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Search Results (1,136)

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Keywords = rice breeding

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17 pages, 1211 KiB  
Review
Physiology, Genetics, and Breeding Strategies for Improving Anaerobic Germinability Under Flooding Stress in Rice
by Panchali Chakraborty and Swapan Chakrabarty
Stresses 2025, 5(3), 49; https://doi.org/10.3390/stresses5030049 - 3 Aug 2025
Viewed by 47
Abstract
Anaerobic germination (AG) is a pivotal trait for successful direct-seeded rice cultivation, encompassing rainfed and irrigated conditions. Elite rice cultivars are often vulnerable to flooding during germination, resulting in poor crop establishment. This drawback has led to the exploration of AG-tolerant rice landraces, [...] Read more.
Anaerobic germination (AG) is a pivotal trait for successful direct-seeded rice cultivation, encompassing rainfed and irrigated conditions. Elite rice cultivars are often vulnerable to flooding during germination, resulting in poor crop establishment. This drawback has led to the exploration of AG-tolerant rice landraces, which offer valuable insights into the genetic underpinnings of AG tolerance. Over the years, substantial progress has been made in identifying significant quantitative trait loci (QTLs) associated with AG tolerance, forming the basis for targeted breeding efforts. However, the intricate gene regulatory network governing AG tolerance remains enigmatic. This comprehensive review presents recent advances in understanding the physiological and genetic mechanisms underlying AG tolerance. It focuses on their practical implications in breeding elite rice cultivars tailored for direct-seeding systems. Full article
(This article belongs to the Collection Feature Papers in Plant and Photoautotrophic Stresses)
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36 pages, 4412 KiB  
Review
CRISPR-Cas Gene Editing Technology in Potato
by Zagipa Sapakhova, Rakhim Kanat, Khanylbek Choi, Dias Daurov, Ainash Daurova, Kabyl Zhambakin and Malika Shamekova
Int. J. Mol. Sci. 2025, 26(15), 7496; https://doi.org/10.3390/ijms26157496 (registering DOI) - 3 Aug 2025
Viewed by 56
Abstract
Potato (Solanum tuberosum L.) is one of the most important food crops in the world, ranking fourth after rice, maize, and wheat. Potatoes are exposed to biotic and abiotic environmental factors, which lead to economic losses and increase the possibility of food [...] Read more.
Potato (Solanum tuberosum L.) is one of the most important food crops in the world, ranking fourth after rice, maize, and wheat. Potatoes are exposed to biotic and abiotic environmental factors, which lead to economic losses and increase the possibility of food security threats in many countries. Traditional potato breeding faces several challenges, primarily due to its genetic complexity and the time-consuming nature of the process. Therefore, gene editing—CRISPR-Cas technology—allows for more precise and rapid changes to the potato genome, which can speed up the breeding process and lead to more effective varieties. In this review, we consider CRISPR-Cas technology as a potential tool for plant breeding strategies to ensure global food security. This review summarizes in detail current and potential technological breakthroughs that open new opportunities for the use of CRISPR-Cas technology for potato breeding, as well as for increasing resistance to abiotic and biotic stresses, and improving potato tuber quality. In addition, the review discusses the challenges and future perspectives of the CRISPR-Cas system in the prospects of the development of potato production and the regulation of gene-edited crops in different countries around the world. Full article
(This article belongs to the Section Molecular Plant Sciences)
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20 pages, 3810 KiB  
Article
Exploring Drought Response: Machine-Learning-Based Classification of Rice Tolerance Using Root and Physiological Traits
by Wuttichai Gunnula, Nantawan Kanawapee, Hathairat Chokthaweepanich and Piyaporn Phansak
Agronomy 2025, 15(8), 1840; https://doi.org/10.3390/agronomy15081840 - 29 Jul 2025
Viewed by 367
Abstract
Drought is a key limitation for rice productivity. While oxidative stress markers like hydrogen peroxide (H2O2) are important for drought adaptation, the predictive value of combining root anatomical and physiological traits is underexplored. We assessed 20 rice cultivars under [...] Read more.
