Volume 31 Issue 5
28 September 2024
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Letters
Review
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Letters
Improving Semi-Dried Brown Rice Noodle Quality via Mixed Fermentation of Lactobacillus and Yeast
Luo Lijuan, Cheng Zixuan, Qiao Fan, Xiong Gangping, Liu Jun, Huang Qingming, Li Jiangtao, Lin Qinlu, Liu Chun
2024, 31(5): 489-493.  DOI: 10.1016/j.rsci.2024.06.005
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Biochar Decreases Soil Cadmium (Cd) Availability and Regulates Expression Levels of Cd Uptake/Transport-Related Genes to Reduce Cd Translocation in Rice
Wang Han, Huang Qina, Zhang Yan, Shao Guosheng, Hu Yijun, Xu Youxiang
2024, 31(5): 494-498.  DOI: 10.1016/j.rsci.2024.04.004
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RISE Method Based on Rare Allele Infusion and Sanger Sequencing Estimation: A Simple, Cheap, and Efficient Method for Detecting Transgene Copy Number in Rice
Liu Tingchang, Huang Lifang, Liu Peng, Cui Yanchun, Chen Caiyan, Mao Donghai
2024, 31(5): 499-502.  DOI: 10.1016/j.rsci.2024.05.001
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Development of Machine Vision-Based Algorithm for Counting and Discriminating Filled and Unfilled Paddy Rice in Overlapping Mode
Mahdieh Hoseingholizadeh-Alashti, Davood Kalantari
2024, 31(5): 503-506.  DOI: 10.1016/j.rsci.2024.04.001
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Review
Advances in Understanding Cadmium Stress and Breeding of Cadmium-Tolerant Crops
Liang Liang, Wang Chenchang, Chen Tao
2024, 31(5): 507-525.  DOI: 10.1016//j.rsci.2024.06.006
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Cadmium (Cd) pollution has emerged as a critical global environmental concern, due to its significant toxicity, environmental persistence, and the pervasiveness of contamination. Significantly, the bioaccumulation of Cd in agricultural crops constitutes a primary vector for its entry into the human diet. This issue warrants urgent attention from both the scientific community and policymakers to develop and implement effective mitigation strategies. This review delves into the physiological impacts of Cd stress on plants, including the suppression of photosynthetic activity, amplification of oxidative stress, and disruptions in mineral nutrient homeostasis. Additionally, the resistance mechanisms deployed by plants in response to Cd stress have been explored, and the prospective contributions of molecular breeding strategies in augmenting crop tolerance to Cd and minimizing its bioaccumulation have been assessed. By integrating and analyzing these findings, we seek to inform future research trajectories and proffer strategic approaches to enhance agricultural sustainability, safeguard human health, and protect environmental integrity.

Next Generation Nutrition: Genomic and Molecular Breeding Innovations for Iron and Zinc Biofortification in Rice
Kunhikrishnan Hemalatha Dhanyalakshmi, Reshma Mohan, Sasmita Behera, Uday Chand Jha, Debashis Moharana, Ahalya Behera, Sini Thomas, Preman Rejitha Soumya, Rameswar Prasad Sah, Radha Beena
2024, 31(5): 526-544.  DOI: 10.1016/j.rsci.2024.04.008
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Global efforts to address malnutrition and hidden hunger, particularly prevalent in low- and middle-income countries, have intensified, with a focus on enhancing the nutritional content of staple crops like rice. Despite serving as a staple for over half of the world’s population, rice falls short in meeting daily nutritional requirements, especially for iron (Fe) and zinc (Zn). Genetic resources, such as wild rice species and specific rice varieties, offer promising avenues for enhancing Fe and Zn content. Additionally, molecular breeding approaches have identified key genes and loci associated with Fe and Zn accumulation in rice grains. This review explores the genetic resources and molecular mechanisms underlying Fe and Zn accumulation in rice grains. The functional genomics involved in Fe uptake, transport, and distribution in rice plants have revealed key genes such as OsFRO1, OsIRT1, and OsNAS3. Similarly, genes associated with Zn uptake and translocation, including OsZIP11 and OsNRAMP1, have been identified. Transgenic approaches, leveraging transporter gene families and genome editing technologies, offer promising avenues for enhancing Fe and Zn content in rice grains. Moreover, strategies for reducing phytic acid (PA) content, a known inhibitor of mineral bioavailability, have been explored, including the identification of low-PA mutants and natural variants. The integration of genomic information, including whole-genome resequencing and pan-genome analyses, provides valuable insights into the genetic basis of micronutrient traits and facilitates targeted breeding efforts. Functional genomics studies have elucidated the molecular mechanisms underlying Fe uptake and translocation in rice. Furthermore, transgenic and genome editing techniques have shown promise in enhancing Fe and Zn content in rice grains through the manipulation of key transporter genes. Overall, the integration of multi-omics approaches holds significant promise for addressing global malnutrition and hidden hunger by enhancing the nutritional quality of rice, thereby contributing to improved food and nutritional security worldwide.

