Phenotyping of rice in salt stress environment using high-throughput infrared imaging

Phenotyping of rice (Oryza sativa L. cv. Donggin) in salt stress environment using infrared imaging was conducted. Results were correlated with the most frequently used physiological parameters such as stomatal conductance, relative water content and photosynthetic parameters. It was observed that stomatal conductance (R2 = –0.618) and relative water content (R2 = –0.852) were significantly negatively correlated with average plant temperature (thermal images), while dark-adapted quantum yield (Fv/Fm, R2 = –0.325) and performance index (R2 = –0.315) were not consistent with plant temperature. Advantages of infrared thermography and utilization of this technology for the selection of stress tolerance physiotypes are discussed in detail

Active Learning of Neural Network Potentials for Rare Events

Atomistic simulation with machine learning-based potentials (MLPs) is an emerging tool for understanding materials\u27 properties and behaviors and predicting novel materials. Neural network potentials (NNPs) are outstanding in this field as they have shown a comparable accuracy to ab initio electronic structure calculations for reproducing potential energy surfaces while being several orders of magnitude faster. However, such NNPs can perform poorly outside their training domain and often fail catastrophically in predicting rare events in molecular dynamics (MD) simulations. The rare events in atomistic modeling typically include chemical bond breaking/formation, phase transitions, and materials failure, which are critical for new materials design, synthesis, and manufacturing processes. In this study, we develop an automated active learning (AL) capability by combining NNPs and enhanced sampling methods for capturing rare events to derive NNPs for targeted applications. We develop a decision engine based on configurational similarity and uncertainty quantification (UQ), using data augmentation for effective AL loops to distinguish the informative data from enhanced sampled configurations, showing that the generated data set achieves an activation energy error of less than 1 kcal/mol. Furthermore, we have devised a strategy to alleviate training uncertainty within AL iterations through a carefully constructed data selection process that leverages an ensemble approach. Our study provides essential insight into the relationship between data and the performance of NNP for the rare event of bond breaking under mechanical loading. It highlights strategies for developing NNPs of broader materials and applications through active learning

Screening for a Novel Gene, <i>OsPSLSq6</i>, Using QTL Analysis for Lodging Resistance in Rice

Lodging is the most common factor that affects crop productivity, reducing yield, grain quality, and harvesting efficiency of rice and other cereal crops. The Cheongcheong (Indica)/Nagdong (Japonica) doubled haploid (CNDH) genetic map was used to develop a lodging-resistant variety. The major agricultural traits of rice related to lodging resistance, such as the pushing strength of the lower stem before the heading date (PSLSB) at reproductive growth period and pushing strength of the lower stem after the heading date (PSLSA) at full ripe period were investigated. A quantitative trait locus (QTL) analysis of PSLSA and PSLSB detected on RM439-RM20318 on chromosome 6 has overlap in three consecutive years. RM439-RM20318 on chromosome 6 contained 15 lodging resistance candidate genes. Among the candidate genes, Os06g0623200, named OsPSLSq6, which is similar to Cinnamoyl-CoA reductase, involved lignin biosynthesis in defense responses. Lignin is the main structural component of vascular plants’ secondary cell wall, which is not only related to plant growth and development but also to mechanical strength. OsPSLSq6 opens new possibilities to control lignin synthesis to improve lodging resistance. OsPSLSq6 can be used as a target gene for further studies to provide important information for the marker-assisted improvement of target traits and cloning genes underlying the QTL of interest

A New Protocol to Mitigate Damage to Germination Caused by Black Layers in Maize (<i>Zea mays</i> L.) Seeds

Maize seeds harvested in the field have higher vitality than those harvested in greenhouses but have higher contamination rates in terms of fungal or bacterial infection. It is important to disinfect maize seeds before sowing because seeds are a source of infection and damage crop production. In this study, we aimed to provide an efficient seed sterilization method to manage fungal or bacterial infections of field-harvested maize seeds. The optimized sterilization protocol was set up according to the disinfectant liquid immersion time, inverting RPM (rotations per minute), number of seeds, and black layer removal. We put 20 grains of maize seeds in 100% commercial bleach disinfectant containing 4–5% NaClO and performed 20 min of inversion at 45 RPM. After standing without inverting for the next 25 min in the sterile hood, inversion at 45 RPM for another 40 min was performed. By using this protocol, microorganisms occurred at a low rate with an average of 11.7%. Moreover, it was shown that microorganisms occurred at the lowest rate (average of 0.29% of seeds) when the black layer was removed. In addition, this sterilization method did not affect the growth and development of maize plants. These results revealed that black layer removal from maize seeds is a highly efficient, easy, and inexpensive sterilization method and can be used for seeds of various maize lines

Nitrogen Fertilization Causes Changes in Agricultural Characteristics and Gas Emissions in Rice Field

