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    Effect of GW8 Gene Editing on Appearance Quality of Erect-Panicle Type (dep1) Japonica Rice
    Mao Ting, Chen Hongfa, Li Xin, Liu Yan, Zhong Shuncheng, Wang Shiyu, Zhao Yizhou, Zhang Zhan, Ni Shanjun, Huang He, Li Xu, Hu Shikai
    Rice Science    2023, 30 (5): 359-363.   DOI: 10.1016/j.rsci.2022.12.002
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    Genome-Wide Dissection of Quan 9311A Breeding Process and Application Advantages
    Li Qianlong, Feng Qi, Wang Heqin, Kang Yunhai, Zhang Conghe, Du Ming, Zhang Yunhu, Wang Hui, Chen Jinjie, Han Bin, Fang Yu, Wang Ahong
    Rice Science    2023, 30 (6): 552-565.   DOI: 10.1016/j.rsci.2023.06.004
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    Germplasm resource innovation is a crucial factor for cultivar development, particularly within the context of hybrid rice breeding based on the three-line system. Quan 9311A, a cytoplasmic male sterile (CMS) line, has been successfully cultivated using rice restoration materials and extensively employed as a female parent in hybrid breeding program in China. This line was developed by crossing the CMS line Zhong 9A with a two-line restorer line 93-11, with the intention of eliminating the restoring ability of 93-11 while retaining the sterility gene WA352c from Zhong 9A. Quan 9311A effectively amalgamates the most favorable agronomic traits from both parental lines. In this study, the relationship between phenotypic characteristics and the known functional genes of Quan 9311A were analyzed using the rice genome navigation technology based on whole-genome sequencing. The findings revealed that Quan 9311A harbors multiple superior alleles from both 93-11 and Zhong 9A, providing exceptional agronomic traits that are unavailable in earlier CMS lines. Despite the removal of the fertility restorer gene Rf3 from 93-11, numerous chromosomal segments from 93-11 persist in the Quan 9311A genome. Furthermore, the hybrid rice Quanyousimiao (QYSM) and the restorer line Wushansimiao (WSSM) were used as examples to illustrate the important role of Quan 9311A as the female parent in heterosis. It was found that QYSM carries a great number of superior alleles, which accounts for its high grain yield and wide adaptability. These insights not only advanced the utilization of hybrid rice pairing groups but also provided guidance for future breeding endeavors. The study introduced innovative concepts to further integrate genomics with traditional breeding techniques. Ultimately, Quan 9311A signified a significant milestone in rice breeding technology, opening up novel avenues for hybrid rice development.

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    Potential Benefits of Bioactive Compounds of Traditional Rice Grown in South and Southeast Asia: A Review
    Md. Forshed Dewan, Md. Ahiduzzaman, Md. Nahidul Islam, Habibul Bari Shozib
    Rice Science    2023, 30 (6): 537-551.   DOI: 10.1016/j.rsci.2023.07.002
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    Traditional rice varieties have been widely cultivated and popularly consumed by Asian people for a very long time and have recently garnered increased consumer concern. Traditional or indigenous rice varieties are known to be rich in a wide range of bioactive compounds, particularly phenolic compounds, flavonoids, tannins, anthocyanins, proanthocyanidins, phytic acids, and γ-oryzanol. We have identified 32 phenolic acids, including hydroxycinnamic acid derivatives, and 7 different flavonoids in rice varieties. These bioactive compounds have unique physiological effects on human health. Additionally, rice grains exhibit nutraceutical potential for antidiabetic, antiarthritic, anti-inflammatory, antibacterial, and antitumor activities. In this review, we critically analyzed the bioactive components of traditional rice and their nutraceutical potential in protecting against harmful microbial activities. To ensure that future generations have access to these beneficial substances, it is crucial to preserve traditional rice varieties.

