Articles

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

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

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

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

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

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

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

Panicle blast 1 (Pb1) resistance is dependent on at least four QTLs in the rice genome

Rice blast is the most serious disease afflicting rice and there is an urgent need for the use of disease resistance (R) genes in blast tolerance breeding programs. Pb1 is classified as a quantitative resistance ...

Authors: Haruhiko Inoue, Mitsuru Nakamura, Tatsumi Mizubayashi, Akira Takahashi, Shoji Sugano, Shuuichi Fukuoka and Nagao Hayashi

GNS4, a novel allele of DWARF11, regulates grain number and grain size in a high-yield rice variety

Rice plays an extremely important role in food safety because it feeds more than half of the world’s population. Rice grain yield depends on biomass and the harvest index. An important strategy to break throug...

Authors: Yong Zhou, Yajun Tao, Jinyan Zhu, Jun Miao, Jun Liu, Yanhua Liu, Chuandeng Yi, Zefeng Yang, Zhiyun Gong and Guohua Liang

Sugary Endosperm is Modulated by Starch Branching Enzyme IIa in Rice (Oryza sativa L.)

Starch biosynthesis is one of the most important pathways that determine both grain quality and yield in rice (Oryza sativa L.). Sugary endosperm, sugary-1 (sug-1), is a mutant trait for starch biosynthesis. Rice...

Authors: Yunjoo Lee, Min-Seon Choi, Gileung Lee, Su Jang, Mi-Ra Yoon, Backki Kim, Rihua Piao, Mi-Ok Woo, Joong Hyoun Chin and Hee-Jong Koh

Updating the elite rice variety Kongyu 131 by improving the Gn1a locus

Kongyu 131 is an elite japonica rice variety of Heilongjiang Province, China. It has the characteristics of early maturity, superior quality, high yield, cold tolerance and wide adaptability. However, there is po...

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

Mesocotyl Elongation is Essential for Seedling Emergence Under Deep-Seeding Condition in Rice

Direct-seeding cultivation by deep-seeding of seeds (drill seeding) is becoming popular due to the scarcity of land and labor. However, poor emergence and inadequate seedling establishment can lead to yield lo...

Authors: Hyun-Sook Lee, Kazuhiro Sasaki, Ju-Won Kang, Tadashi Sato, Won-Yong Song and Sang-Nag Ahn

Phenology, sterility and inheritance of two environment genic male sterile (EGMS) lines for hybrid rice

There is still limited quantitative understanding of how environmental factors affect sterility of Environment-conditioned genic male sterility (EGMS) lines. A model was developed for this purpose and tested b...

Authors: R. El-Namaky and P.A.J. van Oort

Comparative Expression Analysis of Rice and Arabidopsis Peroxiredoxin Genes Suggests Conserved or Diversified Roles Between the Two Species and Leads to the Identification of Tandemly Duplicated Rice Peroxiredoxin Genes Differentially Expressed in Seeds

Peroxiredoxins (PRXs) have recently been identified as plant antioxidants. Completion of various genome sequencing projects has provided genome-wide information about PRX genes in major plant species. Two of t...

Authors: Yun-Shil Gho, Sun-A Park, Sung-Ruyl Kim, Anil Kumar Nalini Chandran, Gynheung An and Ki-Hong Jung

Identification of bakanae disease resistance loci in japonica rice through genome wide association study

Bakanae disease, caused by seed-borne Fusarium species, mainly F. fujikuroi, is a rice disease whose importance is considerably increasing in several rice growing countries, leading to...

Authors: Andrea Volante, Alessandro Tondelli, Maria Aragona, Maria Teresa Valente, Chiara Biselli, Francesca Desiderio, Paolo Bagnaresi, Slavica Matic, Maria Lodovica Gullino, Alessandro Infantino, Davide Spadaro and Giampiero Valè

High Resolution Mapping of QTLs for Heat Tolerance in Rice Using a 5K SNP Array

Heat stress is one of the major abiotic threats to rice production, next to drought and salinity stress. Incidence of heat stress at reproductive phase of the crop results in abnormal pollination leading to fl...

Authors: Shanmugavadivel PS, Amitha Mithra SV, Chandra Prakash, Ramkumar MK, Ratan Tiwari, Trilochan Mohapatra and Nagendra Kumar Singh

Rice Bran Metabolome Contains Amino Acids, Vitamins & Cofactors, and Phytochemicals with Medicinal and Nutritional Properties

Rice bran is a functional food that has shown protection against major chronic diseases (e.g. obesity, diabetes, cardiovascular disease and cancer) in animals and humans, and these health effects have been ass...

