Articles

An In Vivo Targeted Deletion of the Calmodulin-Binding Domain from Rice Glutamate Decarboxylase 3 (OsGAD3) Increases γ-Aminobutyric Acid Content in Grains

Gamma-aminobutyric acid (GABA) is a non-protein amino acid present in all living things. GABA is mainly synthesized from glutamate by glutamate decarboxylase (GAD). In plants the enzymatic activity of GAD is a...

Authors: Kazuhito Akama, Nadia Akter, Hinako Endo, Masako Kanesaki, Masaki Endo and Seiichi Toki

The broad-spectrum rice blast resistance (R) gene Pita2 encodes a novel R protein unique from Pita

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 re...

Authors: 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 and Bo Zhou

Abscisic Acid Negatively Modulates Heat Tolerance in Rolled Leaf Rice by Increasing Leaf Temperature and Regulating Energy Homeostasis

Abscisic acid (ABA) acts as a signaling hormone in plants against abiotic stress, but its function in energy homeostasis under heat stress is unclear.

Authors: Guangyan Li, Caixia Zhang, Guangheng Zhang, Weimeng Fu, Baohua Feng, Tingting Chen, Shaobing Peng, Longxing Tao and Guanfu Fu

Identification and Characterization of a Large Effect QTL from Oryza glumaepatula Revealed Pi68(t) as Putative Candidate Gene for Rice Blast Resistance

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 ...

Authors: 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 and M. S. Madhav

Enhancing xanthine dehydrogenase activity is an effective way to delay leaf senescence and increase rice yield

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 inves...

Authors: Ruicai Han, Xunfeng He, Xiaohua Pan, Qinghua Shi and Ziming Wu

Indeterminate Domain Proteins Regulate Rice Defense to Sheath Blight Disease

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 bligh...

Authors: Qian Sun, Dan Dan Li, Jin Chu, De Peng Yuan, Shuang Li, Li Juan Zhong, Xiao Han and Yuan Hu Xuan

Natural Sequence Variations and Combinations of GNP1 and NAL1 Determine the Grain Number per Panicle in Rice

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 yiel...

Authors: Yun Wang, Laiyuan Zhai, Kai Chen, Congcong Shen, Yuntao Liang, Chunchao Wang, Xiuqin Zhao, Shu Wang and Jianlong Xu

Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice

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 fr...

Authors: Pingping Qu, Jinhui Shi, Tianxiao Chen, Kai Chen, Congcong Shen, Jiankang Wang, Xiangqian Zhao, Guoyou Ye, Jianlong Xu and Luyan Zhang

Comprehensive Evaluation and Analysis of the Mechanism of Cold Tolerance Based on the Transcriptome of Weedy Rice Seedlings

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 1...

Authors: Bing Han, Xiaoding Ma, Di Cui, Yanjie Wang, Leiyue Geng, Guilan Cao, Hui Zhang and Longzhi Han

Genome-Wide Association Studies Reveal the Genetic Basis of Fertility Restoration of CMS-WA and CMS-HL in xian/indica and aus Accessions of Rice (Oryza sativa L.)

Wild-abortive cytoplasmic male sterility (CMS-WA) and Honglian CMS (CMS-HL) are the two main CMS types utilized in production of three-line hybrid rice in xian/indica (XI) rice. Dissection of the genetic basis of...

Authors: Pingbo Li, Hao Zhou, Hanyuan Yang, Duo Xia, Rongjia Liu, Ping Sun, Quanxiu Wang, Guanjun Gao, Qinglu Zhang, Gongwei Wang and Yuqing He

Characterization of a New qLTG3–1 Allele for Low-temperature Germinability in Rice from the Wild Species Oryza rufipogon

Rice (Oryza sativa L.) is generally sensitive to low temperatures, and in production systems that use direct-seeding, low-temperature germinability (LTG) is a desired trait. Previously, the QTLs, qLTG1 and qLTG3,

Authors: Kyu-Chan Shim, Sun Ha Kim, Hyun-Sook Lee, Cheryl Adeva, Yun-A Jeon, Ngoc Ha Luong, Woo-Jin Kim, Mirjalol Akhtamov, Yong-Jin Park and Sang-Nag Ahn

How to start your monocot CRISPR/Cas project: plasmid design, efficiency detection, and offspring analysis

The breakthrough CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9-mediated genome-editing technology has led to great progress in monocot research; however, several factors need to be con...

