PDH) catalyzes a metabolic hub between glycolysis and the pentose phosphate pathway (PPP), which is the oxidation of glucose-6-phosphate (G6P) to 6-phosphogluconolactone concomitantly with the production of nicotinamide adenine dinucleotide phosphate (NADPH), a reducing power. It is considered to be the rate-limiting step that governs carbon flow through the oxidative pentose phosphate pathway (OPPP). The OPPP is the main supplier of reductant (NADPH) for several "reducing" biosynthetic reactions. Although it is involved in multiple physiological processes, current knowledge on its exact role and regulation is still piecemeal. The present review provides a concise and comprehensive picture of the diversity of plant G6PDHs and their role in seed germination, nitrogen assimilation, plant branching, and plant response to abiotic stress. This work will help define future research directions to improve our knowledge of G6PDHs in plant physiology and to integrate this hidden player in plant performance.

Plant phenomics (PP) has been recognized as a bottleneck in studying the interactions of genomics and environment on plants, limiting the progress of smart breeding and precise cultivation. High-throughput plant phenotyping is challenging owing to the spatio-temporal dynamics of traits. Proximal and remote sensing (PRS) techniques are increasingly used for plant phenotyping because of their advantages in multi-dimensional data acquisition and analysis. Substantial progress of PRS applications in PP has been observed over the last two decades and is analyzed here from an interdisciplinary perspective based on 2972 publications. This progress covers most aspects of PRS application in PP, including patterns of global spatial distribution and temporal dynamics, specific PRS technologies, phenotypic research fields, working environments, species, and traits. Subsequently, we demonstrate how to link PRS to multi-omics studies, including how to achieve multi-dimensional PRS data acquisition and processing, how to systematically integrate all kinds of phenotypic information and derive phenotypic knowledge with biological significance, and how to link PP to multi-omics association analysis. Finally, we identify three future perspectives for PRS-based PP: (1) strengthening the spatial and temporal consistency of PRS data, (2) exploring novel phenotypic traits, and (3) facilitating multi-omics communication., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

Background: Brief hypoxic exposures are increasingly applied as interventions for aging-related conditions. To optimize the therapeutic impact of hypoxia, knowledge of the sex-related differences in physiological responses to hypoxia is essential. This study compared hypoxia-induced hypoxemic responses in elderly men and women. Methods : Seven elderly men (70.3 ± 6.0 years old) and nine women (69.4 ± 5.5 years old) breathed 10% O 2 for 5 min while arterial (SaO 2 ; transcutaneous photoplethysmography) and cerebral tissue O 2 saturation (ScO 2 ; near-infrared spectroscopy), ventilatory frequency, tidal volume, minute-ventilation, and partial pressures of end-tidal O 2 (P ET O 2 ) and CO 2 (mass spectrometry) were continuously monitored. Cerebral tissue oxygen extraction fraction (OEF) equaled (SaO 2 -ScO 2 )/SaO 2 . Results: During 5 min hypoxia SaO 2 fell from 97.0 ± 0.8% to 80.6 ± 4.6% in the men and from 96.3 ± 1.4% to 72.6 ± 4.0% in the women. The slope ΔSaO 2 /min was steeper in the women than the men (-4.71 ± 0.96 vs. -3.24 ± 0.76%/min; p = 0.005). Although SaO 2 fell twice as sharply per unit decrease in P ET O 2 in the women than the men (-1.13 ± 0.11 vs. -0.54 ± 0.06%/mmHg; p = 0.003), minute-ventilation per unit hypoxemia increased less appreciably in the women (-0.092 ± 0.014 vs. -0.160 ± 0.021 L/min/%; p = 0.023). OEF fell with hypoxia duration in the women, but remained stable in the men. Conclusion: During 5 min hypoxic breathing, elderly women experience more intense hypoxemia and reduced chemoreflex sensitivity vs. their male counterparts, which may lower OEF stability in women despite augmented O 2 dissociation from hemoglobin during hypoxia. These sex-related differences merit attention when implementing brief hypoxic exposures for therapeutic purposes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Zhao, Ding, Kline, Zhou, Mallet and Shi.)

