Rice Science

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1. Coleoptile Purple Line Regulated by A-P Gene System Is a Valuable Marker Trait for Seed Purity Identification in Hybrid Rice

Du Shuanglin, Wang Zhongwei, Chen Yun, Tan Yao, Li Xiang, Zhu Wenping, He Guanghua, Lei Kairong, Guo Longbiao, Zhang Yi

Rice Science 2022, 29 (5): 451-461. DOI: 10.1016/j.rsci.2022.07.005

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In plants, a large number of anthocyanin biosynthetic genes encoding enzymes and regulatory genes encoding transcription factors are required for anthocyanin synthesis. Coleoptile purple lines are two purple lines on both sides of coleoptiles after seed germination. However, the molecular mechanism of coleoptile purple line is not clear in rice so far. In this study, two major dominant genes, coleoptile purple line 1 (OsCPL1, also known as OsC1) and coleoptile purple line 2 (OsCPL2), were isolated via map-based cloning, and both of them were required for anthocyanin biosynthesis of coleoptile purple line in rice. The knockout and complementation experiments confirmed that OsC1 was required for purple color in most organs, such as coleoptile line, sheath, auricle, stigma and apiculus, whereas OsCPL2 was just required for coleoptile purple line. OsC1 was predominantly expressed in coleoptiles, flag leaves, and green panicles, and highly expressed in young leaves, whereas OsCPL2 was predominantly expressed in coleoptiles, and extremely lowly expressed in the other tested organs. Loss-of-function of either OsC1 or OsCPL2 resulted in significant reduction of transcript levels of multiple anthocyanin biosynthesis genes in coleoptiles. Coleoptile purple line was further used as a marker trait in hybrid rice. Purity identification in hybrid rice seeds via coleoptile purple line just needed a little water, soil and a small plate and could be completed within 5 d. Molecular marker and field identification analyses indicated that coleoptile purple line was reliable for the hybrid seed purity identification. Our findings disclosed that coleoptile purple line in rice was regulated by two major dominant genes, OsC1 and OsCPL2, and can be used as a simple, rapid, accurate and economic marker trait for seed purity identification in hybrid rice.

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2. Characterization of a Novel Weak Allele of RGA1/D1 and Its Potential Application in Rice Breeding

Liu Yantong, Li Ting, Jiang Zhishu, Zeng Chuihai, He Rong, Qiu Jiao, Lin Xiaoli, Peng Limei, Song Yongping, Zhou Dahu, Cai Yicong, Zhu Changlan, Fu Junru, He Haohua, Xu Jie

Rice Science 2022, 29 (6): 522-534. DOI: 10.1016/j.rsci.2022.03.001

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Semi-dwarfing improves the lodging resistance and yield of rice, and the vast majority of modern rice varieties harbor the sd1 allele to decrease plant height, resulting in reduced genetic diversity and negative agronomic traits. Thus, exploring alternative sources of dwarfism is imperative for rice breeding. Here, we identified a novel RGA1 allele, d1-w, from a local indica variety Xiaolixiang (XLX) using a map-based cloning approach. Compared with other rice varieties, RGA1 in XLX contained a unique single nucleotide polymorphism that resulted in an additional transcript and reduced functional RGA1 transcript level. The RGA1 from Nipponbare was introduced into XLX to estimate the value of d1-w in rice breeding. Compared with transgenic XLX plants (XLX^D1), XLX exhibited reduced plant height, increased stem strength, lower reactive oxygen species accumulation, delayed senescence, stronger photosynthesis, higher grain yield and quality (including external, milling and nutritional qualities), and enhanced resistance to drought and Rhizoctonia solani. Therefore, we proposed that the d1-w allele has potential as an excellent dwarfism resource for rice breeding.

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3. OsABT, a Rice WD40 Domain-Containing Protein, Is Involved in Abiotic Stress Tolerance

Chen Eryong, Shen Bo

Rice Science 2022, 29 (3): 247-256. DOI: 10.1016/j.rsci.2021.07.012

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Plant growth and crop productivity are severely affected by abiotic stress on a global scale. WD40 repeat-containing proteins play a significant role in the development and environmental adaptation of eukaryotes. In this study, OsABT, a stress response gene, was cloned from rice (Oryza sativa L. cv. Nipponbare). OsABT encodes a protein containing seven WD40 domains. Expression analysis revealed that the OsABT gene was first up-regulated and then down-regulated following treatment with abscisic acid (ABA) and NaCl, but was down-regulated when treated with PEG8000. Subcellular localization results showed that OsABT was located in the cytoplasm and nucleus of Arabidopsis roots. OsABT transgenic Arabidopsis showed significantly increased tolerance to ABA and salt stress during plant seedling development. However, the transgenic lines were more sensitive to drought stress. Moreover, OsABT can interact with OsABI2, a component of ABA signaling pathway. These results showed that OsABT plays a positive regulatory role in response to salt stress and a negative role in response to drought stress in Arabidopsis.

