Articles

Genome-wide association study and candidate gene analysis of rice cadmium accumulation in grain in a diverse rice collection

Cadmium (Cd) accumulation in rice followed by transfer to the food chain causes severe health problems in humans. Breeding of low Cd accumulation varieties is one of the most economical ways to solve the probl...

Authors: Junliang Zhao, Wu Yang, Shaohong Zhang, Tifeng Yang, Qin Liu, Jingfang Dong, Hua Fu, Xingxue Mao and Bin Liu

Rice UCL8, a plantacyanin gene targeted by miR408, regulates fertility by controlling pollen tube germination and growth

Pollen tube formation and growth are crucial steps that lead to seed production. Despite the importance of pollen tube growth, the molecular mechanisms implicated in its spatial and temporal control are not fu...

Authors: Fan Zhang, Yu-Chan Zhang, Jin-Ping Zhang, Yang Yu, Yan-Fei Zhou, Yan-Zhao Feng, Yu-Wei Yang, Meng-Qi Lei, Huang He, Jian-Pin Lian and Yue-Qin Chen

Constitutive expression of REL1 confers the rice response to drought stress and abscisic acid

Leaf rolling is one of the most significant symptoms of drought stress in plant. Previously, we identified a dominant negative mutant, termed rolled and erect 1 (hereafter referred to rel1-D), regulating leaf rol...

Authors: Jiayan Liang, Shaoying Guo, Bo Sun, Qing Liu, Xionghui Chen, Haifeng Peng, Zemin Zhang and Qingjun Xie

The ATP-binding cassette (ABC) transporter OsABCG3 is essential for pollen development in rice

The pollen wall, which protects male gametophyte against various stresses and facilitates pollination, is essential for successful reproduction in flowering plants. The pollen wall consists of gametophyte-deri...

Authors: Zhenyi Chang, Mingna Jin, Wei Yan, Hui Chen, Shijun Qiu, Shan Fu, Jixing Xia, Yuchen Liu, Zhufeng Chen, Jianxin Wu and Xiaoyan Tang

A northern Chinese origin of Austronesian agriculture: new evidence on traditional Formosan cereals

Genetic data for traditional Taiwanese (Formosan) agriculture is essential for tracing the origins on the East Asian mainland of the Austronesian language family, whose homeland is generally placed in Taiwan. ...

Authors: Laurent Sagart, Tze-Fu Hsu, Yuan-Ching Tsai, Cheng-Chieh Wu, Lin-Tzu Huang, Yu-Chi Chen, Yi-Fang Chen, Yu-Chien Tseng, Hung-Ying Lin and Yue-ie Caroline Hsing

Multivariate-based classification of predicting cooking quality ideotypes in rice (Oryza sativa L.) indica germplasm

For predicting texture suited for South and South East Asia, most of the breeding programs tend to focus on developing rice varieties with intermediate to high amylose content in indica subspecies. However, va...

Authors: Rosa Paula O. Cuevas, Cyril John Domingo and Nese Sreenivasulu

Identification and fine mapping of Bph33, a new brown planthopper resistance gene in rice (Oryza sativa L.)

Host-plant resistance is the most desirable and economic way to overcome BPH damage to rice. As single-gene resistance is easily lost due to the evolution of new BPH biotypes, it is urgent to explore and ident...

Authors: Jie Hu, Xingyuan Chang, Ling Zou, Weiqi Tang and Weiren Wu

A semi-dominant mutation in a CC-NB-LRR-type protein leads to a short-root phenotype in rice

The mechanisms of plant defense against pathogen attack in plant leaves have been extensively studied. However, our understanding of plant defense mechanisms in plant roots is still limited. In this study, a s...

Authors: Zhiming Yu, Lixiang Dong, Zhifang Jiang, Keke Yi, Jianhua Zhang, Zhongchen Zhang, Zhenxing Zhu, Yuhuan Wu, Maojun Xu and Jun Ni

A novel Rice QTL qOPW11 Associated with Panicle Weight Affects Panicle and Plant Architecture

The improvement of rice yield is a crucial global issue, but evaluating yield requires substantial efforts. Rice yield comprises the following indices: panicle number (PN), grain number per panicle (GN), 1000-...