Fertilizer management is vital for sustainable agriculture under climate change. Reduced basal and increased topdressing fertilizer rate (RBIT) has been reported to improve the yield of in-season rice or wheat. However, the effect of RBIT on rice and wheat yield stability and soil organic carbon (SOC) sequestration potential is unknown, especially when combined with straw incorporation. Here, we report the effect of RBIT with/without straw incorporation on crop yields, yield stability, SOC stock, and SOC fractions in the lower Yangtze River rice-wheat system region over nine years. RBIT with/without straw incorporation significantly increased nine-year average and annual rice yields but not wheat yields. Compared with conventional fertilization ( CF ), RBIT did not significantly affect wheat or rice yield stability, but combined with straw incorporation, it increased the sustainable yield index (SYI) of wheat and rice by 7.6 and 12.8%, respectively. RBIT produced a higher C sequestration rate (0.20 Mg C ha -1 year -1 ) than CF (0.06 Mg ha -1 year -1 ) in the 0-20 cm layer due to higher root C input and lower C mineralization rate, and RBIT in combination with straw incorporation produced the highest C sequestration rate (0.47 Mg ha -1 year -1 ). Long-term RBIT had a greater positive effect on silt+clay (0.053 mm)-associated C, microbial biomass C (MBC), dissolved organic C, and hot water organic C in the surface layer (0-10 cm) than in the subsurface layer (10-20 cm). In particular, the increases in SOC pools and mean weight diameter (MWD) of soil aggregates were greater when RBIT was combined with straw incorporation. Correlation analysis indicated that topsoil SOC fractions and MWD were positively correlated with the SYI of wheat and rice. Our findings suggest that the long-term application of RBIT combined with straw incorporation contributed to improving the sustainability of rice production and SOC sequestration in a rice-wheat system., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Zhang, Wang, Zhou, Xu, Chen, Ding, Ning, Liang, Zhang and Li.)

Salt stress severely restricts the growth of plants and threatens the development of agriculture throughout the world. Worldwide studies have shown that exogenous melatonin (MT) can effectively improve the growth of plants under salt stress. Through a meta-analysis of 549 observations, this study first explored the effects of salt stress characteristics and MT application characteristics on MT regulated plant growth under salt stress. The results show that MT has a wide range of regulatory effects on plant growth indicators under salt stress, of which the regulatory effect on root indexes is the strongest, and this regulatory effect is not species-specific. The intensity of salt stress did not affect the positive effect of MT on plant growth, but the application effect of MT in soil was stronger than that in rooting medium. This meta-analysis also revealed that the foliar application of a concentration between 100-200 μM is the best condition for MT to enhance plant growth under salt stress. The results can inspire scientific research and practical production, while seeking the maximum improvement in plant salt tolerance under salt stress.

Sucrose non-fermenting-1-related protein kinase 1 (SnRK1) plays a key role in rice germination. The small molecule drug, A-769662, activates AMP-activated protein kinase, a mammalian homolog of SnRK1. However, it is unknown whether A-769662 activates SnRK1, thereby affecting germination. SnRK1 in desalted extracts from germinating rice seeds was strongly activated by adding A-769662 in vitro. Applying 50 or 100 μM A-769662 accelerated germination and increased the root length, shoot length, and seedling fresh weight. 50 μM A-769662 treatment increased the catalytic activity and phosphorylation of SnRK1 during germination. Transcriptome analysis and biochemical validation were performed to investigate the mechanism whereby A-769662 treatment promoted rice germination. A-769662 treatment promoted starch hydrolysis by increasing the expression and activity of amylase and inhibited starch biosynthesis by decreasing the expression of OsAGPL2, OsAGPS2a, Wx, and SSIIa. The abscisic acid (ABA) level and gene expression of ABA-induced transcription factors, including OsNF-YC9, OsNF-YC12, OsWRKY24, OsPYL8, OsMKKK62, and OsMKKK63, which reduced the inhibition of germination by ABA were decreased under 50 μM A-769662 treatment. The increased expression of the OsACO3 and OsACO5 genes and increased ethylene levels under A-769662 treatment, which counteracted the inhibition of ABA on germination and, thus, promoted germination. These results demonstrate the activation of A-769662 on SnRK1 and further reveal the regulatory mechanism of A-769662 in rice seed germination and nutrient remobilization., (Copyright © 2022 Elsevier Masson SAS. All rights reserved.)