Authors: Jin-Jun Yue, Chwan-Yang Hong, Pengcheng Wei, Yu-Chang Tsai and Choun-Sea Lin

Intron-Based Single Transcript Unit CRISPR Systems for Plant Genome Editing

Expression of either Cas9 or Cas12a and guide RNAs by a single Polymerase II (Pol II) promoter represents a compact CRISPR expression system and has many advantages for different applications. In order to make...

Authors: Zhaohui Zhong, Shishi Liu, Xiaopei Liu, Binglin Liu, Xu Tang, Qiurong Ren, Jianping Zhou, Xuelian Zheng, Yiping Qi and Yong Zhang

MINI SEED 2 (MIS2) Encodes a Receptor-like Kinase that Controls Grain Size and Shape in Rice

Grain size is a key agronomic trait that is directly associated with grain yield in rice. Although several genes related to grain size in rice have been identified, our understanding of the mechanism of grain ...

Authors: Yan Chun, Jingjing Fang, Syed Adeel Zafar, Jiangyuan Shang, Jinfeng Zhao, Shoujiang Yuan and Xueyong Li

Prevalence of Ineffective Haplotypes at the Rice Blast Resistance (R) Gene Loci in Chinese Elite Hybrid Rice Varieties Revealed by Sequence-Based Molecular Diagnosis

Multiple haplotypes at the same rice blast R-gene locus share extremely high sequence similarity, which makes the gene diagnostic method using molecular markers less effective in differentiation from one another....

Authors: Gui Xiao, Jianyuan Yang, Xiaoyuan Zhu, Jun Wu and Bo Zhou

Beyond Seek and Destroy: how to Generate Allelic Series Using Genome Editing Tools

Genome editing tools have greatly facilitated the functional analysis of genes of interest by targeted mutagenesis. Many usable genome editing tools, including different site-specific nucleases and editor data...

Authors: Leo Herbert, Anne-Cécile Meunier, Martine Bes, Aurore Vernet, Murielle Portefaix, Franz Durandet, Remy Michel, Christian Chaine, Patrice This, Emmanuel Guiderdoni and Christophe Périn

Comparison of CRISPR-Cas9/Cas12a Ribonucleoprotein Complexes for Genome Editing Efficiency in the Rice Phytoene Desaturase (OsPDS) Gene

Delivery of CRISPR reagents into cells as ribonucleoprotein (RNP) complexes enables transient editing, and avoids CRISPR reagent integration in the genomes. Another technical advantage is that RNP delivery can...

Authors: Raviraj Banakar, Mollie Schubert, Michael Collingwood, Christopher Vakulskas, Alan L. Eggenberger and Kan Wang

Resistance Genes and their Interactions with Bacterial Blight/Leaf Streak Pathogens (Xanthomonas oryzae) in Rice (Oryza sativa L.)—an Updated Review

Rice (Oryza sativa L.) is a staple food crop, feeding more than 50% of the world’s population. Diseases caused by bacterial, fungal, and viral pathogens constantly threaten the rice production and lead to enormou...

Authors: Nan Jiang, Jun Yan, Yi Liang, Yanlong Shi, Zhizhou He, Yuntian Wu, Qin Zeng, Xionglun Liu and Junhua Peng

OsFPFL4 is Involved in the Root and Flower Development by Affecting Auxin Levels and ROS Accumulation in Rice (Oryza sativa)

FPF1 (flowering-promoting factor 1) is one of the important family involved in the genetic control of flowering time in plant. Until now, limited knowledge concerning FPF1 family in rice has been understood.