Authors: Satoshi Okada, Megumi Sasaki and Masanori Yamasaki

Identification and expression analysis of genes with pathogen-inducible cis-regulatory elements in the promoter regions in Oryza sativa

Complex co-regulatory networks in plants may elicit responses during pathogen infections. A number of genes are activated when these responses take place. Identification of these genes would shed new light on ...

Authors: Weiwen Kong, Li Ding, Jia Cheng and Bin Wang

Overexpression of the Tibetan Plateau annual wild barley (Hordeum spontaneum) HsCIPKs enhances rice tolerance to heavy metal toxicities and other abiotic stresses

The calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) signaling system plays a key regulatory role in plant stress signaling. The roles of plant-specific CIPKs, essential for CBL-CIPK ...

Authors: Weihuai Pan, Jinqiu Shen, Zhongzhong Zheng, Xu Yan, Jianxin Shou, Wenxiang Wang, Lixi Jiang and Jianwei Pan

The transcription factor OsbHLH035 mediates seed germination and enables seedling recovery from salt stress through ABA-dependent and ABA-independent pathways, respectively

Many transcription factors (TFs), such as those in the basic helix-loop-helix (bHLH) family, are important for regulating plant growth and plant responses to abiotic stress. The expression of OsbHLH035 is induced...

Authors: Hung-Chi Chen, Wan-Hsing Cheng, Chwan-Yang Hong, Yu-Sen Chang and Men-Chi Chang

Correction to: A Versatile Vector Toolkit for Functional Analysis of Rice Genes

The caption of Fig. 5 and the figure contained an error [1]. The updated figure and caption are published in this correction article.

Authors: Feng He, Fan Zhang, Wenxian Sun, Yuese Ning and Guo-Liang Wang

Genome-wide analysis of root hair-preferential genes in rice

Root hairs are valuable in taking up nutrients and water from the rhizosphere and serving as sites of interactions with soil microorganisms. By increasing the external surface area of the roots or interacting ...

Authors: Sunok Moon, Anil Kumar Nalini Chandran, Gynheung An, Chanhui Lee and Ki-Hong Jung

Proteomic analysis of the defense response to Magnaporthe oryzae in rice harboring the blast resistance gene Piz-t

Rice blast (caused by Magnaporthe oryzae) is one of the most destructive diseases of rice. While many blast resistance (R) genes have been identified and deployed in rice cultivars, little is known about the R ge...

Authors: Dagang Tian, Liu Yang, Zaijie Chen, Ziqiang Chen, Feng Wang, Yuanchang Zhou, Yuming Luo, Liming Yang and Songbiao Chen

DS1/OsEMF1 interacts with OsARF11 to control rice architecture by regulation of brassinosteroid signaling

Plant height and leaf angle are important determinants of yield in rice (Oryza sativa L.). Genes involved in regulating plant height and leaf angle were identified in previous studies; however, there are many rem...

Authors: X. Liu, C. Y. Yang, R. Miao, C. L. Zhou, P. H. Cao, J. Lan, X. J. Zhu, C. L. Mou, Y. S. Huang, S. J. Liu, Y. L. Tian, T. L. Nguyen, L. Jiang and J. M. Wan

OsRACK1A, encodes a circadian clock-regulated WD40 protein, negatively affect salt tolerance in rice

The receptor for activated C kinase 1 (RACK1) is a WD40 type protein that is involved in multiple signaling pathways and is conserved from prokaryotes to eukaryotes. Here we report that rice RACK1A (OsRACK1A) is ...

Authors: Dongping Zhang, Yuzhu Wang, Jinyu Shen, Jianfeng Yin, Dahong Li, Yan Gao, Weifeng Xu and Jiansheng Liang

Dissection and fine-mapping of two QTL for grain size linked in a 460-kb region on chromosome 1 of rice

Grain size is a key determinant of grain weight and a trait having critical influence on grain quality in rice. While increasing evidences are shown for the importance of minor-effect QTL in controlling comple...

