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Genome-Wide Association Study Dissects Resistance Loci against Bacterial Blight in a Diverse Rice Panel from the 3000 Rice Genomes Project Rice (IF 3.912) Pub Date : 2021-02-27 Jialing Lu, Chunchao Wang, Dan Zeng, Jianmin Li, Xiaorong Shi, Yingyao Shi, Yongli Zhou
Background Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating bacterial diseases of rice in temperate and tropical regions. Breeding and deployment of resistant cultivars carrying major resistance (R) genes has been the most effective approach for BB management. However, because of specific interaction of each R gene with the product of the corresponding
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Combination of High Zn Density and Low Phytic Acid for Improving Zn Bioavailability in Rice ( Oryza stavia L.) Grain Rice (IF 3.912) Pub Date : 2021-02-27 Yin Wang, Yusha Meng, Yanping Ma, Lei Liu, Dianxing Wu, Xiaoli Shu, Liqing Pan, Qixian Lai
Background Zn deficiency is one of the leading public health problems in the world. Staple food crop, such as rice, cannot provide enough Zn to meet the daily dietary requirement because Zn in grain would chelate with phytic acid, which resulted in low Zn bioavailability. Breeding new rice varieties with high Zn bioavailability will be an effective, economic and sustainable strategy to alleviate human
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Strategies to Manage Rice Sheath Blight: Lessons from Interactions between Rice and Rhizoctonia solani Rice (IF 3.912) Pub Date : 2021-02-25 Dayong Li, Shuai Li, Songhong Wei, Wenxian Sun
Rhizoctonia solani is an important phytopathogenic fungus with a wide host range and worldwide distribution. The anastomosis group AG1 IA of R. solani has been identified as the predominant causal agent of rice sheath blight, one of the most devastating diseases of crop plants. As a necrotrophic pathogen, R. solani exhibits many characteristics different from biotrophic and hemi-biotrophic pathogens
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OsPRR37 Alternatively Promotes Heading Date Through Suppressing the Expression of Ghd7 in the Japonica Variety Zhonghua 11 under Natural Long-Day Conditions Rice (IF 3.912) Pub Date : 2021-02-25 Yong Hu, Xin Zhou, Bo Zhang, Shuangle Li, Xiaowei Fan, Hu Zhao, Jia Zhang, Haiyang Liu, Qin He, Qiuping Li, Mohammed Ayaad, Aiqing You, Yongzhong Xing
Heading date is an important agronomic trait of rice (Oryza sativa L.) and is regulated by numerous genes, some of which exhibit functional divergence in a genetic background-dependent manner. Here, we identified a late heading date 7 (lhd7) mutant that flowered later than wild-type Zhonghua 11 (ZH11) under natural long-day (NLD) conditions. Map-based cloning facilitated by the MutMap strategy revealed
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A Semi-Dominant Mutation in OsCESA9 Improves Salt Tolerance and Favors Field Straw Decay Traits by Altering Cell Wall Properties in Rice Rice (IF 3.912) Pub Date : 2021-02-17 Yafeng Ye, Shuoxun Wang, Kun Wu, Yan Ren, Hongrui Jiang, Jianfeng Chen, Liangzhi Tao, Xiangdong Fu, Binmei Liu, Yuejin Wu
Background Cellulose synthase (CESA) mutants have potential use in straw processing due to their lower cellulose content, but almost all of the mutants exhibit defective phenotypes in plant growth and development. Balancing normal plant growth with reduced cellulose content remains a challenge, as cellulose content and normal plant growth are typically negatively correlated with one another. Result
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Two Novel QTLs for the Harvest Index that Contribute to High-Yield Production in Rice ( Oryza sativa L.) Rice (IF 3.912) Pub Date : 2021-02-10 Hiroki Saito, Yoshimichi Fukuta, Mitsuhiro Obara, Asami Tomita, Tsutomu Ishimaru, Kazuhiro Sasaki, Daisuke Fujita, Nobuya Kobayashi
Background The harvest index (HI) is a measure of the biological success of forming harvestable products. However, our understanding of the genetic basis of HI in rice (Oryza sativa L.) is limited, because it is a complex trait consisting of various yield-related traits and physiological attributes. YTH183 is a high-yielding line with large panicles and high HI derived from a cross between the Indica
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Contribution of Small RNA Pathway to Interactions of Rice with Pathogens and Insect Pests Rice (IF 3.912) Pub Date : 2021-02-06 Qin Feng, Yan Li, Zhi-Xue Zhao, Wen-Ming Wang
Small RNAs (sRNAs) are mainly classified into microRNAs (miRNAs) and small interfering RNAs (siRNAs) according to their origin. miRNAs originate from single-stranded RNA precursors, whereas siRNAs originate from double-stranded RNA precursors that are synthesized by RNA-dependent RNA polymerases. Both of single-stranded and double-stranded RNA precursors are processed into sRNAs by Dicer-like proteins
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Efficient Gene Stacking in Rice Using the GA A NTRY System Rice (IF 3.912) Pub Date : 2021-02-06 Leyla T. Hathwaik, James Horstman, James G. Thomson, Roger Thilmony