Drought is a key limitation for rice productivity. While oxidative stress markers like hydrogen peroxide (H2O2) are important for drought adaptation, the predictive value of combining root anatomical and physiological traits is underexplored. We assessed 20 rice cultivars under drought and control conditions using a random forest, a multi-layer perceptron, and a SHAP-optimized stacking ensemble. The stacking ensemble achieved the highest classification accuracy (81.8%) and identified hydrogen peroxide, relative water content, and endodermis inner circumference as key predictors. SHAP analysis revealed important interactions between root anatomical and physiological traits, providing new biological insights into drought tolerance. Our integrative approach, supported by robust cross-validation, improves predictive power and transparency for breeding drought-resilient rice cultivars. Full article
(This article belongs to the Section Precision and Digital Agriculture)
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18 pages, 2752 KiB  
Review
Research Advances in Multiple Embryos and Apomixis in Rice (Oryza sativa L.)
by Junhao Dan, Wuhua Long, Mudan Qiu, Longhui Zhang, Chaoxin Wu, Xue Jiang, Shengyan Fang, Susong Zhu and Huafeng Deng
Int. J. Mol. Sci. 2025, 26(15), 7257; https://doi.org/10.3390/ijms26157257 - 27 Jul 2025
Viewed by 219
Abstract
A typical seed of rice (Oryza sativa L.) gives rise to a single seedling. In contrast, seeds from multiple embryos may develop into two or more seedlings, one of which is generated via sexual reproduction, while the others are likely to originate [...] Read more.
A typical seed of rice (Oryza sativa L.) gives rise to a single seedling. In contrast, seeds from multiple embryos may develop into two or more seedlings, one of which is generated via sexual reproduction, while the others are likely to originate through apomictic pathways. Therefore, the occurrence of multiple embryos is often considered a hallmark of apomixis in rice. Apomixis refers to an asexual reproductive strategy wherein unreduced gametes form through modified meiosis (apomeiosis) without fertilization, thereby generating clonal offspring generally genetically identical to the maternal plant. This process is of great relevance in fixing heterosis in hybrid rice breeding. This review discusses the origin, frequency, genetic regulation, and candidate genes related to multiple embryos in rice and provides a systematic summary of the latest research advances in rice apomixis. The insights presented in this study provide a theoretical foundation for the application of apomixis in rice breeding. Full article
(This article belongs to the Section Molecular Plant Sciences)
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13 pages, 25093 KiB  
Article
Sunflower HaGLK Enhances Photosynthesis, Grain Yields, and Stress Tolerance of Rice
by Jie Luo, Mengyi Zheng, Jiacheng He, Yangyang Lou, Qianwen Ge, Bojun Ma and Xifeng Chen
Biology 2025, 14(8), 946; https://doi.org/10.3390/biology14080946 - 27 Jul 2025
Viewed by 318
Abstract
GOLDEN2-LIKEs (GLKs) are important transcription factors for the chloroplast development influencing photosynthesis, nutrition, senescence, and stress response in plants. Sunflower (Helianthus annuus) is a highly photosynthetic plant; here, a GLK-homologues gene HaGLK was identified from the sunflower genome by bioinformatics. [...] Read more.
GOLDEN2-LIKEs (GLKs) are important transcription factors for the chloroplast development influencing photosynthesis, nutrition, senescence, and stress response in plants. Sunflower (Helianthus annuus) is a highly photosynthetic plant; here, a GLK-homologues gene HaGLK was identified from the sunflower genome by bioinformatics. To analyze the bio-function of HaGLK, transgenic rice plants overexpressing HaGLK (HaGLK-OE) were constructed and characterized via phenotype. Compared to the wild-type control rice variety Zhonghua 11 (ZH11), the HaGLK-OE lines exhibited increased photosynthetic pigment contents, higher net photosynthetic rates, and enlarged chloroplast area; meanwhile, genes involved in both photosynthesis and chlorophyll biosynthesis were also significantly up-regulated. Significantly, the HaGLK-OE plants showed a 12–13% increase in yield per plant. Additionally, the HaGLK-OE plants were demonstrated to have improved salt and drought tolerance compared to the control ZH11. Our results indicated that the HaGLK gene could play multiple roles in photosynthesis and stress response in rice, underscoring its potential value for improving crop productivity and environmental adaptability in breeding. Full article
(This article belongs to the Section Plant Science)
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18 pages, 1724 KiB  
Article
Ecological Product Value Realization in Agricultural Heritage System Sites: A Case Study of Wannian Rice Culture System in China
by Jingyi Li, Zhidong Li, Bojie Wang, Yan Mei, Youyu Luo and Qingwen Min
Sustainability 2025, 17(15), 6791; https://doi.org/10.3390/su17156791 - 25 Jul 2025
Viewed by 224
Abstract
The value realization of ecological products is an important part of rural and agricultural development. As a significant force for protecting traditional agricultural systems and promoting rural revitalization, agricultural heritage systems (AHSs) have formed diverse value realization paths of ecological products in the [...] Read more.
