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Sample records for japonica rice cultivars

  1. Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing.

    PubMed

    Arai-Kichise, Yuko; Shiwa, Yuh; Nagasaki, Hideki; Ebana, Kaworu; Yoshikawa, Hirofumi; Yano, Masahiro; Wakasa, Kyo

    2011-02-01

    Molecular breeding approaches are of growing importance to crop improvement. However, closely related cultivars generally used for crossing material lack sufficient known DNA polymorphisms due to their genetic relatedness. Next-generation sequencing allows the identification of a massive number of DNA polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) between highly homologous genomes. Using this technology, we performed whole-genome sequencing of a landrace of japonica rice, Omachi, which is used for sake brewing and is an important source for modern cultivars. A total of 229 million reads, each comprising 75 nucleotides of the Omachi genome, was generated with 45-fold coverage and uniquely mapped to 89.7% of the Nipponbare genome, a closely related cultivar. We identified 132,462 SNPs, 16,448 insertions and 19,318 deletions between the Omachi and Nipponbare genomes. An SNP array was designed to validate 731 selected SNPs, resulting in validation rates of 95 and 88% for the Omachi and Nipponbare genomes, respectively. Among the 577 SNPs validated in both genomes, 532 are entirely new SNP markers not previously reported between related rice cultivars. We also validated InDels on a part of chromosome 2 as DNA markers and successfully genotyped five japonica rice cultivars. Our results present the methodology and extensive data on SNPs and InDels available for whole-genome genotyping and marker-assisted breeding. The polymorphism information between Omachi and Nipponbare is available at NGRC_Rice_Omachi (http://www.nodai-genome.org/oryza_sativa_en.html).

  2. Identification of SNPs in closely-related temperate japonica rice cultivars using restriction enzyme-phased sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Very low polymorphism in the germplasm typically used by breeding programs poses a significant bottleneck with regarding to molecular breeding and the exploitation of breeding materials for quantitative trait analyses. California rice varieties, derived from a very small base of temperate japonica g...

  3. Outcrossing Potential between U.S. Blackhull Red Rice and Indica Rice Cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Weedy red rice is a major weed pest of rice in the southern U.S. Outcrossing between red rice and commercial tropical japonica rice cultivars has resulted in new weed biotypes that further hinder the effectiveness of weed management. In recent years, indica rice has been used increasingly as a ger...

  4. Rice tungro spherical virus resistance into photoperiod-insensitive japonica rice by marker-assisted selection.

    PubMed

    Shim, Junghyun; Torollo, Gideon; Angeles-Shim, Rosalyn B; Cabunagan, Rogelio C; Choi, Il-Ryong; Yeo, Un-Sang; Ha, Woon-Goo

    2015-09-01

    Rice tungro disease (RTD) is one of the destructive and prevalent diseases in the tropical region. RTD is caused by Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. Cultivation of japonica rice (Oryza sativa L. ssp japonica) in tropical Asia has often been restricted because most japonica cultivars are sensitive to short photoperiod, which is characteristic of tropical conditions. Japonica1, a rice variety bred for tropical conditions, is photoperiod-insensitive, has a high yield potential, but is susceptible to RTD and has poor grain quality. To transfer RTD resistance into Japonica1, we made two backcrosses (BC) and 8 three-way crosses (3-WC) among Japonica1 and RTSV-resistant cultivars. Among 8,876 BC1F2 and 3-WCF2 plants, 342 were selected for photoperiod-insensitivity and good grain quality. Photoperiod-insensitive progenies were evaluated for RTSV resistance by a bioassay and marker-assisted selection (MAS), and 22 BC1F7 and 3-WCF7 lines were selected based on the results of an observational yield trial. The results demonstrated that conventional selection for photoperiod-insensitivity and MAS for RTSV resistance can greatly facilitate the development of japonica rice that is suitable for cultivation in tropical Asia. PMID:26366118

  5. Independent domestication of Asian rice followed by gene flow from japonica to indica.

    PubMed

    Yang, Ching-chia; Kawahara, Yoshihiro; Mizuno, Hiroshi; Wu, Jianzhong; Matsumoto, Takashi; Itoh, Takeshi

    2012-05-01

    Results from studies on the domestication process of Asian rice Oryza sativa have been controversial because of its complicated evolutionary history. Previous studies have yielded two alternative hypotheses about the origin(s) of the two major groups of O. sativa: japonica and indica. One study proposes a single common wild ancestor, whereas the other suggests that there were multiple domestication events of different types of wild rice. Here, we provide clear evidence of the independent domestication of japonica and indica obtained via high-throughput sequencing and a large-scale comparative analysis of two wild rice accessions (W1943 and W0106) and two cultivars (a japonica cultivar called "Nipponbare" and an indica cultivar called "Guangluai-4"). The different domestication processes of the two cultivar groups appear to have led to distinct patterns of molecular evolution in protein-coding regions. The intensity of purifying selection was relaxed only in the japonica group, possibly because of a bottleneck effect. Moreover, a genome-wide comparison between Nipponbare, Guangluai-4, and another indica cultivar (93-11) suggests multiple hybridization events between japonica and indica, both before and after the divergence of the indica cultivars. We found that a large amount of genomic DNA, including domestication-related genes, was transferred from japonica to indica, which might have been important in the development of modern rice. Our study provides an overview of the dynamic process of Asian rice domestication, including independent domestication events and subsequent gene flow.

  6. Molecular Aspect of Good Eating Quality Formation in Japonica Rice

    PubMed Central

    Sun, Ming-Mao; Abdula, Sailila E.; Lee, Hye-Jung; Cho, Young-Chan; Han, Long-Zhi; Koh, Hee-Jong; Cho, Yong-Gu

    2011-01-01

    decreased eating quality. The results indicated the possibility of developing high palatability cultivars through modification of key genes related to japonica rice eating quality formation in starch biosynthesis. PMID:21494675

  7. Indica and Japonica Crosses Resulting in Linkage Block and Recombination Suppression on Rice Chromosome 12

    PubMed Central

    Jia, Yulin; Jia, Melissa H.; Wang, Xueyan; Liu, Guangjie

    2012-01-01

    Understanding linkage block size and molecular mechanisms of recombination suppression is important for plant breeding. Previously large linkage blocks ranging from 14 megabases to 27 megabases were observed around the rice blast resistance gene Pi-ta in rice cultivars and backcross progeny involving an indica and japonica cross. In the present study, the same linkage block was further examined in 456 random recombinant individuals of rice involving 5 crosses ranging from F2 to F10 generation, with and without Pi-ta containing genomic indica regions with both indica and japonica germplasm. Simple sequence repeat markers spanning the entire chromosome 12 were used to detect recombination break points and to delimit physical size of linkage blocks. Large linkage blocks ranging from 4.1 megabases to 10 megabases were predicted from recombinant individuals involving genomic regions of indica and japonica. However, a significantly reduced block from less than 800 kb to 2.1megabases was identified from crosses of indica with indica rice regardless of the existence of Pi-ta. These findings suggest that crosses of indica and japonica rice have significant recombination suppression near the centromere on chromosome 12. PMID:22912788

  8. [Response of yield, quality and nitrogen use efficiency to nitrogen fertilizer from mechanical transplanting super japonica rice].

    PubMed

    Wei, Hai-Yan; Wang, Ya-Jiang; Meng, Tian-Yao; Ge, Meng-Jie; Zhang, Hong-Cheng; Dai, Qi-Gen; Huo, Zhong-Yang; Xu, Ke

    2014-02-01

    Five super japonica rice cultivars were grown by mechanical transplanting in field and seven N treatments with total N application rate of 0, 150, 187.5, 225, 262.5, 300 and 337.5 kg x hm(-2) respectively were adopted to study the effects of N rate on rice yield, quality and N use efficiency. The differences between N requirement for obtaining the highest yield and for achieving the best economic benefit were compared. With the increase of N fertilizer rate, the yields of five super japonica rice cultivars increased firstly and then descended, achieving the highest yield at the N level of 300 kg x hm(-2) ranging from 10.33-10.60 kg x hm(-2). Yield increase mainly attributed to the large number of spikelet, for the total spikelet number of each rice cultivar reached the maximum value at the 300 kg x hm(-2) N level. With the increase of N application, the rates of brown rice, milled rice, head milled rice and the protein content of the five super japonica rice cultivars were all increased, and the rates of brown rice, milled rice, head milled rice and the protein con- tent were higher at 337.5 kg x hm(-2) N level than at 0 kg x hm(-2) N level by 3.3%-4.2%, 2.9%-6.0%, 4.4%-33.7% and 23.8%-44.3%, respectively. While the amylose content, gel consistency and taste value of the five rice cultivars were all decreased, and the amylose content, gel consistency and taste value were lower at 337.5 kg x hm(-2) N level than at 0 kg x hm(-2) N level by 12.4%-38.9%, 10.3%-28.5% and 20.3%-29.7%, respectively. The chalkiness increased firstly and then decreased while the change of chalky rate varied with the cultivars. With the increase of N application, the N use efficiency, agronomic N use efficiency and physiological N use efficiency decreased while the N uptake of grain increased significantly. If the cost of N fertilizer was taken into account, the N fertilizer amount to obtain the optimal economic benefits would be 275.68 kg x hm(-2) with the corresponding yield of 9.97 t x hm

  9. Mutualistic fungal endophytes produce phytohormones and organic acids that promote japonica rice plant growth under prolonged heat stress*

    PubMed Central

    Waqas, Muhammad; Khan, Abdul Latif; Shahzad, Raheem; Ullah, Ihsan; Khan, Abdur Rahim; Lee, In-Jung

    2015-01-01

    This study identifies the potential role in heat-stress mitigation of phytohormones and other secondary metabolites produced by the endophytic fungus Paecilomyces formosus LWL1 in japonica rice cultivar Dongjin. The japonica rice was grown in controlled chamber conditions with and without P. formosus LWL1 under no stress (NS) and prolonged heat stress (HS) conditions. Endophytic association under NS and HS conditions significantly improved plant growth attributes, such as plant height, fresh weight, dry weight, and chlorophyll content. Furthermore, P. formosus LWL1 protected the rice plants from HS compared with controls, indicated by the lower endogenous level of stress-signaling compounds such as abscisic acid (25.71%) and jasmonic acid (34.57%) and the increase in total protein content (18.76%–33.22%). Such fungal endophytes may be helpful for sustainable crop production under high environmental temperatures. PMID:26642184

  10. Mutualistic fungal endophytes produce phytohormones and organic acids that promote japonica rice plant growth under prolonged heat stress.

    PubMed

    Waqas, Muhammad; Khan, Abdul Latif; Shahzad, Raheem; Ullah, Ihsan; Khan, Abdur Rahim; Lee, In-Jung

    2015-12-01

    This study identifies the potential role in heat-stress mitigation of phytohormones and other secondary metabolites produced by the endophytic fungus Paecilomyces formosus LWL1 in japonica rice cultivar Dongjin. The japonica rice was grown in controlled chamber conditions with and without P. formosus LWL1 under no stress (NS) and prolonged heat stress (HS) conditions. Endophytic association under NS and HS conditions significantly improved plant growth attributes, such as plant height, fresh weight, dry weight, and chlorophyll content. Furthermore, P. formosus LWL1 protected the rice plants from HS compared with controls, indicated by the lower endogenous level of stress-signaling compounds such as abscisic acid (25.71%) and jasmonic acid (34.57%) and the increase in total protein content (18.76%-33.22%). Such fungal endophytes may be helpful for sustainable crop production under high environmental temperatures.

  11. Mutualistic fungal endophytes produce phytohormones and organic acids that promote japonica rice plant growth under prolonged heat stress.

    PubMed

    Waqas, Muhammad; Khan, Abdul Latif; Shahzad, Raheem; Ullah, Ihsan; Khan, Abdur Rahim; Lee, In-Jung

    2015-12-01

    This study identifies the potential role in heat-stress mitigation of phytohormones and other secondary metabolites produced by the endophytic fungus Paecilomyces formosus LWL1 in japonica rice cultivar Dongjin. The japonica rice was grown in controlled chamber conditions with and without P. formosus LWL1 under no stress (NS) and prolonged heat stress (HS) conditions. Endophytic association under NS and HS conditions significantly improved plant growth attributes, such as plant height, fresh weight, dry weight, and chlorophyll content. Furthermore, P. formosus LWL1 protected the rice plants from HS compared with controls, indicated by the lower endogenous level of stress-signaling compounds such as abscisic acid (25.71%) and jasmonic acid (34.57%) and the increase in total protein content (18.76%-33.22%). Such fungal endophytes may be helpful for sustainable crop production under high environmental temperatures. PMID:26642184

  12. Genetic Diversity, Rather than Cultivar Type, Determines Relative Grain Cd Accumulation in Hybrid Rice

    PubMed Central

    Sun, Liang; Xu, Xiaxu; Jiang, Youru; Zhu, Qihong; Yang, Fei; Zhou, Jieqiang; Yang, Yuanzhu; Huang, Zhiyuan; Li, Aihong; Chen, Lianghui; Tang, Wenbang; Zhang, Guoyu; Wang, Jiurong; Xiao, Guoying; Huang, Daoyou; Chen, Caiyan

    2016-01-01

    Cadmium (Cd) is a toxic element, and rice is known to be a leading source of dietary Cd for people who consume rice as their main caloric resource. Hybrid rice has dominated rice production in southern China and has been adopted worldwide. The characteristics of high yield heterosis of rice hybrids makes the public think intuitively that the hybrid rice accumulates more Cd in grain than do inbred cultivars. A detailed understanding of the genetic basis of grain Cd accumulation in hybrids and developing Cd-safe rice are one of the top priorities for hybrid rice breeders at present. In this study, we investigated genetic diversity and grain Cd levels in 617 elite rice hybrids collected from the middle and lower Yangtze River Valley in China and 68 inbred cultivars from around the world. We found that there are large variations in grain Cd accumulation in both the hybrids and their inbred counterparts. However, we found grain Cd levels in the rice hybrids to be similar to the levels in indica rice inbreds, suggesting that the hybrids do not accumulate more Cd than do the inbred rice cultivars. Further analysis revealed that the high heritability of Cd accumulation in the grain and the single indica population structure increases the risk of Cd over-accumulation in hybrid rice. The genetic effects of Cd-related QTLs, which have been identified in related Cd-QTL mapping studies, were also determined in the hybrid rice population. Four QTLs were identified as being associated with the variation in grain Cd levels; three of these loci exhibited obvious indica-japonica differentiations. Our study will provide a better understanding of grain Cd accumulations in hybrid rice, and pave the way toward effective breeding for high-yielding, low grain-Cd hybrids in the future. PMID:27708659

  13. Development of Novel Glyphosate-Tolerant Japonica Rice Lines: A Step Toward Commercial Release

    PubMed Central

    Cui, Ying; Huang, Shuqing; Liu, Ziduo; Yi, Shuyuan; Zhou, Fei; Chen, Hao; Lin, Yongjun

    2016-01-01

    Glyphosate is the most widely used herbicide for its low cost and high efficiency. However, it is rarely applied directly in rice field due to its toxicity to rice. Therefore, glyphosate-tolerant rice can greatly decrease the cost of rice production and provide a more effective weed management strategy. Although, several approaches to develop transgenic rice with glyphosate tolerance have been reported, the agronomic performances of these plants have not been well evaluated, and the feasibility of commercial production has not been confirmed yet. Here, a novel glyphosate-tolerant gene cloned from the bacterium Isoptericola variabilis was identified, codon optimized (designated as I. variabilis-EPSPS*), and transferred into Zhonghua11, a widely used japonica rice cultivar. After systematic analysis of the transgene integration via PCR, Southern blot and flanking sequence isolation, three transgenic lines with only one intact I. variabilis-EPSPS* expression cassette integrated into intergenic regions were identified. Seed test results showed that the glyphosate tolerance of the transgenic rice was about 240 times that of wild type on plant medium. The glyphosate tolerance of transgenic rice lines was further evaluated based on comprehensive agronomic performances in the field with T3 and T5generations in a 2-year assay, which showed that they were rarely affected by glyphosate even when the dosage was 8400 g ha−1. To our knowledge, this is the first demonstration of the development of glyphosate-tolerant rice lines based on a comprehensive analysis of agronomic performances in the field. Taken together, the results suggest that the selected glyphosate-tolerant rice lines are highly tolerant to glyphosate and have the possibility of commercial release. I. variabilis-EPSPS* also can be a promising candidate gene in other species for developing glyphosate-tolerant crops. PMID:27625652

  14. Development of Novel Glyphosate-Tolerant Japonica Rice Lines: A Step Toward Commercial Release.

    PubMed

    Cui, Ying; Huang, Shuqing; Liu, Ziduo; Yi, Shuyuan; Zhou, Fei; Chen, Hao; Lin, Yongjun

    2016-01-01

    Glyphosate is the most widely used herbicide for its low cost and high efficiency. However, it is rarely applied directly in rice field due to its toxicity to rice. Therefore, glyphosate-tolerant rice can greatly decrease the cost of rice production and provide a more effective weed management strategy. Although, several approaches to develop transgenic rice with glyphosate tolerance have been reported, the agronomic performances of these plants have not been well evaluated, and the feasibility of commercial production has not been confirmed yet. Here, a novel glyphosate-tolerant gene cloned from the bacterium Isoptericola variabilis was identified, codon optimized (designated as I. variabilis-EPSPS (*)), and transferred into Zhonghua11, a widely used japonica rice cultivar. After systematic analysis of the transgene integration via PCR, Southern blot and flanking sequence isolation, three transgenic lines with only one intact I. variabilis-EPSPS (*) expression cassette integrated into intergenic regions were identified. Seed test results showed that the glyphosate tolerance of the transgenic rice was about 240 times that of wild type on plant medium. The glyphosate tolerance of transgenic rice lines was further evaluated based on comprehensive agronomic performances in the field with T3 and T5generations in a 2-year assay, which showed that they were rarely affected by glyphosate even when the dosage was 8400 g ha(-1). To our knowledge, this is the first demonstration of the development of glyphosate-tolerant rice lines based on a comprehensive analysis of agronomic performances in the field. Taken together, the results suggest that the selected glyphosate-tolerant rice lines are highly tolerant to glyphosate and have the possibility of commercial release. I. variabilis-EPSPS (*) also can be a promising candidate gene in other species for developing glyphosate-tolerant crops. PMID:27625652

  15. Development of Novel Glyphosate-Tolerant Japonica Rice Lines: A Step Toward Commercial Release

    PubMed Central

    Cui, Ying; Huang, Shuqing; Liu, Ziduo; Yi, Shuyuan; Zhou, Fei; Chen, Hao; Lin, Yongjun

    2016-01-01

    Glyphosate is the most widely used herbicide for its low cost and high efficiency. However, it is rarely applied directly in rice field due to its toxicity to rice. Therefore, glyphosate-tolerant rice can greatly decrease the cost of rice production and provide a more effective weed management strategy. Although, several approaches to develop transgenic rice with glyphosate tolerance have been reported, the agronomic performances of these plants have not been well evaluated, and the feasibility of commercial production has not been confirmed yet. Here, a novel glyphosate-tolerant gene cloned from the bacterium Isoptericola variabilis was identified, codon optimized (designated as I. variabilis-EPSPS*), and transferred into Zhonghua11, a widely used japonica rice cultivar. After systematic analysis of the transgene integration via PCR, Southern blot and flanking sequence isolation, three transgenic lines with only one intact I. variabilis-EPSPS* expression cassette integrated into intergenic regions were identified. Seed test results showed that the glyphosate tolerance of the transgenic rice was about 240 times that of wild type on plant medium. The glyphosate tolerance of transgenic rice lines was further evaluated based on comprehensive agronomic performances in the field with T3 and T5generations in a 2-year assay, which showed that they were rarely affected by glyphosate even when the dosage was 8400 g ha−1. To our knowledge, this is the first demonstration of the development of glyphosate-tolerant rice lines based on a comprehensive analysis of agronomic performances in the field. Taken together, the results suggest that the selected glyphosate-tolerant rice lines are highly tolerant to glyphosate and have the possibility of commercial release. I. variabilis-EPSPS* also can be a promising candidate gene in other species for developing glyphosate-tolerant crops.

  16. Development of Novel Glyphosate-Tolerant Japonica Rice Lines: A Step Toward Commercial Release.

    PubMed

    Cui, Ying; Huang, Shuqing; Liu, Ziduo; Yi, Shuyuan; Zhou, Fei; Chen, Hao; Lin, Yongjun

    2016-01-01

    Glyphosate is the most widely used herbicide for its low cost and high efficiency. However, it is rarely applied directly in rice field due to its toxicity to rice. Therefore, glyphosate-tolerant rice can greatly decrease the cost of rice production and provide a more effective weed management strategy. Although, several approaches to develop transgenic rice with glyphosate tolerance have been reported, the agronomic performances of these plants have not been well evaluated, and the feasibility of commercial production has not been confirmed yet. Here, a novel glyphosate-tolerant gene cloned from the bacterium Isoptericola variabilis was identified, codon optimized (designated as I. variabilis-EPSPS (*)), and transferred into Zhonghua11, a widely used japonica rice cultivar. After systematic analysis of the transgene integration via PCR, Southern blot and flanking sequence isolation, three transgenic lines with only one intact I. variabilis-EPSPS (*) expression cassette integrated into intergenic regions were identified. Seed test results showed that the glyphosate tolerance of the transgenic rice was about 240 times that of wild type on plant medium. The glyphosate tolerance of transgenic rice lines was further evaluated based on comprehensive agronomic performances in the field with T3 and T5generations in a 2-year assay, which showed that they were rarely affected by glyphosate even when the dosage was 8400 g ha(-1). To our knowledge, this is the first demonstration of the development of glyphosate-tolerant rice lines based on a comprehensive analysis of agronomic performances in the field. Taken together, the results suggest that the selected glyphosate-tolerant rice lines are highly tolerant to glyphosate and have the possibility of commercial release. I. variabilis-EPSPS (*) also can be a promising candidate gene in other species for developing glyphosate-tolerant crops.

  17. [Characteristics of canopy structure of super high yielding japonica hybrid rice community].

    PubMed

    Chen, Jinhong; Zhang, Guoping; Guo, Hengde; Mao, Guojuan

    2003-06-01

    In this paper, the characteristics of canopy structure, such as the numbers of seedling, panicle and grain, the distribution of dry matters in different canopy layers and different organs, and the distributions of LAI and of solar radiation in different canopy layers of super high yielding community of japonica hybrid rice were studied, in comparison with normal japonica rice. The results showed that the total the dry matter weight and the dry matter weight of layers below 40 cm, 40-60 cm, 60-80 cm and above 80 cm of japonica hybrid rice canopy were 32.29%, 29.12%, 13.95%, 16.45% and 100.17% higher those that of normal japonica rice, respectively. The ratios of dry leaf (photosynthetic organ) and of dry panicle (sink organ) weight to total dry weight were 24.8% and 12.8%, respectively, which were greater than those of normal japonica rice, while the ratios of dry sheath and stem (storage organs) weight were 33.6% and 28.9%, respectively, which were lower than those of normal japonica rice. The allotment of LAI in different layers of japonica hybrid rice canopy was reasonable, and the LAI of above 40 cm layer at full heading stage reached 5.44. The solar radiation was well-distributed inside japonica hybrid rice canopy, for example, the solar radiation in layers below 60 cm were 13.1%-37.0% higher, but 5.9%-12.2% lower above 60 cm than that of normal japonica rice. The extinction coefficients of solar radiation in layers below 20 cm, 20-40 cm, 40-60 cm and 60-80 cm of japonica hybrid rice canopy were 35.1%, 13.5%, 29.1% and 17.2% lower than that of normal japonica rice, respectively.

  18. Identification of low inorganic and total grain arsenic rice cultivars from Bangladesh.

    PubMed

    Norton, Gareth J; Islam, M Rafiqul; Deacon, Claire M; Zhao, Fang-Jie; Stroud, Jacqueline L; McGrath, Steve P; Islam, Shofiqul; Jahiruddin, M; Feldmann, Joerg; Price, Adam H; Meharg, Andrew A

    2009-08-01

    For the world's population, rice consumption is a major source of inorganic arsenic (As), a nonthreshold class 1 carcinogen. Reducing the amount of total and inorganic As within the rice grain would reduce the exposure risk. In this study, grain As was measured in 76 cultivars consisting of Bangladeshi landraces, improved Bangladesh Rice Research Institute (BRRI) cultivars, and parents of permanent mapping populations grown in two field sites in Bangladesh, Faridpur and Sonargaon, irrigated with As-contaminated tubewell water. Grain As ranged from 0.16 to 0.74 mg kg(-1) at Faridpur and from 0.07 to 0.28 mg kg(-1) at Sonargaon. Highly significant cultivar differences were detected and a significant correlation (r = 0.802) in the grain As between the two field sites was observed, indicating stable genetic differences in As accumulation. The cultivars with the highest concentration of grain As were the Bangladeshi landraces. Landraces with red bran had significantly more grain As than the cultivars with brown bran. The percent of inorganic As decreased linearly with increasing total As, but genetic variation within this trend was identified. A number of local cultivars with low grain As were identified. Some tropical japonica cultivars with low grain As have the potential to be used in breeding programs and genetic studies aiming to identify genes which decrease grain As. PMID:19731720

  19. Complexity of indica-japonica varietal differentiation in Bangladesh rice landraces revealed by microsatellite markers.

    PubMed

    Wang, Mumu; Zhu, Zuofeng; Tan, Lubin; Liu, Fengxia; Fu, Yongcai; Sun, Chuanqing; Cai, Hongwei

    2013-06-01

    To understand the genetic diversity and indica-japonica differentiation in Bangladesh rice varieties, a total of 151 accessions of rice varieties mostly Bangladesh traditional varieties including Aus, Boro, broadcast Aman, transplant Aman and Rayada varietal groups were genotyped using 47 rice nuclear SSRs. As a result, three distinct groups were detected by cluster analysis, corresponding to indica, Aus and japonica rice. Among deepwater rice varieties analyzed some having particular morphological features that mainly corresponded to the japonica varietal group. Some small seeded and aromatic varieties from Bangladesh also corresponded to the japonica varietal group. This research for the first time establishes that the japonica varietal group is a prominent component of traditional varieties in Bangladesh, particularly in deepwater areas.

  20. Complexity of indica-japonica varietal differentiation in Bangladesh rice landraces revealed by microsatellite markers

    PubMed Central

    Wang, Mumu; Zhu, Zuofeng; Tan, Lubin; Liu, Fengxia; Fu, Yongcai; Sun, Chuanqing; Cai, Hongwei

    2013-01-01

    To understand the genetic diversity and indica-japonica differentiation in Bangladesh rice varieties, a total of 151 accessions of rice varieties mostly Bangladesh traditional varieties including Aus, Boro, broadcast Aman, transplant Aman and Rayada varietal groups were genotyped using 47 rice nuclear SSRs. As a result, three distinct groups were detected by cluster analysis, corresponding to indica, Aus and japonica rice. Among deepwater rice varieties analyzed some having particular morphological features that mainly corresponded to the japonica varietal group. Some small seeded and aromatic varieties from Bangladesh also corresponded to the japonica varietal group. This research for the first time establishes that the japonica varietal group is a prominent component of traditional varieties in Bangladesh, particularly in deepwater areas. PMID:23853518

  1. Cultivar variability of iron uptake mechanisms in rice (Oryza sativa L.).

    PubMed

    Pereira, Margarida P; Santos, Carla; Gomes, Ana; Vasconcelos, Marta W

    2014-12-01

    Rice (Oryza sativa L.) is the most important staple food in the world. It is rich in genetic diversity and can grow in a wide range of environments. Iron (Fe) deficiency is a major abiotic stress in crop production and in aerobic soils, where Fe forms insoluble complexes, and is not readily available for uptake. To cope with Fe deficiency, plants developed mechanisms for Fe uptake, and although rice was described as a Strategy II plant, recent evidence suggests that it is capable of utilizing mechanisms from both Strategies. The main objective of this work was to compare two cultivars, Bico Branco (japonica) and Nipponbare (tropical japonica), to understand if the regulation of Fe uptake mechanisms could be cultivar (cv.)dependent. Plants of both cultivars were grown under Fe-deficient and -sufficient conditions and physiological and molecular responses to Fe deficiency were evaluated. Bico Branco cv. developed more leaf chlorosis and was more susceptible to Fe deficiency, retaining more nutrients in roots, than Nipponbare cv., which translocated more nutrients to shoots. Nipponbare cv. presented higher levels of Fe reductase activity, which was significantly up-regulated by Fe deficiency, and had higher expression levels of the Strategy I-OsFRO2 gene in roots, while Bico Branco cv. induced more genes involved in Strategy II.These new findings show that rice cultivars have different responses to Fe deficiency and that the induction of Strategy I or II may be rice cultivar-dependent, although the utilization of the reduction mechanisms seems to be an ubiquitous advantage.

  2. Rice root-associated bacteria – insights in community structures across ten cultivars

    PubMed Central

    Hardoim, Pablo Rodrigo; Andreote, Fernando Dini; Reinhold-Hurek, Barbara; Sessitsch, Angela; van Overbeek, Leonard Simon; van Elsas, Jan Dirk

    2015-01-01

    In this study, the effect of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. Thus, total bacteria, Alpha- and Beta-proteobacteria, Pseudomonas and Actinobacteria were studied using PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE). Rice genotype determined to a large extent the composition of the different bacterial communities across cultivars. Several cultivars belonging to Oryza sativa subspecies indica tended to select similar bacterial communities, whereas those belonging to subspecies japonica and aromatica selected ones with divergent community structures. An effect of soil type was pronounced for the Actinobacteria communities, while a small effect of ‘improved’ and ‘traditional’ plants was noted for all communities analysed. A few dominant bands in PCR-DGGE, affiliated with Rhizobium radiobacter, Dickeya zeae, Mycobacterium bolletii and with members of the Rhizobiales, Rhodospirillaceae and Paenibacillaceae were spread across cultivars. In contrast, a majority of bands (e.g. affiliated with Enterobacter cloacae or Burkholderia kururiensis) was only present in particular cultivars or was erratically distributed amongst rice replicates. The data suggested that both bacterial adaptation and plant genotype contribute to the shaping of the dynamic bacterial communities associated with roots of rice plants. PMID:21426364

  3. NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars.

    PubMed

    Fujita, Daisuke; Trijatmiko, Kurniawan Rudi; Tagle, Analiza Grubanzo; Sapasap, Maria Veronica; Koide, Yohei; Sasaki, Kazuhiro; Tsakirpaloglou, Nikolaos; Gannaban, Ritchel Bueno; Nishimura, Takeshi; Yanagihara, Seiji; Fukuta, Yoshimichi; Koshiba, Tomokazu; Slamet-Loedin, Inez Hortense; Ishimaru, Tsutomu; Kobayashi, Nobuya

    2013-12-17

    Increasing crop production is essential for securing the future food supply in developing countries in Asia and Africa as economies and populations grow. However, although the Green Revolution led to increased grain production in the 1960s, no major advances have been made in increasing yield potential in rice since then. In this study, we identified a gene, SPIKELET NUMBER (SPIKE), from a tropical japonica rice landrace that enhances the grain productivity of indica cultivars through pleiotropic effects on plant architecture. Map-based cloning revealed that SPIKE was identical to NARROW LEAF1 (NAL1), which has been reported to control vein pattern in leaf. Phenotypic analyses of a near-isogenic line of a popular indica cultivar, IR64, and overexpressor lines revealed increases in spikelet number, leaf size, root system, and the number of vascular bundles, indicating the enhancement of source size and translocation capacity as well as sink size. The near-isogenic line achieved 13-36% yield increase without any negative effect on grain appearance. Expression analysis revealed that the gene was expressed in all cell types: panicles, leaves, roots, and culms supporting the pleiotropic effects on plant architecture. Furthermore, SPIKE increased grain yield by 18% in the recently released indica cultivar IRRI146, and increased spikelet number in the genetic background of other popular indica cultivars. The use of SPIKE in rice breeding could contribute to food security in indica-growing regions such as South and Southeast Asia.

  4. Flavonoids from the grains of C1/R-S transgenic rice, the transgenic Oryza sativa spp. japonica, and their radical scavenging activities.

    PubMed

    Cho, Jin-Gyeong; Song, Na-Young; Nam, Tae-Gyu; Shrestha, Sabina; Park, Hee-Jung; Lyu, Ha-Na; Kim, Dae-Ok; Lee, Gihwan; Woo, Young-Min; Jeong, Tae-Sook; Baek, Nam-In

    2013-10-30

    The transgenic rice cultivar of Oryza sativa spp. japonica cv. Hwa-Young, C1/R-S transgenic rice (C1/R-S rice), is a flavonoid-rich cultivar of rice. The grains of C1/R-S rice were extracted with aqueous MeOH, and the concentrated extract was partitioned with EtOAc, n-BuOH, and H2O, successively. Repeated silica gel, octadecyl silica gel (ODS), and Sephadex LH-20 column chromatographies for the EtOAc and n-BuOH fractions afforded four new flavonoids (compounds 2, 3, 7, and 8) along with four known flavonoids: (+)-3'-O-methyltaxifolin (1), brassicin (4), isorhamnetin-4'-O-β-D-glucosyranoside (5), and 3'-O-methyltaxifolin-5-O-β-D-glucopyranoside (6). The new flavonoids were identified as 3'-O-methyltaxifolin-7-O-β-D-glucopyranoside (2), 3'-O-methyltaxifolin-4'-O-β-D-glucopyranoside (3), isorhamnetin-7-O-β-D-cellobioside (brassicin-4″-O-β-D-glucopyranoside) (7), and brassicin-4'-O-β-D-glucosyranoside (8) from the result of spectroscopic data including nuclear magnetic resonance spectrometry (NMR), mass spectrometry (MS), and infrared spectroscopy (IR). Also, quantitative analysis of major flavonoids (compounds 2, 3, and 8) in C1/R-S rice, O. sativa spp. japonica cv. Hwa-Young (HY), and a hybrid of two cultivar (C1/R-S rice/HY) extracts was performed using HPLC experiment. The isolated flavonoids were evaluated for their radical-scavenging effect on DPPH and ABTS radicals.

  5. Seed formation in triploid loquat (Eriobotrya japonica) through cross-hybridization with pollen of diploid cultivars.

    PubMed

    Kikuchi, Shinji; Iwasuna, Miwako; Kobori, Aya; Tsutaki, Yasunori; Yoshida, Akihiro; Murota, Yuri; Nishino, Eisho; Sassa, Hidenori; Koba, Takato

    2014-06-01

    As the fruits of loquat (Eriobotrya japonica, 2n = 2x = 34) carry large seeds, the breeding of seedless loquat has long been a goal. The recent creation of triploid cultivars (2n = 3x = 51) and the application of gibberellins allow commercial production of seedless loquat, but the possibility of seed formation in triploid loquats has not been carefully investigated. Through crossing experiments and cytological observations of meiosis and pollen tube growth, we found that the triploid line 3N-N28 was essentially self-sterile, but developed seeds on pollination with pollen from diploid cultivars at rates of up to 5.5%. Almost half of the seedlings survived to 5 months, and carried diploid (2n = 34), tetraploid (2n = 68), or aneuploid chromosome numbers. Our results suggest that triploid loquat cultivars might retain the risk of seed formation. Protection from pollination by diploid cultivars or the development of new triploid cultivars will be necessary to ensure the production of seedless loquat fruits.

  6. Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars.

    PubMed

    Cho, Kyoungwon; Shibato, Junko; Kubo, Akihiro; Kohno, Yoshihisa; Satoh, Kouji; Kikuchi, Shoshi; Sarkar, Abhijit; Agrawal, Ganesh Kumar; Rakwal, Randeep

    2013-11-01

    High ozone (O3) concentrations not only damage plant life but also cause considerable losses in plant productivity. To screen for molecular factors usable as potential biomarkers to identify for O3-sensitive and -tolerant lines and design O3 tolerant crops, our project examines the effects of O3 on rice, using high-throughput omics approaches. In this study, we examined growth and yield parameters of 4 rice cultivars fumigated for a life-time with ambient air (mean O3: 31.4-32.7 ppb) or filtered air (mean O3: 6.6-8.3 ppb) in small open-top chambers (sOTCs) to select O3-sensitive (indica cv Takanari) and O3-tolerant (japonica cv Koshihikari) cultivars for analysis of seed transcriptomes using Agilent 4 × 44K rice oligo DNA chip. Total RNA from dry mature dehusked seeds of Takanari and Koshihikari cultivars was extracted using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment, followed by DNA microarray analysis using the established dye-swap method. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in sOTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in sensitive cv Takanari and tolerant cv Koshihikari. MapMan analysis further mapped the molecular factors activated by O3, confirming Takanari is rightly classified as an O3 sensitive genotype.

  7. Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars

    PubMed Central

    Cho, Kyoungwon; Shibato, Junko; Kubo, Akihiro; Kohno, Yoshihisa; Satoh, Kouji; Kikuchi, Shoshi; Sarkar, Abhijit; Agrawal, Ganesh Kumar; Rakwal, Randeep

    2013-01-01

    High ozone (O3) concentrations not only damage plant life but also cause considerable losses in plant productivity. To screen for molecular factors usable as potential biomarkers to identify for O3-sensitive and -tolerant lines and design O3 tolerant crops, our project examines the effects of O3 on rice, using high-throughput omics approaches. In this study, we examined growth and yield parameters of 4 rice cultivars fumigated for a life-time with ambient air (mean O3: 31.4–32.7 ppb) or filtered air (mean O3: 6.6–8.3 ppb) in small open-top chambers (sOTCs) to select O3-sensitive (indica cv Takanari) and O3-tolerant (japonica cv Koshihikari) cultivars for analysis of seed transcriptomes using Agilent 4 × 44K rice oligo DNA chip. Total RNA from dry mature dehusked seeds of Takanari and Koshihikari cultivars was extracted using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment, followed by DNA microarray analysis using the established dye-swap method. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in sOTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in sensitive cv Takanari and tolerant cv Koshihikari. MapMan analysis further mapped the molecular factors activated by O3, confirming Takanari is rightly classified as an O3 sensitive genotype. PMID:24025514

  8. Artificial selection for a green revolution gene during japonica rice domestication.

    PubMed

    Asano, Kenji; Yamasaki, Masanori; Takuno, Shohei; Miura, Kotaro; Katagiri, Satoshi; Ito, Tomoko; Doi, Kazuyuki; Wu, Jianzhong; Ebana, Kaworu; Matsumoto, Takashi; Innan, Hideki; Kitano, Hidemi; Ashikari, Motoyuki; Matsuoka, Makoto

    2011-07-01

    The semidwarf phenotype has been extensively selected during modern crop breeding as an agronomically important trait. Introduction of the semidwarf gene, semi-dwarf1 (sd1), which encodes a gibberellin biosynthesis enzyme, made significant contributions to the "green revolution" in rice (Oryza sativa L.). Here we report that SD1 was involved not only in modern breeding including the green revolution, but also in early steps of rice domestication. We identified two SNPs in O. sativa subspecies (ssp.) japonica SD1 as functional nucleotide polymorphisms (FNPs) responsible for shorter culm length and low gibberellin biosynthetic activity. Genetic diversity analysis among O. sativa ssp. japonica and indica, along with their wild ancestor O. rufipogon Griff, revealed that these FNPs clearly differentiate the japonica landrace and O. rufipogon. We also found a dramatic reduction in nucleotide diversity around SD1 only in the japonica landrace, not in the indica landrace or O. rufipogon. These findings indicate that SD1 has been subjected to artificial selection in rice evolution and that the FNPs participated in japonica domestication, suggesting that ancient humans already used the green revolution gene.

  9. Registration of a rice gene mapping population of Lemont X Jasmine 85 recombinant inbred lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A mapping population developed from a cross of rice (Oryza sativa L.) tropical japonica cultivar ‘Lemont’ and indica cultivar ‘Jasmine 85’ was developed to facilitate genetic studies for important agronomic traits. The indica- and japonica-based rice recombinant inbred line (RIL) mapping population ...

  10. Methane emissions from rice fields: Effect of plant height among several rice cultivars

    NASA Astrophysics Data System (ADS)

    Ding, A.; Willis, C. R.; Sass, R. L.; Fisher, F. M.

    The effect of rice cultivar and plant height on methane (CH4) emission from rice fields was studied from data of 8-year field experiments. Field experiments were conducted from 1989 to 1996 at the Texas A & M University Agricultural Research and Extension Center near Beaumont, Texas. Eleven rice cultivars and three soil types were involved. The results of this study showed the following: 1) Rice cultivar choice slightly influenced the day-to-day seasonal pattern of methane emission, but it had a significant effect on the seasonal total methane emission. The average seasonal methane emission is 22.8gCH4m-2 for high-emitting cultivars (Mars and Della), ranging from 8.0 to 41.0gCH4m-2 and 17.7gCH4m-2 for low-emitting cultivars (Lemont, Labelle, Lebonnet, Dawn, Katy, IR 36, Cypress, and Jasmine), ranging from 1.7 to 28.4gCH4m-2. 2) Seasonal methane emission has a positive linear correlation with postheading rice plant height. The correlation coefficient r2 is 0.736 (n=24, and p<0.05). In this paper we suggest that plant height may be a good criteria in choosing cultivars for mitigation of methane emission. More importantly, it provides a potential method for estimating methane emission from regional or global rice paddies as plant height can be evaluated by remotely sensed imagery.

  11. Phenolic composition from different loquat (Eriobotrya japonica Lindl.) cultivars grown in China and their antioxidant properties.

    PubMed

    Zhang, Wenna; Zhao, Xiaoyong; Sun, Chongde; Li, Xian; Chen, Kunsong

    2015-01-05

    China is one of the most important centers of diversity for Eriobotrya japonica Lindl. in the world. In this study, seven loquat cultivars grown in China were evaluated for their phenolic compounds and antioxidant activity. Eleven phenolic compounds, i.e., 3-p-coumaroylquinincacid (3-p-CoQA), 5-caffeoylquinic acid (5-CQA), 4-caffeoylquinic acid (4-CQA), 3-caffeoylquinic acid (3-CQA), 5-feruloylquinic acid (5-FQA), quercetin-3-O-galactoside (Q-3-Gal), quercetin-3-O-glucoside (Q-3-Glu), quercetin-3-O-rhamnoside (Q-3-Rha), kaempferol-3-O-galactoside (K-3-Gal), kaempferol-3-O-rhamnoside (K-3-Rha), and kaempferol-3-O-glucoside (K-3-Glu) were identified and quantified in the peel and pulp of the cultivars tested. 3-CQA and 5-CQA were the predominant components in both fruit parts. 2,2-Diphenyl-1-picrylhydrazyl radicals (DPPH), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate (ABTS), and ferric reducing antioxidant power (FRAP) assays were used for the antioxidant evaluation. Results showed that peel extracts had higher antioxidant activities than their pulp counterparts in all the cultivars tested, which was correlated with their higher total phenolic contents. The antioxidant potency composite (APC) index showed obvious variations ranging from 64.15 to 100 in the peel and from 59.49 to 97.95 in the pulp of different cultivars, where "Dahongpao" (DHP) and "Luoyangqing" (LYQ) had the highest APC index in the peel and pulp, respectively. Overall, loquat cultivars rich in hydroxycinnamic acids (HCAs) such as 3-p-CoQA, 5-CQA, 4-CQA, 3-CQA and 5-FQA showed relatively higher antioxidant activities, and may be excellent sources of phytochemicals and natural antioxidants.

  12. Decoding regulatory landscape of somatic embryogenesis reveals differential regulatory networks between japonica and indica rice subspecies.

    PubMed

    Indoliya, Yuvraj; Tiwari, Poonam; Chauhan, Abhisekh Singh; Goel, Ridhi; Shri, Manju; Bag, Sumit Kumar; Chakrabarty, Debasis

    2016-01-01

    Somatic embryogenesis is a unique process in plants and has considerable interest for biotechnological application. Compare to japonica, indica rice has been less responsive to in vitro culture. We used Illumina Hiseq 2000 sequencing platform for comparative transcriptome analysis between two rice subspecies at six different developmental stages combined with a tag-based digital gene expression profiling. Global gene expression among different samples showed greater complexity in japonica rice compared to indica which may be due to polyphyletic origin of two rice subspecies. Expression pattern in initial stage indicate major differences in proembryogenic callus induction phase that may serve as key regulator to observe differences between both subspecies. Our data suggests that phytohormone signaling pathways consist of elaborate networks with frequent crosstalk, thereby allowing plants to regulate somatic embryogenesis pathway. However, this crosstalk varies between the two rice subspecies. Down regulation of positive regulators of meristem development (i.e. KNOX, OsARF5) and up regulation of its counterparts (OsRRs, MYB, GA20ox1/GA3ox2) in japonica may be responsible for its better regeneration and differentiation of somatic embryos. Comprehensive gene expression information in the present experiment may also facilitate to understand the monocot specific meristem regulation for dedifferentiation of somatic cell to embryogenic cells.

  13. Decoding regulatory landscape of somatic embryogenesis reveals differential regulatory networks between japonica and indica rice subspecies

    PubMed Central

    Indoliya, Yuvraj; Tiwari, Poonam; Chauhan, Abhisekh Singh; Goel, Ridhi; Shri, Manju; Bag, Sumit Kumar; Chakrabarty, Debasis

    2016-01-01

    Somatic embryogenesis is a unique process in plants and has considerable interest for biotechnological application. Compare to japonica, indica rice has been less responsive to in vitro culture. We used Illumina Hiseq 2000 sequencing platform for comparative transcriptome analysis between two rice subspecies at six different developmental stages combined with a tag-based digital gene expression profiling. Global gene expression among different samples showed greater complexity in japonica rice compared to indica which may be due to polyphyletic origin of two rice subspecies. Expression pattern in initial stage indicate major differences in proembryogenic callus induction phase that may serve as key regulator to observe differences between both subspecies. Our data suggests that phytohormone signaling pathways consist of elaborate networks with frequent crosstalk, thereby allowing plants to regulate somatic embryogenesis pathway. However, this crosstalk varies between the two rice subspecies. Down regulation of positive regulators of meristem development (i.e. KNOX, OsARF5) and up regulation of its counterparts (OsRRs, MYB, GA20ox1/GA3ox2) in japonica may be responsible for its better regeneration and differentiation of somatic embryos. Comprehensive gene expression information in the present experiment may also facilitate to understand the monocot specific meristem regulation for dedifferentiation of somatic cell to embryogenic cells. PMID:26973288

  14. Preferential Association of Endophytic Bradyrhizobia with Different Rice Cultivars and Its Implications for Rice Endophyte Evolution

    PubMed Central

    Piromyou, Pongdet; Greetatorn, Teerana; Teamtisong, Kamonluck; Okubo, Takashi; Shinoda, Ryo; Nuntakij, Achara; Tittabutr, Panlada; Boonkerd, Nantakorn

    2015-01-01

    Plant colonization by bradyrhizobia is found not only in leguminous plants but also in nonleguminous species such as rice. To understand the evolution of the endophytic symbiosis of bradyrhizobia, the effect of the ecosystems of rice plantations on their associations was investigated. Samples were collected from various rice (Oryza sativa) tissues and crop rotational systems. The rice endophytic bradyrhizobia were isolated on the basis of oligotrophic properties, selective medium, and nodulation on siratro (Macroptilium atropurpureum). Six bradyrhizobial strains were obtained exclusively from rice grown in a crop rotational system. The isolates were separated into photosynthetic bradyrhizobia (PB) and nonphotosynthetic bradyrhizobia (non-PB). Thai bradyrhizobial strains promoted rice growth of Thai rice cultivars better than the Japanese bradyrhizobial strains. This implies that the rice cultivars possess characteristics that govern rice-bacterium associations. To examine whether leguminous plants in a rice plantation system support the persistence of rice endophytic bradyrhizobia, isolates were tested for legume nodulation. All PB strains formed symbioses with Aeschynomene indica and Aeschynomene evenia. On the other hand, non-PB strains were able to nodulate Aeschynomene americana, Vigna radiata, and M. atropurpureum but unable to nodulate either A. indica or A. evenia. Interestingly, the nodABC genes of all of these bradyrhizobial strains seem to exhibit low levels of similarity to those of Bradyrhizobium diazoefficiens USDA110 and Bradyrhizobium sp. strain ORS285. From these results, we discuss the evolution of the plant-bradyrhizobium association, including nonlegumes, in terms of photosynthetic lifestyle and nod-independent interactions. PMID:25710371

  15. Screening Rice Cultivars for Resistance to Bacterial Leaf Blight.

    PubMed

    Fred, Agaba Kayihura; Kiswara, Gilang; Yi, Gihwan; Kim, Kyung-Min

    2016-05-28

    Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious threats to rice production. In this study, screening of rice for resistance to BLB was carried out at two different times and locations; that is, in a greenhouse during winter and in an open field during summer. The pathogenicity of Xoo race K1 was tested on 32 Korean rice cultivars. Inoculation was conducted at the maximum tillering stage, and the lesion length was measured after 14 days of inoculation. Five cultivars, Hanareum, Namcheon, Samgdeok, Samgang, and Yangjo, were found to be resistant in both the greenhouse and open-field screenings. Expression of the plant defense-related genes JAmyb, OsNPR1, OsPR1a, OsWRKY45, and OsPR10b was observed in resistant and susceptible cultivars by qRT-PCR. Among the five genes tested, only OsPR10b showed coherent expression with the phenotypes. Screening of resistance to Xoo in rice was more accurate when conducted in open fields in the summer cultivation period than in greenhouses in winter. The expression of plant defenserelated genes after bacterial inoculation could give another perspective in elucidating defense mechanisms by using both resistant and susceptible individuals.