Authors: Qing Dong, Zhen-Hua Zhang, Lin-Lin Wang, Yu-Jun Zhu, Ye-Yang Fan, Tong-Min Mou, Liang-Yong Ma and Jie-Yun Zhuang

Physiological mechanisms contributing to the QTL qDTY_3.2 effects on improved performance of rice Moroberekan x Swarna BC₂F_3:4 lines under drought

Traditional rice (Oryza sativa) varieties are valuable resources for the improvement of drought resistance. qDTY_3.2 is a drought-yield quantitative trait locus that was identified in a population derived from the...

Authors: Alexandre Grondin, Shalabh Dixit, Rolando Torres, Challa Venkateshwarlu, Eric Rogers, Thomas Mitchell-Olds, Philip N. Benfey, Arvind Kumar and Amelia Henry

Guanine Nucleotide Exchange Factor 7B (RopGEF7B) is involved in floral organ development in Oryza sativa

RAC/ROP GTPase are versatile signaling molecules controlling diverse biological processes including cell polarity establishment, cell growth, morphogenesis, hormone responses and many other cellular processes ...

Authors: Jiaqing Huang, Huili Liu, Thomas Berberich, Yuting Liu, Li-zhen Tao and Taibo Liu

Overexpression of OsbHLH107, a member of the basic helix-loop-helix transcription factor family, enhances grain size in rice (Oryza sativa L.)

Grain size, which is determined by grain length, grain width, and grain thickness, is an important determinant for grain yield in rice. Identification and characterization of new genes that are associated with...

Authors: Xiaoming Yang, Yulong Ren, Yue Cai, Mei Niu, Zhiming Feng, Ruonan Jing, Changling Mou, Xi Liu, Lianjie Xiao, Xin Zhang, Fuqing Wu, Xiuping Guo, Ling Jiang and Jianmin Wan

Expression Profile of Defense Genes in Rice Lines Pyramided with Resistance Genes Against Bacterial Blight, Fungal Blast and Insect Gall Midge

Rice, a major food crop of the world, endures many major biotic stresses like bacterial blight (BB), fungal blast (BL) and the insect Asian rice gall midge (GM) that cause significant yield losses. Progress in...

Authors: Dhanasekar Divya, Kanaparthi Ratna Madhavi, Muralidharan Ayyappa Dass, Roshan Venkata Maku, Garladinne Mallikarjuna, Raman Meenakshi Sundaram, Gouri Sankar Laha, Ayyagari Phani Padmakumari, Hitendra Kumar Patel, Madamsetty Srinivas Prasad, Ramesh Venkata Sonti and Jagadish Sanmallappa Bentur

The rice white green leaf 2 gene causes defects in chloroplast development and affects the plastid ribosomal protein S9

Plastid ribosomal proteins (PRPs) play important roles in the translation of key proteins involved in chloroplast development and photosynthesis. PRPs have been widely studied in many plant species; however, f...

Authors: Zhennan Qiu, Dongdong Chen, Lei He, Sen Zhang, Zenan Yang, Yu Zhang, Zhongwei Wang, Deyong Ren, Qian Qian, Longbiao Guo and Li Zhu

Suppression of OsMDHAR4 enhances heat tolerance by mediating H₂O₂-induced stomatal closure in rice plants

Monodehydroascorbate reductase (MDAR or MDHAR), which is responsible for growth, development and stress response in plants, is a key enzyme in the maintenance of the ascorbate acid (AsA) pool through the AsA–g...

Authors: Jianping Liu, Xinjiao Sun, Feiyun Xu, Yingjiao Zhang, Qian Zhang, Rui Miao, Jianhua Zhang, Jiansheng Liang and Weifeng Xu

Genetic analysis for the grain number heterosis of a super-hybrid rice WFYT025 combination using RNA-Seq

Despite the great contributions of utilizing heterosis to crop productivity worldwide, the molecular mechanism of heterosis remains largely unexplored. Thus, the present research is focused on the grain number...

