Articles

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

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

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

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

A non-radioactive method for small RNA detection by northern blotting

Small non-coding RNAs are essential regulators of gene expression at the transcriptional and posttranscriptional levels. High-throughput sequencing has revealed thousands of predicted small RNAs; however, only...

Authors: Qi Huang, Zhinang Mao, Shaoqing Li, Jun Hu and Yingguo Zhu

Meloidogyne incognita - rice (Oryza sativa) interaction: a new model system to study plant-root-knot nematode interactions in monocotyledons

Plant-parasitic nematodes developed strategies to invade and colonize their host plants, including expression of immune suppressors to overcome host defenses. Meloidogyne graminicola and M. incognita are root-kno...

Authors: Phong Vũ Nguyễn, Stéphane Bellafiore, Anne-Sophie Petitot, Rana Haidar, Aurélie Bak, Amina Abed, Pascal Gantet, Itamara Mezzalira, Janice de Almeida Engler and Diana Fernandez

Genetic interaction between rice PLASTOCHRON genes and the gibberellin pathway in leaf development

The rice PLASTOCHRON (PLA) genes PLA1 and PLA2 regulate leaf maturation and the temporal pattern of leaf initiation. Although the function of PLA genes in the leaf initiation process has been analyzed, little is ...

Authors: Manaki Mimura and Jun-Ichi Itoh

Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"

Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yield rice variety derived from a three-way cross between indica and japonica varieties. Tongil contributed to the self-sufficiency of staple food producti...

Authors: Backki Kim, Dong-Gwan Kim, Gileung Lee, Jeonghwan Seo, Ik-Young Choi, Beom-Soon Choi, Tae-Jin Yang, Kwang Soo Kim, Joohyun Lee, Joong Hyoun Chin and Hee-Jong Koh

Transcriptomic analysis of rice in response to iron deficiency and excess

Iron (Fe) is essential micronutrient for plants and its deficiency as well as toxicity is a serious agricultural problem. The mechanisms of Fe deficiency are reasonably understood, however our knowledge about ...

Authors: Khurram Bashir, Kousuke Hanada, Minami Shimizu, Motoaki Seki, Hiromi Nakanishi and Naoko K Nishizawa

Differentially-expressed genes in rice infected by Xanthomonas oryzae pv. oryzae relative to a flagellin-deficient mutant reveal potential functions of flagellin in host–pathogen interactions

Plants have evolved a sensitive defense response system that detects and recognizes various pathogen-associated molecular patterns (PAMPs) (e.g. flagellin) and induces immune responses to protect against invas...

Authors: Chao Yu, Huamin Chen, Fang Tian, Jan E Leach and Chenyang He

Genome duplication improves rice root resistance to salt stress

Salinity is a stressful environmental factor that limits the productivity of crop plants, and roots form the major interface between plants and various abiotic stresses. Rice is a salt-sensitive crop and its p...

Authors: Yi Tu, Aiming Jiang, Lu Gan, Mokter Hossain, Jinming Zhang, Bo Peng, Yuguo Xiong, Zhaojian Song, Detian Cai, Weifeng Xu, Jianhua Zhang and Yuchi He

OsSUV3 transgenic rice maintains higher endogenous levels of plant hormones that mitigates adverse effects of salinity and sustains crop productivity

The SUV3 (suppressor of Var 3) gene encodes a DNA and RNA helicase, which is localized in the mitochondria. Plant SUV3 has not yet been characterized in detail. However, the Arabidopsis ortholog of SUV3 (AT4G1479...

Authors: Ranjan Kumar Sahoo, Mohammad Wahid Ansari, Renu Tuteja and Narendra Tuteja

Generation of transgenic rice with reduced content of major and novel high molecular weight allergens

Rice seed proteins contain antigens that provoke allergic responses in some individuals with food allergy, particularly in those with cereal allergy, and these antigens can elicit clinical symptoms such as ecz...

Authors: Yuko Ogo, Yuhya Wakasa, Kana Hirano, Atsuo Urisu, Tsukasa Matsuda and Fumio Takaiwa

Response of an aspartic protease gene OsAP77 to fungal, bacterial and viral infections in rice

Aspartic protease (APs) plays important roles in plant growth, development and biotic and abiotic stresses. We previously reported that the expression of a rice AP gene (OsAP77, Os10g0537800) was induced by probe...