Genetic engineering of rice provides a means for improving rice grain quality and yield, and the introduction and expression of multiple genes can produce new traits that would otherwise be difficult to obtain through conventional breeding. GAANTRY (Gene Assembly in Agrobacterium by Nucleic acid Transfer using Recombinase technologY) was previously shown to be a precise and robust system to stably
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Genomics Analyses Reveal Unique Classification, Population Structure and Novel Allele of Neo-Tetraploid Rice Rice (IF 3.912) Pub Date : 2021-02-06 Hang Yu, Qihang Li, Yudi Li, Huijing Yang, Zijun Lu, Jinwen Wu, Zemin Zhang, Muhammad Qasim Shahid, Xiangdong Liu
Background Neo-tetraploid rice (NTR) is a useful new germplasm that developed from the descendants of the autotetraploid rice (ATR) hybrids. NTR showed improved fertility and yield potential, and produced high yield heterosis when crossed with indica ATR for commercial utilization. However, their classification, population structure and genomic feature remain elusive. Results Here, high-depth genome
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Analysis of Rice Transcriptome Reveals the LncRNA/CircRNA Regulation in Tissue Development Rice (IF 3.912) Pub Date : 2021-01-28 Run Zhou, Pablo Sanz-Jimenez, Xi-Tong Zhu, Jia-Wu Feng, Lin Shao, Jia-Ming Song, Ling-Ling Chen
Background Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) can play important roles in many biological processes. However, no study of the influence of epigenetics factors or the 3D structure of the genome in their regulation is available in plants. Results In the current analysis, we identified a total of 15,122 lncRNAs and 7902 circRNAs in three tissues (root, leaf and panicle) in the
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Decreased Vascular Bundle 1 affects mitochondrial and plant development in rice Rice (IF 3.912) Pub Date : 2021-01-25 Lisha Zhang, Ping Feng, Yao Deng, Wuzhong Yin, Yingchun Wan, Ting Lei, Guanghua He, Nan Wang
Background Mitochondria are vital regulators of plant growth and development, constitute the predominant source of ATP, and participate in multiple anabolic and catabolic metabolic pathways. But the mechanism by which dysfunctional mitochondria affect plant growth remains unknown, and more mitochondria-defective mutants need to be identified. Results A mitochondria-defective mutant decreased vascular
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The Fungal Effector Avr-Pita Suppresses Innate Immunity by Increasing COX Activity in Rice Mitochondria Rice (IF 3.912) Pub Date : 2021-01-14 Jingluan Han, Xiaoyu Wang, Fengpin Wang, Zhe Zhao, Gousi Li, Xiaoyuan Zhu, Jing Su, Letian Chen
Background Avr-Pita was the first effector identified in the blast fungus (Magnaporthe oryzae)–rice (Oryza sativa) pathosystem. However, the molecular mechanism underlying its effects on the host plant has remained a long-standing mystery. Results Here, we report that ectopically expressing Avr-Pita in rice enhances susceptibility to M. oryzae and suppresses pathogen-associated molecular pattern (PAMP)-triggered
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Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage Rice (IF 3.912) Pub Date : 2021-01-09 Leila Nayyeripasand, Ghasem Ali Garoosi, Asadollah Ahmadikhah
Background Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant
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Genetic Analysis of S5 -Interacting Genes Regulating Hybrid Sterility in Rice Rice (IF 3.912) Pub Date : 2021-01-09 Jianglei Rao, Xing Wang, Zhongquan Cai, Yourong Fan, Jiangyi Yang
Background Asian cultivated rice (Oryza sativa L.) comprises two subspecies, O. sativa subsp. indica and subsp. japonica, and the hybrids between them display strong heterosis. However, hybrid sterility (HS) limits practical use of the heterosis between these two subspecies. S5 is a major-effect locus controlling the HS of female gametes in rice, consisting of three closely-linked genes ORF3, ORF4
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OsNBL1, a Multi-Organelle Localized Protein, Plays Essential Roles in Rice Senescence, Disease Resistance, and Salt Tolerance Rice (IF 3.912) Pub Date : 2021-01-09 Xiaosheng Zhao, Tianbo Zhang, Huijing Feng, Tiancheng Qiu, Zichao Li, Jun Yang, You-Liang Peng, Wensheng Zhao
Background Plant senescence is a complicated process involving multiple regulations, such as temperature, light, reactive oxygen species (ROS), endogenous hormone levels, and diseases. Although many such genes have been characterized to understand the process of leaf senescence, there still remain many unknowns, and many more genes need to be characterized. Results We identified a rice mutant nbl1
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Genetics and Genomics of African Rice ( Oryza glaberrima Steud) Domestication Rice (IF 3.912) Pub Date : 2021-01-07 Peterson W. Wambugu, Marie-Noelle Ndjiondjop, Robert Henry