  16. Overcoming inter-subspecific hybrid sterility in rice by developing indica-compatible japonica lines.

    PubMed

    Guo, Jie; Xu, Xiaomei; Li, Wentao; Zhu, Wenyin; Zhu, Haitao; Liu, Ziqiang; Luan, Xin; Dai, Ziju; Liu, Guifu; Zhang, Zemin; Zeng, Ruizhen; Tang, Guang; Fu, Xuelin; Wang, Shaokui; Zhang, Guiquan

    2016-06-01

    Rice (Oryza sativa L.) is an important staple crop. The exploitation of the great heterosis that exists in the inter-subspecific crosses between the indica and japonica rice has long been considered as a promising way to increase the yield potential. However, the male and female sterility frequently occurred in the inter-subspecific hybrids hampered the utilization of the heterosis. Here we report that the inter-subspecific hybrid sterility in rice is mainly affected by the genes at Sb, Sc, Sd and Se loci for F1 male sterility and the gene at S5 locus for F1 female sterility. The indica-compatible japonica lines (ICJLs) developed by pyramiding the indica allele (S-i) at Sb, Sc, Sd and Se loci and the neutral allele (S-n) at S5 locus in japonica genetic background through marker-assisted selection are compatible with indica rice in pollen fertility and in spikelet fertility. These results showed a great promise of overcoming the inter-subspecific hybrid sterility and exploiting the heterosis by developing ICJLs.

  17. The cadmium and lead content of the grain produced by leading Chinese rice cultivars.

    PubMed

    Xie, L H; Tang, S Q; Wei, X J; Shao, G N; Jiao, G A; Sheng, Z H; Luo, J; Hu, P S

    2017-02-15

    The cadmium (Cd) and lead (Pb) content in both white and wholemeal flour milled from 110 leading rice cultivars was assessed. The white flour Cd content ranged from <0.0025 to 0.2530mg/kg (geometric mean (GM)=0.0150mg/kg), while its Pb content ranged from <0.0250 to 0.3830mg/kg (GM=0.0210mg/kg). The indica types took up higher amounts of Cd and Pb than did the japonica types. Although the heavy metal content of wholemeal flour tended to higher than that of white flour, nevertheless 84.5% (Cd) and 95.4% (Pb) of the entries were compliant with the national maximum allowable concentration of 0.2000mg/kg of each contaminant. An analysis of the Cd content in the white flour of three indica type cultivars grown in two consecutive years at two locations indicated that Cd content may be significantly affected by the conditions prevailing in the growing season. PMID:27664629

  18. Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

    PubMed Central

    Wang, C-H; Zheng, X-M; Xu, Q; Yuan, X-P; Huang, L; Zhou, H-F; Wei, X-H; Ge, S

    2014-01-01

    Despite extensive studies on cultivated rice, the genetic structure and subdivision of this crop remain unclear at both global and local scales. Using 84 nuclear simple sequence repeat markers, we genotyped a panel of 153 global rice cultivars covering all previously recognized groups and 826 cultivars representing the diversity of Chinese rice germplasm. On the basis of model-based grouping, neighbour-joining tree and principal coordinate analysis, we confirmed the widely accepted five major groups of rice cultivars (indica, aus, aromatic, temperate japonica and tropical japonica), and demonstrated that rayada rice was unique in genealogy and should be treated as a new (the sixth) major group of rice germplasm. With reference to the global classification of rice cultivars, we identified three major groups (indica, temperate japonica and tropical japonica) in Chinese rice germplasm and showed that Chinese temperate japonica contained higher diversity than that of global samples, whereas Chinese indica and tropical japonica maintained slightly lower diversity than that present in the global samples. Particularly, we observed that all seasonal, drought-tolerant and endosperm types occurred within each of three major groups of Chinese cultivars, which does not support previous claims that seasonal differentiation exists in Indica and drought-tolerant differentiation is present in Japonica. It is most likely that differentiation of cultivar types arose multiple times stemming from artificial selection for adaptation to local environments. PMID:24326293

  19. Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm.

    PubMed

    Wang, C-H; Zheng, X-M; Xu, Q; Yuan, X-P; Huang, L; Zhou, H-F; Wei, X-H; Ge, S

    2014-05-01

    Despite extensive studies on cultivated rice, the genetic structure and subdivision of this crop remain unclear at both global and local scales. Using 84 nuclear simple sequence repeat markers, we genotyped a panel of 153 global rice cultivars covering all previously recognized groups and 826 cultivars representing the diversity of Chinese rice germplasm. On the basis of model-based grouping, neighbour-joining tree and principal coordinate analysis, we confirmed the widely accepted five major groups of rice cultivars (indica, aus, aromatic, temperate japonica and tropical japonica), and demonstrated that rayada rice was unique in genealogy and should be treated as a new (the sixth) major group of rice germplasm. With reference to the global classification of rice cultivars, we identified three major groups (indica, temperate japonica and tropical japonica) in Chinese rice germplasm and showed that Chinese temperate japonica contained higher diversity than that of global samples, whereas Chinese indica and tropical japonica maintained slightly lower diversity than that present in the global samples. Particularly, we observed that all seasonal, drought-tolerant and endosperm types occurred within each of three major groups of Chinese cultivars, which does not support previous claims that seasonal differentiation exists in Indica and drought-tolerant differentiation is present in Japonica. It is most likely that differentiation of cultivar types arose multiple times stemming from artificial selection for adaptation to local environments.

  20. A genome-wide microsatellite polymorphism database for the indica and japonica rice.

    PubMed

    Zhang, Zhonghua; Deng, Yajun; Tan, Jun; Hu, Songnian; Yu, Jun; Xue, Qingzhong

    2007-02-28

    Microsatellite (MS) polymorphism is an important source of genetic diversity, providing support for map-based cloning and molecular breeding. We have developed a new database that contains 52 845 polymorphic MS loci between indica and japonica, composed of ample Class II MS markers, and integrated 18 828 MS loci from IRGSP and genetic markers from RGP. Based on genetic marker positions on the rice genome (http://rise.genomics.org.cn/rice2/index.jsp ), we determined the approximate genetic distances of these MS loci and validated 100 randomly selected markers experimentally with 90% success rate. In addition, we recorded polymorphic MS positions in indica cv. 9311 that is the most important paternal parent of the two-line hybrid rice in China. Our database will undoubtedly facilitate the application of MS markers in genetic researches and marker-assisted breeding. The data set is freely available from www.wigs.zju.edu.cn/achievment/polySSR. PMID:17452422

  1. [Effects of spacing on the yields and canopy structure of japonica rice at full heading stage].

    PubMed

    Li, Xiao-peng; Wang, Shu; Huang, Yuan-cai; Jia, Bao-yan; Wang, Yan; Zeng, Qun-yun

    2015-11-01

    With three panicle types of rice varieties and hybrids in Liaoning as entries, the effects of spacing of Japonica rice on light interception capacity, population light distribution, light conversion efficiency at full heading stage and yield were studied. The results showed that the leaf area indices at full heading stage, closely related to light interception, increased first and then decreased with the decrease of transplanting density. The extinction coefficient in one day increased first and then decreased, and the K value increased with the increase of planting density. Yield was positively correlated with canopy extinction coefficient and inclinations of the upper three leaves. In terms of energy efficiency, the yields were positively correlated to flag leaf stomatal conductance, intercellular CO2 concentration and transpiration rate. At the configuration of high (15 cm x 25 cm) and low (20 cm x 30 cm and 20 cm x 35 cm) densities, Japonica rice could increase light interception capability and optical conversion efficiency, but could not obtain high and stable yields due to limitation by lodging and panicles of per unit area, respectively. At the configurations of 15 cm x 30 cm and 20 cm x 25 cm, it was easy to get adequate panicles, optimize the structure of the canopy, reduce lodging risk, and obtain high yield. PMID:26915187

  2. Effect of rice cultivars on root-associated methanotrophic communities

    NASA Astrophysics Data System (ADS)

    Lüke, C.; Frenzel, P.

    2009-04-01

    Rice agriculture represents a major source of the greenhouse gas methane. However, a large amount of methane is oxidized by methanotrophic bacteria before being released to the atmosphere. Methanotrophs are characterized by their unique ability to use methane as sole source for carbon and energy. They are located at oxic-anoxic interfaces where methane and oxygen are present, such as the rhizosphere. Although they have been studied extensively in the past, only little is known about natural or anthropogenic factors influencing their large diversity. In this study, we investigated the effect of 20 different rice cultivars on methanotrophic communities associated with the roots of rice plants. The pmoA gene encoding a subunit of the particulate methane monooxygenase (catalyzing the first step of methane oxidation) was used as a functional and phylogenetic marker and analyzed using two different fingerprinting methods. The well established terminal restriction fragment length polymorphism (T-RFLP) analysis was compared to results obtained using a diagnostic pmoA microarray. Both methods indicated that type Ib (Methylococcus/Methylocaldum) and type II (Methylosinus/Methylocystis) were the predominat methanotrophs located on rice roots. Interestingly, analysis of pmoA transcripts suggested Methylobacter/Methylomonas (type Ia) to present the actively methane oxidizing population in this environment.

  3. Consumption of Bt rice pollen containing Cry1C or Cry2A does not pose a risk to Propylea japonica (Thunberg) (Coleoptera: Coccinellidae).

    PubMed

    Li, Yunhe; Zhang, Xiaojie; Chen, Xiuping; Romeis, Jörg; Yin, Xinming; Peng, Yufa

    2015-01-01

    As a pollen feeder, Propylea japonica would be directly exposed to Cry proteins in Bacillus thuringiensis (Bt)-transgenic rice fields. The effect of Cry1C- or Cry2A-containing transgenic rice pollen on the fitness of P. japonica was assessed using two dietary-exposure experiments in the laboratory. In the first experiment, larval developmental time of P. japonica was significantly longer when fed pollen from Bt rice lines rather than control pollen but other life table parameters were not significantly affected. In the second experiment, P. japonica was not affected when fed a rapeseed pollen-based diet containing purified Cry1C or Cry2A at concentrations that were >10-times higher than in pollen, but P. japonica was affected when the diet contained E-64 as a positive control. In both experiments, the stability and bioactivity of the Cry proteins in the food sources and the uptake of the proteins by P. japonica were confirmed. The results show that P. japonica is not sensitive to Cry1C or Cry2A proteins; the effect observed in the first experiment was likely attributable to unknown differences in the nutritional composition of Bt rice pollen. Overall, the data indicate that the growing of Cry1C- or Cry2A-transgenic rice should pose a negligible risk to P. japonica.

  4. Consumption of Bt rice pollen containing Cry1C or Cry2A does not pose a risk to Propylea japonica (Thunberg) (Coleoptera: Coccinellidae).

    PubMed

    Li, Yunhe; Zhang, Xiaojie; Chen, Xiuping; Romeis, Jörg; Yin, Xinming; Peng, Yufa

    2015-01-01

    As a pollen feeder, Propylea japonica would be directly exposed to Cry proteins in Bacillus thuringiensis (Bt)-transgenic rice fields. The effect of Cry1C- or Cry2A-containing transgenic rice pollen on the fitness of P. japonica was assessed using two dietary-exposure experiments in the laboratory. In the first experiment, larval developmental time of P. japonica was significantly longer when fed pollen from Bt rice lines rather than control pollen but other life table parameters were not significantly affected. In the second experiment, P. japonica was not affected when fed a rapeseed pollen-based diet containing purified Cry1C or Cry2A at concentrations that were >10-times higher than in pollen, but P. japonica was affected when the diet contained E-64 as a positive control. In both experiments, the stability and bioactivity of the Cry proteins in the food sources and the uptake of the proteins by P. japonica were confirmed. The results show that P. japonica is not sensitive to Cry1C or Cry2A proteins; the effect observed in the first experiment was likely attributable to unknown differences in the nutritional composition of Bt rice pollen. Overall, the data indicate that the growing of Cry1C- or Cry2A-transgenic rice should pose a negligible risk to P. japonica. PMID:25567127

  5. Consumption of Bt rice pollen containing Cry1C or Cry2A does not pose a risk to Propylea japonica (Thunberg) (Coleoptera: Coccinellidae)

    PubMed Central

    Li, Yunhe; Zhang, Xiaojie; Chen, Xiuping; Romeis, Jörg; Yin, Xinming; Peng, Yufa

    2015-01-01

    As a pollen feeder, Propylea japonica would be directly exposed to Cry proteins in Bacillus thuringiensis (Bt)-transgenic rice fields. The effect of Cry1C- or Cry2A-containing transgenic rice pollen on the fitness of P. japonica was assessed using two dietary-exposure experiments in the laboratory. In the first experiment, larval developmental time of P. japonica was significantly longer when fed pollen from Bt rice lines rather than control pollen but other life table parameters were not significantly affected. In the second experiment, P. japonica was not affected when fed a rapeseed pollen-based diet containing purified Cry1C or Cry2A at concentrations that were >10-times higher than in pollen, but P. japonica was affected when the diet contained E-64 as a positive control. In both experiments, the stability and bioactivity of the Cry proteins in the food sources and the uptake of the proteins by P. japonica were confirmed. The results show that P. japonica is not sensitive to Cry1C or Cry2A proteins; the effect observed in the first experiment was likely attributable to unknown differences in the nutritional composition of Bt rice pollen. Overall, the data indicate that the growing of Cry1C- or Cry2A-transgenic rice should pose a negligible risk to P. japonica. PMID:25567127

  6. Water management affects arsenic and cadmium accumulation in different rice cultivars.

    PubMed

    Hu, Pengjie; Huang, Jiexue; Ouyang, Younan; Wu, Longhua; Song, Jing; Wang, Songfeng; Li, Zhu; Han, Cunliang; Zhou, Liqiang; Huang, Yujuan; Luo, Yongming; Christie, Peter

    2013-12-01

    Paddy rice (Oryza sativa L.) is a staple food and one of the major sources of dietary arsenic (As) and cadmium (Cd) in Asia. A field experiment was conducted to investigate the effects of four water management regimes (aerobic, intermittent irrigation, conventional irrigation and flooding) on As and Cd accumulation in seven major rice cultivars grown in Zhejiang province, east China. With increasing irrigation from aerobic to flooded conditions, the soil HCl-extractable As concentrations increased significantly and the HCl-extractable Cd concentrations decreased significantly. These trends were consistent with the As and Cd concentrations in the straw, husk and brown rice. Water management both before and after the full tillering stage affected As and Cd accumulation in the grains. The intermittent and conventional treatments produced higher grain yields than the aerobic and flooded treatments. Cd concentrations in brown rice varied 13.1-40.8 times and As varied 1.75-8.80 times among the four water management regimes. Cd and As accumulation in brown rice varied among the rice cultivars, with Guodao 6 (GD6) was a low Cd but high-As-accumulating cultivar while Indonesia (IR) and Yongyou 9 (YY9) were low As but high-Cd-accumulating cultivars. Brown rice Cd and As concentrations in the 7 cultivars were significantly negatively correlated. The results indicate that As and Cd accumulated in rice grains with opposite trends that were influenced by both water management and rice cultivar. Production of 'safe' rice with respect to As and Cd might be possible by balancing water management and rice cultivar according to the severity of soil pollution. PMID:23719663

  7. Evidence for divergence of response in Indica, Japonica, and wild rice to high CO2 x temperature interaction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Evaluating variability of rice response to concurrent increases in CO2 and temperature forecasted for future climates is a prerequisite step towards characterizing the genetic architecture underlying this response. Expanding on previous single cultivar studies, we evaluated eleven biogeographically ...

  8. Phytochemical content, antioxidants and cell wall metabolism of two loquat (Eriobotrya japonica) cultivars under different storage regimes.

    PubMed

    Goulas, V; Minas, I S; Kourdoulas, P M; Vicente, A R; Manganaris, G A

    2014-07-15

    Changes in quality, phytochemical content and cell wall metabolism of two loquat cultivars (Eriobotrya japonica cvs. 'Morphitiki', 'Karantoki') under different storage regimes were studied. The fruit were harvested at commercial maturity stage and analyzed after 1, 3, 5, 7, and 11 days maintenance at room temperature (RT, ∼ 20°C) or after cold storage (14 days at 4°C) and additional ripening at RT for 1, 3 and 5 days, respectively. Compositional analysis revealed substantial cultivar differences; the 'Morphitiki' fruit was more acidic and showed higher contents of total phenolics, flavonoids and hydroxycinnamic acid-derivatives as well as greater antioxidant potency. Although firmness did not change markedly during storage, the cell wall exhibited extensive remodeling. Greater changes were observed in the pectin backbones than in polyuronide side chains and cross-linking glycans. Polygalacturonase (PG) showed better association with cell wall solubilization at RT than the enzymes involved in arabinan or galactan disassembly. During postharvest ripening after harvest, 'Karantoki' showed more extensive pectin solubilization than 'Morphitiki'. Interestingly, cold storage inhibited the cell wall disassembly in 'Karantoki' but not in 'Morphitiki', suggesting that the cultivars may differ in their susceptibility to chilling-related wall disorders. Low temperature-induced alterations in wall disassembly may impact juice and phytochemical release upon consumption.

  9. Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses

    PubMed Central

    Shankar, Rama; Bhattacharjee, Annapurna; Jain, Mukesh

    2016-01-01

    Drought and salinity are the major environmental factors that affect rice productivity. Comparative transcriptome analysis between tolerant and sensitive rice cultivars can provide insights into the regulatory mechanisms involved in these stress responses. In this study, the comparison of transcriptomes of a drought-tolerant [Nagina 22 (N22)] and a salinity-tolerant (Pokkali) rice cultivar with IR64 (susceptible cultivar) revealed variable transcriptional responses under control and stress conditions. A total of 801 and 507 transcripts were exclusively differentially expressed in N22 and Pokkali rice cultivars, respectively, under stress conditions. Gene ontology analysis suggested the enrichment of transcripts involved in response to abiotic stress and regulation of gene expression in stress-tolerant rice cultivars. A larger number of transcripts encoding for members of NAC and DBP transcription factor (TF) families in N22 and members of bHLH and C2H2 TF families in Pokkali exhibited differential regulation under desiccation and salinity stresses, respectively. Transcripts encoding for thioredoxin and involved in phenylpropanoid metabolism were up-regulated in N22, whereas transcripts involved in wax and terpenoid metabolism were up-regulated in Pokkali. Overall, common and cultivar-specific stress-responsive transcripts identified in this study can serve as a helpful resource to explore novel candidate genes for abiotic stress tolerance in rice. PMID:27029818

  10. Seasonal methane and nitrous oxide emissions of several rice cultivars in direct-seeded systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding cultivar effects on field greenhouse gas (GHG) emissions in rice (Oryza sativa L.) systems is needed to improve the accuracy of predictive models used for estimating GHG emissions and determine to what extent choice of cultivar may have on GHG mitigation. We compared methane (CH4) and...

  11. Effect of nitrogen rate and the environment on physicochemical properties of selected high amylose rice cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic marker haplotypes for the Waxy and alk genes are associated with amylose content and gelatinization temperature, respectively, and are used by breeders to develop rice cultivars that have physicochemical properties desired by the parboiling and canning industries. Cultivars that provide cons...

  12. Use of SSR markers to discern reciprocal outcrossing rates between weedy red rice types and rice cultivars having different degrees of flowering synchronization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A broad range of flowering synchronization between red rice and rice was established by planting rice cultivars that flowered earlier, similar to, or later than red rice. Five SSR markers were used to identify hybrids. Outcrossing rates differed greatly depending on the degree of synchronization a...

  13. Evidence for divergence of response in Indica, Japonica, and wild rice to high CO2 × temperature interaction.

    PubMed

    Wang, Diane R; Bunce, James A; Tomecek, Martha B; Gealy, David; McClung, Anna; McCouch, Susan R; Ziska, Lewis H

    2016-07-01

    High CO2 and high temperature have an antagonistic interaction effect on rice yield potential and present a unique challenge to adapting rice to projected future climates. Understanding how the differences in response to these two abiotic variables are partitioned across rice germplasm accessions may be key to identifying potentially useful sources of resilient alleles for adapting rice to climate change. In this study, we evaluated eleven globally diverse rice accessions under controlled conditions at two carbon dioxide concentrations (400 and 600 ppm) and four temperature environments (29 °C day/21 °C night; 29 °C day/21 °C night with additional heat stress at anthesis; 34 °C day/26 °C night; and 34 °C day/26 °C night with additional heat stress at anthesis) for a suite of traits including five yield components, five growth characteristics, one phenological trait, and four photosynthesis-related measurements. Multivariate analyses of mean trait data from these eight treatments divide our rice panel into two primary groups consistent with the genetic classification of INDICA/INDICA-like and JAPONICA populations. Overall, we find that the productivity of plants grown under elevated [CO2 ] was more sensitive (negative response) to high temperature stress compared with that of plants grown under ambient [CO2 ] across this diversity panel. We report differential response to CO2 × temperature interaction for INDICA/INDICA-like and JAPONICA rice accessions and find preliminary evidence for the beneficial introduction of exotic alleles into cultivated rice genomic background. Overall, these results support the idea of using wild or currently unadapted gene pools in rice to enhance breeding efforts to secure future climate change adaptation.

  14. Agronomic potential of southern rice cultivars under organic management

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Organic rice production is expanding in the United States as a result of increasing market demand. Although acreage of conventional produced rice has declined in Texas over the last twenty years, organic rice production has increased to almost ten percent of the Texas rice acreage. Organic growers ...

  15. Heat-tolerant rice cultivars retain grain appearance quality under free-air CO2 enrichment

    PubMed Central

    2014-01-01

    Background Heat-tolerant rice cultivars have been developed as a countermeasure to poor grain appearance quality under high temperatures. Recent studies showed that elevated CO2 concentrations (E-[CO2]) also reduce grain quality. To determine whether heat-tolerant cultivars also tolerate E-[CO2], we conducted a free-air CO2 enrichment (FACE) experiment with 12 rice cultivars differing in heat tolerance. Results The percentage of undamaged grains of five standard cultivars (Akitakomachi, Kinuhikari, Koshihikari, Matsuribare, Nipponbare) averaged 61.7% in the ambient [CO2] (AMB) plot and 51.7% in the FACE plot, whereas that of heat-tolerant cultivars (Eminokizuna, Wa2398, Kanto 257, Toyama 80, Mineharuka, Kanto 259, Saikai 290) averaged 73.5% in AMB and 71.3% in FACE. This resulted in a significant [CO2] by cultivar interaction. The percentage of white-base or white-back grains increased from 8.4% in AMB to 17.1% in FACE in the sensitive cultivars, but from only 2.1% in AMB to only 4.4% in FACE in the heat-tolerant cultivars. Conclusion Heat-tolerant cultivars retained their grain appearance quality at E-[CO2] under present air temperatures. Further improvements in appearance quality under present conditions will be needed to achieve improvements under E-[CO2], because E-[CO2] will likely lower the threshold temperature for heat stress. PMID:24920972

  16. Arsenic accumulation and phosphorus status in two rice (Oryza sativa L.) cultivars surveyed from fields in South China.

    PubMed

    Lu, Ying; Dong, Fei; Deacon, Claire; Chen, Huo-Jun; Raab, Andrea; Meharg, Andrew A

    2010-05-01

    The consumption of paddy rice (Oryza sativa L.) is a major inorganic arsenic exposure pathway in S.E. Asia. A multi-location survey was undertaken in Guangdong Province, South China to assess arsenic accumulation and speciation in 2 rice cultivars, one an Indica and the other a hybrid Indica. The results showed that arsenic concentrations in rice tissue increased in the order grain < husk < straw < root. Rice grain arsenic content of 2 rice cultivars was significant different and correlated with phosphorus concentration and molar ratio of P/As in shoot, being higher for the Indica cultivar than for the hybrid Indica, which suggests altering shoot phosphorus status as a promising route for breeding rice cultivars with reduced grain arsenic. Speciation of grain arsenic, performed using HPLC-ICP-MS, identified inorganic arsenic as the dominant arsenic species present in the rice grain. PMID:20045585

  17. Variation of As concentration between soil types and rice genotypes and the selection of cultivars for reducing As in the diet.

    PubMed

    Ye, X X; Sun, B; Yin, Y L

    2012-04-01

    Human exposure to toxic heavy metals via the food chain is of increasing concern. In the present study, the effects of soil type and genotype on variation in arsenic (As) concentrations of different organs were investigated by using nine rice cultivars grown in two soils, with two levels of As contamination. There were significant genotypic differences (P<0.05) in As concentrations of all organs, and As concentrations of polished grain were significantly affected by genotype and soil type. The As concentration in polished grain was higher in red paddy soil under As treatment, with range from 0.24 to 1.03 mg kg(-1), and the As concentration of three cultivars exceeded the concentration of Chinese Food Hygiene Standard (0.7 mg kg(-1)). The As concentrations in stems, leaves and polished grain were all significantly and positively correlated. The As concentrations in polished grain were positively and significantly (P<0.01) correlated with As root-grain translocation factor. The results indicated that As concentration in grain was partially governed by As uptake and the transfer of As from root to grain. The grain As concentration of the nine cultivars was significantly correlated between the two soil types at different levels of As contamination. Some genotypes, such as japonica rice (e.g. Ning jing 1 and Nan jing 32) had consistently low grain As concentrations. The results suggest the possibility of breeding the As rice cultivars to produce grain for safe consumption from soils with slight and moderate levels of As. PMID:22221666

  18. A Relative Resistance Ratio for Evaluation of Mexican Rice Borer (Lepidoptera: Crambidae) Susceptibility Among Sugarcane Cultivars.

    PubMed

    Wilson, Blake E; VanWeelden, Matthew T; Beuzelin, Julien M; Reagan, Thomas E; Way, Michael O; White, William H; Wilson, Lloyd T; Showler, Allan T

    2015-06-01

    The Mexican rice borer, Eoreuma loftini (Dyar), is a major pest of sugarcane (hybrids of Saccharum spp.) in Louisiana and Texas. Resistance to E. loftini was evaluated in 51 commercial and experimental cultivars of sugarcane, energycane (hybrids of Saccharum spp.), and sorghum [Sorghum bicolor (L.) Moench and hybrids of Sorghum spp.] in four replicated small plot field experiments from 2009 to 2012. A relative resistance ratio was developed to compare levels of susceptibility among cultivars based on the percentage of bored internodes and survival to adulthood. This index was able to separate cultivars into five resistance categories and provides a new method for comparing levels of resistance among cultivars. E. loftini pest pressure in 2009 was among the highest recorded with injury ranging from 55 to 88% bored internodes. Commercial sugarcane cultivar HoCP 85-845 was identified as resistant in three of four experiments, whereas HoCP 04-838 was identified as susceptible in all experiments. Of the five sugarcane cultivars in commercial production in the Rio Grande Valley of Texas, only TCP 87-3388 was categorized as resistant. Of the cultivars with potential for bioenergy production, all of the energycane cultivars demonstrated higher levels of resistance than high-biomass and sweet sorghum cultivars. Continued evaluation of cultivar resistance to E. loftini is important to development of effective integrated pest management strategies for this pest. PMID:26470265

  19. A Relative Resistance Ratio for Evaluation of Mexican Rice Borer (Lepidoptera: Crambidae) Susceptibility Among Sugarcane Cultivars.

    PubMed

    Wilson, Blake E; VanWeelden, Matthew T; Beuzelin, Julien M; Reagan, Thomas E; Way, Michael O; White, William H; Wilson, Lloyd T; Showler, Allan T

    2015-06-01

    The Mexican rice borer, Eoreuma loftini (Dyar), is a major pest of sugarcane (hybrids of Saccharum spp.) in Louisiana and Texas. Resistance to E. loftini was evaluated in 51 commercial and experimental cultivars of sugarcane, energycane (hybrids of Saccharum spp.), and sorghum [Sorghum bicolor (L.) Moench and hybrids of Sorghum spp.] in four replicated small plot field experiments from 2009 to 2012. A relative resistance ratio was developed to compare levels of susceptibility among cultivars based on the percentage of bored internodes and survival to adulthood. This index was able to separate cultivars into five resistance categories and provides a new method for comparing levels of resistance among cultivars. E. loftini pest pressure in 2009 was among the highest recorded with injury ranging from 55 to 88% bored internodes. Commercial sugarcane cultivar HoCP 85-845 was identified as resistant in three of four experiments, whereas HoCP 04-838 was identified as susceptible in all experiments. Of the five sugarcane cultivars in commercial production in the Rio Grande Valley of Texas, only TCP 87-3388 was categorized as resistant. Of the cultivars with potential for bioenergy production, all of the energycane cultivars demonstrated higher levels of resistance than high-biomass and sweet sorghum cultivars. Continued evaluation of cultivar resistance to E. loftini is important to development of effective integrated pest management strategies for this pest.

  20. Genome-Wide Association Mapping of Root Traits in a Japonica Rice Panel

    PubMed Central

    Courtois, Brigitte; Audebert, Alain; Dardou, Audrey; Roques, Sandrine; Ghneim- Herrera, Thaura; Droc, Gaëtan; Frouin, Julien; Rouan, Lauriane; Gozé, Eric; Kilian, Andrzej; Ahmadi, Nourollah; Dingkuhn, Michael

    2013-01-01

    Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r2>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates. PMID:24223758

  1. Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellites.

    PubMed

    Gao, Li-Zhi; Innan, Hideki

    2008-06-01

    The origins of the Asian cultivated rice Oryza sativa from its wild ancestor O. rufipogon have been debated for decades. The question mainly concerns whether it originated monophyletically or polyphyletically. To shed light on the origins and demographic history of rice domestication, we genotyped a total of 92 individual plants from the two O. sativa subspecies and O. rufipogon for 60 microsatellites. An approximate Bayesian method was applied to estimate demographic parameters for O. rufipogon vs. O. sativa ssp. indica and O. rufipogon vs. O. sativa ssp. japonica. We showed that the japonica subspecies suffered a more severe bottleneck than the indica subspecies and thus a greater loss of genetic variation during its domestication. Across microsatellite loci there is a significant positive correlation in the reduction of genetic diversity between the two subspecies. The results suggest that completely independent domestication of indica and japonica subspecies may not explain our data and that there is at least partial sharing of their ancestral populations and/or recent gene flow between them. PMID:18505887

  2. Retrogenes in Rice (Oryza sativa L. ssp. japonica) Exhibit Correlated Expression with Their Source Genes

    PubMed Central

    Sakai, Hiroaki; Mizuno, Hiroshi; Kawahara, Yoshihiro; Wakimoto, Hironobu; Ikawa, Hiroshi; Kawahigashi, Hiroyuki; Kanamori, Hiroyuki; Matsumoto, Takashi; Itoh, Takeshi; Gaut, Brandon S.

    2011-01-01

    Gene duplication occurs by either DNA- or RNA-based processes; the latter duplicates single genes via retroposition of messenger RNA. The expression of a retroposed gene copy (retrocopy) is expected to be uncorrelated with its source gene because upstream promoter regions are usually not part of the retroposition process. In contrast, DNA-based duplication often encompasses both the coding and the intergenic (promoter) regions; hence, expression is often correlated, at least initially, between DNA-based duplicates. In this study, we identified 150 retrocopies in rice (Oryza sativa L. ssp japonica), most of which represent ancient retroposition events. We measured their expression from high-throughput RNA sequencing (RNAseq) data generated from seven tissues. At least 66% of the retrocopies were expressed but at lower levels than their source genes. However, the tissue specificity of retrogenes was similar to their source genes, and expression between retrocopies and source genes was correlated across tissues. The level of correlation was similar between RNA- and DNA-based duplicates, and they decreased over time at statistically indistinguishable rates. We extended these observations to previously identified retrocopies in Arabidopsis thaliana, suggesting they may be general features of the process of retention of plant retrogenes. PMID:22042334

  3. Growth characteristics of a weed-suppressive indica x non-suppressive tropical japonica rice mapping population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The indica rice cultivar, PI 312777, can be highly productive as well as suppressive to C4 grass species such as barnyardgrass (Echinochloa crus-galli). A recombinant inbred line (RIL) mapping population was developed using single seed descent from a cross between ‘Katy’ (non-weed-suppressive) and ...

  4. Low uptake affinity cultivars with biochar to tackle Cd-tainted rice--A field study over four rice seasons in Hunan, China.

    PubMed

    Chen, De; Guo, Hu; Li, Ruiyue; Li, Lianqing; Pan, Genxing; Chang, Andrew; Joseph, Stephen

    2016-01-15

    Biochar is becoming an environmentally friendly material for remediation of heavy metal contaminated soils and improving food safety. A field trial over four rice seasons was conducted to investigate the use of biochar and low Cd accumulating cultivars on Cd uptake in a heavy metal contaminated soil. Wheat straw derived biochar was applied at 0, 20 and 40 t ha(-1). Two rice cultivars with differing Cd accumulation abilities were selected in each season. The results showed that both biochar and low Cd affinity cultivars significantly reduced rice grain Cd accumulation. Biochar had no significant effect the first season but thereafter consistently reduced rice grain Cd by a maximum of 61, 86 and 57% over the next three seasons. Zn accumulation in the rice grains was not decreased by biochar application, although available soil Zn was sharply reduced (35-91%). Indica conventional rice cultivars had much lower Cd, but higher Zn and lower Cd/Zn ratios in the grain than indica hybrid cultivars. Biochar was more effective for mitigating grain Cd accumulation in low Cd affinity cultivars than in high affinity cultivars. Soil pH was sustainably increased (up to nearly 1 unit) while available Cd significantly decreased by a maximum of 85% after biochar addition. The translocation of Cd from rice roots to shoots was reduced from 20 to 80% by biochar. Low uptake affinity cultivars combined with biochar reduced late rice grain Cd concentration and Cd/Zn ratios by 69-80% and 72-80%, respectively. It indicated that the management of combining biochar and low Cd affinity cultivars should be an efficient way to remediate Cd contaminated rice paddies and reduce health risk associated with consuming rice from these soils.

  5. Physiological and biochemical parameters for evaluation and clustering of rice cultivars differing in salt tolerance at seedling stage.

    PubMed

    Chunthaburee, Sumitahnun; Dongsansuk, Anoma; Sanitchon, Jirawat; Pattanagul, Wattana; Theerakulpisut, Piyada

    2016-07-01

    Salinity tolerance levels and physiological changes were evaluated for twelve rice cultivars, including four white rice and eight black glutinous rice cultivars, during their seedling stage in response to salinity stress at 100 mM NaCl. All the rice cultivars evaluated showed an apparent decrease in growth characteristics and chlorophyll accumulation under salinity stress. By contrast an increase in proline, hydrogen peroxide, peroxidase (POX) activity and anthocyanins were observed for all cultivars. The K(+)/Na(+) ratios evaluated for all rice cultivars were noted to be highly correlated with the salinity scores thus indicating that the K(+)/Na(+) ratio serves as a reliable indicator of salt stress tolerance in rice. Principal component analysis (PCA) based on physiological salt tolerance indexes could clearly distinguish rice cultivars into 4 salt tolerance clusters. Noteworthy, in comparison to the salt-sensitive ones, rice cultivars that possessed higher degrees of salt tolerance displayed more enhanced activity of catalase (CAT), a smaller increase in anthocyanin, hydrogen peroxide and proline content but a smaller drop in the K(+)/Na(+) ratio and chlorophyll accumulation. PMID:27298579

  6. Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia.

    PubMed

    Song, Beng-Kah; Chuah, Tse-Seng; Tam, Sheh May; Olsen, Kenneth M

    2014-10-01

    Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild-to-weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed-shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations.

  7. The assessment of the rice cultivars/lines resistance to blast disease in Mazandaran province, Iran.

    PubMed

    Amanzadeh, M; Okhovvat, S M; Moumeni, A; Javan-Nikkhah, M; Khosravi, V

    2004-01-01

    Blast, caused by Magnaporthe grisea, is one of the most important diseases in rice production regions of the world including Iran. To determine progress of rice blast disease on the selective cultivars and lines also to assay some components of partial resistance, a set of Iranian rice cultivars (Local and breeding) along with near-isogenic lines (NILs) and breeding lines from International Rice Research Institute (IRRI) were tested with some field races of the fungus in blast nursery and five of selective races in greenhouse. These experiments were conducted in a Randomized complete Block Design (RCBD) with three replications (except greenhouse experiment on the leaves). Traits in this study consisted of Infection Neck Number (INN), Neck Lesion Size (NLS), Infection Type (IT), percent Diseased Leaf Area (DLA) and Area Under Disease Progress Curve (AUDPC); also IT, Sporulation Lesion Number (SLN), Sporulating Region Diameter (SRD) and percent DLA were measured in leaf blast in greenhouse (one replication). The Iranian local cultivars and NILs i.e. Co-39 and C104-PKT located as susceptible group for AUDPC, IT, INN and NLS. Iranian breeding cultivars, breeding lines from IRRI and NILs (except Co-39 and C104-PKT) were resistant or indicated hypersensivity reaction (HR). Some cultivars (Fujiminori, Onda, and Hassan Saraii) were semi susceptible to leaf blast in nursery. The main point is correlation in 1% (a = 0.0001) between the traits in greenhouse and blast nursery. Neck node infection of Haraz cultivar in greenhouse experiment to IA-89 race is very important, because Haraz is a resistant cultivar to blast disease in Iran. PMID:15756856

  8. Physiological and Biochemical Mechanisms of Seed Priming-Induced Chilling Tolerance in Rice Cultivars

    PubMed Central

    Hussain, Saddam; Khan, Fahad; Hussain, Hafiz A.; Nie, Lixiao

    2016-01-01

    Rice belongs to tropical and subtropical environments and is extremely sensitive to chilling stress particularly during emergence and early stages of seedling development. Seed priming can be a good approach to enhance rice germination and stand establishment under chilling stress. The present study examined the role of different seed priming techniques viz., hydropriming, osmopriming, redox priming, chemical priming, and hormonal priming, in enhancing the chilling tolerance in rice. The most effective reagents and their pre-optimized concentrations based on preliminary experiments were used in this study. Two different rice cultivars were sown under chilling stress (18°C) and normal temperatures (28°C) in separate growth chambers. A non-primed control treatment was also maintained for comparison. Chilling stress caused erratic and delayed germination, poor seedling growth, reduced starch metabolism, and lower respiration rate, while higher lipid peroxidation and hydrogen peroxide accumulation in rice seedlings of both cultivars. Nevertheless, all the seed priming treatments effectively alleviated the negative effects of chilling stress. In addition, seed priming treatments triggered the activities of superoxide dismutase, peroxidase, and catalase, and enhanced the accumulations of glutathione and free proline in rice seedlings, which suggests that these measures help prevent the rice seedlings from chilling induced oxidative stress. Chemical priming with selenium and hormonal priming with salicylic acid remained more effective treatments for both rice cultivars under chilling stress than all other priming treatments. The better performance and greater tolerance of primed rice seedlings was associated with enhanced starch metabolism, high respiration rate, lower lipid peroxidation, and strong antioxidative defense system under chilling stress. PMID:26904078

  9. Physiological and Biochemical Mechanisms of Seed Priming-Induced Chilling Tolerance in Rice Cultivars.

    PubMed

    Hussain, Saddam; Khan, Fahad; Hussain, Hafiz A; Nie, Lixiao

    2016-01-01

    Rice belongs to tropical and subtropical environments and is extremely sensitive to chilling stress particularly during emergence and early stages of seedling development. Seed priming can be a good approach to enhance rice germination and stand establishment under chilling stress. The present study examined the role of different seed priming techniques viz., hydropriming, osmopriming, redox priming, chemical priming, and hormonal priming, in enhancing the chilling tolerance in rice. The most effective reagents and their pre-optimized concentrations based on preliminary experiments were used in this study. Two different rice cultivars were sown under chilling stress (18°C) and normal temperatures (28°C) in separate growth chambers. A non-primed control treatment was also maintained for comparison. Chilling stress caused erratic and delayed germination, poor seedling growth, reduced starch metabolism, and lower respiration rate, while higher lipid peroxidation and hydrogen peroxide accumulation in rice seedlings of both cultivars. Nevertheless, all the seed priming treatments effectively alleviated the negative effects of chilling stress. In addition, seed priming treatments triggered the activities of superoxide dismutase, peroxidase, and catalase, and enhanced the accumulations of glutathione and free proline in rice seedlings, which suggests that these measures help prevent the rice seedlings from chilling induced oxidative stress. Chemical priming with selenium and hormonal priming with salicylic acid remained more effective treatments for both rice cultivars under chilling stress than all other priming treatments. The better performance and greater tolerance of primed rice seedlings was associated with enhanced starch metabolism, high respiration rate, lower lipid peroxidation, and strong antioxidative defense system under chilling stress.

  10. Differential morphological, cytological and biochemical responses of two rice cultivars to coumarin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plants are often exposed to allelochemicals in the environment produced by neighboring plants. Coumarin is a common allelochemical produced by many higher plants. Two cultivars (susceptible BS-2000 and less susceptible BR-41) of rice (Oryza sativa L.) were selected to compare their differential root...

  11. Understanding salinity responses and adopting 'omics-based' approaches to generate salinity tolerant cultivars of rice.

    PubMed

    Das, Priyanka; Nutan, Kamlesh K; Singla-Pareek, Sneh L; Pareek, Ashwani

    2015-01-01

    Soil salinity is one of the main constraints affecting production of rice worldwide, by reducing growth, pollen viability as well as yield of the plant. Therefore, detailed understanding of the response of rice towards soil salinity at the physiological and molecular level is a prerequisite for its effective management. Various approaches have been adopted by molecular biologists or breeders to understand the mechanism for salinity tolerance in plants and to develop salt tolerant rice cultivars. Genome wide analysis using 'omics-based' tools followed by identification and functional validation of individual genes is becoming one of the popular approaches to tackle this task. On the other hand, mutation breeding and insertional mutagenesis has also been exploited to obtain salinity tolerant crop plants. This review looks into various responses at cellular and whole plant level generated in rice plants toward salinity stress thus, evaluating the suitability of intervention of functional genomics to raise stress tolerant plants. We have tried to highlight the usefulness of the contemporary 'omics-based' approaches such as genomics, proteomics, transcriptomics and phenomics towards dissecting out the salinity tolerance trait in rice. In addition, we have highlighted the importance of integration of various 'omics' approaches to develop an understanding of the machinery involved in salinity response in rice and to move forward to develop salt tolerant cultivars of rice. PMID:26442026

  12. High-quality Italian rice cultivars: chemical indices of ageing and aroma quality.

    PubMed

    Griglione, Alessandra; Liberto, Erica; Cordero, Chiara; Bressanello, Davide; Cagliero, Cecilia; Rubiolo, Patrizia; Bicchi, Carlo; Sgorbini, Barbara

    2015-04-01

    The volatile fractions of six Italian high-quality rice cultivars were investigated by HS-SPME-GC-MS to define fingerprinting and identify chemical markers and/or indices of ageing and aroma quality. In particular, four non-aromatic (Carnaroli, Carnise, Cerere and Antares) and two aromatic (Apollo and Venere) rices, harvested in 2010 and 2011, were monitored over 12months. Twenty-five aroma components were considered and, despite considerable inter-annual variability, some of them showed similar trends over time, including 2-(E)-octenal as a marker of ageing for all cultivars, and heptanal, octanal and 2-ethyl hexanol as cultivar-specific indicators. The area ratios 2-acetyl-1-pyrroline/1-octen-3-ol, for Venere, and 3-methyl-1-butanol/2-methyl-1-butanol, for Apollo, were also found to act as ageing indices. Additional information on release of key-aroma compounds was also obtained from quantitation and its dependence on grain shape and chemical composition. Heptanal/1-octen-3-ol and heptanal/octanal ratios were also defined as characterising the aroma quality indices of the six Italian rice cultivars investigated.

  13. Nutritionally important starch fractions of rice cultivars grown in southern United States.

    PubMed

    Patindol, James A; Guraya, Harmeet S; Champagne, Elaine T; McClung, Anna M

    2010-06-01

    Dietary starches can be classified into 3 major fractions according to in vitro digestibility as rapidly digestible (RDS), slowly digestible (SDS), and resistant starch (RS). Literature indicates that SDS and/or RS have significant implications on human health, particularly glucose metabolism, diabetes management, colon cancer prevention, mental performance, and satiety. In this study, the nutritionally important starch fractions (RDS, SDS, and RS) in cooked rice were assayed in vitro, making use of 16 cultivars grown in 5 southern U.S. rice growing locations (Arkansas, Louisiana, Mississippi, Missouri, and Texas). RDS, SDS, and RS were 52.4% to 69.4%, 10.3% to 26.6%, and 1.2% to 9.0%, respectively, of cooked rice dry weight. Cultivar, location, and cultivar-by-location interaction contributed to the variations in RDS, SDS, and RS contents. Means pooled across locations indicated that SDS was higher for the Louisiana samples than those from Texas, whereas RS was higher for the Texas samples than those from Arkansas, Louisiana, and Mississippi. Some cultivars were identified to possess high levels of RS (for example, Bowman and Rondo) or SDS (for example, Dixiebelle and Tesanai-2) and were also stable across growing locations. Apparent amylose content correlated positively with RS (n = 80, r = 0.54, P 0.05). RS and SDS were not collinear (n = 80, r =or-0.18, P > 0.05); it does not follow that a cultivar high in RS will also be high in SDS, and vice versa. The observed differences in RDS, SDS, and RS among the samples are indicative of wide genetic diversity in rice.

