Articles

Phylogenetic analysis and protein structure modelling identifies distinct Ca²⁺/Cation antiporters and conservation of gene family structure within Arabidopsis and rice species

The Ca²⁺/Cation Antiporter (CaCA) superfamily is an ancient and widespread family of ion-coupled cation transporters found in nearly all kingdoms of life. In animals, K⁺-dependent and K⁺-indendent Na⁺/Ca²⁺ exchan...

Authors: Jon K. Pittman and Kendal D. Hirschi

Physiological Responses and Expression Profile of NADPH Oxidase in Rice (Oryza Sativa) Seedlings under Different Levels of Submergence

Flooding due to global climate change is a serious problem that frequently decreases crop yields. Rice fields in flood-prone areas often experience full or partial submergence. Submergence has an adverse effec...

Authors: Yu-Sian Wu and Chin-Ying Yang

Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India

Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, ...

Authors: Pinky Agarwal, Swarup K. Parida, Saurabh Raghuvanshi, Sanjay Kapoor, Paramjit Khurana, Jitendra P. Khurana and Akhilesh K. Tyagi

Genetic Mapping of Anaerobic Germination-Associated QTLs Controlling Coleoptile Elongation in Rice

Increasing numbers of rice farmers are adopting direct-seeding methods to save on costs associated with labor and transplanting. Successful seedling establishment in flooded conditions requires rapid coleoptil...

Authors: Sheng-Kai Hsu and Chih-Wei Tung

Artificial Selection of Gn1a Plays an Important role in Improving Rice Yields Across Different Ecological Regions

Rice is one of the most important crops, and it is essential to improve rice productivity to satisfy the future global food supply demands. Gn1a (OsCKX2), which encodes cytokinin oxidase/dehydrogenase, plays an i...

Authors: Jie Wang, Huaxue Xu, Nengwu Li, Fengfeng Fan, Liuting Wang, Yingguo Zhu and Shaoqing Li

Down-Regulation of Cytokinin Oxidase 2 Expression Increases Tiller Number and Improves Rice Yield

Cytokinins are plant-specific hormones that affect plant growth and development. The endogenous level of cytokinins in plant cells is regulated in part by irreversible degradation via cytokinin oxidase/dehydro...

Authors: Su-Ying Yeh, Hau-Wen Chen, Chun-Yeung Ng, Chu-Yin Lin, Tung-Hai Tseng, Wen-Hsiung Li and Maurice S. B. Ku

Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal

Genetic diversity among rice cultivars from Bangladesh and North East India was assessed using a custom 384-SNP microarray assay. A total of 511 cultivars were obtained from several sources, choosing landraces...

Authors: Anthony J. Travis, Gareth J. Norton, Sutapa Datta, Ramendra Sarma, Tapash Dasgupta, Filipe L. Savio, Malcolm Macaulay, Peter E. Hedley, Kenneth L. McNally, Mahmud H. Sumon, M. Rafiqul Islam and Adam H. Price

Allele mining and enhanced genetic recombination for rice breeding

Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been f...

Authors: Hei Leung, Chitra Raghavan, Bo Zhou, Ricardo Oliva, Il Ryong Choi, Vanica Lacorte, Mona Liza Jubay, Casiana Vera Cruz, Glenn Gregorio, Rakesh Kumar Singh, Victor Jun Ulat, Frances Nikki Borja, Ramil Mauleon, Nickolai N. Alexandrov, Kenneth L. McNally and Ruaraidh Sackville Hamilton

Influence of Multi-Gene Allele Combinations on Grain Size of Rice and Development of a Regression Equation Model to Predict Grain Parameters

Grain size is one of the key factors determining yield and quality in rice. A large number of genes are involved in the regulation of grain size parameters such as grain length and grain width. Different allel...

Authors: Chan-Mi Lee, Jonghwa Park, Backki Kim, Jeonghwan Seo, Gileung Lee, Su Jang and Hee-Jong Koh

Rice arbuscular mycorrhiza as a tool to study the molecular mechanisms of fungal symbiosis and a potential target to increase productivity

Rice (Oryza sativa L.) is a monocot model crop for cereal molecular biology. Following the emergence of molecular genetics of arbuscular mycorrhizal (AM) symbiosis in model legumes in the 1990s, studies on rice g...

Authors: Tomomi Nakagawa and Haruko Imaizumi-Anraku

Photoprotection as a Trait for Rice Yield Improvement: Status and Prospects

Solar radiation is essential for photosynthesis and global crop productivity but it is also variable in space and time, frequently being limiting or in excess of plant requirements depending on season, environ...