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4. Rational Design of Grain Size to Improve Rice Yield and Quality

Tao Yajun, Wang Jun, Xu Yang, Wang Fangquan, Li Wenqi, Jiang Yanjie, Chen Zhihui, Fan Fangjun, Zhu Jianping, Li Xia, Yang Jie

Rice Science 2023, 30 (1): 1-5. DOI: 10.1016/j.rsci.2022.04.003

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5. Polycomb Repressive Complex 2-Mediated H3K27 Trimethylation Is Required for Pathogenicity in Magnaporthe oryzae

Wu Zhongling, Qiu Jiehua, Shi Huanbin, Lin Chuyu, Yue Jiangnan, Liu Zhiquan, Xie Wei, Naweed I. Naqvi, Kou Yanjun, Tao Zeng

Rice Science 2022, 29 (4): 363-374. DOI: 10.1016/j.rsci.2021.11.006

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Polycomb repressive complex 2 (PRC2) contributes to catalyze the methylation of histone H3 at lysine 27 and plays vital roles in transcriptional silencing and growth development in various organisms. In Magnaporthe oryzae, histone H3K27 is found to associate with altered transcription of in planta induced genes. However, it is still unknown whether and how H3K27me3 modification is involved in pathogenicity to rice and stress response. In this study, we found that core subunits of PRC2, Kmt6-Suz12-Eed, were required for fungal pathogenicity to rice in M. oryzae. Kmt6-Suz12-Eed localized in the nuclei and was necessary for the establishment of H3K27me3 modification. With ChIP-seq analysis, 9.0% of genome regions enriched with H3K27me3 occupancy, which corresponded to 1033 genes in M. oryzae. Furthermore, deletion of Kmt6, Suz12 or Eed altered genome-wide transcriptional expression, while the de-repression genes in the ∆kmt6 strain were highly associated with H3K27me3 occupancy. Notably, plenty of genes which encode effectors and secreted enzymes, secondary metabolite synthesis genes, and cell wall stress-responsive genes were directly occupied with H3K27me3 modification and de-repression in the ∆kmt6 strain. These results elaborately explained how PRC2 was required for pathogenicity, which is closely related to effector modulated host immunity and host environment adaption.

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6. Stay-Green Panicle Branches Improve Processing Quality of Elite Rice Cultivars

Chen Yibo, Zhao Lei, Wang Chongrong, Li Hong, Huang Daoqiang, Wang Zhidong, Zhou Degui, Pan Yangyang, Gong Rong, Zhou Shaochuan

Rice Science 2023, 30 (1): 11-14. DOI: 10.1016/j.rsci.2022.08.001

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7. A Simple and Rapid Oxidative Stress Screening Method of Small Molecules for Functional Studies of Transcription Factor

Vanitha Adhinarayanreddy, Preethi Vijayaraghavareddy, Ashwin Vargheese, Sujitha Dadi, Akshay Uttarkar, Vidya Niranjan, Anuradha Venkatraman, Sheshshayee M. Sreeman, Ramu S. Vemanna

Rice Science 2022, 29 (5): 402-406. DOI: 10.1016/j.rsci.2022.07.002

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8. Transcriptome Analysis Provides Novel Insights into Salt Stress Response in Two Egyptian Rice Varieties with Different Tolerance Levels

Shehab Mohamed, Iovene Marina, Ciancio Aurelio, Colagiero Mariantonietta, Finetti-Sialer Mariella

Rice Science 2022, 29 (6): 499-502. DOI: 10.1016/j.rsci.2022.09.001

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9. Nucleus-Encoded Thylakoid Protein, OsY3IP1, Confers Enhanced Tolerance to Saline and Alkaline Stresses in Rice

Hyeran Moon, Young-Ah Kim, Ryoung Shin, Chang-Jin Park

Rice Science 2022, 29 (3): 225-236. DOI: 10.1016/j.rsci.2021.08.004

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Abiotic stress confers serious damage to the photosynthetic machinery, often resulting in plant growth inhibition. Hypothetical chloroplast open reading frame 3 (Ycf3)-interacting protein 1 (Y3IP1) is a nucleus-encoded thylakoid protein and plays an essential role in the assembly of photosystem I. The full-length cDNA over-expresser (FOX) gene-hunting system is an approach using systemically generated gain-of-function mutants. Among the FOX-rice lines, a line CE175 overexpressing rice Y3IP1 gene (OsY3IP1) displayed less inhibition of root growth under saline (NaCl) stress. The expression of OsY3IP1 was up-regulated under saline and alkaline (Na₂CO₃) stresses in the rice variety Kitaake. After saline and alkaline treatments, transgenic Kitaake overexpressing OsY3IP1-GFP (OsY3IP1-GFPox/Kit) displayed higher levels of chlorophyll content compared to Kitaake. Under the stress conditions, the maximum quantum yield of photosystem II photochemistry levels was higher in OsY3IP1-GFPox/Kit than in Kitaake. The increased tolerance conferred by OsY3IP1 overexpression correlated with reduced reactive oxygen species accumulation. Our data provide new insights into the possible role of OsY3IP1 in the pathway suppressing photooxidative damage under stress conditions. These features can be further exploited to improve saline and alkaline tolerances of rice plants in future.