Authors: Yaomin Guo, Qi Wu, Zizhao Xie, Bo Yu, Rongfeng Zeng, Qian Min and Junli Huang

Development of Whole-Genome Agarose-Resolvable LInDel Markers in Rice

The level of difficulty involved in separating marker genotypes greatly determines the utilization of such marker-aided selection (MAS) by breeders. Genotyping by use of agarose gel electrophoresis is easily a...

Authors: Wei Hu, Tianhao Zhou, Pengfei Wang, Bo Wang, Jiaming Song, Zhongmin Han, Lingling Chen, Kede Liu and Yongzhong Xing

Genome-Wide Association Analysis Dissects the Genetic Basis of the Grain Carbon and Nitrogen Contents in Milled Rice

Carbon (C) and nitrogen (N) are two fundamental components of starch and protein, which are important determinants of grain yield and quality. The food preferences of consumers and the expected end-use of grai...

Authors: Liang Tang, Fan Zhang, Anjin Liu, Jian Sun, Song Mei, Xin Wang, Zhongyuan Liu, Wanying Liu, Qing Lu and Shuangjie Chen

Lose-of-Function of a Rice Nucleolus-Localized Pentatricopeptide Repeat Protein Is Responsible for the floury endosperm14 Mutant Phenotypes

The endosperm of rice (Oryza sativa) has been usually used for the study of starch synthesis. Although several related factors have been revealed, other unknown members remain to be identified, given that starch ...

Authors: Mengyao Xue, Linglong Liu, Yanfang Yu, Jianping Zhu, Hao Gao, Yihua Wang and Jianmin Wan

Genomic and transcriptomic analysis reveal molecular basis of salinity tolerance in a novel strong salt-tolerant rice landrace Changmaogu

Salt stress is an important factor that limits rice yield. We identified a novel, strongly salt tolerant rice landrace called Changmaogu (CMG) collected from a coastal beach of Zhanjiang, Guangdong Province, C...

Authors: Bing-Rui Sun, Chong-Yun Fu, Zhi-Lan Fan, Yu Chen, Wen-Feng Chen, Jing Zhang, Li-Qun Jiang, Shuwei Lv, Da-Jian Pan and Chen Li

In Loving Memory of Professor Joachim Messing, a Pioneer from Molecular Genetics to Plant Genomics

Authors: Yin Li, Jennifer Ayer, Paul Fourounjian, Jiaqiang Dong, Zhiyong Zhang, Chenxu Liu and Fan Feng

Rice Stress-Resistant SNP Database

Rice (Oryza sativa L.) yield is limited inherently by environmental stresses, including biotic and abiotic stresses. Thus, it is of great importance to perform in-depth explorations on the genes that are closely ...

Authors: Samuel Tareke Woldegiorgis, Shaobo Wang, Yiruo He, Zhenhua Xu, Lijuan Chen, Huan Tao, Yu Zhang, Yang Zou, Andrew Harrison, Lina Zhang, Yufang Ai, Wei Liu and Huaqin He

Competition between Granule Bound Starch Synthase and Starch Branching Enzyme in Starch Biosynthesis

Starch branching enzymes (SBE) and granule-bound starch synthase (GBSS) are two important enzymes for starch biosynthesis. SBE mainly contributes to the formation of side branches, and GBSS mainly contributes ...

Authors: Huaxin Han, Chuantian Yang, Jihui Zhu, Lixia Zhang, Yeming Bai, Enpeng Li and Robert G. Gilbert

Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants

Continuing crop domestication/redomestication and modification is a key determinant of the adaptation and fulfillment of the food requirements of an exploding global population under increasingly challenging c...