Authors: Erik H. Murchie, Asgar Ali and Tiara Herman

Analysis of Population Structure and Genetic Diversity in Rice Germplasm Using SSR Markers: An Initiative Towards Association Mapping of Agronomic Traits in Oryza Sativa

Genetic diversity is the main source of variability in any crop improvement program. It serves as a reservoir for identifying superior alleles controlling key agronomic and quality traits through allele mining...

Authors: Vishnu Varthini Nachimuthu, Raveendran Muthurajan, Sudhakar Duraialaguraja, Rajeswari Sivakami, Balaji Aravindhan Pandian, Govinthraj Ponniah, Karthika Gunasekaran, Manonmani Swaminathan, Suji K K and Robin Sabariappan

The Usefulness of Known Genes/Qtls for Grain Quality Traits in an Indica Population of Diverse Breeding Lines Tested using Association Analysis

A number of studies reported major genes/QTLs for rice grain shapes, chalkiness and starch physicochemical properties. For these finely mapped QTLs or cloned genes to make an impact in practical breeding, it i...

Authors: Xiangqian Zhao, Lijie Zhou, Kimberley Ponce and Guoyou Ye

Characterization and Functional Analysis of Pyrabactin Resistance-Like Abscisic Acid Receptor Family in Rice

Abscisic acid (ABA) plays crucial roles in regulating plant growth and development, especially in responding to abiotic stress. The pyrabactin resistance-like (PYL) abscisic acid receptor family has been ident...

Authors: Xiaojie Tian, Zhenyu Wang, Xiufeng Li, Tianxiao Lv, Huazhao Liu, Lizhi Wang, Hongbin Niu and Qingyun Bu

Development of Genome-Wide Insertion and Deletion Polymorphism Markers from Next-Generation Sequencing Data in Rice

Next-generation sequencing technologies enable the re-sequencing of a large number of genomes and provide an unprecedented opportunity to discover numerous DNA polymorphisms throughout the genome of a species....

Authors: Jian Liu, Jingwei Li, Jingtao Qu and Shuangyong Yan

Phylogenomics databases for facilitating functional genomics in rice

The completion of whole genome sequence of rice (Oryza sativa) has significantly accelerated functional genomics studies. Prior to the release of the sequence, only a few genes were assigned a function each year....

Authors: Ki-Hong Jung, Peijian Cao, Rita Sharma, Rashmi Jain and Pamela C Ronald

Mapping Consistent Rice (Oryza sativa L.) Yield QTLs under Drought Stress in Target Rainfed Environments

Drought stress is a major limitation to rainfed rice production and yield stability. Identifying yield-associated quantitative trait loci (QTLs) that are consistent under drought stress predominant in target p...

Authors: Silvas J Prince, R Beena, S Michael Gomez, S Senthivel and R Chandra Babu

Coexpression Network Analysis of Macronutrient Deficiency Response Genes in Rice

Macronutrients are pivotal elements for proper plant growth and development. Although extensive gene expression profiling revealed a large number of genes differentially expressed under various nutrient depriv...

Authors: Hinako Takehisa, Yutaka Sato, Baltazar Antonio and Yoshiaki Nagamura

The Rice Floral Repressor Early flowering1 Affects Spikelet Fertility By Modulating Gibberellin Signaling

Gibberellic acid (GA; or gibberellin) affects the development of floral organs, especially anthers and pollen, and perturbation of development of male floral organs can cause sterility. Many studies of GA sign...

Authors: Choon-Tak Kwon, Suk-Hwan Kim, Dami Kim and Nam-Chon Paek

Laser microdissection-based gene expression analysis in the aleurone layer and starchy endosperm of developing rice caryopses in the early storage phase

Rice endosperm is composed of aleurone cells in the outermost layers and starchy endosperm cells in the inner part. The aleurone layer accumulates lipids, whereas starchy endosperm mainly accumulates starch. D...

Authors: Tsutomu Ishimaru, Masashi Ida, Sakiko Hirose, Satoshi Shimamura, Takehiro Masumura, Naoko K. Nishizawa, Mikio Nakazono and Motohiko Kondo

Genome-wide investigation and expression analysis of Sodium/Calcium exchanger gene family in rice and Arabidopsis

The Na⁺/Ca²⁺ Exchanger (NCX) protein family is a member of the Cation/Ca²⁺ exchanger superfamily and its members play important roles in cellular Ca²⁺ homeostasis. While the functions of NCX family of proteins is...