African rice (Oryza glaberrima Steud) is one of the two independently domesticated rice species, the other one being Asian rice (Oryza sativa L.). Despite major progress being made in understanding the evolutionary and domestication history of African rice, key outstanding issues remain controversial. There appears to be an underlying difficulty in identifying the domestication centre and number of
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Genomic Regions Involved in Differences in Eating and Cooking Quality Other than Wx and Alk Genes between indica and japonica Rice Cultivars Rice (IF 3.912) Pub Date : 2021-01-07 Kiyosumi Hori, Keitaro Suzuki, Haruka Ishikawa, Yasunori Nonoue, Kazufumi Nagata, Shuichi Fukuoka, Junichi Tanaka
Background In temperate rice cultivation regions, japonica rice cultivars are grown preferentially because consumers deem them to have good eating quality, whereas indica rice cultivars have high grain yields and strong heat tolerance but are considered to have poor eating quality. To mitigate the effects of global warming on rice production, it is important to develop novel rice cultivars with both
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Adaptation Mechanism of Roots to Low and High Nitrogen Revealed by Proteomic Analysis Rice (IF 3.912) Pub Date : 2021-01-07 Wei Xin, Lina Zhang, Jiping Gao, Wenzhong Zhang, Jun Yi, Xiaoxi Zhen, Congyuan Bi, Dawei He, Shiming Liu, Xinyu Zhao
Background Nitrogen-based nutrients are the main factors affecting rice growth and development. Root systems play an important role in helping plants to obtain nutrients from the soil. Root morphology and physiology are often closely related to above-ground plant organs performance. Therefore, it is important to understand the regulatory effects of nitrogen (N) on rice root growth to improve nitrogen
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Exploring Natural Allelic Variations of the β-Triketone Herbicide Resistance Gene HIS1 for Application in indica Rice and Particularly in Two-Line Hybrid Rice Rice (IF 3.912) Pub Date : 2021-01-07 Qiming Lv, Xiuli Zhang, Dingyang Yuan, Zhiyuan Huang, Rui Peng, Jiming Peng, Zuren Li, Li Tang, Ducai Liu, Xiaomao Zhou, Lifeng Wang, Lang Pan, Ye Shao, Bigang Mao, Yeyun Xin, Lihuang Zhu, Bingran Zhao, Lianyang Bai
Background Benzobicyclon (BBC) is a β-triketone herbicide (bTH) used in rice paddy fields. It has the advantages of high efficiency, low toxicity, high crop safety, and good environmental compatibility, and shows efficacy against paddy weeds resistant to other types of herbicides. However, as some important indica rice varieties are susceptible to BBC, BBC is currently only registered and applied in
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OsMS188 Is a Key Regulator of Tapetum Development and Sporopollenin Synthesis in Rice Rice (IF 3.912) Pub Date : 2021-01-06 Yu Han, Si-Da Zhou, Jiong-Jiong Fan, Lei Zhou, Qiang-Sheng Shi, Yan-Fei Zhang, Xing-Lu Liu, Xing Chen, Jun Zhu, Zhong-Nan Yang
Background During anther development, the tapetum provides essential nutrients and materials for pollen development. In rice, multiple transcription factors and enzymes essential for tapetum development and pollen wall formation have been cloned from male-sterile lines. Results In this study, we obtained several lines in which the MYB transcription factor OsMS188 was knocked out through the CRISPR-Cas9
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Generation and Starch Characterization of Non-Transgenic BEI and BEIIb Double Mutant Rice ( Oryza sativa ) with Ultra-High Level of Resistant Starch Rice (IF 3.912) Pub Date : 2021-01-06 Satoko Miura, Nana Koyama, Naoko Crofts, Yuko Hosaka, Misato Abe, Naoko Fujita
Background Cereals high in resistant starch (RS) are gaining popularity, as their intake is thought to help manage diabetes and prediabetes. Number of patients suffering from diabetes is also increasing in Asian countries where people consume rice as a staple food, hence generation of practically growable high RS rice line has been anticipated. It is known that suppression of starch branching enzyme
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The Amino Acid Transporter OsAAP4 Contributes to Rice Tillering and Grain Yield by Regulating Neutral Amino Acid Allocation through Two Splicing Variants Rice (IF 3.912) Pub Date : 2021-01-06 Zhongming Fang, Bowen Wu, Yuanyuan Ji
Background Amino acids, which are transported by amino acid transporters, are the major forms of organic nitrogen utilized by higher plants. Among the 19 Amino Acid Permease transporters (AAPs) in rice, only a small number of these genes have been reported to influence rice growth and development. However, whether other OsAAPs are responsible for rice growth and development is unclear. Results In this
