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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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • WSL9 Encodes an HNH Endonuclease Domain-Containing Protein that Is Essential for Early Chloroplast Development in Rice.
    Rice (IF 3.912) Pub Date : 2020-07-11
    Xingjie Zhu,Changling Mou,Fulin Zhang,Yunshuai Huang,Chunyan Yang,Jingli Ji,Xi Liu,Penghui Cao,Thanhliem Nguyen,Jie Lan,Chunlei Zhou,Shijia Liu,Ling Jiang,Jianmin Wan

    BackgroundThe plant chloroplast is essential for photosynthesis and other cellular processes, but an understanding of the biological mechanisms of plant chloroplast development are incomplete. ResultsA new temperature-sensitive white stripe leaf 9(wsl9) rice mutant is described. The mutant develops white stripes during early leaf development, but becomes green after the three-leaf stage under field

  • Re-Analysis of 16S Amplicon Sequencing Data Reveals Soil Microbial Population Shifts in Rice Fields under Drought Condition.
    Rice (IF 3.912) Pub Date : 2020-07-02
    Seok-Won Jang,Myeong-Hyun Yoou,Woo-Jong Hong,Yeon-Ju Kim,Eun-Jin Lee,Ki-Hong Jung

    Rice (Oryza sativa. L) has been intensively studied to ensure a stable global supply of this commodity in the face of rapid global climate change. A critical factor that decreases crop yield is drought, which has been analyzed in various ways through many researches. Microbiome-based studies of rice investigate the symbiosis between rice and bacteria, which has been proposed as a way to overcome problems

  • Effect of Root Colonization by Arbuscular Mycorrhizal Fungi on Growth, Productivity and Blast Resistance in Rice.
    Rice (IF 3.912) Pub Date : 2020-06-22
    Sonia Campo,Héctor Martín-Cardoso,Marta Olivé,Eva Pla,Mar Catala-Forner,Maite Martínez-Eixarch,Blanca San Segundo

    BackgroundArbuscular mycorrhizal (AM) fungi form symbiotic associations with roots in most land plants. AM symbiosis provides benefits to host plants by improving nutrition and fitness. AM symbiosis has also been associated with increased resistance to pathogen infection in several plant species. In rice, the effects of AM symbiosis is less studied, probably because rice is mostly cultivated in wetland

  • Transcriptome Sequencing and iTRAQ of Different Rice Cultivars Provide Insight into Molecular Mechanisms of Cold-Tolerance Response in Japonica Rice.
    Rice (IF 3.912) Pub Date : 2020-06-22
    Yan Jia,Hualong Liu,Zhaojun Qu,Jin Wang,Xinpeng Wang,Zhuoqian Wang,Liang Yang,Dong Zhang,Detang Zou,Hongwei Zhao

    BackgroundRice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions. However, it has a high sensitivity to cold stress and chilling stress limits its nitrogen uptake and metabolism. To identify the genes and pathways involved in cold tolerance, specifically within nitrogen metabolism pathways, we compared gene and protein expression differences between

  • The Rice BZ1 Locus Is Required for Glycosylation of Arabinogalactan Proteins and Galactolipid and Plays a Role in both Mechanical Strength and Leaf Color.
    Rice (IF 3.912) Pub Date : 2020-06-17
    Sitong Liu,Yijun Tang,Nan Ruan,Zhengjun Dang,Yuwei Huang,Wei Miao,Zhengjin Xu,Fengcheng Li

    BackgroundThe cell wall and chloroplast are two fundamental structures determining plant mechanical strength and grain yield. Therefore, understanding mechanisms that improve plants’ ability to develop a robust cell wall and well-developed chloroplast is of utmost importance for agricultural activities. ResultsIn this study, we report the functional characterization of a novel rice mutant, brittle

  • Genetic Dissection and Functional Differentiation of ALKa and ALKb, Two Natural Alleles of the ALK/SSIIa Gene, Responding to Low Gelatinization Temperature in Rice.
    Rice (IF 3.912) Pub Date : 2020-06-11
    Zhuanzhuan Chen,Yan Lu,Linhao Feng,Weizhuo Hao,Chuang Li,Yong Yang,Xiaolei Fan,Qianfeng Li,Changquan Zhang,Qiaoquan Liu