Authors: Anil Kumar Singh, Ritesh Kumar, Amit K. Tripathi, Brijesh K. Gupta, Ashwani Pareek and Sneh L. Singla-Pareek

Improved understanding of rice amylose biosynthesis from advanced starch structural characterization

It has been shown from the chain length distributions (CLDs) that amylose chains can be divided into at least two groups: long and short amylose chains. These molecular structures influence some functional pro...

Authors: Enpeng Li, Alex Chi Wu, Juan Li, Qiaoquan Liu and Robert G Gilbert

Pyramiding of three bacterial blight resistance genes for broad-spectrum resistance in deepwater rice variety, Jalmagna

Jalmagna is a popular deepwater rice variety with farmers of India because of its good yield under waterlogged condition. However, the variety is highly susceptible to bacterial blight (BB) disease. The develo...

Authors: Sharat Kumar Pradhan, Deepak Kumar Nayak, Soumya Mohanty, Lambodar Behera, Saumya Ranjan Barik, Elssa Pandit, Srikanta Lenka and Annamalai Anandan

Transcriptome profiling of the spl5 mutant reveals that SPL5 has a negative role in the biosynthesis of serotonin for rice disease resistance

Rice mutant, spl5 (spotted leaf 5), has spontaneous hypersensitive-like lesions on its leaves and shows enhanced resistance to pathogens, indicating that SPL5 plays a role in programmed cell death (PCD) and disea...

Authors: Bin Jin, Xinru Zhou, Baolin Jiang, Zhimin Gu, Pinghua Zhang, Qian Qian, Xifeng Chen and Bojun Ma

The rice ALS3 encoding a novel pentatricopeptide repeat protein is required for chloroplast development and seedling growth

Pentatricopeptide repeat (PPR) proteins play essential roles in modulating the expression of organelle genes and have expanded greatly in higher plants. However, molecular mechanisms of most rice PPR genes rem...

Authors: Dongzhi Lin, Xiaodi Gong, Quan Jiang, Kailun Zheng, Hua Zhou, Jianlong Xu, Sheng Teng and Yanjun Dong

QTLs underlying natural variation of root growth angle among rice cultivars with the same functional allele of DEEPER ROOTING 1

The functional allele of the rice gene DEEPER ROOTING 1 (DRO1) increases the root growth angle (RGA). However, wide natural variation in RGA is observed among rice cultivars with the functional DRO1 allele. To el...

Authors: Yuka Kitomi, Noriko Kanno, Sawako Kawai, Tatsumi Mizubayashi, Shuichi Fukuoka and Yusaku Uga

Allelic effects on starch structure and properties of six starch biosynthetic genes in a rice recombinant inbred line population

The genetic diversity of six starch biosynthetic genes (Wx, SSI, SSIIa, SBEI, SBEIIa and SBEIIb) in indica and japonica rices opens an opportunity to produce a new variety with more favourable grain starch qualit...

Authors: Jixun Luo, Stephen A Jobling, Anthony Millar, Matthew K Morell and Zhongyi Li

Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining

Dissecting the upstream regulatory architecture of rice genes and their cognate regulator proteins is at the core of network biology and its applications to comparative functional genomics. With the rapidly ad...

Authors: Benildo G de los Reyes, Bijayalaxmi Mohanty, Song Joong Yun, Myoung-Ryoul Park and Dong-Yup Lee

Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice

Iron toxicity is a root related abiotic stress, occurring frequently in flooded soils. It can affect the yield of rice in lowland production systems. This toxicity is associated with high concentrations of red...

Authors: Taciane Finatto, Antonio Costa de Oliveira, Cristian Chaparro, Luciano C da Maia, Daniel R Farias, Leomar G Woyann, Claudete C Mistura, Adriana P Soares-Bresolin, Christel Llauro, Olivier Panaud and Nathalie Picault

Multiple tissue-specific expression of rice seed-shattering gene SH4 regulated by its promoter pSH4

Rice seed shattering is an important domestication syndrome encoded by a gene named as SH4. The coding region of SH4 has been well studied regarding its function and roles in evolution. However, its promoter has ...

Authors: Huanxin Yan, Li Ma, Zhe Wang, Zhimin Lin, Jun Su and Bao-Rong Lu

Molecular breeding of thermo-sensitive genic male sterile (TGMS) lines of rice for blast resistance using Pi2 gene

Blast disease caused by the fungal pathogen Magnaporthe oryzae is one of the big problems in rice production in China, especially for high yield hybrid varieties made from a two-line system in which thermo-sensit...