  14. Root Morphology Was Improved in a Late-Stage Vigor Super Rice Cultivar

    PubMed Central

    Huang, Min; Chen, Jiana; Cao, Fangbo; Jiang, Ligeng; Zou, Yingbin

    2015-01-01

    This study aimed to test the hypothesis that root morphology might be improved and consequently contributing to superior post-heading shoot growth and grain yield in late-stage vigor super rice. A pot experiment was carried out to compare yield attributes, shoot growth and physiological properties and root morphological traits between a late-stage vigor super rice cultivar (Y-liangyou 087) and an elite rice cultivar (Teyou 838). Grain yield and total shoot biomass were 7–9% higher in Y-liangyou 087 than in Teyou 838. Y-liangyou 087 had 60–64% higher post-heading shoot growth rate and biomass production than Teyou 838. Average relative chlorophyll concentration and net photosynthetic rate in flag leaves were 7–11% higher in Y-liangyou 087 than in Teyou 838 during heading to 25 days after heading. Y-liangyou 087 had 41% higher post-heading shoot N uptake but 17–25% lower root biomass and root-shoot ratio at heading and maturity than Teyou 838. Specific root length and length and surface area of fine roots were higher in Y-liangyou 087 than in Teyou 838 at heading and maturity by more than 15%. These results indicated that root-shoot relationships were well balanced during post-heading phase in the late-stage vigor super rice cultivar Y-liangyou 087 by improving root morphology including avoiding a too great root biomass and developing a large fine root system. PMID:26566229

  15. Classification of rice (oryza sativa l. japonica nipponbare) immunophilins (fkbps, cyps) and expression patterns under water stress

    PubMed Central

    2010-01-01

    Background FK506 binding proteins (FKBPs) and cyclophilins (CYPs) are abundant and ubiquitous proteins belonging to the peptidyl-prolyl cis/trans isomerase (PPIase) superfamily, which regulate much of metabolism through a chaperone or an isomerization of proline residues during protein folding. They are collectively referred to as immunophilin (IMM), being present in almost all cellular organs. In particular, a number of IMMs relate to environmental stresses. Results FKBP and CYP proteins in rice (Oryza sativa cv. Japonica) were identified and classified, and given the appropriate name for each IMM, considering the ortholog-relation with Arabidopsis and Chlamydomonas or molecular weight of the proteins. 29 FKBP and 27 CYP genes can putatively be identified in rice; among them, a number of genes can be putatively classified as orthologs of Arabidopsis IMMs. However, some genes were novel, did not match with those of Arabidopsis and Chlamydomonas, and several genes were paralogs by genetic duplication. Among 56 IMMs in rice, a significant number are regulated by salt and/or desiccation stress. In addition, their expression levels responding to the water-stress have been analyzed in different tissues, and some subcellular IMMs located by means of tagging with GFP protein. Conclusion Like other green photosynthetic organisms such as Arabidopsis (23 FKBPs and 29 CYPs) and Chlamydomonas (23 FKBs and 26 CYNs), rice has the highest number of IMM genes among organisms reported so far, suggesting that the numbers relate closely to photosynthesis. Classification of the putative FKBPs and CYPs in rice provides the information about their evolutional/functional significance when comparisons are drawn with the relatively well studied genera, Arabidopsis and Chlamydomonas. In addition, many of the genes upregulated by water stress offer the possibility of manipulating the stress responses in rice. PMID:21087465

  16. Novel method for preparation of the template DNA and selection of primers to differentiate the material rice cultivars of rice wine by PCR.

    PubMed

    Ohtsubo, Ken'ichi; Suzuki, Keitaro; Haraguchi, Kazutomo; Nakamura, Sumiko

    2008-04-24

    As many rice wine brewers label the name of the cultivar of the material rice, authentication technology is necessary. The problems are (1) decomposition of DNAs during the fermentation, (2) contamination of DNAs from microorganisms, (3) co-existence of PCR inhibitors, such as polyphenols. The present authors improved the PCR method by (1) lyophilizing and pulverizing the rice wine to concentrate DNAs, (2) decomposition of starches and proteins so as not to inhibit DNA extraction by the use of heat-resistant amylase and proteinase K, (3) purification of the template DNA by the combination of CTAB method and fractional precipitation by 70% EtOH. To prevent the amplification of microorganism's DNAs during PCR, the present authors selected the suitable plant-specific primers. It became possible to prepare the template DNAs for PCR from the rice wine. The sequences of the amplified DNAs by PCR were ascertained to be same with those of material rice. Mislabeling of material rice cultivar was detected by PCR using the commercial rice wine. It became possible to extract and purify the template DNAs for PCR from the rice wine and to differentiate the material rice cultivars by the PCR using the rice wine as a sample.

  17. [Cd uptake in rice cultivars and Cd fractions in soil treated with organic acids and EDTA].

    PubMed

    Zhang, Hai-Bo; Li, Yang-Rui; Xu, Wei-Hong; Chen, Gui-Qing; Wang, Hui-Xian; Han, Gui-Qi; Zhang, Xiao-Jing; Xiong, Zhi-Ting; Zhang, Jin-Zhong; Xie, De-Ti

    2011-09-01

    A pot experiment was conducted to examine the yield, quality and cadmium (Cd) uptake in different rice cultivars, and Cd speciation in soil after exposing to Cd (0, 1 and 5 mg x kg(-1)) in the presence of organic acids and ethylenediamine tetraacetic acid (EDTA). The results showed that general increase in the yield for cultivars Xiushui63 and II you527 was observed. Yield of two rice cultivars were in order of organic acids treatment or organic acids + 1/2EDTA treatment > EDTA treatment. The exchangeable, carbonate related and ferric-manganese oxidation related Cd increased; while organic complexation Cd and residules decreased in the presence of organic acids and EDTA. Cadmium concentrations in grain, straw and roots of both cultivars markedly reduced in the presence of organic acids and EDTA. Grain Cd concentration was the lowest for plants treated with EDTA, followed by organic acids + 1/2EDTA, and the highest Cd concentration in grain was found in the treatment with organic acids. Grain Cd concentration decreased by 9.0% to 49.3% and 16.5% to 30.6% at 1 mg x kg(-1) Cd in the presence of organic acids and EDTA, and by 12.7% to 28.5% and 4.3% to 19.1% at 5 mg x kg(-1) Cd. Cadmium concentration and accumulation in plants and total Cd content in soil were higher in Xiushui63 than in that in II you527. Grain Cd concentration decreased, and yield and quality of two rice cultivars increased at the same time in the presence of organic acids + 1/2EDTA.

  18. Differentially expressed membrane transporters in rice roots may contribute to cultivar dependent salt tolerance.

    PubMed

    Senadheera, Prasad; Singh, R K; Maathuis, Frans J M

    2009-01-01

    Salinity tolerance in rice, like in other glycophytes, is a function of cellular ion homeostasis. The large divergence in ion homeostasis between the salt-tolerant FL478 and salt-sensitive IR29 rice varieties can be exploited to understand mechanisms of salinity tolerance. Physiological studies indicate that FL478 shows a lower Na(+) influx, a reduced Na(+) translocation to the shoot, and maintains a lower Na(+):K(+) ratio. To understand the basis of these differences, a comparative investigation of transcript regulation in roots of the two cultivars was undertaken. This analysis revealed that genes encoding aquaporins, a silicon transporter, and N transporters are induced in both cultivars. However, transcripts for cation transport proteins including OsCHX11, OsCNGC1, OsCAX, and OsTPC1 showed differential regulation between the cultivars. The encoded proteins are likely to participate in reducing Na(+) influx, lowering the tissue Na(+):K(+) ratio and limiting the apoplastic bypass flow in roots of FL478 and are therefore important new targets to improve salt tolerance in rice. PMID:19395386

  19. Genome-wide DNA polymorphisms in Kavuni, a traditional rice cultivar with nutritional and therapeutic properties.

    PubMed

    Rathinasabapathi, Pasupathi; Purushothaman, Natarajan; Parani, Madasamy

    2016-05-01

    Although rice genome was sequenced in the year 2002, efforts in resequencing the large number of available accessions, landraces, traditional cultivars, and improved varieties of this important food crop are limited. We have initiated resequencing of the traditional cultivars from India. Kavuni is an important traditional rice cultivar from South India that attracts premium price for its nutritional and therapeutic properties. Whole-genome sequencing of Kavuni using Illumina platform and SNPs analysis using Nipponbare reference genome identified 1 150 711 SNPs of which 377 381 SNPs were located in the genic regions. Non-synonymous SNPs (62 708) were distributed in 19 251 genes, and their number varied between 1 and 115 per gene. Large-effect DNA polymorphisms (7769) were present in 3475 genes. Pathway mapping of these polymorphisms revealed the involvement of genes related to carbohydrate metabolism, translation, protein-folding, and cell death. Analysis of the starch biosynthesis related genes revealed that the granule-bound starch synthase I gene had T/G SNPs at the first intron/exon junction and a two-nucleotide combination, which were reported to favour high amylose content and low glycemic index. The present study provided a valuable genomics resource to study the rice varieties with nutritional and medicinal properties.

  20. Genetic diversity analysis reveals that geographical environment plays a more important role than rice cultivar in Villosiclava virens population selection.

    PubMed

    Wang, Fei; Zhang, Shu; Liu, Mei-Gang; Lin, Xian-Song; Liu, Hui-Jiang; Peng, You-Liang; Lin, Yang; Huang, Jun-Bin; Luo, Chao-Xi

    2014-05-01

    Rice false smut caused by Villosiclava virens is an economically important disease of grains worldwide. The genetic diversity of 153 isolates from six fields located in Wuhan (WH), Yichang Wangjia (YCW), Yichang Yaohe (YCY), Huanggang (HG), Yangxin (YX), and Jingzhou (JZ) in Hubei province of China were phylogenetically analyzed to evaluate the influence of environments and rice cultivars on the V. virens populations. Isolates (43) from Wuhan were from two rice cultivars, Wanxian 98 and Huajing 952, while most of the other isolates from fields YCW, YCY, HG, YX, and JZ originated from different rice cultivars with different genetic backgrounds. Genetic diversity of isolates was analyzed using random amplified polymorphic DNA (RAPD) and single-nucleotide polymorphisms (SNP). The isolates from the same cultivars in Wuhan tended to group together, indicating that the cultivars had an important impact on the fungal population. The 110 isolates from individual fields tended to cluster according to geographical origin. The values of Nei's gene diversity (H) and Shannon's information index (I) showed that the genetic diversity among isolates was higher between than within geographical populations. Furthermore, mean genetic distance between groups (0.006) was higher than mean genetic distance within groups (0.0048) according to MEGA 5.2. The pairwise population fixation index (FST) values also showed significant genetic differentiation between most populations. Higher genetic similarity of isolates from individual fields but different rice cultivars suggested that the geographical factor played a more important role in the selection of V. virens isolates than rice cultivars. This information could be used to improve the management strategy for rice false smut by adjusting the cultivation measures, such as controlling fertilizer, water, and planting density, in the rice field to change the microenvironment.

  1. Comparative transcriptome profiling of developing caryopses from two rice cultivars with differential dormancy.

    PubMed

    Huh, Sun Mi; Hwang, Yong-sic; Shin, Young Seop; Nam, Myung Hee; Kim, Dool Yi; Yoon, In Sun

    2013-08-15

    Pre-harvest sprouting (PHS) in rice causes poor grain quality and results in significant reductions in yield, leading to significant economic losses. In contrast, deep dormancy can lead to equally unwanted non-uniform germination. Therefore, a suitable level of dormancy is a critically important agronomic trait. In this study, an analysis of PHS in developing seeds of two Korean rice cultivars (vivipary), Gopum and Samgwang, revealed differences in dormancy in caryopses at 25 d after heading (DAH). To assess the transcriptomic characteristics associated with vivipary, we compared RNA profiles at early (3-6 DAH), middle (25 DAH), and late (40 DAH) developmental stages. Transcriptomic differentiation was most pronounced in caryopses at 25 DAH, the developmental stage at which differential dormancy was also the most prominent. A k-means clustering analysis of the two cultivars revealed groups of genes with similar or dissimilar expression profiles. Many of the genes that showed distinct differential expression profiles were those involved in seed maturation. Intriguingly, differential gene expression levels between the two cultivars were positively correlated with fold-changes in their expression during the early half of caryopsis development. This implies that the establishment of seed dormancy is strongly correlated with the altered transcriptomic patterns related to the progression of maturation. Our global RNA profiling suggests that caryopsis development in Gopum proceeds at a greater speed than in the Samgwang cultivar. Thus, a high degree of maturity and early dormancy release may be present in 25 DAH caryopses of Gopum, although we cannot exclude the possibility of genetic defects modifying dormancy. The comparative transcriptomic analysis of the two cultivars did not reveal noticeable differences in RNA profiles with respect to differences in abscisic acid (ABA) content or ABA sensitivity. Therefore, it is unlikely that ABA is directly involved in the

  2. A genome-wide survey reveals abundant rice blast R-genes in resistant cultivars

    PubMed Central

    Tan, Shengjun; Zhong, Yan; Wang, Ling; Gu, Longjiang; Chen, Jian-Qun; Pan, Qinghua; Bergelson, Joy; Tian, Dacheng

    2015-01-01

    Summary Plant resistance genes (R-genes) harbor tremendous allelic diversity, constituting a robust immune system effective against microbial pathogens. Nevertheless, few functional R-genes have been identified for even the best-studied pathosystems. Does this limited repertoire reflect specificity, with most R-genes having been defeated by former pests, or do plants harbor a rich diversity of functional R-genes whose composite behavior is yet to be characterized? Here, we survey 332 NBS-LRR genes cloned from 5 resistant rice cultivars for their ability to confer recognition of 12 rice blast isolates when transformed into susceptible cultivars. Our survey reveals that 48.5% of the 132 NBS-LRR loci tested contain functional rice blast R-genes, with most R-genes deriving from multi-copy clades containing especially diversified loci. Each R-gene recognized, on average, 2.42 of the 12 isolates screened. The abundant R-genes identified in resistant genomes provide extraordinary redundancy in the ability of host genotypes to recognize particular isolates. If the same is true for other pathogens, many extant NBS-LRR genes retain functionality. Our success at identifying rice blast R-genes also validates a highly efficient cloning and screening strategy. PMID:26248689

  3. Identification of rice cultivars resistant to Lissorhoptrus oryzophilus (Coleoptera: Curculionidae), and their use in an integrated management program.

    PubMed

    Stout, M J; Rice, W C; Linscombe, S D; Bollich, P K

    2001-08-01

    The rice water weevil, Lissorhoptrus oryzophilus Kuschel, is the most destructive insect pest of rice in the United States and is a particularly severe pest in Louisiana. The current management program for this insect in Louisiana relies heavily on insecticides, most notably the seed treatment fipronil (Icon). Diversification of the management program by incorporation of alternative strategies is needed to improve the effectiveness and long-term stability of the program. In the three experiments reported here, three components of a diversified management program for the rice water weevil in Louisiana--host plant resistance, treatment of seeds with Icon, aid the cultural practice of delayed flooding--were investigated. Comparison of the densities of weevil larvae on the roots of several commercial cultivars indicated that the long-grain cultivar 'Jefferson' was more resistant to infestation by the rice water weevil than the other cultivars. The medium-grain cultivars 'Bengal', 'Earl' and 'Mars' and the long-grain variety 'Cocodrie' were the most susceptible to infestation. Comparison of yield data from untreated plots and plots treated with Icon indicated that the long-grain cultivars Cocodrie, Lemont, and Jefferson were more tolerant of weevil injury than the other cultivars. A 2-wk delay in flooding was associated with yield benefits in plots not treated with Icon. Treatment of seeds with Icon controlled weevils in all three screening experiments. The implications of these results for the development of an integrated management program for the rice water weevil are discussed.

  4. Uptake Kinetics of Arsenic in Upland Rice Cultivar Zhonghan 221 Inoculated with Arbuscular Mycorrhizal Fungi.

    PubMed

    Chan, W F; Li, W C; Wong, M H

    2015-01-01

    Arbuscular mycorrhizal fungi (AMF) appear to be highly associated with arsenic (As) uptake in host plants because arsenate (As(V)) and phosphorus (P) share the same transporter, whereby AMF can enhance P uptake. A short-term experiment was conducted for low- (0 to 0.05 mM As) and high-affinity (0 to 2.5 mM As) uptake systems, to investigate the AMF role on As uptake mechanism in plants, which may explain As uptake kinetics in upland rice cultivar: Zhonghan 221. When concentration of As ranged from 0 to 0.05 mM, Funneliformis geosporum (Fg) significantly decreased arsenite (As(III)) and monomethylarsonicacid (MMA) uptake when (p < 0.05) compared to non-mycorrhizal (NM) treatment, since the major route for (As(III)) in rice roots-rice silicon transporter Lsi1 would be influenced by Fg inoculation at high As concentrations. Fg can also reduce As(V) uptake significantly (p < 0.05) under both uptake systems relative to NM treatment, whereas, Funneliformis mosseae (Fm) increased As(V) and MMA uptake in rice roots, with MMA uptake rate generally lower than As(III) and As(V). Using suitable AMF species inoculation with rice, As uptake and accumulation in rice grains can be reduced and the risk to human health, once consumed, can be minimized.

  5. Uptake Kinetics of Arsenic in Upland Rice Cultivar Zhonghan 221 Inoculated with Arbuscular Mycorrhizal Fungi.

    PubMed

    Chan, W F; Li, W C; Wong, M H

    2015-01-01

    Arbuscular mycorrhizal fungi (AMF) appear to be highly associated with arsenic (As) uptake in host plants because arsenate (As(V)) and phosphorus (P) share the same transporter, whereby AMF can enhance P uptake. A short-term experiment was conducted for low- (0 to 0.05 mM As) and high-affinity (0 to 2.5 mM As) uptake systems, to investigate the AMF role on As uptake mechanism in plants, which may explain As uptake kinetics in upland rice cultivar: Zhonghan 221. When concentration of As ranged from 0 to 0.05 mM, Funneliformis geosporum (Fg) significantly decreased arsenite (As(III)) and monomethylarsonicacid (MMA) uptake when (p < 0.05) compared to non-mycorrhizal (NM) treatment, since the major route for (As(III)) in rice roots-rice silicon transporter Lsi1 would be influenced by Fg inoculation at high As concentrations. Fg can also reduce As(V) uptake significantly (p < 0.05) under both uptake systems relative to NM treatment, whereas, Funneliformis mosseae (Fm) increased As(V) and MMA uptake in rice roots, with MMA uptake rate generally lower than As(III) and As(V). Using suitable AMF species inoculation with rice, As uptake and accumulation in rice grains can be reduced and the risk to human health, once consumed, can be minimized. PMID:25901895

  6. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.

    PubMed

    Duitama, Jorge; Silva, Alexander; Sanabria, Yamid; Cruz, Daniel Felipe; Quintero, Constanza; Ballen, Carolina; Lorieux, Mathias; Scheffler, Brian; Farmer, Andrew; Torres, Edgar; Oard, James; Tohme, Joe

    2015-01-01

    Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops. PMID:25923345

  7. Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection

    PubMed Central

    Duitama, Jorge; Silva, Alexander; Sanabria, Yamid; Cruz, Daniel Felipe; Quintero, Constanza; Ballen, Carolina; Lorieux, Mathias; Scheffler, Brian; Farmer, Andrew; Torres, Edgar; Oard, James; Tohme, Joe

    2015-01-01

    Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops. PMID:25923345

  8. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.

    PubMed

    Duitama, Jorge; Silva, Alexander; Sanabria, Yamid; Cruz, Daniel Felipe; Quintero, Constanza; Ballen, Carolina; Lorieux, Mathias; Scheffler, Brian; Farmer, Andrew; Torres, Edgar; Oard, James; Tohme, Joe

    2015-01-01

    Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.

  9. Evaluation of the agronomic performance of atrazine-tolerant transgenic japonica rice parental lines for utilization in hybrid seed production.

    PubMed

    Zhang, Luhua; Chen, Haiwei; Li, Yanlan; Li, Yanan; Wang, Shengjun; Su, Jinping; Liu, Xuejun; Chen, Defu; Chen, Xiwen

    2014-01-01

    Currently, the purity of hybrid seed is a crucial limiting factor when developing hybrid japonica rice (Oryza sativa L.). To chemically control hybrid seed purity, we transferred an improved atrazine chlorohydrolase gene (atzA) from Pseudomonas ADP into hybrid japonica parental lines (two maintainers, one restorer), and Nipponbare, by using Agrobacterium-mediated transformation. We subsequently selected several transgenic lines from each genotype by using PCR, RT-PCR, and germination analysis. In the presence of the investigated atrazine concentrations, particularly 150 µM atrazine, almost all of the transgenic lines produced significantly larger seedlings, with similar or higher germination percentages, than did the respective controls. Although the seedlings of transgenic lines were taller and gained more root biomass compared to the respective control plants, their growth was nevertheless inhibited by atrazine treatment compared to that without treatment. When grown in soil containing 2 mg/kg or 5 mg/kg atrazine, the transgenic lines were taller, and had higher total chlorophyll contents than did the respective controls; moreover, three of the strongest transgenic lines completely recovered after 45 days of growth. After treatment with 2 mg/kg or 5 mg/kg of atrazine, the atrazine residue remaining in the soil was 2.9-7.0% or 0.8-8.7% respectively, for transgenic lines, and 44.0-59.2% or 28.1-30.8%, respectively, for control plants. Spraying plants at the vegetative growth stage with 0.15% atrazine effectively killed control plants, but not transgenic lines. Our results indicate that transgenic atzA rice plants show tolerance to atrazine, and may be used as parental lines in future hybrid seed production.

  10. Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress

    PubMed Central

    2010-01-01

    Background The transcriptional regulatory network involved in low temperature response leading to acclimation has been established in Arabidopsis. In japonica rice, which can only withstand transient exposure to milder cold stress (10°C), an oxidative-mediated network has been proposed to play a key role in configuring early responses and short-term defenses. The components, hierarchical organization and physiological consequences of this network were further dissected by a systems-level approach. Results Regulatory clusters responding directly to oxidative signals were prominent during the initial 6 to 12 hours at 10°C. Early events mirrored a typical oxidative response based on striking similarities of the transcriptome to disease, elicitor and wounding induced processes. Targets of oxidative-mediated mechanisms are likely regulated by several classes of bZIP factors acting on as1/ocs/TGA-like element enriched clusters, ERF factors acting on GCC-box/JAre-like element enriched clusters and R2R3-MYB factors acting on MYB2-like element enriched clusters. Temporal induction of several H2O2-induced bZIP, ERF and MYB genes coincided with the transient H2O2 spikes within the initial 6 to 12 hours. Oxidative-independent responses involve DREB/CBF, RAP2 and RAV1 factors acting on DRE/CRT/rav1-like enriched clusters and bZIP factors acting on ABRE-like enriched clusters. Oxidative-mediated clusters were activated earlier than ABA-mediated clusters. Conclusion Genome-wide, physiological and whole-plant level analyses established a holistic view of chilling stress response mechanism of japonica rice. Early response regulatory network triggered by oxidative signals is critical for prolonged survival under sub-optimal temperature. Integration of stress and developmental responses leads to modulated growth and vigor maintenance contributing to a delay of plastic injuries. PMID:20100339

  11. Photosynthesis enhanced oxidative stress tolerance in high-yield rice varieties (Oryza sativa var. japonica L.) in the field.

    PubMed

    Wei, X D

    2016-01-01

    The objective of this study was to understand varietal differences in photosynthetic characteristics, chlorophyll fluorescence, antioxidant capability, and yield of japonica rice varieties. Nanjing 44, Oryza sativa var. japonica (average yield of 12.7 t/ha), Nanjing 46, and Nanjing 5055 (average yields of 11.3 and 11.5 t/ha) were included as "super" and high-yield varieties, respectively, whereas Wuyunjing 7 (average yield of 10.2 t/ha) was included as a control variety. These varieties were grown under field conditions in Jiangsu Province, China, in 2010-2012. Different organs (panicle, grain, etc.) were measured, before and after flowering, to identify differences of dry matter accumulation and transformation properties. Photosynthesis, the chlorophyll content, and antioxidant enzyme activities of the flag leaf in the days after flowering (DAF) were also investigated. The results showed that, compared with the other three rice varieties, Nanjing 44 had the highest plant dry weight and number of grains per panicle. It also had a relatively high net flag leaf photosynthetic rate and showed the least inhibition of photosynthesis at noon in DAF, which probably explains the higher yield in this variety. Furthermore, Nanjing 44 also had the highest stem export and conversion rate from stem to grain, exhibiting a strong ability to convert and distribute photosynthetic products. After DAF 42, Nanjing 44 still maintained a high-soluble protein content and a high antioxidant ability in the leaves to clear peroxidation products, which could protect the photosynthetic apparatus of the flag leaves, and maintain the grain-filling activity for longer. The high-yield capability of Nanjing 44 was attributed to its photosynthetic advantages in the leaves during the late developmental stage. PMID:27525885

  12. Development and molecular characterization of a doubled haploid population derived from a hybrid between japonica rice and wide compatible indica rice

    PubMed Central

    Nguyen, Hung; Chen, Xiao-Yang; Jiang, Meng; Wang, Qing; Deng, Li; Zhang, Wei-Zhang; Shu, Qing-Yao

    2016-01-01

    Doubled haploid (DH) populations, particularly those from subspecies crosses possessing the wide compatible gene S5n, are important germplasm resources for rice genetic studies and breeding, but their feature and potential have not been fully assessed and explored. In the present study, we produced a DH population from the hybrid of japonica 668B and wide compatible indica T23. Genotyping of the S5 locus with allele-specific markers for ORF3, ORF4 and ORF5 revealed a potential recombination hot spot in the ORF3-ORF4 region. Haplotyping analysis revealed that 21/34 subspecies specific Indel markers segregated in distortion in the DH population, with a few lines having indica alleles either extremely low (1.7%) or high (98.3%), with little effect of the S5 allele. While DH lines with the S5n allele had higher frequency of indica alleles, no effect of the S5n allele was observed on all agronomic traits but flowering time. Taken together, the present study advanced understanding of the genetics of wide crosses in general, and DH production in particular between the two rice subspecies, and the new DH population generated will become a useful resource for rice genetic study and breeding in the future. PMID:27795680

  13. Difference in cesium accumulation among rice cultivars grown in the paddy field in Fukushima Prefecture in 2011 and 2012.

    PubMed

    Ohmori, Yoshihiro; Inui, Yayoi; Kajikawa, Masataka; Nakata, Atsumi; Sotta, Naoyuki; Kasai, Koji; Uraguchi, Shimpei; Tanaka, Nobuhiro; Nishida, Sho; Hasegawa, Takahiro; Sakamoto, Takuya; Kawara, Yuko; Aizawa, Kayoko; Fujita, Haruka; Li, Ke; Sawaki, Naoya; Oda, Koshiro; Futagoishi, Ryuichiro; Tsusaka, Takahiro; Takahashi, Satomi; Takano, Junpei; Wakuta, Shinji; Yoshinari, Akira; Uehara, Masataka; Takada, Shigeki; Nagano, Hayato; Miwa, Kyoko; Aibara, Izumi; Ojima, Takuya; Ebana, Kaoru; Ishikawa, Satoru; Sueyoshi, Kuni; Hasegawa, Hiroshi; Mimura, Tetsuro; Mimura, Mari; Kobayashi, Natsuko I; Furukawa, Jun; Kobayashi, Daisuke; Okouchi, Toshiyasu; Tanoi, Keitaro; Fujiwara, Toru

    2014-01-01

    After the accident of the Fukushima 1 Nuclear Power Plant in March 2011, radioactive cesium was released and paddy fields in a wide area including Fukushima Prefecture were contaminated. To estimate the levels of radioactive Cs accumulation in rice produced in Fukushima, it is crucial to obtain the actual data of Cs accumulation levels in rice plants grown in the actual paddy field in Fukushima City. We herein conducted a two-year survey in 2011 and 2012 of radioactive and non-radioactive Cs accumulation in rice using a number of rice cultivars grown in the paddy field in Fukushima City. Our study demonstrated a substantial variation in Cs accumulation levels among the cultivars of rice.

  14. Pomological Traits, Sensory Profile and Nutraceutical Properties of Nine Cultivars of Loquat (Eriobotrya japonica Lindl.) Fruits Grown in Mediterranean Area.

    PubMed

    Gentile, C; Reig, C; Corona, O; Todaro, A; Mazzaglia, A; Perrone, A; Gianguzzi, G; Agusti, M; Farina, V

    2016-09-01

    In this paper the diversity of fruit quality within nine loquat cultivars, including five international affirmed cultivars (Algerie, Golden Nugget, Peluche, Bueno, El Buenet) and four local cultivars (Sanfilippara, Nespolone di Trabia, BRT20 and Claudia), were investigated in order to discriminate the variation in pomological characteristics, sensory profile, and antioxidant properties. Finally, to evaluate potential bioactivity, antiproliferative activity of hydrophilic extracts from loquat fruits was assessed, at dietary relevant concentrations, against three human epithelial cell lines. Even though the international cultivars confirmed an appropriate level of commercial qualities in association to high levels in antioxidant compounds, the local cultivars revealed the best performances in a wide range of chemical-physical and sensory characteristics. Concerning bioactivity, our results indicate that hydrophilic extracts from all tested cultivars showed concentration-dependent antiproliferative activity with a significant variability of effects between different cell lines and between different cultivars. HeLa cells, the most sensitive and hydrophilic extracts from Peluche, showed the highest inhibitory effect followed by Nespolone di Trabia and Claudia. The results of this trial provide useful information on the pomological traits and the not yet known specific nutritional and functional properties of loquat fruits. Our data, besides helping to promote specific local cultivars, could serve to establish a database that will permit to improve the utilization of specific genetic resources in breeding programs.

  15. [Effects of different ecological conditions on grain quality and RVA profile of japonica rice from Yunnan of China and Korea].

    PubMed

    Zhu, Zhen-hua; Kim, Ki-young; Yuan, Ping-rong; Zhao, Guo-zhen; Su, Zhen-xi; Liao, Xin-hua; Yang, Sea-jun; Dai, Lu-yuan

    2009-12-01

    Taking sixteen japonica rice varieties from Yunnan of China and Korea growing at three locations with different altitudes in Yunnan Plateau as test materials, this paper studied the effects of different ecological conditions on their grain quality, including brown rice length (BRL), brown rice width (BRW), length-width ratio (L/W), chalky rate (CR), whiteness (WH), amylose content (AC), protein content (PC), and alkali digestion value (ADV), and their starch RVA profile, including peak viscosity (PKV), hot viscosity (HTV), final viscosity (FLV), breakdown viscosity (BDV), setback viscosity (SBV), consistence viscosity( CTV), peak time (PeT), and pasting temperature (PaT). Of all the test parameters, SBV had the largest coefficient of variation. The coefficients of variation of BRL, CR, AC, PC, ADV, FLV, SBV, and PeT of Yunnan varieties were higher than those of Korean varieties, while the BRW, L/W, WH, PKV, HTV, BDV, CTV, and PaT of Korean varieties had higher coefficients of variation than those of Yunnan varieties. With increasing altitude, the BRL, BRW, L/W, WH, AC, ADV, FLV, and CTV of Yunnan varieties, and the BRL, BRW, WH, PC, PKV, HTV and BDV of Korean varieties decreased significantly, while the CR, PC, HTV, and PeT of Yunnan varieties, and the L/W, AC, ADV, SBV and CTV of Korean varieties increased significantly. The CR of Korean varieties had no obvious change. The PKV, BDV, and PaT of Yunnan varieties and the PaT of Korean varieties increased after an initial decrease, whereas the SBV of Yunnan varieties and the FLV and PeT of Korean varieties were in reverse. PMID:20353061

  16. Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining

    PubMed Central

    2014-01-01

    Background Apparent Amylose Content (AAC), regulated by the Waxy gene, represents the key determinant of rice cooking properties. In occidental countries high AAC rice represents the most requested market class but the availability of molecular markers allowing specific selection of high AAC varieties is limited. Results In this study, the effectiveness of available molecular markers in predicting AAC was evaluated in a collection of 127 rice accessions (125 japonica ssp. and 2 indica ssp.) characterized by AAC values from glutinous to 26%. The analyses highlighted the presence of several different allelic patterns identifiable by a few molecular markers, and two of them, i.e., the SNPs at intron1 and exon 6, were able to explain a maximum of 79.5% of AAC variation. However, the available molecular markers haplotypes did not provide tools for predicting accessions with AAC higher than 24.5%. To identify additional polymorphisms, the re-sequencing of the Waxy gene and 1kbp of the putative upstream regulatory region was performed in 21 genotypes representing all the AAC classes identified. Several previously un-characterized SNPs were identified and four of them were used to develop dCAPS markers. Conclusions The addition of the SNPs newly identified slightly increased the AAC explained variation and allowed the identification of a haplotype almost unequivocally associated to AAC higher than 24.5%. Haplotypes at the waxy locus were also associated to grain length and length/width (L/W) ratio. In particular, the SNP at the first intron, which identifies the Wx a and Wx b alleles, was associated with differences in the width of the grain, the L/W ratio and the length of the kernel, most likely as a result of human selection. PMID:24383761

  17. Evaluation of methane emissions of some rice cultivars of Sri Lanka

    SciTech Connect

    Namaratne, S.Y.; Alwis, H.P.W. de

    1996-12-31

    A field experiment on three local rice cultivars, namely BG 300, BG 304 and AT 303, showed no statistically significant difference (p<0.05) among them with-respect to the methane flux emitted. The methane flux profiles of all three varieties indicated a more or less constant emission during the vegetative and reproductive periods, a peak emission during late flowering/early ripening stage and a dramatic increase in the flux during the late ripening period. The seasonal methane flux of BG 300, BG 304 and AT 303 were 200 {+-} 48, 156 {+-} 52 and 129 {+-} 40 g m{sup {minus}2}, respectively for a 92 day cropping period.

  18. Comparison of soil acetate concentrations and methane production, transport, and emission in two rice cultivars

    NASA Astrophysics Data System (ADS)

    Sigren, L. K.; Byrd, G. T.; Fisher, F. M.; Sass, R. L.

    1997-03-01

    The amount of methane emitted from irrigated rice paddies is dependent on the variety of rice grown. In this study we examined two varieties of rice with differing methane emission rates to determine if the primary mechanism for these differences was related to transport processes or the rate of methane production. The cultivars used were Mars and Lemont, with 1994 seasonal emissions of 34 and 18 g m-2, respectively. Seasonal methane emission and soil acetate concentration data were measured weekly over two seasons in both varieties. In addition, gas transport through the two rice varieties was investigated in both field and laboratory experiments in 1995. We found no significant differences in gas transport between the two varieties. However, significant differences between the two varieties were detected in the soil acetate concentrations during the vegetative growth stage. Mars exhibited higher seasonal methane emissions and higher soil acetate concentrations than Lemont. This suggests that the intervarietal differences in methane emissions are the result of different soil substrate levels and hence different rates of methane production. The turnover time of soil acetate was found to be small, about 1 hour in the last half of the season. Calculations of methane oxidation, using two methods, support previous findings that the fraction of methane oxidized in the soil prior to emission increases from 10 to 30% before heading to 30-70% after heading.

  19. Photosynthetic Diffusional Constraints Affect Yield in Drought Stressed Rice Cultivars during Flowering

    PubMed Central

    Lauteri, Marco; Haworth, Matthew; Serraj, Rachid; Monteverdi, Maria Cristina; Centritto, Mauro

    2014-01-01

    Global production of rice (Oryza sativa) grain is limited by water availability and the low ‘leaf-level’ photosynthetic capacity of many cultivars. Oryza sativa is extremely susceptible to water-deficits; therefore, predicted increases in the frequency and duration of drought events, combined with future rises in global temperatures and food demand, necessitate the development of more productive and drought tolerant cultivars. We investigated the underlying physiological, isotopic and morphological responses to water-deficit in seven common varieties of O. sativa, subjected to prolonged drought of varying intensities, for phenotyping purposes in open field conditions. Significant variation was observed in leaf-level photosynthesis rates (A) under both water treatments. Yield and A were influenced by the conductance of the mesophyll layer to CO2 (gm) and not by stomatal conductance (gs). Mesophyll conductance declined during drought to differing extents among the cultivars; those varieties that maintained gm during water-deficit sustained A and yield to a greater extent. However, the variety with the highest gm and yield under well-watered conditions (IR55419-04) was distinct from the most effective cultivar under drought (Vandana). Mesophyll conductance most effectively characterises the photosynthetic capacity and yield of O. sativa cultivars under both well-watered and water-deficit conditions; however, the desired attributes of high gm during optimal growth conditions and the capacity for gm to remain constant during water-deficit may be mutually exclusive. Nonetheless, future genetic and physiological studies aimed at enhancing O. sativa yield and drought stress tolerance should investigate the biochemistry and morphology of the interface between the sub-stomatal pore and mesophyll layer. PMID:25275452

  20. RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions

    PubMed Central

    Sato, Yutaka; Antonio, Baltazar A.; Namiki, Nobukazu; Takehisa, Hinako; Minami, Hiroshi; Kamatsuki, Kaori; Sugimoto, Kazuhiko; Shimizu, Yuji; Hirochika, Hirohiko; Nagamura, Yoshiaki

    2011-01-01

    Elucidating the function of all predicted genes in rice remains as the ultimate goal in cereal genomics in order to ensure the development of improved varieties that will sustain an expanding world population. We constructed a gene expression database (RiceXPro, URL: http://ricexpro.dna.affrc.go.jp/) to provide an overview of the transcriptional changes throughout the growth of the rice plant in the field. RiceXPro contains two data sets corresponding to spatiotemporal gene expression profiles of various organs and tissues, and continuous gene expression profiles of leaf from transplanting to harvesting. A user-friendly web interface enables the extraction of specific gene expression profiles by keyword and chromosome search, and basic data analysis, thereby providing useful information as to the organ/tissue and developmental stage specificity of expression of a particular gene. Analysis tools such as t-test, calculation of fold change and degree of correlation facilitate the comparison of expression profiles between two random samples and the prediction of function of uncharacterized genes. As a repository of expression data encompassing growth in the field, this database can provide baseline information of genes that underlie various agronomically important traits in rice. PMID:21045061

  1. Genome-Wide Association Studies Reveal that Diverse Heading Date Genes Respond to Short and Long Day Lengths between Indica and Japonica Rice

    PubMed Central

    Han, Zhongmin; Zhang, Bo; Zhao, Hu; Ayaad, Mohammed; Xing, Yongzhong

    2016-01-01

    Rice is a short-day plant. Short-day length promotes heading, and long-day length suppresses heading. Many studies have evaluated rice heading in field conditions in which some individuals in the population were exposed to various day lengths, including short and long days, prior to a growth phase transition. In this study, we investigated heading date under natural short-day conditions (SD) and long-day conditions (LD) for 100s of accessions and separately conducted genome-wide association studies within indica and japonica subpopulations. Under LD, three and four quantitative trait loci (QTLs) were identified in indica and japonica subpopulations, respectively, two of which were less than 80 kb from the known genes Hd17 and Ghd7. But no common QTLs were detected in both subpopulations. Under SD, six QTLs were detected in indica, three of which were less than 80 kb from the known heading date genes Ghd7, Ehd1, and RCN1. But no QTLs were detected in japonica subpopulation. qHd3 under SD and qHd4 under LD were two novel major QTLs, which deserve isolation in the future. Eleven known heading date genes were used to test the power of association mapping at the haplotype level. Hd17, Ghd7, Ehd1, and RCN1 were again detected at more significant level and three additional genes, Hd3a, OsMADS56, and Ghd7.1, were detected. However, of the detected seven genes, only one gene, Hd17, was commonly detected in both subpopulations and two genes, Ghd7 and Ghd7.1, were commonly detected in indica subpopulation under both conditions. Moreover, haplotype analysis identified favorable haplotypes of Ghd7 and OsMADS56 for breeding design. In conclusion, diverse heading date genes/QTLs between indica and japonica subpopulations responded to SD and LD, and haplotype-level association mapping was more powerful than SNP-level association in rice.

  2. Different responses of low grain-Cd-accumulating and high grain-Cd-accumulating rice cultivars to Cd stress.

    PubMed

    Wang, Feijuan; Wang, Min; Liu, Zhouping; Shi, Yan; Han, Tiqian; Ye, Yaoyao; Gong, Ning; Sun, Junwei; Zhu, Cheng

    2015-11-01

    Cadmium (Cd) is a major heavy metal pollutant which is highly toxic to plants and animals. The accumulation of Cd in rice grains is a major agricultural problem in regions with Cd pollution. A hydroponics experiment using low grain-Cd-accumulating rice (xiushui 11) and high grain-Cd-accumulating rice (xiushui 110) was carried out to characterize the different responses of rice cultivars to Cd stress. We found that xiushui 11 was more tolerant to Cd than xiushui 110, and xiushui 11 suffered less oxidative damage. Cell walls played an important role in limiting the amount of Cd that entered the protoplast, especially in xiushui 11. Cd stored in organelles as soluble fractions, leading to greater physiological stress of Cd detoxification. We found that Cd can disturb the ion homeostasis in rice roots because Cd(2+) and Ca(2+) may have a similar uptake route. Xiushui 11 had a faster root-to-shoot transport of Cd, and the expression level of OsPCR1 gene which was predicted related with Cd accumulation in rice was consist with the Cd transport of root-to-shoot in rice and maintain the greater Cd tolerance of xiushui 11. These results suggest there are different Cd detoxification and accumulation mechanisms in rice cultivars.

  3. Different responses of low grain-Cd-accumulating and high grain-Cd-accumulating rice cultivars to Cd stress.

    PubMed

    Wang, Feijuan; Wang, Min; Liu, Zhouping; Shi, Yan; Han, Tiqian; Ye, Yaoyao; Gong, Ning; Sun, Junwei; Zhu, Cheng

    2015-11-01

    Cadmium (Cd) is a major heavy metal pollutant which is highly toxic to plants and animals. The accumulation of Cd in rice grains is a major agricultural problem in regions with Cd pollution. A hydroponics experiment using low grain-Cd-accumulating rice (xiushui 11) and high grain-Cd-accumulating rice (xiushui 110) was carried out to characterize the different responses of rice cultivars to Cd stress. We found that xiushui 11 was more tolerant to Cd than xiushui 110, and xiushui 11 suffered less oxidative damage. Cell walls played an important role in limiting the amount of Cd that entered the protoplast, especially in xiushui 11. Cd stored in organelles as soluble fractions, leading to greater physiological stress of Cd detoxification. We found that Cd can disturb the ion homeostasis in rice roots because Cd(2+) and Ca(2+) may have a similar uptake route. Xiushui 11 had a faster root-to-shoot transport of Cd, and the expression level of OsPCR1 gene which was predicted related with Cd accumulation in rice was consist with the Cd transport of root-to-shoot in rice and maintain the greater Cd tolerance of xiushui 11. These results suggest there are different Cd detoxification and accumulation mechanisms in rice cultivars. PMID:26318143

  4. Do NERICA rice cultivars express resistance to Striga hermonthica (Del.) Benth. and Striga asiatica (L.) Kuntze under field conditions?

    PubMed Central

    Rodenburg, Jonne; Cissoko, Mamadou; Kayeke, Juma; Dieng, Ibnou; Khan, Zeyaur R.; Midega, Charles A.O.; Onyuka, Enos A.; Scholes, Julie D.

    2015-01-01

    The parasitic weeds Striga asiatica and Striga hermonthica cause high yield losses in rain-fed upland rice in Africa. Two resistance classes (pre- and post-attachment) and several resistant genotypes have been identified among NERICA (New Rice for Africa) cultivars under laboratory conditions (in vitro) previously. However, little is known about expression of this resistance under field conditions. Here we investigated (1) whether resistance exhibited under controlled conditions would express under representative Striga-infested field conditions, and (2) whether NERICA cultivars would achieve relatively good grain yields under Striga-infested conditions. Twenty-five rice cultivars, including all 18 upland NERICA cultivars, were screened in S. asiatica-infested (in Tanzania) and S. hermonthica-infested (in Kenya) fields during two seasons. Additionally, a selection of cultivars was tested in vitro, in mini-rhizotron systems. For the first time, resistance observed under controlled conditions was confirmed in the field for NERICA-2, -5, -10 and -17 (against S. asiatica) and NERICA-1 to -5, -10, -12, -13 and -17 (against S. hermonthica). Despite high Striga-infestation levels, yields of around 1.8 t ha−1 were obtained with NERICA-1, -9 and -10 (in the S. asiatica-infested field) and around 1.4 t ha−1 with NERICA-3, -4, -8, -12 and -13 (in the S. hermonthica-infested field). In addition, potential levels of tolerance were identified in vitro, in NERICA-1, -17 and -9 (S. asiatica) and in NERICA-1, -17 and -10 (S. hermonthica). These findings are highly relevant to rice agronomists and breeders and molecular geneticists working on Striga resistance. In addition, cultivars combining broad-spectrum resistance with good grain yields in Striga-infested fields can be recommended to rice farmers in Striga-prone areas. PMID:26089591

  5. Fine mapping of a gene causing hybrid pollen sterility between Yunnan weedy rice and cultivated rice (Oryza sativa L.) and phylogenetic analysis of Yunnan weedy rice.

    PubMed

    Wang, Yong; Zhong, Zheng Zheng; Zhao, Zhi Gang; Jiang, Ling; Bian, Xiao Feng; Zhang, Wen Wei; Liu, Ling Long; Ikehashi, H; Wan, Jian Min

    2010-02-01

    Weedy rice represents an important resource for rice improvement. The F(1) hybrid between the japonica wide compatibility rice cultivar 02428 and a weedy rice accession from Yunnan province (SW China) suffered from pollen sterility. Pollen abortion in the hybrid occurred at the early bicellular pollen stage, as a result of mitotic failure in the microspore, although the tapetum developed normally. Genetic mapping in a BC(1)F(1) population (02428//Yunnan weedy rice (YWR)/02428) showed that a major QTL for hybrid pollen sterility (qPS-1) was present on chromosome 1. qPS-1 was fine-mapped to a 110 kb region known to contain the hybrid pollen sterility gene Sa, making it likely that qPS-1 is either identical to, or allelic with Sa. Interestingly, F(1) hybrid indicated that Dular and IR36 were assumed to carry the sterility-neutral allele, Sa ( n ). Re-sequencing SaM and SaF, the two component genes present at Sa, suggested that variation for IR36 and Dular may be responsible for the loss of male sterility, and the qPS-1 sequence might be derived from wild rice or indica cultivars. A phylogenetic analysis based on microsatellite genotyping suggested that the YWR accession is more closely related to wild rice and indica type cultivars than to japonica types. Thus it is probable that the YWR accession evolved from a spontaneous hybrid between wild rice and an ancient cultivated strain of domesticated rice.

  6. Incorporation of Bacterial Blight Resistance Genes Into Lowland Rice Cultivar Through Marker-Assisted Backcross Breeding.

    PubMed

    Pradhan, Sharat Kumar; Nayak, Deepak Kumar; Pandit, Elssa; Behera, Lambodar; Anandan, Annamalai; Mukherjee, Arup Kumar; Lenka, Srikanta; Barik, Durga Prasad

    2016-07-01

    Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae is a major disease of rice in many rice growing countries. Pyramided lines carrying two BB resistance gene combinations (Xa21+xa13 and Xa21+xa5) were developed in a lowland cultivar Jalmagna background through backcross breeding by integrating molecular markers. In each backcross generation, markers closely linked to the disease resistance genes were used to select plants possessing the target genes. Background selection was continued in those plants carrying resistant genes until BC(3) generation. Plants having the maximum contribution from the recurrent parent genome were selected in each generation and hybridized with the recipient parent. The BB-pyramided line having the maximum recipient parent genome recovery of 95% was selected among BC3F1 plants and selfed to isolate homozygous BC(3)F(2) plants with different combinations of BB resistance genes. Twenty pyramided lines with two resistance gene combinations exhibited high levels of tolerance against the BB pathogen. In order to confirm the resistance, the pyramided lines were inoculated with different X. oryzae pv. oryzae strains of Odisha for bioassay. The genotypes with combination of two BB resistance genes conferred high levels of resistance to the predominant X. oryzae pv. oryzae isolates prevalent in the region. The pyramided lines showed similarity with the recipient parent with respect to major agro-morphologic traits.

  7. An improved Agrobacterium-mediated transformation of recalcitrant indica rice (Oryza sativa L.) cultivars.

    PubMed

    Shri, Manju; Rai, Arti; Verma, Pankaj Kumar; Misra, Prashant; Dubey, Sonali; Kumar, Smita; Verma, Sikha; Gautam, Neelam; Tripathi, Rudra Deo; Trivedi, Prabodh Kumar; Chakrabarty, Debasis

    2013-04-01

    Agrobacterium-mediated transformation of indica rice varieties has been quite difficult as these are recalcitrant to in vitro responses. In the present study, we established a high-efficiency Agrobacterium tumefaciens-mediated transformation system of rice (Oryza sativa L. ssp. indica) cv. IR-64, Lalat, and IET-4786. Agrobacterium strain EHA-101 harboring binary vector pIG121-Hm, containing a gene encoding for β-glucuronidase (GUS) and hygromycin resistance, was used in the transformation experiments. Manipulation of different concentrations of acetosyringone, days of co-culture period, bacterial suspension of different optical densities (ODs), and the concentrations of L-cysteine in liquid followed by solid co-culture medium was done for establishing the protocol. Among the different co-culture periods, 5 days of co-culture with bacterial cells (OD600 nm = 0.5-0.8) promoted the highest frequency of transformation (83.04 %) in medium containing L-cysteine (400 mg l(-1)). Putative transformed plants were analyzed for the presence of a transgene through genomic PCR and GUS histochemical analyses. Our results also suggest that different cultural conditions and the addition of L-cysteine in the co-culture medium improve the Agrobacterium-mediated transformation frequencies from an average of 12.82 % to 33.33 % in different indica rice cultivars.