Rice Cultivation under Film Mulching Can Improve Soil Environment and Be Beneficial for Rice Production in China
Zhang Youliang, Zhu Kaican, Tang Yongqi, Feng Shaoyuan
2024, 31(5): 545-555.  DOI: 10.1016/j.rsci.2024.06.009
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Rice cultivation under film mulching is an integrated management technology that can conserve water, increase soil temperature, improve yield, and enhance water and nitrogen use efficiencies. Despite these advantages, the system does have its drawbacks, such as soil organic matter reduction and microplastic pollution, which impede the widespread adoption of film mulching cultivation in China. Nonetheless, the advent of degradable film, controlled-release fertilizer, organic fertilizer, and film mulching machinery is promoting the development of rice film mulching cultivation. This review outlines the impact of rice cultivation under film mulching on soil moisture, soil temperature, soil fertility, greenhouse gas emissions, weed control, and disease and pest management. It also elucidates the mechanism of changes in rice growth, yield and quality, water use efficiency, and nitrogen use efficiency. This paper incorporates a review of published research articles and discusses some uncertainties and shortcomings associated with rice cultivation under film mulching. Consequently, prospective research directions for the technology of rice film mulching cultivation are outlined, and recommendations for future research into rice cultivation under film mulching are proposed.

Research Papers
Bulked Segregant RNA-Seq Analysis of Pollinated Pistils Reveals Genes Influencing Spikelet Fertility in Rice
Kanokwan Kaewmungkun, Keasinee Tongmark, Sriprapai Chakhonkaen, Numphet Sangarwut, Theerachai Thanananta, Amorntip Muangprom
2024, 31(5): 556-571.  DOI: 10.1016/j.rsci.2024.06.001
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Prezygotic isolation is important for successful fertilization in rice, significantly affecting yield. This study focused on F5:6 generation plants derived from inter-subspecific crosses (Nipponbare × KDML105) with low (LS) and high seed-setting rates (HS), in which normal pollen fertility was observed. However, LS plants showed a reduced number of pollen grains adhering to the stigma and fewer pollen tubes reaching the ovules at 4‒5 h post-pollination, compared with HS plants. Bulked segregant RNA-Seq analysis of pollinated pistils from the HS and LS groups revealed 249 and 473 differentially expressed genes (DEGs), respectively. Kyoto Encyclopedia of Genes and Genomes analysis of the HS and LS- specific DEGs indicated enrichment in metabolic pathways, pentose and glucuronate interconversions, and flavonoid biosynthesis. Several of these DEGs exhibited co-expression with pollen development genes and formed extensive clusters of co-expression networks. Compared with LS pistils, enzyme genes controlling pectin degradation, such as OsPME35 and OsPLL9, showed similar expression patterns, with higher levels in HS pistils pre-pollination. Os02g0467600, similar to cinnamate 4-hydroxylase gene (CYP73), involved in flavonoid biosynthesis, displayed higher expression in HS pistils post-pollination. Our findings suggest that OsPME35, OsPLL9, and Os02g0467600 contribute to prezygotic isolation by potentially modifying the stigma cell wall (OsPME35 and OsPLL9) and controlling later processes such as pollen-stigma adhesion (Os02g0467600) genes. Furthermore, several DEGs specific to HS and LS were co-localized with QTLs and functional genes associated with spikelet fertility. These findings provide valuable insights for further research on rice spikelet fertility, ultimately contributing to the development of high-yielding rice varieties.

