Articles

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

Accelerated molecular breeding of a novel P/TGMS line with broad-spectrum resistance to rice blast and bacterial blight in two-line hybrid rice

Breeding two-line hybrid rice with disease resistance is an effective approach to stabilize rice yield in commercial rice production of China.

Authors: Jiaming Mi, Dabing Yang, Yi Chen, Jiefeng Jiang, Haipeng Mou, Junbin Huang, Yidan Ouyang and Tongmin Mou

Preferential Geographic Distribution Pattern of Abiotic Stress Tolerant Rice

Crop productivity and stability of the food system are threatened by climate change, mainly through the effects of predicted abiotic stresses. Despite extensive research on abiotic stress tolerance in the past...

Authors: A N M Rubaiyath Bin Rahman and Jianhua Zhang

Exploring traditional aus-type rice for metabolites conferring drought tolerance

Traditional varieties and landraces belonging to the aus-type group of rice (Oryza sativa L.) are known to be highly tolerant to environmental stresses, such as drought and heat, and are therefore recognized as a...

Authors: Alberto Casartelli, David Riewe, Hans Michael Hubberten, Thomas Altmann, Rainer Hoefgen and Sigrid Heuer

Effect of qGN4.1 QTL for Grain Number per Panicle in Genetic Backgrounds of Twelve Different Mega Varieties of Rice

Rice is a major source of food, particularly for the growing Asian population; hence, the utilization of genes for enhancing its yield potential is important for ensuring food security. Earlier, we have mapped...

Authors: Vijay Kumar Singh, Ranjith Kumar Ellur, Ashok Kumar Singh, M. Nagarajan, Brahma Deo Singh and Nagendra Kumar Singh

Deciphering the Environmental Impacts on Rice Quality for Different Rice Cultivated Areas

Rice (Oryza sativa L.) is cultivated in a wide range of climatic conditions, and is one of mankind’s major staple foods. The interaction of environmental factors with genotype effects major agronomic traits such ...

Authors: Xiukun Li, Lian Wu, Xin Geng, Xiuhong Xia, Xuhong Wang, Zhengjin Xu and Quan Xu

Genetic Evidence for the Role of a Rice Vacuolar Invertase as a Molecular Sink Strength Determinant

Rice is a major crop feeding the majority of the global population, and increasing its sink strength is one of the modes to alleviate the declining availability of food for the rapidly growing world population...

Authors: Shamitha Rao Morey, Tatsuro Hirose, Yoichi Hashida, Akio Miyao, Hirohiko Hirochika, Ryu Ohsugi, Junko Yamagishi and Naohiro Aoki

Rice WRKY11 Plays a Role in Pathogen Defense and Drought Tolerance

Plants are frequently subjected to abiotic and biotic stresses, and WRKY proteins play a pivotal role in the response to such stress. OsWRKY11 is induced by pathogens, drought, and heat, suggesting a function in ...

Authors: Heyoung Lee, Jooyoung Cha, Changhyun Choi, Naeyoung Choi, Hyun-So Ji, Sang Ryeol Park, Seungbum Lee and Duk-Ju Hwang

Manipulating the Phytic Acid Content of Rice Grain Toward Improving Micronutrient Bioavailability

Myo-inositol hexaphosphate, also known as phytic acid (PA), is the most abundant storage form of phosphorus in seeds. PA acts as a strong chelator of metal cations to form phytate and is considered an anti-nutrie...

Authors: Ishara Perera, Saman Seneweera and Naoki Hirotsu

Molecular mapping of qBK1 ^WD , a major QTL for bakanae disease resistance in rice

Bakanae or foot rot disease is a prominent disease of rice caused by Gibberella fujikuroi. This disease may infect rice plants from the pre-emergence stage to the mature stage. In recent years, raising rice seedl...

Authors: Sais-Beul Lee, Yeon-Jae Hur, Jun-Hyeon Cho, Jong-Hee Lee, Tae-Heon Kim, Soo-Min Cho, You-Chun Song, Young-Su Seo, Jungkwan Lee, Tae-sung Kim, Yong-Jin Park, Myung-Kyu Oh and Dong-Soo Park

Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice

Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to esca...

Authors: Niharika Sharma, Trang Minh Dang, Namrata Singh, Slobodan Ruzicic, Bernd Mueller-Roeber, Ute Baumann and Sigrid Heuer

The rice zebra3 (z3) mutation disrupts citrate distribution and produces transverse dark-green/green variegation in mature leaves

Rice zebra mutants are leaf variegation mutants that exhibit transverse sectors of green/yellow or green/white in developing or mature leaves. In most cases, leaf variegation is caused by defects in chloroplast b...