The value realization of ecological products is an important part of rural and agricultural development. As a significant force for protecting traditional agricultural systems and promoting rural revitalization, agricultural heritage systems (AHSs) have formed diverse value realization paths of ecological products in the process of dynamic protection and adaptive management. Through theoretical research, this article analyzed the characteristics of ecological products in AHS sites (EPAHSSs) and summarized the framework of value realization paths of EPAHSSs. Then, the Wannian Rice Culture System in China was selected as a case for conducting empirical research. The results showed that EPAHSSs exhibit obvious uniqueness in terms of climate environment, germplasm resources, farming and breeding models, and cultural heritage. The value realization paths of EPAHSSs mainly include industrial development support, such as the extension of agricultural industrial chains and the development of tourism, as well as fiscal transfer payments. The case analysis results indicated that Wannian County contains a rich variety of ecological products and developed a value realization pathway mainly based on the integration of industries and supplemented by fiscal transfer payments during the process of protection and development. However, further optimization is needed to promote the development of tourism and other paths. This study not only contributes to the sustainable development of the Wannian Rice Culture System, but the proposed framework is also applicable to other heritage systems and similar regions. Full article
(This article belongs to the Section Social Ecology and Sustainability)
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18 pages, 2659 KiB  
Article
Salt Stress Responses of Different Rice Varieties at Panicle Initiation: Agronomic Traits, Photosynthesis, and Antioxidants
by Yusheng Li, Yuxiang Xue, Zhuangzhuang Guan, Zhenhang Wang, Daijie Hou, Tingcheng Zhao, Xutong Lu, Yucheng Qi, Yanbo Hao, Jinqi Liu, Lin Li, Haider Sultan, Xiayu Guo, Zhiyong Ai and Aibin He
Plants 2025, 14(15), 2278; https://doi.org/10.3390/plants14152278 - 24 Jul 2025
Viewed by 320
Abstract
The utilization of saline–alkali land for rice cultivation is critical for global food security. However, most existing studies on rice salt tolerance focus on the seedling stage, with limited insights into tolerance mechanisms during reproductive growth, particularly at the panicle initiation stage (PI). [...] Read more.
The utilization of saline–alkali land for rice cultivation is critical for global food security. However, most existing studies on rice salt tolerance focus on the seedling stage, with limited insights into tolerance mechanisms during reproductive growth, particularly at the panicle initiation stage (PI). Leveraging precision salinity-control facilities, this study imposed four salt stress gradients (0, 3, 5, and 7‰) to dissect the differential response mechanisms of six rice varieties (YXYZ: Yuxiangyouzhan, JLY3261: Jingliangyou3261, SLY91: Shuangliangyou91, SLY138: Shuangliangyou138, HLYYHSM: Hualiangyouyuehesimiao, and SLY11:Shuangliangyou111) during PI. The results revealed that increasing salinity significantly reduced tiller number (13.14–68.04%), leaf area index (18.58–57.99%), canopy light interception rate (11.91–44.08%), and net photosynthetic rate (2.63–52.42%) (p < 0.001), accompanied by reactive oxygen species (ROS)-induced membrane lipid peroxidation. Integrative analysis of field phenotypic and physiological indices revealed distinct adaptation strategies: JLY3261 rapidly activated antioxidant enzymes under 3‰ salinity, alleviating lipid peroxidation (no significant difference in H2O2 or malondialdehyde content compared to 0‰ salinity) and maintaining tillering and aboveground biomass. SLY91 tolerated 7‰ salinity via CAT/POD-mediated lipid peroxide degradation, with H2O2 and malondialdehyde contents increasing initially but decreasing with escalating stress. These findings highlight genotype-specific antioxidant strategies underlying salt-tolerance mechanisms and the critical need for integrating phenomics–physiological assessments at reproductive stages into salt-tolerance breeding pipelines. Full article
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55 pages, 1315 KiB  
Review
Rice Adaptation to Abiotic Stresses Caused by Soil Inorganic Elements
by Giulia Vitiello, Daniela Goretti, Caterina Marè, Edoardo Delmastro, Giorgia Siviero, Silvio Collani, Erica Mica and Giampiero Valè
Int. J. Mol. Sci. 2025, 26(15), 7116; https://doi.org/10.3390/ijms26157116 - 23 Jul 2025
Viewed by 223
Abstract
Soil contamination with toxic inorganic elements poses a major challenge to rice cultivation, affecting plant physiology, yield, and grain safety. While natural variation in tolerance exists among rice genotypes and related species, recent advances in genomics, breeding, and biotechnology offer new opportunities to [...] Read more.