    BackgroundALK is the key gene controlling rice gelatinization temperature (GT), which is closely associated with the eating and cooking quality (ECQ) in rice (Oryza sativa L.). To date, at least three ALK alleles are thought to be responsible for the diversity of GT among rice cultivars. The ALKc/SSIIai allele with high activity of the soluble starch synthase IIa (SSIIa) controls high GT, but the accurate

  • Analysis of QTL for Grain Size in a Rice Chromosome Segment Substitution Line Z1392 with Long Grains and Fine Mapping of qGL-6.
    Rice (IF 3.912) Pub Date : 2020-06-11
    Ting Zhang,Shiming Wang,Shuangfei Sun,Yi Zhang,Juan Li,Jing You,Tian Su,Wenbo Chen,Yinghua Ling,Guanghua He,Fangming Zhao

    BackgroundGrain size affects not only rice yield but is also an important element in quality of appearance. However, the mechanism for inheritance of grain size is unclear. ResultsA rice chromosome segment substitution line Z1392, which harbors three substitution segments and produces grains of increased length, was identified. The three chromosome segments were located on chromosomes 1, 5, and 6,

  • Osa-miR162a fine-tunes rice resistance to Magnaporthe oryzae and Yield.
    Rice (IF 3.912) Pub Date : 2020-06-10
    Xu-Pu Li,Xiao-Chun Ma,He Wang,Yong Zhu,Xin-Xian Liu,Ting-Ting Li,Ya-Ping Zheng,Ji-Qun Zhao,Ji-Wei Zhang,Yan-Yan Huang,Mei Pu,Hui Feng,Jing Fan,Yan Li,Wen-Ming Wang

    MicroRNAs (miRNAs) play essential roles in rice immunity against Magnaporthe oryzae, the causative agent of rice blast disease. Here we demonstrate that Osa-miR162a fine-tunes rice immunity against M. oryzae and yield traits. Overexpression of Osa-miR162a enhances rice resistance to M. oryzae accompanying enhanced induction of defense-related genes and accumulation of hydrogen peroxide (H2O2). In contrast

  • Substitution Mapping of the Major Quantitative Trait Loci Controlling Stigma Exsertion Rate from Oryza glumaepatula.
    Rice (IF 3.912) Pub Date : 2020-06-09
    Quanya Tan,Tuo Zou,Mingmin Zheng,Yuerong Ni,Xin Luan,Xiaohui Li,Weifeng Yang,Zifeng Yang,Haitao Zhu,Ruizhen Zeng,Guifu Liu,Shaokui Wang,Xuelin Fu,Guiquan Zhang

    BackgroundStigma exsertion rate (SER) is a key determinant for the outcrossing ability of male sterility lines (MSLs) in hybrid rice seed production. In the process of domestication, the outcrossing ability of cultivated rice varieties decreased, while that of wild Oryza species kept strong. Here, we detected the quantitative trait loci (QTLs) controlling SER using a set of single-segment substitution

  • SAPK2 contributes to rice yield by modulating nitrogen metabolic processes under reproductive stage drought stress.
    Rice (IF 3.912) Pub Date : 2020-06-08
    Dengji Lou,Zhen Chen,Diqiu Yu,Xiaoyan Yang

    BackgroundThe sucrose non-fermenting 1-related kinases 2 (SnRK2s) play important roles in osmotic stress responses in A. thaliana and rice (Oryza sativa L.). Osmotic stress/ABA–activated protein kinase 2 (SAPK2) is a member of SnRK2s subclass II in rice, but its function in rice yield under drought stress is unclear. ResultsCompared with wild-type (Oryza.Sativa L.spp.japonica, WT) plants, the sapk2

  • Research and Development Strategies for Hybrid japonica Rice.
    Rice (IF 3.912) Pub Date : 2020-06-08
    Wenjing Zheng,Zuobin Ma,Mingzhu Zhao,Minggang Xiao,Jiaming Zhao,Changhua Wang,Hong Gao,Yuanjun Bai,Hui Wang,Guomin Sui