  8. Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response

    PubMed Central

    Garg, Rohini; Narayana Chevala, VVS; Shankar, Rama; Jain, Mukesh

    2015-01-01

    DNA methylation is an epigenetic mechanism that play an important role in gene regulation in response to environmental conditions. The understanding of DNA methylation at the whole genome level can provide insights into the regulatory mechanisms underlying abiotic stress response/adaptation. We report DNA methylation patterns and their influence on transcription in three rice (Oryza sativa) cultivars (IR64, stress-sensitive; Nagina 22, drought-tolerant; Pokkali, salinity-tolerant) via an integrated analysis of whole genome bisulphite sequencing and RNA sequencing. We discovered extensive DNA methylation at single-base resolution in rice cultivars, identified the sequence context and extent of methylation at each site. Overall, methylation levels were significantly different in the three rice cultivars. Numerous differentially methylated regions (DMRs) among different cultivars were identified and many of which were associated with differential expression of genes important for abiotic stress response. Transposon-associated DMRs were found coupled to the transcript abundance of nearby protein-coding gene(s). Small RNA (smRNA) abundance was found to be positively correlated with hypermethylated regions. These results provide insights into interplay among DNA methylation, gene expression and smRNA abundance, and suggest a role in abiotic stress adaptation in rice. PMID:26449881

  9. Phytochemicals characterization of solvent extracts from taro-scented japonica rice bran.

    PubMed

    Chen, Hua Han; Chiu, Tsai Hsin

    2011-05-01

    The major phytochemicals and antioxidant properties of taro-scented rice bran (TaiNung 71; TN71) extracts using 3 different solvents are characterized. Some progress is realized in creating an economic value for rice bran that has long been considered an agricultural waste. Various solvent extracts reveal the presence of phenolic compounds, oryzanols, tocopherols, and tocotrienols. Ethyl acetate (EtOAc) can extract more oryzanols (1.55 ± 0.20 g/kg rice bran). Meanwhile, the methanol (MeOH) extract possesses a higher yield in total contents (15.42 ± 1.41 g/kg bran), which includes phenolic compounds (2.69 ± 0.29 g gallic acid equivalent/kg bran), tocopherols (251 ± 26 mg/kg bran) and tocotrienols (111 ± 4 mg/kg bran). The MeOH extract exhibits more effective antioxidant activity against various oxidative systems in vitro, including the inhibition of linoleic acid peroxidation (33.89%), scavenging of DPPH radicals (83.88%), and reducing power. It is found that the yield, total content in phenolic compounds and tocols of the extracts increase with increasing Synder's polarity value and viscosity, which can then be used as the indices in isolation of the desired rice bran phytochemicals extracts.

  10. Comparison of aroma active and sulfur volatiles in three fragrant rice cultivars using GC-olfactometry and GC-PFPD.

    PubMed

    Mahattanatawee, Kanjana; Rouseff, Russell L

    2014-07-01

    Aroma volatiles from three cooked fragrant rice types (Jasmine, Basmati and Jasmati) were characterised and identified using SPME GC-O, GC-PFPD and confirmed using GC-MS. A total of 26, 23, and 22 aroma active volatiles were observed in Jasmine, Basmati and Jasmati cooked rice samples. 2-Acetyl-1-pyrroline was aroma active in all three rice types, but the sulphur-based, cooked rice character impact volatile, 2-acetyl-2-thiazoline was aroma active only in Jasmine rice. Five additional sulphur volatiles were found to have aroma activity: dimethyl sulphide, 3-methyl-2-butene-1-thiol, 2-methyl-3-furanthiol, dimethyl trisulphide, and methional. Other newly-reported aroma active rice volatiles were geranyl acetate, β-damascone, β-damascenone, and ɑ-ionone, contributing nutty, sweet floral attributes to the aroma of cooked aromatic rice. The first two principal components from the principal component analysis of sulphur volatiles explained 60% of the variance. PC1 separated Basmati from the other two cultivars and PC2 completely separated Jasmine from Jasmati cultivars. PMID:24518308

  11. Understanding salinity responses and adopting ‘omics-based’ approaches to generate salinity tolerant cultivars of rice

    PubMed Central

    Das, Priyanka; Nutan, Kamlesh K.; Singla-Pareek, Sneh L.; Pareek, Ashwani

    2015-01-01

    Soil salinity is one of the main constraints affecting production of rice worldwide, by reducing growth, pollen viability as well as yield of the plant. Therefore, detailed understanding of the response of rice towards soil salinity at the physiological and molecular level is a prerequisite for its effective management. Various approaches have been adopted by molecular biologists or breeders to understand the mechanism for salinity tolerance in plants and to develop salt tolerant rice cultivars. Genome wide analysis using ‘omics-based’ tools followed by identification and functional validation of individual genes is becoming one of the popular approaches to tackle this task. On the other hand, mutation breeding and insertional mutagenesis has also been exploited to obtain salinity tolerant crop plants. This review looks into various responses at cellular and whole plant level generated in rice plants toward salinity stress thus, evaluating the suitability of intervention of functional genomics to raise stress tolerant plants. We have tried to highlight the usefulness of the contemporary ‘omics-based’ approaches such as genomics, proteomics, transcriptomics and phenomics towards dissecting out the salinity tolerance trait in rice. In addition, we have highlighted the importance of integration of various ‘omics’ approaches to develop an understanding of the machinery involved in salinity response in rice and to move forward to develop salt tolerant cultivars of rice. PMID:26442026

  12. Simple sequence repeat markers in genetic divergence and marker-assisted selection of rice cultivars: a review.

    PubMed

    Kaur, Shubhneet; Panesar, Parmjit S; Bera, Manab B; Kaur, Varinder

    2015-01-01

    Sequencing of rice genome has facilitated the understanding of rice evolution and has been utilized extensively for mining of DNA markers to facilitate marker-assisted breeding. Simple sequence repeat (SSR) markers that are tandemly repeated nucleotide sequence motifs flanked by unique sequences are presently the maker of choice in rice improvement due to their abundance, co-dominant inheritance, high levels of allelic diversity, and simple reproducible assay. The current level of genome coverage by SSR markers in rice is sufficient to employ them for genotype identification and marker-assisted selection in breeding for mapping of genes and quantitative trait loci analysis. This review provides comprehensive information on the mapping and applications of SSR markers in investigation of rice cultivars to study their genetic divergence and marker-assisted selection of important agronomic traits.

  13. Divergent responses of methanogenic archaeal communities in two rice cultivars to elevated ground-level O3.

    PubMed

    Zhang, Jianwei; Tang, Haoye; Zhu, Jianguo; Lin, Xiangui; Feng, Youzhi

    2016-06-01

    Inhibitive effect of elevated ground-level ozone (O3) on paddy methane (CH4) emission varies with rice cultivars. However, little information is available on its microbial mechanism. For this purpose, the responses of methane-metabolizing microorganisms, methanogenic archaea and methanotrophic bacteria to O3 pollution were investigated in the O3-tolerant (YD6) and the O3-sensitive (IIY084) cultivars at two rice growth stages in Free Air Concentration Elevation of O3 (O3-FACE) system of China. It was found that O3 pollution didn't change the abundances of Type I and Type II methanotrophic bacteria at two rice stages. For methanogenic archaea, their abundances in both cultivars were decreased by O3 pollution at the tillering stage. Furthermore, a greater negative influence on methanogenic archaeal community was observed on IIY084 than on YD6: at tillering stage, the alpha diversity indices of methanogenic archaeal community in IIY084 was decreased to a greater extent than in YD6; IIY084 shifted methanogenic archaeal community composition and decreased the abundances and the diversities of Methanosarcinaceae and Methanosaetaceae as well as the abundance of Methanomicrobiales, while the diversity of Methanocellaceae were increased in YD6. These findings indicate that the variations in the responses of paddy CH4 emission to O3 pollution between cultivars could result from the divergent responses of their methanogenic archaea. PMID:26895536

  14. Isolation and characterization of plant growth promoting endophytic diazotrophic bacteria from Korean rice cultivars.

    PubMed

    Ji, Sang Hye; Gururani, Mayank Anand; Chun, Se-Chul

    2014-01-20

    We have isolated 576 endophytic bacteria from the leaves, stems, and roots of 10 rice cultivars and identified 12 of them as diazotrophic bacteria using a specific primer set of nif gene. Through 16S rDNA sequence analysis, nifH genes were confirmed in the two species of Penibacillus, three species of Microbacterium, three Bacillus species, and four species of Klebsiella. Rice seeds treated with these plant growth-promoting bacteria (PGPB) showed improved plant growth, increased height and dry weight and antagonistic effects against fungal pathogens. In addition, auxin and siderophore producing ability, and phosphate solubilizing activity were studied for the possible mechanisms of plant growth promotion. Among 12 isolates tested, 10 strains have shown higher auxin producing activity, 6 isolates were confirmed as strains with high siderophore producing activity while 4 isolates turned out to have high phosphate-solubilizing activity. These results strongly suggest that the endophytic diazotrophic bacteria characterized in this study could be successfully used to promote plant growth and inducing fungal resistance in plants.

  15. Regeneration of plantlets from mature embryo calli of Western Ghats land race cultivar of rice, Oryza sativa L.

    PubMed

    Gnanesh, A U; Krishna, V; Kumar, R Shashi; Venkatesh; Kumar, S R Santosh; Shashidhar, H E

    2012-02-01

    The Malnad region located in the Western Ghats of Karnataka is known for the cultivation of indigenous rain fed land race cultivar of rice. The present study was to investigate the callogenic and caulogenic potentialities of the two indigenous rice cultivar namely Karimundaga and Kanadatumba using dehusked mature embryo explants. For callus and shoot bud differentiation, the explants were cultured on Murashige and Skoog (MS) medium supplemented with 2,4-D (1-3 mg/L), IAA (1-2 mg/L), Kn (1-4 mg/L) and BAP (1-4 mg/L). The morphogenic potentialities of the two rice cultivar differed in texture of callus. In both the cultivar callogenic frequency was optimized at 1 mg/L 2,4-D concentration, it was 94% in Karimundaga and 58% in Kanadatumba. Supplementation of IAA either alone (1-2 mg/L) or in combination with Kn or BAP at 1 to 4 mg/L concentration of each induces shoot bud differentiation from the calli. In the cultivar Karimundaga caulogenic frequency was highest (10.60 +/- 2.55) at 1.0 mg/L IAA and 4.0 mg/L BAP concentration. While in the cultivar Kanadatumba highest number of shoot buds (7.90 +/- 2.69) was differentiated at 1.0 mg/L IAA and 4.0 mg/L Kn concentration. The calli derived regenerants were successfully acclimatized in the greenhouse and agro-morphological variations were evaluated. The growth characteristics and yield related parameters exhibited by in vitro plants were lower than the in vivo plants.

  16. Genome-Wide Association Studies Reveal that Diverse Heading Date Genes Respond to Short and Long Day Lengths between Indica and Japonica Rice

    PubMed Central

    Han, Zhongmin; Zhang, Bo; Zhao, Hu; Ayaad, Mohammed; Xing, Yongzhong

    2016-01-01

    Rice is a short-day plant. Short-day length promotes heading, and long-day length suppresses heading. Many studies have evaluated rice heading in field conditions in which some individuals in the population were exposed to various day lengths, including short and long days, prior to a growth phase transition. In this study, we investigated heading date under natural short-day conditions (SD) and long-day conditions (LD) for 100s of accessions and separately conducted genome-wide association studies within indica and japonica subpopulations. Under LD, three and four quantitative trait loci (QTLs) were identified in indica and japonica subpopulations, respectively, two of which were less than 80 kb from the known genes Hd17 and Ghd7. But no common QTLs were detected in both subpopulations. Under SD, six QTLs were detected in indica, three of which were less than 80 kb from the known heading date genes Ghd7, Ehd1, and RCN1. But no QTLs were detected in japonica subpopulation. qHd3 under SD and qHd4 under LD were two novel major QTLs, which deserve isolation in the future. Eleven known heading date genes were used to test the power of association mapping at the haplotype level. Hd17, Ghd7, Ehd1, and RCN1 were again detected at more significant level and three additional genes, Hd3a, OsMADS56, and Ghd7.1, were detected. However, of the detected seven genes, only one gene, Hd17, was commonly detected in both subpopulations and two genes, Ghd7 and Ghd7.1, were commonly detected in indica subpopulation under both conditions. Moreover, haplotype analysis identified favorable haplotypes of Ghd7 and OsMADS56 for breeding design. In conclusion, diverse heading date genes/QTLs between indica and japonica subpopulations responded to SD and LD, and haplotype-level association mapping was more powerful than SNP-level association in rice. PMID:27621738

  17. Genome-Wide Association Studies Reveal that Diverse Heading Date Genes Respond to Short and Long Day Lengths between Indica and Japonica Rice.

    PubMed

    Han, Zhongmin; Zhang, Bo; Zhao, Hu; Ayaad, Mohammed; Xing, Yongzhong

    2016-01-01

    Rice is a short-day plant. Short-day length promotes heading, and long-day length suppresses heading. Many studies have evaluated rice heading in field conditions in which some individuals in the population were exposed to various day lengths, including short and long days, prior to a growth phase transition. In this study, we investigated heading date under natural short-day conditions (SD) and long-day conditions (LD) for 100s of accessions and separately conducted genome-wide association studies within indica and japonica subpopulations. Under LD, three and four quantitative trait loci (QTLs) were identified in indica and japonica subpopulations, respectively, two of which were less than 80 kb from the known genes Hd17 and Ghd7. But no common QTLs were detected in both subpopulations. Under SD, six QTLs were detected in indica, three of which were less than 80 kb from the known heading date genes Ghd7, Ehd1, and RCN1. But no QTLs were detected in japonica subpopulation. qHd3 under SD and qHd4 under LD were two novel major QTLs, which deserve isolation in the future. Eleven known heading date genes were used to test the power of association mapping at the haplotype level. Hd17, Ghd7, Ehd1, and RCN1 were again detected at more significant level and three additional genes, Hd3a, OsMADS56, and Ghd7.1, were detected. However, of the detected seven genes, only one gene, Hd17, was commonly detected in both subpopulations and two genes, Ghd7 and Ghd7.1, were commonly detected in indica subpopulation under both conditions. Moreover, haplotype analysis identified favorable haplotypes of Ghd7 and OsMADS56 for breeding design. In conclusion, diverse heading date genes/QTLs between indica and japonica subpopulations responded to SD and LD, and haplotype-level association mapping was more powerful than SNP-level association in rice. PMID:27621738

  18. Origin of seed shattering in rice (Oryza sativa L.).

    PubMed

    Lin, Zhongwei; Griffith, Megan E; Li, Xianran; Zhu, Zuofeng; Tan, Lubing; Fu, Yongcai; Zhang, Wenxu; Wang, Xiangkun; Xie, Daoxin; Sun, Chuanqing

    2007-06-01

    A critical evolutionary step during rice domestication was the elimination of seed shattering. Wild rice disperses seeds freely at maturity to guarantee the propagation, while cultivated rice retains seeds on the straws to make easy harvest and decrease the loss of production. The molecular basis for this key event during rice domestication remains to be elucidated. Here we show that the seed shattering is controlled by a single dominant gene, Shattering1 (SHA1), encoding a member of the trihelix family of plant-specific transcription factors. SHA1 was mapped to a 5.5 kb genomic fragment, which contains a single open reading frame, using a backcrossed population between cultivated rice Teqing and an introgression line IL105 with the seed shattering habit derived from perennial common wild rice, YJCWR. The predicted amino acid sequence of SHA1 in YJCWR and IL105 is distinguished from that in eight domesticated rice cultivars, including Teqing, by only a single amino acid substitution (K79N) caused by a single nucleotide change (g237t). Further sequence verification on the g237t mutation site revealed that the g237t mutation is present in all the domesticated rice cultivars, including 92 indica and 108 japonica cultivars, but not in any of the 24 wild rice accessions examined. Our results demonstrate that the g237t mutation in SHA1 accounts for the elimination of seed shattering, and that all the domesticated rice cultivars harbor the mutant sha1 gene and therefore have lost the ability to shed their seeds at maturity. In addition, our data support the theory that the non-shattering trait selection during rice domestication occurred prior to the indica-japonica differentiation in rice evolutionary history. PMID:17216230

  19. Development of formulae for estimating amylose content and resistant starch content based on the pasting properties measured by RVA of Japonica polished rice and starch.

    PubMed

    Nakamura, Sumiko; Katsura, Junji; Kato, Kiyoko; Ohtsubo, Ken'ichi

    2016-01-01

    We searched for the easy and simple method to measure the novel indicators which reflect not only AAC, but also (RS) based on pasting properties using RVA. Novel indexes such as SB/Con and Max/Fin (Maximum viscosity/Minimum viscosity) ratios had a very high correlation with proportion of intermediate and long chains of amylopectin; Fb1+2+3 (DP ≧ 13). In Japonica polished rice, estimation formulae for AAC and RS content were developed using novel indexes based on pasting properties by RVA, and these equations showed determination coefficients of 0.89 and 0.80 for calibration and 0.71 and 0.75 for validation test. We developed the estimation formulae for AAC and RS content for Japonica starch samples. These equations showed determination coefficients of 0.86 and 1.00 for calibration and 0.76 and 0.83 for validation test, which showed that these equations can be applied to the unknown rice samples.

  20. Analysis of transcript and metabolite levels in Italian rice (Oryza sativa L.) cultivars subjected to osmotic stress or benzothiadiazole treatment.

    PubMed

    Baldoni, Elena; Mattana, Monica; Locatelli, Franca; Consonni, Roberto; Cagliani, Laura R; Picchi, Valentina; Abbruscato, Pamela; Genga, Annamaria

    2013-09-01

    One of the major objectives of rice (Oryza sativa L.) breeding programs is the development of new varieties with higher tolerance/resistance to both abiotic and biotic stresses. In this study, Italian rice cultivars were subjected to osmotic stress or benzothiadiazole (BTH) treatments. An analysis of the expression of selected genes known to be involved in the stress response and (1)H nuclear magnetic resonance ((1)H NMR) metabolic profiling were combined with multivariate statistical analyses to elucidate potential correlations between gene expression or metabolite content and observed tolerant/resistant phenotypes. We observed that the expression of three chosen genes (two WRKY genes and one peroxidase encoding gene) differed between susceptible and resistant cultivars in response to BTH treatments. Moreover, the analysis of metabolite content, in particular in the osmotic stress experiment, enabled discrimination between selected cultivars based on differences in the accumulation of some primary metabolites, primarily sugars. This research highlights the potential usefulness of this approach to characterise rice varieties based on transcriptional or metabolic changes due to adverse environmental conditions.

  1. Crop performance and weed suppression by weed-suppressive rice cultivars in furrow- and flood-irrigated systems under reduced herbicide inputs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Weed control in rice is challenging, particularly in light of increased resistance to herbicides in weed populations and diminishing availability of irrigation water. Certain indica rice cultivars can produce high yields and suppress weeds in conventional flood-irrigated, drill-seeded systems in the...

  2. Seasonal CH4 and N2O emissions and plant growth characteristics of several cultivars in direct seeded rice systems

    NASA Astrophysics Data System (ADS)

    Simmonds, M.; Anders, M. M.; Adviento-Borbe, M. A.; Van Kessel, C.; McClung, A.; Linquist, B.

    2014-12-01

    Understanding cultivar effects on field greenhouse gas (GHG) emissions in rice (Oryza sativa L.) systems is needed to improve the accuracy of predictive models used for estimating GHG emissions, and to determine to what extent choice of cultivar may have on GHG mitigation. We compared CH4 and N2O emissions, global warming potential (GWP = N2O + CH4), yield-scaled GWP (GWPY = GWP Mg-1 grain), and plant growth characteristics of 8 cultivars within 4 study sites in California and Arkansas. Seasonal CH4 emissions differed between cultivars by a factor of 2.1 and 1.3 at one California and one Arkansas site, respectively. Nitrous oxide emissions were negligible, comprised <10% of GWP, and were not different among cultivars. When sites and cultivars were pooled, and data were normalized to site averages, there was a positive correlation (r = 0.33) between root biomass at heading and seasonal CH4 emissions, but no correlation with shoot biomass at heading, or grain or straw biomass at maturity. Although differences in GWP and GWPY were observed, the consistency of some of the trends was variable across sites, indicating the importance of the genotype x environment interaction. While no high-yielding and low CH4-emitting cultivars were identified at the California sites, among the Southern varieties tested at the Arkansas site, the lowest emitting cultivar had the highest yield. This highlights the potential for breeding high-yielding varieties with low GWP, the ideal scenario to achieve low GWPY due to simultaneously mitigating GHG emissions and improving global food security.

  3. Root-Derived Short-Chain Suberin Diacids from Rice and Rape Seed in a Paddy Soil under Rice Cultivar Treatments.

    PubMed

    Ji, Haishi; Ding, Yuanjun; Liu, Xiaoyu; Li, Lianqing; Zhang, Dengxiao; Li, Zichuan; Sun, Jingling; Lashari, Muhammad Siddique; Joseph, Stephen; Meng, Yuanduo; Kuzyakov, Yakov; Pan, Genxing

    2015-01-01

    Suberin-derived substituted fatty acids have been shown to be potential biomarkers for plant-derived carbon (C) in soils across ecosystems. Analyzing root derived suberin compounds bound in soil could help to understand the root input into a soil organic carbon pool. In this study, bound lipids were extracted and identified in root and topsoil samples. Short-chain suberin diacids were quantified under rice (Oryza sativa L.) and rape (Brassica campestris) rotations with different cultivar combinations in a Chinese rice paddy. After removal of free lipids with sequential extraction, the residual bound lipids were obtained with saponification and derivatization before analysis using gas chromatography-mass spectrometry (GC-MS). Diacids C16 and C18 in bound lipids were detected both in rice and rape root samples, while diacids C20 and C22 were detected only in rape root samples. Accordingly, diacids were quantified in both rhizosphere and bulk soil (0-15 cm). The amount of total root-derived diacids in bulk soil varied in a range of 5.6-9.6 mg/kg across growth stages and crop seasons. After one year-round rice-rape rotation, root-derived suberin diacids were maintained at a level of 7-9 mg/kg in bulk soil; this was higher under a super rice cultivar LY than under a hybrid cultivar IIY. While concentrations of the analyzed diacids were generally higher in rhizosphere than in bulk soil, the total diacid (DA) concentration was higher at the time of rape harvest than at rice harvest, suggesting that rape roots made a major contribution to the preservation of diacids in the paddy. Moreover, the net change in the concentration and the ratios of C16:0 DA to C18:1 DA, and of C16:0 DA to C18:0 DA, over a whole growing season, were greater under LY than under IIY, though there was no difference between cultivars within a single growth stage. Overall, total concentration of root-derived suberin diacids was found to be positively correlated to soil organic carbon concentration

  4. Root-Derived Short-Chain Suberin Diacids from Rice and Rape Seed in a Paddy Soil under Rice Cultivar Treatments

    PubMed Central

    Ji, Haishi; Ding, Yuanjun; Liu, Xiaoyu; Li, Lianqing; Zhang, Dengxiao; Li, Zichuan; Sun, Jingling; Lashari, Muhammad Siddique; Joseph, Stephen; Meng, Yuanduo; Kuzyakov, Yakov; Pan, Genxing

    2015-01-01

    Suberin-derived substituted fatty acids have been shown to be potential biomarkers for plant-derived carbon (C) in soils across ecosystems. Analyzing root derived suberin compounds bound in soil could help to understand the root input into a soil organic carbon pool. In this study, bound lipids were extracted and identified in root and topsoil samples. Short-chain suberin diacids were quantified under rice (Oryza sativa L.) and rape (Brassica campestris) rotations with different cultivar combinations in a Chinese rice paddy. After removal of free lipids with sequential extraction, the residual bound lipids were obtained with saponification and derivatization before analysis using gas chromatography–mass spectrometry (GC-MS). Diacids C16 and C18 in bound lipids were detected both in rice and rape root samples, while diacids C20 and C22 were detected only in rape root samples. Accordingly, diacids were quantified in both rhizosphere and bulk soil (0–15 cm). The amount of total root-derived diacids in bulk soil varied in a range of 5.6–9.6 mg/kg across growth stages and crop seasons. After one year-round rice-rape rotation, root-derived suberin diacids were maintained at a level of 7–9 mg/kg in bulk soil; this was higher under a super rice cultivar LY than under a hybrid cultivar IIY. While concentrations of the analyzed diacids were generally higher in rhizosphere than in bulk soil, the total diacid (DA) concentration was higher at the time of rape harvest than at rice harvest, suggesting that rape roots made a major contribution to the preservation of diacids in the paddy. Moreover, the net change in the concentration and the ratios of C16:0 DA to C18:1 DA, and of C16:0 DA to C18:0 DA, over a whole growing season, were greater under LY than under IIY, though there was no difference between cultivars within a single growth stage. Overall, total concentration of root-derived suberin diacids was found to be positively correlated to soil organic carbon

  5. Root-Derived Short-Chain Suberin Diacids from Rice and Rape Seed in a Paddy Soil under Rice Cultivar Treatments.

    PubMed

    Ji, Haishi; Ding, Yuanjun; Liu, Xiaoyu; Li, Lianqing; Zhang, Dengxiao; Li, Zichuan; Sun, Jingling; Lashari, Muhammad Siddique; Joseph, Stephen; Meng, Yuanduo; Kuzyakov, Yakov; Pan, Genxing

    2015-01-01

    Suberin-derived substituted fatty acids have been shown to be potential biomarkers for plant-derived carbon (C) in soils across ecosystems. Analyzing root derived suberin compounds bound in soil could help to understand the root input into a soil organic carbon pool. In this study, bound lipids were extracted and identified in root and topsoil samples. Short-chain suberin diacids were quantified under rice (Oryza sativa L.) and rape (Brassica campestris) rotations with different cultivar combinations in a Chinese rice paddy. After removal of free lipids with sequential extraction, the residual bound lipids were obtained with saponification and derivatization before analysis using gas chromatography-mass spectrometry (GC-MS). Diacids C16 and C18 in bound lipids were detected both in rice and rape root samples, while diacids C20 and C22 were detected only in rape root samples. Accordingly, diacids were quantified in both rhizosphere and bulk soil (0-15 cm). The amount of total root-derived diacids in bulk soil varied in a range of 5.6-9.6 mg/kg across growth stages and crop seasons. After one year-round rice-rape rotation, root-derived suberin diacids were maintained at a level of 7-9 mg/kg in bulk soil; this was higher under a super rice cultivar LY than under a hybrid cultivar IIY. While concentrations of the analyzed diacids were generally higher in rhizosphere than in bulk soil, the total diacid (DA) concentration was higher at the time of rape harvest than at rice harvest, suggesting that rape roots made a major contribution to the preservation of diacids in the paddy. Moreover, the net change in the concentration and the ratios of C16:0 DA to C18:1 DA, and of C16:0 DA to C18:0 DA, over a whole growing season, were greater under LY than under IIY, though there was no difference between cultivars within a single growth stage. Overall, total concentration of root-derived suberin diacids was found to be positively correlated to soil organic carbon concentration

  6. Effects of tire rubber ash and zinc sulfate on crop productivity and cadmium accumulation in five rice cultivars under field conditions.

    PubMed

    Fahad, Shah; Hussain, Saddam; Khan, Fahad; Wu, Chao; Saud, Shah; Hassan, Shah; Ahmad, Naeem; Gang, Deng; Ullah, Abid; Huang, Jianliang

    2015-08-01

    Cadmium (Cd) is among the most widespread and toxic heavy metals becoming a severe threat to humans. A field study was conducted to examine the role of various zinc (Zn) fertilization treatments and cultivars on crop productivity and Zn and Cd concentrations in brown rice and rice straw. The Zn fertilization treatments included an unfertilized control, foliar applied Zn sulfate (ZnSO4) at panicle initiation stage, foliar applied ZnSO4 at milky stage, soil application of rubber ash, and soil-applied ZnSO4, while five rice cultivars were Swat-1, Shadab, Shua-92, Swat-2, and Sada Hayat. All the Zn fertilization treatments resulted in significantly higher number of panicles, number of spikelets per panicles, spikelet fertility, 1,000-grain weight, grain yield, brown rice and rice straw Zn concentrations, and significantly lower Cd concentrations. Soil application of rubber ash remained the best among all Zn fertilization treatments as it resulted in 73% higher grain yield and reduced Cd concentration by 51% as compared with control. Variations were also apparent among cultivars, and Shua-92 and Swat-2 performed better in terms of all studied attributes as compared with other cultivars. Conclusively, cultivar selection and Zn application are effective strategies to improve rice grain yield as well as quality. Rubber ash appeared a viable source of Zn having the ability to increase yield along with reducing Cd accumulation.

  7. Regulation of glutamine synthetase isoforms in two differentially drought-tolerant rice (Oryza sativa L.) cultivars under water deficit conditions.

    PubMed

    Singh, Kamal Krishna; Ghosh, Shilpi

    2013-02-01

    KEY MESSAGE : The regulation of GS isoforms by WD was organ specific. Two GS isoforms i.e. OsGS1;1 and OsGS2 were differentially regulated in IR-64 (drought-sensitive) and Khitish (drought-tolerant) cultivars of rice. Water deficit (WD) has adverse effect on rice (Oryza sativa L.) and acclimation requires essential reactions of primary metabolism to continue. Rice plants utilize ammonium as major nitrogen source, which is assimilated into glutamine by the reaction of Glutamine synthetase (GS, EC 6.3.1.2). Rice plants possess one gene (OsGS2) for chloroplastic GS2 and three genes (OsGS1;1, OsGS1;2 and OsGS1;3) for cytosolic GS1. Here, we report the effect of WD on regulation of GS isoforms in drought-sensitive (cv. IR-64) and drought-tolerant (cv. Khitish) rice cultivars. Under WD, total GS activity in root and leaf decreased significantly in IR-64 seedlings in comparison to Khitish seedlings. The reduced GS activity in IR-64 leaf was mainly due to decrease in GS2 activity, which correlated with decrease in corresponding transcript and polypeptide contents. GS1 transcript and polypeptide accumulated in leaf during WD, however, GS1 activity was maintained at a constant level. Total GS activity in stem of both the varieties was insensitive to WD. Among GS1 genes, OsGS1;1 expression was differently regulated by WD in the two rice varieties. Its transcript accumulated more abundantly in IR-64 leaf than in Khitish leaf. Following WD, OsGS1;1 mRNA level in stem and root tissues declined in IR-64 and enhanced in Khitish. A steady OsGS1;2 expression patterns were noted in leaf, stem and root of both the cultivars. Results suggest that OsGS2 and OsGS1;1 expression may contribute to drought tolerance of Khitish cultivar under WD conditions.

  8. Impact of rice cultivar and organ on elemental composition of phytoliths and the release of bio-available silicon

    PubMed Central

    Li, Zimin; Song, Zhaoliang; Cornelis, Jean-Thomas

    2014-01-01

    The continental bio-cycling of silicon (Si) plays a key role in global Si cycle and as such partly controls global carbon (C) budget through nutrition of marine and terrestrial biota, accumulation of phytolith-occluded organic carbon (PhytOC) and weathering of silicate minerals. Despite the key role of elemental composition of phytoliths on their solubility in soils, the impact of plant cultivar and organ on the elemental composition of phytoliths in Si high-accumulator plants, such as rice (Oryza sativa) is not yet fully understood. Here we show that rice cultivar significantly impacts the elemental composition of phytoliths (Si, Al, Fe, and C) in different organs of the shoot system (grains, sheath, leaf and stem). The amount of occluded OC within phytoliths is affected by contents of Si, Al, and Fe in plants, while independent of the element composition of phytoliths. Our data document, for different cultivars, higher bio-available Si release from phytoliths of leaves and sheaths, which are characterized by higher enrichment with Al and Fe (i.e., lower Si/Al and Si/Fe ratios), compared to grains and stems. We indicate that phytolith solubility in soils may be controlled by rice cultivar and type of organs. Our results highlight that the role of the morphology, the hydration rate and the chemical composition in the solubility of phytoliths and the kinetic release of Si in soil solution needs to be studied further. This is central to a better understanding of the impact of soil amendment with different plant organs and cultivars on soil OC stock and on the delivery of dissolved Si as we show that sheath and leaf rice organs are both characterized by higher content of OC occluded in phytolith and higher phytolith solubility compared to grains and stems. Our study shows the importance of studying the impact of the agro-management on the evolution of sinks and sources of Si and C in soils used for Si-high accumulator plants. PMID:25346741

  9. Soil Texture and Cultivar Effects on Rice (Oryza sativa, L.) Grain Yield, Yield Components and Water Productivity in Three Water Regimes.

    PubMed

    Dou, Fugen; Soriano, Junel; Tabien, Rodante E; Chen, Kun

    2016-01-01

    The objective of this study was to determine the effects of water regime/soil condition (continuous flooding, saturated, and aerobic), cultivar ('Cocodrie' and 'Rondo'), and soil texture (clay and sandy loam) on rice grain yield, yield components and water productivity using a greenhouse trial. Rice grain yield was significantly affected by soil texture and the interaction between water regime and cultivar. Significantly higher yield was obtained in continuous flooding than in aerobic and saturated soil conditions but the latter treatments were comparable to each other. For Rondo, its grain yield has decreased with soil water regimes in the order of continuous flooding, saturated and aerobic treatments. The rice grain yield in clay soil was 46% higher than in sandy loam soil averaged across cultivar and water regime. Compared to aerobic condition, saturated and continuous flooding treatments had greater panicle numbers. In addition, panicle number in clay soil was 25% higher than in sandy loam soil. The spikelet number of Cocodrie was 29% greater than that of Rondo, indicating that rice cultivar had greater effect on spikelet number than soil type and water management. Water productivity was significantly affected by the interaction of water regime and cultivar. Compared to sandy loam soil, clay soil was 25% higher in water productivity. Our results indicated that cultivar selection and soil texture are important factors in deciding what water management option to practice.

  10. Soil Texture and Cultivar Effects on Rice (Oryza sativa, L.) Grain Yield, Yield Components and Water Productivity in Three Water Regimes

    PubMed Central

    Dou, Fugen; Soriano, Junel; Tabien, Rodante E.; Chen, Kun

    2016-01-01

    The objective of this study was to determine the effects of water regime/soil condition (continuous flooding, saturated, and aerobic), cultivar (‘Cocodrie’ and ‘Rondo’), and soil texture (clay and sandy loam) on rice grain yield, yield components and water productivity using a greenhouse trial. Rice grain yield was significantly affected by soil texture and the interaction between water regime and cultivar. Significantly higher yield was obtained in continuous flooding than in aerobic and saturated soil conditions but the latter treatments were comparable to each other. For Rondo, its grain yield has decreased with soil water regimes in the order of continuous flooding, saturated and aerobic treatments. The rice grain yield in clay soil was 46% higher than in sandy loam soil averaged across cultivar and water regime. Compared to aerobic condition, saturated and continuous flooding treatments had greater panicle numbers. In addition, panicle number in clay soil was 25% higher than in sandy loam soil. The spikelet number of Cocodrie was 29% greater than that of Rondo, indicating that rice cultivar had greater effect on spikelet number than soil type and water management. Water productivity was significantly affected by the interaction of water regime and cultivar. Compared to sandy loam soil, clay soil was 25% higher in water productivity. Our results indicated that cultivar selection and soil texture are important factors in deciding what water management option to practice. PMID:26978525

  11. Soil Texture and Cultivar Effects on Rice (Oryza sativa, L.) Grain Yield, Yield Components and Water Productivity in Three Water Regimes.

    PubMed

    Dou, Fugen; Soriano, Junel; Tabien, Rodante E; Chen, Kun

    2016-01-01

    The objective of this study was to determine the effects of water regime/soil condition (continuous flooding, saturated, and aerobic), cultivar ('Cocodrie' and 'Rondo'), and soil texture (clay and sandy loam) on rice grain yield, yield components and water productivity using a greenhouse trial. Rice grain yield was significantly affected by soil texture and the interaction between water regime and cultivar. Significantly higher yield was obtained in continuous flooding than in aerobic and saturated soil conditions but the latter treatments were comparable to each other. For Rondo, its grain yield has decreased with soil water regimes in the order of continuous flooding, saturated and aerobic treatments. The rice grain yield in clay soil was 46% higher than in sandy loam soil averaged across cultivar and water regime. Compared to aerobic condition, saturated and continuous flooding treatments had greater panicle numbers. In addition, panicle number in clay soil was 25% higher than in sandy loam soil. The spikelet number of Cocodrie was 29% greater than that of Rondo, indicating that rice cultivar had greater effect on spikelet number than soil type and water management. Water productivity was significantly affected by the interaction of water regime and cultivar. Compared to sandy loam soil, clay soil was 25% higher in water productivity. Our results indicated that cultivar selection and soil texture are important factors in deciding what water management option to practice. PMID:26978525

  12. Morphological and starch structural characteristics of the Japonica rice mutant variety Seolgaeng for dry-milled flour

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Producing fine, good quality rice flour is more difficult than wheat flour because the rice grain is harder. In this study, we analyzed the relationship between the morphology and starch of kernels from genetically different rice varieties that can be used to make dry-milled flour. The non-glutinous...

  13. Genotypic variation in the uptake, accumulation, and translocation of di-(2-ethylhexyl) phthalate by twenty cultivars of rice (Oryza sativa L.).

    PubMed

    Cai, Quan-Ying; Xiao, Pei-Yun; Chen, Tong; Lü, Huixiong; Zhao, Hai-Ming; Zeng, Qiao-Yun; Li, Yan-Wen; Li, Hui; Xiang, Lei; Mo, Ce-Hui

    2015-06-01

    Agricultural soil in China contains high levels of di-(2-ethylhexyl) phthalate (DEHP), especially in paddy-field soil of Guangdong province of China, but the accumulation and translocation of DEHP by rice (Oryza sativa L.) remains unknown. In the present study, twenty rice cultivars were cultivated in paddy soil spiked with DEHP, and variations in DEHP accumulation and translocation among various cultivars were investigated. Our results showed that DEHP concentrations in roots and shoots of different rice cultivars at four growth stages (i.e., ripening, tillering, jointing, and flowering stages) varied greatly from 0.26 to 11.8 mg/kg (dry weight, dw) and 0.40 to 7.58 mg/kg (dw), respectively. No obvious change over time was observed. The greatest variation in DEHP concentrations among the rice cultivars occurred at ripening stage, whereas the lowest variation at flowering stage. During ripening stage, the largest variation in DEHP concentrations among cultivars were observed in stems (varying from 0.35 to 13.2 mg/kg), whereas the least one was observed in roots (ranging from 1.01 to 5.72 mg/kg). Significant differences in DEHP concentrations in the roots, stems, leaves and grains of most rice cultivars were found. The translocation factors of DEHP from roots to stems or stems to leaves were higher than those from shoots to grains. Overall, cultivars Tianfengyou 316, Wuyou 308, and Peizataifeng, which contained low levels of DEHP in grains but high levels in shoots, were ideal cultivars for simultaneous production of safe food and phytoremediation of contaminated soil.

  14. Cadmium accumulation retard activity of functional components of photo assimilation and growth of rice cultivars amended with vermicompost.

    PubMed

    Sebastian, Abin; Prasad, M N V

    2013-01-01

    Cadmium (Cd) uptake mediated alterations in functional components of photo assimilation during conversion of cow dung and poultry cast to vermicompost were studied in two Indian rice cultivars; MO 16 and MTU 7029. It was found that higher amount of Cd accumulate in plants grown in soil amended with vermicompost which in turn damaged functional components in photo assimilation. Enhancement of root growth was recognized as reason for Cd accumulation. Metabolic alterations noticed among plants were not taken place during application of raw materials used for vermicomposting such as cow dung and poultry cast amendment. Rice varieties accumulated Cd differentially where MTU 7029 accumulated more Cd compare to MO 16. It was also noticed that existence of negative correlation between zinc status of the plant and Cd accumulation.

  15. Economics of weed suppressive rice cultivars in flood- and furrow-irrigated systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Weeds are a major constraint to rice production. In the U.S, weeds in rice are controlled primarily with synthetic herbicides. Intensive herbicide application in rice also has many potential drawbacks, resulting in environmental pollution, human health concerns, and development of weed resistance. B...

  16. Disease severity and yield potential of rice cultivars in organic production systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The market demand for organically produced rice has driven the steady increase in the acreage of organic rice in the U. S., with Texas and California being the largest states. Yield potential and disease management are among the principal challenges associated with organic rice production. We evalua...

  17. Sequence, expression and tissue localization of a gene encoding a makorin RING zinc-finger protein in germinating rice (Oryza sativa L. ssp. Japonica) seeds.

    PubMed

    Arumugam, Thangavelu U; Davies, Eric; Morita, Eugene Hayato; Abe, Shunnosuke

    2007-01-01

    The makorin (MKRN) RING finger protein gene family encodes proteins (makorins) with a characteristic array of zinc-finger motifs and which are present in a wide array of eukaryotes. In the present study, we analyzed the structure and expression of a putative makorin RING finger protein gene in rice (Oryza sativa L. ssp. Japonica cv. Nipponbare). From the analysis of the genomic (AP003543), mRNA (AK120250) and deduced protein (BAD61603) sequences of the putative MKRN gene of rice, obtained from GenBank, we found that it was indeed a bona fide member of the MKRN gene family. The rice MKRN cDNA encoded a protein with four C3H zinc-finger-motifs, one putative Cys-His zinc-finger motif, and one RING zinc-finger motif. The presence of this distinct motif organization and overall amino acid identity clearly indicate that this gene is indeed a true MKRN ortholog. We isolated RNA from embryonic axes of rice seeds at various stages of imbibition and germination and studied the temporal expression profile of MKRN by RT-PCR. This analysis revealed that MKRN transcripts were present at all the time points studied. It was at very low levels in dry seeds, increased slowly during imbibition and germination, and slightly declined in the seedling growth stage. After 6days of germination, an organ-dependent expression pattern of MKRN was observed: highest in roots and moderate in leaves. Similarly to MKRN transcripts, transcripts of cytoskeletal actin and tubulin were also detected in dry embryos, steadily increased during imbibition and germination and leveled off after 24h of germination. We studied the spatial expression profile of MKRN in rice tissues, by using a relatively fast, simple and effective non-radioactive mRNA in situ hybridization (NRISH) technique, which provided the first spatial experimental data that hints at the function of a plant makorin. This analysis revealed that MKRN transcripts were expressed in young plumules, lateral root primordia, leaf primordia

  18. Soil amendments and cultivar selection can improve rice yield in salt-influenced (tsunami-affected) paddy fields in Sri Lanka.

    PubMed

    Reichenauer, Thomas G; Panamulla, Sunil; Subasinghe, Siripala; Wimmer, Bernhard

    2009-10-01

    The tsunami disaster in the Indian Ocean in December 2004 caused devastation of agricultural soils by salt water over wide areas. Many rice fields located close to the coast were affected by the flood of seawater. Electric conductivity (EC) of soils in tsunami-affected rice fields was found to be higher compared to unaffected fields 2 years after the tsunami. Four soil amendments (gypsum, dolomite, cinnamon ash and rice-husk-charcoal) were tested for their influence on improving the yield parameters of rice grown in a tsunami-affected and a non-affected area. Yield parameters were compared with an untreated control of the same cultivar (AT362) and with a salt resistant rice variety (AT354). The salt resistant variety had the highest grain yield. The two amendments gypsum and rice-husk-charcoal led to an increase in grain yield compared to the untreated control, whereas dolomite and cinnamon ash had no significant effect on grain yield.

  19. [Effects of Rice Cultivar and Typical Soil Improvement Measures on the Uptake of Cd in Rice Grains].

    PubMed

    Wang, Mei-e; Peng, Chi; Chen, Wei-ping

    2015-11-01

    Cadmium pollution of rice is a big problem in agricultural food safety. The accident "Cd rice" occurred last year in Youxian County, Hunan Province caused serious social panic. In this study, trials on "Cd rice" controlling techniques specific to the Cd pollution in paddy soil in Youxian were investigated. It was suggested that the average Cd contents in rice grains of the rice variety "Zhu Liang You 06" in Datongqiao and Wangling were 0.167 and 0.127 mg x kg(-1), respectively, which were only equal to 20% of the contents of other varieties. The trials for stabilizing agents revealed that treatments of lime and mineral fertilizer decreased Cd contents in rice grains to 20-30% of the control. Plastic film-mulched treatment decreased the rice grain Cd to 50%. And combined treatment of plastic film-mulched and biochar and silicon foliar-fertilizer decreased 80% of rice Cd content. Single treatments of silicon foliar-fertilizer and combined treatment of silicon foliar-fertilizer and topdressing fertilizer decreased more than 90% of Cd content. Results of BCR revealed that the percentage of cationic exchangeable and/or carbonate associated Cd fraction was more than 55% for most of the soil samples. Lime treatment significantly decreased the percentage of cationic exchangeable and/or carbonate and oxides of Fe and Mn associated Cd and increased the crystalline structure of clay minerals associated Cd. The change rate reached about 20%. Our results suggested concentration of soil Cd and pH were the two significant factors impacting the uptake of Cd by rice grains. PMID:26911020

  20. [Effects of Rice Cultivar and Typical Soil Improvement Measures on the Uptake of Cd in Rice Grains].

    PubMed

    Wang, Mei-e; Peng, Chi; Chen, Wei-ping

    2015-11-01

    Cadmium pollution of rice is a big problem in agricultural food safety. The accident "Cd rice" occurred last year in Youxian County, Hunan Province caused serious social panic. In this study, trials on "Cd rice" controlling techniques specific to the Cd pollution in paddy soil in Youxian were investigated. It was suggested that the average Cd contents in rice grains of the rice variety "Zhu Liang You 06" in Datongqiao and Wangling were 0.167 and 0.127 mg x kg(-1), respectively, which were only equal to 20% of the contents of other varieties. The trials for stabilizing agents revealed that treatments of lime and mineral fertilizer decreased Cd contents in rice grains to 20-30% of the control. Plastic film-mulched treatment decreased the rice grain Cd to 50%. And combined treatment of plastic film-mulched and biochar and silicon foliar-fertilizer decreased 80% of rice Cd content. Single treatments of silicon foliar-fertilizer and combined treatment of silicon foliar-fertilizer and topdressing fertilizer decreased more than 90% of Cd content. Results of BCR revealed that the percentage of cationic exchangeable and/or carbonate associated Cd fraction was more than 55% for most of the soil samples. Lime treatment significantly decreased the percentage of cationic exchangeable and/or carbonate and oxides of Fe and Mn associated Cd and increased the crystalline structure of clay minerals associated Cd. The change rate reached about 20%. Our results suggested concentration of soil Cd and pH were the two significant factors impacting the uptake of Cd by rice grains.

  1. Improving salt tolerance of lowland rice cultivar 'Rassi' through marker-aided backcross breeding in West Africa.

    PubMed

    Bimpong, Isaac Kofi; Manneh, Baboucarr; Sock, Mamadou; Diaw, Faty; Amoah, Nana Kofi Abaka; Ismail, Abdelbagi M; Gregorio, Glenn; Singh, Rakesh Kumar; Wopereis, Marco

    2016-01-01

    Salt stress affects about 25% of the 4.4 million ha of irrigated and lowland systems for rice cultivation in West Africa (WA). A major quantitative trait locus (QTLs) on chromosome 1 (Saltol) that enhances tolerance to salt stress at the vegetative stage has enabled the use of marker-assisted selection (MAS) to develop salt-tolerant rice cultivar(s) in WA. We used 3 cycles of backcrossing with selection based on DNA markers and field-testing using 'FL478' as tolerant donor and the widely grown 'Rassi' as recurrent parent. In the BC3F2 stage, salt-tolerant lines with over 80% Rassi alleles except in the region around Saltol segment were selected. 429 introgression lines (Saltol-ILs) were identified as tolerant at vegetative stage, of which 116 were field-tested for four seasons at the reproductive stage. Sixteen Saltol-ILs had less yield loss (3-26% relative to control trials), and 8 Saltol-ILs showed high yield potential under stress and non-stress conditions. The 16 Saltol-ILs had been included for further African-wide testing prior to release in 6 WA countries. MAS reduced the time for germplasm improvement from at least 7 to about 4 years. Our objective is to combine different genes/QTLs conferring tolerance to stresses under one genetic background using MAS. PMID:26566846

  2. The relative contribution of climate and cultivar renewal to shaping rice yields in China since 1981

    NASA Astrophysics Data System (ADS)

    Song, Yanling; Wang, Chunyi; Ren, Guoyu; Zhao, Yanxia; Linderholm, Hans W.