Rice is a source of food for the majority of the global population. Currently, the rice yield is declining owing to extreme climate change. Farmers use nitrogen fertilizers to increase the yield; however, excessive nitrogen fertilizer application has a negative impact on plants and the environment. Nitrogen fertilizer is necessary for the growth of rice, but it is an important cause of environ-mental pollution. Carbon monoxide (CO) emitted from rice fields due to nitrogen fertilizer reacts with greenhouse gases such as carbon dioxide or methane, affecting global warming. Although CO does not directly affect global warming, it is a gas that needs attention because it reacts with various other gases. In this study, a chamber was designed and manufactured to collect the CO emitted from the paddy field after nitrogen fertilizer application in 2021 and 2022. In paddy fields, nitrogen fertilizer treatment affected the pH, EC, and soil temperature, and affected various agricultural traits. Various agricultural characteristics and the number of spikes, number of tillers, and chlorophyll content increased with nitrogen fertilizer application, whereas the amylose content decreased. Adequate nitrogen fertilizer should be applied to increase the rice yield; however, excessive nitrogen fertilizer application has a serious negative effect on grain quality and can accelerate global warming by releasing CO from paddy fields. The appropriate application of nitrogen fertilizer can have a positive effect on farmers by increasing yield. However, caution should be exercised in the application of excessive nitrogen fertilizers, as excessive nitrogen fertilizers increase the emission of CO, which affects greenhouse gases

Genotype and Phenotype Interaction between <i>OsWKRYq6</i> and BLB after <i>Xanthomonas oryzae</i> pv. <i>Oryzae</i> Inoculation in the Field

Bacterial leaf blight (BLB) is an important and devastating rice disease caused by the pathogen Xanthomonas oryzae pv. Oryzae (Xoo). In particular, in recent years, the occurrence of abnormal climate and warming phenomena has produced a good environment for the occurrence of BLB, and the rice yield due to the occurrence of BLB continues to decrease. Currently, molecular breeding is applied by searching for resistant genes to development of BLB resistance cultivar. In addition, there are many methods for screening resistant genes, and among them, phenotype analysis in the field and applied research is rarely conducted. Due to recent rapid climate change, BLB is a major problem that has a more serious negative effect on rice yield. Therefore, we suggest OsWRKYq6 to be effectively used for breeding BLB-resistant cultivars by screening BLB-resistant genes. In this study, the BLB-resistant gene was screened using the lesion length, which most definitely changes to the phenotype when Xoo is infected. OsWRKYq6 was finally selected as a BLB resistance gene by analyzing the phenotype and genotype after inoculating Xoo in 120 Cheongcheong/Nagdong double haploid (CNDH) lines in the field. After Xoo inoculation, lesion length and yield were investigated, and 120 CNDH lines were divided from BLB-resistant and susceptible lines. Moreover, when the transcription level of OsWRKYq6 was analyzed in the resistant and susceptible lines after Xoo inoculation in the field, the expression level was regulated to a high level in the resistant line. In this study, we propose OsWRKYq6 as a transcription factor involved in BLB resistance. Currently, the differentiation of various races is proceeding rapidly due to rapid climate change. In addition, screening of transcription factor genes involved in BLB resistance in the field can be effectively applied to molecular breeding to develop resistant cultivars in preparation for rapid climate change

Overexpressing <i>OsPYL/RCAR7</i> Improves Drought Tolerance of Maize Seedlings by Reducing Stomatal Conductance

Drought stress is a serious abiotic factor limiting the quality and yield of maize (Zea mays). To produce maize plants with enhanced drought tolerance, we generated transgenic maize plants overexpressing OsPYL/RCAR7, encoding an abscisic acid receptor. We crossed the selected lines with maize variety B73 and obtained F1 hybrid seeds. Initial screening suggested that the transgenic lines were more drought tolerant than wild-type plants. Analysis using the DroughtSpotter platform indicated that expressing OsPYL/RCAR7 enhanced drought resistance in transgenic maize seedlings by reducing water loss. In addition, the stomatal conductance of the leaf surface was 30% lower in OsPYL/RCAR7-overexpressing plants than in wild-type ones. After drought treatment, OsPYL/RCAR7-overexpressing maize showed a much higher survival rate than the wild type, suggesting that expressing OsPYL/RCAR7 reduced the negative effects of drought exposure on stomatal conductance and enhanced water use efficiency. Furthermore, the expression levels of drought-tolerance–related abscisic acid–signaling genes ABP2 and RAB16A were higher in the transgenic plants than in the wild type. Taken together, our data indicate that the seedlings of transgenic maize expressing the gene OsPYL/RCAR7 showed increased tolerance to drought stress, raising the possibility that stress-related genes from monocotyledonous crops could be used as genetic resources to improve the agricultural traits of maize