The remobilization of nonstructural carbohydrates (NSCs) reserved in rice (Oryza sativa) sheaths is essential for grain filling. This assimilate distribution between plant tissues and organs is determined by sucrose non-fermenting-1-related protein kinase 1 (SnRK1). However, the SnRK1-mediated mechanism regulating the sheath-to-panicle transport of NSCs in rice remains unknown. In this study, leaf cutting treatment was used to accelerate NSC transport in the rice sheaths. Accelerated NSC transport was accompanied by increased levels of OsSnRK1a mRNA expression, SnRK1a protein expression, catalytic subunit phosphorylation of SnRK1, and SnRK1 activity, indicating that SnRK1 activity plays an important role in sheath NSC transport. We also discovered that trehalose-6-phosphate, a signal of sucrose availability, slightly reduced SnRK1 activity in vitro. Since SnRK1 activity is mostly regulated by OsSnRK1a transcription in response to low sucrose content, we constructed an snrk1a mutant to verify the function of SnRK1 in NSC transport. NSCs accumulated in the sheaths of snrk1a mutant plants and resulted in a low seed setting rate and grain weight, verifying that SnRK1 activity is essential for NSC remobilization. Using phosphoproteomics and parallel reaction monitoring, we identified 20 SnRK1-dependent phosphosites that are involved in NSC transport. In addition, the SnRK1-mediated phosphorylation of the phosphosites directly affected starch degradation, sucrose metabolism, phloem transport, sugar transport across the tonoplast, and glycolysis in rice sheaths to promote NSC transport. Therefore, our findings reveal the importance, function, and possible regulatory mechanism of SnRK1 in the sheath-to-panicle transport of NSCs in rice., (© American Society of Plant Biologists 2022. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Cytokinins play key roles in plant growth and development, and hence their biosynthesis and degradation have been extensively studied. Cytokinin oxidase/dehydrogenases (CKXs) are a group of enzymes that regulate oxidative cleavage to maintain cytokinin homeostasis. In rice, 11 CKX genes have been identified to date; however, most of their functions remain unknown. In this study, we comprehensively examined the expression patterns and functions of the CKXs in rice by using CRISPR/Cas9 technology to construct mutants of all 11 genes. The results revealed that the ckx single-mutants and higher-order ckx4 ckx9 mutant lines showed functional overlaps and sub-functionalization. Notably, the ckx1 ckx2 and ckx4 ckx9 double-mutants displayed contrasting phenotypic changes in tiller number and panicle size compared to the wild-type. In addition, we identified several genes with significantly altered expression in both the ckx4 and ckx9 single-mutant and double-mutant plants. Many of the differentially expressed genes were found to be associated with auxin and cytokinin pathways, and cytokinins in the ckx4 ckx9 double-mutant were increased compared to the wild-type. Taken together, our findings provide new insights into the functions of CKX genes in rice growth and may provide the foundations for future studies aimed at improving rice yield., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Key Message: Chromatin remodeling ATPases OsSYD and OsBRM are involved in shoot establishment, and both affect OSH gene transcription. OsSYD protein interacts with RFL, but OsBRM does not. In plants, SPLAYED (SYD) and BRAHMA (BRM) encode chromatin remodeling ATPases that use the energy derived from ATP hydrolysis to restructure nucleosomes and render certain genomic regions available to transcription factors. However, the function of SYD and BRM on rice growth and development is unknown. Here, we constructed ossyd and osbrm mutants using CRISPR/Cas9 technology and analyzed the effects of mutations on rice embryo development. We discovered that the ossyd and osbrm mutants exhibited severe defects during embryonic development, whereas endosperm development was normal. These results indicated that the development of the embryo and endosperm is independent of each other. Consequently, the ossyd- and osbrm-null mutants did not germinate due to the abnormal embryos. Furthermore, we observed the embryos of ossyd- and osbrm-null mutants, and they indeed had distinct differentiation defects in shoot establishment, acquired during embryogenesis. To verify the function of OsSYD and OsBRM in embryogenesis, we measured the transcript levels of marker genes at different stages. Compared with wild type, the expression levels of multiple OSH genes were significantly reduced in the mutants, which was consistent with the defective shoot establishment phenotypes. The interaction between SYD and RICE FLORICAULA/LFY (RFL) was revealed using a yeast two-hybrid screening system, suggesting that the interaction between the LFY homolog and chromatin remodeling ATPases is ubiquitous in plants. Collectively, our findings provide the basis for elucidating the function of OsSYD and OsBRM during embryo development in rice., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Podocyte injury induced by hyperglycemia is the main cause of kidney dysfunction in diabetic nephropathy. However, the underlying mechanism is unclear. Store-operated Ca 2+ entry (SOCE) regulates a diversity of cellular processes in a variety of cell types. Calpain, a Ca 2+ -dependent cysteine protease, was recently shown to be involved in podocyte injury. In the present study, we sought to determine whether increased SOCE contributed to high glucose (HG)-induced podocyte injury through activation of the calpain pathway. In cultured human podocytes, whole-cell patch clamp indicated the presence of functional store-operated Ca 2+ channels, which are composed of Orai1 proteins and mediate SOCE. Western blots showed that HG treatment increased the protein abundance of Orai1 in a dose-dependent manner. Consistently, calcium imaging experiments revealed that SOCE was significantly enhanced in podocytes following HG treatment. Furthermore, HG treatment caused overt podocyte F-actin disorganization as well as a significant decrease in nephrin protein abundance, both of which are indications of podocyte injury. These podocyte injury responses were significantly blunted by both pharmacological inhibition of Orai1 using the small molecule inhibitor BTP2 or by genetic deletion of Orai1 using CRISPR-Cas9 lentivirus. Moreover, activation of SOCE by thapsigargin, an inhibitor of Ca 2+ pump on the endoplasmic/sarcoplasmic reticulum membrane, significantly increased the activity of calpain, which was inhibited by BTP2. Finally, the calpain-1/calpain-2 inhibitor calpeptin significantly blunted the nephrin protein reduction induced by HG treatment. Taken together, our results suggest that enhanced signaling via an Orai1/SOCE/Calpain axis contributes to HG-induced podocyte injury., Competing Interests: Conflict of interests The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