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    ORYZA SATIVA SPOTTED-LEAF 41 (OsSPL41) Negatively Regulates Plant Immunity in Rice
    Tan Jingyi, Zhang Xiaobo, Shang Huihui, Li Panpan, Wang Zhonghao, Liao Xinwei, Xu Xia, Yang Shihua, Gong Junyi, Wu Jianli
    Rice Science    2023, 30 (5): 426-436.   DOI: 10.1016/j.rsci.2023.02.004
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    Identification of immunity-associated leucine-rich repeat receptor-like protein kinases (LRR-RLK) is critical to elucidate the LRR-RLK mediated mechanism of plant immunity. Here, we reported the map-based cloning of a novel rice SPOTTED-LEAF 41 (OsSPL41) encoding a putative LRR-RLK protein (OsLRR-RLK41/OsSPL41) that regulated disease responses to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo). An 8-bp insertion at position 865 bp in a mutant spotted-leaf 41 (spl41) allele led to the formation of purple-brown lesions on leaves. Functional complementation by the wild type allele (OsSPL41) can rescue the mutant phenotype, and the complementary lines showed similar performance to wild type in a number of agronomic, physiological and molecular indices. OsSPL41 was constitutively expressed in all tissues tested, and OsSPL41 contains a typical transmembrane domain critical for its localization to the cell membrane. The mutant exhibited an enhanced level of resistance to Xoo in companion of markedly up-regulated expression of pathogenesis-related genes such as OsPR10a, OsPAL1 and OsNPR1, while the level of salicylic acid was significantly increased in spl41. In contrast, the over-expression lines exhibited a reduced level of H2O2 and were much susceptible to Xoo with down-regulated expression of pathogenesis-related genes. These results suggested that OsSPL41 might negatively regulate plant immunity through the salicylic acid signaling pathway in rice.

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    Development and Application of Prime Editing in Plants
    Liu Tingting, Zou Jinpeng, Yang Xi, Wang Kejian, Rao Yuchun, Wang Chun
    Rice Science    2023, 30 (6): 509-522.   DOI: 10.1016/j.rsci.2023.07.005
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    Clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)-mediated genome editing has greatly accelerated progress in plant genetic research and agricultural breeding by enabling targeted genomic modifications. Moreover, the prime editing system, derived from the CRISPR/Cas system, has opened the door for even more precise genome editing. Prime editing has the capability to facilitate all 12 types of base-to-base conversions, as well as desired insertions or deletions of fragments, without inducing double-strand breaks and requiring donor DNA templet. In a short time, prime editing has been rapidly verified as functional in various plants, and can be used in plant genome functional analysis as well as precision breeding of crops. In this review, we summarize the emergence and development of prime editing, highlight recent advances in improving its efficiency in plants, introduce the current applications of prime editing in plants, and look forward to future prospects for utilizing prime editing in genetic improvement and precision molecular breeding.

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    Iron Toxicity Tolerance of Rice Genotypes in Relation to Growth, Yield and Physiochemical Characters
    Sheikh Faruk Ahmed, Hayat Ullah, May Zun Aung, Rujira Tisarum, Suriyan Cha-Um, Avishek Datta
    Rice Science    2023, 30 (4): 321-334.   DOI: 10.1016/j.rsci.2023.02.002
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    Iron (Fe) toxicity, generated from excess reduced ferrous Fe (Fe2+) ion formation within the soil under submerged condition, is a potent environmental stress that limits lowland rice production. Total 11 diverse Thai rice genotypes, including a recognized tolerant genotype Azucena and a susceptible genotype IR64, were evaluated against 5 Fe2+ levels [0 (control), 150, 300, 600 and 900 mg/L] to screen the tested genotypes for their Fe-toxicity tolerance and to classify them as a sensitive/tolerant category. The evaluation was conducted by a germination study, followed by a polyhouse study on growth, yield and physiochemical performances. Results showed significant variations in Fe2+-tolerance across genotypes. Increasing Fe2+ level beyond 300 mg/L was detrimental for germination and growth of all the tested genotypes, although germination responses were negatively affected at Fe2+ ≥ 300 mg/L. Physiochemical responses in the form of leaf greenness, net photosynthetic rate, membrane stability index and Fe contents in leaf and root were the most representative of Fe2+-toxicity-mediated impairments on overall growth and yield. Difference in physiochemical responses was effectively correlated with the contrasting ability of the genotypes on lowering excess Fe2+ in tissues. Analysis of average tolerance and stress tolerance index unveiled that the genotypes RD85 and RD31 were the closest to the tolerant check Azucena and the sensitive check IR64, respectively. The unweighted pair group method with arithmetic means clustering revealed three major clusters, with cluster II (four genotypes) being Fe2+ tolerant and cluster I (four genotypes) being Fe2+ sensitive. Principal component (PC) analysis and genotype by trait-biplot analysis showed that the first two components explained 90.5% of the total variation, with PC1 accounting for 56.6% and PC2 for 33.9% of the total variation. The identified tolerant rice genotypes show potentials for cultivation in Fe2+-toxic lowlands for increased productivity. The findings contribute to the present understanding on Fe2+-toxicity response and provide a basis for future genotype selection or rice crop improvement programs against Fe2+-toxicity.