    2015-04-01

    Rice is one of China's most important staple food crops, where the yields are strongly influenced by climate and rice variety renewal. Using high-quality weather data, rice growth, and agricultural practice data, the contribution of climatic variation on rice yield increases was analyzed from 1981 to 2009 in Wuchang, Northeast China. In this region, the annual mean surface air temperature increased by 0.6 °C/decade, and the accumulated temperature (>10 °C) increased by 120.1 °C/decade from 1981 to 2009, mainly related to global warming. During the same period, rice yields increased by 2,095 kg/ha*decade. To quantify the contribution of climate change to rice yield increases, a "climate similarity index" was devised, where the most important climate parameters for rice growth were compared among years. If the rice variety was changed between 2 years, while the climate conditions were similar, any yield change would be attributed to a rice variety renewal effect. Conversely, changes in rice yields that were not associated with variety changes were attributed to climate change. Our results showed that over the analyzed period, the influence of climate on yields was estimated to 805 kg/ha per decade, while the increasing trend due to rice variety renewal was estimated to 1,290 kg/ha per decade. Thus, 38 % of the yield increases can be related to climatic variation and the remaining 62 % to changes in rice varieties. Furthermore, the effect of variety renewal on the rice yield increases was more pronounced before the 1990s, while afterward, the yield increases were mainly influenced by climatic variations in Northeast China.

  3. Deficiencies in both starch synthase IIIa and branching enzyme IIb lead to a significant increase in amylose in SSIIa-inactive japonica rice seeds

    PubMed Central

    Asai, Hiroki; Abe, Natsuko; Matsushima, Ryo; Crofts, Naoko; Oitome, Naoko F.; Nakamura, Yasunori; Fujita, Naoko

    2014-01-01

    Starch synthase (SS) IIIa has the second highest activity of the total soluble SS activity in developing rice endosperm. Branching enzyme (BE) IIb is the major BE isozyme, and is strongly expressed in developing rice endosperm. A mutant (ss3a/be2b) was generated from wild-type japonica rice which lacks SSIIa activity. The seed weight of ss3a/be2b was 74–94% of that of the wild type, whereas the be2b seed weight was 59–73% of that of the wild type. There were significantly fewer amylopectin short chains [degree of polymerization (DP) ≤13] in ss3a/be2b compared with the wild type. In contrast, the amount of long chains (DP ≥25) connecting clusters of amylopectin in ss3a/be2b was higher than in the wild type and lower than in be2b. The apparent amylose content of ss3a/be2b was 45%, which was >1.5 times greater than that of either ss3a or be2b. Both SSIIIa and BEIIb deficiencies led to higher activity of ADP-glucose pyrophosphorylase (AGPase) and granule-bound starch synthase I (GBSSI), which partly explains the high amylose content in the ss3a/be2b endosperm. The percentage apparent amylose content of ss3a and ss3a/be2b at 10 days after flowering (DAF) was higher than that of the wild type and be2b. At 20 DAF, amylopectin biosynthesis in be2b and ss3a/be2b was not observed, whereas amylose biosynthesis in these lines was accelerated at 30 DAF. These data suggest that the high amylose content in the ss3a/be2b mutant results from higher amylose biosynthesis at two stages, up to 20 DAF and from 30 DAF to maturity. PMID:25071222

  4. Indica rice cultivar IRGA 424, transformed with cry genes of B. thuringiensis, provided high resistance against Spodoptera frugiperda (Lepidoptera: Noctuidae).

    PubMed

    Pinto, Laura Massochin Nunes; Fiuza, Lidia Mariana; Ziegler, Denize; De Oliveira, Jaime Vargas; Menezes, Valmir Gaedke; Bourrié, Isabelle; Meynard, Donaldo; Guiderdoni, Emmanuel; Breitler, Jean-Christophe; Altosaar, Illimar; Gantet, Pascal

    2013-12-01

    Plant expression of the entomopathogenic bacteria Bacillus thuringiensis cry gene has reduced the damage created by insect pests in several economically important cultures. For this study, we have conducted genetic transformation of the indica rice "IRGA 424", via Agrobacterium tumefaciens, using the B. thuringiensis cry1Aa and cry1B genes, with the objective of obtaining rice plants resistant to the insect pests from this culture. The gene constructions harbor the promoters maize proteinase inhibitor and ubiquitin. The results showed that high concentration of the hormone 2,4-dichlorophenoxyacetic acid and agarose as the gelling agent helped the production of embryogenic calli for the analyzed cultivar. More than 80% of the obtained transformed plants revealed the integration, using polymerase chain reaction, of the cry1Aa and cry1B genes. Analysis of the expression of the heterologous protein by Western blotting revealed the expression of the Cry1B delta-endotoxin in IRGA 424 plants transformed with the ubiquitin promoter. Data showed the production and dissemination of a high number of embryogenic calli in addition to obtaining plants transformed with the cry1Aa and cry1B genes until the reproductive phase. The feed bioassays with the transformed plants and Spodoptera frugiperda (JE Smith) larvae indicated high rates of mortality to the insect target. The highest corrected mortality rate achieved under laboratory conditions with Bt-rice plants transformed with the cry1B and cry1Aa genes was 94 and 84%, respectively. Thus, our results demonstrated the great potential of transformed Bt-rice plants in controlling the damage caused by these insect pests in rice paddy fields.

  5. Effects of Organic Fertility Management on Physicochemical Properties and Sensory Quality of Diverse Rice Cultivars.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The demand for organically-grown rice has increased with consumer demand for organic foods. The objective of this research was to determine if there are physicochemical differences in organically- and conventionally-grown rice that contribute to flavor and texture differences, as determined by desc...

  6. Uptake, translocation and transformation of antimony in rice (Oryza sativa L.) seedlings.

    PubMed

    Cai, Fei; Ren, Jinghua; Tao, Shu; Wang, Xilong

    2016-02-01

    Antimony (Sb), as a toxic metalloid, has been gaining increasing research concerns due mainly to its severe pollution in many places. Rice has been identified to be the dominant intake route of Sb by residents close to the Sb mining areas. A hydroponic experiment was conducted to investigate the difference in uptake, translocation and transformation of Sb in rice seedlings of four cultivars exposed to 0.2 or 1.0 mg/L of Sb(V). The results showed that mass concentration of iron plaque (mg/kg FW) formed at the root surfaces of cultivar N was the highest among all tested cultivars at both low and high exposure levels of Sb(V). The accumulated Sb concentration in iron plaque significantly increased with an increase in mass concentration of iron plaque formed at the rice root. The total amount of iron plaque (mg/pot) at rice root generally increased with increasing exposed Sb(V) concentration, which was closely associated with the increasing lipid peroxidation in roots. Concentration percentage of Sb in rice root significantly reduced as the corresponding value in the iron plaque increased, suggesting that iron plaque formation strongly suppressed uptake of Sb by rice root. Sb concentration in rice tissues followed an order: root > stem, leaf. The japonica rice (cultivars N and Z) exhibited a stronger translocation tendency of Sb from root to stem than indica hybrid rice (cultivars F and G). Translocation of Sb from root of cultivar F to its stem and leaf was sharply enhanced with increasing Sb exposure concentration. Sb(V) could be reduced to Sb(III) in rice tissues, especially in stems (10-26% of the total Sb). For the sake of food safety, the difference in uptake, translocation and transformation of Sb in rice species planted in Sb-contaminated soils should be taken into consideration.

  7. Uptake, translocation and transformation of antimony in rice (Oryza sativa L.) seedlings.

    PubMed

    Cai, Fei; Ren, Jinghua; Tao, Shu; Wang, Xilong

    2016-02-01

    Antimony (Sb), as a toxic metalloid, has been gaining increasing research concerns due mainly to its severe pollution in many places. Rice has been identified to be the dominant intake route of Sb by residents close to the Sb mining areas. A hydroponic experiment was conducted to investigate the difference in uptake, translocation and transformation of Sb in rice seedlings of four cultivars exposed to 0.2 or 1.0 mg/L of Sb(V). The results showed that mass concentration of iron plaque (mg/kg FW) formed at the root surfaces of cultivar N was the highest among all tested cultivars at both low and high exposure levels of Sb(V). The accumulated Sb concentration in iron plaque significantly increased with an increase in mass concentration of iron plaque formed at the rice root. The total amount of iron plaque (mg/pot) at rice root generally increased with increasing exposed Sb(V) concentration, which was closely associated with the increasing lipid peroxidation in roots. Concentration percentage of Sb in rice root significantly reduced as the corresponding value in the iron plaque increased, suggesting that iron plaque formation strongly suppressed uptake of Sb by rice root. Sb concentration in rice tissues followed an order: root > stem, leaf. The japonica rice (cultivars N and Z) exhibited a stronger translocation tendency of Sb from root to stem than indica hybrid rice (cultivars F and G). Translocation of Sb from root of cultivar F to its stem and leaf was sharply enhanced with increasing Sb exposure concentration. Sb(V) could be reduced to Sb(III) in rice tissues, especially in stems (10-26% of the total Sb). For the sake of food safety, the difference in uptake, translocation and transformation of Sb in rice species planted in Sb-contaminated soils should be taken into consideration. PMID:26686058

  8. Effects of cultivars, organic cropping management and environment on antioxidants in whole grain rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Whole grain rice contains functional antioxidants such as phenolics, flavonoids (including proanthocyanidins), vitamin E homologues (tocopherols and tocotrienols) and gamma-oryzanol that have positive effects on human health. These antioxidants are secondary metabolites in plants that can be induced...

  9. Identification and Characterization of Differentially Expressed Genes in Inferior and Superior Spikelets of Rice Cultivars with Contrasting Panicle-Compactness and Grain-Filling Properties

    PubMed Central

    Panda, Binay Bhushan; Mohaptra, Trupti; Das, Kaushik; Kariali, Ekamber; Mohapatra, Pravat Kumar; Shaw, Birendra Prasad

    2015-01-01

    Breeding programs for increasing spikelet number in rice have resulted in compactness of the panicle, accompanied by poor grain filling in inferior spikelets. Although the inefficient utilization of assimilate has been indicated as responsible for this poor grain filling, the underlying cause remains elusive. The current study utilized the suppression subtractive hybridization technique to identify 57 and 79 genes that overexpressed in the superior and inferior spikelets (with respect to each other), respectively, of the compact-panicle rice cultivar Mahalaxmi. Functional categorization of these differentially expressed genes revealed a marked metabolic difference between the spikelets according to their spatial location on the panicle. The expression of genes encoding seed storage proteins was dominant in inferior spikelets, whereas genes encoding regulatory proteins, such as serine-threonine kinase, zinc finger protein and E3 ligase, were highly expressed in superior spikelets. The expression patterns of these genes in the inferior and superior spikelets of Mahalaxmi were similar to those observed in another compact-panicle cultivar, OR-1918, but differed from those obtained in two lax-panicle cultivars, Upahar and Lalat. The results first suggest that the regulatory proteins abundantly expressed in the superior spikelets of compact-panicle cultivars and in both the superior and inferior spikelets of lax-panicle cultivars but poorly expressed in the inferior spikelets of compact-panicle cultivars promote grain filling. Second, the high expression of seed-storage proteins observed in the inferior spikelets of compact-panicle cultivars appears to inhibit the grain filling process. Third, the low expression of enzymes of the Krebs cycle in inferior spikelets compared with superior spikelets of compact-panicle cultivars is bound to lead to poor ATP generation in the former and consequently limit starch biosynthesis, an ATP-consuming process, resulting in poor grain

  10. Identification and Characterization of Differentially Expressed Genes in Inferior and Superior Spikelets of Rice Cultivars with Contrasting Panicle-Compactness and Grain-Filling Properties.

    PubMed

    Sekhar, Sudhanshu; Gharat, Sachin Ashruba; Panda, Binay Bhushan; Mohaptra, Trupti; Das, Kaushik; Kariali, Ekamber; Mohapatra, Pravat Kumar; Shaw, Birendra Prasad

    2015-01-01

    Breeding programs for increasing spikelet number in rice have resulted in compactness of the panicle, accompanied by poor grain filling in inferior spikelets. Although the inefficient utilization of assimilate has been indicated as responsible for this poor grain filling, the underlying cause remains elusive. The current study utilized the suppression subtractive hybridization technique to identify 57 and 79 genes that overexpressed in the superior and inferior spikelets (with respect to each other), respectively, of the compact-panicle rice cultivar Mahalaxmi. Functional categorization of these differentially expressed genes revealed a marked metabolic difference between the spikelets according to their spatial location on the panicle. The expression of genes encoding seed storage proteins was dominant in inferior spikelets, whereas genes encoding regulatory proteins, such as serine-threonine kinase, zinc finger protein and E3 ligase, were highly expressed in superior spikelets. The expression patterns of these genes in the inferior and superior spikelets of Mahalaxmi were similar to those observed in another compact-panicle cultivar, OR-1918, but differed from those obtained in two lax-panicle cultivars, Upahar and Lalat. The results first suggest that the regulatory proteins abundantly expressed in the superior spikelets of compact-panicle cultivars and in both the superior and inferior spikelets of lax-panicle cultivars but poorly expressed in the inferior spikelets of compact-panicle cultivars promote grain filling. Second, the high expression of seed-storage proteins observed in the inferior spikelets of compact-panicle cultivars appears to inhibit the grain filling process. Third, the low expression of enzymes of the Krebs cycle in inferior spikelets compared with superior spikelets of compact-panicle cultivars is bound to lead to poor ATP generation in the former and consequently limit starch biosynthesis, an ATP-consuming process, resulting in poor grain

  11. Identification and Characterization of Differentially Expressed Genes in Inferior and Superior Spikelets of Rice Cultivars with Contrasting Panicle-Compactness and Grain-Filling Properties.

    PubMed

    Sekhar, Sudhanshu; Gharat, Sachin Ashruba; Panda, Binay Bhushan; Mohaptra, Trupti; Das, Kaushik; Kariali, Ekamber; Mohapatra, Pravat Kumar; Shaw, Birendra Prasad

    2015-01-01

    Breeding programs for increasing spikelet number in rice have resulted in compactness of the panicle, accompanied by poor grain filling in inferior spikelets. Although the inefficient utilization of assimilate has been indicated as responsible for this poor grain filling, the underlying cause remains elusive. The current study utilized the suppression subtractive hybridization technique to identify 57 and 79 genes that overexpressed in the superior and inferior spikelets (with respect to each other), respectively, of the compact-panicle rice cultivar Mahalaxmi. Functional categorization of these differentially expressed genes revealed a marked metabolic difference between the spikelets according to their spatial location on the panicle. The expression of genes encoding seed storage proteins was dominant in inferior spikelets, whereas genes encoding regulatory proteins, such as serine-threonine kinase, zinc finger protein and E3 ligase, were highly expressed in superior spikelets. The expression patterns of these genes in the inferior and superior spikelets of Mahalaxmi were similar to those observed in another compact-panicle cultivar, OR-1918, but differed from those obtained in two lax-panicle cultivars, Upahar and Lalat. The results first suggest that the regulatory proteins abundantly expressed in the superior spikelets of compact-panicle cultivars and in both the superior and inferior spikelets of lax-panicle cultivars but poorly expressed in the inferior spikelets of compact-panicle cultivars promote grain filling. Second, the high expression of seed-storage proteins observed in the inferior spikelets of compact-panicle cultivars appears to inhibit the grain filling process. Third, the low expression of enzymes of the Krebs cycle in inferior spikelets compared with superior spikelets of compact-panicle cultivars is bound to lead to poor ATP generation in the former and consequently limit starch biosynthesis, an ATP-consuming process, resulting in poor grain

  12. Dorsoventral asymmetry of photosynthesis and photoinhibition in flag leaves of two rice cultivars that differ in nitrogen response and leaf angle.

    PubMed

    Kumagai, Etsushi; Hamaoka, Norimitsu; Araki, Takuya; Ueno, Osamu

    2014-08-01

    Rice is believed to show photosynthetic symmetry between adaxial and abaxial leaf sides. To verify this, we re-examined dorsoventral asymmetry in photosynthesis, chlorophyll fluorescence and anatomical traits in flag leaves of two Oryza sativa cultivars that differ in nitrogen (N) response and in leaf angle: 'Akenohoshi', a cultivar that can adapt to low-N (LN), with low leaf angle (more erect leaves), and 'Shirobeniya', a cultivar that is unable to adapt to LN, with higher leaf angle. Plants were grown under standard-N (SN) and LN conditions. LN leaves of both cultivars became more erect than SN, but LN Akenohoshi still had more erect ones than Shirobeniya. Contrary to results of previous studies, leaves of both cultivars showed an asymmetry in photosynthetic rate between adaxial and abaxial sides (higher on the adaxial side) under SN. SN leaves of both cultivars showed lower susceptibility to photoinhibition on the adaxial side than on the abaxial side. However, leaves of Akenohoshi showed less asymmetry in these traits under LN than under SN, whereas leaves of Shirobeniya had similar degrees of asymmetry in these traits under both SN and LN. Both cultivars also showed dorsoventral asymmetry in anatomical traits of mesophyll tissue regardless of N level, but the degree of asymmetry was lower in LN Akenohoshi. These data reveal that rice leaves exhibit dorsoventral asymmetry in photosynthetic and anatomical features, and that the degree of asymmetry varies with cultivar and N level. It is suggested that lower leaf angles (particularly in Akenohoshi) in the presence of LN represent a light acclimation to prevent photoinhibition.

  13. Proposal of a growth chamber for growing Super-Dwarf Rice in Space Agriculture

    NASA Astrophysics Data System (ADS)

    Hirai, Hiroaki; Kitaya, Yoshiaki; Tsukamoto, Koya; Yamashita, Youichirou; Hirai, Takehiro

    Space agriculture needs to be considered to supply food for space crew who stay in space over an extended time period. So far crops such as wheat, onion, oat, pea and lettuce grew to explore the possibility of space agriculture. Although rice is a staple food for most of the world, research on rice cultivation in space has not been done much. Rice grains are nutrient-rich with carbohydrate, protein and dietary fiber. Moreover, rice is a high yield crop and harvested grains have a long shelf life. However, the plant height of standard rice cultivars is relatively long, requiring much space. In addition, rice plants require higher light intensities for greater yield. For these reasons, it is difficult to establish facilities for rice culture in a limited space with a low cost. We propose to employee a super-dwarf cultivar and a small growth chamber with a new type of LEDs. The super-dwarf rice is a short-grain japonica variety and the plant height is approximately 20 cm that is one-fifth as tall as standard cultivars. The LED light used as a light source for this study can provide full spectrum of 380 nm to 750 nm. Air temperature and humidity were controlled by a Peltier device equipped in the chamber. The characteristics of the new type of LEDs and other equipments of the chamber and the ground based performance of super-dwarf rice plants grown in the chamber will be reported.

  14. GS6, a member of the GRAS gene family, negatively regulates grain size in rice.

    PubMed

    Sun, Lianjun; Li, Xiaojiao; Fu, Yongcai; Zhu, Zuofeng; Tan, Lubin; Liu, Fengxia; Sun, Xianyou; Sun, Xuewen; Sun, Chuanqing

    2013-10-01

    Grain size is an important yield-related trait in rice. Intensive artificial selection for grain size during domestication is evidenced by the larger grains of most of today's cultivars compared with their wild relatives. However, the molecular genetic control of rice grain size is still not well characterized. Here, we report the identification and cloning of Grain Size 6 (GS6), which plays an important role in reducing grain size in rice. A premature stop at the +348 position in the coding sequence (CDS) of GS6 increased grain width and weight significantly. Alignment of the CDS regions of GS6 in 90 rice materials revealed three GS6 alleles. Most japonica varieties (95%) harbor the Type I haplotype, and 62.9% of indica varieties harbor the Type II haplotype. Association analysis revealed that the Type I haplotype tends to increase the width and weight of grains more than either of the Type II or Type III haplotypes. Further investigation of genetic diversity and the evolutionary mechanisms of GS6 showed that the GS6 gene was strongly selected in japonica cultivars. In addition, a "ggc" repeat region identified in the region that encodes the GRAS domain of GS6 played an important historic role in the domestication of grain size in rice. Knowledge of the function of GS6 might aid efforts to elucidate the molecular mechanisms that control grain development and evolution in rice plants, and could facilitate the genetic improvement of rice yield. PMID:23650998

  15. Molecular evaluation of genetic diversity and association studies in rice (Oryza sativa L.).

    PubMed

    Vanniarajan, C; Vinod, K K; Pereira, Andy

    2012-01-01

    In the present study, we tested rice genotypes that included un(der)exploited landraces of Tamil Nadu along with indica and japonica test cultivars to ascertain their genetic diversity structure. Highly polymorphic microsatellite markers were used for generating marker segregation data. A novel measure, allele discrimination index, was used to determine subpopulation differentiation power of each marker. Phenotypic data were collected for yield and component traits. Pattern of molecular differentiation separated indica and japonica genotypes; indica genotypes had two subpopulations within. Landraces were found to have indica genome, but formed a separate subgroup with low linkage disequilibrium. The landraces further separated into distinct group in both hierarchical clustering analysis using neighbour-joining method as well as in the model based population structure analysis. Japonica and the remaining indica cultivars formed two other distinct groups. Linkage disequilibrium observed in the whole population was considerably reduced in subpopulations. Low linkage disequilibrium of landforms suggests their narrow adaptation in local geographical niche. Many population specific alleles could be identified particularly for japonica cultivars and landraces. Association analysis revealed nine marker-trait associations with three agronomic traits, of which 67% were previously reported. Although the testing landraces together with known cultivars had permitted genomewide association mapping, the experiment offers scope to study more landraces collected from the entire geographical region for drawing more reliable information. PMID:22546822

  16. Effects of water management on arsenic and cadmium speciation and accumulation in an upland rice cultivar.

    PubMed

    Hu, Pengjie; Ouyang, Younan; Wu, Longhua; Shen, Libo; Luo, Yongming; Christie, Peter

    2015-01-01

    Pot and field experiments were conducted to investigate the effects of water regimes on the speciation and accumulation of arsenic (As) and cadmium (Cd) in Brazilian upland rice growing in soils polluted with both As and Cd. In the pot experiment constant and intermittent flooding treatments gave 3-16 times higher As concentrations in soil solution than did aerobic conditions but Cd showed the opposite trend. Compared to arsenate, there were more marked changes in the arsenite concentrations in the soil solution as water management shifted, and therefore arsenite concentrations dominated the As speciation and bioavailability in the soil. In the field experiment As concentrations in the rice grains increased from 0.14 to 0.21 mg/kg while Cd concentrations decreased from 0.21 to 0.02 mg/kg with increasing irrigation ranging from aerobic to constantly flooding conditions. Among the various water regimes the conventional irrigation treatment produced the highest rice grain yield of 6.29 tons/ha. The As speciation analysis reveals that the accumulation of dimethylarsinic acid (from 11.3% to 61.7%) made a greater contribution to the increase in total As in brown rice in the intermittent and constant flooding treatments compared to the intermittent-aerobic treatment. Thus, water management exerted opposite effects on Cd and As speciation and bioavailability in the soil and consequently on their accumulation in the upland rice. Special care is required when irrigation regime methods are employed to mitigate the accumulation of metal(loid)s in the grain of rice grown in soils polluted with both As and Cd. PMID:25597681

  17. Differences in responses to flooding by germinating seeds of two contrasting rice cultivars and two species of economically important grass weeds.

    PubMed

    Estioko, Lucy P; Miro, Berta; Baltazar, Aurora M; Merca, Florinia E; Ismail, Abdelbagi M; Johnson, David E

    2014-01-01

    Crop productivity is largely affected by abiotic factors such as flooding and by biotic factors such as weeds. Although flooding after direct seeding of rice helps suppress weeds, it also can adversely affects germination and growth of rice, resulting in poor crop establishment. Barnyard grasses (Echinochloa spp.) are among the most widespread weeds affecting rice, especially under direct seeding. The present work aimed to establish effective management options to control these weeds. We assessed the effects of variable depths and time of submergence on germination, seedling growth and carbohydrate metabolism of (i) two cultivars of rice known to differ in their tolerance to flooding during germination and (ii) two barnyard grasses (Echinochloa colona and E. crus-galli) that commonly infest rice fields. Flooding barnyard grasses with 100-mm-deep water immediately after seeding was effective in suppressing germination and growth. Echinochloa colona showed greater reductions in emergence, shoot and root growth than E. crus-galli. Delaying flooding for 2 or 4 days was less injurious to both species. Echinochloa colona was also more susceptible to flooding than the flood-sensitive rice cultivar 'IR42'. The activity of alcohol dehydrogenase (ADH) and pyruvate decarboxylase (PDC) in rice seedlings was increased by flooding after sowing but with greater increases in 'Khao Hlan On' compared with 'IR42'. The activity of ADH and PDC was enhanced to a similar extent in both barnyard grasses. Under aerobic conditions, the activity of ADH and PDC in the two barnyard grasses was downregulated, which might contribute to their inherently faster growth compared with rice. Aldehyde dehydrogenase activity was significantly enhanced in flood-tolerant 'Khao Hlan On' and E. crus-galli, but did not increase in flood-sensitive E. colona and 'IR42', implying a greater ability of the flood-tolerant types to detoxify acetaldehyde generated during anaerobic fermentation. Confirmation of this

  18. Relative abundance of Delta(5)-sterols in plasma membrane lipids of root-tip cells correlates with aluminum tolerance of rice.

    PubMed

    Khan, M Shahadat Hossain; Tawaraya, Keitarou; Sekimoto, Hiroshi; Koyama, Hiroyuki; Kobayashi, Yuriko; Murayama, Tetsuya; Chuba, Masaru; Kambayashi, Mihoko; Shiono, Yoshihito; Uemura, Matsuo; Ishikawa, Satoru; Wagatsuma, Tadao

    2009-01-01

    We investigated variations in aluminum (Al) tolerance among rice plants, using ancestor cultivars from the family line of the Al-tolerant and widely cultivated Japonica cultivar, Sasanishiki. The cultivar Rikuu-20 was Al sensitive, whereas a closely related cultivar that is a descendant of Rikuu-20, Rikuu-132, was Al tolerant. These two cultivars were compared to determine mechanisms underlying variations in Al tolerance. The sensitive cultivar Rikuu-20 showed increased permeability of the plasma membrane (PM) and greater Al uptake within 1 h of Al treatment. This could not be explained by organic acid release. Lipid composition of the PM differed between these cultivars, and may account for the difference in Al tolerance. The tolerant cultivar Rikuu-132 had a lower ratio of phospholipids to Delta(5)-sterols than the sensitive cultivar Rikuu-20, suggesting that the PM of Rikuu-132 is less negatively charged and less permeabilized than that of Rikuu-20. We used inhibitors of Delta(5)-sterol synthesis to alter the ratio of phospholipids to Delta(5)-sterols in both cultivars. These inhibitors reduced Al tolerance in Rikuu-132 and its Al-tolerant ancestor cultivars Kamenoo and Kyoku. In addition, Rikuu-132 showed a similar level of Al sensitivity when the ratio of phospholipids to Delta(5)-sterols was increased to match that of Rikuu-20 after treatment with uniconazole-P, an inhibitor of obtusifoliol-14alpha-demethylase. These results indicate that PM lipid composition is a factor underlying variations in Al tolerance among rice cultivars.

  19. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Current advances in sequencing technologies and bioinformatics allow to determine a nearly complete genomic background of rice, a staple food for the poor people. Consequently, comprehensive databases of variation among thousands of varieties is currently being assembled and released. Proper analysi...

  20. Molecular Genetic Diversity of Major Indian Rice Cultivars over Decadal Periods

    PubMed Central

    Deborah, Dondapati Annekitty; Vipparla, Abhilash; Anuradha, Ghanta; Siddiq, Ebrahimali Abubacker; Vemireddy, Lakshminarayana Reddy

    2013-01-01

    Genetic diversity in representative sets of high yielding varieties of rice released in India between 1970 and 2010 was studied at molecular level employing hypervariable microsatellite markers. Of 64 rice SSR primer pairs studied, 52 showed polymorphism, when screened in 100 rice genotypes. A total of 184 alleles was identified averaging 3.63 alleles per locus. Cluster analysis clearly grouped the 100 genotypes into their respective decadal periods i.e., 1970s, 1980s, 1990s and 2000s. The trend of diversity over the decadal periods estimated based on the number of alleles (Na), allelic richness (Rs), Nei’s genetic diversity index (He), observed heterozygosity (Ho) and polymorphism information content (PIC) revealed increase of diversity over the periods in year of releasewise and longevitywise classification of rice varieties. Analysis of molecular variance (AMOVA) suggested more variation in within the decadal periods than among the decades. Pairwise comparison of population differentiation (Fst) among decadal periods showed significant difference between all the pairs except a few. Analysis of trends of appearing and disappearing alleles over decadal periods showed an increase in the appearance of alleles and decrease in disappearance in both the categories of varieties. It was obvious from the present findings, that genetic diversity was progressively on the rise in the varieties released during the decadal periods, between 1970s and 2000s. PMID:23805204

  1. Can southern US rice cultivars be used to mitigate greenhouse gas emissions? A preliminary study.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Most rice in the world is produced under flooded paddy conditions as a means of producing high stable yields and controlling non-aquatic weeds. However, the anaerobic soil conditions that occur as a result of the flooded fields cause high levels of methane production due to bacterial methanogenesis....

  2. Comparing the defence-related gene expression changes upon root-knot nematode attack in susceptible versus resistant cultivars of rice

    PubMed Central

    Kumari, Chanchal; Dutta, Tushar K.; Banakar, Prakash; Rao, Uma

    2016-01-01

    Rice is one of the major staple food crops in the world and an excellent model system for studying monocotyledonous plants. Diseases caused by nematodes in rice are well documented and among them, root-knot nematode (RKN), Meloidogyne graminicola, causes extensive yield decline. It is therefore necessary to identify novel sources of natural resistance to RKN in rice and to investigate the rice-RKN interaction in detail to understand the basal plant defence mechanisms and nematode manipulation of the host physiology. To this end, six different cultivars of rice were initially screened for RKN infection and development; Pusa 1121 and Vandana were found to be most susceptible and resistant to RKN infection, respectively. In order to investigate the role of major hormone-regulated plant defence pathways in compatible/incompatible rice-RKN interaction, some well-identified marker genes involved in salicylate/jasmonate/ethylene pathway were evaluated for their differential expression through qRT-PCR. In general, our study shows a remarkable discrepancy in the expression pattern of those genes between compatible and incompatible rice-RKN interaction. As most information on the molecular interplay between plants and nematodes were generated on dicotyledonous plants, the current study will strengthen our basic understanding of plant-nematode interaction in the monocot crops, which will aid in defining future strategies for best plant health measures. PMID:26961568

  3. A genome-wide view of miniature inverted-repeat transposable elements (MITEs) in rice, Oryza sativa ssp. japonica.

    PubMed

    Oki, Nobuhiko; Yano, Kentaro; Okumoto, Yutaka; Tsukiyama, Takuji; Teraishi, Masayoshi; Tanisaka, Takatoshi

    2008-08-01

    Transposable elements (TEs) have played important roles in the evolution of genes and genomes of higher eukaryotes. Among the TEs in the rice genome, miniature inverted-repeat transposable elements (MITEs) exist at the highest copy number. Some of MITEs in the rice genome contain poly(A) signals and putative cis-acting regulatory domains. Insertion events of such MITEs may have caused many structural and functional changes of genomes. The genome-wide examination of MITE-derived sequences could elucidate the contribution of MITEs to gene evolution. Here we report on the MITEs in the rice genome that have contributed to the emergence of novel genes and the expansion of the sequence diversity of the genome and mRNAs. Of the MITE-derived sequences, approximately 6000 were found in gene regions (exons and introns) and 67,000 in intergenic regions. In gene regions, most MITEs are located in introns rather than exons. For over 300 protein-coding genes, coding sequences, poly(A) sites, transcription start sites, and splicing sites overlap with MITEs. These sequence alterations via MITE insertions potentially affect the biological functions of gene products. Many MITE insertions also exist in 5'-untranslated regions (UTRs), 3'-UTRs, and in the proximity of genes. Although mutations in these non-protein coding regions do not alter protein sequences, these regions have key roles for gene regulation. Moreover, MITE family sequences (Tourist, Stowaway, and others) are unevenly distributed in introns. Our findings suggest that MITEs may have contributed to expansion of genome diversity by causing alterations not only in gene functions but also in regulation of many genes. PMID:18931457

  4. Agrobacterium-mediated transformation: rice transformation.

    PubMed

    Slamet-Loedin, Inez H; Chadha-Mohanty, Prabhjit; Torrizo, Lina

    2014-01-01

    Agrobacterium is a common soil bacterium with natural capacity for trans-kingdom transfer of genetic information by transferring its T-DNA into the eukaryotic genome. In agricultural plant biotechnology, combination of non-phytopathogenic strain of Agrobacterium tumefaciens with modified T-DNA and vir-genes in a binary vector system is the most widely utilized system for genetic improvement in diverse plant species and for gene function validation. Here we have described a highly efficient A. tumefaciens-mediated transformation system for indica and japonica rice cultivars based on an immature embryo system.

  5. HapRice, an SNP haplotype database and a web tool for rice.

    PubMed

    Yonemaru, Jun-ichi; Ebana, Kaworu; Yano, Masahiro

    2014-01-01

    Genome-wide single nucleotide polymorphism (SNP) analysis is a promising tool to examine the genetic diversity of rice populations and genetic traits of scientific and economic importance. Next-generation sequencing technology has accelerated the re-sequencing of diverse rice varieties and the discovery of genome-wide SNPs. Notably, validation of these SNPs by a high-throughput genotyping system, such as an SNP array, could provide a manageable and highly accurate SNP set. To enhance the potential utility of genome-wide SNPs for geneticists and breeders, analysis tools need to be developed. Here, we constructed an SNP haplotype database, which allows visualization of the allele frequency of all SNPs in the genome browser. We calculated the allele frequencies of 3,334 SNPs in 76 accessions from the world rice collection and 3,252 SNPs in 177 Japanese rice accessions; all these SNPs have been validated in our previous studies. The SNP haplotypes were defined by the allele frequency in each cultivar group (aus, indica, tropical japonica and temperate japonica) for the world rice accessions, and in non-irrigated and three irrigated groups (three variety registration periods) for Japanese rice accessions. We also developed web tools for finding polymorphic SNPs between any two rice accessions and for the primer design to develop cleaved amplified polymorphic sequence markers at any SNP. The 'HapRice' database and the web tools can be accessed at http://qtaro.abr.affrc.go.jp/index.html. In addition, we established a core SNP set consisting of 768 SNPs uniformly distributed in the rice genome; this set is of a practically appropriate size for use in rice genetic analysis.

  6. [Micromorphology of leaf epidermis of some Venezuelan rice cultivars (Poaceae) associated with the mechanical damage of Sogata T. orizicolus (Homoptera: Delphacidae)].

    PubMed

    Velásquez-Salazar, Rosalia; Diamont, Diego

    2014-06-01

    Rice cultivars are affected directly and indirectly by the insect sogata. The mechanical damage or direct loss, is produced after feeding and ovoposition on the young leaves tissues, while the indirect damage is produced after the transmission of the Rice hoja blanca virus. We studied the morpho-anatomic structures associated with the resistance of the mechanical damage produced by the insect, in six rice cultivars, including controls for resistance and susceptibility (Makalioka and Bluebonnet 50), during August 2011, in Fundacion Danac, Venezuela. Samples were taken from leaf 3, where cuticle thickness, presence of macrohair, microhair and silica bodies in the second third of the leaf was evaluated. A significant difference to thickness of the cuticle, the presence of microhair in the leaves, and presence of silica bodies was observed among cultivars, determining a significant correlation among the number of macrohair and microhair in the adaxial leaf blade with the presence of silica bodies, and thickness of the cuticle and number of posed insects. Thickness of the cuticle and presence of silica bodies in the intercostals space of microhair and macrohair showed to be the variables most related to mechanical damage and resistance mechanism. PMID:25102661

  7. Study of water stress effects in different growth stages on yield and yield components of different rice (Oryza sativa L.) cultivars.

    PubMed

    Sarvestani, Zinolabedin Tahmasebi; Pirdashti, Hemmatollah; Sanavy, Seyed Ali Mohammad Modarres; Balouchi, Hamidreza

    2008-05-15

    A field experiment was conducted during 2001-2003 to evaluate the effect of water stress on the yield and yield components of four rice cultivars commonly grown in Mazandaran province, Iran. In northern Iran irrigated lowland rice usually experiences water deficit during the growing season include of land preparation time, planting, tillering stage, flowering and grain filing period. Recently drought affected 20 of 28 provinces in Iran; with the southeastern, central and eastern parts of the country being most severely affected. The local and improved cultivars used were Tarom, Khazar, Fajr and Nemat. The different water stress conditions were water stress during vegetative, flowering and grain filling stages and well watered was the control. Water stress at vegetative stage significantly reduced plant height of all cultivars. Water stress at flowering stage had a greater grain yield reduction than water stress at other times. The reduction of grain yield largely resulted from the reduction in fertile panicle and filled grain percentage. Water deficit during vegetative, flowering and grain filling stages reduced mean grain yield by 21, 50 and 21% on average in comparison to control respectively. The yield advantage of two semidwarf varieties, Fajr and Nemat, were not maintained under drought stress. Total biomass, harvest index, plant height, filled grain, unfilled grain and 1000 grain weight were reduced under water stress in all cultivars. Water stress at vegetative stage effectively reduced total biomass due to decrease of photosynthesis rate and dry matter accumulation. PMID:18817260

  8. Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes.

    PubMed

    Wang, Xi-liang; Song, Shu-hui; Wu, Yong-Sheng; Li, Yu-Li; Chen, Ting-ting; Huang, Zhi-yuan; Liu, Shuo; Dunwell, Thomas L; Pfeifer, Gerd P; Dunwell, Jim M; Wamaedeesa, Raheema; Ullah, Ihsan; Wang, Yinsheng; Hu, Song-nian

    2015-11-01

    5-Hydroxymethylcytosine (5hmC), a modified form of cytosine that is considered the sixth nucleobase in DNA, has been detected in mammals and is believed to play an important role in gene regulation. In this study, 5hmC modification was detected in rice by employing a dot-blot assay, and its levels was further quantified in DNA from different rice tissues using liquid chromatography-multistage mass spectrometry (LC-MS/MS/MS). The results showed large intertissue variation in 5hmC levels. The genome-wide profiles of 5hmC modification in three different rice cultivars were also obtained using a sensitive chemical labelling followed by a next-generation sequencing method. Thousands of 5hmC peaks were identified, and a comparison of the distributions of 5hmC among different rice cultivars revealed the specificity and conservation of 5hmC modification. The identified 5hmC peaks were significantly enriched in heterochromatin regions, and mainly located in transposable elements (TEs), especially around retrotransposons. The correlation analysis of 5hmC and gene expression data revealed a close association between 5hmC and silent TEs. These findings provide a resource for plant DNA 5hmC epigenetic studies and expand our knowledge of 5hmC modification. PMID:26272901

  9. New Rice for Africa (NERICA) cultivars exhibit different levels of post-attachment resistance against the parasitic weeds Striga hermonthica and Striga asiatica.

    PubMed

    Cissoko, Mamadou; Boisnard, Arnaud; Rodenburg, Jonne; Press, Malcolm C; Scholes, Julie D

    2011-12-01

    Striga hermonthica and S. asiatica are root parasitic weeds that infect the major cereal crops of sub-Saharan Africa causing severe losses in yield. The interspecific upland NEw RICe for Africa (NERICA) cultivars are popular amongst subsistence farmers, but little is known about their post-attachment resistance against Striga. Here, we evaluate the post-attachment resistance levels of the NERICA cultivars and their parents against ecotypes of S. hermonthica and S.asiatica, characterize the phenotype of the resistance mechanisms and determine the effect of Striga on host biomass. Some NERICA cultivars showed good broad-spectrum resistance against several Striga ecotypes, whereas others showed intermediate resistance or were very susceptible. The phenotype of a resistant interaction was often characterized by an inability of the parasite to penetrate the endodermis. Moreover, some parasites formed only a few connections to the host xylem, grew slowly and remained small. The most resistant NERICA cultivars were least damaged by Striga, although even a small number of parasites caused a reduction in above-ground host biomass. The elucidation of the molecular genetic basis of the resistance mechanisms and tolerance would allow the development of cultivars with multiple, durable resistance for use in farmers' fields.

  10. Comparative quantitative analysis of headspace volatiles and their association with BADH2 marker in non-basmati scented, basmati and non-scented rice (Oryza sativa L.) cultivars of India.

    PubMed

    Mathure, Sarika V; Jawali, Narendra; Thengane, Ratnakar J; Nadaf, Altafhusian B

    2014-01-01

    For the first time, 91 Indian rice (Oryza sativa L.) cultivars, belonging to non-basmati scented (77), basmati (9) and non-scented (5) categories, were quantitatively analysed for 23 headspace volatiles. In addition, the BADH2 marker related to 2-acetyl-1-pyrroline (2AP) synthesis is validated among the cultivars representing these categories. The non-basmati scented cultivars (15) excelled in 2-acetyl-1-pyrroline (2AP) content compared to basmati cultivars. The major aroma volatile (2AP) correlated positively with 1-tetradecene and indole, and negatively with benzyl alcohol. On the basis of nonanal, octanal, decanal and 1-octen-3-ol contents, basmati cultivars were different from non-scented cultivars. Benzyl alcohol, 2-phenylethanol, 2-amino acetophenone, indole, 1-hexanol and nonanoic acid exhibited significant variation among rice categories under study. This study reports 16 non-basmati scented cultivars with variations in the BADH2 locus rendering a marker based on 8bp deletion in BADH2 as unsuitable for MAS in rice cultivars under study.

  11. Genomewide association analysis for awn length linked to the seed shattering gene qSH1 in rice.

    PubMed

    Magwa, Risper Auma; Zhao, Hu; Yao, Wen; Xie, Weibo; Yang, Lin; Xing, Yongzhong; Bai, Xufeng

    2016-09-01

    Awn is one of the most important domesticated traits in rice (Oryza sativa). Understanding the genetic basis of awn length is important for grain harvest and production, because long awn length is disadvantageous for both grain harvest and milling. We investigated the awn length of 529 rice cultivars and performed a Genomewide association studies (GWAS) in the indica and japonica subpopulations, and the whole population. In total, we found 17 loci associated with awn length. Of these loci, seven were linked to previously reported quantitative trait loci, and one was linked to the awn gene An-1. Nine novel loci were repeatedly identified in different environments. One of the nine associations was identified in both the whole and japonica populations. Special interest was the detection of the most significant association SNP, sf0136352825, which was less than 95 kb from the seed shattering gene qSH1. These results may provide potentially favourable haplotypes for molecular breeding in rice. PMID:27659335

  12. Differential activation of genes related to aluminium tolerance in two contrasting rice cultivars.

    PubMed

    Roselló, Maite; Poschenrieder, Charlotte; Gunsé, Benet; Barceló, Juan; Llugany, Mercè

    2015-11-01

    Rice (Oryza sativa) is a highly Al-tolerant crop. Among other mechanisms, a higher expression of STAR1/STAR2 (sensitive to Al rhizotoxicity1/2) genes and of Nrat1 (NRAMP Aluminium Transporter 1), and ALS1 (Aluminium sensitive 1) can at least in part be responsible for the inducible Al tolerance in this species. Here we analysed the responses to Al in two contrasting rice varieties. All analysed toxicity/tolerance markers (root elongation, Evans blue, morin and haematoxylin staining) indicated higher Al-tolerance in variety Nipponbare, than in variety Modan. Nipponbare accumulated much less Al in the roots than Modan. Aluminium supply caused stronger expression of STAR1 in Nipponbare than in Modan. A distinctively higher increase of Al-induced abscisic acid (ABA) accumulation was found in the roots of Nipponbare than in Modan. Highest ABA levels were observed in Nipponbare after 48 h exposure to Al. This ABA peak was coincident in time with the highest expression level of STAR1. It is proposed that ABA may be required for cell wall remodulation facilitated by the enhanced UDP-glucose transport to the walls through STAR1/STAR2. Contrastingly, in the roots of Modan the expression of both Nrat1 coding for a plasma membrane Al-transporter and of ALS1 coding for a tonoplast-localized Al transporter was considerably enhanced. Moreover, Modan had a higher Al-induced expression of ASR1 a gene that has been proposed to code for a reactive oxygen scavenging protein. In conclusion, the Al-exclusion strategy of Nipponbare, at least in part mediated by STAR1 and probably regulated by ABA, provided better protection against Al toxicity than the accumulation and internal detoxification strategy of Modan mediated by Nrat1, ALS1 and ARS1.

  13. The rice mitochondrial genomes and their variations.

    PubMed

    Tian, Xiangjun; Zheng, Jing; Hu, Songnian; Yu, Jun

    2006-02-01

    Based on highly redundant and high-quality sequences, we assembled rice (Oryza sativa) mitochondrial genomes for two cultivars, 93-11 (an indica variety) and PA64S (an indica-like variety with maternal origin of japonica), which are paternal and maternal strains of an elite superhybrid rice Liang-You-Pei-Jiu (LYP-9), respectively. Following up with a previous analysis on rice chloroplast genomes, we divided mitochondrial sequence variations into two basic categories, intravarietal and intersubspecific. Intravarietal polymorphisms are variations within mitochondrial genomes of an individual variety. Intersubspecific polymorphisms are variations between subspecies among their major genotypes. In this study, we identified 96 single nucleotide polymorphisms (SNPs), 25 indels, and three segmental sequence variations as intersubspecific polymorphisms. A signature sequence fragment unique to indica varieties was confirmed experimentally and found in two wild rice samples, but absent in japonica varieties. The intersubspecific polymorphism rate for mitochondrial genomes is 0.02% for SNPs and 0.006% for indels, nearly 2.5 and 3 times lower than that of their chloroplast counterparts and 21 and 38 times lower than corresponding rates of the rice nuclear genome, respectively. The intravarietal polymorphism rates among analyzed mitochondrial genomes, such as 93-11 and PA64S, are 1.26% and 1.38% for SNPs and 1.13% and 1.09% for indels, respectively. Based on the total number of SNPs between the two mitochondrial genomes, we estimate that the divergence of indica and japonica mitochondrial genomes occurred approximately 45,000 to 250,000 years ago. PMID:16384910

  14. Comparative proteomics of the superior and inferior spikelets at the early grain filling stage in rice cultivars contrast for panicle compactness and ethylene evolution.