The stress of transplanting injury adversely affects rice growth and productivity worldwide. N-acetylcysteine (NAC), the precursor of glutathione, is a potent ROS scavenger with powerful antioxidant activity. Previous studies on the application of NAC in plants mainly focused on alleviating the stress of heavy metals, UV-B, herbicides, etc. However, the role of NAC in alleviating transplanting injury is still not clear. A barrel experiment was carried out to explain the mechanism of NAC regulating the transplanting injury to machine-transplanted rice during the recovery stage. The results showed that NAC priming shortened the time of initiation of tillering and increased the tiller numbers within 3 weeks after transplanting. In addition, NAC priming increased the chlorophyll content, net photosynthetic rate, and sucrose content, thereby improving the dry weight at the recovery stage, especially root dry weight. At the same time, NAC priming significantly increased the activity of ascorbate peroxidase (APX), glutathione reductase (GR), catalase (CAT), and superoxide dismutase (SOD). In addition, it also regulated flavonoids and total phenols contents to reduce hydrogen peroxide (H 2 O 2 ) and malondialdehyde (MDA) contents, especially at the initial days after transplanting. These results suggest that NAC priming improves the tolerance of rice seedlings against transplanting injury by enhancing photosynthesis and antioxidant systems at initial days after transplanting, thereby promoting the accumulation of dry matter and tillering for higher yield returns.