Authors: Jiefeng Jiang, Tongmin Mou, Huihui Yu and Fasong Zhou

Exploring the power of plants to overcome environmental stresses

Authors: Motoyuki Ashikari and Jian Feng Ma

Shading during the grain filling period increases 2-acetyl-1-pyrroline content in fragrant rice

Fragrant rice, including Thai jasmine and Indian basmati varieties, is highly valued by consumers globally. 2-acetyl-1-proline (2-AP) is the major compound responsible for the aromatic character of fragrant ri...

Authors: Zhaowen Mo, Wu Li, Shenggang Pan, Timothy L Fitzgerald, Feng Xiao, Yongjian Tang, Yilei Wang, Meiyang Duan, Hua Tian and Xiangru Tang

A QTL for root growth angle on rice chromosome 7 is involved in the genetic pathway of DEEPER ROOTING 1

Root growth angle (RGA) is an important trait that influences the ability of rice to avoid drought stress. DEEPER ROOTING 1 (DRO1), which is a major quantitative trait locus (QTL) for RGA, is responsible for the ...

Authors: Yusaku Uga, Yuka Kitomi, Eiji Yamamoto, Noriko Kanno, Sawako Kawai, Tatsumi Mizubayashi and Shuichi Fukuoka

Pseudo-backcrossing design for rapidly pyramiding multiple traits into a preferential rice variety

Pyramiding multiple genes into a desirable genetic background can take years to accomplish. In this paper, a pseudo-backcrossing scheme was designed to shorten the backcrossing cycle needed. PinK3, an aromatic...

Authors: Siriphat Ruengphayak, Ekawat Chaichumpoo, Supaporn Phromphan, Wintai Kamolsukyunyong, Wissarut Sukhaket, Ekapol Phuvanartnarubal, Siripar Korinsak, Siriporn Korinsak and Apichart Vanavichit

Delving deeper into technological innovations to understand differences in rice quality

Increasing demand for better quality rice varieties, which are also more suited to growth under sub-optimal cultivation conditions, is driving innovation in rice research. Here we have used a multi-disciplinar...

Authors: Mariafe Calingacion, Lu Fang, Lenie Quiatchon-Baeza, Roland Mumm, Arthur Riedel, Robert D Hall and Melissa Fitzgerald

Functional diversity of jasmonates in rice

Phytohormone jasmonates (JA) play essential roles in plants, such as regulating development and growth, responding to environmental changes, and resisting abiotic and biotic stresses. During signaling, JA inte...

Authors: Zheng Liu, Shumin Zhang, Ning Sun, Hongyun Liu, Yanhong Zhao, Yuling Liang, Liping Zhang and Yuanhuai Han

Transcriptome-based analysis of mitogen-activated protein kinase cascades in the rice response to Xanthomonas oryzae infection

Mitogen-activated protein (MAP) kinase cascades, with each cascade consisting of a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK), and a MAP kinase (MAPK), play important roles in dicot plant r...

Authors: Zeyu Yang, Haigang Ma, Hanming Hong, Wen Yao, Weibo Xie, Jinghua Xiao, Xianghua Li and Shiping Wang

Forward screening for seedling tolerance to Fe toxicity reveals a polymorphic mutation in ferric chelate reductase in rice

Rice contains the lowest grain Fe content among cereals. One biological limiting factor is the tolerance of rice to Fe toxicity. Reverse and forward genetic screenings were used to identify tolerance to Fe tox...

Authors: Siriphat Ruengphayak, Vinitchan Ruanjaichon, Chatree Saensuk, Supaporn Phromphan, Somvong Tragoonrung, Ratchanee Kongkachuichai and Apichart Vanavichit

Genetic analysis of flag leaf size and candidate genes determination of a major QTL for flag leaf width in rice

Flag leaf is the most essential organ for photosynthesis in rice and its size plays an important role in rice breeding for ideal plant-type. Flag leaf size affect photosynthesis to a certain extent, thereby in...

Authors: Bin Zhang, Weijun Ye, Deyong Ren, Peng Tian, Youlin Peng, Yang Gao, Banpu Ruan, Li Wang, Guangheng Zhang, Longbiao Guo, Qian Qian and Zhenyu Gao

A receptor like kinase gene with expressional responsiveness on Xanthomonas oryzae pv. oryzae is essential for Xa21-mediated disease resistance

Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent a large class of proteins in regulating plant development and immunity. The LRR-RLK XA21 confers resistance to the bacterial disease caused by the...