    PubMed

    Das, Kaushik; Panda, Binay B; Sekhar, Sudhanshu; Kariali, Ekamber; Mohapatra, Pravat K; Shaw, Birendra P

    2016-09-01

    The breeding programmes in rice aimed at increasing the number of spikelets per panicle have been accompanied by poor grain filling in the inferior spikelets of large panicle rice, leading to yield disadvantage. The present study attempted to understand the reason for differential grain filling in the inferior and superior spikelets by comparative proteomics considering a compact-panicle rice cultivar Mahalaxmi and a lax-panicle rice cultivar Upahar, which show poor and good grain filling, respectively. An initial study of two rice cultivars for panicle compactness and grain filling revealed an inverse correlation between the two parameters. It was further observed that the panicle compactness in Mahalaxmi was associated with a higher evolution of ethylene by the spikelets, both superior and inferior, compared with the lax-panicle Upahar. The proteomic studies revealed that the superior and inferior spikelets of Mahalaxmi differentially expressed 21 proteins that were also expressed in Upahar. However, in Upahar, only two of these proteins were differentially expressed between the superior and inferior spikelets, indicating that the metabolic activities of the spikelets occupying the superior and inferior positions on the panicle were very different in Mahalaxmi compared with those in Upahar. Among the proteins that were downregulated in the inferior spikelets compared with the superior ones in Mahalaxmi were importin-α, elongation factor 1-β and cell division control protein 48, which are essential for cell cycle progression and cell division. Low expression of these proteins might inhibit endosperm cell division in the inferior spikelets, limiting their sink capacity and leading to poor grain filling compared to that in the superior spikelets. The poor grain filling in Mahalaxmi may also be a result of the high evolution of ethylene in the inferior spikelets, which is reflected from the observation that these spikelets showed significantly higher expression of

  15. The Nipponbare genome and the next-generation of rice genomics research in Japan.

    PubMed

    Matsumoto, Takashi; Wu, Jianzhong; Itoh, Takeshi; Numa, Hisataka; Antonio, Baltazar; Sasaki, Takuji

    2016-12-01

    The map-based genome sequence of the japonica rice cultivar Nipponbare remains to date as the only monocot genome that has been sequenced to a high-quality level. It has become the reference sequence for understanding the diversity among thousands of rice cultivars and its wild relatives as well as the major cereal crops that comprised the food source for the entire human race. This review focuses on the accomplishments in rice genomics in Japan encompassing the last 10 years which have led into deeper understanding of the genome, characterization of many agronomic traits, comprehensive analysis of the transcriptome, and the map-based cloning of many genes associated with agronomic traits.

  16. The Nipponbare genome and the next-generation of rice genomics research in Japan.

    PubMed

    Matsumoto, Takashi; Wu, Jianzhong; Itoh, Takeshi; Numa, Hisataka; Antonio, Baltazar; Sasaki, Takuji

    2016-12-01

    The map-based genome sequence of the japonica rice cultivar Nipponbare remains to date as the only monocot genome that has been sequenced to a high-quality level. It has become the reference sequence for understanding the diversity among thousands of rice cultivars and its wild relatives as well as the major cereal crops that comprised the food source for the entire human race. This review focuses on the accomplishments in rice genomics in Japan encompassing the last 10 years which have led into deeper understanding of the genome, characterization of many agronomic traits, comprehensive analysis of the transcriptome, and the map-based cloning of many genes associated with agronomic traits. PMID:27447712

  17. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes.

    PubMed

    Long, Yunming; Zhao, Lifeng; Niu, Baixiao; Su, Jing; Wu, Hao; Chen, Yuanling; Zhang, Qunyu; Guo, Jingxin; Zhuang, Chuxiong; Mei, Mantong; Xia, Jixing; Wang, Lan; Wu, Haibin; Liu, Yao-Guang

    2008-12-01

    Sterility is common in hybrids between divergent populations, such as the indica and japonica subspecies of Asian cultivated rice (Oryza sativa). Although multiple loci for plant hybrid sterility have been identified, it remains unknown how alleles of the loci interact at the molecular level. Here we show that a locus for indica-japonica hybrid male sterility, Sa, comprises two adjacent genes, SaM and SaF, encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein, respectively. Most indica cultivars contain a haplotype SaM(+)SaF(+), whereas all japonica cultivars have SaM(-)SaF(-) that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM(-). This allele-specific gamete elimination results from a selective interaction of SaF(+) with SaM(-), a truncated protein, but not with SaM(+) because of the presence of an inhibitory domain, although SaM(+) is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility. We propose a two-gene/three-component interaction model for this hybrid male sterility system. The findings have implications for overcoming male sterility in inter-subspecific hybrid rice breeding.

  18. Identification of Conserved and Diverse Metabolic Shifts during Rice Grain Development

    PubMed Central

    Hu, Chaoyang; Tohge, Takayuki; Chan, Shen-An; Song, Yue; Rao, Jun; Cui, Bo; Lin, Hong; Wang, Lei; Fernie, Alisdair R.; Zhang, Dabing; Shi, Jianxin

    2016-01-01

    Seed development dedicates to reserve synthesis and accumulation and uncovering its genetic and biochemical mechanisms has been a major research focus. Although proteomic and transcriptomic analyses revealed dynamic changes of genes and enzymes involved, the information regarding concomitant metabolic changes is missing. Here we investigated the dynamic metabolic changes along the rice grain development of two japonica and two indica cultivars using non-targeted metabolomics approach, in which we successfully identified 214 metabolites. Statistical analyses revealed both cultivar and developmental stage dependent metabolic changes in rice grains. Generally, the stage specific metabolic kinetics corresponded well to the physiological status of the developing grains, and metabolic changes in developing rice grain are similar to those of dicot Arabidopsis and tomato at reserve accumulation stage but are different from those of dicots at seed desiccation stage. The remarkable difference in metabolite abundances between japonica and indica rice grain was observed at the reserve accumulation stage. Metabolite-metabolite correlation analysis uncovered potential new pathways for several metabolites. Taken together, this study uncovered both conserved and diverse development associated metabolic kinetics of rice grains, which facilitates further study to explore fundamental questions regarding the evolution of seed metabolic capabilities as well as their potential applications in crop improvement. PMID:26860358

  19. Genetic Diversity and Population Structure in Aromatic and Quality Rice (Oryza sativa L.) Landraces from North-Eastern India.

    PubMed

    Roy, Somnath; Banerjee, Amrita; Mawkhlieng, Bandapkuper; Misra, A K; Pattanayak, A; Harish, G D; Singh, S K; Ngachan, S V; Bansal, K C

    2015-01-01

    The North-eastern (NE) India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland, Sikkim and Tripura, possess diverse array of locally adapted non-Basmati aromatic germplasm. The germplasm collections from this region could serve as valuable resources in breeding for abiotic stress tolerance, grain yield and cooking/eating quality. To utilize such collections, however, breeders need information about the extent and distribution of genetic diversity present within collections. In this study, we report the result of population genetic analysis of 107 aromatic and quality rice accessions collected from different parts of NE India, as well as classified these accessions in the context of a set of structured global rice cultivars. A total of 322 alleles were amplified by 40 simple sequence repeat (SSR) markers with an average of 8.03 alleles per locus. Average gene diversity was 0.67. Population structure analysis revealed that NE Indian aromatic rice can be subdivided into three genetically distinct population clusters: P1, joha rice accessions from Assam, tai rices from Mizoram and those from Sikkim; P2, aromatic rice accessions from Nagaland; and P3, chakhao rice germplasm from Manipur [corrected]. Pair-wise FST between three groups varied from 0.223 (P1 vs P2) to 0.453 (P2 vs P3). With reference to the global classification of rice cultivars, two major groups (Indica and Japonica) were identified in NE Indian germplasm. The aromatic accessions from Assam, Manipur and Sikkim were assigned to the Indica group, while the accessions from Nagaland exhibited close association with Japonica. The tai accessions of Mizoram along with few chakhao accessions collected from the hill districts of Manipur were identified as admixed. The results highlight the importance of regional genetic studies for understanding diversification of aromatic rice in India. The data also suggest that there is scope for exploiting the genetic diversity of aromatic and

  20. Genetic Diversity and Population Structure in Aromatic and Quality Rice (Oryza sativa L.) Landraces from North-Eastern India

    PubMed Central

    Mawkhlieng, Bandapkuper; Misra, A. K.; Pattanayak, A.; Harish, G. D.; Singh, S. K.; Ngachan, S. V.; Bansal, K. C.

    2015-01-01

    The North-eastern (NE) India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland, Sikkim and Tripura, possess diverse array of locally adapted non-Basmati aromatic germplasm. The germplasm collections from this region could serve as valuable resources in breeding for abiotic stress tolerance, grain yield and cooking/eating quality. To utilize such collections, however, breeders need information about the extent and distribution of genetic diversity present within collections. In this study, we report the result of population genetic analysis of 107 aromatic and quality rice accessions collected from different parts of NE India, as well as classified these accessions in the context of a set of structured global rice cultivars. A total of 322 alleles were amplified by 40 simple sequence repeat (SSR) markers with an average of 8.03 alleles per locus. Average gene diversity was 0.67. Population structure analysis revealed that NE Indian aromatic rice can be subdivided into three genetically distinct population clusters: P1, joha rice accessions from Assam, tai rices from Mizoram and those from Sikkim; P2, chakhao rice germplasm from Manipur; and P3, aromatic rice accessions from Nagaland. Pair-wise FST between three groups varied from 0.223 (P1 vs P2) to 0.453 (P2 vs P3). With reference to the global classification of rice cultivars, two major groups (Indica and Japonica) were identified in NE Indian germplasm. The aromatic accessions from Assam, Manipur and Sikkim were assigned to the Indica group, while the accessions from Nagaland exhibited close association with Japonica. The tai accessions of Mizoram along with few chakhao accessions collected from the hill districts of Manipur were identified as admixed. The results highlight the importance of regional genetic studies for understanding diversification of aromatic rice in India. The data also suggest that there is scope for exploiting the genetic diversity of aromatic and quality rice

  1. Comparative Characterization of Aroma Volatiles and Related Gene Expression Analysis at Vegetative and Mature Stages in Basmati and Non-Basmati Rice (Oryza sativa L.) Cultivars.

    PubMed

    Hinge, Vidya; Patil, Hemant; Nadaf, Altafhusain

    2016-02-01

    Aroma volatiles in Basmati-370, Ambemohar-157 (non-basmati scented), and IR-64 (non-scented) rice cultivars were qualitatively and quantitatively analyzed at vegetative and maturity stages to study their differential accumulation using headspace solid-phase microextraction, followed by gas chromatography mass spectrometry (HS-SPME-GCMS) with selected ion monitoring (SIM) approach. In addition, expression analysis of major aroma volatile 2-acetyl-1-pyrroline (2AP)-related genes, betaine aldehyde dehydrogenase 2 (badh2) and Δ(1)-pyrolline-5-carboxylic acid synthetase (P5CS), were studied by real-time PCR. Maximum number of volatiles recorded at vegetative (72-58) than at mature stage (54-39). Twenty new compounds (12 in scented and 8 in both) were reported in rice. N-containing aromatic compounds were major distinguishing class separating scented from non-scented. Among quantified 26 volatiles, 14 odor-active compounds distinguished vegetative and mature stage. Limit of detection (LOD) and limit of quantification (LOQ) for 2AP was 0.001 mg/kg of 2AP and 0.01 g of rice, respectively. 2AP accumulation in mature grains was found three times more than in leaves of scented rice. Positive correlation of 2AP with 2-pentylfuran, 6-methyl-5-hepten-2-one, and (E)-2-nonenal suggests their major role as aroma contributors. The badh2 expression was inversely and P5CS expression was positively correlated with 2AP accumulation in scented over non-scented cultivar.

  2. An indica rice genotype showed a similar yield enhancement to that of hybrid rice under free air carbon dioxide enrichment.

    PubMed

    Zhu, Chunwu; Xu, Xi; Wang, Dan; Zhu, Jianguo; Liu, Gang

    2015-07-31

    Although the rice growth response to FACE (free-air CO2 enrichment) has been widely studied and is considered important within the scientific community, few studies have attempted to examine the effects of FACE on the yield of indica rice, which is typically the parent of indica hybrids in China. The effects of FACE on the yield, yield components, biomass, N uptake and leaf photosynthesis of Yangdao 6 Hao (an indica rice) in China were examined over 2 years. The grain yield increased over 30%, the panicle number increased 12.4% on average, and the spikelet number per panicle also showed an average increase of 8.2% at elevated CO2. FACE caused a significant enhancement in both the filled spikelet percentage (+5.9%) and the individual grain weight (+3.0%). Compared with three prior FACE studies on rice, a similar enhancement of yield in hybrid indica was shown under FACE, with much a higher value than for the japonica rice cultivar (approximately + 13%) because of indica's stronger sink generation and N uptake capacity, which help coordinate the C/N balance to avoid photosynthetic acclimation. The high enhancement of the indica rice yield under FACE holds promise for improved cultivar selection for future food security.

  3. An indica rice genotype showed a similar yield enhancement to that of hybrid rice under free air carbon dioxide enrichment

    NASA Astrophysics Data System (ADS)

    Zhu, Chunwu; Xu, Xi; Wang, Dan; Zhu, Jianguo; Liu, Gang

    2015-07-01

    Although the rice growth response to FACE (free-air CO2 enrichment) has been widely studied and is considered important within the scientific community, few studies have attempted to examine the effects of FACE on the yield of indica rice, which is typically the parent of indica hybrids in China. The effects of FACE on the yield, yield components, biomass, N uptake and leaf photosynthesis of Yangdao 6 Hao (an indica rice) in China were examined over 2 years. The grain yield increased over 30%, the panicle number increased 12.4% on average, and the spikelet number per panicle also showed an average increase of 8.2% at elevated CO2. FACE caused a significant enhancement in both the filled spikelet percentage (+5.9%) and the individual grain weight (+3.0%). Compared with three prior FACE studies on rice, a similar enhancement of yield in hybrid indica was shown under FACE, with much a higher value than for the japonica rice cultivar (approximately + 13%) because of indica’s stronger sink generation and N uptake capacity, which help coordinate the C/N balance to avoid photosynthetic acclimation. The high enhancement of the indica rice yield under FACE holds promise for improved cultivar selection for future food security.

  4. An indica rice genotype showed a similar yield enhancement to that of hybrid rice under free air carbon dioxide enrichment.

    PubMed

    Zhu, Chunwu; Xu, Xi; Wang, Dan; Zhu, Jianguo; Liu, Gang

    2015-01-01

    Although the rice growth response to FACE (free-air CO2 enrichment) has been widely studied and is considered important within the scientific community, few studies have attempted to examine the effects of FACE on the yield of indica rice, which is typically the parent of indica hybrids in China. The effects of FACE on the yield, yield components, biomass, N uptake and leaf photosynthesis of Yangdao 6 Hao (an indica rice) in China were examined over 2 years. The grain yield increased over 30%, the panicle number increased 12.4% on average, and the spikelet number per panicle also showed an average increase of 8.2% at elevated CO2. FACE caused a significant enhancement in both the filled spikelet percentage (+5.9%) and the individual grain weight (+3.0%). Compared with three prior FACE studies on rice, a similar enhancement of yield in hybrid indica was shown under FACE, with much a higher value than for the japonica rice cultivar (approximately + 13%) because of indica's stronger sink generation and N uptake capacity, which help coordinate the C/N balance to avoid photosynthetic acclimation. The high enhancement of the indica rice yield under FACE holds promise for improved cultivar selection for future food security. PMID:26228872

  5. Differential competence of redox-regulatory mechanism under extremes of temperature determines growth performances and cross tolerance in two indica rice cultivars.

    PubMed

    Chakraborty, Ananya; Bhattacharjee, Soumen

    2015-03-15

    The present study investigated the relationship between reactive oxygen species (ROS) accumulation (total and individual), antioxidant and radical scavenging capacity (total and individual), transcript abundance of some antioxidative genes and oxidative damages to membrane protein and lipid in germinating tissues of a salt resistant (SR26B) and salt sensitive (Ratna) rice cultivars under extremes of temperature to elucidate redox-regulatory mechanism governing differential oxidative stress tolerance associated with better growth and yield potential and identification of cross tolerance, if any. Imbibitional heat and chilling stress caused disruption of redox-homeostasis and oxidative damage to a newly assembled membrane system by increasing pro-oxidant/antioxidant ratio and by aggravating membrane lipid peroxidation and protein oxidation [measured in terms of accumulation of thiobarbituric acid reactive substances (TBARS), free carbonyl content (CO groups), and membrane protein thiol level (MPTL)]. A concomitant increase in accumulation of individual ROS (superoxide and hydrogen peroxide) and significant reduction of radical scavenging activity (assessed in terms of ABTS, FRAP and DPPH methods), non-enzymatic and enzymatic anti-oxidative defense [assessed in terms of total thiol content and activities of superoxide dismutase (EC 1.15.1.1), catalase (EC 1.11.1.6), ascorbate peroxidase (EC 1.11.1.11), and glutathione reductase (EC 1.6.4.2)] are also noticed in both the salt sensitive (Ratna) and resistant (SR26B) germinating tissues of rice cultivars. When compared, salt resistant cultivar SR26B was found to suffer significantly less redox-imbalance and related oxidative damages to membrane protein and lipid as compared to salt sensitive cultivar Ratna. The salt tolerant cultivar SR26B resisted imbibitional chilling and heat stress due to its early preparedness to combat oxidative stress by up-regulation of gene expression of anti-oxidative enzymes and better

  6. Anaerobic conditions improve germination of a gibberellic acid deficient rice

    NASA Technical Reports Server (NTRS)

    Frantz, Jonathan M.; Bugbee, Bruce

    2002-01-01

    Dwarf plants are useful in research because multiple plants can be grown in a small area. Rice (Oryza sativa L.) is especially important since its relatively simple genome has recently been sequenced. We are characterizing a gibberellic acid (GA) mutant of rice (japonica cv 'Shiokari,' line N-71) that is extremely dwarf (20 cm tall). Unfortunately, this GA mutation is associated with poor germination (70%) under aerobic conditions. Neither exogenous GA nor a dormancy-breaking heat treatment improved germination. However, 95% germination was achieved by germinating the seeds anaerobically, either in a pure N2 environment or submerged in unstirred tap water. The anaerobic conditions appear to break a mild post-harvest dormancy in this rice cultivar. Copyright 2002 Crop Science Society of America.

  7. Effect of succinylation on functional and morphological properties of starches from broken kernels of Pakistani Basmati and Irri rice cultivars.

    PubMed

    Moin, Abeera; Ali, Tahira Mohsin; Hasnain, Abid

    2016-01-15

    Starch extracted from broken kernels of Basmati and Irri rice varieties of Pakistani rice were subjected to modification by addition of succinic anhydride at levels of 2%, 4% and 5% based on dried weight of starch. The succinyl content of Irri rice starch increased with the concentration of succinic anhydride. Scanning electron micrographs revealed presence of dents and fusion of rice starch granules. Swelling power and water retention capacity (WRC) significantly improved after succinylation while on refrigerated storage percent decline in paste clarity of modified rice starches was stable as compared to native Basmati (BC) and Irri (IC) rice starches. Succinylation also reduced solubility, pasting temperature (PT) and gel hardness of starch gels. Improvement was observed in cold storage stability of rice starch succinates as evident from textural profile analysis. PMID:26258701

  8. Analysis of the early-flowering mechanisms and generation of T-DNA tagging lines in Kitaake, a model rice cultivar

    PubMed Central

    An, Gynheung

    2013-01-01

    As an extremely early flowering cultivar, rice cultivar Kitaake is a suitable model system for molecular studies. Expression analyses revealed that transcript levels of the flowering repressor Ghd7 were decreased while those of its downstream genes, Ehd1, Hd3a, and RFT1, were increased. Sequencing the known flowering-regulator genes revealed mutations in Ghd7 and OsPRR37 that cause early translation termination and amino acid substitutions, respectively. Genetic analysis of F2 progeny from a cross between cv. Kitaake and cv. Dongjin indicated that those mutations additively contribute to the early-flowering phenotype in cv. Kitaake. Because the short life cycle facilitates genetics research, this study generated 10 000 T-DNA tagging lines and deduced 6758 flanking sequence tags (FSTs), in which 3122 were genic and 3636 were intergenic. Among the genic lines, 367 (11.8%) were inserted into new genes that were not previously tagged. Because the lines were generated by T-DNA that contained the promoterless GUS reporter gene, which had an intron with triple splicing donors/acceptors in the right border region, a high efficiency of GUS expression was shown in various organs. Sequencing of the GUS-positive lines demonstrated that the third splicing donor and the first splicing acceptor of the vector were extensively used. The FST data have now been released into the public domain for seed distribution and facilitation of rice research. PMID:23966593

  9. A novel two T-DNA binary vector allows efficient generation of marker-free transgenic plants in three elite cultivars of rice (Oryza sativa L.).

    PubMed

    Breitler, Jean-Christophe; Meynard, Donaldo; Van Boxtel, Jos; Royer, Monique; Bonnot, François; Cambillau, Laurence; Guiderdoni, Emmanuel

    2004-06-01

    A pilot binary vector was constructed to assess the potential of the 2 T-DNA system for generating selectable marker-free progeny plants in three elite rice cultivars (ZhongZuo321, Ariete and Khao Dawk Mali 105) known to exhibit contrasting amenabilities to transformation. The first T-DNA of the vector, delimited by Agrobacterium tumefaciens borders, contains the hygromycin phosphotransferase (hpt) selectable gene and the green fluorescent protein (gfp) reporter gene while the second T-DNA, delimited by Agrobacterium rhizogenes borders, bears the phosphinothricin acetyl transferase (bar) gene, featuring the gene of interest. 82-90% of the hygromycin-resistant primary transformants exhibited tolerance to ammonium glufosinate mediated by the bar gene suggesting very high co-transformation frequency in the three cultivars. All of the regenerated plants were analyzed by Southern blot which confirmed co-integration of the T-DNAs at frequencies consistent with those of co-expression and allowed determination of copy number for each gene as well as detection of two different vector backbone fragments extending between the two T-DNAs. Hygromycin susceptible, ammonium glufosinate tolerant phenotypes represented 14.4, 17.4 and 14.3% of the plants in T1 progenies of ZZ321, Ariete and KDML105 primary transformants, respectively. We developed a statistical model for deducing from the observed copy number of each T-DNA in T0 plants and phenotypic segregations in T1 progenies the most likely constitution and linkage of the T-DNA integration locus. Statistical analysis identified in 40 out of 42 lines a most likely linkage configuration theoretically allowing genetic separation of the two T-DNA types and out segregation of the T-DNA bearing the bar gene. Overall, though improvements of the technology would be beneficial, the 2 T-DNA system appeared to be a useful approach to generate selectable marker-free rice plants with a consistent frequency among cultivars. PMID:15359604

  10. Analysis of Stress-Responsive Gene Expression in Cultivated and Weedy Rice Differing in Cold Stress Tolerance

    PubMed Central

    Pereira, Andy; Tseng, Te-Ming; Zimmer, Paulo Dejalma; Burgos, Nilda Roma

    2015-01-01

    Rice (Oryza sativa L.) cultivars show impairment of growth in response to environmental stresses such as cold at the early seedling stage. Locally adapted weedy rice is able to survive under adverse environmental conditions, and can emerge in fields from greater soil depth. Cold-tolerant weedy rice can be a good genetic source for developing cold-tolerant, weed-competitive rice cultivars. An in-depth analysis is presented here of diverse indica and japonica rice genotypes, mostly weedy rice, for cold stress response to provide an understanding of different stress adaptive mechanisms towards improvement of the rice crop performance in the field. We have tested a collection of weedy rice genotypes to: 1) classify the subspecies (ssp.) grouping (japonica or indica) of 21 accessions; 2) evaluate their sensitivity to cold stress; and 3) analyze the expression of stress-responsive genes under cold stress and a combination of cold and depth stress. Seeds were germinated at 25°C at 1.5- and 10-cm sowing depth for 10d. Seedlings were then exposed to cold stress at 10°C for 6, 24 and 96h, and the expression of cold-, anoxia-, and submergence-inducible genes was analyzed. Control plants were seeded at 1.5cm depth and kept at 25°C. The analysis revealed that cold stress signaling in indica genotypes is more complex than that of japonica as it operates via both the CBF-dependent and CBF-independent pathways, implicated through induction of transcription factors including OsNAC2, OsMYB46 and OsF-BOX28. When plants were exposed to cold + sowing depth stress, a complex signaling network was induced that involved cross talk between stresses mediated by CBF-dependent and CBF-independent pathways to circumvent the detrimental effects of stresses. The experiments revealed the importance of the CBF regulon for tolerance to both stresses in japonica and indica ssp. The mechanisms for cold tolerance differed among weedy indica genotypes and also between weedy indica and cultivated

  11. Development and evaluation of rice giant embryo mutants for high oil content originated from a high-yielding cultivar ‘Mizuhochikara’

    PubMed Central

    Sakata, Mitsukazu; Seno, Mari; Matsusaka, Hiroaki; Takahashi, Kiyomi; Nakamura, Yuki; Yamagata, Yoshiyuki; Angeles, Enrique R.; Mochizuki, Toshihiro; Kumamaru, Toshihiro; Sato, Masao; Enomoto, Akiko; Tashiro, Kosuke; Kuhara, Satoru; Satoh, Hikaru; Yoshimura, Atsushi

    2016-01-01

    Rice bran oil is a byproduct of the milling of rice (Oryza sativa L.). It offers various health benefits and has a beneficial fatty acid composition. To increase the amount of rice bran as a sink for triacylglycerol (TAG), we developed and characterized new breeding materials with giant embryos. To induce mutants, we treated fertilized egg cells of the high-yielding cultivar ‘Mizuhochikara’ with N-methyl-N-nitrosourea (MNU). By screening M2 seeds, we isolated four giant embryo mutant lines. Genetic analysis revealed that the causative loci in lines MGE12 and MGE13 were allelic to giant embryo (ge) on chromosome 7, and had base changes in the causal gene Os07g0603700. On the other hand, the causative loci in lines MGE8 and MGE14 were not allelic to ge, and both were newly mapped on chromosome 3. The TAG contents of all four mutant lines increased relative to their wild type, ‘Mizuhochikara’. MGE13 was agronomically similar to ‘Mizuhochikara’ and would be useful for breeding for improved oil content. PMID:27436953

  12. Effects of Fertilizer Inputs and Conventional Versus Organic Management on the Physiocochemical Properties and Sensory Quality of Diverse Rice Cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The demand for organically-grown rice has increased with consumer demand for organic foods. The objective of this research was to determine if there are physicochemical differences in organically- and conventionally-grown rice that contribute to flavor and texture differences, as determined by desc...

  13. Three QTLs conferring resistance to kernel fissuring in rice (Oryza sativa L.) identified by selective genotyping in two tropical japonica populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Kernel fissures caused by pre- or post-harvest stresses are the leading cause of breakage among milled rice, causing economic losses for producers, millers, and processors. Being an environmentally sensitive trait, it is difficult to reliably select for rice fissure resistance among breeding progen...

  14. [Effects of different barnyardgrass species on grain yield of rice and their physiological characteristics under alternate wetting and drying irrigation].

    PubMed

    Zhang, Zi-chang; Li, Yong-feng; Yang, Xia; Gu, Tao; Li, Gui

    2015-11-01

    In order to investigate the influence of different barnyardgrass species on rice yield and physiological characteristics of rice, two rice cultivars, Liangyoupeijiu (an indica hybrid cultivar) and Nanjing 9108 (a japonica cultivar) , were employed to co-culture with four barnyardgrass species during the period from transplanting to maturity under alternate wetting and moderate drying ir- rigation condition. The treatments were separately designed as follow: weed free ( control) , rice with Echinochloa crusgalli var. mitis (T1), rice with E. crusgalli (T2), rice with E. crusgali var. zelayensis (T3) and rice with E. colonum (T4). The results showed that T1, T2, T3 and T4 treatments reduced the Liangyoupeijiu yield by 13.8%, 10.6%, 23.8% and 0.5%, but the corresponding yield loss of Nanjing 9108 could reach up to 45.5%, 36.9%, 60.7% and 15.1%, respectively. The results above showed that T1, T2 and T3 treatments all significantly reduced grain yield, and T4 treatment only reduced grain yield for Nanjing 9108 but not for Liangyoupeijiu. All treatments elevated malondialehyde contents of rice leaf, but the activities of peroxidase, catalase, superoxide dimutase, dry matter accumulation in maturity stage, root oxidation activities and contents of indole-3-acetic acid as well as zeatin + zeatin riboside in roots during rice grain filling stage were all decreased. The influence degree of four barnyardgrass against physiological indices of rice had the order of T3 > T1 >T2 > T4. It showed that the reductions in enzyme activities of antioxidant system, root oxidation activities, contents of indole-3-acetic acid, zeatin + zeatin riboside during grain filling stage and accumulation of dry matter in maturity as well as increase in contents of malondialehyde of rice during grain filling stage might be important reasons for grain yield reduction when grew with barnyardgrass. PMID:26915195

  15. Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication[W

    PubMed Central

    Yu, Yanchun; Tang, Tian; Qian, Qian; Wang, Yonghong; Yan, Meixian; Zeng, Dali; Han, Bin; Wu, Chung-I; Shi, Suhua; Li, Jiayang

    2008-01-01

    Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reflect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1; here, we report the cloning of Phr1, which encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar. Phr1 is defective in all japonica lines but functional in nearly all indica and wild strains. Phylogenetic analysis showed that the defects in Phr1 arose independently three times. The multiple recent origins and rapid spread of phr1 in japonica suggest the action of positive selection, which is further supported by several population genetic tests. This case may hence represent an example of artificial selection driving the differentiation among domesticated varieties. PMID:19033526

  16. [Using liquid chromatography-mass spectrometry based metabolomics to discriminate between cold pressed rice bran oils produced from two different cultivars of Oryza sativa L. ssp. indica in Thailand].

    PubMed

    Charoonratana, Tossaton; Songsak, Thanapat; Sakunpak, Apirak; Pathompak, Pathamaporn; Charoenchai, Laksana

    2015-09-01

    A newly developed liquid chromatography-mass spectrometry (LC-MS) method for the analysis of cold pressed rice bran oil (RBO) was established and used to discriminate between RBOs produced from two different cultivars of major Thai fragrant rice species. The cold pressed RBO was prepared using the screw compression method. The LC-MS data were preprocessed with MZmine 2.10 program before evaluating with principal component analysis using SIMCA 13 software. The LC-MS method was able to detect and quantify several kinds of valuable constituents such as fatty acids, vitamin E, and γ-oryzanol. The chromatographic condition was feasible; short time for analysis and simple method were achieved. From score plot and loading plot of principle component analysis (PCA) , two rice cultivar samples were clearly separated, and it was revealed that Khao-Hom-Pathum was more suitable than Khao-Hom-Mali for cold pressed RBO production since it contained high total γ-oryzanol and less saturated free fatty acids. As with the fixed price of all the rice brans, this information can be used in order to, if possible, preserve the price of rice brans from different cultivars. PMID:26753285

  17. [Using liquid chromatography-mass spectrometry based metabolomics to discriminate between cold pressed rice bran oils produced from two different cultivars of Oryza sativa L. ssp. indica in Thailand].

    PubMed

    Charoonratana, Tossaton; Songsak, Thanapat; Sakunpak, Apirak; Pathompak, Pathamaporn; Charoenchai, Laksana

    2015-09-01

    A newly developed liquid chromatography-mass spectrometry (LC-MS) method for the analysis of cold pressed rice bran oil (RBO) was established and used to discriminate between RBOs produced from two different cultivars of major Thai fragrant rice species. The cold pressed RBO was prepared using the screw compression method. The LC-MS data were preprocessed with MZmine 2.10 program before evaluating with principal component analysis using SIMCA 13 software. The LC-MS method was able to detect and quantify several kinds of valuable constituents such as fatty acids, vitamin E, and γ-oryzanol. The chromatographic condition was feasible; short time for analysis and simple method were achieved. From score plot and loading plot of principle component analysis (PCA) , two rice cultivar samples were clearly separated, and it was revealed that Khao-Hom-Pathum was more suitable than Khao-Hom-Mali for cold pressed RBO production since it contained high total γ-oryzanol and less saturated free fatty acids. As with the fixed price of all the rice brans, this information can be used in order to, if possible, preserve the price of rice brans from different cultivars.

  18. A comparison of spider communities in Bt and non-Bt rice fields.

    PubMed

    Lee, Sue Yeon; Kim, Seung Tae; Jung, Jong Kook; Lee, Joon-Ho

    2014-06-01

    To assess the potential adverse effects of a Bt rice line (Japonica rice cultivar, Nakdong) expressing a synthetic cry1Ac1 gene, C7-1-9-1-B, which was highly active against all larval stages of Cnaphalocrocis medinalis (Guenée) (Lepidoptera: Crambidae), we investigated the community structure of spiders in Bt and non-Bt rice fields during the rice-growing season in 2007 and 2008 in Chungcheongnam-do, Korea. Spiders were surveyed with a sweep net and suction device. Suction sampling captured more spiders, measured in terms of species level and abundance, than sweeping. Araneidae and Thomisidae were captured more by sweeping, and certain species were captured only by sweeping. These findings show that both suction and sweep sampling methods should be used because these methods are most likely complementary. In total, 29 species in 23 genera and nine families were identified from the 4,937 spiders collected, and both Bt and non-Bt rice fields showed a typical Korean spider assemblage. The temporal patterns of spider species richness and spider abundance were very similar between Bt and non-Bt rice, although significant differences in species richness were observed on a few occasions. Overall, spider community structure, including diversity, the dominant species, and abundance did not differ between Bt and non-Bt rice. The results of the study indicated that the transgenic Cry1Ac rice lines tested in this study had no adverse effects on the spider community structure of the rice fields.

  19. Developing rice mapping populations as a genetic resource for validation of GWAS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Asian rice (Oryza sativa L.) is divided into two major subspecies, Indica and Japonica with the temperate and tropical japonica subpopulations being part of Japonica. These two subpopulations encompass the majority of the rice grown in the USA. Recently, a genome-wide association study (GWAS) iden...

  20. Assimilate translocation and expression of sucrose transporter, OsSUT1, contribute to high-performance ripening under heat stress in the heat-tolerant rice cultivar Genkitsukushi.

    PubMed

    Miyazaki, Masayuki; Araki, Masato; Okamura, Kenta; Ishibashi, Yushi; Yuasa, Takashi; Iwaya-Inoue, Mari

    2013-12-15

    High temperature reduces the grain quality of rice, a situation likely to become more frequent because of global warming. We studied the effects of high-temperature stress on grain quality of heat-tolerant cultivar 'Genkitsukushi' and heat-sensitive cultivar 'Tsukushiroman'. When day/night temperatures were 31/26 °C from heading until maturity, the grain quality of 'Genkitsukushi' was rated at the first inspection grade (high quality), whereas 'Tsukushiroman' showed a remarkable increase in the percentage of white immature kernels (low quality). Nonstructural carbohydrate content in the stem of 'Genkitsukushi' the early maturation was significantly higher than in 'Tsukushiroman' and greatly decreased under high temperature. From 14 to 21 days after heading, the expression of the sucrose transporter gene, OsSUT1, was higher in the stem of 'Genkitsukushi' grown under high temperature than in 'Tsukushiroman'. In addition, the expression of OsSUT1 in the grains of 'Genkitsukushi' was significantly higher than in 'Tsukushiroman' during the ripening period. These results indicate that sugar transport functions more effectively in 'Genkitsukushi' than in 'Tsukushiroman', and that the effectiveness of sugar transport contributes to maintaining high grain quality in 'Genkitsukushi' under high-temperature conditions.

  1. Comparing simple root phenotyping methods on a core set of rice genotypes.

    PubMed

    Shrestha, R; Al-Shugeairy, Z; Al-Ogaidi, F; Munasinghe, M; Radermacher, M; Vandenhirtz, J; Price, A H

    2014-05-01

    Interest in belowground plant growth is increasing, especially in relation to arguments that shallow-rooted cultivars are efficient at exploiting soil phosphorus while deep-rooted ones will access water at depth. However, methods for assessing roots in large numbers of plants are diverse and direct comparisons of methods are rare. Three methods for measuring root growth traits were evaluated for utility in discriminating rice cultivars: soil-filled rhizotrons, hydroponics and soil-filled pots whose bottom was sealed with a non-woven fabric (a potential method for assessing root penetration ability). A set of 38 rice genotypes including the OryzaSNP set of 20 cultivars, additional parents of mapping populations and products of marker-assisted selection for root QTLs were assessed. A novel method of image analysis for assessing rooting angles from rhizotron photographs was employed. The non-woven fabric was the easiest yet least discriminatory method, while the rhizotron was highly discriminatory and allowed the most traits to be measured but required more than three times the labour of the other methods. The hydroponics was both easy and discriminatory, allowed temporal measurements, but is most likely to suffer from artefacts. Image analysis of rhizotrons compared favourably to manual methods for discriminating between cultivars. Previous observations that cultivars from the indica subpopulation have shallower rooting angles than aus or japonica cultivars were confirmed in the rhizotrons, and indica and temperate japonicas had lower maximum root lengths in rhizotrons and hydroponics. It is concluded that rhizotrons are the preferred method for root screening, particularly since root angles can be assessed.

  2. Spikelet-specific variation in ethylene production and constitutive expression of ethylene receptors and signal transducers during grain filling of compact- and lax-panicle rice (Oryza sativa) cultivars.

    PubMed

    Sekhar, Sudhanshu; Panda, Binay B; Mohapatra, Trupti; Das, Kaushik; Shaw, Birendra P; Kariali, Ekamber; Mohapatra, Pravat K

    2015-05-01

    Grain yields in modern super rice cultivars do not always meet the expectations because many spikelets are located on secondary branches in closely packed homogeneous distribution in these plants, and they do not fill properly. The factors limiting grain filling of such spikelets, especially in the lower panicle branches, are elusive. Two long-duration rice cultivars differing in panicle density, Mahalaxmi (compact) and Upahar (lax), were cultivated in an open field plot. Grain filling, ethylene production and constitutive expression of ethylene receptors and ethylene signal transducers in apical and basal spikelets of the panicle were compared during the early post-anthesis stage, which is the most critical period for grain development. In another experiment, a similar assessment was made for the medium-duration cultivars compact-panicle OR-1918 and lax-panicle Lalat. Grain weight of the apical spikelets was always higher than that of the basal spikelets. This gradient of grain weight was wide in the compact-panicle cultivars and narrow in the lax-panicle cultivars. Compared to apical spikelets, the basal spikelets produced more ethylene at anthesis and retained the capacity for post-anthesis expression of ethylene receptors and ethylene signal transducers longer. High ethylene production enhanced the expression of the RSR1 gene, but reduced expression of the GBSS1 gene. Ethylene inhibited the partitioning of assimilates of developing grains resulting in low starch biosynthesis and high accumulation of soluble carbohydrates. It is concluded that an increase in grain/spikelet density in rice panicles reduces apical dominance to the detriment of grain filling by production of ethylene and/or enhanced perception of the ethylene signal. Ethylene could be a second messenger for apical dominance in grain filling. The manipulation of the ethylene signal would possibly improve rice grain yield.

  3. Close linkage of a blast resistance gene, Pias(t), with a bacterial leaf blight resistance gene, Xa1-as(t), in a rice cultivar 'Asominori'.

    PubMed

    Endo, Takashi; Yamaguchi, Masayuki; Kaji, Ryota; Nakagomi, Koji; Kataoka, Tomomori; Yokogami, Narifumi; Nakamura, Toshiki; Ishikawa, Goro; Yonemaru, Jun-Ichi; Nishio, Takeshi

    2012-12-01

    It has long been known that a bacterial leaf blight-resistant line in rice obtained from a crossing using 'Asominori' as a resistant parent also has resistance to blast, but a blast resistance gene in 'Asominori' has not been investigated in detail. In the present study, a blast resistance gene in 'Asominori', tentatively named Pias(t), was revealed to be located within 162-kb region between DNA markers YX4-3 and NX4-1 on chromosome 4 and to be linked with an 'Asominori' allele of the bacterial leaf blight resistance gene Xa1, tentatively named Xa1-as(t). An 'Asominori' allele of Pias(t) was found to be dominant and difference of disease severity between lines having the 'Asominori' allele of Pias(t) and those without it was 1.2 in disease index from 0 to 10. Pias(t) was also closely linked with the Ph gene controlling phenol reaction, suggesting the possibility of successful selection of blast resistance using the phenol reaction. Since blast-resistant commercial cultivars have been developed using 'Asominori' as a parent, Pias(t) is considered to be a useful gene in rice breeding for blast resistance. PMID:23341747

  4. Genetic variation in the chloroplast genome suggests multiple domestication of cultivated Asian rice (Oryza sativa L.).

    PubMed

    Kawakami, Shin-ichi; Ebana, Kaworu; Nishikawa, Tomotaro; Sato, Yo-ichiro; Vaughan, Duncan A; Kadowaki, Koh-ichi

    2007-02-01

    Two hundred and seventy-five accessions of cultivated Asian rice and 44 accessions of AA genome Oryza species were classified into 8 chloroplast (cp) genome types (A-H) based on insertion-deletion events at 3 regions (8K, 57K, and 76K) of the cp genome. The ancestral cp genome type was determined according to the frequency of occurrence in Oryza species and the likely evolution of the variable 57K region of the cp genome. When 2 nucleotide substitutions (AA or TT) were taken into account, these 8 cp types were subdivided into 11 cp types. Most indica cultivars had 1 of 3 cp genome types that were also identified in the wild relatives of rice, O. nivara and O. rufipogon, suggesting that the 3 indica cp types had evolved from distinct gene pools of the O. rufipogon - O. nivara complex. The majority of japonica cultivars had 1 of 3 different cp genome types. One of these 3 was identified in O. rufipogon, suggesting that at least 1 japonica type is derived from O. rufipogon with the same cp genome type. These results provide evidence to support a polyphyletic origin of cultivated Asian rice from at least 4 principal lineages in the O. rufipogon - O. nivara complex.

  5. Variations in CYP78A13 coding region influence grain size and yield in rice.

    PubMed

    Xu, Fan; Fang, Jun; Ou, Shujun; Gao, Shaopei; Zhang, Fengxia; Du, Lin; Xiao, Yunhua; Wang, Hongru; Sun, Xiaohong; Chu, Jinfang; Wang, Guodong; Chu, Chengcai

    2015-04-01

    Grain size is one of the most important determinants of crop yield in cereals. Here, we identified a dominant mutant, big grain2 (bg2-D) from our enhancer-trapping population. Genetic analysis and SiteFinding PCR (polymerase chain reaction) revealed that BG2 encodes a cytochrome P450, OsCYP78A13. Sequence search revealed that CYP78A13 has a paralogue Grain Length 3.2 (GL3.2, LOC_Os03g30420) in rice with distinct expression patterns, analysis of transgenic plants harbouring either CYP78A13 or GL3.2 showed that both can promote grain growth. Sequence polymorphism analysis with 1529 rice varieties showed that the nucleotide diversity at CYP78A13 gene body and the 20 kb flanking region in the indica varieties were markedly higher than those in japonica varieties. Further, comparison of the genomic sequence of CYP78A13 in the japonica cultivar Nipponbare and the indica cultivar 9311 showed that there were three InDels in the promoter region and eight SNPs (single nucleotide polymorphism) in its coding sequence. Detailed examination of the transgenic plants with chimaeric constructs suggested that variation in CYP78A13 coding region is responsible for the variation of grain yield. Taken together, our results suggest that the variations in CYP78A13 in the indica varieties hold potential in rice breeding for application of grain yield improvement.

  6. The Tyrosine Aminomutase TAM1 Is Required for β-Tyrosine Biosynthesis in Rice

    PubMed Central

    Yan, Jian; Aboshi, Takako; Teraishi, Masayoshi; Strickler, Susan R.; Spindel, Jennifer E.; Tung, Chih-Wei; Takata, Ryo; Matsumoto, Fuka; Maesaka, Yoshihiro; McCouch, Susan R.; Okumoto, Yutaka; Mori, Naoki; Jander, Georg

    2015-01-01

    Non-protein amino acids, often isomers of the standard 20 protein amino acids, have defense-related functions in many plant species. A targeted search for jasmonate-induced metabolites in cultivated rice (Oryza sativa) identified (R)-β-tyrosine, an isomer of the common amino acid (S)-α-tyrosine in the seeds, leaves, roots, and root exudates of the Nipponbare cultivar. Assays with 119 diverse cultivars showed a distinct presence/absence polymorphism, with β-tyrosine being most prevalent in temperate japonica cultivars. Genetic mapping identified a candidate gene on chromosome 12, which was confirmed to encode a tyrosine aminomutase (TAM1) by transient expression in Nicotiana benthamiana and in vitro enzyme assays. A point mutation in TAM1 eliminated β-tyrosine production in Nipponbare. Rice cultivars that do not produce β-tyrosine have a chromosome 12 deletion that encompasses TAM1. Although β-tyrosine accumulation was induced by the plant defense signaling molecule jasmonic acid, bioassays with hemipteran and lepidopteran herbivores showed no negative effects at physiologically relevant β-tyrosine concentrations. In contrast, root growth of Arabidopsis thaliana and other tested dicot plants was inhibited by concentrations as low as 1 μM. As β-tyrosine is exuded into hydroponic medium at higher concentrations, it may contribute to the allelopathic potential of rice. PMID:25901084

  7. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

    PubMed

    Sakai, Hiroaki; Lee, Sung Shin; Tanaka, Tsuyoshi; Numa, Hisataka; Kim, Jungsok; Kawahara, Yoshihiro; Wakimoto, Hironobu; Yang, Ching-chia; Iwamoto, Masao; Abe, Takashi; Yamada, Yuko; Muto, Akira; Inokuchi, Hachiro; Ikemura, Toshimichi; Matsumoto, Takashi; Sasaki, Takuji; Itoh, Takeshi

    2013-02-01

    The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.

  8. Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis

    PubMed Central

    2012-01-01

    Background GDSL esterases/lipases are a newly discovered subclass of lipolytic enzymes that are very important and attractive research subjects because of their multifunctional properties, such as broad substrate specificity and regiospecificity. Compared with the current knowledge regarding these enzymes in bacteria, our understanding of the plant GDSL enzymes is very limited, although the GDSL gene family in plant species include numerous members in many fully sequenced plant genomes. Only two genes from a large rice GDSL esterase/lipase gene family were previously characterised, and the majority of the members remain unknown. In the present study, we describe the rice OsGELP (Oryza sativa GDSL esterase/lipase protein) gene family at the genomic and proteomic levels, and use this knowledge to provide insights into the multifunctionality of the rice OsGELP enzymes. Results In this study, an extensive bioinformatics analysis identified 114 genes in the rice OsGELP gene family. A complete overview of this family in rice is presented, including the chromosome locations, gene structures, phylogeny, and protein motifs. Among the OsGELPs and the plant GDSL esterase/lipase proteins of known functions, 41 motifs were found that represent the core secondary structure elements or appear specifically in different phylogenetic subclades. The specification and distribution of identified putative conserved clade-common and -specific peptide motifs, and their location on the predicted protein three dimensional structure may possibly signify their functional roles. Potentially important regions for substrate specificity are highlighted, in accordance with protein three-dimensional model and location of the phylogenetic specific conserved motifs. The differential expression of some representative genes were confirmed by quantitative real-time PCR. The phylogenetic analysis, together with protein motif architectures, and the expression profiling were analysed to predict the

  9. Differences in CH4 oxidation and pathways of production between rice cultivars deduced from measurements of CH4 flux and δ13C of CH4 and CO2

    NASA Astrophysics Data System (ADS)

    Bilek, Rebecca S.; Tyler, Stanley C.; Sass, Ronald L.; Fisher, Frank M.

    We report measurements of CH4 flux and δ13C and δD values of emitted CH4 and sediment CH4 and CO2 during the 1995 rice growing season in Beaumont, Texas. Four rice plant cultivars, Lemont, Mars, Cypress, and Della, and an unplanted plot were studied to provide possible explanations for the differences in CH4 emissions between cultivars. Using the measured isotope values, along with data of CH4 and CO2 concentrations and other ecosystem data, we determined differences between cultivars in the processes of oxidation and production throughout the growing season. For instance, rhizospheric CH4 oxidation increased as the season progressed in both Mars and Lemont cultivars. Late in the season, however, 71+/-10% of CH4 produced in the Mars plot was oxidized compared to only 39+/-10% in the Lemont plot. The contribution of acetate fermentation to methanogenesis at specific times during the season was calculated using measured isotopic values and assuming identical isotopic fractionation factors in methanogenic pathways for the cultivars. In these calculations a range of values for the contribution to CH4 production from acetate fermentation and CO2 reduction with H2 was estimated by considering different fractionation factors for the methanogenic CO2 reduction pathway and the possibility of a 10% contribution to CH4 production from acetate produced by homoacetogenesis. In general, a steady increase in the CH4 portion produced by acetate fermentation was noted in the Lemont cultivar, while an increase followed by a decrease near the end of the season was observed for the Mars cultivar.