Authors: Tien Van Vu, Yeon Woo Sung, Jihae Kim, Duong Thi Hai Doan, Mil Thi Tran and Jae-Yean Kim

Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars

Rice grain production is susceptible to a changing environment that imposes both biotic and abiotic stress conditions. Cold episodes are becoming more frequent in the last years and directly affect rice yield ...

Authors: Nahuel González-Schain, Irma Roig-Villanova and Martin M. Kater

Genome-Wide Association Analysis of the Genetic Basis for Sheath Blight Resistance in Rice

Sheath blight (ShB), caused by Rhizoctonia solani Kühn, is one of the most destructive rice diseases. Developing ShB-resistant rice cultivars represents the most economical and environmentally sound strategy for ...

Authors: Fan Zhang, Dan Zeng, Cong-Shun Zhang, Jia-Ling Lu, Teng-Jun Chen, Jun-Ping Xie and Yong-Li Zhou

OsIAGT1 Is a Glucosyltransferase Gene Involved in the Glucose Conjugation of Auxins in Rice

In cereal crop rice, auxin is known as an important class of plant hormone that regulates a plethora of plant growth and development. Glycosylation of auxin is known to be one of the important mechanisms media...

Authors: Qian Liu, Ting-Ting Chen, Dong-Wang Xiao, Shu-Man Zhao, Ji-Shan Lin, Ting Wang, Yan-Jie Li and Bing-Kai Hou

The Rice G Protein γ Subunit DEP1/qPE9–1 Positively Regulates Grain-Filling Process by Increasing Auxin and Cytokinin Content in Rice Grains

Heterotrimeric G protein-mediated signal transduction is one of the most important and highly conserved signaling pathways in eukaryotes, which involves in the regulation of many important biological processes...

Authors: Dongping Zhang, Minyan Zhang, Yong Zhou, Yuzhu Wang, Jinyu Shen, Hongyingxue Chen, Lin Zhang, Bing Lü, Guohua Liang and Jiansheng Liang

OsPGIP1-Mediated Resistance to Bacterial Leaf Streak in Rice is Beyond Responsive to the Polygalacturonase of Xanthomonas oryzae pv. oryzicola

Polygalacturonase-inhibiting proteins (PGIPs) have been shown to recognize fungal polygalacturonases (PGs), which initiate innate immunity in various plant species. Notably, the connection between rice OsPGIPs...

Authors: Tao Wu, Chune Peng, Beibei Li, Wei Wu, Lingguang Kong, Fuchuan Li, Zhaohui Chu, Fang Liu and Xinhua Ding

Harmonizing technological advances in phenomics and genomics for enhanced salt tolerance in rice from a practical perspective

Half of the global human population is dependent on rice as a staple food crop and more than 25% increase in rice productivity is required to feed the global population by 2030. With increase in irrigation, gl...

Authors: Sarika Jaiswal, R. K. Gautam, R. K. Singh, S. L. Krishnamurthy, S. Ali, K. Sakthivel, M. A. Iquebal, Anil Rai and Dinesh Kumar

Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study

Soil salinity is one of the main environmental conditions that affects rice production. Identifying the genetic loci that affect rice salt tolerance (ST)-related traits at the seedling stage, especially under ...

Authors: Chen Liu, Kai Chen, Xiuqin Zhao, Xiaoqian Wang, Congcong Shen, Yajun Zhu, Mingli Dai, Xianjin Qiu, Rongwei Yang, Danying Xing, Yunlong Pang and Jianlong Xu

Improving the Glossiness of Cooked Rice, an Important Component of Visual Rice Grain Quality

Rice is one of the few cereals consumed as a whole grain, and therefore the appearance of the final milled product, both before and after cooking, strongly influences the consumer’s perception of product quali...