Authors: Md Mahfuz Alam, Hidemitsu Nakamura, Hiroaki Ichikawa, Akio Miyao, Hirohiko Hirochika, Kappei Kobayashi, Naoto Yamaoka and Masamichi Nishiguchi

High-density mapping of quantitative trait loci for grain-weight and spikelet number in rice

High grain yield is one of the most important traits requiring improvement in rice breeding programs. Consequently, the genetic basis of spikelets per panicle (SPP) and grain weight (TGW) have received much re...

Authors: Dong-Min Kim, Hyun-Sook Lee, Soo-Jin Kwon, Mark Edward Fabreag, Ju-Won Kang, Yeo-Tae Yun, Chong-Tae Chung and Sang-Nag Ahn

Image-based phenotyping for non-destructive screening of different salinity tolerance traits in rice

Soil salinity is an abiotic stress wide spread in rice producing areas, limiting both plant growth and yield. The development of salt-tolerant rice requires efficient and high-throughput screening techniques t...

Authors: Aris Hairmansis, Bettina Berger, Mark Tester and Stuart John Roy

Workable male sterility systems for hybrid rice: Genetics, biochemistry, molecular biology, and utilization

The exploitation of male sterility systems has enabled the commercialization of heterosis in rice, with greatly increased yield and total production of this major staple food crop. Hybrid rice, which was adopt...

Authors: Jian-Zhong Huang, Zhi-Guo E, Hua-Li Zhang and Qing-Yao Shu

Analysis of segregation distortion and its relationship to hybrid barriers in rice

Segregation distortion (SD) is a frequently observed occurrence in mapping populations generated from crosses involving divergent genotypes. In the present study, ten genetic linkage maps constructed from reci...

Authors: Reflinur, Backki Kim, Sun Mi Jang, Sang-Ho Chu, Yogendra Bordiya, Md Babul Akter, Joohyun Lee, Joong Hyoun Chin and Hee-Jong Koh

Update on Bacterial Blight of Rice: Fourth International Conference on Bacterial Blight

Authors: Raman M Sundaram, Subhadeep Chatterjee, Ricardo Oliva, Gouri Sankar Laha, Casiana Vera Cruz, Jan E Leach and Ramesh V Sonti

Application of resequencing to rice genomics, functional genomics and evolutionary analysis

Rice is a model system used for crop genomics studies. The completion of the rice genome draft sequences in 2002 not only accelerated functional genome studies, but also initiated a new era of resequencing ric...

Authors: Longbiao Guo, Zhenyu Gao and Qian Qian

Nuclear and chloroplast diversity and phenotypic distribution of rice (Oryza sativa L.) germplasm from the democratic people’s republic of Korea (DPRK; North Korea)

Rice accounts for 43% of staple food production in the Democratic People’s Republic of Korea (DPRK). The most widely planted rice varieties were developed from a limited number of ancestral lines that were rep...

Authors: HyunJung Kim, Eung Gi Jeong, Sang-Nag Ahn, Jeffrey Doyle, Namrata Singh, Anthony J Greenberg, Yong Jae Won and Susan R McCouch

Split luciferase complementation assay to detect regulated protein-protein interactions in rice protoplasts in a large-scale format

The rice interactome, in which a network of protein-protein interactions has been elucidated in rice, is a useful resource to identify functional modules of rice signal transduction pathways. Protein-protein i...

Authors: Yukichi Fujikawa, Takahiro Nakanishi, Hiroko Kawakami, Kanako Yamasaki, Masa H Sato, Hiroyuki Tsuji, Makoto Matsuoka and Naohiro Kato

Gene response in rice plants treated with continuous fog influenced by pH, was similar to that treated with biotic stress

Throughout Asia, including Japan, rice plants are cultivated in a wide range of areas from lowlands to highlands and are frequently exposed to fog, including acid fog. Some physiological studies have shown tha...

Authors: Kouji Satoh, Shoko Saji, Shoko Ito, Hideyuki Shimizu, Hikaru Saji and Shoshi Kikuchi

Genetic and physiological analysis of tolerance to acute iron toxicity in rice

Fe toxicity occurs in lowland rice production due to excess ferrous iron (Fe²⁺) formation in reduced soils. To contribute to the breeding for tolerance to Fe toxicity in rice, we determined quantitative trait loc...

Authors: Lin-Bo Wu, Mohamad Yusser Shhadi, Glenn Gregorio, Elsa Matthus, Mathias Becker and Michael Frei