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28 November 2023, Volume 30 Issue 6 Previous Issue   
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Letter

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Novel Sources of Combined Resistance Against Rice Root-Knot Nematode and Brown Spot Disease in Oryza rufipogon Griff Anupam SEKHON, Narpinderjeet Kaur DHILLON, Dharminder BHATIA, Jagjeet Singh LORE, Harwinder Singh BUTTAR 2023, 30(6): 1.  Abstract ( )   PDF (458KB) ( )

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Efficient Improvement of Nutritional Contents 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 2023, 30(6): 2.  Abstract ( )   PDF (845KB) ( )

Review

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Development and Application of Prime Editing in Plants LIU Tingting, ZOU Jinpeng, YANG Xi, WANG Kejian, RAO Yuchun, WANG Chun 2023, 30(6): 3.  Abstract ( )   PDF (1205KB) ( )   Clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)-mediated genome editing has greatly accelerated the progress in plant genetic research and agricultural breeding by enabling targeted genomic modifications. Moreover, the prime editing system developed from the CRISPR/Cas system has opened the door for even more precise genome editing. Prime editing has the ability to make all 12 types of base-to-base conversions, as well as desired insertions or deletions of fragments, without double-strand breaks and 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 the recent advances in improving its efficiency in plants, introduce the current applications of prime editing in plants, and look forward to future prospects using prime editing in genetic improvement and precision molecular breeding.

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Recent Advances to Enhance Nutritional Quality of Rice Sundus ZAFAR, XU Jianlong 2023, 30(6): 4.  Abstract ( )   PDF (903KB) ( )   Rice nutritional quality is one of the main concerns along with the productivity enhancement to feed the continuously growing population. Thus, high-yield rice varieties with improved nutritional quality need to be bred that can address malnutrition influencing global health. Undoubtedly, breeding approaches assisted in enhancing the rice yield with nutrition and helped to fulfill the crop demand. Apart from breeding techniques, other recent approaches such as genetic engineering, gene editing, omics approaches and agronomic practices also need to be employed to fulfill the nutritional requirement of the current population. In this review, we provided detailed information on the generation of nutritionally improved rice varieties by enhancing protein content, micro- and macro-nutrients, vitamins, and oil nutritional quality by genetic engineering approaches and also identified QTLs for amino acid, protein, and micro-nutrients in rice. Furthermore, omics approaches provide different tools and techniques for effectively exploring resources and understanding the molecular mechanism involved in trait development. Omics branches (transcriptomics, proteomics, ionomics and metabolomics) are efficiently utilized for rice nutritional improvement. Thus, utilizing the information acquired from these techniques and incorporating all these recent approaches can efficiently modify the genome and will directly enrich the nutritional value of rice varieties that will address the malnutrition challenges in years to come.

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Potential Benefits of Bioactive Compounds of Traditional Rice Grown in South and South-East Asia: A Review Md. Forshed DEWAN, Md. AHIDUZZAMAN, Md. Nahidul ISLAM, Habibul Bari SHOZIB 2023, 30(6): 5.  Abstract ( )   PDF (1167KB) ( )   Traditional rice varieties have been widely cultivated and popularly consumed by Asian people for a very long time. In recent times, consumers concern regarding traditional rice has increased. Traditional or indigenous rice varieties have been found to be rich in a wide range of bioactive compounds, particularly phenolic compounds, flavonoids, tannins, anthocyanins, proanthocyanidins, phytic acid and γ-oryzanol. We have found 32 phenolic acids, including hydroxycinnamic acid derivatives, and 7 different flavonoids in rice varieties. All the mentioned bioactive compounds have unique physiological effects on human health. Besides that, the grains showed their nutraceutical potential for antidiabetic, antiarthritic, antiinflammatory, antibacterial and antitumor activities. In this review, we critically analyzed the bioactive components of traditional rice and its nutraceutical potential to shield against hazardous microbial activities. To ensure that future generations have access to these beneficial substances, traditional rice varieties must be preserved.