Authors: Suk-Hwan Kim, Choon-Tak Kwon, Giha Song, Hee-Jong Koh, Gynheung An and Nam-Chon Paek

OsLAP6/OsPKS1, an orthologue of Arabidopsis PKSA/LAP6, is critical for proper pollen exine formation

Male fertility is crucial for rice yield, and the improvement of rice yield requires hybrid production that depends on male sterile lines. Although recent studies have revealed several important genes in male ...

Authors: Ting Zou, Qiao Xiao, Wenjie Li, Tao Luo, Guoqiang Yuan, Zhiyuan He, Mingxing Liu, Qiao Li, Peizhou Xu, Jun Zhu, Yueyang Liang, Qiming Deng, Shiquan Wang, Aiping Zheng, Lingxia Wang, Ping Li…

Characterization of the rice NLA family reveals a key role for OsNLA1 in phosphate homeostasis

Phosphate (Pi), an essential mineral nutrient for plant development and reproduction, is one of the main components of fertilizers in modern agriculture. Previous research demonstrated that AtNLA1 mediates ubi...

Authors: Jian Yang, Lan Wang, Chuanzao Mao and Honghui Lin

Marker assisted pyramiding of Bph6 and Bph9 into elite restorer line 93–11 and development of functional marker for Bph9

The brown planthopper (BPH) has become the most destructive and a serious threat to the rice production in Asia. Breeding the resistant varieties with improved host resistance is the most effective and ecosyst...

Authors: Yang Wang, Weihua Jiang, Hongmei Liu, Ya Zeng, Bo Du, Lili Zhu, Guangcun He and Rongzhi Chen

Root cone angle is enlarged in docs1 LRR-RLK mutants in rice

The DEFECTIVE IN OUTER CELL LAYER SPECIFICATION 1 (DOCS1) gene belongs to the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) subfamily. It has been discovered few years ago in Oryza sativa (rice) in a screen ...

Authors: M. Bettembourg, M. Dal-Soglio, C. Bureau, A. Vernet, A. Dardoux, M. Portefaix, M. Bes, D. Meynard, D. Mieulet, B. Cayrol, C. Perin, B. Courtois, J. F. Ma and A. Dievart

Pervasive interactions of Sa and Sb loci cause high pollen sterility and abrupt changes in gene expression during meiosis that could be overcome by double neutral genes in autotetraploid rice

Intersubspecific autotetraploid rice hybrids possess high hybrid vigor; however, low pollen fertility is a critical hindrance in its commercial utilization. Our previous study demonstrated that polyploidy coul...

Authors: Jinwen Wu, Lin Chen, Muhammad Qasim Shahid, Minyi Chen, Qinglei Dong, Jirui Li, Xiaosong Xu and Xiangdong Liu

Delineation of Inheritance Pattern of Aleurone Layer Colour Through Chemical Tests in Rice

Rice aleurone layer develops different colours with various chemical tests that may help to develop some rapid tests for identification/grouping of rice varieties. Understanding the colour inheritance pattern ...

Authors: Chandu Singh, Sripathy K.V., Jeevan Kumar S.P., Bhojaraja Naik K., Govind Pal, Udaya Bhaskar K., Ramesh K.V. and Somasundaram G.

Mapping QTLs using a novel source of salinity tolerance from Hasawi and their interaction with environments in rice

Salinity is one of the most severe and widespread abiotic stresses that affect rice production. The identification of major-effect quantitative trait loci (QTLs) for traits related to salinity tolerance and un...

Authors: M. Akhlasur Rahman, Isaac Kofi Bimpong, J. B. Bizimana, Evangeline D. Pascual, Marydee Arceta, B. P. Mallikarjuna Swamy, Faty Diaw, M. Sazzadur Rahman and R. K. Singh

The Race Structure of the Rice Blast Pathogen Across Southern and Northeastern China

Rice blast, caused by the ascomycete Magnaporthe oryzae (Mo), imposes a major constraint on rice productivity. Managing the disease through the deployment of host resistance requires a close understanding of race...