Authors: Iman Zarei, Dustin G. Brown, Nora Jean Nealon and Elizabeth P. Ryan

Overexpression of Rice Auxilin-Like Protein, XB21, Induces Necrotic Lesions, up-Regulates Endocytosis-Related Genes, and Confers Enhanced Resistance to Xanthomonas oryzae pv. oryzae

The rice immune receptor XA21 confers resistance to the bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo). To elucidate the mechanism of XA21-mediated immunity, we previously performed a yeast two-hybrid sc...

Authors: Chang-Jin Park, Tong Wei, Rita Sharma and Pamela C. Ronald

Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa)

Lectins, defined as ‘Proteins that can recognize and bind specific carbohydrate structures’, are widespread among all kingdoms of life and play an important role in various biological processes in the cell. Mo...

Authors: Kristof De Schutter, Mariya Tsaneva, Shubhada R. Kulkarni, Pierre Rougé, Klaas Vandepoele and Els J. M. Van Damme

08SG2/OsBAK1 regulates grain size and number, and functions differently in Indica and Japonica backgrounds in rice

Both grain size and grain number are significant for rice yield. In the past decade, a number of genes related to grain size and grain number have been documented, however, the regulatory mechanisms underlying...

Authors: Hua Yuan, Shijun Fan, Juan Huang, Shijie Zhan, Shifu Wang, Peng Gao, Weilan Chen, Bin Tu, Bingtian Ma, Yuping Wang, Peng Qin and Shigui Li

Silencing of the Rice Gene LRR1 Compromises Rice Xa21 Transcript Accumulation and XA21-Mediated Immunity

The rice immune receptor XA21 confers resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial leaf blight. We previously demonstrated that an auxilin-like protein, XA21 BINDING PROTEIN 21...

Authors: Daniel F. Caddell, Chang-Jin Park, Nicholas C. Thomas, Patrick E. Canlas and Pamela C. Ronald

Genome-Based Identification of Heterotic Patterns in Rice

Hybrid rice breeding facilitates to increase grain yield and yield stability. Long-term success of hybrid breeding depends on the recognition of high-yielding complementary heterotic patterns, which is lacking...

Authors: Ulrike Beukert, Zuo Li, Guozheng Liu, Yusheng Zhao, Nadhigade Ramachandra, Vilson Mirdita, Fabiano Pita, Klaus Pillen and Jochen Christoph Reif

Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.)

The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present stu...

Authors: B. P. Mallikarjuna Swamy, Noraziyah Abd Aziz Shamsudin, Site Noorzuraini Abd Rahman, Ramil Mauleon, Wickneswari Ratnam, Ma. Teressa Sta. Cruz and Arvind Kumar

A hairy-leaf gene, BLANKET LEAF, of wild Oryza nivara increases photosynthetic water use efficiency in rice

High water use efficiency is essential to water-saving cropping. Morphological traits that affect photosynthetic water use efficiency are not well known. We examined whether leaf hairiness improves photosynthe...

Authors: Norimitsu Hamaoka, Hideshi Yasui, Yoshiyuki Yamagata, Yoko Inoue, Naruto Furuya, Takuya Araki, Osamu Ueno and Atsushi Yoshimura

Erratum to: Aldo-ketoreductase 1 (AKR1) improves seed longevity in tobacco and rice by detoxifying reactive cytotoxic compounds generated during ageing

Authors: Kodadinne Narayana Nisarga, Ramu S. Vemanna, Babitha Kodekallu Chandrashekar, Hanumantha Rao, Amaranatha Reddy Vennapusa, Ashwini Narasimaha, Udayakumar Makarla and Mohan Raju Basavaiah

Dissection of broad-spectrum resistance of the Thai rice variety Jao Hom Nin conferred by two resistance genes against rice blast

Rice (Oryza sativa) is one of the most important food crops in the world. Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most destructive rice diseases worldwide. To effectively cope ...

Authors: Chaivarakun Chaipanya, Mary Jeanie Telebanco-Yanoria, Berlaine Quime, Apinya Longya, Siripar Korinsak, Siriporn Korinsak, Theerayut Toojinda, Apichart Vanavichit, Chatchawan Jantasuriyarat and Bo Zhou

Erratum to: Population dynamics among six major groups of the Oryza rufipogon species complex, wild relative of cultivated Asian rice

Authors: HyunJung Kim, Janelle Jung, Namrata Singh, Anthony Greenberg, Jeff J. Doyle, Wricha Tyagi, Jong-Wook Chung, Jennifer Kimball, Ruaraidh Sackville Hamilton and Susan R. McCouch