Research Paper

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Seed-Specific Expression of Apolipoprotein A-IMilano Dimer in Rice Engineered Lines Serena REGGI, Elisabetta ONELLI, Alessandra MOSCATELLI, Nadia STROPPA, Matteo Dell’ANNO, Kiril PERFANOV, Luciana ROSSI 2023, 30(6): 6.  Abstract ( )   PDF (852KB) ( )   Apolipoprotein A-IMilano (ApoA-IM) has been shown to significantly reduce coronary atherosclerotic plaques. However, the preparation of cost-effective pharmaceutical formulations of ApoA-IMilano can be limited by the high cost and difficulty of purifying the protein and producing the highly effective dimeric form. The aim of this study was to create an expression cassette driving the specific expression of dimeric ApoA-IMilano in protein bodies of rice seeds. The ApoA-IMilano protein under control of the 13 kDa prolamin promoter is expressed in dimeric form only in the seeds, and immunocytochemical and immunogold analysis confirm its expression in different caryopsis tissue such as seed coat, aleurone cell and endosperm, particularly into amyloplast and storage vacuoles. A plant-based ApoA-IMilano production system offers numerous advantages over current production systems, including direct production of the most therapeutically effective dimeric ApoA-IMilano forms, long-term storage of protein in seeds, and ease of protein production by simply growing plants. Therefore, seeds could provide a cost-effective source of ApoA-IMilano for use as a therapeutic.

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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 2023, 30(6): 7.  Abstract ( )   PDF (1651KB) ( )   Germplasm resource innovation is a crucial factor for cultivar development, particularly in hybrid rice breeding based on the three-line system. Quan 9311A, a cytoplasmic male sterile (CMS) line, has been successfully cultivated with rice restoration materials and widely applied as a female parent for hybrid breeding in China, which was developed by crossing the CMS line Zhong 9A with a two-line restorer line 93-11. By removing the restoring ability of 93-11 and retaining the sterility gene WA352c of Zhong 9A, Quan 9311A combined the best agronomic traits of both the 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 analysis technology based on whole-genome sequencing. The results revealed that Quan 9311A harbors multiple superior alleles from both 93-11 and Zhong 9A, providing excellent agronomic traits that were unavailable in earlier CMS lines. Although the fertility restorer gene Rf3 from 93-11 was removed, there were still many 93-11 chromosomal segments in the Quan 9311A genome background. Moreover, the hybrid rice Quanyousimiao (QYSM) and restorer line Wushansimiao (WSSM) were used as examples to further analyze the important role of Quan 9311A as the female parent in heterosis. It was found that QYSM harbors more superior alleles, which explained its high grain yield and wide adaptability. These findings not only promoted the utilization of hybrid rice pairing groups but also guided future breeding efforts. The study also provided fresh ideas for further promoting the closer integration of genomics with traditional breeding methods. Ultimately, Quan 9311A represents a significant advancement in rice breeding technology and has opened up new avenues for hybrid rice breeding.

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Phosphorus Starvation Tolerance in Rice Through a Combined Physiological, Biochemical and Proteome Analysis Prathap V, Suresh KUMAR, Nand Lal MEENA, Chirag MAHESHWARI, Monika DALAL, Aruna TYAGI 2023, 30(6): 8.  Abstract ( )   PDF (1221KB) ( )   Phosphorus (P) deficiency in rice limits its growth, development, and productivity. To better understand the underlying mechanisms in P-deficiency tolerance and the role of Pup1 QTL in enhancing P use efficiency (PUE) towards the development of P-efficient rice cultivars, a pair of contrasting rice genotypes (Pusa-44 and NIL-23) was used to investigate the morpho-physio-biochemical and proteomic changes under P-starvation stress. The rice genotypes were grown hydroponically in a PusaRich medium with P (16 mg/kg, +P) or without P (0 mg/kg, -P) for 30 d. P-starvation manifested a significant reduction in root and shoot biomass, shoot length, leaf area, total chlorophyll, phosphorus, nitrogen, and starch contents as well as the protein kinase activity. The stress increased root-to-shoot biomass ratio, root length, sucrose content, and acid phosphatase activity, particularly in the tolerant (NIL-23) genotype. Comparative proteome analysis revealed several P metabolism-associated proteins (including OsCDPKs, OsMAPKs, OsCPKs, OsLecRK2 and OsSAPks) to be expressed in shoot of NIL-23 indicating that multiple protein kinases are involved in P-starvation/deficiency tolerance. Moreover, up-regulated expression of OsrbcL, OsABCG32, OsSUS5, OsPolI-like B and ClpC2 proteins in shoot, while OsACA9, OsACA8, OsSPS2F, OsPP2C15 and OsBiP3 in root of NIL-23 indicate their role in P-starvation stress control through Pup1 QTL. Thus, our findings indicate that -P stress-responsive proteins in conjugation with morpho-physio-biochemical modulations improve PUE and make NIL-23 a P-deficiency tolerant genotype due to the introgression of Pup1 QTL in Pusa-44 background.