Soil contamination with toxic inorganic elements poses a major challenge to rice cultivation, affecting plant physiology, yield, and grain safety. While natural variation in tolerance exists among rice genotypes and related species, recent advances in genomics, breeding, and biotechnology offer new opportunities to enhance adaptation. This review synthesizes the current knowledge on the physiological effects of toxic elements and explores strategies to improve tolerance, from harnessing genetic diversity to genome editing and transgenic approaches. Attention is also paid to the role of microbiota in mitigating toxicity and reducing translocation to seeds, highlighting emerging solutions for sustainable rice production in contaminated environments. Full article
(This article belongs to the Special Issue Plant Resilience: Insights into Abiotic and Biotic Stress Adaptations)
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13 pages, 980 KiB  
Article
Determination of Rice Accession Status Using Infochemical and Visual Cues Emitted to Sustainably Control Diopsis apicalis Dalman
by Roland Bocco, Esther Pegalepo, Abou Togola, Francis Nwilene, Christophe Bernard Gandonou, Yedomon Ange Bovys Zoclanclounon, Marie Noelle Ndjiondjop, Mounirou Sow, Jeong Jun Kim and Manuele Tamò
Insects 2025, 16(8), 752; https://doi.org/10.3390/insects16080752 - 23 Jul 2025
Viewed by 283
Abstract
This study assessed the host plant selection behavior of female stalk-eyed flies (SEFs) or Diopsis apicalis, where a Y-tube olfactometer was used to compare SEF attraction to the odor of leaves from four rice varieties (ITA306, WAB56-104, CG14, and RAM55). Another step [...] Read more.
This study assessed the host plant selection behavior of female stalk-eyed flies (SEFs) or Diopsis apicalis, where a Y-tube olfactometer was used to compare SEF attraction to the odor of leaves from four rice varieties (ITA306, WAB56-104, CG14, and RAM55). Another step of the evaluation consisted of pairing leaf odors from two rice varieties. Also, potted plants of the tested varieties were displayed in a screened cage and submitted to female SEF selection. The results indicated that the odor produced by leaves from rice varieties CG14, WAB56-104, and ITA306 significantly attracted SEFs, at rates of 81%, 70%, and 97%, respectively, while SEF females were rarely attracted by the odor of leaves from the resistant rice variety RAM55, at a rate of 35%. The results suggested that the use of a Y-tube olfactometer was similar to the use of a screened cage. The resistance exhibited by rice variety CG14 against SEFs is related to an antibiosis interaction acting as bait, while that in RAM55 is an antixenosis one. Farmers can plant the traditional CG14 variety on the edge of rice fields to draw SEFs and poison their larvae. However, RAM55 can be inserted in an intercropping system to repel SEFs from laying eggs. The authors recommend CG14 and RAM55 as candidates for breeding to create resistant lines against SEF. Full article
(This article belongs to the Section Insect Behavior and Pathology)
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18 pages, 1169 KiB  
Article
Multi-Dimensional Analysis of Quality-Related Traits Affecting the Taste of Main Cultivated Japonica Rice Varieties in Northern China
by Hongwei Yang, Liying Zhang, Xiangquan Gao, Shi Han, Zuobin Ma and Lili Wang
Agronomy 2025, 15(8), 1757; https://doi.org/10.3390/agronomy15081757 - 22 Jul 2025
Viewed by 316
Abstract
The quality of rice, one of the most important food crops in the world, is directly related to people’s dietary experience and nutritional health. With the improvement in living standards, consumer requirements for the taste quality of rice are becoming increasingly strict. Japonica [...] Read more.