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    LHD3 Encoding a J-Domain Protein Controls Heading Date in Rice
    Liu Qiao, Qiu Linlin, Hua Yangguang, Li Jing, Pang Bo, Zhai Yufeng, Wang Dekai
    Rice Science    2023, 30 (5): 437-448.   DOI: 10.1016/j.rsci.2023.03.015
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    Heading date is one of the most important agronomic traits of rice, which critically affects rice ecogeographical adaptation, yield and quality. In this study, a late heading date 3 (lhd3) mutant was screened from the 60Co-γ irradiation mutant library. The lhd3 delayed heading date in rice under both short day and long day conditions. Map-based cloning combined with Mutmap strategy was adopted to isolate the causal LHD3 gene. The LHD3 gene encodes a DNA_J domain protein, which was ubiquitously expressed in various plant organs, and dominant expressed in stems and leaves. Subcellular localization analysis showed that LHD3 was localized to nucleus, indicating that LHD3 may interact with other elements to regulate the expression of flowering genes. The transcriptions of the heading activators Ehd1, Hd3a and RFT1 significantly decreased in the lhd3 mutant, suggesting that LHD3 may control the heading date through the Ehd1-Hd3a/RFT1 photoperiodic flowering pathway. The variation and haplotype analyses of the genomic region of LHD3 showed that there were 7 haplotypes in the LHD3 region from 4 702 accessions. The haplotypes of LHD3 can be divided into two classes: class a and class b, and the heading dates of these two classes were significantly different. Further study showed that two single nucleotide polymorphisms (SNPs), SNP10 (G2100C) in Hap II and SNP3 (C861T) in Hap VII, may be the functional sites causing early and late heading in accessions. Nucleotide diversity analysis showed LHD3 had been selected in the indica population, rather than in the japonica population. Therefore, the present study sheds light on the regulation of LHD3 on heading date in rice and suggests that LHD3 is a novel promising new target for rice molecular design and breeding improvement.

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    Genome-Wide Association Study for Milled Grain Appearance Traits Using Multi-Parent Advanced Generation Intercross Population in Rice
    Li Xiaoxiang, Liu Jindong, Guo Liang, Wei Xiucai, Wang Yamei, Pan Xiaowu, Dong Zheng, Liu Wenqiang, Liu Licheng, Min Jun, Liu Sanxiong, Ye Guoyou, Li Yongchao
    Rice Science    2023, 30 (5): 364-368.   DOI: 10.1016/j.rsci.2023.04.001
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    Effects of Root Growth of Deep and Shallow Rooting Rice Cultivars in Compacted Paddy Soils on Subsequent Rice Growth
    Md. Dhin Islam, Adam H. Price, Paul D. Hallett
    Rice Science    2023, 30 (5): 459-472.   DOI: 10.1016/j.rsci.2023.03.017
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    Rice is often grown as multiple seasons in one year, alternating between flooded and upland systems. A major constraint, introduced from the flooded system, is a plough pan that may decrease rooting depth and productivity of follow-on upland rice. Roots penetrating the plough pan under flooded rice system can leave a legacy of weaker root growth pathways. Deeper rooting rice cultivars could have a bigger impact, but no direct evidence is available. To explore whether a deep rather than a shallow rooting rice cultivar grown in a flooded cropping cycle benefited deeper root growth of follow-on rice in an upland, reduced tillage cropping cycle, a simulated flooded paddy in greenhouse was planted with deep (Black Gora) and shallow (IR64) rooting cultivars and a plant-free control. Artificial plough pans were made in between the topsoil and subsoil to form different treatments with no plough pan (0.35 MPa), soft plough pan (1.03 MPa) and hard plough pan (1.70 MPa). After harvest of this ‘first season’ rice, the soil was drained and undisturbed to simulate zero-tillage upland and planted rice cultivar BRRI Dhan 28. The overall root length density (RLD), root surface area, the numbers of root tips and branching of BRRI Dhan 28 did not vary between plough pan and no plough pan treatments. Compared with the shallow rooting rice genotype, the deep rooting rice genotype as ‘first season’ crop produced 19% greater RLD, 34% greater surface area and 29% more branching of BRRI Dhan 28 in the subsoil. In the topsoil, however, BRRI Dhan 28 had 28% greater RLD, 35% greater surface area and 43% more branching for the shallow rather than deep rooting genotype planted in the ‘first season’. The results suggested that rice cultivar selection for a paddy cycle affects root growth of a follow-on rice crop grown under no-till, with benefits to subsoil access from deep rooting cultivars and topsoil proliferation for shallow rooting cultivars.