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Effect of Sulfur Fertilization on Productivity and Grain Zinc Yield of Rice Grown under Low and Adequate Soil Zinc Applications Kankunlanach KHAMPUANG, Nanthana CHAIWONG, Atilla YAZICI, Baris DEMIRER, Ismail CAKMAK, Chanakan PROM-U-THAI 2023, 30(6): 9.  Abstract ( )   PDF (1086KB) ( )   This study explored the responses in production and grain zinc (Zn) accumulation of rice (Oryza sativa cv. Osmancik 97) to a combination of Zn and sulfur (S) fertilization. The experiment was arranged in factorial with two Zn and three S rates of soil application in a completely randomized design with four replications. Plants were grown under greenhouse conditions at low (0.25 mg/kg) and adequate (5 mg/kg) Zn rates using a combination of S (CaSO4·2H2O) applied at low (2.5 mg/kg), moderate (10 mg/kg), and adequate (50 mg/kg) concentrations. Applying the lowest rate of S under adequate soil Zn treatment increased grain yield by 68% compared to the same S rate at low Zn supply, while plants with the adequate S rate produced the highest grain yield by 247% and 143% compared to low S rate at low Zn and adequate Zn supply, respectively. Grain Zn and S concentrations responded to the applied S rates differently depending on the soil Zn condition. The highest grain Zn concentration was 41.5 mg/kg associated with the adequate Zn supply at low S rates. Applying an adequate S at the low soil Zn conditions yielded the highest grain S concentration. The total grain Zn uptake per plant showed particular increases in grain Zn yield when applied with adequate S rates by 208% and 111% compared to low S rates in low and adequate soil Zn conditions, respectively. The results indicate that soil Zn and S application synergistically improves grain production and grain Zn yield, suggesting that attention should be given to the total grain Zn yield beside grain Zn concentration, especially under the growth conditions where grain yield shows particular increases as the dilution of grain Zn due to increase grain yield by increasing S fertilization.

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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 2023, 30(6): 10.  Abstract ( )   PDF (1124KB) ( )   Rice blast is regarded as one of the major diseases of rice. Screening rice genotypes with high resistance to rice blast is a key option for ensuring global food security. Unmanned aerial vehicle (UAV)-based imaging coupled with deep learning can high-throughput get imagery traits about rice blast infection. In this study, a segmented detection model (RiceblastSegMask) was made for rice blast detection and resistance evaluation. The feasibility of different backbones and target detection models was further investigated. RiceblastSegMask was a two-stage instance segmentation model, which included an image denoising backbone network, feature pyramid and trinomial tree fine-grained feature extraction combination network, and image pixel codec module. The results showed that the model combining the image-denoising and fine-grained feature extraction based on Swin Transformer and the feature pixels matching feature labels with the trinomial tree recursive algorithm presented the best performance. Overall accuracy for instance segmentation of RiceblastSegMask reached 97.56%. It achieved a satisfying result of 90.29% accuracy for grading unique resistance to rice blast. The results demonstrated that UAV low-altitude remote sensing coupled with the proposed RiceblastSegMask model can efficiently calculate the infected area of rice blast, providing a new phenotypic tool to evaluate the resistance to rice blast in rice at field scale for the breeding program

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Phenolic Profile, Antioxidant, Antihyperlipidemic and Cardiac Risk Preventive Effect of Chakhao Poireiton (A Pigmented Black Rice) in High-Fat High-Sugar induced Rats Raja CHAKRABORTY, Pratap KALITA, Saikat SEN 2023, 30(6): 11.  Abstract ( )   PDF (1121KB) ( )   The present study aimed to investigate the hypolipidemic, antioxidant, and cardiac risk-suppressing effects of Chakhao poireiton (CP), a GI-tagged pigmented black rice of India. In vitro and ex vivo studies confirmed that whole rice extracts of CP have potent antioxidant, HMG-CoA reductase, cholesterol esterase inhibitory and antilipase effects. An in vivo study was conducted to evaluate the effects of the ethanol extracts of CP in high-fat high-sugar induced hyperlipidemic rats. The ethanol extract significantly ameliorated lipid parameters and liver enzymes to normal. Levels of lactate dehydrogenase, creatine kinase-NAC, C-reactive protein and lipoprotein (a) were significantly lower in extract-treated groups compared to disease control group. A marked reduction of ApoB/ApoA1 and imported atherogenic indices were observed in extract treated groups. Twelve phenolic compounds, i.e. rosamarinic acid, gallic acid, protocatechuic acid etc., were quantified in CP. This study provides the first evidence of the antihyperlipidemic and cardiac risk inhibitory effect of CP, which may be beneficial in preventing and managing hyperlipidemia, associated oxidative stress and cardiac complications.