The quality of rice, one of the most important food crops in the world, is directly related to people’s dietary experience and nutritional health. With the improvement in living standards, consumer requirements for the taste quality of rice are becoming increasingly strict. Japonica rice occupies an important position in rice production due to its rich genetic diversity and excellent agronomic characteristics. In this study, LJ433, JY653, LJ218, LJ177, LY66, and LX21, which are mainly popularized in northern China and have different taste values, were selected as the experimental subjects, and YJ219, which won the gold award in the third China high-quality rice variety taste quality evaluation, was taken as the control (CK). Low-field nuclear magnetic resonance and spectral analysis were adopted as the main detection techniques. The effects of free water (peak area increased by 13.24–86.68% when p < 0.05), bound water, appearance characteristics (such as chalkiness, which decreased by 18.48–86.48%), and chemical composition (amylose content decreased by 3.76–26.47%) on the taste value of rice were systematically analyzed, and a multi-dimensional “appearance–palatability–nutrition” evaluation system was constructed. The experimental results indicated that increasing the free water content, reducing the chalkiness and chemical component content could significantly improve the taste value of rice (p < 0.05). The results of this research provide a theoretical basis for breeding new high-yield and high-quality rice varieties and have guiding significance for the practice of rice planting and processing. Full article
(This article belongs to the Section Plant-Crop Biology and Biochemistry)
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14 pages, 9617 KiB  
Article
Disruption of FW2.2-like Genes Enhances Metallic Micronutrient Accumulation in Brown Rice
by Qingsong Gao, Rumeng Sun, Jiayi Ding, Xingdang Xu, Xun Ma, Xi Liu and Hao Zhang
Agronomy 2025, 15(7), 1747; https://doi.org/10.3390/agronomy15071747 - 20 Jul 2025
Viewed by 299
Abstract
Micronutrient deficiencies adversely affect human health and pose a significant global threat. Enhancing the accumulation of micronutrients in the edible parts of crops through genetic breeding is a promising strategy to mitigate micronutrient deficiencies in humans. FW2.2-like (FWL) genes play [...] Read more.
Micronutrient deficiencies adversely affect human health and pose a significant global threat. Enhancing the accumulation of micronutrients in the edible parts of crops through genetic breeding is a promising strategy to mitigate micronutrient deficiencies in humans. FW2.2-like (FWL) genes play crucial roles in regulating heavy metal homeostasis in plants. We previously obtained two allelic mutants for each of the rice OsFWL1 (osfwl1a and osfwl1b) and OsFWL2 (osfwl2a and osfwl2b) genes. In this study, we showed that disruption of either OsFWL1 or OsFWL2 significantly enhanced the accumulation of metallic micronutrients in brown rice. Compared with that in the wild type, the iron (Fe) concentration in brown rice was higher in the osfwl1a (+166.7%), osfwl1b (+24.3%), and osfwl2a (+99.2%) mutants; the manganese (Mn) concentration was elevated in all four mutants (+25.1% to 35.6%); the copper (Cu) concentration increased in osfwl2a (+31.0%) and osfwl2b (+29.0%); and the zinc (Zn) concentration increased in osfwl2a (+10.2%). Additionally, disruption of OsFWL1 or OsFWL2 affected the homeostasis of metallic micronutrients in seedlings. Transcriptome analysis suggested that OsFWL1 and OsFWL2 might regulate cell wall polysaccharide metabolism and the expression of heavy metal transporter genes. Protein interaction analysis revealed that OsFWL1 interacted with OsFWL2 on the cell membrane. These findings suggest that OsFWL1 and OsFWL2 can serve as genetic biofortification tools to increase the concentrations of metallic micronutrients in rice grains. Full article
(This article belongs to the Special Issue Innovative Research on Rice Breeding and Genetics)
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19 pages, 2262 KiB  
Article
Epidemiological Profile and Risk Factors for Malaria in Rural Communities Before the Operationalization of the Singrobo–Ahouaty Dam, Southern Côte d’Ivoire
by Taki Jean Deles Avenié, Kigbafori Dieudonné Silué, Négnorogo Guindo-Coulibaly, Naférima Koné, Sadikou Touré, Kouamé Laurent Valian, Kouassi Séraphin Kouadio, Alloua Marie Joelle Bédia, Boza Fulgence Déabo, Klotcholman Diabagaté, Christian Nsanzabana and Jean Tenena Coulibaly
Trop. Med. Infect. Dis. 2025, 10(7), 197; https://doi.org/10.3390/tropicalmed10070197 - 15 Jul 2025
Viewed by 332
Abstract
Malaria remains a major public health issue, especially near hydroelectric dams that often promote mosquito breeding. This study aimed to establish baseline epidemiological data during the construction of the Singrobo–Ahouaty dam to support assessment and decision-making for short- and long-term health impacts on [...] Read more.