Authors: Yaling Zhang, Qiongle Zhu, Yongxiang Yao, Zhenghong Zhao, James C. Correll, Ling Wang and Qinghua Pan

Genome-wide association mapping for root cone angle in rice

Plant root systems play a major role in anchoring and in water and nutrient uptake from the soil. The root cone angle is an important parameter of the root system architecture because, combined with root depth...

Authors: Mathilde Bettembourg, Audrey Dardou, Alain Audebert, Emilie Thomas, Julien Frouin, Emmanuel Guiderdoni, Nourollah Ahmadi, Christophe Perin, Anne Dievart and Brigitte Courtois

Identification and validation of a novel major QTL for harvest index in rice (Oryza sativa L.)

Harvest index (HI) in rice is defined as the ratio of grain yield (GY) to biomass (BM). Although it has been demonstrated that HI is significantly related to yield and is considered as one of the most importan...

Authors: Shaohong Zhang, Xiuying He, Junliang Zhao, Yongsheng Cheng, Zhimei Xie, Yuehan Chen, Tifeng Yang, Jingfang Dong, Xiaofei Wang, Qing Liu, Wei Liu, Xingxue Mao, Hua Fu, Zhaoming Chen, Yaoping Liao and Bin Liu

Higher yields of hybrid rice do not depend on nitrogen fertilization under moderate to high soil fertility conditions

Increasing rice yield with fewer external inputs is critical to ensuring food security, reducing environmental costs, and improving returns. Use of hybrid rice has expanded greatly in China due to its higher y...

Authors: Min Huang, Peng Jiang, Shuanglü Shan, Wei Gao, Guohui Ma, Yingbin Zou, Norman Uphoff and Longping Yuan

Physiological and molecular responses of seedlings of an upland rice (‘Tung Lu 3’) to total submergence compared to those of a submergence-tolerant lowland rice (‘FR13A’)

Understanding the responses of rice to environmental stresses such as unscheduled submergence is of pressing important owing to increasing severity of weather thought to arise from global climate change. When ...

Authors: Si-Yu Yang, Yu-Sian Wu, Chung-Tse Chen, Ming-Hsin Lai, Hsing-Mu Yen and Chin-Ying Yang

Identification and fine mapping of a new gene, BPH31 conferring resistance to brown planthopper biotype 4 of India to improve rice, Oryza sativa L

Rice (Oryza sativa L.) is the staple food for more than 3.5 billion people, mainly in Asia. Brown planthopper (BPH) is one of the most destructive insect pests of rice that limits rice production. Host-plant resi...

Authors: G. D. Prahalada, N. Shivakumar, H. C. Lohithaswa, D. K. Sidde Gowda, G. Ramkumar, Sung-Ryul Kim, C. Ramachandra, Shailaja Hittalmani, Trilochan Mohapatra and Kshirod K. Jena

Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A...

Authors: Michael J. Thomson, Namrata Singh, Maria S. Dwiyanti, Diane R. Wang, Mark H. Wright, Francisco Agosto Perez, Genevieve DeClerck, Joong Hyoun Chin, Geraldine A. Malitic-Layaoen, Venice Margarette Juanillas, Christine J. Dilla-Ermita, Ramil Mauleon, Tobias Kretzschmar and Susan R. McCouch

Dissecting combining ability effect in a rice NCII-III population provides insights into heterosis in indica-japonica cross

Combining ability is a measure for selecting elite parents that make the highest contributions to hybrid performance. However, the genetic bases of combining ability and how they contributed to heterosis is se...

Authors: Hao Zhou, Duo Xia, Jing Zeng, Gonghao Jiang and Yuqing He

Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs

The next-generation sequencing (NGS) technology has revolutionized our previous understanding of the plant genomes, relying on its innate advantages, such as high throughput and deep sequencing depth. In addit...

Authors: Dongliang Yu, Xiaoxia Ma, Ziwei Zuo, Weishan Shao, Huizhong Wang and Yijun Meng

Identification of resistant germplasm containing novel resistance genes at or tightly linked to the Pi2/9 locus conferring broad-spectrum resistance against rice blast

The rice Pi2/9 locus harbors multiple resistance (R) genes each controlling broad-spectrum resistance against diverse isolates of Magnaporthe oryzae, a fungal pathogen causing devastating blast disease to rice. I...

Authors: Gui Xiao, Frances Nikki Borja, Ramil Mauleon, Jonas Padilla, Mary Jeanie Telebanco-Yanoria, Jianxia Yang, Guodong Lu, Maribel Dionisio-Sese and Bo Zhou