Higher Grain-Filling Rate in Inferior Spikelets of Tolerant Rice Genotype Offset Grain Yield Loss under Post-Anthesis High Night Temperatures
Nitin Sharma, Bhupinder Singh, Subbaiyan Gopala Krishnan, Haritha Bollinedi, Pranab Kumar Mandal, Milan Kumar Lal, Prakash Kumar Jha, P. V. Vara Prasad, Anjali Anand
2024, 31(5): 572-586.  DOI: 10.1016/j.rsci.2024.06.003
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Increased nighttime respiratory losses decrease the amount of photoassimilates available for plant growth and yield. We hypothesized that the increased respiratory carbon loss under high night temperatures (HNT) could be compensated for by increased photosynthesis during the day following HNT exposure. Two rice genotypes, Vandana (HNT-sensitive) and Nagina 22 (HNT-tolerant), were exposed to HNT (4 °C above the control) from flowering to physiological maturity. They were assessed for alterations in the carbon balance of the source (flag leaf) and its subsequent impact on grain filling dynamics and the quality of spatially differentiated sinks (superior and inferior spikelets). Both genotypes exhibited significantly higher night respiration rates. However, only Nagina 22 compensated for the high respiration rates with an increased photosynthetic rate, resulting in a steady production of total dry matter under HNT. Nagina 22 also recorded a higher grain-filling rate, particularly at 5 and 10 d after flowering, with 1.5- and 4.0-fold increases in the translocation of 14C sugars to the superior and inferior spikelets, respectively. The ratio of photosynthetic rate to respiratory rate on a leaf area basis was negatively correlated with spikelet sterility, resulting in a higher filled spikelet number and grain weight per plant, particularly for inferior grains in Nagina 22. Grain quality parameters such as head rice recovery, high-density grains, and gelatinization temperature were maintained in Nagina 22. An increase in the rheological properties of rice flour starch in Nagina 22 under HNT indicated the stability of starch and its ability to reorganize during the cooling process of product formation. Thus, our study showed that sink adjustments between superior and inferior spikelets favored the growth of inferior spikelets, which helped to offset the reduction in grain weight under HNT in the tolerant genotype Nagina 22.

Appropriate Supply of Ammonium Nitrogen and Ammonium Nitrate Reduces Cadmium Content in Rice Seedlings by Inhibiting Cadmium Uptake and Transport
Hu Yunchao, Yan Tiancai, Gao Zhenyu, Wang Tiankang, Lu Xueli, Yang Long, Shen Lan, Zhang Qiang, Hu Jiang, Ren Deyong, Zhang Guangheng, Zhu Li, Li Li, Zeng Dali, Qian Qian, Li Qing
2024, 31(5): 587-602.  DOI: 10.1016/j.rsci.2024.02.007
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Reasonable nitrogen (N) application is a promising strategy for reducing crop cadmium (Cd) toxicity. However, the specific form of N and the required amount that affect Cd tolerance and accumulation in rice remain unclear. This study explored the influence of different N-fertilizer forms (NH4NO3, NH4Cl, and KNO3) and dosages on Cd tolerance and uptake in Cd-stressed N-sensitive and N-insensitive indica rice accessions. The results indicated that the Cd tolerance of N-sensitive indica accessions is more robust than that of N-insensitive ones. Furthermore, the shoot Cd content and Cd translocation rate in both N-sensitive and N-insensitive indica accessions decreased with an appropriate supply of NH4NO3 and NH4Cl, whereas they were comparable or slightly increased with increased KNO3. Unfortunately, we did not find significant and regular differences in Cd accumulation or translocation between N-sensitive and N-insensitive rice accessions. Consistent with the reduction of shoot Cd content, the addition of NH4NO3 and NH4Cl also inhibited the instantaneous root Cd2+ uptake. The expression changes of Cd transport-related genes under different N forms and dosages suggested that the decreased shoot Cd content, caused by the increased supply of NH4NO3 and NH4Cl, is likely achieved by reducing the transcription of OsNRAMP1 and OsIRT1. In summary, our findings reveal that an appropriate supply of NH4NO3 and NH4Cl could reduce Cd uptake and transport in rice seedlings, suggesting that rational N management could reduce the Cd risk in rice production.