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10. Feasibility of Improving Unmanned Aerial Vehicle-Based Seeding Efficiency by Using Rice Varieties with Low Seed Weight

Wang Xinyu, Yang Guodong, Pan Xiangcheng, Xiang Hongshun, Peng Shaobing, Xu Le

Rice Science 2022, 29 (4): 299-303. DOI: 10.1016/j.rsci.2022.05.001

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Unmanned aerial vehicle (UAV) has offered a promising platform for rice direct seeding that can substantially reduce labor input in the crop establishment process. However, the insufficient payload capacity of UAV-based seeders is currently limiting its intensive and large-scale use for rice direct seeding. This study indicated a large variation in seed weight across varieties, ranging from 15.0 to 36.5 mg and 14.0 to 31.3 mg for inbred and hybrid varieties, respectively, with average seed weights of 25.3 mg for inbred and 24.7 mg for hybrid varieties. Seed weights of 160 out of 4 106 inbred varieties and 17 out of 311 hybrid varieties ranged from 15.0 to 20.0 mg. Reducing seed weight from 25.0 to 15.0 mg increased the seeding area per UAV flight by 67% regardless of inbred and hybrid varieties, although the absolute increase in seeding area for hybrid variety was greater than that for inbred variety because of the difference in seeding rate. The grain yield of inbred varieties was reduced when the seed weight was less than 24 mg. Moreover, 87% of inbred varieties with a seed weight ≤ 20 mg were distributed in South China where rice consumers prefer small rice grains. Therefore, the use of low-seed-weight inbred varieties for improving UAV seeding efficiency might be considered in South China. Unlike inbred rice, 64% of hybrid varieties had higher grain weights compared with their seed weights, and reducing seed weights did not necessarily cause yield loss. Therefore, the small-seed-and-large-grain strategy in hybrid rice could be used for improving UAV seeding efficiency without yield loss. This strategy can be considered for improving UAV seeding efficiency in rice production regions other than South China.

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11. Conservation and Utilization of Genetic Resources of Wild Rice in China

Yang Ziyi, Xu Zhijian, Yang Qingwen, Qiao Weihua

Rice Science 2022, 29 (3): 216-224. DOI: 10.1016/j.rsci.2021.08.003

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The abundant genetic resources of wild rice in China represent a key gene pool for modern rice breeding, contributing to food production and agricultural development in China and worldwide. Between the 1970s and the 2010s, two national wild rice surveys were carried out in China. More than 20 000 accessions of three species Oryza rufipogon, O. officinalis and O. meyeriana have been conserved ex situ. An in situ conservation system has also been set up to protect notable and endangered populations. This review summarized the geographical distribution of wild rice in China, the current status of conservation, the discovery of elite genes, and the application of research into the origin and domestication of rice.

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12. 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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13. Saline-Alkali Tolerance in Rice: Physiological Response, Molecular Mechanism, and QTL Identification and Application to Breeding

Ratan Kumar Ganapati, Shahzad Amir Naveed, Sundus Zafar, Wang Wensheng, Xu Jianlong

Rice Science 2022, 29 (5): 412-434. DOI: 10.1016/j.rsci.2022.05.002

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Salinity-alkalinity is incipient abiotic stress that impairs plant growth and development. Rice (Oryza sativa) is a major food crop greatly affected by soil salinity and alkalinity, requiring tolerant varieties in the saline-alkali prone areas. Understanding the molecular and physiological mechanisms of saline-alkali tolerance paves the base for improving saline-alkali tolerance in rice and leads to progress in breeding. This review illustrated the physiological consequences, and molecular mechanisms especially signaling and function of regulating genes for saline-alkali tolerance in rice plants. We also discussed QTLs regarding saline-alkali tolerance accordingly and ways of deployment for improvement. More efforts are needed to identify and utilize the identified QTLs for saline-alkali tolerance in rice.