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    Grain Shape Genes: Shaping the Future of Rice Breeding
    Lu Xuedan, Li Fan, Xiao Yunhua, Wang Feng, Zhang Guilian, Deng Huabing, Tang Wenbang
    Rice Science    2023, 30 (5): 379-404.   DOI: 10.1016/j.rsci.2023.03.014
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    The main goals of rice breeding nowadays include increasing yield, improving grain quality, and promoting complete mechanized production to save labor costs. Rice grain shape, specified by three dimensions, including grain length, width and thickness, has a more precise meaning than grain size, contributing to grain appearance quality as well as grain weight and thus yield. Furthermore, the divergence of grain shape characters could be utilized in mechanical seed sorting in hybrid rice breeding systems, which has been succeeded in utilizing heterosis to achieve substantial increase in rice yield in the past decades. Several signaling pathways that regulate rice grain shape have been elucidated, including G protein signaling, ubiquitination-related pathway, mitogen-activated protein kinase signaling, phytohormone biosynthesis and signaling, microRNA process, and some other transcriptional regulatory pathways and regulators. This review summarized the recent progress on molecular mechanisms underlying rice grain shape determination and the potential of major genes in future breeding applications.

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    Efficient Improvement of Nutritional Content in Rice Grains by Precise Base Editing of OsROS1
    Xu Yang, Wang Fangquan, Li Wenqi, Wang Jun, Tao Yajun, Fan Fangjun, Chen Zhihui, Jiang Yanjie, Zhu Jianping, Li Xia, Zhu Qianhao, Yang Jie
    Rice Science    2023, 30 (6): 499-503.   DOI: 10.1016/j.rsci.2023.06.002
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    Screening Rice Germplasm with Different Genetic Backgrounds for Cadmium Accumulation in Brown Rice in Cadmium-Polluted Soils
    Zhang Weixing, Guan Meiyan, Wang Jie, Wang Yulei, Zhang Weigui, Lu Xinzhe, Xu Ping, Chen Mingxue, Zhu Youwei
    Rice Science    2023, 30 (4): 267-270.   DOI: 10.1016/j.rsci.2023.01.009
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    Diversity of Arbuscular Mycorrhizal Fungi Associated with Six Rice Cultivars in Italian Agricultural Ecosystem Managed with Alternate Wetting and Drying
    Veronica Volpe, Franco Magurno, Paola Bonfante, Stefano Ghignone, Erica Lumini
    Rice Science    2023, 30 (4): 348-358.   DOI: 10.1016/j.rsci.2023.02.003
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    Alternate wetting and drying (AWD) system, in which water has been reduced by approximately 35% with an increased occurrence of beneficial arbuscular mycorrhizal (AM) symbiosis and no negative impact on rice yield, was proposed to utilize water and nutrients more sustainable. In this study, we selected six rice cultivars (Centauro, Loto, Selenio, Vialone nano, JSendra and Puntal) grown under AWD conditions, and investigated their responsiveness to AM colonization and how they select diverse AM taxa. In order to investigate root-associated AM fungus communities, molecular cloning-Sanger sequencing on small subunit rDNA data were obtained from five out of the six rice cultivars and compared with Next Generation Sequencing (NGS) data, which were previously obtained in Vialone nano. The results showed that all the cultivars were responsive to AM colonization with the development of AM symbiotic structures, even if with differences in the colonization and arbuscule abundance in the root systems. We identified 16 virtual taxa (VT) in the soil compartment and 7 VT in the root apparatus. We emphasized that the NGS analysis gives additional value to the results thanks to a more in-depth reading of the less represented AM fungus taxa.