Authors: Liang Chen, Jianmin Bian, Shilai Shi, Jianfeng Yu, Hira Khanzada, Ghulam Mustafa Wassan, Changlan Zhu, Xin Luo, Shan Tong, Xiaorong Yang, Xiaosong Peng, Shuang Yong, Qiuying Yu, Xiaopeng He, Junru Fu, Xiaorong Chen…

OsSND2, a NAC family transcription factor, is involved in secondary cell wall biosynthesis through regulating MYBs expression in rice

As one of the most important staple food crops, rice produces huge agronomic biomass residues that contain lots of secondary cell walls (SCWs) comprising cellulose, hemicelluloses and lignin. The transcription...

Authors: Yafeng Ye, Kun Wu, Jianfeng Chen, Qian Liu, Yuejin Wu, Binmei Liu and Xiangdong Fu

Marker-assisted selection strategy to pyramid two or more QTLs for quantitative trait-grain yield under drought

Marker-assisted breeding will move forward from introgressing single/multiple genes governing a single trait to multiple genes governing multiple traits to combat emerging biotic and abiotic stresses related t...

Authors: Arvind Kumar, Nitika Sandhu, Shalabh Dixit, Shailesh Yadav, B. P. M. Swamy and Noraziyah Abd Aziz Shamsudin

Inoculation with the endophyte Piriformospora indica significantly affects mechanisms involved in osmotic stress in rice

Rice is a drought susceptible crop. A symbiotic association between rice and mycorrhizal fungi could effectively protect the plant against sudden or frequent episodes of drought. Due to its extensive network o...

Authors: Muhammad Abu Bakar Saddique, Zulfiqar Ali, Abdus Salam Khan, Iqrar Ahmad Rana and Imran Haider Shamsi

Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

Increasing rice demand is one of the consequences of the steadily improving socio-economic status of the African countries. New Rice for Africa (NERICA), which are interspecific hybrids between Asian and Afric...

Authors: Naoki Yamamoto, Richard Garcia, Tomohiro Suzuki, Celymar Angela Solis, Yuichi Tada, Ramaiah Venuprasad and Ajay Kohli

Genomic selection of agronomic traits in hybrid rice using an NCII population

Hybrid breeding is an effective tool to improve yield in rice, while parental selection remains the key and difficult issue. Genomic selection (GS) provides opportunities to predict the performance of hybrids ...

Authors: Yang Xu, Xin Wang, Xiaowen Ding, Xingfei Zheng, Zefeng Yang, Chenwu Xu and Zhongli Hu

Outgrowth of Rice Tillers Requires Availability of Glutamine in the Basal Portions of Shoots

Our previous studies concluded that metabolic disorder in the basal portions of rice shoots caused by a lack of cytosolic glutamine synthetase1;2 (GS1;2) resulted in a severe reduction in the outgrowth of till...

Authors: Miwa Ohashi, Keiki Ishiyama, Soichi Kojima, Noriyuki Konishi, Kazuhiro Sasaki, Mitsue Miyao, Toshihiko Hayakawa and Tomoyuki Yamaya

Genetic analysis of male sterility obtained from a rice cultivar Lebed backcrossed with Taichung 65

Male sterility is a useful agronomic trait for breeding of self-pollinating crops and is often observed in the progenies of hybrids of distantly related species, for example, Oryza sativa L. subsp. indica and O. ...

Authors: Tetsuya Murakami, Tomohiko Kazama and Kinya Toriyama

Correction to: Genetic diversity of arsenic accumulation in rice and QTL analysis of methylated arsenic in rice grains

The authors of article “Genetic diversity of arsenic accumulation in rice and QTL analysis of methylated arsenic in rice grains” (Kuramata et al. 2013) would like to note that the original version of the artic...