The remobilization of non-structural carbohydrates (NSCs) in the stem is essential for rice grain filling so as to improve grain yield. We conducted a two-year field experiment to deeply investigate their relationship. Two large-panicle rice varieties with similar spikelet size, CJ03 and W1844, were used to conduct two treatments (removing-spikelet group and control group). Compared to CJ03, W1844 had higher 1000-grain weight, especially for the grain growth of inferior spikelets (IS) after removing the spikelet. These results were mainly ascribed to the stronger sink strength of W1844 than that of CJ03 contrasting in the same group. The remobilization efficiency of NSC in the stem decreased significantly after removing the spikelet for both CJ03 and W1844, and the level of sugar signaling in the T6P-SnRK1 pathway was also significantly changed. However, W1844 outperformed CJ03 in terms of the efficiency of carbon reserve remobilization under the same treatments. More precisely, there was a significant difference during the early grain-filling stage in terms of the conversion of sucrose and starch. Interestingly, the sugar signaling of the T6P and SnRK1 pathways also represented an obvious change. Hence, sugar signaling may be promoted by sink strength to remobilize the NSCs of the rice stem during grain filling to further advance crop yield.

Global warming is expected to affect methane (CH 4 ) emissions from rice paddies, one of the largest human-induced sources of this potent greenhouse gas. However, the large variability in warming impacts on CH 4 emissions makes it difficult to extrapolate the experimental results over large regions. Here, we show, through meta-analysis and multi-site warming experiments using the free air temperature increase facility, that warming stimulates CH 4 emissions most strongly at background air temperatures during the flooded stage of ∼26 °C, with smaller responses of CH 4 emissions to warming at lower and higher temperatures. This pattern can be explained by divergent warming responses of plant growth, methanogens, and methanotrophs. The effects of warming on rice biomass decreased with the background air temperature. Warming increased the abundance of methanogens more strongly at the medium air temperature site than the low and high air temperature sites. In contrast, the effects of warming on the abundance of methanotrophs were similar across the three temperature sites. We estimate that 1 °C warming will increase CH 4 emissions from paddies in China by 12.6%─substantially higher than the estimates obtained from leading ecosystem models. Our findings challenge model assumptions and suggest that the estimates of future paddy CH 4 emissions need to consider both plant and microbial responses to warming.

The essential role of auxin in plant growth and development is well known. Pathways related to auxin synthesis, transport and signaling have been extensively studied in recent years, and the PIN-FORMED (PIN) protein family has been identified as being pivotal for polar auxin transport and distribution. However, research focused on the functional characterization of PIN proteins in rice is still lacking. In this study, we investigated the expression and function of OsPIN1c and OsPIN1d in the japonica rice variety (Nipponbare) using gene knockout and high-throughput RNA sequencing analysis. The results showed that OsPIN1c and OsPIN1d were mainly expressed in young panicles and exhibited a redundant function. Furthermore, OsPIN1c or OsPIN1d loss-of-function mutants presented a mild phenotype compared with the wild type. However, in addition to significantly decreased plant height and tiller number, panicle development was severely disrupted in double-mutant lines of OsPIN1c and OsPIN1d. Severe defects included smaller inflorescence meristem and panicle sizes, fewer primary branches, elongated bract leaves, non-degraded hair and no spikelet growth. Interestingly, ospin1cd-3, a double-mutant line with functional retention of OsPIN1d, showed milder defects than those observed in other mutants. Additionally, several critical regulators of reproductive development, such as OsPID, LAX1, OsMADS1 and OsSPL14/IPA1, were differentially expressed in ospin1c-1 ospin1d-1, supporting the hypothesis that OsPIN1c and OsPIN1d are involved in regulating panicle development. Therefore, this study provides novel insights into the auxin pathways that regulate plant reproductive development in monocots., (© The Author(s) 2021. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Grain chalkiness is a key quality trait of the rice grain, whereas its underlying mechanism is still not thoroughly understood because of the complex genetic and environmental interactions. We identified a notched-belly (NB) mutant that has a notched-line on the belly of grains. The line dissects the endosperm into two distinct parts, the upper translucent part, and the bottom chalky part in the vicinity of the embryo. Using this mutant, our previous studies clued the negative influence of embryo on the biochemical makeup of the endosperm, suggesting the need for the in-depth study of the embryo effect on the metabolome of developing endosperm. This study continued to use the NB mutant to evolve a novel comparison method to clarify the role of embryo in the formation of a chalky endosperm. Grain samples of the wild-type (WT) and NB were harvested at 10, 20, and 30 days after fertilization (DAF), and then divided into subsamples of the embryo, the upper endosperm, and the bottom endosperm. Using non-targeted metabolomics and whole-genome RNA sequencing (RNA-seq), a nearly complete catalog of expressed metabolites and genes was generated. Results showed that the embryo impaired the storage of sucrose, amino acid, starch, and storage proteins in the bottom endosperm of NB by enhancing the expression of sugar, amino acids, and peptide transporters, and declining the expression of starch, prolamin, and glutelin synthesis-related genes. Importantly, the competitive advantage of the developing embryo in extracting the nutrients from the endosperm, transformed the bottom endosperm into an "exhaustive source" by diverting the carbon (C) and nitrogen (N) metabolism from synthetic storage to secondary pathways, resulting in impaired filling of the bottom endosperm and subsequently the formation of chalky tissue. In summary, this study reveals that embryo-induced metabolic shift in the endosperm is associated with the occurrence of grain chalkiness, which is of relevance to the development of high-quality rice by balancing the embryo-endosperm interaction., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Tao, Mohi Ud Din, An, Chen, Li, Ding and Liu.)