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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, Tom Matthew HARRISON, LIU Ke, WANG Zhiqin, WANG Weilu, YANG Jianchang 2023, 30(6): 12.  Abstract ( )   PDF (1236KB) ( )   Due to climate change, extreme heat stress events have become more frequent, adversely affecting rice yield and grain quality. 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 organs, as well as its effects on rice yield and grain quality, pot experiments with indica rice Yangdao 6 (YD6) and japonica rice Jinxiangyu 1 (JXY1) were conducted under normal temperature (NT, 32 ºC / 26 ºC) and HTS (38 ºC / 29 ºC). 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. In addition, 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 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 deterioration of grain quality. These findings contribute significantly 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 adaptation of rice varieties to climate change in near future.

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Mapping and Functional Analysis of LE Gene in a Lethal Etiolated Rice Mutant at Seedling Stage XIA Xiaodong, ZHANG Xiaobo, WANG Zhonghao, CHENG Benyi, Sun Huifeng, XU Xia, GONG Junyi, YANG Shihua, WU Jianli, SHI Yongfeng, XU Rugen 2023, 30(6): 13.  Abstract ( )   PDF (924KB) ( )   An EMS-induced mutant le (lethal etiolated) obtained from a rice variety Zhongjian 100, was characterized by lethal etiolated phenotypes with significantly lower contents of chlorophyll a, chlorophyll b, total chlorophyll and carotenoids, as well as significantly decreased the number of chloroplast grana and irregular and less-stacked grana lamella. The root length, root surface area and root volume of le plants were markedly reduced relative to the wild type. The mutant le showed significantly lower catalase activity and total protein content, significantly higher peroxidase activity,. Using the map-based cloning method, LE gene was mapped to an interval of 48 kb between markers RM16107 and RM16110 on rice chromosome 3. A mutation (from T to C) at the nucleotide position 692 bp of LOC_Os03g59640 (ChlD) occurred, resulting in a change from leucine to proline. By crossing HM133 (a pale green mutant with a single-base substitution of A for G on the exon 10 of ChlD subunit) with a heterozygous line of le (LEle), two plant lines heterozygous at the LE locus and HM133 locus were obtained. Among 15 transgenic plants, 3 complementation lines displayed normal leaf color with significant higher total chlorophyll and chlorophyll a and b contents. The ChlD subunit of the mutant was unable to interact with the ChlI subunit, as demonstrated by a yeast two-hybrid assay. The mutation in le led to lethal etiolated phenotype, but no such phenomenon was observed in the mutants. The interaction between the ChlD and ChlI subunits, chlorophyll synthesis, and chloroplast development may all be impacted by the mutation, which could ultimately result in plant death. The mutation in the AAA+ domain of ChlD blocked the interaction of ChlDle with ChlI, leading to the loss of function of ChlD and hindering chlorophyll synthesis and chloroplast development, and ultimately causing lethal etiolated phenotype of the mutant.

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Novel QTLs from Wild Rice Oryza longistaminata Confer Rice Strong Tolerance to High Temperature at Seedling Stage FAN Fengfeng, CAI Meng, LUO Xiong, LIU Manman, YUAN Huanran, CHENG Mingxing, Ayaz AHMAD, LI Nengwu, LI Shaoqing 2023, 30(6): 14.  Abstract ( )   PDF (2372KB) ( )   Global warming poses a threat to rice production. Breeding heat-tolerant rice is an effective and economic way to meet this challenge. African rice is a valuable genetic resource for developing heat-tolerant crops due to its delicate mechanism for adapting to high temperatures. Oryza longistaminata, a wild rice species widely distributed in Africa, may contain an even richer gene pool for heat tolerance, which has yet to be harnessed. In this study, we have identified three heat-tolerant QTLs from O. longistaminata at the seedling stage. Of these, qTT4 and qTT5 are novel heat-tolerant sites found in O. longistaminata. Our findings show that the O. longistaminata allele for these two QTLs can improve the heat tolerance of rice seedlings. Notably, qTT5 was mapped to a region of about 287.2 kb containing 46 expressing genes, and four candidate genes were identified by the analysis of gene ontology and expression difference under heat induction. Our results provide a basis for identifying the heat-tolerant genes underlying O. longistaminata and for developing new genetic resources for rice heat tolerance breeding.