    The utilization of heterosis has resulted in significant breakthroughs in rice breeding. However, the development of hybrid japonica has been slow in comparison with that of hybrid indica. The present review explores the history and current status of hybrid japonica breeding. With the creation of japonica cytoplasmic male sterility and photo-thermo-sensitive genic male sterile lines, both three-line

  • Proteome-Wide Analyses Reveal the Diverse Functions of Lysine 2-Hydroxyisobutyrylation in Oryza sativa.
    Rice (IF 3.912) Pub Date : 2020-06-05
    Chao Xue,Zhongying Qiao,Xu Chen,Penghui Cao,Kai Liu,Shuai Liu,Lu Ye,Zhiyun Gong

    BackgroundLysine 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, is known to regulate transcriptional activity in animals. However, extensive studies of the lysine 2-hydroxyisobutyrylome in plants and animals have yet to be performed. ResultsIn this study, using LC-MS/MS qualitative proteomics strategies, we identified 4163 Khib sites on 1596 modified proteins in

  • Production Assessment and Genome Comparison Revealed High Yield Potential and Novel Specific Alleles Associated with Fertility and Yield in Neo-Tetraploid Rice.
    Rice (IF 3.912) Pub Date : 2020-06-03
    Hang Yu,Muhammad Qasim Shahid,Qihang Li,Yudi Li,Cong Li,Zijun Lu,Jinwen Wu,Zemin Zhang,Xiangdong Liu

    BackgroundNeo-tetraploid rice (NTR) is a new tetraploid rice germplasm that developed from the crossing and directional selection of different autotetraploid rice lines, which showed high fertility and promising yield potential. However, systematic yield assessment, genome composition and functional variations associated with fertility and yield remain elusive. ResultsTwo season’s field trials of 15

  • Agrobacterium-Mediated Genetic Transformation of Wild Oryza Species Using Immature Embryos.
    Rice (IF 3.912) Pub Date : 2020-06-03
    Sae Shimizu-Sato,Katsutoshi Tsuda,Misuzu Nosaka-Takahashi,Toshiya Suzuki,Seijiro Ono,Kim Nhung Ta,Yuri Yoshida,Ken-Ichi Nonomura,Yutaka Sato

    Genetic transformation is one of the most important technologies for revealing or modulating gene function. It is used widely in both functional genomics and molecular breeding of rice. Demands on its use in wild Oryza species is increasing because of their high genetic diversity. Given the difficulties in genetic crosses between distantly related species, genetic transformation offers a way to alter

  • Identification of Blast Resistance QTLs Based on Two Advanced Backcross Populations in Rice.
    Rice (IF 3.912) Pub Date : 2020-06-01
    Haichao Jiang,Yutao Feng,Lei Qiu,Guanjun Gao,Qinglu Zhang,Yuqing He

    BackgroundRice blast is an economically important and mutable disease of rice. Using host resistance gene to breed resistant varieties has been proven to be the most effective and economical method to control rice blast and new resistance genes or quantitative trait loci (QTLs) are then needed. ResultsIn this study, we constructed two advanced backcross population to mapping blast resistance QTLs.

  • Proteomic Analysis of Rice Subjected to Low Light Stress and Overexpression of OsGAPB Increases the Stress Tolerance.
    Rice (IF 3.912) Pub Date : 2020-06-01
    Yangxuan Liu,Ting Pan,Yuying Tang,Yong Zhuang,Zhijian Liu,Penghui Li,Hui Li,Weizao Huang,Shengbin Tu,Guangjun Ren,Tao Wang,Songhu Wang

    BackgroundLight provides the energy for photosynthesis and determines plant morphogenesis and development. Low light compromises photosynthetic efficiency and leads to crop yield loss. It remains unknown how rice responds to low light stress at a proteomic level. ResultsIn this study, the quantitative proteomic analysis with isobaric tags for relative and absolute quantitation (iTRAQ) was used and