Authors: Haitao Hu, Jing Wang, Chan Shi, Can Yuan, Chunfang Peng, Junjie Yin, Weitao Li, Min He, Jichun Wang, Bintian Ma, Yuping Wang, Shigui Li and Xuewei Chen

Phenotypic analyses of rice lse2 and lse3 mutants that exhibit hyperaccumulation of starch in the leaf blades

To identify genes that potentially regulate the accumulation, mobilization, and transport of photoassimilates in rice (Oryza sativa L.) leaves, we recently screened a mutant collection of rice by iodine staining ...

Authors: Chenggang Liang, Tatsuro Hirose, Masaki Okamura, Rei Tanimoto, Akio Miyao, Hirohiko Hirochika, Tomio Terao, Tian Li, Ryu Ohsugi and Naohiro Aoki

Marker-assisted breeding of Indonesia local rice variety Siputeh for semi-dwarf phonetype, good grain quality and disease resistance to bacterial blight

Rice is one of the most important staple food crops in Asia. Since the first green revolution beginning in 1960s, high-yield semidwarf modern rice varieties have been widely planted; however, traditional rice ...

Authors: Yanchang Luo, Sabaruddin Zakaria, Bakhtiar Basyah, Tingchen Ma, Zefu Li, Jianbo Yang and Zhongchao Yin

The roots of future rice harvests

Rice production faces the challenge to be enhanced by 50% by year 2030 to meet the growth of the population in rice-eating countries. Whereas yield of cereal crops tend to reach plateaus and a yield is likely ...

Authors: Nourollah Ahmadi, Alain Audebert, Malcolm J Bennett, Anthony Bishopp, Antonio Costa de Oliveira, Brigitte Courtois, Abdala Diedhiou, Anne Diévart, Pascal Gantet, Alain Ghesquière, Emmanuel Guiderdoni, Amelia Henry, Yoshiaki Inukai, Leon Kochian, Laurent Laplaze, Mikael Lucas…

Genes controlling root development in rice

In this review, we report on the recent developments made using both genetics and functional genomics approaches in the discovery of genes controlling root development in rice. QTL detection in classical bipar...

Authors: Chung D Mai, Nhung TP Phung, Huong TM To, Mathieu Gonin, Giang T Hoang, Khanh L Nguyen, Vinh N Do, Brigitte Courtois and Pascal Gantet

Rice miR172 induces flowering by suppressing OsIDS1 and SNB, two AP2 genes that negatively regulate expression of Ehd1 and florigens

Rice is a facultative short-day plant that flowers under long days (LD) after a lengthy vegetative phase. Although several inhibitors that delay flowering have been identified, the process by which rice eventu...

Authors: Yang-Seok Lee, Dong-Yeon Lee, Lae-Hyeon Cho and Gynheung An

A fertility restorer gene, Rf4, widely used for hybrid rice breeding encodes a pentatricopeptide repeat protein

Uncontrolled expression of a certain mitochondrial gene often causes cytoplasmic male sterility (CMS) in plants. This phenotype is prevented by the presence of a fertility restorer (Rf) gene in the nuclear genome...

Authors: Tomohiko Kazama and Kinya Toriyama

Iron deficiency responses in rice roots

Iron (Fe) is an essential element for most living organisms. To acquire sparingly soluble Fe from the rhizosphere, rice roots rely on two Fe acquisition pathways. The first of these pathways involves Fe(III) c...

Authors: Takanori Kobayashi, Reiko Nakanishi Itai and Naoko K. Nishizawa

A candidate factor that interacts with RF2, a restorer of fertility of Lead rice-type cytoplasmic male sterility in rice

The pollen function of cytoplasmic male sterile (CMS) plants is often recovered by the Restorer of fertility (Rf) gene encoded by the nuclear genome. An Rf gene of Lead rice type CMS, Rf2, encodes a small mitocho...

Authors: Shinya Fujii, Tomohiko Kazama, Yukihiro Ito, Soichi Kojima and Kinya Toriyama

Rice and cold stress: methods for its evaluation and summary of cold tolerance-related quantitative trait loci

Cold stress adversely affects rice (Oryza sativa L.) growth and productivity, and has so far determined its geographical distribution. Dissecting cold stress-mediated physiological changes and understanding their...

Authors: Qi Zhang, Qiuhong Chen, Shaoling Wang, Yahui Hong and Zhilong Wang