  10. LABA1, a Domestication Gene Associated with Long, Barbed Awns in Wild Rice.

    PubMed

    Hua, Lei; Wang, Diane R; Tan, Lubin; Fu, Yongcai; Liu, Fengxia; Xiao, Langtao; Zhu, Zuofeng; Fu, Qiang; Sun, Xianyou; Gu, Ping; Cai, Hongwei; McCouch, Susan R; Sun, Chuanqing

    2015-07-01

    Common wild rice (Oryza rufipogon), the wild relative of Asian cultivated rice (Oryza sativa), flaunts long, barbed awns, which are necessary for efficient propagation and dissemination of seeds. By contrast, O. sativa cultivars have been selected to be awnless or to harbor short, barbless awns, which facilitate seed processing and storage. The transition from long, barbed awns to short, barbless awns was a crucial event in rice domestication. Here, we show that the presence of long, barbed awns in wild rice is controlled by a major gene on chromosome 4, LONG AND BARBED AWN1 (LABA1), which encodes a cytokinin-activating enzyme. A frame-shift deletion in LABA1 of cultivated rice reduces the cytokinin concentration in awn primordia, disrupting barb formation and awn elongation. Sequencing analysis demonstrated low nucleotide diversity and a selective sweep encompassing an ∼800-kb region around the derived laba1 allele in cultivated rice. Haplotype analysis revealed that the laba1 allele originated in the japonica subspecies and moved into the indica gene pool via introgression, suggesting that humans selected for this locus in early rice domestication. Identification of LABA1 provides new insights into rice domestication and also sheds light on the molecular mechanism underlying awn development.

  11. Dissipation of phenanthrene and pyrene at the aerobic-anaerobic soil interface: differentiation induced by the rhizosphere of PAH-tolerant and PAH-sensitive rice (Oryza sativa L.) cultivars.

    PubMed

    He, Yan; Xia, Wen; Li, Xinfeng; Lin, Jiajiang; Wu, Jianjun; Xu, Jianming

    2015-03-01

    A pot experiment was conducted to reveal the removal of two polycyclic aromatic hydrocarbons (PAHs) (phenanthrene, PHE, and pyrene, PYR) during rice cultivation in a paddy field. The rhizosphere effect on facilitating dissipation of PAHs varied simultaneously as a function of soil properties, PAH types, cultivation time, and genotypes within rice cultivars, with differences performed for PYR but not PHE. Changes in soil PLFA profiles evidenced that the growth of rice roots modified the dominant species within rhizosphere microbial communities and induced a selective enrichment of Gram-negative aerobic bacteria capable of degrading, thereby resulting in the differentiated dissipation of PYR. While the insignificant differences in PHE dissipation might be attributed to its higher solubility and availability under flooded condition that concealed the differences in improvement of bioavailability for microorganisms between rhizosphere and non-rhizosphere, and between both soils and both rice cultivars. Our findings illustrate that the removal of PAHs in paddy soils was more complex relative to those in dryland soils. This was possibly due to the specialty of rice roots for oxygen secretion that provides development of redox heterogeneous microbial habitats at root-soil interface under flooded condition.

  12. Detection of QTLs for white-back and basal-white grains caused by high temperature during ripening period in japonica rice.

    PubMed

    Wada, Takuya; Miyahara, Katsunori; Sonoda, Jun-Ya; Tsukaguchi, Tadashi; Miyazaki, Masayuki; Tsubone, Masao; Ando, Tsuyu; Ebana, Kaworu; Yamamoto, Toshio; Iwasawa, Norio; Umemoto, Takayuki; Kondo, Motohiko; Yano, Masahiro

    2015-06-01

    There is increasing evidence that global warming affects the development of rice. High temperatures during ripening increase the ratio of undesirable chalky grains followed by deteriorating grain appearance quality. In order to detect quantitative trait loci (QTLs) controlling the occurrence of white-back and basal-white chalky grains of brown rice, QTL analysis was performed using recombinant inbred lines derived from a cross between two strains, 'Tsukushiroman' (sensitive to heat stress) and 'Chikushi 52' (tolerant of heat stress). The F7 and F8 lines were exposed to heat stress during the ripening period in two locations, Fukuoka and Kagoshima, in Japan. QTLs for white-back grains and basal-white grains were detected on chromosomes 1, 3, and 8, and those for basal-white grains were detected on chromosomes 2, 3, and 12. QTLs on chromosome 8 for white-back grains were shared in the plants grown in both locations. Near-isogenic lines (NILs), which harbored a segment from 'Chikushi 52' on chromosome 8 with the genetic background of 'Tsukushiroman', showed relatively lower ratios of white-back grains than 'Tsukushiroman'. Therefore, insertion of the 'Chikushi 52' genomic region of the QTL on chromosome 8 can improve the quality of rice when it is grown under heat stress conditions.

  13. Detection of QTLs for white-back and basal-white grains caused by high temperature during ripening period in japonica rice

    PubMed Central

    Wada, Takuya; Miyahara, Katsunori; Sonoda, Jun-ya; Tsukaguchi, Tadashi; Miyazaki, Masayuki; Tsubone, Masao; Ando, Tsuyu; Ebana, Kaworu; Yamamoto, Toshio; Iwasawa, Norio; Umemoto, Takayuki; Kondo, Motohiko; Yano, Masahiro

    2015-01-01

    There is increasing evidence that global warming affects the development of rice. High temperatures during ripening increase the ratio of undesirable chalky grains followed by deteriorating grain appearance quality. In order to detect quantitative trait loci (QTLs) controlling the occurrence of white-back and basal-white chalky grains of brown rice, QTL analysis was performed using recombinant inbred lines derived from a cross between two strains, ‘Tsukushiroman’ (sensitive to heat stress) and ‘Chikushi 52’ (tolerant of heat stress). The F7 and F8 lines were exposed to heat stress during the ripening period in two locations, Fukuoka and Kagoshima, in Japan. QTLs for white-back grains and basal-white grains were detected on chromosomes 1, 3, and 8, and those for basal-white grains were detected on chromosomes 2, 3, and 12. QTLs on chromosome 8 for white-back grains were shared in the plants grown in both locations. Near-isogenic lines (NILs), which harbored a segment from ‘Chikushi 52’ on chromosome 8 with the genetic background of ‘Tsukushiroman’, showed relatively lower ratios of white-back grains than ‘Tsukushiroman’. Therefore, insertion of the ‘Chikushi 52’ genomic region of the QTL on chromosome 8 can improve the quality of rice when it is grown under heat stress conditions. PMID:26175618

  14. Effects of nitrogen fertilization strategies on nitrogen use efficiency in physiology, recovery, and agronomy and redistribution of dry matter accumulation and nitrogen accumulation in two typical rice cultivars in Zhejiang, China.

    PubMed

    Xie, Wen-xia; Wang, Guang-huo; Zhang, Qi-chun; Guo, Hai-chao

    2007-03-01

    Field experiments were conducted in farmers' rice fields in 2001 and 2002 to study the effects of nitrogen (N) management strategies on N use efficiency in recovery (RE), agronomy (AE) and physiology (PE) and redistribution of dry matter accumulation (DMA) and nitrogen accumulation (NA) in two typical rice cultivars in Jinhua, Zhejiang Province. This study aimed mainly at identifying the possible causes of poor fertilizer N use efficiency (NUE) of rice in Zhejiang by comparing farmers' fertilizer practice (FFP) with advanced site-specific nutrient management (SSNM) and real-time N management (RTNM). The results showed that compared to FFP, SSNM and RTNM reduced DMA and NA before panicle initiation and increased DMA and NA at post-flowering. There is no significant difference between SSNM and FFP in post-flowering dry matter redistribution (post-DMR) and post-flowering nitrogen redistribution (post-NR). These results suggest that high input rate of fertilizer N and improper fertilizer N timing are the main factors causing low NUE of irrigated rice in the farmer's routine practice of Zhejiang. With SSNM, about 15% of the current total N input in direct-seeding early rice and 45% in single rice could be reduced without yield loss in Zhejiang, China.

  15. Dissecting root proteome of transgenic rice cultivars unravels metabolic alterations and accumulation of novel stress responsive proteins under drought stress.

    PubMed

    Paul, Soumitra; Gayen, Dipak; Datta, Swapan K; Datta, Karabi

    2015-05-01

    Generation of drought tolerant rice plants by overexpressing Arabidopsis DREB1A is a significant development for abiotic stress research. However, the metabolic network regulated in the drought tolerant transgenic rice plants is poorly understood. In this research study, we have demonstrated the comparative proteome analysis between the roots of wild type and transgenic DREB1A overexpressing homozygous plants under drought stress condition. After 7d of dehydration stress at reproductive stage, the plants were re-watered for 24h. The roots were collected separately from wild type and transgenic plants grown under water, drought stress and re-watering conditions and total proteins were analyzed by two-dimensional gel electrophoresis (2-DE) coupled with mass spectrometry (MS). Among the large number of differentially accumulated spots, 30, 27 and 20 spots were successfully identified as differentially expressed proteins in three different conditions respectively. The major class of identified proteins belongs to carbohydrate and energy metabolism category while stress and defense related proteins are especially up-accumulated under drought stress in both the plants. A novel protein, R40C1 was reported to be up-accumulated in roots of transgenic plants which may play an important role in generation of drought tolerant plants. Protein-protein interaction helps to identify the network of drought stress signaling pathways. PMID:25804816

  16. Comparison of the role of gibberellins and ethylene in response to submergence of two lowland rice cultivars, Senia and Bomba.

    PubMed

    Dubois, Vincent; Moritz, Thomas; García-Martínez, José L

    2011-02-15

    We examined the gibberellin (GA) and ethylene regulation of submergence-induced elongation in seedlings of the submergence-tolerant lowland rice (Oryza sativa L.) cvs Senia and Bomba. Elongation was enhanced after germination to facilitate water escape and reach air. We found that submergence-induced elongation depends on GA because it was counteracted by paclobutrazol (an inhibitor of GA biosynthesis), an effect that was negated by GA(3). Moreover, in the cv Senia, submergence increased the content of active GA(1) and its immediate precursors (GA(53), GA(19) and GA(20)) by enhancing expression of several GA biosynthesis genes (OsGA20ox1 and -2, and OsGA3ox2), but not by decreasing expression of several OsGA2ox (GA inactivating genes). Senia seedlings, in contrast to Bomba seedlings, did not elongate in response to ethylene or 1-aminocyclopropane-1-carboxylic-acid (ACC; an ethylene precursor) application, and submergence-induced elongation was not reduced in the presence of 1-methylcyclopropene (1-MCP; an ethylene perception inhibitor). Ethylene emanation was similar in Senia seedlings grown in air and in submerged-grown seedlings following de-submergence, while it increased in Bomba. The expression of ethylene biosynthesis genes (OsACS1, -2 and -3, and OsACO1) was not affected in Senia, but expression of OsACS5 was rapidly enhanced in Bomba upon submergence. Our results support the conclusion that submergence elongation enhancement of lowland rice is due to alteration of GA metabolism leading to an increase in active GA (GA(1)) content. Interestingly, in the cv Senia, in contrast to cv Bomba, this was triggered through an ethylene-independent mechanism.

  17. Proteomics insight into the biological safety of transgenic modification of rice as compared with conventional genetic breeding and spontaneous genotypic variation.

    PubMed

    Gong, Chun Yan; Li, Qi; Yu, Hua Tao; Wang, Zizhang; Wang, Tai

    2012-05-01

    The potential of unintended effects caused by transgenic events is a key issue in the commercialization of genetically modified (GM) crops. To investigate whether transgenic events cause unintended effects, we used comparative proteomics approaches to evaluate proteome differences in seeds from 2 sets of GM indica rice, herbicide-resistant Bar68-1 carrying bar and insect-resistant 2036-1a carrying cry1Ac/sck, and their respective controls D68 and MH86, as well as indica variety MH63, a parental line for breeding MH86, and japonica variety ZH10. This experimental design allowed for comparing proteome difference caused by transgenes, conventional genetic breeding, and natural genetic variation. Proteomics analysis revealed the maximum numbers of differentially expressed proteins between indica and japonica cultivars, second among indica varieties with relative small difference between MH86 and MH63, and the minimum between GM rice and respective control, thus indicating GM events do not substantially alter proteome profiles as compared with conventional genetic breeding and natural genetic variation. Mass spectrometry analysis revealed 234 proteins differentially expressed in the 6 materials, and these proteins were involved in different cellular and metabolic processes with a prominent skew toward metabolism (31.2%), protein synthesis and destination (25.2%), and defense response (22.4%). In these seed proteomes, proteins implicated in the 3 prominent biological processes showed significantly different composite expression patterns and were major factors differentiating japonica and indica cultivars, as well as indica varieties. Thus, metabolism, protein synthesis and destination, and defense response in seeds are important in differentiating rice cultivars and varieties.

  18. Biology and epidemiology of rice viruses.

    PubMed

    Hibino, H

    1996-01-01

    The 15 known viruses that occur in rice are rice black-streaked dwarf, rice bunchy stunt, rice dwarf, rice gall dwarf, rice giallume, rice grassy stunt, rice hoja blanca, rice necrosis mosaic, rice ragged stunt, rice stripe necrosis, rice stripe, rice transitory yellowing, rice tungro bacilliform, rice tungro spherical, and rice yellow mottle viruses. This paper describes their geographical distribution, relation to vectors, infection cycles, field dispersal, and development, and lists recorded outbreaks of the viruses. Many rice viruses have become serious problems since rice cultivation has been intensified. Double-cropping of rice using improved, photo-insensitive cultivars of short growth duration has significantly influenced the incidence of these viruses. PMID:15012543

  19. Whole Mitochondrial Genome Sequencing and Re-Examination of a Cytoplasmic Male Sterility-Associated Gene in Boro-Taichung-Type Cytoplasmic Male Sterile Rice

    PubMed Central

    Kazama, Tomohiko; Toriyama, Kinya

    2016-01-01

    Nuclear genome substitutions between subspecies can lead to cytoplasmic male sterility (CMS) through incompatibility between nuclear and mitochondrial genomes. Boro-Taichung (BT)-type CMS rice was obtained by substituting the nuclear genome of Oryza sativa subsp. indica cultivar Chinsurah Boro II with that of Oryza sativa subsp. japonica cultivar Taichung 65. In BT-type CMS rice, the mitochondrial gene orf79 is associated with male sterility. A complete sequence of the Boro-type mitochondrial genome responsible for BT-type CMS has not been determined to date. Here, we used pyrosequencing to construct the Boro-type mitochondrial genome. The contiguous sequences were assembled into five circular DNA molecules, four of which could be connected into a single circle. The two resulting subgenomic circles were unable to form a reliable master circle, as recombination between them was scarcely detected. We also found an unequal abundance of DNA molecules for the two loci of atp6. These results indicate the presence of multi-partite DNA molecules in the Boro-type mitochondrial genome. Expression patterns were investigated for Boro-type mitochondria-specific orfs, which were not found in the mitochondria from the standard japonica cultivar Nipponbare. Restorer of fertility 1 (RF1)-dependent RNA processing has been observed in orf79-containing RNA but was not detected in other Boro-type mitochondria-specific orfs, supporting the conclusion that orf79 is a unique CMS-associated gene in Boro-type mitochondria. PMID:27414645

  20. The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice.

    PubMed

    Reagon, Michael; Thurber, Carrie S; Olsen, Kenneth M; Jia, Yulin; Caicedo, Ana L

    2011-09-01

    Growth-related traits, such as greater height, greater biomass, faster growth rate and early flowering, are thought to enhance competitiveness of agricultural weeds. However, weedy rice, a conspecific weed of cultivated rice (Oryza sativa L.), displays variation for growth traits. In the United States, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. Through a common garden experiment, we investigated whether growth trait divergence has occurred among U.S. weeds and their putative cultivated progenitors. We also determined polymorphism patterns in the growth candidate gene, SD1, to assess its possible role in the evolution of divergent phenotypes. We found considerable growth trait variation among weed groups, suggesting that growth trait convergence is not evident among weedy populations. Phenotypic divergence of weedy rice from cultivated ancestors is most apparent for flowering time. Introgression of a chromosomal block containing the SD1 allele from tropical japonica, the predominant U.S. rice cultivar, was detected in one weedy rice population and is associated with a change in growth patterns in this group. This study demonstrates the role of introgressive hybridization in evolutionary divergence of an important weed. PMID:21854475

  1. Molecular marker assisted gene stacking for biotic and abiotic stress resistance genes in an elite rice cultivar

    PubMed Central

    Das, Gitishree; Rao, G. J. N.

    2015-01-01

    Severe yield loss due to various biotic stresses like bacterial blight (BB), gall midge (insect) and Blast (disease) and abiotic stresses like submergence and salinity are a serious constraint to the rice productivity throughout the world. The most effective and reliable method of management of the stresses is the enhancement of host resistance, through an economical and environmentally friendly approach. Through the application of marker assisted selection (MAS) technique, the present study reports a successful pyramidization of genes/QTLs to confer resistance/tolerance to blast (Pi2, Pi9), gall Midge (Gm1, Gm4), submergence (Sub1), and salinity (Saltol) in a released rice variety CRMAS2621-7-1 as Improved Lalat which had already incorporated with three BB resistance genes xa5, xa13, and Xa21 to supplement the Xa4 gene present in Improved Lalat. The molecular analysis revealed clear polymorphism between the donor and recipient parents for all the markers that are tagged to the target traits. The conventional backcross breeding approach was followed till BC3F1 generation and starting from BC1F1 onwards, marker assisted selection was employed at each step to monitor the transfer of the target alleles with molecular markers. The different BC3F1s having the target genes/QTLs were inter crossed to generate hybrids with all 10 stress resistance/tolerance genes/QTLs into a single plant/line. Homozygous plants for resistance/tolerance genes in different combinations were recovered. The BC3F3 lines were characterized for their agronomic and quality traits and promising progeny lines were selected. The SSR based background selection was done. Most of the gene pyramid lines showed a high degree of similarity to the recurrent parent for both morphological, grain quality traits and in SSR based background selection. Out of all the gene pyramids tested, two lines had all the 10 resistance/tolerance genes and showed adequate levels of resistance/tolerance against the five target

  2. Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species.

    PubMed

    Singh, Sangeeta; Chand, Suresh; Singh, N K; Sharma, Tilak Raj

    2015-01-01

    The resistance (R) genes and defense response (DR) genes have become very important resources for the development of disease resistant cultivars. In the present investigation, genome-wide identification, expression, phylogenetic and synteny analysis was done for R and DR-genes across three species of rice viz: Oryza sativa ssp indica cv 93-11, Oryza sativa ssp japonica and wild rice species, Oryza brachyantha. We used the in silico approach to identify and map 786 R -genes and 167 DR-genes, 672 R-genes and 142 DR-genes, 251 R-genes and 86 DR-genes in the japonica, indica and O. brachyanth a genomes, respectively. Our analysis showed that 60.5% and 55.6% of the R-genes are tandemly repeated within clusters and distributed over all the rice chromosomes in indica and japonica genomes, respectively. The phylogenetic analysis along with motif distribution shows high degree of conservation of R- and DR-genes in clusters. In silico expression analysis of R-genes and DR-genes showed more than 85% were expressed genes showing corresponding EST matches in the databases. This study gave special emphasis on mechanisms of gene evolution and duplication for R and DR genes across species. Analysis of paralogs across rice species indicated 17% and 4.38% R-genes, 29% and 11.63% DR-genes duplication in indica and Oryza brachyantha, as compared to 20% and 26% duplication of R-genes and DR-genes in japonica respectively. We found that during the course of duplication only 9.5% of R- and DR-genes changed their function and rest of the genes have maintained their identity. Syntenic relationship across three genomes inferred that more orthology is shared between indica and japonica genomes as compared to brachyantha genome. Genome wide identification of R-genes and DR-genes in the rice genome will help in allele mining and functional validation of these genes, and to understand molecular mechanism of disease resistance and their evolution in rice and related species.

  3. Combination Patterns of Major R Genes Determine the Level of Resistance to the M. oryzae in Rice (Oryza sativa L.).

    PubMed

    Wu, Yunyu; Xiao, Ning; Yu, Ling; Pan, Cunhong; Li, Yuhong; Zhang, Xiaoxiang; Liu, Guangqing; Dai, Zhengyuan; Pan, Xuebiao; Li, Aihong

    2015-01-01

    Rice blast caused by Magnaporthe oryzae is the most devastating disease of rice and poses a serious threat to world food security. In this study, the distribution and effectiveness of 18 R genes in 277 accessions were investigated based on pathogenicity assays and molecular markers. The results showed that most of the accessions exhibited some degree of resistance (resistance frequency, RF >50%). Accordingly, most of the accessions were observed to harbor two or more R genes, and the number of R genes harbored in accessions was significantly positively correlated with RF. Some R genes were demonstrated to be specifically distributed in the genomes of rice sub-species, such as Pigm, Pi9, Pi5 and Pi1, which were only detected in indica-type accessions, and Pik and Piz, which were just harbored in japonica-type accessions. By analyzing the relationship between R genes and RF using a multiple stepwise regression model, the R genes Pid3, Pi5, Pi9, Pi54, Pigm and Pit were found to show the main effects against M. oryzae in indica-type accessions, while Pita, Pb1, Pik, Pizt and Pia were indicated to exhibit the main effects against M. oryzae in japonica-type accessions. Principal component analysis (PCA) and cluster analysis revealed that combination patterns of major R genes were the main factors determining the resistance of rice varieties to M. oryzae, such as 'Pi9+Pi54', 'Pid3+Pigm', 'Pi5+Pid3+Pigm', 'Pi5+Pi54+Pid3+Pigm', 'Pi5+Pid3' and 'Pi5+Pit+Pid3' in indica-type accessions and 'Pik+Pib', 'Pik+Pita', 'Pik+Pb1', 'Pizt+Pia' and 'Pizt+Pita' in japonica-type accessions, which were able to confer effective resistance against M. oryzae. The above results provide good theoretical support for the rational utilization of combinations of major R genes in developing rice cultivars with broad-spectrum resistance.

  4. Combination Patterns of Major R Genes Determine the Level of Resistance to the M. oryzae in Rice (Oryza sativa L.).

    PubMed

    Wu, Yunyu; Xiao, Ning; Yu, Ling; Pan, Cunhong; Li, Yuhong; Zhang, Xiaoxiang; Liu, Guangqing; Dai, Zhengyuan; Pan, Xuebiao; Li, Aihong

    2015-01-01

    Rice blast caused by Magnaporthe oryzae is the most devastating disease of rice and poses a serious threat to world food security. In this study, the distribution and effectiveness of 18 R genes in 277 accessions were investigated based on pathogenicity assays and molecular markers. The results showed that most of the accessions exhibited some degree of resistance (resistance frequency, RF >50%). Accordingly, most of the accessions were observed to harbor two or more R genes, and the number of R genes harbored in accessions was significantly positively correlated with RF. Some R genes were demonstrated to be specifically distributed in the genomes of rice sub-species, such as Pigm, Pi9, Pi5 and Pi1, which were only detected in indica-type accessions, and Pik and Piz, which were just harbored in japonica-type accessions. By analyzing the relationship between R genes and RF using a multiple stepwise regression model, the R genes Pid3, Pi5, Pi9, Pi54, Pigm and Pit were found to show the main effects against M. oryzae in indica-type accessions, while Pita, Pb1, Pik, Pizt and Pia were indicated to exhibit the main effects against M. oryzae in japonica-type accessions. Principal component analysis (PCA) and cluster analysis revealed that combination patterns of major R genes were the main factors determining the resistance of rice varieties to M. oryzae, such as 'Pi9+Pi54', 'Pid3+Pigm', 'Pi5+Pid3+Pigm', 'Pi5+Pi54+Pid3+Pigm', 'Pi5+Pid3' and 'Pi5+Pit+Pid3' in indica-type accessions and 'Pik+Pib', 'Pik+Pita', 'Pik+Pb1', 'Pizt+Pia' and 'Pizt+Pita' in japonica-type accessions, which were able to confer effective resistance against M. oryzae. The above results provide good theoretical support for the rational utilization of combinations of major R genes in developing rice cultivars with broad-spectrum resistance. PMID:26030358

  5. Aquaporins are major determinants of water use efficiency of rice plants in the field.

    PubMed

    Nada, Reham M; Abogadallah, Gaber M

    2014-10-01

    This study aimed at specifying the reasons of unbalanced water relations of rice in the field at midday which results in slowing down photosynthesis and reducing water use efficiency (WUE) in japonica and indica rice under well-watered and droughted conditions. Leaf relative water content (RWC) decreased in the well-watered plants at midday in the field, but more dramatically in the droughted indica (75.6 and 71.4%) than japonica cultivars (85.5 and 80.8%). Gas exchange was measured at three points during the day (9:00, 13:00 and 17:00). Leaf internal CO2 (Ci) was not depleted when midday stomatal depression was highest indicating that Ci was not limiting to photosynthesis. Most aquaporins were predominantly expressed in leaves suggesting higher water permeability in leaves than in roots. The expression of leaf aquaporins was further induced by drought at 9:00 without comparable responses in roots. The data suggest that aquaporin expression in the root endodermis was limiting to water uptake. Upon removal of the radial barriers to water flow in roots, transpiration increased instantly and photosynthesis increased after 4h resulting in increasing WUE after 4h, demonstrating that WUE in rice is largely limited by the inadequate aquaporin expression profiles in roots.

  6. Rice ( Oryza) hemoglobins

    PubMed Central

    Arredondo-Peter, Raúl; Moran, Jose F.; Sarath, Gautam

    2014-01-01

    Hemoglobins (Hbs) corresponding to non-symbiotic (nsHb) and truncated (tHb) Hbs have been identified in rice ( Oryza). This review discusses the major findings from the current studies on rice Hbs. At the molecular level, a family of the nshb genes, consisting of hb1, hb2, hb3, hb4 and hb5, and a single copy of the thb gene exist in Oryza sativa var. indica and O. sativa var. japonica, Hb transcripts coexist in rice organs and Hb polypeptides exist in rice embryonic and vegetative organs and in the cytoplasm of differentiating cells. At the structural level, the crystal structure of rice Hb1 has been elucidated, and the structures of the other rice Hbs have been modeled. Kinetic analysis indicated that rice Hb1 and 2, and possibly rice Hb3 and 4, exhibit a very high affinity for O 2, whereas rice Hb5 and tHb possibly exhibit a low to moderate affinity for O 2. Based on the accumulated information on the properties of rice Hbs and data from the analysis of other plant and non-plant Hbs, it is likely that Hbs play a variety of roles in rice organs, including O 2-transport, O 2-sensing, NO-scavenging and redox-signaling. From an evolutionary perspective, an outline for the evolution of rice Hbs is available. Rice nshb and thb genes vertically evolved through different lineages, rice nsHbs evolved into clade I and clade II lineages and rice nshbs and thbs evolved under the effect of neutral selection. This review also reveals lacunae in our ability to completely understand rice Hbs. Primary lacunae are the absence of experimental information about the precise functions of rice Hbs, the properties of modeled rice Hbs and the cis-elements and trans-acting factors that regulate the expression of rice hb genes, and the partial understanding of the evolution of rice Hbs. PMID:25653837

  7. Rice ( Oryza) hemoglobins.

    PubMed

    Arredondo-Peter, Raúl; Moran, Jose F; Sarath, Gautam

    2014-01-01

    Hemoglobins (Hbs) corresponding to non-symbiotic (nsHb) and truncated (tHb) Hbs have been identified in rice ( Oryza). This review discusses the major findings from the current studies on rice Hbs. At the molecular level, a family of the nshb genes, consisting of hb1, hb2, hb3, hb4 and hb5, and a single copy of the thb gene exist in Oryza sativa var. indica and O. sativa var. japonica, Hb transcripts coexist in rice organs and Hb polypeptides exist in rice embryonic and vegetative organs and in the cytoplasm of differentiating cells. At the structural level, the crystal structure of rice Hb1 has been elucidated, and the structures of the other rice Hbs have been modeled. Kinetic analysis indicated that rice Hb1 and 2, and possibly rice Hb3 and 4, exhibit a very high affinity for O 2, whereas rice Hb5 and tHb possibly exhibit a low to moderate affinity for O 2. Based on the accumulated information on the properties of rice Hbs and data from the analysis of other plant and non-plant Hbs, it is likely that Hbs play a variety of roles in rice organs, including O 2-transport, O 2-sensing, NO-scavenging and redox-signaling. From an evolutionary perspective, an outline for the evolution of rice Hbs is available. Rice nshb and thb genes vertically evolved through different lineages, rice nsHbs evolved into clade I and clade II lineages and rice nshbs and thbs evolved under the effect of neutral selection. This review also reveals lacunae in our ability to completely understand rice Hbs. Primary lacunae are the absence of experimental information about the precise functions of rice Hbs, the properties of modeled rice Hbs and the cis-elements and trans-acting factors that regulate the expression of rice hb genes, and the partial understanding of the evolution of rice Hbs.

  8. Differentiation of weedy traits in ALS-resistant red rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Red rice is a weedy form of cultivated rice (Oryza sativa) that competes aggressively with rice in the southern U.S., reduces yields and contaminates rice grains. The introduction of ClearfieldTM rice, a nontransgenic, herbicide-resistant rice cultivar a decade ago has led to increased use of imazet...

  9. Outcrossing potential between U.S. red rice (Oryza sativa) and Chinese indica rice (Oryza sativa) lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Red rice in southern U.S. rice fields remains a widespread, economically challenging problem despite nearly a decade of rice production systems that include true-breeding rice cultivars and indica-derived hybrid rice with resistance to imazethapyr. Both of these herbicide-resistant rice systems hav...

  10. Genetic analysis of durable resistance to Magnaporthe oryzae in the rice accession Gigante Vercelli identified two blast resistance loci.

    PubMed

    Urso, Simona; Desiderio, Francesca; Biselli, Chiara; Bagnaresi, Paolo; Crispino, Laura; Piffanelli, Pietro; Abbruscato, Pamela; Assenza, Federica; Guarnieri, Giada; Cattivelli, Luigi; Valè, Giampiero

    2016-02-01

    Rice cultivars exhibiting durable resistance to blast, the most important rice fungal disease provoking up to 30 % of rice losses, are very rare and searching for sources of such a resistance represents a priority for rice-breeding programs. To this aim we analyzed Gigante Vercelli (GV) and Vialone Nano (VN), two temperate japonica rice cultivars in Italy displaying contrasting response to blast, with GV showing a durable and broad-spectrum resistance, whereas VN being highly susceptible. An SSR-based genetic map developed using a GV × VN population segregating for blast resistance identified two blast resistance loci, localized to the long arm of chromosomes 1 and 4 explaining more than 78 % of the observed phenotypic variation for blast resistance. The pyramiding of two blast resistance QTLs was therefore involved in the observed durable resistance in GV. Mapping data were integrated with information obtained from RNA-seq expression profiling of all classes of resistance protein genes (resistance gene analogs, RGAs) and with the map position of known cloned or mapped blast resistance genes to search candidates for the GV resistant response. A co-localization of RGAs with the LOD peak or the marker interval of the chromosome 1 QTL was highlighted and a valuable tool for selecting the resistance gene during breeding programs was developed. Comparative analysis with known blast resistance genes revealed co-positional relationships between the chromosome 1 QTL with the Pi35/Pish blast resistance alleles and showed that the chromosome 4 QTL represents a newly identified blast resistance gene. The present genetic analysis has therefore allowed the identification of two blast resistance loci in the durable blast-resistant rice cultivar GV and tools for molecular selection of these resistance genes.

  11. Association Mapping for Aluminum Tolerance in a Core Collection of Rice Landraces

    PubMed Central

    Zhang, Peng; Zhong, Kaizhen; Tong, Hanhua; Shahid, Muhammad Qasim; Li, Jinquan

    2016-01-01

    Trivalent aluminum (Al3+) has drastic effect on the rice production in acidic soils. Elite genes for aluminum (Al) tolerance might exist in rice landraces. Therefore, the purpose of this research is to mine the elite genes within rice landraces. Association mapping for Al tolerance traits [i.e., relative root elongation (RRE)] was performed by using a core collection of 150 accessions of rice landraces (i.e., Ting’s rice core collection). Our results showed that the Ting’s rice core collection possessed a wide-range of phenotypic variation for Al tolerance, and the index of Al tolerance (RRE) was ranged from 0.22 to 0.89. Moreover, the groups with different origins and compositions of indica and japonica rice showed different degrees of tolerance to varying levels of Al. These rice landraces were further screened with 274 simple sequence repeat markers, and association mapping was performed using a mixed linear model approach. The mapping results showed that a total of 23 significant (P < 0.05) trait–marker associations were detected for Al tolerance. Of these, three associations (13%) were identical to the quantitative trait loci reported previously, and other 20 associations were reported for the first time in this study. The proportion of phenotypic variance (R2) explained by 23 significant associations ranged from 5.03 to 20.03% for Al tolerance. We detected several elite alleles for Al tolerance based on multiple comparisons of allelic effects, which could be used to develop Al tolerant rice cultivars through marker-assisted breeding. PMID:27757115

  12. Escape to Ferality: The Endoferal Origin of Weedy Rice from Crop Rice through De-Domestication

    PubMed Central

    Gettler, Kyle A.; Burgos, Nilda R.; Fischer, Albert J.

    2016-01-01

    Domestication is the hallmark of evolution and civilization and harnesses biodiversity through selection for specific traits. In regions where domesticated lines are grown near wild relatives, congeneric sources of aggressive weedy genotypes cause major economic losses. Thus, the origins of weedy genotypes where no congeneric species occur raise questions regarding management effectiveness and evolutionary mechanisms responsible for weedy population success. Since eradication in the 1970s, California growers avoided weedy rice through continuous flood culture and zero-tolerance guidelines, preventing the import, presence, and movement of weedy seeds. In 2003, after decades of no reported presence in California, a weedy rice population was confirmed in dry-seeded fields. Our objectives were to identify the origins and establishment of this population and pinpoint possible phenotypes involved. We show that California weedy rice is derived from a different genetic source among a broad range of AA genome Oryzas and is most recently diverged from O. sativa temperate japonica cultivated in California. In contrast, other weedy rice ecotypes in North America (Southern US) originate from weedy genotypes from China near wild Oryza, and are derived through existing crop-wild relative crosses. Analyses of morphological data show that California weedy rice subgroups have phenotypes like medium-grain or gourmet cultivars, but have colored pericarp, seed shattering, and awns like wild relatives, suggesting that reversion to non-domestic or wild-like traits can occur following domestication, despite apparent fixation of domestication alleles. Additionally, these results indicate that preventive methods focused on incoming weed sources through contamination may miss burgeoning weedy genotypes that rapidly adapt, establish, and proliferate. Investigating the common and unique evolutionary mechanisms underlying global weed origins and subsequent interactions with crop relatives sheds

  13. A hydroponic rice seedling culture model system for investigating proteome of salt stress in rice leaf.

    PubMed

    Kim, Dea-Wook; Rakwal, Randeep; Agrawal, Ganesh Kumar; Jung, Young-Ho; Shibato, Junko; Jwa, Nam-Soo; Iwahashi, Yumiko; Iwahashi, Hitoshi; Kim, Du Hyun; Shim, Ie-Sung; Usui, Kenji

    2005-12-01

    By using an in vivo hydroponic rice seedling culture system, we investigated the physiological and biochemical responses of a model rice japonica cultivar Nipponbare to salt stress using proteomics and classical biochemical methods. Yoshida's nutrient solution (YS) was used to grow rice seedlings. YS-grown 18-day-old seedlings manifested highly stable and reproducible symptoms, prominently the wilting and browning of the 3rd leaf, reduced photosynthetic activity, inhibition in overall seedling growth, and failure to develop new (5th) leaf, when subjected to salt stress by transferring them to YS containing 130 mM NaCl for 4 days. As leaf response to salt stress is least investigated in rice by proteomics, we used the 3rd leaf as source material. A comparison of 2-DE protein profiles between the untreated control and salt-stressed 3rd leaves revealed 55 differentially expressed CBB-stained spots, where 47 spots were increased over the control. Of these changed spots, the identity of 33 protein spots (27 increased and 5 decreased) was determined by nESI-LC-MS/MS. Most of these identified proteins belonged to major metabolic processes like photosynthetic carbon dioxide assimilation and photorespiration, suggesting a good correlation between salt stress-responsive proteins and leaf morphology. Moreover, 2-DE immunoblot and enzymatic activity analyses of 3rd leaves revealed remarkable changes in the key marker enzymes associated with oxidative damage to salt stress: ascorbate peroxidase and lipid peroxidation were induced, and catalase was suppressed. These results demonstrate that hydroponic culture system is best suited for proteomics of salt stress in rice seedling.

  14. Genetic structural analysis for germplasm accessions in the USDA Rice World Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice is grouped into five genetic structures including indica, aus, aromatic, temperate japonica, and tropical japonica. A core collection having 1,785 accessions from 114 countries has been developed that is representative of the USDA rice world collection which includes over 18,000 accessions. The...

  15. Identification and mapping of expressed genes, simple sequence repeats and transposable elements in centromeric regions of rice chromosomes.

    PubMed

    Mizuno, Hiroshi; Ito, Kazue; Wu, Jianzhong; Tanaka, Tsuyoshi; Kanamori, Hiroyuki; Katayose, Yuichi; Sasaki, Takuji; Matsumoto, Takashi

    2006-12-31

    The genomic sequences derived from rice centromeric regions were analyzed to facilitate the comprehensive understanding of the rice genome. A rice centromere-specific satellite sequence, RCS2/TrsD/CentO, was used to screen P1-derived artificial chromosome (PAC) and bacterial artificial chromosome (BAC) genomic libraries derived from Oryza sativa L. ssp. japonica cultivar Nipponbare. Physical maps of the centromeric regions were constructed by DNA fingerprinting methods and the aligned clones were analyzed by end sequencing. BLAST analysis revealed the composition of genes, centromeric satellites and other repetitive elements, such as RIRE7/CRR, RIRE8, Squiq, Anaconda, CACTA and miniature inverted-repeat transposable elements. Fiber-fluorescent in situ hybridization analysis also indicated the presence of distinct clusters of RCS2/TrsD/CentO satellite interspersed with other elements, instead of a long homogeneous region. Several expressed genes, sequences representative of ancestral organellar insertions, relatively long simple sequence repeats (SSRs), and sequences corresponding to 5S and 45S ribosomal RNA genes were also identified. Thirty-one gene sequences showed high-similarity to rice full-length cDNA sequences that had not been matched to the published rice genome sequence in silico. These results suggest the presence of expressed genes within and around the clusters of RCS2/TrsD/CentO satellites in unsequenced centromeric regions of the rice chromosomes.

  16. Brome mosaic virus Infection of Rice Results in Decreased Accumulation of RNA1.

    PubMed

    Kitayama, Masahiko; Hoover, Haley; Middleton, Stefani; Kao, C Cheng

    2015-05-01

    Brome mosaic virus (BMV) (the Russian strain) infects monocot plants and has been studied extensively in barley and wheat. Here, we report BMV can systemically infect rice (Oryza sativa var. japonica), including cultivars in which the genomes have been determined. The BMV capsid protein can be found throughout the inoculated plants. However, infection in rice exhibits delayed symptom expression or no symptoms when compared with wheat (Triticum aestivum). The sequences of BMV RNAs isolated from rice did not reveal any nucleotide changes in RNA1 or RNA2, while RNA3 had only one synonymous nucleotide change from the inoculum sequence. Preparations of purified BMV virions contained RNA1 at a significantly reduced level relative to the other two RNAs. Analysis of BMV RNA replication in rice revealed that minus-strand RNA1 was replicated at a reduced rate when compared with RNA2. Thus, rice appears to either inhibit RNA1 replication or lacks a sufficient amount of a factor needed to support efficient RNA1 replication.

  17. Rice-produced MSP142 of Plasmodium falciparum elicits antibodies that inhibit parasite growth in vitro.

    PubMed

    Chen, Q; Liang, W; Qian, F; Qian, B; Cao, J; Zhang, D; Xu, Y; Tang, L

    2016-10-01

    Many malaria antigens contain multiple disulphide bonds involved in the formation of inhibitory B-cell epitopes. Producing properly folded malaria antigens in sufficient quantities for vaccination is often a challenge. The 42-kDa fragment of Plasmodium falciparum merozoite surface protein 1 (MSP142 ) is such a kind of malaria antigen. In this study, we investigated the expression of MSP142 in a rice system (9522, a cultivar of Oryza sativa ssp. japonica), which was used as a bioreactor for protein production. The MSP142 gene was synthesized according to rice-preferred codons and transformed into rice plants via an Agrobacterium-mediated method. The recombinant antigen was efficiently expressed in rice seeds with a level up to 1.56% of total soluble protein and was recognized by both the conformational monoclonal antibody 5.2 (mAb5.2) and the pooled sera of P. falciparum malaria patients. Rabbits were immunized intramuscularly with the purified MSP142 formulated with Freund's adjuvant. High antibody titres against MSP142 were elicited. The rabbit immune sera reacted well with the native protein of P. falciparum parasite and strongly inhibited the in vitro growth of blood-stage P. falciparum parasites, demonstrating that transgenic rice can become an efficient bioreactor for the production of malaria vaccine antigens. PMID:27493141

  18. Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection.

    PubMed

    Li, Xiaobai; Yan, Wengui; Agrama, Hesham; Hu, Biaolin; Jia, Limeng; Jia, Melissa; Jackson, Aaron; Moldenhauer, Karen; McClung, Anna; Wu, Dianxing

    2010-12-01

    A rice mini-core collection consisting of 217 accessions has been developed to represent the USDA core and whole collections that include 1,794 and 18,709 accessions, respectively. To improve the efficiency of mining valuable genes and broadening the genetic diversity in breeding, genetic structure and diversity were analyzed using both genotypic (128 molecular markers) and phenotypic (14 numerical traits) data. This mini-core had 13.5 alleles per locus, which is the most among the reported germplasm collections of rice. Similarly, polymorphic information content (PIC) value was 0.71 in the mini-core which is the highest with one exception. The high genetic diversity in the mini-core suggests there is a good possibility of mining genes of interest and selecting parents which will improve food production and quality. A model-based clustering analysis resulted in lowland rice including three groups, aus (39 accessions), indica (71) and their admixtures (5), upland rice including temperate japonica (32), tropical japonica (40), aromatic (6) and their admixtures (12) and wild rice (12) including glaberrima and four other species of Oryza. Group differentiation was analyzed using both genotypic distance Fst from 128 molecular markers and phenotypic (Mahalanobis) distance D(2) from 14 traits. Both dendrograms built by Fst and D(2) reached similar-differentiative relationship among these genetic groups, and the correlation coefficient showed high value 0.85 between Fst matrix and D(2) matrix. The information of genetic and phenotypic differentiation could be helpful for the association mapping of genes of interest. Analysis of genotypic and phenotypic diversity based on genetic structure would facilitate parent selection for broadening genetic base of modern rice cultivars via breeding effort.

  19. Impacts of climate change on paddy rice yield in a temperate climate.

    PubMed

    Kim, Han-Yong; Ko, Jonghan; Kang, Suchel; Tenhunen, John

    2013-02-01

    The crop simulation model is a suitable tool for evaluating the potential impacts of climate change on crop production and on the environment. This study investigates the effects of climate change on paddy rice production in the temperate climate regions under the East Asian monsoon system using the CERES-Rice 4.0 crop simulation model. This model was first calibrated and validated for crop production under elevated CO2 and various temperature conditions. Data were obtained from experiments performed using a temperature gradient field chamber (TGFC) with a CO2 enrichment system installed at Chonnam National University in Gwangju, Korea in 2009 and 2010. Based on the empirical calibration and validation, the model was applied to deliver a simulated forecast of paddy rice production for the region, as well as for the other Japonica rice growing regions in East Asia, projecting for years 2050 and 2100. In these climate change projection simulations in Gwangju, Korea, the yield increases (+12.6 and + 22.0%) due to CO2 elevation were adjusted according to temperature increases showing variation dependent upon the cultivars, which resulted in significant yield decreases (-22.1% and -35.0%). The projected yields were determined to increase as latitude increases due to reduced temperature effects, showing the highest increase for any of the study locations (+24%) in Harbin, China. It appears that the potential negative impact on crop production may be mediated by appropriate cultivar selection and cultivation changes such as alteration of the planting date. Results reported in this study using the CERES-Rice 4.0 model demonstrate the promising potential for its further application in simulating the impacts of climate change on rice production from a local to a regional scale under the monsoon climate system.

  20. Identification of rice blast resistance genes using international monogenic differentials

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice blast disease, caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases of rice that severely affects crop production in Jilin Province, Northeast China, where temperate japonica rice is primarily grown. In the present study, 44 representative local blast isolat...

  1. The wheat durable, multipathogen resistance gene Lr34 confers partial blast resistance in rice.

    PubMed

    Krattinger, Simon G; Sucher, Justine; Selter, Liselotte L; Chauhan, Harsh; Zhou, Bo; Tang, Mingzhi; Upadhyaya, Narayana M; Mieulet, Delphine; Guiderdoni, Emmanuel; Weidenbach, Denise; Schaffrath, Ulrich; Lagudah, Evans S; Keller, Beat

    2016-05-01

    The wheat gene Lr34 confers durable and partial field resistance against the obligate biotrophic, pathogenic rust fungi and powdery mildew in adult wheat plants. The resistant Lr34 allele evolved after wheat domestication through two gain-of-function mutations in an ATP-binding cassette transporter gene. An Lr34-like fungal disease resistance with a similar broad-spectrum specificity and durability has not been described in other cereals. Here, we transformed the resistant Lr34 allele into the japonica rice cultivar Nipponbare. Transgenic rice plants expressing Lr34 showed increased resistance against multiple isolates of the hemibiotrophic pathogen Magnaporthe oryzae, the causal agent of rice blast disease. Host cell invasion during the biotrophic growth phase of rice blast was delayed in Lr34-expressing rice plants, resulting in smaller necrotic lesions on leaves. Lines with Lr34 also developed a typical, senescence-based leaf tip necrosis (LTN) phenotype. Development of LTN during early seedling growth had a negative impact on formation of axillary shoots and spikelets in some transgenic lines. One transgenic line developed LTN only at adult plant stage which was correlated with lower Lr34 expression levels at seedling stage. This line showed normal tiller formation and more importantly, disease resistance in this particular line was not compromised. Interestingly, Lr34 in rice is effective against a hemibiotrophic pathogen with a lifestyle and infection strategy that is different from obligate biotrophic rusts and mildew fungi. Lr34 might therefore be used as a source in rice breeding to improve broad-spectrum disease resistance against the most devastating fungal disease of rice. PMID:26471973

  2. The wheat durable, multipathogen resistance gene Lr34 confers partial blast resistance in rice.

    PubMed

    Krattinger, Simon G; Sucher, Justine; Selter, Liselotte L; Chauhan, Harsh; Zhou, Bo; Tang, Mingzhi; Upadhyaya, Narayana M; Mieulet, Delphine; Guiderdoni, Emmanuel; Weidenbach, Denise; Schaffrath, Ulrich; Lagudah, Evans S; Keller, Beat

    2016-05-01

    The wheat gene Lr34 confers durable and partial field resistance against the obligate biotrophic, pathogenic rust fungi and powdery mildew in adult wheat plants. The resistant Lr34 allele evolved after wheat domestication through two gain-of-function mutations in an ATP-binding cassette transporter gene. An Lr34-like fungal disease resistance with a similar broad-spectrum specificity and durability has not been described in other cereals. Here, we transformed the resistant Lr34 allele into the japonica rice cultivar Nipponbare. Transgenic rice plants expressing Lr34 showed increased resistance against multiple isolates of the hemibiotrophic pathogen Magnaporthe oryzae, the causal agent of rice blast disease. Host cell invasion during the biotrophic growth phase of rice blast was delayed in Lr34-expressing rice plants, resulting in smaller necrotic lesions on leaves. Lines with Lr34 also developed a typical, senescence-based leaf tip necrosis (LTN) phenotype. Development of LTN during early seedling growth had a negative impact on formation of axillary shoots and spikelets in some transgenic lines. One transgenic line developed LTN only at adult plant stage which was correlated with lower Lr34 expression levels at seedling stage. This line showed normal tiller formation and more importantly, disease resistance in this particular line was not compromised. Interestingly, Lr34 in rice is effective against a hemibiotrophic pathogen with a lifestyle and infection strategy that is different from obligate biotrophic rusts and mildew fungi. Lr34 might therefore be used as a source in rice breeding to improve broad-spectrum disease resistance against the most devastating fungal disease of rice.