  • Marker Assisted Forward Breeding to Combine Multiple Biotic-Abiotic Stress Resistance/Tolerance in Rice.
    Rice (IF 3.912) Pub Date : 2020-05-29
    Shilpi Dixit,Uma Maheshwar Singh,Arun Kumar Singh,Shamshad Alam,Challa Venkateshwarlu,Vishnu Varthini Nachimuthu,Shailesh Yadav,Ragavendran Abbai,Ramchander Selvaraj,M Nagamallika Devi,Perumalla Janaki Ramayya,Jyothi Badri,T Ram,Jhansi Lakshmi,G Lakshmidevi,Jai Vidhya Lrk,Ayyagari Phani Padmakumari,G S Laha,M S Prasad,Malathi Seetalam,Vikas Kumar Singh,Arvind Kumar

    Background Unfavorable climatic changes have led to an increased threat of several biotic and abiotic stresses over the past few years. Looking at the massive damage caused by these stresses, we undertook a study to develop high yielding climate-resilient rice, using genes conferring resistance against blast (Pi9), bacterial leaf blight (BLB) (Xa4, xa5, xa13, Xa21), brown planthopper (BPH) (Bph3, Bph17)

  • OsHsfB4d Binds the Promoter and Regulates the Expression of OsHsp18.0-CI to Resistant Against Xanthomonas Oryzae.
    Rice (IF 3.912) Pub Date : 2020-05-27
    Wei Yang,Yanhu Ju,Liping Zuo,Luyue Shang,Xinru Li,Xiaoming Li,Shangzong Feng,Xinhua Ding,Zhaohui Chu

    BackgroundBacterial leaf streak (BLS) and bacterial blight (BB) are two major prevalent and devastating rice bacterial diseases caused by the Gram-negative bacteria of Xanthomonas oryzae pv. oryzicola (Xoc) and Xanthomonas oryzae pv. oryzae (Xoo), respectively. Previously, we identified a defence-related (DR) gene encoding a small heat shock protein, OsHsp18.0-CI, that positively regulates BLS and

  • Evaluation of Domestication Loci Associated with Awnlessness in Cultivated Rice, Oryza sativa.
    Rice (IF 3.912) Pub Date : 2020-04-28
    Yaddehige Priya Jayantha Amarasinghe,Rie Kuwata,Akinori Nishimura,Phuong Dang Thai Phan,Ryo Ishikawa,Takashige Ishii

    BackgroundAwns are bristle-like organs at the tips of the glumes. Wild rice has maintained long awns for successful seed propagation through seed dispersal. Seed awning is an interesting trait in rice domestication. Long awns might have been beneficial for seed gatherers in the initial phase of domestication; however, awnless phenotypes were preferably selected in a later phase with non-seed-shattering

  • Abscisic Acid Negatively Modulates Heat Tolerance in Rolled Leaf Rice by Increasing Leaf Temperature and Regulating Energy Homeostasis
    Rice (IF 3.912) Pub Date : 2020-03-13
    Guangyan Li, Caixia Zhang, Guangheng Zhang, Weimeng Fu, Baohua Feng, Tingting Chen, Shaobing Peng, Longxing Tao, Guanfu Fu

    Background Abscisic acid (ABA) acts as a signaling hormone in plants against abiotic stress, but its function in energy homeostasis under heat stress is unclear. Results Two rice genotypes, Nipponbare (wild-type, WT) with flat leaves and its mutant high temperature susceptibility (hts) plant with semi-rolled leaves, were subjected to heat stress. We found significantly higher tissue temperature, respiration

  • The broad-spectrum rice blast resistance ( R ) gene Pita2 encodes a novel R protein unique from Pita
    Rice (IF 3.912) Pub Date : 2020-03-13
    Xiuli Meng, Gui Xiao, Mary Jeanie Telebanco-Yanoria, Paolo Miguel Siazon, Jonas Padilla, Rina Opulencia, Joseph Bigirimana, Georges Habarugira, Jun Wu, Mingyang Li, Baohua Wang, Guo-dong Lu, Bo Zhou

    Background Rice blast is generally considered the most devastating rice disease worldwide. The development of resistant varieties has been proven to be the most economical strategy to control the disease. A cluster of resistant (R) genes on rice chromosome 12 including Pita, Pita2 and Ptr has been studies for decades. However, the relationship between these R genes has not been well established. Results