Authors: Seul-Gi Park, Hyun-Su Park, Man-Kee Baek, Jong-Min Jeong, Young-Chan Cho, Gun-Mi Lee, Chang-Min Lee, Jung-Pil Suh, Choon-Song Kim and Suk-Man Kim

Genome-wide Profiling of Histone Lysine Butyrylation Reveals its Role in the Positive Regulation of Gene Transcription in Rice

Histone modifications play important roles in growth and development of rice (Oryza sativa L.). Lysine butyrylation (Kbu) with a four-carbon chain is a newly-discovered histone acylation modification in rice.

Authors: Shuai Liu, Guanqing Liu, Peifeng Cheng, Chao Xue, Yong Zhou, Xu Chen, Lu Ye, Zhongying Qiao, Tao Zhang and Zhiyun Gong

Genome-wide association mapping of gene loci affecting disease resistance in the rice-Fusarium fujikuroi pathosystem

Rice bakanae disease has emerged as a new threat to rice production. In recent years, an increase in the occurrence and severity of bakanae disease has been reported in several areas in Asia. Although bakanae ...

Authors: Szu-Yu Chen, Ming-Hsin Lai, Chih-Wei Tung, Dong-Hong Wu, Fang-Yu Chang, Tsung-Chun Lin and Chia-Lin Chung

Functional Haplotype and eQTL Analyses of Genes Affecting Cadmium Content in Cultivated Rice

Rice is a major food resource for Asian countries including Korea. However, most Asian countries are facing food safety problems due to cropland contamination by heavy metals. Thus, this study was conducted to...

Authors: Sang-Beom Lee, Gyeong-Jin Kim, Kyu-Won Kim, Sang-Ho Chu, Jung-Du Shin, Yu-Ji Lee, Yong-Jin Park and Sang-Won Park

Zebra leaf 15, a receptor-like protein kinase involved in moderate low temperature signaling pathway in rice

Zebra leaf mutants are an important resource for studying leaf colour in rice. In most such mutants, the zebra leaf phenotype results from defective chloroplast biogenesis. The molecular mechanism by which zeb...

Authors: Ping Feng, Junqiong Shi, Ting Zhang, Yuqin Zhong, Lisha Zhang, Guoling Yu, Tianquan Zhang, Xiaoyan Zhu, Yadi Xing, Wuzhong Yin, Xianchun Sang, Yinghua Ling, Changwei Zhang, Zhenglin Yang, Guanghua He and Nan Wang

Involvement of OsGF14b Adaptation in the Drought Resistance of Rice Plants

Drought stress is one of the major abiotic stresses that restrict plant growth and development. 14–3-3 proteins have been validated to regulate many biological processes in plants. Previous research demonstrat...

Authors: Jianping Liu, Xinjiao Sun, Wencheng Liao, Jianhua Zhang, Jiansheng Liang and Weifeng Xu

A novel approach to carotenoid accumulation in rice callus by mimicking the cauliflower Orange mutation via genome editing

β-carotene (provitamin A) is an important target for biofortification of crops as a potential solution to the problem of vitamin A deficiency that is prevalent in developing countries. A previous report showed...

Authors: Akira Endo, Hiroaki Saika, Miho Takemura, Norihiko Misawa and Seiichi Toki

Stress-Activated Protein Kinase OsSAPK9 Regulates Tolerance to Salt Stress and Resistance to Bacterial Blight in Rice

Salt stress and bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) are key limiting factors of rice (Oryza sativa L.) yields. Members of sucrose non-fermenting 1 (SNF1)-related protein kinase 2 (SnRK2...

Authors: Fan Zhang, Dan Zeng, Liyu Huang, Yingyao Shi, Tengjun Chen, Fan Zhang and Yongli Zhou

OsProT1 and OsProT3 Function to Mediate Proline- and γ-aminobutyric acid-specific Transport in Yeast and are Differentially Expressed in Rice (Oryza sativa L.)

Proline (Pro) and γ-aminobutyric acid (GABA) play important roles in plant development and stress tolerance. However, the molecular components responsible for the transport of these molecules in rice remain la...

