Rice Science

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1. Rice Heat Tolerance Breeding: A Comprehensive Review and Forward Gaze

Ravindran Lalithambika Visakh, Sreekumar Anand, Sukumaran Nair Arya, Behera Sasmita, Uday Chand Jha, Rameswar Prasad Sah, Radha Beena

Rice Science 2024, 31 (4): 375-400. DOI: 10.1016/j.rsci.2024.02.004

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The yield potential of rice is seriously affected by heat stress due to climate change. Since rice is a staple food globally, it is imperative to develop heat-resistant rice varieties. Thus, a thorough understanding of the complex molecular mechanisms underlying heat tolerance and the impact of high temperatures on various critical stages of the crop is needed. Adoption of both conventional and innovative breeding strategies offers a long-term advantage over other methods, such as agronomic practices, to counter heat stress. In this review, we summarize the effects of heat stress, regulatory pathways for heat tolerance, phenotyping strategies, and various breeding methods available for developing heat-tolerant rice. We offer perspectives and knowledge to guide future research endeavors aimed at enhancing the ability of rice to withstand heat stress and ultimately benefit humanity.

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2. 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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3. 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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4. Random Amplification Polymorphic DNA and Agro-Morphological Traits-Based Fingerprinting for Detection of Genetic Divergence in Indian Black Rice

Manisha Sharma, Dhananjay Raturi, Vijay Rani Rajpal, Manju Chaudhary, Soom Nath Raina, Apekshita Singh

Rice Science 2024, 31 (4): 366-370. DOI: 10.1016/j.rsci.2024.03.002

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5. Progress on Molecular Mechanism of Heat Tolerance in Rice

Fu Yiwei, Wu Jiayelu, Wu Mingming, Ye Shenghai, Zhai Rongrong, Ye Jing, Zhu Guofu, Yu Faming, Lu Yanting, Zhang Xiaoming

Rice Science 2024, 31 (6): 673-687. DOI: 10.1016/j.rsci.2024.07.001

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Rice (Oryza sativa L.) is a major food crop in China, and its high and stable yield is crucial for ensuring food security in the country. However, over the past few years, extreme weather events induced by global climate change have impacted rice growth. For example, the effects of heat stress on rice quality and yield have been significant. Therefore, it is fundamental to conduct in-depth research on the heat-tolerance mechanisms of rice and to cultivate superior new thermotolerant rice varieties. This review summarizes the adverse effects of high temperatures on rice growth at various stages, the heat-tolerance mechanisms in rice, and the heat-tolerance genes and QTLs that have been identified in recent years. We also discuss strategies to enhance the heat tolerance of rice, offering new insights for rice breeding research.

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6. Response of Rice Growth and Nutrient Absorption in a Saline- Alkali Paddy to Different Nitrogen Fertilizer Applications

Wang Xinyi, Zhu Hui, Yan Baixing, Brian Shutes, Zeng Yuan

Rice Science 2024, 31 (3): 245-250. DOI: 10.1016/j.rsci.2024.03.001

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7. Novel Sources of Combined Resistance Against Rice Root- Knot Nematode and Brown Spot Disease in Oryza rufipogon

Anupam Sekhon, Narpinderjeet Kaur Dhillon, Dharminder Bhatia, Jagjeet Singh Lore, Harwinder Singh Buttar

Rice Science 2023, 30 (6): 504-508. DOI: 10.1016/j.rsci.2023.08.001

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8. 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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9. 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 H₂O₂and 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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10. 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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11. Research Progress of Genomes of Insect Pests in Paddy Field

Xu Hongxing, Zhao Xianxin, Lü Zhongxian, Li Fei

Rice Science 2023, 30 (5): 369-373. DOI: 10.1016/j.rsci.2023.03.013

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12. 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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13. 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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14. 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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15. Effects of Biochar Inoculation with Bacillus megaterium on Rice Soil Phosphorus Fraction Transformation and Bacterial Community Dynamics

Yu Keru, Xue Zhaokun, Fang Xianzhi, Ma Jiawei, Wang Yongjun, Liu Dan, Ye Zhengqian

Rice Science 2024, 31 (4): 361-365. DOI: 10.1016/j.rsci.2024.04.003

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16. 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 the⁶⁰Co-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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17. 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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18. 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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19. 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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20. Translocation and Distribution of Carbon-Nitrogen in Relation to Rice Yield and Grain Quality as Affected by High Temperature at Early Panicle Initiation Stage

Ji Dongling, Xiao Wenhui, Sun Zhiwei, Liu Lijun, Gu Junfei, Zhang Hao, Matthew Tom Harrison, Liu Ke, Wang Zhiqin, Wang Weilu

Rice Science 2023, 30 (6): 598-612. DOI: 10.1016/j.rsci.2023.06.003

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Due to climate change, extreme heat stress events have become more frequent, adversely affecting rice yield and grain quality. The accumulation and translocation of dry matter and nitrogen substances are essential for rice yield and grain quality. To assess the impact of high temperature stress (HTS) at the early panicle initiation (EPI) stage on the accumulation, transportation, and distribution of dry matter and nitrogen substances in various organs of rice, as well as the resulting effects on rice yield and grain quality, pot experiments were conducted using an indica rice cultivar Yangdao 6 (YD6) and a japonica rice cultivar Jinxiangyu 1 (JXY1) under both normal temperature (32 ºC / 26 ºC) and high temperature (38 ºC / 29 ºC) conditions. The results indicated that exposure to HTS at the EPI stage significantly decreased rice yield by reducing spikelet number per panicle, grain-filling rate, and grain weight. However, it improved the nutritional quality of rice grains by increasing protein and amylose contents. The reduction in nitrogen and dry matter accumulation accounted for the changes in spikelet number per panicle, grain-filling rate, and grain size. Under HTS, the decrease in nitrogen accumulation accompanied by the reduction in dry matter may be due to the down-regulation of leaf net photosynthesis and senescence, as evidenced by the decrease in nitrogen content. Furthermore, the decrease in sink size limited the translocation of dry matter and nitrogen substances to grains, which was closely related to the reduction in grain weight and the deterioration of grain quality. These findings significantly contribute to our understanding of the mechanisms of HTS on grain yield and quality formation from the perspective of dry matter and nitrogen accumulation and translocation. Further efforts are needed to improve the adaptability of rice varieties to climate change in the near future.

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