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    Transcriptome Analysis of oserf922 Mutants Reveals New Insights into Rice Blast Resistance
    Qin Mengchao, Tao Hui, Shi Xuetao, Zhang Chongyang, He Feng, Wang Min, Liu Zheng, Wang Jisong, Zhang Rongxue, Wang Shutong, Wang Guoliang, Ning Yuese, Wang Ruyi
    Rice Science    2023, 30 (5): 374-378.   DOI: 10.1016/j.rsci.2023.05.002
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    Hydrogen Sulfide Improves Rice Seed Germination by Regulating Aluminum Absorption, Internal Antioxidant Enzyme System and Osmotic Balance under Aluminum Toxicity Conditions
    Wei Qianqian, Kong Yali, Xiang Xingjia, Zhu Lianfeng, Liu Jia, Tian Wenhao, Jin Qianyu, Yu Yijun, Zhang Junhua, Zhu Chunquan
    Rice Science    2023, 30 (4): 271-275.   DOI: 10.1016/j.rsci.2023.05.001
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    Morphophysiological Diversity and Haplotype Analysis of Saltol QTL Region in Diverse Rice Landraces for Salinity Tolerance
    B. M. Lokeshkumar, S. L. Krishnamurthy, Suman Rathor, Arvinder Singh Warriach, N. M. Vinaykumar, B. M. Dushyanthakumar, Parbodh Chander Sharma
    Rice Science    2023, 30 (4): 306-320.   DOI: 10.1016/j.rsci.2023.02.001
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    Rice is sensitive to salinity stress at both the seedling and reproductive stages. The present study used 145 rice genotypes comprising of 100 landraces and 45 advanced breeding lines collected from different regions of India. These genotypes were evaluated in hydroponics under control [electrical conductivity (ECe) ~1.2 dS/m] and saline (ECe ~10.0 dS/m) environments along with susceptible (IR29) and tolerant (FL478) checks. The stress susceptibility index for eight morphophysiological traits was estimated. Analysis of variance showed significant differences among the genotypes for all the parameters studied in control, stress and relative stress conditions. We identified 3 landraces (Kuttimanja, Tulasimog and IET-13713I) as tolerant and 14 lines as moderately tolerant to salt stress. Strong correlations in the morphological (root and shoot lengths) and physiological traits (shoot Na+, Ca2+ and Mg2+ contents, and Na+/K+ ratio) were observed under all the conditions. The hierarchical cluster analysis grouped the genotypes into five clusters, among which cluster II comprised salt-tolerant lines. Haplotyping of Saltol region using 11 simple sequence repeat markers on 17 saline tolerant and moderately tolerant lines was conducted. Markers AP3206F, RM10793 and RM3412b, located close to SKC1 gene (11.23-12.55 Mb), displayed diverse allelic variations and they were not related to the FL478 type. In this region, tolerant lines like Kuttimanja, IET-13713I and Tulasimog have new alleles. As a result, these lines may be suitable candidates for novel genomic regions governing rice salinity tolerance. Salt-tolerance ability of Kuttimanja, Tulasimog and IET-13713I was validated in two years in three salinity stress environments. These promising lines can be used in breeding programs to broaden the genetic base of salinity tolerance in rice, and it may help to dissect key genomic regions responsible for salinity tolerance.

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    Effects of Zinc Oxide Particles with Different Sizes on Root Development in Oryza sativa
    Monica Ruffini Castiglione, Stefania Bottega, Carlo Sorce, Carmelina SpanÒ
    Rice Science    2023, 30 (5): 449-458.   DOI: 10.1016/j.rsci.2023.03.016
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    Given the consistent release of zinc oxide (ZnO) nanoparticles into the environment, it is urgent to study their impact on plants in depth. In this study, grains of rice were treated with two different concentrations of ZnO nanoparticles (NP-ZnO, 10 and 100 mg/L), and their bulk counterpart (B-ZnO) were used to evaluate whether ZnO action could depend on particle size. To test this hypothesis, root growth and development assessment, oxidative stress parameters, indole-3-acetic acid (IAA) content and molecules/enzymes involved in IAA metabolism were analyzed. In situ localization of Zn in control and treated roots was also performed. Though Zn was visible inside root cells only following nanoparticle treatment, both materials (NP-ZnO and B-ZnO) were able to affect seedling growth and root morphology, with alteration in the concentration/pattern of localization of oxidative stress markers and with a different action depending on particle size. In addition, only ZnO supplied as bulk material induced a significant increase in both IAA concentration and lateral root density, supporting our hypothesis that bulk particles might enhance lateral root development through the rise of IAA concentration. Apparently, IAA concentration was influenced more by the activity of the catabolic peroxidases than by the protective action of phenols.