Authors: Masato Kuramata, Tadashi Abe, Akira Kawasaki, Kaworu Ebana, Taeko Shibaya, Masahiro Yano and Satoru Ishikawa

Genome-wide analyses of late pollen-preferred genes conserved in various rice cultivars and functional identification of a gene involved in the key processes of late pollen development

Understanding late pollen development, including the maturation and pollination process, is a key component in maintaining crop yields. Transcriptome data obtained through microarray or RNA-seq technologies ca...

Authors: Sunok Moon, Moe Moe Oo, Backki Kim, Hee-Jong Koh, Sung Aeong Oh, Gihwan Yi, Gynheung An, Soon Ki Park and Ki-Hong Jung

A Versatile Vector Toolkit for Functional Analysis of Rice Genes

Rice (Oryza sativa) is the main food for half of the world’s population, and is considered the model for molecular biology studies of monocotyledon species. Although the rice genome was completely sequenced about...

Authors: Feng He, Fan Zhang, Wenxian Sun, Yuese Ning and Guo-Liang Wang

Comparative analysis of the root transcriptomes of cultivated and wild rice varieties in response to Magnaporthe oryzae infection revealed both common and species-specific pathogen responses

Magnaporthe oryzae, the causal fungus of rice blast disease, negatively impacts global rice production. Wild rice (Oryza rufipogon), a relative of cultivated rice (O. sativa), possesses unique attributes that ena...

Authors: Lei Tian, Shaohua Shi, Fahad Nasir, Chunling Chang, Weiqiang Li, Lam-Son Phan Tran and Chunjie Tian

Finding the superior allele of japonica-type for increasing stem lodging resistance in indica rice varieties using chromosome segment substitution lines

In cereal crops, stem lodging can be classified into two types: stem-breaking type and stem-bending type. To improve stem-lodging resistance, the strong culm traits of superior lodging-resistant varieties must...

Authors: Indria Wahyu Mulsanti, Toshio Yamamoto, Tadamasa Ueda, Ahmad Fahim Samadi, Eri Kamahora, Indrastuti Apri Rumanti, Vo Cong Thanh, Shunsuke Adachi, Sakae Suzuki, Motoki Kanekatsu, Tadashi Hirasawa and Taiichiro Ookawa

Identification of a cold-tolerant locus in rice (Oryza sativa L.) using bulked segregant analysis with a next-generation sequencing strategy

Cold stress can cause serious abiotic damage that limits the growth, development and yield of rice. Cold tolerance during the booting stage of rice is a key factor that can guarantee a high and stable yield un...

Authors: Jian Sun, Luomiao Yang, Jingguo Wang, Hualong Liu, Hongliang Zheng, Dongwei Xie, Minghui Zhang, Mingfang Feng, Yan Jia, Hongwei Zhao and Detang Zou

Sub-cellular markers highlight intracellular dynamics of membrane proteins in response to abiotic treatments in rice

Cell biology approach using membrane protein markers tagged with fluorescent proteins highlights the dynamic behaviour of plant cell membranes, not only in the standard but also in changing environmental condi...

Authors: Thi Thu Huyen Chu, Thi Giang Hoang, Duy Chi Trinh, Charlotte Bureau, Donaldo Meynard, Aurore Vernet, Mathieu Ingouff, Nang Vinh Do, Christophe Périn, Emmanuel Guiderdoni, Pascal Gantet, Christophe Maurel and Doan-Trung Luu

Evaluation and breeding application of six brown planthopper resistance genes in rice maintainer line Jin 23B

The brown planthopper (BPH), an insect species that feeds on rice plants (Oryza sativa L.), is one of the most destructive insect pests of rice. BPH can be controlled with chemical pesticides, but they are expens...

Authors: Haichao Jiang, Jie Hu, Zhi Li, Jia Liu, Guanjun Gao, Qinglu Zhang, Jinghua Xiao and Yuqing He

Improving rice grain length through updating the GS3 locus of an elite variety Kongyu 131

Traditional crop breeding has made significant achievement meet food needs worldwide. However, the way has some inevitable problems including time-consuming, laborious, low predictability and reproducibility. ...