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Dynamic genome-wide association analysis and identification of candidate genes involved in anaerobic germination tolerance in rice Rice (IF 3.912) Pub Date : 2021-01-06 Ling Su, Jing Yang, Dandan Li, Ziai Peng, Aoyun Xia, Meng Yang, Lixin Luo, Cuihong Huang, Jiafeng Wang, Hui Wang, Zhiqiang Chen, Tao Guo
Background In Asian rice production, an increasing number of countries now choose the direct seeding mode because of rising costs, labour shortages and water shortages. The ability of rice seeds to undergo anaerobic germination (AG) plays an important role in the success of direct seeding. Results In this study, we used 2,123,725 single nucleotide polymorphism (SNP) markers based on resequencing to
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Genetic Diversity of Landraces and Improved Varieties of Rice ( Oryza sativa L.) in Taiwan Rice (IF 3.912) Pub Date : 2020-12-14 Ai-ling Hour, Wei-hsun Hsieh, Su-huang Chang, Yong-pei Wu, Han-shiuan Chin, Yann-rong Lin
Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter
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Weighted Gene Co-Expression Network Coupled with a Critical-Time-Point Analysis during Pathogenesis for Predicting the Molecular Mechanism Underlying Blast Resistance in Rice Rice (IF 3.912) Pub Date : 2020-12-11 Dagang Tian, Zaijie Chen, Yan Lin, Ziqiang Chen, Khuynh The Bui, Zonghua Wang, Feng Wang
Background Rice blast, caused by the ascomycete fungus M. oryzae, is one of the most important diseases of rice. Although many blast resistance (R) genes have been identified and deployed in rice varieties, the molecular mechanisms responsible for the R gene-mediated defense responses are yet not fully understood. Results In this study, we used comparative transcriptomic analysis to explore the molecular
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Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining Rice (IF 3.912) Pub Date : 2020-12-07 Ying Zhou, Fang Lei, Qiong Wang, Weicong He, Bin Yuan, Wenya Yuan
Background As rice (Oryza sativa) is the staple food of more than half the world’s population, rice production contributes greatly to global food security. Rice blast caused by the fungus Magnaporthe oryzae (M. oryzae) is a devastating disease that affects rice yields and grain quality, resulting in substantial economic losses annually. Because the fungus evolves rapidly, the resistance conferred by
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OsNAC45 is Involved in ABA Response and Salt Tolerance in Rice Rice (IF 3.912) Pub Date : 2020-12-07 Xiang Zhang, Yan Long, Jingjing Huang, Jixing Xia
Background Salt stress threatens crop yields all over the world. Many NAC transcription factors have been reported to be involved in different abiotic stress responses, but it remains unclear how loss of these transcription factors alters the transcriptomes of plants. Previous reports have demonstrated that overexpression of OsNAC45 enhances salt and drought tolerance in rice, and that OsNAC45 may
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Auxin, Abscisic Acid and Jasmonate Are the Central Players in Rice Sheath Rot Caused by Sarocladium oryzae and Pseudomonas fuscovaginae Rice (IF 3.912) Pub Date : 2020-11-26 K. J. Peeters, M. Ameye, K. Demeestere, K. Audenaert, M. Höfte
Sheath rot is an emerging rice disease that causes severe yield losses worldwide. The main causal agents are the toxin producers Sarocladium oryzae and Pseudomonas fuscovaginae. The fungus S. oryzae produces helvolic acid and cerulenin and the bacterium P. fuscovaginae produces cyclic lipopeptides. Helvolic acid and the lipopeptide, fuscopeptin, inhibit membrane-bound H+-ATPase pumps in the rice plant
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Long Non-coding RNAs Responsive to Blast Fungus Infection in Rice Rice (IF 3.912) Pub Date : 2020-11-12 Lan-Lan Wang, Jing-Jing Jin, Li-Hua Li, Shao-Hong Qu
Background Long non-coding RNAs (LncRNAs) have emerged as important regulators in many physiological processes in plant. By high-throughput RNA-sequencing, many pathogen-associated LncRNAs were mapped in various plants, and some of them were proved to be involved in plant defense responses. The rice blast disease caused by Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases in rice
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RGG1 , Involved in the Cytokinin Regulatory Pathway, Controls Grain Size in Rice Rice (IF 3.912) Pub Date : 2020-11-10 Yajun Tao, Jun Miao, Jun Wang, Wenqi Li, Yang Xu, Fangquan Wang, Yanjie Jiang, Zhihui Chen, Fangjun Fan, Mengbin Xu, Yong Zhou, Guohua Liang, Jie Yang
Heterotrimeric GTP binding proteins (G proteins) and cytokinin play important roles in regulating plant growth and development. However, little is known about the mechanism by which they coordinate the regulation of grain size in rice. We functionally characterized one gene, RGG1, encoding a type-A Gγ subunit. Strong GUS staining was detected in young panicles and spikelets, suggesting a role for this