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14. CRISPR/Cas9-Targeted Knockout of Rice Susceptibility Genes OsDjA2 and OsERF104 Reveals Alternative Sources of Resistance to Pyricularia oryzae

Fabiano T. P. K. Távora, Anne Cécile Meunier, Aurore Vernet, Murielle Portefaix, Joëlle Milazzo, Henri Adreit, Didier Tharreau, Octávio L. Franco, Angela Mehta

Rice Science 2022, 29 (6): 535-544. DOI: 10.1016/j.rsci.2022.04.001

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Rice genes OsDjA2 and OsERF104, encoding a chaperone protein and an APETELA2/ ethylene-responsive factor, respectively, are strongly induced in a compatible interaction with blast fungus, and also have function in plant susceptibility validated through gene silencing. Here, we reported the CRISPR/Cas9 knockout of OsDjA2 and OsERF104 genes resulting in considerable improvement of blast resistance. A total of 15 OsDjA2 (62.5%) and 17 OsERF104 (70.8%) T₀ transformed lines were identified from 24 regenerated plants for each target and used in downstream experiments. Phenotyping of homozygous T₁ mutant lines revealed not only a significant decrease in the number of blast lesions but also a reduction in the percentage of diseased leaf area, compared with the infected control plants. Our results supported CRISPR/Cas9-mediated target mutation in rice susceptibility genes as a potential and alternative breeding strategy for building resistance to blast disease.

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15. 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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16. Evaluation of Medicinal Plant Extracts for Rice Blast Disease Control

Tan Yanping, Deng Shiqi, Qin Yonghua, Xu Xin, Yu You, Cui Liu, Wang Chuntai, Jiang Changjie, Liu Xinqiong

Rice Science 2023, 30 (1): 6-10. DOI: 10.1016/j.rsci.2022.03.003

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17. Adoption of Improved Rice Varieties in the Global South: A Review

Julia Checco, Fathin Ayuni Azizan, Jaquie Mitchell, Ammar Abdul Aziz

Rice Science 2023, 30 (3): 186-206. DOI: 10.1016/j.rsci.2023.03.004

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Improved rice varieties (IRVs) play a significant role in establishing food security and improving livelihood in the Global South since its introduction in the 1960s. However, the adoption of new IRVs has remained relatively low. This low adoption poses a challenge to rice-producing and consuming countries as they are increasingly threatened by production shortages, malnutrition, and poor rice quality. Many empirical studies have attempted to identify the determinants influencing the adoption of IRVs by distinguishing the characteristics between adopters and non-adopters. This review showed a consensus on the important determinants influencing the adoption of IRVs in the Global South. Findings synthesized from 99 studies suggested that variables (farm size, education, information access and farm location) examined extensively are not necessarily the most important determinants of adoption when undertaking a weighted analysis. Terrain, source of seed and technology-related attributes (perceived yield, maturity, ease of use, marketability and technical efficiency) are more important determinants of adoption, with determinants changing according to adoption type (probability or intensity of adoption), variety type and region. The recommendations for future adoption studies include: incorporating more technology-specific variables, increasing research for overlooked regions and variety types, shifting away from predominant static analysis by capturing the dynamics of the adoption process, and considering the potential biases in analyses. This review will facilitate the development of targeted interventions and policies that promote IRV adoption in the Global South.

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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. Novel Deletion in Exon 7 of Betaine Aldehyde Dehydrogenase 2 (BADH2)

Van Quoc Giang, Huynh Ky, Nguyen Chau Thanh Tung, Nguyen Loc Hien, Nguyen van Manh, Nguyen Nhut Thanh, Vo Cong Thanh, Swee Keong Yeap

Rice Science 2023, 30 (2): 104-112. DOI: 10.1016/j.rsci.2023.01.003

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The fragrance of rice is one of the premium characteristics that breeders want to include in rice varieties due to the higher market value. Nucleotide deletions in exons 2 (7 bp) and 7 (8 bp) of Betaine Aldehyde Dehydrogenase 2 (BADH2) are associated with fragrance in rice. In this study, a new 13 bp deletion in exon 7 of the BADH2 gene was discovered in the Nang Thom Cho Dao (NTCD) variety, and the mutation has been closely related to the genetic background of indica subspecies through the Bayesian phylogenetic approach and haplotype network analysis of the 3 000 Rice Genomes Project. In addition, a set of functional markers (EX07-13F, EX07-13RN, and EX07-13RM) identified the 13 bp deletion only within NTCD (no amplified band) compared with both non-aromatic and other aromatic rice varieties (110 bp band). The deletion of 13 bases instead of 8 bases in exon 7 of BADH2 caused a premature stop codon, which down-regulated the expression of the BADH2 transcript while associated with up-regulation of OsP5CS and the high amount of 2-acetyl-1-pyrroline. It is potential to use the deletion in exon 7 of the BADH2 gene as a novel marker for adulteration and breeding of fragrant rice varieties, particularly for NTCD.

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20. 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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