Authors: Jianzong Nan, Xiaomin Feng, Chen Wang, Xiaohui Zhang, Rongsheng Wang, Jiaxin Liu, Qingbo Yuan, Guoqiang Jiang and Shaoyang Lin

Thai Hom Mali Rice: Origin and Breeding for Subsistence Rainfed Lowland Rice System

The world-renowned Thai Hom Mali Rice has been the most important aromatic rice originating in Thailand. The aromatic variety was collected from Chachoengsao, a central province, and after pure-line selection,...

Authors: Apichart Vanavichit, Wintai Kamolsukyeunyong, Meechai Siangliw, Jonaliza L. Siangliw, Suniyom Traprab, Siriphat Ruengphayak, Ekawat Chaichoompu, Chatree Saensuk, Ekapol Phuvanartnarubal, Theerayut Toojinda and Somvong Tragoonrung

Pusa Basmati 1121 – a rice variety with exceptional kernel elongation and volume expansion after cooking

Pusa Basmati 1121 (PB 1121) is a landmark Basmati rice variety having Basmati quality traits introgressed from traditional Basmati varieties such as Basmati 370 and Type 3. It was released for commercial culti...

Authors: Vijaipal Singh, Ashok Kumar Singh, Trilochan Mohapatra, Gopala Krishnan S and Ranjith Kumar Ellur

IR64: a high-quality and high-yielding mega variety

High-yielding varieties developed in the 1960s and 1970s at the International Rice Research Institute (IRRI) and elsewhere benefited farmers and the public, ultimately increasing yields and reducing the cost o...

Authors: David J. Mackill and Gurdev S. Khush

Shanyou 63: an elite mega rice hybrid in China

Hybrid rice has been successfully used for commercial rice production for 40 years in China. Shanyou 63, a mega rice hybrid, derived from the parents Zhenshan 97A and Minghui 63, was a milestone for China’s hy...

Authors: Fangming Xie and Jianfu Zhang

Special Issue: Iconic Rice Varieties

Authors: David J. Mackill

Koshihikari: a premium short-grain rice cultivar – its expansion and breeding in Japan

Koshihikari, a Japanese short-grain rice cultivar, was developed in 1956, more than 60 years ago. Despite its age, it has been the most widely grown cultivar in Japan for more than 35 years, making it the most...

Authors: Asako Kobayashi, Kiyosumi Hori, Toshio Yamamoto and Masahiro Yano

Heat stress induces spikelet sterility in rice at anthesis through inhibition of pollen tube elongation interfering with auxin homeostasis in pollinated pistils

Pollen tube elongation in the pistil is a key step for pollination success in plants, and auxins play an important role in this process. However, the function of auxins in pollen tube elongation in the pistil ...

Authors: Caixia Zhang, Guangyan Li, Tingting Chen, Baohua Feng, Weimeng Fu, Jinxiang Yan, Mohammad Rezaul Islam, Qianyu Jin, Longxing Tao and Guanfu Fu

QTL mapping and candidate gene analysis of peduncle vascular bundle related traits in rice by genome-wide association study

The vascular bundle especially in the peduncle is one of crucial limiting factors of rice yield, and it determines how plants efficiently transport photosynthetic products, mineral nutrients and water from lea...

Authors: Laiyuan Zhai, Tianqing Zheng, Xinyu Wang, Yun Wang, Kai Chen, Shu Wang, Yun Wang, Jianlong Xu and Zhikang Li

Rice nitrate transporter OsNPF7.2 positively regulates tiller number and grain yield

Rice tiller number is one of the most important factors that determine grain yield, while nitrogen is essential for the crop growth and development, especially for tiller formation. Genes involved in nitrogen ...

Authors: Jie Wang, Kai Lu, Haipeng Nie, Qisen Zeng, Bowen Wu, Junjie Qian and Zhongming Fang