To investigate the differential responses of super rice grain filling to low filling stage temperature (LT) and the regulative effect of nitrogen panicle fertilizer (NPF), physiological and molecular experiments were conducted with two super rice varieties (Nanjing 7th: N7 and Nanjing 9108th: N9108) on two different filling stage temperature treatments implemented by applying two sowing dates [Normal filling stage temperature (CK): Sowed on May 30, T mean = 24.7°C and low filling stage temperature (LT): Sowed on July 1, T mean = 20.3°C], and two NPF levels (0 and 150 kg N ha -1 ). In this study, LT, NPF, and simultaneous LT and NPF treatments suppressed the grain filling in all varieties with different levels. Under LT or NPF treatments, the reduction of grain weight, seed setting rate, and filling rate were closely associated with suppressed starch biosynthesis rate in inferior seeds, suggesting that reduced starch biosynthesis rate, expression, and activities of enzymes encoded by related genes, Floury endosperm-4 ( FLO4 ), Starch branching enzyme-I ( SBE1 ), and Starch phosphorylase-L ( PHO-l ), were responsible for the grain filling reduction. Under LT or NPF treatments, significantly higher grain filling rates and lower variance were found in N9108 compared to that in N7, which were closely related to their higher starch biosynthesis ability, related gene expression, and enzymes activities. One of the probable explanations of the grain filling difference was the variation in the relative amount of key regulative hormones, Abscisic acid (ABA) and 1-aminocyclopropane-1-carboxylic acid (ACC). These results raise a possibility that super rice with higher sink activities has superior adaptability to LT and NPF due to their higher sink activities., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Xu, Yang, Tang, Lu, Li, Liu, Ding, Ding and Li.)

With the intensification of global warming, rice production is facing new challenges. Field evidence indicates that elevated temperature during rice grain-filling leads to the further deterioration of grain quality. In order to clarify the potential regulatory mechanism of elevated temperature on the formation of rice quality, the DIA mass spectrometry method under the background of field warming was conducted to investigate the regulatory effects of high temperature on grain development and material accumulation pathways. The results showed that a total of 840 differentially expressed proteins were identified during the grain-filling process under elevated temperature. These differentially expressed proteins participated in carbon metabolism, amino acid biosynthesis, signal transduction, protein synthesis, and alternately affected the material accumulation of rice grains. The significant up-regulation of PPROL 14E, PSB28, granule-bound starch synthase I, and the significant down-regulation of 26.7 kDa heat shock protein would lead to the component difference in grain starch and storage proteins, and that could be responsible for the degradation of rice quality under elevated temperature. Results suggested that proteins specifically expressed under elevated temperature could be the key candidates for elucidating the potential regulatory mechanism of warming on rice development and quality formation. In-depth study on the metabolism of storage compounds would be contributed in further proposing high-quality cultivation control measures suitable for climate warming., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Liu, Yin, Zhao, Wang, Wang, Shen, Ding and Tang.)