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RICE ACYL-COA-BINDING PROTEIN6 Affects Acyl-CoA Homeostasis and Growth in Rice Rice (IF 3.912) Pub Date : 2020-11-06 Wei Meng, Lijian Xu, Zhi-Yan Du, Fang Wang, Rui Zhang, Xingshun Song, Sin Man Lam, Guanghou Shui, Yuhua Li, Mee-Len Chye
Backgrounds Acyl-coenzyme A (CoA) esters are important intermediates in lipid metabolism with regulatory properties. Acyl-CoA-binding proteins bind and transport acyl-CoAs to fulfill these functions. RICE ACYL-COA-BINDING PROTEIN6 (OsACBP6) is currently the only one peroxisome-localized plant ACBP that has been proposed to be involved in β-oxidation in transgenic Arabidopsis. The role of the peroxisomal
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The Candidate Genes Underlying a Stably Expressed QTL for Low Temperature Germinability in Rice ( Oryza sativa L.) Rice (IF 3.912) Pub Date : 2020-10-19 Tifeng Yang, Lian Zhou, Junliang Zhao, Jingfang Dong, Qing Liu, Hua Fu, Xingxue Mao, Wu Yang, Yamei Ma, Luo Chen, Jian Wang, Song Bai, Shaohong Zhang, Bin Liu
Background Direct seeding is an efficient cultivation technique in rice. However, poor low temperature germinability (LTG) of modern rice cultivars limits its application. Identifying the genes associated with LTG and performing molecular breeding is the fundamental way to address this issue. However, few LTG QTLs have been fine mapped and cloned so far. Results In the present study, the LTG evaluation
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Characterization of the ‘Oat-Like Rice’ Caused by a Novel Allele OsMADS1 Olr Reveals Vital Importance of OsMADS1 in Regulating Grain Shape in Oryza sativa L. Rice (IF 3.912) Pub Date : 2020-10-15 Penghui Li, Hui Li, Zhijian Liu, Yong Zhuang, Ming Wei, Yuanyang Gu, Yangxuan Liu, Xiuqiang Sun, Yuying Tang, Lu Yue, Longxiang Lu, Dagang Luo, Weizao Huang, Shengbin Tu, Songhu Wang
Background Grain shape is a critical agronomic trait affecting grain yield and quality. Exploration and functional characterization of grain shape-related genes will facilitate rice breeding for higher quality and yield. Results Here, we characterized a recessive mutant named Oat-like rice for its unique grain shape which highly resembles oat grains. The Oat-like rice displayed abnormal floral organs
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Characterization of the Leaf Microbiome from Whole-Genome Sequencing Data of the 3000 Rice Genomes Project Rice (IF 3.912) Pub Date : 2020-10-09 Veronica Roman-Reyna, Dale Pinili, Frances N. Borja, Ian L. Quibod, Simon C. Groen, Nickolai Alexandrov, Ramil Mauleon, Ricardo Oliva
Background The crop microbial communities are shaped by interactions between the host, microbes and the environment, however, their relative contribution is beginning to be understood. Here, we explore these interactions in the leaf bacterial community across 3024 rice accessions. Findings By using unmapped DNA sequencing reads as microbial reads, we characterized the structure of the rice bacterial
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Genome wide association studies for japonica rice resistance to blast in field and controlled conditions Rice (IF 3.912) Pub Date : 2020-10-08 Andrea Volante, Alessandro Tondelli, Francesca Desiderio, Pamela Abbruscato, Barbara Menin, Chiara Biselli, Laura Casella, Namrata Singh, Susan R. McCouch, Didier Tharreau, Elisa Zampieri, Luigi Cattivelli, Giampiero Valè
Background Rice blast, caused by the fungus Pyricularia oryzae, represents the most damaging fungal disease of rice worldwide. Utilization of rice resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in
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RICE CENTRORADIALIS 1, a TFL1-like Gene, Responses to Drought Stress and Regulates Rice Flowering Transition. Rice (IF 3.912) Pub Date : 2020-09-24 Yan Wang,Yuyang Lu,Ziyu Guo,Yanfeng Ding,Chengqiang Ding
Background The initiation of flowering transition in rice (Oryza sativa) is a complex process regulated by genes and environment. In particular, drought can interfere with flowering; therefore, many plants hasten this process to shorten their life cycle under water scarcity, and this is known as drought-escape response. However, rice has other strategies; for example, drought stress can delay flowering
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Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima. Rice (IF 3.912) Pub Date : 2020-09-16 Philippe Cubry,Hélène Pidon,Kim Nhung Ta,Christine Tranchant-Dubreuil,Anne-Céline Thuillet,Maria Holzinger,Hélène Adam,Honoré Kam,Harold Chrestin,Alain Ghesquière,Olivier François,François Sabot,Yves Vigouroux,Laurence Albar,Stefan Jouannic
BackgroundAfrican rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation
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3D Visualization and Volume-Based Quantification of Rice Chalkiness In Vivo by Using High Resolution Micro-CT. Rice (IF 3.912) Pub Date : 2020-09-16 Yi Su,Lang-Tao Xiao