Malaria remains a major public health issue, especially near hydroelectric dams that often promote mosquito breeding. This study aimed to establish baseline epidemiological data during the construction of the Singrobo–Ahouaty dam to support assessment and decision-making for short- and long-term health impacts on surrounding communities. A cross-sectional survey was carried out in randomly selected households. Blood samples were analyzed using thick/thin smears and rapid diagnostic tests, while sociodemographic and behavioral data were collected via questionnaires. Statistical analyses included chi-square, Mann–Whitney, Kruskal–Wallis tests, and logistic regression. The malaria prevalence was 43.1% (394/915). The parasite density averaged 405.7 parasites/µL. School-age children (6–13 years) showed the highest prevalence (74.3%, p < 0.0001), while younger children (0–5 years) had the highest parasite density (1218.0 parasites/µL, p < 0.0001). Highly elevated infection rates (>51%) occurred in Sokrogbo, N’Dènou, and Amani-Menou, with the highest density in Ahérémou 1 (5663.9 parasites/µL). Risk factors included being an informal worker (ORa = 1.5), working in the raw material sector (ORa = 1.4) or market gardening/rice farming (ORa = 0.9; p = 0.043), and frequent mosquito bites (OR = 0.4; p = 0.017). These results underscore the need for stronger vector control strategies, improved bed net distribution and follow-up, and enhanced intersectoral collaboration in dam-influenced areas to reduce malaria transmission. Full article
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17 pages, 2826 KiB  
Article
Fine Mapping and Genetic Effect Analysis of Rf21(t) for the Fertility Restoration of Chinsurah-Boro-II-Type Cytoplasmic Male Sterile Oryza sativa (ssp. japonica) Lines
by Yuanyue Du, Liying Fan, Yunhua Gu, Chen Wang, Kai Shi, Yebin Qin, Zhejun Li, Qiaoquan Liu, Shuzhu Tang, Honggen Zhang and Zuopeng Xu
Agronomy 2025, 15(7), 1690; https://doi.org/10.3390/agronomy15071690 - 12 Jul 2025
Viewed by 287
Abstract
The combination of Chinsurah Boro II (BT)-type cytoplasmic male sterility (CMS) and Rf1, the main fertility restorer gene (Rf) for CMS-BT, has been extensively utilized for the production of three-line commercial japonica hybrid seeds. The identification of new Rf genes [...] Read more.