Plant phenomics bridges the gap between traits of agricultural importance and genomic information. Limitations of current field-based phenotyping solutions include mobility, affordability, throughput, accuracy, scalability, and the ability to analyze big data collected. Here, we present a large-scale phenotyping solution that combines a commercial backpack Light Detection and Ranging (LiDAR) device and our analytic software, CropQuant-3D, which have been applied jointly to phenotype wheat (Triticum aestivum) and associated 3D trait analysis. The use of LiDAR can acquire millions of 3D points to represent spatial features of crops, and CropQuant-3D can extract meaningful traits from large, complex point clouds. In a case study examining the response of wheat varieties to three different levels of nitrogen fertilization in field experiments, the combined solution differentiated significant genotype and treatment effects on crop growth and structural variation in the canopy, with strong correlations with manual measurements. Hence, we demonstrate that this system could consistently perform 3D trait analysis at a larger scale and more quickly than heretofore possible and addresses challenges in mobility, throughput, and scalability. To ensure our work could reach non-expert users, we developed an open-source graphical user interface for CropQuant-3D. We, therefore, believe that the combined system is easy-to-use and could be used as a reliable research tool in multi-location phenotyping for both crop research and breeding. Furthermore, together with the fast maturity of LiDAR technologies, the system has the potential for further development in accuracy and affordability, contributing to the resolution of the phenotyping bottleneck and exploiting available genomic resources more effectively., (© The Author(s) 2021. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

A series of modified polysaccharide microparticles have been fabricated and their potential application for scavenging reactive oxygen species (ROS) and their derivatives to achieve osteoarthritis (OA) treatment has been explored. These microparticles were cross-linked dextran (Sephadex) with different carbazate substitution ratios determined by the TNBS assay and elemental analysis. It has been demonstrated that they could effectively scavenge carbonylated proteins and ROS including hydroxyl radicals (˙OH), superoxide anions (˙O 2 - ) and H 2 O 2 and their derivatives with high efficiency, improve the viability of H 2 O 2 -treated chondrocytes by reducing their ROS levels, as well as lower their inflammatory factors. The above ability of antioxidation and inflammation resistance improved with the increase of carbazate substitution ratio. Significantly, this work provided the proof that modified Sephadex successfully alleviated the deterioration of cartilage and the progression of OA in vivo . The proposed microparticles showed a very promising capability for reducing ROS levels and further treating OA.

The poor grain-filling initiation often causes the poor development of inferior spikelets (IS) which limits the yield potential of large panicle rice ( Oryza sativa L.). However, it remains unclear why IS often has poor grain-filling initiation. In addressing this problem, this study conducted a field experiment involving two large panicle rice varieties, namely CJ03 and W1844, in way of removing the superior spikelets (SS) during flowering to force enough photosynthate transport to the IS. The results of this study showed that the grain-filling initiation of SS was much earlier than the IS in CJ03 and W1844, whereas the grain-filling initiation of IS in W1844 was evidently more promoted compared with the IS of CJ03 by removing spikelets. The poor sucrose-unloading ability, i.e., carbohydrates contents, the expression patterns of OsSUTs , and activity of CWI, were highly improved in IS of CJ03 and W1844 by removing spikelets. However, there was a significantly higher rise in the efficiency of sucrose to starch metabolism, i.e., the expression patterns of OsSUS4 and OsAGPL1 and activities of SuSase and AGPase, for IS of W1844 than that of CJ03. Removing spikelets also led to the changes in sugar signaling of T6P and SnRK1 level. These changes might be related to the regulation of sucrose to starch metabolism. The findings of this study suggested that poor sucrose-unloading ability delays the grain-filling initiation of IS. Nonetheless, the efficiency of sucrose to starch metabolism is also strongly linked with the grain-filling initiation of IS., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Jiang, Chen, Chen, Yang, Zhu, Ding, Li, Liu, Jiang and Li.)

Plant growth rhythm in structural traits is important for better understanding plant response to the ever-changing environment. Terrestrial laser scanning (TLS) is a well-suited tool to study structural rhythm under field conditions. Recent studies have used TLS to describe the structural rhythm of trees, but no consistent patterns have been drawn. Meanwhile, whether TLS can capture structural rhythm in crops is unclear. Here, we aim to explore the seasonal and circadian rhythms in maize structural traits at both the plant and leaf levels from time-series TLS. The seasonal rhythm was studied using TLS data collected at four key growth periods, including jointing, bell-mouthed, heading, and maturity periods. Circadian rhythms were explored by using TLS data acquired around every 2 hours in a whole day under standard and cold stress conditions. Results showed that TLS can quantify the seasonal and circadian rhythm in structural traits at both plant and leaf levels. (1) Leaf inclination angle decreased significantly between the jointing stage and bell-mouthed stage. Leaf azimuth was stable after the jointing stage. (2) Some individual-level structural rhythms (e.g., azimuth and projected leaf area/PLA) were consistent with leaf-level structural rhythms. (3) The circadian rhythms of some traits (e.g., PLA) were not consistent under standard and cold stress conditions. (4) Environmental factors showed better correlations with leaf traits under cold stress than standard conditions. Temperature was the most important factor that significantly correlated with all leaf traits except leaf azimuth. This study highlights the potential of time-series TLS in studying outdoor agricultural chronobiology., Competing Interests: The authors declare that there is no conflict of interest regarding the publication of this article., (Copyright © 2021 Shichao Jin et al.)

Our previous study has shown that nitrogen plays an important role in dealing with significantly increased chalkiness caused by elevated temperature. However, the role of nitrogen metabolites has not been given sufficient attention, and its regulatory mechanism is not clear. This study investigated the effects of high temperature and nitrogen fertilizer on the synthesis of grain storage protein and further explored the quality mechanism under the actual scenario of field warming. Results showed that increased temperature and nitrogen fertilizer could affect the activities of nitrogen metabolism enzymes, namely, glutamate synthetase, glutamine synthetase, glutamic pyruvic transaminase, and glutamic oxaloacetic transaminase, and the expressions of storage protein synthesis factor genes, namely, GluA and GluB , and subfamily genes, namely, pro14, BiP1 , and PDIL1 , which co-induced the changes of storage protein synthesis in rice grains. Furthermore, the increased temperature changed the balance of grain storage substances which may lead to the significantly increased chalky rate (197.67%) and chalkiness (532.92%). Moreover, there was a significant negative correlation between prolamin content and chalkiness, indicating that nitrogen fertilizer might regulate the formation of chalkiness by affecting the synthesis of prolamin. Results suggested that nitrogen application could regulate the related core factors involved in nitrogen metabolism pathways, which, in turn, affects the changes in the storage protein components in the grain and further affects quality. Therefore, as a conventional cultivation measure, nitrogen application would have a certain value in future rice production in response to climate warming., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Wang, Wang, Yin, Zhao, Liu, Shen, Ding and Tang.)

Melatonin mediates multiple physiological processes in plants and is involved in many reactions related to the protection of plants from abiotic stress. In this paper, the effect of melatonin on the antioxidant capacity of rice under salt stress was studied. Melatonin alleviated the inhibition of salt stress on the growth of rice seedlings, mainly by increasing the dry weight and fresh weight of shoots and roots. Melatonin alleviated the membrane damage caused by salt stress, which was mainly manifested by the decrease of TBARS content and the decrease of leaf and root damage. During the whole salt stress period, rice after melatonin pretreatment showed lower ROS (H 2 O 2 , O 2 •- ,OH - ) accumulation. In the early stage (1-3 d) of stress, the rice after melatonin pretreatment showed a strong increase in antioxidant enzyme activity, while in the later stage (5,7 d), it showed a strong increase in antioxidant content. During the whole period of salt stress, melatonin had a weak regulatory effect on AsA-GSH cycle. Through the above regulation process, the decreasing effect of melatonin on ROS content of rice under salt stress did not decrease with prolonged stress time in a short time (1-7 d). In conclusion, melatonin improved the antioxidant capacity of rice under continuous salt stress, and rice showed variable antioxidant strategies after melatonin pretreatment., (Copyright © 2021. Published by Elsevier Masson SAS.)