Ameliorative Effects of Paclobutrazol via Physio-Biochemical and Molecular Manifestation in Rice under Water Deficit Stress
Chirag Maheshwari, Nitin Kumar Garg, Archana Singh, Aruna Tyagi
2024, 31(5): 603-616.  DOI: 10.1016/j.rsci.2024.03.004
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To comprehensively explore the physio-biochemical and molecular changes of paclobutrazol (PBZ) at the ideal dose under water deficit stress (WDS) conditions, we investigated the effects of 100 mg/kg PBZ applied via drenching on various physio-biochemical and molecular parameters in three rice varieties (N22, IR64, and IR64 DTY1.1) under both mild [75%‒80% relative water content (RWC)] and severe (60%‒65% RWC) WDS conditions. The results showed that PBZ treatment positively influenced the physio-biochemical parameters, significantly increasing dry matter (16.27%‒61.91%), RWC (6.48%‒ 16.34%), membrane stability index (4.37%‒10.35%), and total chlorophyll content (8.97%‒29.09%) in the rice varieties under both mild and severe WDS. Moreover, PBZ treatment reduced drought susceptibility (0.83‒0.95) and enhanced drought tolerance efficiency (60.92%‒86.78%), indicating its potential as a stress-mitigating agent. Global methylation analysis revealed changes in DNA methylation patterns, indicating the regulatory influence of PBZ on gene expression. The expression analysis of genes involved in the diversification of geranylgeranyl pyrophosphate towards the biosynthesis of abscisic acid, gibberellin acid, and chlorophyll showed alterations in their expression levels, suggesting the involvement of PBZ in the isoprenoid pathway. Overall, this study provides valuable insights into the potential mechanisms by which PBZ modulates physiological and molecular responses in rice plants under WDS. The findings highlight the importance of PBZ as a promising agent for enhancing drought tolerance in rice and offer valuable information for future research in crop stress management.

Estimating Key Phenological Dates of Multiple Rice Accessions Using Unmanned Aerial Vehicle-Based Plant Height Dynamics for Breeding
Hong Weiyuan, Li Ziqiu, Feng Xiangqian, Qin Jinhua, Wang Aidong, Jin Shichao, Wang Danying, Chen Song
2024, 31(5): 617-628.  DOI: 10.1016/j.rsci.2024.04.007
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Efficient and high-quality estimation of key phenological dates in rice is of great significance in breeding work. Plant height (PH) dynamics are valuable for estimating phenological dates. However, research on estimating the key phenological dates of multiple rice accessions based on PH dynamics has been limited. In 2022, field traits were collected using unmanned aerial vehicle (UAV)-based images across 435 plots, including 364 rice varieties. PH, dates of initial heading (IH) and full heading (FH), and panicle initiation (PI), and growth period after transplanting (GPAT) were collected during the rice growth stage. PHs were extracted using a digital surface model (DSM) and fitted using Fourier and logistic models. Machine learning algorithms, including multiple linear regression, random forest (RF), support vector regression, least absolute shrinkage and selection operator, and elastic net regression, were employed to estimate phenological dates. Results indicated that the optimal percentile of the DSM for extracting rice PH was the 95th (R2 = 0.934, RMSE = 0.056 m). The Fourier model provided a better fit for PH dynamics compared with the logistic models. Additionally, curve features (CF) and GPAT were significantly associated with PI, IH, and FH. The combination of CF and GPAT outperformed the use of CF alone, with RF demonstrating the best performance among the algorithms. Specifically, the combination of CF extracted from the logistic models, GPAT, and RF yielded the best performance for estimating PI (R2 = 0.834, RMSE = 4.344 d), IH (R2 = 0.877, RMSE = 2.721 d), and FH (R2 = 0.883, RMSE = 2.694 d). Overall, UAV-based rice PH dynamics combined with machine learning effectively estimated the key phenological dates of multiple rice accessions, providing a novel approach for investigating key phenological dates in breeding work.