  3. Unlocking the variation hidden in rice germplasm collections with genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cultivated Asian rice (Oryza sativa) was domesticated from O. rufipogon (O. nivara). The O. sativa subspecies indica and japonica diverged in ancient times, and based on DNA markers, further subdivided into the five major subpopulations, aus, indica, aromatic, tropical japonica and temperate japoni...

  4. SSR MARKER CONFIRMATION OF RECIPROCAL OUTCROSSING RATES BETWEEN RICE AND RED RICE LINES IN ARKANSAS OVER A FIVE-YEAR PERIOD

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Outcrossing between rice and red rice can negatively impact the rice industry, especially when herbicide-resistant rice cultivars are grown. Previous research has indicated that outcrossing between rice and red rice in Arkansas farm fields can occur with either plant type serving as the pollen dono...

  5. Mutation in CSA creates a new photoperiod-sensitive genic male sterile line applicable for hybrid rice seed production.

    PubMed

    Zhang, Hui; Xu, Chenxi; He, Yi; Zong, Jie; Yang, Xijia; Si, Huamin; Sun, Zongxiu; Hu, Jianping; Liang, Wanqi; Zhang, Dabing

    2013-01-01

    Rice is a major staple food worldwide. Making hybrid rice has proved to be an effective strategy to significantly increase grain yield. Current hybrid rice technologies rely on male sterile lines and have been used predominantly in indica cultivars. However, intrinsic problems exist in the implementation of these technologies, such as limited germplasms and unpredictable conversions from sterility to fertility in the field. Here, we describe a photoperiod-controlled male sterile line, carbon starved anther (csa), which contains a mutation in an R2R3 MYB transcription regulator of pollen development. This mutation was introduced into indica and japonica rice, and it rendered male sterility under short-day conditions and male fertility under long-day conditions in both lines. Furthermore, F(1) plants of csa and a restorer line JP69 exhibited heterosis (hybrid vigor), suggesting the feasibility of using this mutation to create hybrid rice. The csa-based photoperiod-sensitive male sterile line allows the establishment of a stable two-line hybrid system, which promises to have a significant impact on agriculture.

  6. Introgression of Blast Resistance Genes (Putative Pi-b and Pi-kh) into Elite Rice Cultivar MR219 through Marker-Assisted Selection.

    PubMed

    Tanweer, Fatah A; Rafii, Mohd Y; Sijam, Kamaruzaman; Rahim, Harun A; Ahmed, Fahim; Ashkani, Sadegh; Latif, Mohammad A

    2015-01-01

    Blast is the most common biotic stress leading to the reduction of rice yield in many rice-growing areas of the world, including Malaysia. Improvement of blast resistance of rice varieties cultivated in blast endemic areas is one of the most important objectives of rice breeding programs. In this study, the marker-assisted backcrossing strategy was applied to improve the blast resistance of the most popular Malaysian rice variety MR219 by introgressing blast resistance genes from the Pongsu Seribu 2 variety. Two blast resistance genes, Pi-b and Pi-kh, were pyramided into MR219. Foreground selection coupled with stringent phenotypic selection identified 15 plants homozygous for the Pi-b and Pi-kh genes, and background selection revealed more than 95% genome recovery of MR219 in advanced blast resistant lines. Phenotypic screening against blast disease indicated that advanced homozygous blast resistant lines were strongly resistant against pathotype P7.2 in the blast disease endemic areas. The morphological, yield, grain quality, and yield-contributing characteristics were significantly similar to those of MR219. The newly developed blast resistant improved lines will retain the high adoptability of MR219 by farmers. The present results will also play an important role in sustaining the rice production of Malaysia. PMID:26734013

  7. Introgression of Blast Resistance Genes (Putative Pi-b and Pi-kh) into Elite Rice Cultivar MR219 through Marker-Assisted Selection

    PubMed Central

    Tanweer, Fatah A.; Rafii, Mohd Y.; Sijam, Kamaruzaman; Rahim, Harun A.; Ahmed, Fahim; Ashkani, Sadegh; Latif, Mohammad A.

    2015-01-01

    Blast is the most common biotic stress leading to the reduction of rice yield in many rice-growing areas of the world, including Malaysia. Improvement of blast resistance of rice varieties cultivated in blast endemic areas is one of the most important objectives of rice breeding programs. In this study, the marker-assisted backcrossing strategy was applied to improve the blast resistance of the most popular Malaysian rice variety MR219 by introgressing blast resistance genes from the Pongsu Seribu 2 variety. Two blast resistance genes, Pi-b and Pi-kh, were pyramided into MR219. Foreground selection coupled with stringent phenotypic selection identified 15 plants homozygous for the Pi-b and Pi-kh genes, and background selection revealed more than 95% genome recovery of MR219 in advanced blast resistant lines. Phenotypic screening against blast disease indicated that advanced homozygous blast resistant lines were strongly resistant against pathotype P7.2 in the blast disease endemic areas. The morphological, yield, grain quality, and yield-contributing characteristics were significantly similar to those of MR219. The newly developed blast resistant improved lines will retain the high adoptability of MR219 by farmers. The present results will also play an important role in sustaining the rice production of Malaysia. PMID:26734013

  8. Switchgrass cultivar

    DOEpatents

    Wu, Yanqi; Taliaferro, Charles M.

    2012-10-02

    A new cultivar of switchgrass `Cimarron` (SL93 2001-1) having increased biomass yield is provided. The switchgrass comprises all the morphological and physiological properties of the cultivar grown from a seed deposited under American Type Culture Collection (ATCC) No. PTA-10116. The invention also provides seeds, progeny, parts and methods of use of Cimarron, such as for the production of biofuels.

  9. Fine mapping of the lesion mimic and early senescence 1 (lmes1) in rice (Oryza sativa).

    PubMed

    Li, Zhi; Zhang, Yingxin; Liu, Lin; Liu, Qunen; Bi, Zhenzhen; Yu, Ning; Cheng, Shihua; Cao, Liyong

    2014-07-01

    A novel rice mutant, lesion mimic and early senescence 1 (lmes1), was induced from the rice 93-11 cultivar in a γ-ray field. This mutant exhibited spontaneous disease-like lesions in the absence of pathogen attack at the beginning of the tillering stage. Moreover, at the booting stage, lmes1 mutants exhibited a significantly increased MDA but decreased chlorophyll content, soluble protein content and photosynthetic rate in the leaves, which are indicative of an early senescence phenotype. The lmes1 mutant was significantly more resistant than 93-11 against rice bacterial blight infection, which was consistent with a marked increase in the expression of three resistance-related genes. Here, we employed a map-based cloning approach to finely map the lmes1 gene. In an initial mapping with 94 F2 individuals derived from a cross between the lmes1 mutant and Nipponbare, the lmes1 gene was located in a 10.6-cM region on the telomere of the long arm of chromosome 7 using simple sequence repeat (SSR) markers. To finely map lmes1, we derived two F2 populations with 940 individuals from two crosses between the lmes1 mutant and two japonica rice varieties, Nipponbare and 02428. Finally, the lmes1 gene was mapped to an 88-kb region between two newly developed inDel markers, Zl-3 and Zl-22, which harbored 15 ORFs.

  10. Changes in Lignin and Polysaccharide Components in 13 Cultivars of Rice Straw following Dilute Acid Pretreatment as Studied by Solution-State 2D 1H-13C NMR.

    PubMed

    Teramura, Hiroshi; Sasaki, Kengo; Oshima, Tomoko; Aikawa, Shimpei; Matsuda, Fumio; Okamoto, Mami; Shirai, Tomokazu; Kawaguchi, Hideo; Ogino, Chiaki; Yamasaki, Masanori; Kikuchi, Jun; Kondo, Akihiko

    2015-01-01

    A renewable raw material, rice straw is pretreated for biorefinery usage. Solution-state two-dimensional (2D) 1H-13 C hetero-nuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy, was used to analyze 13 cultivars of rice straw before and after dilute acid pretreatment, to characterize general changes in the lignin and polysaccharide components. Intensities of most (15 of 16) peaks related to lignin aromatic regions, such as p-coumarate, guaiacyl, syringyl, p-hydroxyphenyl, and cinnamyl alcohol, and methoxyl, increased or remained unchanged after pretreatment. In contrast, intensities of most (11 of 13) peaks related to lignin aliphatic linkages or ferulate decreased. Decreased heterogeneity in the intensities of three peaks related to cellulose components in acid-insoluble residues resulted in similar glucose yield (0.45-0.59 g/g-dry biomass). Starch-derived components showed positive correlations (r = 0.71 to 0.96) with glucose, 5-hydroxymethylfurfural (5-HMF), and formate concentrations in the liquid hydrolysates, and negative correlations (r = -0.95 to -0.97) with xylose concentration and acid-insoluble residue yield. These results showed the fate of lignin and polysaccharide components by pretreatment, suggesting that lignin aromatic regions and cellulose components were retained in the acid insoluble residues and starch-derived components were transformed into glucose, 5-HMF, and formate in the liquid hydrolysate.

  11. Close linkage of a blast resistance gene, Pias(t), with a bacterial leaf blight resistance gene, Xa1-as(t), in a rice cultivar ‘Asominori’

    PubMed Central

    Endo, Takashi; Yamaguchi, Masayuki; Kaji, Ryota; Nakagomi, Koji; Kataoka, Tomomori; Yokogami, Narifumi; Nakamura, Toshiki; Ishikawa, Goro; Yonemaru, Jun-ichi; Nishio, Takeshi

    2012-01-01

    It has long been known that a bacterial leaf blight-resistant line in rice obtained from a crossing using ‘Asominori’ as a resistant parent also has resistance to blast, but a blast resistance gene in ‘Asominori’ has not been investigated in detail. In the present study, a blast resistance gene in ‘Asominori’, tentatively named Pias(t), was revealed to be located within 162-kb region between DNA markers YX4-3 and NX4-1 on chromosome 4 and to be linked with an ‘Asominori’ allele of the bacterial leaf blight resistance gene Xa1, tentatively named Xa1-as(t). An ‘Asominori’ allele of Pias(t) was found to be dominant and difference of disease severity between lines having the ‘Asominori’ allele of Pias(t) and those without it was 1.2 in disease index from 0 to 10. Pias(t) was also closely linked with the Ph gene controlling phenol reaction, suggesting the possibility of successful selection of blast resistance using the phenol reaction. Since blast-resistant commercial cultivars have been developed using ‘Asominori’ as a parent, Pias(t) is considered to be a useful gene in rice breeding for blast resistance. PMID:23341747

  12. Changes in Lignin and Polysaccharide Components in 13 Cultivars of Rice Straw following Dilute Acid Pretreatment as Studied by Solution-State 2D 1H-13C NMR

    PubMed Central

    Teramura, Hiroshi; Sasaki, Kengo; Oshima, Tomoko; Aikawa, Shimpei; Matsuda, Fumio; Okamoto, Mami; Shirai, Tomokazu; Kawaguchi, Hideo; Ogino, Chiaki; Yamasaki, Masanori; Kikuchi, Jun; Kondo, Akihiko

    2015-01-01

    A renewable raw material, rice straw is pretreated for biorefinery usage. Solution-state two-dimensional (2D) 1H-13 C hetero-nuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy, was used to analyze 13 cultivars of rice straw before and after dilute acid pretreatment, to characterize general changes in the lignin and polysaccharide components. Intensities of most (15 of 16) peaks related to lignin aromatic regions, such as p-coumarate, guaiacyl, syringyl, p-hydroxyphenyl, and cinnamyl alcohol, and methoxyl, increased or remained unchanged after pretreatment. In contrast, intensities of most (11 of 13) peaks related to lignin aliphatic linkages or ferulate decreased. Decreased heterogeneity in the intensities of three peaks related to cellulose components in acid-insoluble residues resulted in similar glucose yield (0.45–0.59 g/g-dry biomass). Starch-derived components showed positive correlations (r = 0.71 to 0.96) with glucose, 5-hydroxymethylfurfural (5-HMF), and formate concentrations in the liquid hydrolysates, and negative correlations (r = –0.95 to –0.97) with xylose concentration and acid-insoluble residue yield. These results showed the fate of lignin and polysaccharide components by pretreatment, suggesting that lignin aromatic regions and cellulose components were retained in the acid insoluble residues and starch-derived components were transformed into glucose, 5-HMF, and formate in the liquid hydrolysate. PMID:26083431

  13. Changes in DNA methylation and transgenerational mobilization of a transposable element (mPing) by the Topoisomerase II inhibitor, Etoposide, in rice

    PubMed Central

    2012-01-01

    Background Etoposide (epipodophyllotoxin) is a chemical commonly used as an anti-cancer drug which inhibits DNA synthesis by blocking topoisomerase II activity. Previous studies in animal cells have demonstrated that etoposide constitutes a genotoxic stress which may induce genomic instability including mobilization of normally quiescent transposable elements (TEs). However, it remained unknown whether similar genetically mutagenic effects could be imposed by etoposide in plant cells. Also, no information is available with regard to whether the drug may cause a perturbation of epigenetic stability in any organism. Results To investigate whether etoposide could generate genetic and/or epigenetic instability in plant cells, we applied etoposide to germinating seeds of six cultivated rice (Oryza sativa L.) genotypes including both subspecies, japonica and indica. Based on the methylation-sensitive gel-blotting results, epigenetic changes in DNA methylation of three TEs (Tos17, Osr23 and Osr36) and two protein-encoding genes (Homeobox and CDPK-related genes) were detected in the etoposide-treated plants (S0 generation) in four of the six studied japonica cultivars, Nipponbare, RZ1, RZ2, and RZ35, but not in the rest japonica cultivar (Matsumae) and the indica cultivar (93-11). DNA methylation changes in the etoposide-treated S0 rice plants were validated by bisulfite sequencing at both of two analyzed loci (Tos17 and Osr36). Transpositional activity was tested for eight TEs endogenous to the rice genome in both the S0 plants and their selfed progenies (S1 and S2) of one of the cultivars, RZ1, which manifested heritable phenotypic variations. Results indicated that no transposition occurred in the etoposide-treated S0 plants for any of the TEs. Nonetheless, a MITE transposon, mPing, showed rampant mobilization in the S1 and S2 progenies descended from the drug-treated S0 plants. Conclusions Our results demonstrate that etoposide imposes a similar genotoxic stress on

  14. Rice Domestication Revealed by Reduced Shattering of Archaeological rice from the Lower Yangtze valley

    PubMed Central

    Zheng, Yunfei; Crawford, Gary W.; Jiang, Leping; Chen, Xugao

    2016-01-01

    Plant remains dating to between 9000 and 8400 BP from a probable ditch structure at the Huxi site include the oldest rice (Oryza sativa) spikelet bases and associated plant remains recovered in China. The remains document an early stage of rice domestication and the ecological setting in which early cultivation was taking place. The rice spikelet bases from Huxi include wild (shattering), intermediate, and domesticated (non-shattering) forms. The relative frequency of intermediate and non-shattering spikelet bases indicates that selection for, at the very least, non-shattering rice was underway at Huxi. The rice also has characteristics of japonica rice (Oryza sativa subsp. japonica), helping to clarify the emergence of a significant lineage of the crop. Seeds, phytoliths and their context provide evidence of increasing anthropogenesis and cultivation during the occupation. Rice spikelet bases from Kuahuqiao (8000–7700 BP), Tianluoshan (7000–6500 BP), Majiabang (6300–6000 BP), and Liangzhu (5300–4300 BP) sites indicate that rice underwent continuing selection for reduced shattering and japonica rice characteristics, confirming a prolonged domestication process for rice. PMID:27324699

  15. Rice Domestication Revealed by Reduced Shattering of Archaeological rice from the Lower Yangtze valley.

    PubMed

    Zheng, Yunfei; Crawford, Gary W; Jiang, Leping; Chen, Xugao

    2016-01-01

    Plant remains dating to between 9000 and 8400 BP from a probable ditch structure at the Huxi site include the oldest rice (Oryza sativa) spikelet bases and associated plant remains recovered in China. The remains document an early stage of rice domestication and the ecological setting in which early cultivation was taking place. The rice spikelet bases from Huxi include wild (shattering), intermediate, and domesticated (non-shattering) forms. The relative frequency of intermediate and non-shattering spikelet bases indicates that selection for, at the very least, non-shattering rice was underway at Huxi. The rice also has characteristics of japonica rice (Oryza sativa subsp. japonica), helping to clarify the emergence of a significant lineage of the crop. Seeds, phytoliths and their context provide evidence of increasing anthropogenesis and cultivation during the occupation. Rice spikelet bases from Kuahuqiao (8000-7700 BP), Tianluoshan (7000-6500 BP), Majiabang (6300-6000 BP), and Liangzhu (5300-4300 BP) sites indicate that rice underwent continuing selection for reduced shattering and japonica rice characteristics, confirming a prolonged domestication process for rice. PMID:27324699

  16. Impacts of rice varieties and management on yield-scaled greenhouse gas emissions from rice fields in China: A meta-analysis

    NASA Astrophysics Data System (ADS)

    Zheng, H.; Huang, H.; Yao, L.; Liu, J.; He, H.; Tang, J.

    2014-07-01

    Increasing numbers of studies have suggested that a comprehensive assessment of the impacts of cropping practices on greenhouse gas (GHG) emissions per unit yield (yield-scaled), rather than by land area (area-scaled), is needed to inform trade-off decisions to increase yields and reduce GHG emissions. We conducted a meta-analysis to quantify impacts of rice varieties on the global warming potential (GWP) of GHG emissions at the yield scale in China. Our results showed that significantly higher yield-scaled GWP occurred with indica rice varieties (1101.72 kg CO2 equiv. Mg-1) than japonica rice varieties (711.38 kg CO2 equiv. Mg-1). Lower yield-scaled GHG emissions occurred within 120-130 days of growth duration after transplanting (GDAT; 613.66 kg CO2 equiv. Mg-1), followed by 90-100 days of GDAT (749.72 kg CO2 equiv. Mg-1, 100-110 days of GDAT (794.29 kg CO2 equiv. Mg-1), and 70-80 days of GDAT (800.85 kg CO2 equiv. Mg-1). The fertilizer rate of 150-200 kg N ha-1 resulted in the lowest yield-scaled GWP. Consequently, appropriate cultivar choice and pairs were of vital importance in the rice cropping system. A further life cycle assessment of GHG emissions among rice varieties at the yield scale is urgently needed to develop win-win policies for rice production to achieve higher yield with lower emissions.

  17. Mapping of Novel QTL Regulating Grain Shattering Using Doubled Haploid Population in Rice (Oryza sativa L.).

    PubMed

    Lee, Gyu-Ho; Kang, In-Kyu; Kim, Kyung-Min

    2016-01-01

    The critical evolutionary step during domestication of major cereals was elimination of seed shattering because the easy-to-shatter trait in wild relatives results in a severe reduction in yield. In this study, we analyzed the QTLs associated with shattering employing a high-density genetic map in doubled haploid (DH) population of rice (Oryza sativa L.). A genetic linkage map was generated with 217 microsatellite markers spanning 2082.4 cM and covering 12 rice chromosomes with an average interval of 9.6 cM between markers based on 120 DHLs derived from a cross between Cheongcheong indica type cultivar and Nagdong japonica type cultivar. In the QTL analysis, five QTLs pertaining to the breaking tensile strength (BTS) were detected in 2013 and 2015. Two regions of the QTLs related to BTS on chromosome 1 and chromosome 6 were detected. Several important genes are distributed in 1 Mbp region of the QTL on chromosome 6 and they are related to the formation of abscission layer. We decide to name this QTL qSh6 and the candidate genes in the qSh6 region can be employed usefully in further research for cloning. PMID:27419124

  18. Mapping of Novel QTL Regulating Grain Shattering Using Doubled Haploid Population in Rice (Oryza sativa L.)

    PubMed Central

    Lee, Gyu-Ho; Kang, In-Kyu

    2016-01-01

    The critical evolutionary step during domestication of major cereals was elimination of seed shattering because the easy-to-shatter trait in wild relatives results in a severe reduction in yield. In this study, we analyzed the QTLs associated with shattering employing a high-density genetic map in doubled haploid (DH) population of rice (Oryza sativa L.). A genetic linkage map was generated with 217 microsatellite markers spanning 2082.4 cM and covering 12 rice chromosomes with an average interval of 9.6 cM between markers based on 120 DHLs derived from a cross between Cheongcheong indica type cultivar and Nagdong japonica type cultivar. In the QTL analysis, five QTLs pertaining to the breaking tensile strength (BTS) were detected in 2013 and 2015. Two regions of the QTLs related to BTS on chromosome 1 and chromosome 6 were detected. Several important genes are distributed in 1 Mbp region of the QTL on chromosome 6 and they are related to the formation of abscission layer. We decide to name this QTL qSh6 and the candidate genes in the qSh6 region can be employed usefully in further research for cloning. PMID:27419124

  19. Response of two rice cultivars differing in their sensitivity towards arsenic, differs in their expression of glutaredoxin and glutathione S transferase genes and antioxidant usage.

    PubMed

    Dubey, Arvind Kumar; Kumar, Navin; Sahu, Nayan; Verma, Pankaj Kumar; Ranjan, Ruma; Chakrabarty, Debasis; Behera, Soumit K; Mallick, Shekhar

    2016-02-01

    Embodied study investigates the role of GRX and associated antioxidant enzymes in the detoxification mechanism between arsenic (As) sensitive (Usar-3) and tolerant cultivar (Pant Dhan 11) of Oryza sativa against As(III) and As(V), under GSH enriched, and GSH deprived conditions. The overall growth and physiological parameters in sensitive cultivar were lower than the tolerant cultivar, against various treatments of As(III) and As(V). The As accumulation in sensitive cv. against both As(III) and As(V) was lower than the corresponding treatments in tolerant cv. However, the As translocation against As(V) was lower (35% and 64%, resp.) than that of As(III), in both the cultivars. In sensitive cv. translocation of Zn and Cu was influenced by both As(V) and As(III) whereas, in tolerant cv. the translocation of Cu, Mn and Zn was influenced only by As(III). Translocation of Fe was negatively influenced by translocation of As in sensitive cv. and positively in tolerant cv. Strong correlation between H2O2, SOD, GRX, GR, GST and GSH/GSSG in sensitive cv. and between DHAR, APX, MDHAR and AsA in tolerant cv. demonstrates the underlying preference of GSH as electron donor for detoxification of H2O2 in sensitive cv. and AsA in tolerant cv. Higher expression of the four GRX and two GST genes in the sensitive cv. than tolerant cv, suggests that under As stress, GRX are synthesized more in the sensitive cv. than tolerant cv. Also, the expression of four GRX genes were higher against As(V) than As(III). The higher As accumulation in the tolerant cv. is due to lower GST expression, is attributed to the absence of thiolation and sequestration of As in roots, the translocation of As to shoots is higher.

  20. Postharvest physiology and technology of loquat (Eriobotrya japonica Lindl.) fruit.

    PubMed

    Pareek, Sunil; Benkeblia, Noureddine; Janick, Jules; Cao, Shifeng; Yahia, Elhadi M

    2014-06-01

    Loquat (Eriobotrya japonica Lindl.) is a subtropical evergreen tree whose fruit is consumed both fresh and processed. Loquat fruit is a good source of minerals and carotenoids, while the kernel is rich in protein and carbohydrates. It has been considered a non-climacteric fruit, but there is evidence that some cultivars have a ripening pattern similar to that of climacteric fruits. The fruit has a short postharvest life at ambient temperatures and is susceptible to physical and mechanical damage, loss of moisture and nutrients, and decay. Low-temperature storage extends the shelf life of loquat fruit, but some cultivars are severely affected by chilling injury and flesh browning during cold storage. Purple spot, browning and leatheriness are major postharvest disorders. The shelf life of loquat can be extended by modified or controlled atmosphere storage as well as by postharvest treatment with 1-methyl cyclopropene or methyl jasmonate.

  1. Effect of Removing Superior Spikelets on Grain Filling of Inferior Spikelets in Rice

    PubMed Central

    You, Cuicui; Zhu, Honglei; Xu, Beibei; Huang, Wenxiao; Wang, Shaohua; Ding, Yanfeng; Liu, Zhenghui; Li, Ganghua; Chen, Lin; Ding, Chengqiang; Tang, She

    2016-01-01

    Large-panicle rice cultivars often fail to reach their yield potential due to the poor grain filling of inferior spikelets (IS). Thus, it is important to determine the causes of poor IS grain filling. In this study, we attempted to identify whether inferior grain filling of large panicles is restricted by superior spikelets (SS) and their physiological mechanism. SS were removed from two homozygous japonica rice strains (W1844 and WJ165) during flowering in an attempt to force photosynthate transport to the IS. We measured the effects of SS removal on seed setting rate, grain weight, grain filling rate, sucrose content, as well as hormone levels, activities of key enzymes, and expression of genes involved in sucrose to starch metabolism in rice IS during grain filling. The results showed that SS removal improved IS grain filling by increasing the seed setting rate, grain weight, sucrose content, and hormone levels. SS removal also enhanced the activities of key enzymes and the expression levels of genes involved in sucrose to starch metabolism. These results suggest that sucrose and several hormones act as signal substances and play a vital role in grain filling by regulating enzyme activities and gene expression. Therefore, IS grain filling is restricted by SS, which limit assimilate supply and plant hormones, leading to poor grain filling of IS. PMID:27547210

  2. Identification and characterization of Mini1, a gene regulating rice shoot development.

    PubMed

    Fang, Yunxia; Hu, Jiang; Xu, Jie; Yu, Haiping; Shi, Zhenyuan; Xiong, Guosheng; Zhu, Li; Zeng, Dali; Zhang, Guangheng; Gao, Zhenyu; Dong, Guojun; Yan, Meixian; Guo, Longbiao; Wang, Yonghong; Qian, Qian

    2015-02-01

    The aerial parts of higher plants are generated from the shoot apical meristem (SAM). In this study, we isolated a small rice (Oryza sativa L.) mutant that showed premature termination of shoot development and was named mini rice 1 (mini1). The mutant was first isolated from a japonica cultivar Zhonghua11 (ZH11) subjected to ethyl methanesulfonate (EMS) treatment. With bulked segregant analysis (BSA) and map-based cloning method, Mini1 gene was finally fine-mapped to an interval of 48.6 kb on chromosome 9. Sequence analyses revealed a single base substitution from G to A was found in the region, which resulted in an amino acid change from Gly to Asp. The candidate gene Os09g0363900 was predicted to encode a putative adhesion of calyx edges protein ACE (putative HOTHEAD precursor) and genetic complementation experiment confirmed the identity of Mini1. Os09g0363900 contains glucose-methanol-choline (GMC) oxidoreductase and NAD(P)-binding Rossmann-like domain, and exhibits high similarity to Arabidopsis HOTHEAD (HTH). Expression analysis indicated Mini1 was highly expressed in young shoots but lowly in roots and the expression level of most genes involved in auxin biosynthesis and signal transduction were reduced in mutant. We conclude that Mini1 plays an important role in maintaining SAM activity and promoting shoot development in rice.

  3. Effect of Removing Superior Spikelets on Grain Filling of Inferior Spikelets in Rice.

    PubMed

    You, Cuicui; Zhu, Honglei; Xu, Beibei; Huang, Wenxiao; Wang, Shaohua; Ding, Yanfeng; Liu, Zhenghui; Li, Ganghua; Chen, Lin; Ding, Chengqiang; Tang, She

    2016-01-01

    Large-panicle rice cultivars often fail to reach their yield potential due to the poor grain filling of inferior spikelets (IS). Thus, it is important to determine the causes of poor IS grain filling. In this study, we attempted to identify whether inferior grain filling of large panicles is restricted by superior spikelets (SS) and their physiological mechanism. SS were removed from two homozygous japonica rice strains (W1844 and WJ165) during flowering in an attempt to force photosynthate transport to the IS. We measured the effects of SS removal on seed setting rate, grain weight, grain filling rate, sucrose content, as well as hormone levels, activities of key enzymes, and expression of genes involved in sucrose to starch metabolism in rice IS during grain filling. The results showed that SS removal improved IS grain filling by increasing the seed setting rate, grain weight, sucrose content, and hormone levels. SS removal also enhanced the activities of key enzymes and the expression levels of genes involved in sucrose to starch metabolism. These results suggest that sucrose and several hormones act as signal substances and play a vital role in grain filling by regulating enzyme activities and gene expression. Therefore, IS grain filling is restricted by SS, which limit assimilate supply and plant hormones, leading to poor grain filling of IS. PMID:27547210

  4. Unraveling the rich phenotypic and genetic diversity in rice for varietal improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Asian cultivated rice (Oryza sativa L.) has two distinct varietal groups identified as the indica and japonica subspecies. With the advent of molecular markers the indica subspecies was divided into the indica and aus subpopulation groups and the japonica subspecies into the aromatic, tropical japon...

  5. Combination Patterns of Major R Genes Determine the Level of Resistance to the M. oryzae in Rice (Oryza sativa L.)

    PubMed Central

    Yu, Ling; Pan, Cunhong; Li, Yuhong; Zhang, Xiaoxiang; Liu, Guangqing; Dai, Zhengyuan; Pan, Xuebiao; Li, Aihong

    2015-01-01

    Rice blast caused by Magnaporthe oryzae is the most devastating disease of rice and poses a serious threat to world food security. In this study, the distribution and effectiveness of 18 R genes in 277 accessions were investigated based on pathogenicity assays and molecular markers. The results showed that most of the accessions exhibited some degree of resistance (resistance frequency, RF >50%). Accordingly, most of the accessions were observed to harbor two or more R genes, and the number of R genes harbored in accessions was significantly positively correlated with RF. Some R genes were demonstrated to be specifically distributed in the genomes of rice sub-species, such as Pigm, Pi9, Pi5 and Pi1, which were only detected in indica-type accessions, and Pik and Piz, which were just harbored in japonica-type accessions. By analyzing the relationship between R genes and RF using a multiple stepwise regression model, the R genes Pid3, Pi5, Pi9, Pi54, Pigm and Pit were found to show the main effects against M. oryzae in indica-type accessions, while Pita, Pb1, Pik, Pizt and Pia were indicated to exhibit the main effects against M. oryzae in japonica-type accessions. Principal component analysis (PCA) and cluster analysis revealed that combination patterns of major R genes were the main factors determining the resistance of rice varieties to M. oryzae, such as ‘Pi9+Pi54’, ‘Pid3+Pigm’, ‘Pi5+Pid3+Pigm’, ‘Pi5+Pi54+Pid3+Pigm’, ‘Pi5+Pid3’ and ‘Pi5+Pit+Pid3’ in indica-type accessions and ‘Pik+Pib’, ‘Pik+Pita’, ‘Pik+Pb1’, ‘Pizt+Pia’ and ‘Pizt+Pita’ in japonica-type accessions, which were able to confer effective resistance against M. oryzae. The above results provide good theoretical support for the rational utilization of combinations of major R genes in developing rice cultivars with broad-spectrum resistance. PMID:26030358

  6. Early Embryogenesis-Specific Expression of the Rice Transposon Ping Enhances Amplification of the MITE mPing

    PubMed Central

    Teramoto, Shota; Tsukiyama, Takuji; Okumoto, Yutaka; Tanisaka, Takatoshi

    2014-01-01

    Miniature inverted-repeat transposable elements (MITEs) are numerically predominant transposable elements in the rice genome, and their activities have influenced the evolution of genes. Very little is known about how MITEs can rapidly amplify to thousands in the genome. The rice MITE mPing is quiescent in most cultivars under natural growth conditions, although it is activated by various stresses, such as tissue culture, gamma-ray irradiation, and high hydrostatic pressure. Exceptionally in the temperate japonica rice strain EG4 (cultivar Gimbozu), mPing has reached over 1000 copies in the genome, and is amplifying owing to its active transposition even under natural growth conditions. Being the only active MITE, mPing in EG4 is an appropriate material to study how MITEs amplify in the genome. Here, we provide important findings regarding the transposition and amplification of mPing in EG4. Transposon display of mPing using various tissues of a single EG4 plant revealed that most de novo mPing insertions arise in embryogenesis during the period from 3 to 5 days after pollination (DAP), and a large majority of these insertions are transmissible to the next generation. Locus-specific PCR showed that mPing excisions and insertions arose at the same time (3 to 5 DAP). Moreover, expression analysis and in situ hybridization analysis revealed that Ping, an autonomous partner for mPing, was markedly up-regulated in the 3 DAP embryo of EG4, whereas such up-regulation of Ping was not observed in the mPing-inactive cultivar Nipponbare. These results demonstrate that the early embryogenesis-specific expression of Ping is responsible for the successful amplification of mPing in EG4. This study helps not only to elucidate the whole mechanism of mPing amplification but also to further understand the contribution of MITEs to genome evolution. PMID:24921928

  7. Effect of volunteer rice infestation on grain quality and yield of rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Volunteer rice (Oryza sativa L.) plants arise from shattered seeds of the previous crop, which could reduce the yield of cultivated rice and the commercial value of harvested grain. Volunteer rice plants from a cultivar other than the current crop produce grains that may differ in physico-chemical t...

  8. Segregation for endosperm lysine in F2, F 3 and F 4 progeny from a cross of in vitro-selected and unselected cultivar of rice.

    PubMed

    Schaeffer, G W; Sharpe, F T; Dudley, J T

    1989-02-01

    Lysine is a limiting amino acid for optimal nutritional quality in rice grain. In vitro selections using inhibitory levels of lysine plus threonine or s-aminoethylcysteine allow the predictable recovery of variants with elevated levels of lysine and protein. These methods may generate useful starting germplasm for plant breeders. This study was conducted to define the genetics of lysine mutants in progeny from crosses of mutants derived from cells cultured in vitro in the presence of inhibitory levels of lysine plus threonine and s-(2-aminoethyl)-cysteine. In vitro selections produce a wide range of mutants, including endosperm mutants with elevated lysine and protein levels as well as mutants for high and low seed weights. Mutants were analyzed for lysine content by the endosperm half-seed method in which the halves without the embryo were ground and acid hydrolyzed for amino acid determinations. The halves with the embryos were preserved for later germination. In two different F2 populations derived from a cross of a selected mutant x M-101, a parental marker, there was an inverse relationship between seed weight and percent lysine in endosperm protein (R(2) 0.52 and 0.56). The F2 segregation patterns show that elevated lysine is inherited as a recessive gene and that increased lysine is correlated with decreased seed size. F3 and F4 data provide evidence for the transmission of high lysine genes to advanced germplasm in rice. This work supports our earlier conclusions that high lysine phenotypes can be recovered predictably from in vitro selections. The elevated lysine phenotypes are frequently, but not exclusively, associated with opaque seed. Some segregants from crosses produced increased lysine in plants with near normal seed weight and good fertility. PMID:24232525

  9. Bioactive compounds in pigmented rice bran inhibit growth of human cancer cells

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice bran contains both lipophilic and hydrophilic antioxidants. Our previous studies have shown that pigmented rice cultivars contained several-fold higher total phenolic concentrations and antioxidant capacities than non-pigmented cultivars. We investigated three rice brans (purple, red and light-...

  10. A fragment of the Xanthomonas oryzae pv. oryzicola harpin HpaG Xooc reduces disease and increases yield of rice in extensive grower plantings.

    PubMed

    Chen, Lei; Zhang, Shu-Jian; Zhang, Shao-Song; Qu, Shuping; Ren, Xiuyan; Long, Juying; Yin, Qian; Qian, Jun; Sun, Feng; Zhang, Chunling; Wang, Lingxian; Wu, Xiaojing; Wu, Tingquan; Zhang, Zhongkai; Cheng, Zaiquan; Hayes, Marshall; Beer, Steven V; Dong, Hansong

    2008-07-01

    Harpins of phytopathogenic bacteria stimulate defense and plant growth in many types of plants, conferring disease resistance and enhanced yield. In a previous study, we characterized nine fragments of the harpin protein HpaG(Xooc) from Xanthomonas oryzae pv. oryzicola for plant defense elicitation and plant growth stimulation activity relative to the intact protein. In plants grown under controlled conditions, the fragment HpaG10-42 was more active in both regards than HpaG(Xooc). Here, we demonstrate that the activity of HpaG10-42 in rice under field conditions significantly exceeds that of HpaG(Xooc), stimulating resistance to three important diseases and increasing grain yield. We carried out tests in 672 experimental plots with nine cultivars of rice planted at three locations. Application protocols were optimized by testing variations in application rate, frequency, and timing with respect to rice growth stage. Of the concentrations (24, 24, 12, and 6 microg/ml), and number and timing of applications (at one to four different stages of growth) tested, HpaG10-42 at 6 microg/ml applied to plants once at nursery seedling stage and three times in the field was most effective. Bacterial blight, rice blast, and sheath blight were reduced 61.6 and 56.4, 93.6 and 76.0, and 93.2 and 55.0% in indica and japonica cultivars, respectively, relative to controls. Grain yields were 22 to 27% greater. These results are similar to results obtained with typical local management practices, including use of chemicals, to decrease disease severities and increase yield in rice. Our results demonstrate that the HpaG10-42 protein fragment can be used effectively to control diseases and increase yield of this staple food crop. PMID:18943255

  11. Increased α-tocotrienol content in seeds of transgenic rice overexpressing Arabidopsis γ-tocopherol methyltransferase.

    PubMed

    Zhang, Gui-Yun; Liu, Ru-Ru; Xu, Geng; Zhang, Peng; Li, Yin; Tang, Ke-Xuan; Liang, Guo-Hua; Liu, Qiao-Quan

    2013-02-01

    Vitamin E comprises a group of eight lipid soluble antioxidant compounds that are an essential part of the human diet. The α-isomers of both tocopherol and tocotrienol are generally considered to have the highest antioxidant activities. γ-tocopherol methyltransferase (γ-TMT) catalyzes the final step in vitamin E biosynthesis, the methylation of γ- and δ-isomers to α- and β-isomers. In present study, the Arabidopsis γ-TMT (AtTMT) cDNA was overexpressed constitutively or in the endosperm of the elite japonica rice cultivar Wuyujing 3 (WY3) by Agrobacterium-mediated transformation. HPLC analysis showed that, in brown rice of the wild type or transgenic controls with empty vector, the α-/γ-tocotrienol ratio was only 0.7, much lower than that for tocopherol (~19.0). In transgenic rice overexpressing AtTMT driven by the constitutive Ubi promoter, most of the γ-isomers were converted to α-isomers, especially the γ- and δ-tocotrienol levels were dramatically decreased. As a result, the α-tocotrienol content was greatly increased in the transgenic seeds. Similarly, over-expression of AtTMT in the endosperm also resulted in an increase in the α-tocotrienol content. The results showed that the α-/γ-tocopherol ratio also increased in the transgenic seeds, but there was no significant effect on α-tocopherol level, which may reflect the fact that γ-tocopherol is present in very small amounts in wild type rice seeds. AtTMT overexpression had no effect on the absolute total content of either tocopherols or tocotrienols. Taken together, these results are the first demonstration that the overexpression of a foreign γ-TMT significantly shift the tocotrienol synthesis in rice, which is one of the world's most important food crops.

  12. Selenium addition alters mercury uptake, bioavailability in the rhizosphere and root anatomy of rice (Oryza sativa)

    PubMed Central

    Wang, Xun; Tam, Nora Fung-Yee; Fu, Shi; Ametkhan, Aray; Ouyang, Yun; Ye, Zhihong

    2014-01-01

    Background and Aims Mercury (Hg) is an extremely toxic pollutant, especially in the form of methylmercury (MeHg), whereas selenium (Se) is an essential trace element in the human diet. This study aimed to ascertain whether addition of Se can produce rice with enriched Se and lowered Hg content when growing in Hg-contaminated paddy fields and, if so, to determine the possible mechanisms behind these effects. Methods Two cultivars of rice (Oryza sativa, japonica and indica) were grown in either hydroponic solutions or soil rhizobags with different Se and Hg treatments. Concentrations of total Hg, MeHg and Se were determined in the roots, shoots and brown rice, together with Hg uptake kinetics and Hg bioavailability in the soil. Root anatonmy was also studied. Key Results The high Se treatment (5 μg g–1) significantly increased brown rice yield by 48 % and total Se content by 2·8-fold, and decreased total Hg and MeHg by 47 and 55 %, respectively, compared with the control treatments. The high Se treatment also markedly reduced ‘water-soluble’ Hg and MeHg concentrations in the rhizosphere soil, decreased the uptake capacity of Hg by roots and enhanced the development of apoplastic barriers in the root endodermis. Conclusions Addition of Se to Hg-contaminated soil can help produce brown rice that is simultaneously enriched in Se and contains less total Hg and MeHg. The lowered accumulation of total Hg and MeHg appears to be the result of reduced bioavailability of Hg and production of MeHg in the rhizosphere, suppression of uptake of Hg into the root cells and an enhancement of the development of apoplastic barriers in the endodermis of the roots. PMID:24948669

  13. A genome-wide association study of a global rice panel reveals resistance in Oryza sativa to root-knot nematodes

    PubMed Central

    Dimkpa, Stanley O. N.; Lahari, Zobaida; Shrestha, Roshi; Douglas, Alex; Gheysen, Godelieve; Price, Adam H.

    2016-01-01

    The root-knot nematode Meloidogyne graminicola is one of the most serious nematode pests worldwide and represents a major constraint on rice production. While variation in the susceptibility of Asian rice (Oryza sativa) exists, so far no strong and reliable resistance has been reported. Quantitative trait loci for partial resistance have been reported but no underlying genes have been tagged or cloned. Here, 332 accessions of the Rice Diversity Panel 1 were assessed for gall formation, revealing large variation across all subpopulations of rice and higher susceptibility in temperate japonica accessions. Accessions Khao Pahk Maw and LD 24 appeared to be resistant, which was confirmed in large pot experiments where no galls were observed. Detailed observations on these two accessions revealed no nematodes inside the roots 2 days after inoculation and very few females after 17 days (5 in Khao Pahk Maw and <1 in LD 24, in comparison with >100 in the susceptible controls). These two cultivars appear ideal donors for breeding root-knot nematode resistance. A genome-wide association study revealed 11 quantitative trait loci, two of which are close to epistatic loci detected in the Bala x Azucena population. The discussion highlights a small number of candidate genes worth exploring further, in particular many genes with lectin domains and genes on chromosome 11 with homology to the Hordeum Mla locus. PMID:26552884

  14. A positive feedback loop between HEAT SHOCK PROTEIN101 and HEAT STRESS-ASSOCIATED 32-KD PROTEIN modulates long-term acquired thermotolerance illustrating diverse heat stress responses in rice varieties.

    PubMed

    Lin, Meng-yi; Chai, Kuo-hsing; Ko, Swee-suak; Kuang, Lin-yun; Lur, Huu-sheng; Charng, Yee-yung

    2014-04-01

    Heat stress is an important factor that has a negative impact on rice (Oryza sativa) production. To alleviate this problem, it is necessary to extensively understand the genetic basis of heat tolerance and adaptability to heat stress in rice. Here, we report the molecular mechanism underlying heat acclimation memory that confers long-term acquired thermotolerance (LAT) in this monocot plant. Our results showed that a positive feedback loop formed by two heat-inducible genes, HEAT SHOCK PROTEIN101 (HSP101) and HEAT STRESS-ASSOCIATED 32-KD PROTEIN (HSA32), at the posttranscriptional level prolongs the effect of heat acclimation in rice seedlings. The interplay between HSP101 and HSA32 also affects basal thermotolerance of rice seeds. These findings are similar to those reported for the dicot plant Arabidopsis (Arabidopsis thaliana), suggesting a conserved function in plant heat stress response. Comparison between two rice cultivars, japonica Nipponbare and indica N22 showed opposite performance in basal thermotolerance and LAT assays. 'N22' seedlings have a higher basal thermotolerance level than cv Nipponbare and vice versa at the LAT level, indicating that these two types of thermotolerance can be decoupled. The HSP101 and HSA32 protein levels were substantially higher in cv Nipponbare than in cv N22 after a long recovery following heat acclimation treatment, at least partly explaining the difference in the LAT phenotype. Our results point out the complexity of thermotolerance diversity in rice cultivars, which may need to be taken into consideration when breeding for heat tolerance for different climate scenarios.

  15. The organelle genomes of Hassawi rice (Oryza sativa L.) and its hybrid in saudi arabia: genome variation, rearrangement, and origins.

    PubMed

    Zhang, Tongwu; Hu, Songnian; Zhang, Guangyu; Pan, Linlin; Zhang, Xiaowei; Al-Mssallem, Ibrahim S; Yu, Jun

    2012-01-01

    Hassawi rice (Oryza sativa L.) is a landrace adapted to the climate of Saudi Arabia, characterized by its strong resistance to soil salinity and drought. Using high quality sequencing reads extracted from raw data of a whole genome sequencing project, we assembled both chloroplast (cp) and mitochondrial (mt) genomes of the wild-type Hassawi rice (Hassawi-1) and its dwarf hybrid (Hassawi-2). We discovered 16 InDels (insertions and deletions) but no SNP (single nucleotide polymorphism) is present between the two Hassawi cp genomes. We identified 48 InDels and 26 SNPs in the two Hassawi mt genomes and a new type of sequence variation, termed reverse complementary variation (RCV) in the rice cp genomes. There are two and four RCVs identified in Hassawi-1 when compared to 93-11 (indica) and Nipponbare (japonica), respectively. Microsatellite sequence analysis showed there are more SSRs in the genic regions of both cp and mt genomes in the Hassawi rice than in the other rice varieties. There are also large repeats in the Hassawi mt genomes, with the longest length of 96,168 bp and 96,165 bp in Hassawi-1 and Hassawi-2, respectively. We believe that frequent DNA rearrangement in the Hassawi mt and cp genomes indicate ongoing dynamic processes to reach genetic stability under strong environmental pressures. Based on sequence variation analysis and the breeding history, we suggest that both Hassawi-1 and Hassawi-2 originated from the Indonesian variety Peta since genetic diversity between the two Hassawi cultivars is very low albeit an unknown historic origin of the wild-type Hassawi rice. PMID:22870184

  16. Isolation of a novel mutant gene for soil-surface rooting in rice (Oryza sativa L.)

    PubMed Central

    2013-01-01

    Background Root system architecture is an important trait affecting the uptake of nutrients and water by crops. Shallower root systems preferentially take up nutrients from the topsoil and help avoid unfavorable environments in deeper soil layers. We have found a soil-surface rooting mutant from an M2 population that was regenerated from seed calli of a japonica rice cultivar, Nipponbare. In this study, we examined the genetic and physiological characteristics of this mutant. Results The primary roots of the mutant showed no gravitropic response from the seedling stage on, whereas the gravitropic response of the shoots was normal. Segregation analyses by using an F2 population derived from a cross between the soil-surface rooting mutant and wild-type Nipponbare indicated that the trait was controlled by a single recessive gene, designated as sor1. Fine mapping by using an F2 population derived from a cross between the mutant and an indica rice cultivar, Kasalath, revealed that sor1 was located within a 136-kb region between the simple sequence repeat markers RM16254 and 2935-6 on the terminal region of the short arm of chromosome 4, where 13 putative open reading frames (ORFs) were found. We sequenced these ORFs and detected a 33-bp deletion in one of them, Os04g0101800. Transgenic plants of the mutant transformed with the genomic fragment carrying the Os04g0101800 sequence from Nipponbare showed normal gravitropic responses and no soil-surface rooting. Conclusion These results suggest that sor1, a rice mutant causing soil-surface rooting and altered root gravitropic response, is allelic to Os04g0101800, and that a 33-bp deletion in the coding region of this gene causes the mutant phenotypes. PMID:24280269

  17. A whole-genome SNP array (RICE6K) for genomic breeding in rice.

    PubMed

    Yu, Huihui; Xie, