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A new rice gene, OsMFT1, was identified that both regulates rice heading date and panicle architecture and is different from its homologs in other species. Abstract Heading date and panicle architecture are important agronomic traits in rice. Here, we identified a gene MOTHER OF FT AND TFL1 (OsMFT1) that regulates rice heading and panicle architecture. Overexpressing OsMFT1 delayed heading date by over 7 d and greatly increased spikelets per panicle and the number of branches. In contrast, OsMFT1 knockout mutants had an advanced heading date and reduced spikelets per panicle. Overexpression of OsMFT1 significantly suppressed Ehd1 expression, and Ghd7 up-regulated OsMFT1 expression. Double mutants showed that OsMFT1 acted downstream of Ghd7. In addition, transcription factor OsLFL1 was verified to directly bind to the promoter of OsMFT1 via an RY motif and activate the expression of OsMFT1 in vivo and in vitro. RNA-seq and RNA in situ hybridization analysis confirmed that OsMFT1 repressed expression of FZP and five SEPALLATA-like genes, indicating that the transition from branch meristem to spikelet meristem was delayed and thus more panicle branches were produced. Therefore, OsMFT1 is a suppressor of flowering acting downstream of Ghd7 and upstream of Ehd1, and a positive regulator of panicle architecture.

Summary Panicle architecture is a key determinant of grain yield in cereals, but the mechanisms governing panicle morphogenesis and organ development remain elusive. Here, we have identified a quantitative trait locus (qPA1) associated with panicle architecture using chromosome segment substitution lines from parents Nipponbare and 9311. The panicle length, branch number and grain number of Nipponbare were significantly higher than CSSL‐9. Through map‐based cloning and complementation tests, we confirmed that qPA1 was identical to SD1 (Semi Dwarf1), which encodes a gibberellin 20‐oxidase enzyme participating in gibberellic acid (GA) biosynthesis. Transcript analysis revealed that SD1 was widely expressed during early panicle development. Analysis of sd1/osga20ox2 and gnp1/ osga20ox1 single and double mutants revealed that the two paralogous enzymes have non‐redundant functions during panicle development, likely due to differences in spatiotemporal expression; GNP1 expression under control of the SD1 promoter could rescue the sd1 phenotype. The DELLA protein SLR1, a component of the GA signalling pathway, accumulated more highly in sd1 plants. We have demonstrated that SLR1 physically interacts with the meristem identity class I KNOTTED1‐LIKE HOMEOBOX (KNOX) protein OSH1 to repress OSH1‐mediated activation of downstream genes related to panicle development, providing a mechanistic link between gibberellin and panicle architecture morphogenesis.

• MicroRNAs (miRNAs) are a class of small noncoding RNAs that play important roles in plant growth and development as well as in stress responses. However, little is known about their regulatory functions affecting rice grain yield. • We functionally characterized a novel miRNA in rice, OsmiR530, its target OsPL3, and its upstream regulator phytochrome-interacting factor-like 15 (OsPIL15). Their effects on rice yield were dissected comprehensively. • We determined that OsmiR530 negatively regulates grain yield. Blocking OsmiR530 increases grain yield, whereas OsmiR530 overexpression significantly decreases grain size and panicle branching, leading to yield loss. Additionally, OsPL3, which encodes a PLUS3 domain-containing protein, is targeted directly by OsmiR530. Knocking out OsPL3 decreases the grain yield. In-depth analyses indicated that OsPIL15 activates OsMIR530 expression by directly binding to the G-box elements in the promoter. Analyses of genetic variations suggested that the OsMIR530 locus has likely been subjected to artificial selection during rice breeding. • The results presented herein reveal a novel OsPIL15–OsmiR530 module controlling rice grain yield, thus providing researchers with a new target for the breeding of high-yielding rice.

• Degeneration of apical spikelets and reduced panicle fertility are common reasons for low seed-setting rate in rice (Oryza sativa). However, little is known about the underlying molecular mechanisms. • Here, we report a novel degenerated panicle and partial sterility 1 (dps1) mutant that showed panicle apical degeneration and reduced fertility in middle spikelets. dps1 plants were characterized by small whitish anthers with altered cuticle morphology and absence of pollen grains. Amounts of cuticular wax and cutin were significantly reduced in dps1 anthers. Panicles of dps1 plants showed an accumulation of reactive oxygen species (ROS), lower antioxidant activity, and increased programmed cell death. • Map-based cloning revealed that DPS1 encodes a mitochondrial-localized protein containing a cystathionine β-synthase domain that showed the highest expression in panicles and anthers. DPS1 physically interacted with mitochondrial thioredoxin proteins Trx1 and Trx20, and it participated in ROS scavenging. Global gene expression analysis in dps1 revealed that biological processes related to fatty acid metabolism and ROS homeostasis were significantly affected, and the expression of key genes involved in wax and cutin biosynthesis were downregulated. • These results suggest that DPS1 plays a vital role in regulating ROS homeostasis, anther cuticle formation, and panicle development in rice.

Panicle number is directly related to rice yield, so panicle detection and counting has always been one of the most important scientific research topics. Panicle counting is a challenging task due to many factors such as high density, high occlusion, and large variation in size, shape, posture et.al. Deep learning provides state-of-the-art performance in object detection and counting. Generally, the large images need to be resized to fit for the video memory. However, small panicles would be missed if the image size of the original field rice image is extremely large. In this paper, we proposed a rice panicle detection and counting method based on deep learning which was especially designed for detecting rice panicles in rice field images with large image size. Different object detectors were compared and YOLOv5 was selected with MAPE of 3.44% and accuracy of 92.77%. Specifically, we proposed a new method for removing repeated detections and proved that the method outperformed the existing NMS methods. The proposed method was proved to be robust and accurate for counting panicles in field rice images of different illumination, rice accessions, and image input size. Also, the proposed method performed well on UAV images. In addition, an open-access and user-friendly web portal was developed for rice researchers to use the proposed method conveniently.

Summary Yield in rice is determined mainly by panicle architecture. Using map‐based cloning, we identified an R2R3 MYB transcription factor REGULATOR OF GRAIN NUMBER1 (RGN1) affecting grain number and panicle architecture. Mutation of RGN1 caused an absence of lateral grains on secondary branches. We demonstrated that RGN1 controls lateral grain formation by regulation of LONELY GUY (LOG) expression, thus controlling grain number and shaping panicle architecture. A novel favourable allele, RGN1C, derived from the Or‐I group in wild rice affected panicle architecture by means longer panicles. Identification of RGN1 provides a theoretical basis for understanding the molecular mechanism of lateral grain formation in rice; RGN1 will be an important gene resource for molecular breeding for higher yield.

The emergence of rice panicle substantially changes the spectral reflectance of rice canopy and, as a result, decreases the accuracy of leaf area index (LAI) that was derived from vegetation indices (VIs). From a four-year field experiment with using rice varieties, nitrogen (N) rates, and planting densities, the spectral reflectance characteristics of panicles and the changes in canopy reflectance after panicle removal were investigated. A rice “panicle line”—graphical relationship between red-edge and near-infrared bands was constructed by using the near-infrared and red-edge spectral reflectance of rice panicles. Subsequently, a panicle-adjusted renormalized difference vegetation index (PRDVI) that was based on the “panicle line” and the renormalized difference vegetation index (RDVI) was developed to reduce the effects of rice panicles and background. The results showed that the effects of rice panicles on canopy reflectance were concentrated in the visible region and the near-infrared region. The red band (670 nm) was the most affected by panicles, while the red-edge bands (720–740 nm) were less affected. In addition, a combination of near-infrared and red-edge bands was for the one that best predicted LAI, and the difference vegetation index (DI) (976, 733) performed the best, although it had relatively low estimation accuracy (R2 = 0.60, RMSE = 1.41 m2/m2). From these findings, correcting the near-infrared band in the RDVI by the panicle adjustment factor (θ) developed the PRDVI, which was obtained while using the “panicle line”, and the less-affected red-edge band replaced the red band. Verification data from an unmanned aerial vehicle (UAV) showed that the PRDVI could minimize the panicle and background influence and was more sensitive to LAI (R2 = 0.77; RMSE = 1.01 m2/m2) than other VIs during the post-heading stage. Moreover, of all the assessed VIs, the PRDVI yielded the highest R2 (0.71) over the entire growth period, with an RMSE of 1.31 (m2/m2). These results suggest that the PRDVI is an efficient and suitable LAI estimation index.

Bacterial panicle blight is caused by Burkholderia glumae and results in damage to rice crops worldwide. Virulence of B. glumae requires quorum sensing (QS)‐dependent synthesis and export of toxoflavin, responsible for much of the damage to rice. The DedA family is a conserved membrane protein family found in all bacterial species. B. glumae possesses a member of the DedA family, named DbcA, which we previously showed is required for toxoflavin secretion and virulence in a rice model of infection. B. glumae secretes oxalic acid as a “common good” in a QS‐dependent manner to combat toxic alkalinization of the growth medium during the stationary phase. Here, we show that B. glumae Δ dbcA fails to secrete oxalic acid, leading to alkaline toxicity and sensitivity to divalent cations, suggesting a role for DbcA in oxalic acid secretion. B. glumae Δ dbcA accumulated less acyl‐homoserine lactone (AHL) QS signalling molecules as the bacteria entered the stationary phase, probably due to nonenzymatic inactivation of AHL at alkaline pH. Transcription of toxoflavin and oxalic acid operons was down‐regulated in Δ dbcA . Alteration of the proton motive force with sodium bicarbonate also reduced oxalic acid secretion and expression of QS‐dependent genes. Overall, the data show that DbcA is required for oxalic acid secretion in a proton motive force‐dependent manner, which is critical for QS of B. glumae . Moreover, this study supports the idea that sodium bicarbonate may serve as a chemical for treatment of bacterial panicle blight.

• Inflorescence architecture in plants is often complex and challenging to quantify, particularly for inflorescences of cereal grasses. Methods for capturing inflorescence architecture and for analyzing the resulting data are limited to a few easily captured parameters that may miss the rich underlying diversity. • Here, we apply X-ray computed tomography combined with detailed morphometrics, offering new imaging and computational tools to analyze three-dimensional inflorescence architecture. To show the power of this approach, we focus on the panicles of Sorghum bicolor, which vary extensively in numbers, lengths, and angles of primary branches, as well as the three-dimensional shape, size, and distribution of the seed. • We imaged and comprehensively evaluated the panicle morphology of 55 sorghum accessions that represent the five botanical races in the most common classification system of the species, defined by genetic data. We used our data to determine the reliability of the morphological characters for assigning specimens to race and found that seed features were particularly informative. • However, the extensive overlap between botanical races in multivariate trait space indicates that the phenotypic range of each group extends well beyond its overall genetic background, indicating unexpectedly weak correlation between morphology, genetic identity, and domestication history.