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    Application of UAV-Based Imaging and Deep Learning in Assessment of Rice Blast Resistance
    Lin Shaodan, Yao Yue, Li Jiayi, Li Xiaobin, Ma Jie, Weng Haiyong, Cheng Zuxin, Ye Dapeng
    Rice Science    2023, 30 (6): 652-660.   DOI: 10.1016/j.rsci.2023.06.005
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    Rice blast is regarded as one of the major diseases of rice. Screening rice genotypes with high resistance to rice blast is a key strategy for ensuring global food security. Unmanned aerial vehicles (UAV)-based imaging, coupled with deep learning, can acquire high-throughput imagery related to rice blast infection. In this study, we developed a segmented detection model (called RiceblastSegMask) for rice blast detection and resistance evaluation. The feasibility of different backbones and target detection models was further investigated. RiceblastSegMask is a two-stage instance segmentation model, comprising an image-denoising backbone network, a feature pyramid, a trinomial tree fine-grained feature extraction combination network, and an image pixel codec module. The results showed that the model combining the image-denoising and fine-grained feature extraction based on the Swin Transformer and the feature pixel matching feature labels with the trinomial tree recursive algorithm performed the best. The overall accuracy for instance segmentation of RiceblastSegMask reached 97.56%, and it demonstrated a satisfactory accuracy of 90.29% for grading unique resistance to rice blast. These results indicated that low-altitude remote sensing using UAV, in conjunction with the proposed RiceblastSegMask model, can efficiently calculate the extent of rice blast infection, offering a new phenotypic tool for evaluating rice blast resistance on a field scale in rice breeding programs.

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    Germplasm Resources, Genes and Perspective for Aromatic Rice
    Prafulla Kumar Behera, Debabrata Panda
    Rice Science    2023, 30 (4): 294-305.   DOI: 10.1016/j.rsci.2023.03.011
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    Aromatic rice is considered an important commodity in the global market because of its strong aroma and eating and cooking quality. Asian countries, such as India and Pakistan, are the leading traders of Basmati rice, whereas Thailand is the major supplier of Jasmine rice in the international market. The strong aroma of rice is associated with more than 300 volatile compounds, among which 2-acetyl-1-pyrroline (2-AP) is the principal component. 2-AP is a phenotypic expression of spontaneous mutations in the recessive gene OsBadh2 or Badh2. The present review focuses on the origin, evolution and diversity of genetic resources of aromatic rice available worldwide. A brief discussion is presented on the genes responsible for quality traits along with details of their molecular genetics. This compilation and discussion will be useful for future breeding programs and the biofortification of quality traits of aromatic rice to ensure food security and nutritional need.

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    Priming for Saline-Alkaline Tolerance in Rice: Current Knowledge and Future Challenges
    Jiang Changjie, Liang Zhengwei, Xie Xianzhi
    Rice Science    2023, 30 (5): 417-425.   DOI: 10.1016/j.rsci.2023.05.003
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    Soil salinization and/or alkalization is a major constraint to crop production worldwide. Approximately 60% of the cultivated land is affected by salt, over half of which is alkalized. Alkaline soils are characterized by high alkalinity and typically high salinity, which creates a complex saline-alkaline (SA) stress that affects plant growth. Rice cultivation has been accepted as an important strategy for effective utilization of SA land if water is available for irrigation. Nevertheless, as a salt-sensitive plant, rice plants suffer severe SA-induced damage, which results in poor plant growth and grain yield. Various approaches have been employed to improve rice productivity in SA land. Among them, the priming technique has emerged as a powerful method for enhancing SA tolerance in rice plants. In this review, we summarized how SA stress damages rice plants, and then presented how priming treatment can mitigate such damage.

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