The combination of Chinsurah Boro II (BT)-type cytoplasmic male sterility (CMS) and Rf1, the main fertility restorer gene (Rf) for CMS-BT, has been extensively utilized for the production of three-line commercial japonica hybrid seeds. The identification of new Rf genes holds significance for the breeding of BT-type restorer lines, aiming to enhance the heterosis level of BT-type japonica hybrids. In the present study, ‘02428’, a wide-compatibility japonica variety, was observed to partially restore fertility to BT-type CMS lines. Genetic analysis revealed that ‘02428’ carries a dominant Rf gene, Rf21(t), responsible for the fertility restoration of BT-type CMS lines. Leveraging bulked segregant analysis (BSA) resequencing technology and molecular markers, the Rf21(t) locus was identified, and mapped within a candidate interval of 6–12.5 Mb on chromosome 2. Using the iso-cytoplasmic restorer populations, Rf21(t) was ultimately mapped to an interval of approximately 77 kb, encompassing 12 predicted genes, including LOC_Os02g17360, encoding a PPR-domain-containing protein and LOC_Os02g17380 (Rf2), a cloned Rf for Lead-rice-type CMS. A comparative sequence analysis, gene expression profiling and gene knockout experiments confirmed that LOC_Os02g17360 and LOC_Os02g17380 are the most likely candidates of Rf21(t). Furthermore, Rf21(t) showed the dosage effect on the fertility restoration of BT-type CMS lines. This newly identified Rf21(t) represents a valuable genetic resource for the breeding of BT-type japonica restorer lines. Our findings offer practical insights for breeders interested in advancing BT-type japonica hybrid development. Full article
(This article belongs to the Section Crop Breeding and Genetics)
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17 pages, 1609 KiB  
Article
Meta-Analysis of Wild Relatives and Domesticated Species of Rice, Tomato, and Soybean Using Publicly Available Transcriptome Data
by Makoto Yumiya and Hidemasa Bono
Life 2025, 15(7), 1088; https://doi.org/10.3390/life15071088 - 11 Jul 2025
Viewed by 422
Abstract
The domesticated species currently available in the market have been developed through the breeding of wild relatives. Breeding strategies using wild relatives with high genetic diversity are attracting attention as an important approach for addressing climate change and ensuring sustainable food supply. However, [...] Read more.
The domesticated species currently available in the market have been developed through the breeding of wild relatives. Breeding strategies using wild relatives with high genetic diversity are attracting attention as an important approach for addressing climate change and ensuring sustainable food supply. However, studies examining gene expression variation in multiple wild and domesticated species are limited. Therefore, we aimed to investigate the changes in gene expression associated with domestication. We performed a meta-analysis of public gene expression data of domesticated species of rice, tomato, and soybean and their presumed ancestral species using 21 pairs for rice, 36 pairs for tomato, and 56 pairs for soybean. In wild relatives, the expression of genes involved in osmotic, drought, and wound stress tolerance was upregulated, with 18 genes included in the top 5% of DW scores. In domesticated species, upregulated expression was observed in genes related to auxin and those involved in the efflux of heavy metals and harmful substances, with 36 genes included in the top 5% of DW scores. These findings provide insights into how domestication influences changes in crop traits. Thus, our findings may contribute to rapid breeding and the development of new varieties capable of growing in harsh natural environments. Hence, a new cultivation method called “de novo domestication” has been proposed, which combines the genetic diversity of currently unused wild relatives and wild relatives with genome editing technologies that enable rapid breeding. Full article
(This article belongs to the Special Issue Recent Advances in Crop Genetics and Breeding)
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26 pages, 1985 KiB  
Review
Stomatal and Non-Stomatal Leaf Traits for Enhanced Water Use Efficiency in Rice
by Yvonne Fernando, Mark Adams, Markus Kuhlmann and Vito Butardo Jr
Biology 2025, 14(7), 843; https://doi.org/10.3390/biology14070843 - 10 Jul 2025
Viewed by 600
Abstract
Globally, rice cultivation consumes large amounts of fresh water, and urgent improvements in water use efficiency (WUE) are needed to ensure sustainable production, given increasing water scarcity. While stomatal traits have been a primary focus for enhancing WUE, complex interactions between stomatal and [...] Read more.
Globally, rice cultivation consumes large amounts of fresh water, and urgent improvements in water use efficiency (WUE) are needed to ensure sustainable production, given increasing water scarcity. While stomatal traits have been a primary focus for enhancing WUE, complex interactions between stomatal and non-stomatal leaf traits remain poorly understood. In this review, we present an analysis of stomatal and non-stomatal leaf traits influencing WUE in rice. The data suggests that optimising stomatal density and size will be insufficient to maximise WUE because non-stomatal traits such as mesophyll conductance, leaf anatomy, and biochemical composition significantly modulate the relationship between stomatal conductance and the photosynthetic rate. Integrating recent advances in high-throughput phenotyping, multi-omics technologies, and crop modelling, we suggest that combinations of seemingly contradictory traits can enhance WUE without compromising yield potential. We propose a multi-trait breeding framework that leverages both stomatal and non-stomatal adaptations to develop rice varieties with superior WUE and climate resilience. This integrated approach provides a roadmap for accelerating the development of water-efficient rice cultivars, with broad implications for improving WUE in other crops. Full article
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