  • Identification and Characterization of a Large Effect QTL from Oryza glumaepatula Revealed Pi68(t) as Putative Candidate Gene for Rice Blast Resistance
    Rice (IF 3.912) Pub Date : 2020-03-12
    S. J. S. Rama Devi, Kuldeep Singh, B. Umakanth, B. Vishalakshi, K. Vijaya Sudhakara Rao, B. Suneel, S. K. Sharma, Gopala Krishna Murthy Kadambari, M. S. Prasad, P. Senguttvel, Divya P. Syamaladevi, M. S. Madhav

    Background Field resistance is often effective and durable as compared to vertical resistance. The introgression line (INGR15002) derived from O. glumaepatula has proven broad spectrum field resistance for both leaf and neck blast. Results Quantitative Trait Loci (QTL) analysis of INGR15002, led to the identification of two major QTL - qBL3 contributing about 34% and 32% phenotypic variance towards

  • Enhancing xanthine dehydrogenase activity is an effective way to delay leaf senescence and increase rice yield
    Rice (IF 3.912) Pub Date : 2020-03-11
    Ruicai Han, Xunfeng He, Xiaohua Pan, Qinghua Shi, Ziming Wu

    Xanthine dehydrogenase (XDH) is an important enzyme in purine metabolism. It is involved in regulation of the normal growth and non-biological stress-induced ageing processes in plants. The present study investigated XDH’s role in regulating rice leaf senescence. We measured physical characteristics, chlorophyll content and fluorescence parameters, active oxygen metabolism, and purine metabolism in

  • Indeterminate Domain Proteins Regulate Rice Defense to Sheath Blight Disease
    Rice (IF 3.912) Pub Date : 2020-03-06
    Qian Sun, Dan Dan Li, Jin Chu, De Peng Yuan, Shuang Li, Li Juan Zhong, Xiao Han, Yuan Hu Xuan

    Background Loose Plant Architecture 1 (LPA1), an indeterminate domain (IDD) protein, exhibits almost no expression in the leaves, but the overexpression of LPA1 significantly increases the resistance of rice to sheath blight disease (ShB) via the activation of PIN-FORMED 1a (PIN1a). Results In this study, we determined that Rhizoctonia solani infection significantly induced LPA1 expression in the leaves

  • Natural Sequence Variations and Combinations of GNP1 and NAL1 Determine the Grain Number per Panicle in Rice
    Rice (IF 3.912) Pub Date : 2020-02-28
    Yun Wang, Laiyuan Zhai, Kai Chen, Congcong Shen, Yuntao Liang, Chunchao Wang, Xiuqin Zhao, Shu Wang, Jianlong Xu

    Background The grain number per panicle (GNP), which is one of three grain yield components, is an important trait for the genetic improvement of rice. Although the NAL1 and GNP1 genes regulating the rice GNP and grain yield have been cloned, their allelic diversity, functional differences in rice germplasms, and effects of their combination on GNP and grain yield remain unclear. Results Based on DNA

  • Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice
    Rice (IF 3.912) Pub Date : 2020-02-14
    Pingping Qu, Jinhui Shi, Tianxiao Chen, Kai Chen, Congcong Shen, Jiankang Wang, Xiangqian Zhao, Guoyou Ye, Jianlong Xu, Luyan Zhang

    Background The construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies. Pure lines derived from multiple parents provide more abundant genetic variation than those from bi-parent populations. Two four-parent pure-line populations (4PL1 and 4PL2) and one eight-parent pure-line population (8PL) were developed from eight homozygous indica varieties

  • Comprehensive Evaluation and Analysis of the Mechanism of Cold Tolerance Based on the Transcriptome of Weedy Rice Seedlings
    Rice (IF 3.912) Pub Date : 2020-02-13
    Bing Han, Xiaoding Ma, Di Cui, Yanjie Wang, Leiyue Geng, Guilan Cao, Hui Zhang, Longzhi Han

    Abstract In this study, the cold-tolerance capacity of 133 varieties of weedy rice was evaluated based on the comprehensive evaluation index D, with Kongyu 131 used as a cold-tolerant control. A total of 39.8% of the 133 varieties were considered ‘strong’, indicating that weedy rice populations indeed have relatively strong cold-tolerance capacity as a whole, and the robust cold-tolerant varieties

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