Authors: Jin-Hong Lin, Zhi-Jun Xu, Jia-Shi Peng, Jing Zhao, Guo-Bin Zhang, Jun Xie, Zhen-Xie Yi, Jian-Hua Zhang, Ji-Ming Gong, Neng-Hui Ye and Shuan Meng

Improvement of rice blast resistance by developing monogenic lines, two-gene pyramids and three-gene pyramid through MAS

Rice blast caused by Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases in rice production. Development of resistant varieties through pyramiding of resistant (R) genes is considered as an eff...

Authors: Wuming Xiao, Qiyun Yang, Ming Huang, Tao Guo, Yongzhu Liu, Jiafeng Wang, Guili Yang, Jiyong Zhou, Jianyuan Yang, Xiaoyuan Zhu, Zhiqiang Chen and Hui Wang

Correction to: Nitrogen application and different water regimes at booting stage improved yield and 2-acetyl-1-pyrroline (2AP) formation in fragrant rice

It was highlighted that the original article (Mo et al. 2019) contained an error in Fig. 1f which revealed the biosynthesis pathway of 2AP. This Correction article shows the correct Fig. 1 and incorrect Fig. 1...

Authors: Zhaowen Mo, Yanhong Li, Jun Nie, Longxin He, Shenggang Pan, Meiyang Duan, Hua Tian, Lizhong Xiao, Keyou Zhong and Xiangru Tang

Overexpression of a microRNA-targeted NAC transcription factor improves drought and salt tolerance in Rice via ABA-mediated pathways

The NAC (NAM, AFAT, and CUC) transcription factors play critical roles in rice (Oryza sativa) development and stress regulation. Overexpressing a microRNA (miR164b)-resistant OsNAC2 mutant gene, which generates t...

Authors: Dagang Jiang, Lingyan Zhou, Weiting Chen, Nenghui Ye, Jixing Xia and Chuxiong Zhuang

The Initiation of Inferior Grain Filling is Affected by Sugar Translocation Efficiency in Large Panicle Rice

Large panicle rice has a large sink capacity, but inferior spikelet filling is poor in this variety of rice due to asynchronous grain filling. The understanding of the factors that cause asynchronous grain fil...

Authors: Lin Chen, Yao Deng, Honglei Zhu, Yuxiang Hu, Zhengrong Jiang, She Tang, Shaohua Wang and Yanfeng Ding

Nitrogen application and different water regimes at booting stage improved yield and 2-acetyl-1-pyrroline (2AP) formation in fragrant rice

Water (W) and nitrogen (N) management generally cause regulations in the 2-acetyl-1-pyrroline (2AP) accumulation in fragrant rice; nevertheless, the feasibility of such management strategies at booting stage i...

Authors: Zhaowen Mo, Yanhong Li, Jun Nie, Longxin He, Shenggang Pan, Meiyang Duan, Hua Tian, Lizhong Xiao, Keyou Zhong and Xiangru Tang

Development of cytoplasmic male sterile lines and restorer lines of various elite Indica Group rice cultivars using CW-CMS/Rf17 system

A cytoplasm of CW-type cytoplasmic male sterile (CMS) line is derived from Oryza rufipogon strain W1 and fertility is restored by a single nuclear gene, Rf17. We have previously reported that CW-CMS were effectiv...

Authors: Kinya Toriyama, Tomohiko Kazama, Tadashi Sato, Yoshimichi Fukuta and Masaaki Oka

Genome-wide association analysis of panicle exsertion and uppermost internode in rice (Oryza sativa L.)

Rice (Oryza sativa L.) yield is seriously influenced by panicle exsertion (PE) and the uppermost internode (UI) through panicle enclosure or energy transport during grain-filling stages. We evaluated the traits o...

Authors: Chengfang Zhan, Jiaxiao Hu, Qiao Pang, Bin Yang, Yanhao Cheng, Enshun Xu, Peiwen Zhu, Yingyi Li, Hongsheng Zhang and Jinping Cheng