BackgroundRice quality research attracts attention worldwide. Rice chalkiness is one of the key indexes determining rice kernel quality. The traditional rice chalkiness measurement methods only use milled rice as materials and are mainly based on naked-eye observation or area-based two-dimensional (2D) image analysis and the results could not represent the three-dimensional (3D) characteristics of
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Phenotyping Root Systems in a Set of Japonica Rice Accessions: Can Structural Traits Predict the Response to Drought? Rice (IF 3.912) Pub Date : 2020-09-15 Paulo Henrique Ramos Guimarães,Isabela Pereira de Lima,Adriano Pereira de Castro,Anna Cristina Lanna,Patrícia Guimarães Santos Melo,Marcel de Raïssac
BackgroundThe root system plays a major role in plant growth and development and root system architecture is reported to be the main trait related to plant adaptation to drought. However, phenotyping root systems in situ is not suited to high-throughput methods, leading to the development of non-destructive methods for evaluations in more or less controlled root environments. This study used a root
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Marker Assisted Development and Characterization of Herbicide Tolerant Near Isogenic Lines of a Mega Basmati Rice Variety, "Pusa Basmati 1121". Rice (IF 3.912) Pub Date : 2020-09-15 Nitasha Grover,Aruna Kumar,Ashutosh Kumar Yadav,S Gopala Krishnan,Ranjith Kumar Ellur,Prolay Kumar Bhowmick,K K Vinod,Haritha Bollinedi,M Nagarajan,C Viswanathan,Amitha Mithra V Sevanthi,Nagendra Kumar Singh,Trilochan Mohapatra,Ashok Kumar Singh
BackgroundDirect-seeded rice (DSR) is a potential technology for sustainable rice farming as it saves water and labor. However, higher incidence of weed under DSR limits productivity. Therefore, there is a need to develop herbicide tolerant (HT) rice varieties. ResultsWe used marker assisted backcross breeding (MABB) to transfer a mutant allele of Acetohydroxy acid synthase (AHAS) gene, which confers
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Transcriptome Analysis of Early Defenses in Rice against Fusarium fujikuroi. Rice (IF 3.912) Pub Date : 2020-09-10 An-Po Cheng,Szu-Yu Chen,Ming-Hsin Lai,Dong-Hong Wu,Shih-Shun Lin,Chieh-Yi Chen,Chia-Lin Chung
BackgroundBakanae is a seedborne disease caused by Fusarium fujikuroi. Rice seedlings emerging from infected seeds can show diverse symptoms such as elongated and slender stem and leaves, pale coloring, a large leaf angle, stunted growth and even death. Little is known about rice defense mechanisms at early stages of disease development. ResultsThis study focused on investigating early defenses against
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A Cyclophilin OsCYP20-2 Interacts with OsSYF2 to Regulate Grain Length by Pre-mRNA Splicing. Rice (IF 3.912) Pub Date : 2020-09-10 Qiang Ge,Yongyan Tang,Wei Luo,Jingyu Zhang,Kang Chong,Yunyuan Xu
BackgroundGrain size is one of the key agronomic traits that impact grain yield. Several regulatory pathways had been reported to participate in grain size determination via cell expansion or proliferation in rice. However, little is known about cyclophilin and spliceosome participation in grain shape regulation. ResultsHere, we identified OsCYP20–2, a cyclophilin that influences spliceosome assembly
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Grain Size Selection Using Novel Functional Markers Targeting 14 Genes in Rice. Rice (IF 3.912) Pub Date : 2020-09-09 Lin Zhang,Bin Ma,Zhong Bian,Xiaoyuan Li,Changquan Zhang,Jiyun Liu,Qun Li,Qiaoquan Liu,Zuhua He
BackgroundGrain size is an extremely important aspect of rice breeding, affecting both grain yield and quality traits. It is controlled by multiple genes and tracking these genes in breeding schemes should expedite selection of lines with superior grain yield and quality, thus it is essential to develop robust, efficient markers. ResultIn this study, 14 genes related to grain size (GW2, GS2, qLGY3
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Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains. Rice (IF 3.912) Pub Date : 2020-09-07 Ting-Ying Wu,Marlen Müller,Wilhelm Gruissem,Navreet K Bhullar
BackgroundRice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular the contributions of different grain tissues to these processes, are not understood. Main
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Architectural and Physiological Features to Gain High Yield in an Elite Rice Line YLY1. Rice (IF 3.912) Pub Date : 2020-08-26 Shuoqi Chang,Tiangen Chang,Qingfeng Song,Jun Wu,Yi Luo,Xiaolong Chen,Xin-Guang Zhu,Qiyun Deng
Identification of traits strongly associated with high yield can help future gene engineering towards improvements of productivity. Here we systematically determine the major architectural and physiological features associated with high yield in two elite historical hybrid rice cultivars, i.e., YLY1 and LYP9. Data from a six-year experiment show that high yield of YLY1 are related to a number of architectural
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OsProDH Negatively Regulates Thermotolerance in Rice by Modulating Proline Metabolism and Reactive Oxygen Species Scavenging. Rice (IF 3.912) Pub Date : 2020-08-26 Mingxin Guo,Xiaotian Zhang,Jiajia Liu,Linlin Hou,Hanxiao Liu,Xusheng Zhao
BackgroundGlobal warming threatens rice growth and reduces yields. Proline plays important roles in plant abiotic stress tolerance. Previous research demonstrated that engineering proline metabolism-related genes can enhance tolerance to freezing and salinity in Arabidopsis. OsProDH encodes a putative proline dehydrogenase and is a single copy gene in rice. However, whether OsProDH plays roles in abiotic
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Genome-Wide Association Study of Rice Rooting Ability at the Seedling Stage. Rice (IF 3.912) Pub Date : 2020-08-24 Xin Xu,Junhua Ye,Yingying Yang,Mengchen Zhang,Qun Xu,Yue Feng,Xiaoping Yuan,Hanyong Yu,Yiping Wang,Yaolong Yang,Xinghua Wei
BackgroundRice rooting ability is a complex agronomical trait that displays heterosis and plays an important role in rice growth and production. Only a few quantitative trait loci (QTLs) have been identified by bi-parental population. More genes or QTLs are required to dissect the genetic architecture of rice rooting ability. ResultsTo characterize the genetic basis for rice rooting ability, we used
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Natural Diversity in Stomatal Features of Cultivated and Wild Oryza Species. Rice (IF 3.912) Pub Date : 2020-08-20 Jolly Chatterjee,Vivek Thakur,Robert Nepomuceno,Robert A Coe,Jacqueline Dionora,Abigail Elmido-Mabilangan,Abraham Darius Llave,Anna Mae Delos Reyes,Apollo Neil Monroy,Irma Canicosa,Anindya Bandyopadhyay,Kshirod K Jena,Darshan S Brar,William Paul Quick
BackgroundStomata in rice control a number of physiological processes by regulating gas and water exchange between the atmosphere and plant tissues. The impact of the structural diversity of these micropores on its conductance level is an important area to explore before introducing stomatal traits into any breeding program in order to increase photosynthesis and crop yield. Therefore, an intensive
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Multiple Cold Tolerance Trait Phenotyping Reveals Shared Quantitative Trait Loci in Oryza sativa. Rice (IF 3.912) Pub Date : 2020-08-14 Naoki Shimoyama,Melineeh Johnson,André Beaumont,Michael Schläppi
BackgroundDeveloping chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important cereal crop that can gain significantly from improved tolerance to low temperatures. However, mechanisms underlying this complex trait are not fully understood
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UvAtg8-Mediated Autophagy Regulates Fungal Growth, Stress Responses, Conidiation, and Pathogenesis in Ustilaginoidea virens. Rice (IF 3.912) Pub Date : 2020-08-12 Shuai Meng,Meng Xiong,Jane Sadhna Jagernath,Congcong Wang,Jiehua Qiu,Huanbin Shi,Yanjun Kou
BackgroundUstilaginoidea virens has become one of the most devastating rice pathogens in China, as well as other rice-growing areas. Autophagy is an important process in normal cell differentiation and development among various organisms. To date, there has been no optimized experimental system introduced for the study of autophagy in U. virens. In addition, the function of autophagy in pathogenesis
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Identification of a Major QTL and Candidate Gene Analysis of Salt Tolerance at the Bud Burst Stage in Rice (Oryza sativa L.) Using QTL-Seq and RNA-Seq. Rice (IF 3.912) Pub Date : 2020-08-10 Lei Lei,Hongliang Zheng,Yanli Bi,Luomiao Yang,Hualong Liu,Jingguo Wang,Jian Sun,Hongwei Zhao,Xianwei Li,Jiaming Li,Yongcai Lai,Detang Zou
BackgroundSalt stress is one of the main abiotic stresses that limits rice production worldwide. Rice salt tolerance at the bud burst stage directly affects the seedling survival rate and the final yield in the direct seeding cultivation model. However, the reports on quantitative trait locus (QTL) mapping and map-based cloning for salt tolerance at the bud burst stage are limited. ResultsHere, an
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Chloroplast SRP54s are Essential for Chloroplast Development in Rice. Rice (IF 3.912) Pub Date : 2020-08-06 Yongfeng Shi,Yan He,Xiangguang Lv,Yanlin Wei,Xiaobo Zhang,Xia Xu,Liangjian Li,Jian-Li Wu
BackgroundThe chloroplast signal recognition particle 54 (cpSRP54) is known for targeting the light-harvesting complex proteins to thylakoids and plays a critical role for chloroplast development in Arabidopsis, but little is known in rice. Here, we reported two homologous cpSRP54s that affect chloroplast development and plant survival in rice. ResultsTwo rice cpSRP54 homologues, OscpSRP54a and OscpSRP54b
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Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel. Rice (IF 3.912) Pub Date : 2020-08-06 Aditi Bhandari,Nitika Sandhu,Jérôme Bartholome,Tuong-Vi Cao-Hamadoun,Nourollah Ahmadi,Nilima Kumari,Arvind Kumar
BackgroundReproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution
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Genetic Dissection of Seed Dormancy in Rice (Oryza sativa L.) by Using Two Mapping Populations Derived from Common Parents. Rice (IF 3.912) Pub Date : 2020-08-05 Chaopu Zhang,Zhiyang Yuan,Yuntong Wang,Wenqiang Sun,Xinxin Tang,Yongjian Sun,Sibin Yu
BackgroundSeed dormancy, a quality characteristic that plays a role in seed germination, seedling establishment and grain yield, is affected by multiple genes and environmental factors. The genetic and molecular mechanisms underlying seed dormancy in rice remain largely unknown. ResultsQuantitative trait loci (QTLs) for seed dormancy were identified in two different mapping populations, a chromosome
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Disruption of a Rice Chloroplast-Targeted Gene OsHMBPP Causes a Seedling-Lethal Albino Phenotype. Rice (IF 3.912) Pub Date : 2020-07-25 X Liu,P H Cao,Q Q Huang,Y R Yang,D D Tao
BackgroundChloroplast development is coordinately regulated by plastid- and nuclear-encoding genes. Although many regulators have been reported to be involved in chloroplast development, new factors remain to be identified, given the complexity of this process. ResultsIn this study, we characterized a rice mutant lethal albinic seedling 1(las1)form of a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
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Overexpression of the Transcription Factor Gene OsSTAP1 Increases Salt Tolerance in Rice. Rice (IF 3.912) Pub Date : 2020-07-23 Yinxiao Wang,Juan Wang,Xiuqin Zhao,Sheng Yang,Liyu Huang,Fengping Du,Zhikang Li,Xiangqiang Zhao,Binying Fu,Wensheng Wang
BackgroundHigh soil salinity can cause significant losses in rice productivity worldwide, mainly because salt inhibits plant growth and reduces grain yield. To cope with environmental changes, plants have evolved several adaptive mechanisms that involve the regulation of many stress-responsive genes. ResultsIn this study, we identified OsSTAP1, which encodes an AP2/ERF-type transcription factor, was
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Isolation of TSCD11 Gene for Early Chloroplast Development under High Temperature in Rice. Rice (IF 3.912) Pub Date : 2020-07-17 Guonan Fang,Shenglong Yang,Banpu Ruan,Chaolei Liu,Anpeng Zhang,Hongzhen Jiang,Shilin Ding,Biao Tian,Yu Zhang,Noushin Jahan,Li Zhu,Guangheng Zhang,Guojun Dong,Qiang Zhang,Dali Zeng,Longbiao Guo,Zhenyu Gao,Qian Qian
BackgroundChloroplasts are essential for photosynthesis and play key roles in plant development. High temperature affects structure of chloroplasts and metabolism in plants. The seryl-tRNA synthetase plays an important role in translation of proteins. Although seryl-tRNA synthetase has been widely studied in microbes and animals, few studies have reported about its role in chloroplast development under
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QTL Mapping and Candidate Gene Analysis for Alkali Tolerance in Japonica Rice at the bud Stage Based on Linkage Mapping and Genome-Wide Association Study. Rice (IF 3.912) Pub Date : 2020-07-16 Xianwei Li,Hongliang Zheng,Wenshen Wu,Hualong Liu,Jingguo Wang,Yan Jia,Jiaming Li,Luomiao Yang,Lei Lei,Detang Zou,Hongwei Zhao
BackgroundSalinity-alkalinity stress is one of the major factors limiting rice production. Damage caused by alkaline salt stress is more severe than that caused by neutral salt stress. Alkali tolerance at the bud stage in rice directly affects seedling survival and final yield when using the direct seeding cultivation model. However, genetic resources (QTLs and genes) for rice breeders to improve alkali
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Characterization of Haplotype Diversity in the BADH2 Aroma Gene and Development of a KASP SNP Assay for Predicting Aroma in U.S. Rice. Rice (IF 3.912) Pub Date : 2020-07-14 Christopher K Addison,Brijesh Angira,Manoch Kongchum,Dustin L Harrell,Niranjan Baisakh,Steven D Linscombe,Adam N Famoso
BackgroundAroma is an important grain quality trait in rice, controlled by mutations within the BADH2 gene. The trait is simply inherited, and its importance in variety development makes it a practical target for marker-assisted selection in applied breeding programs. The predominant functional mutation within BADH2, an 8-bp indel, can be reliably detected using a PCR-based assay, but the available
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Genetic Effects of Soluble Starch Synthase IV-2 and It with ADPglucose Pyrophorylase Large Unit and Pullulanase on Rice Qualities. Rice (IF 3.912) Pub Date : 2020-07-13 Liang Xu,Hui You,Ouling Zhang,Xunchao Xiang
BackgroundRice amylose content and amylopectin structure corporately determine rice eating and cooking qualities (ECQs). Soluble starch synthase (SS) IV-2 is a member of the soluble starch synthesis gene family but with unknown effects on ECQs. ResultsIn this study, three populations derived from a cross of two parents who possess the same major genes of starch bio-synthesis were employed to investigate
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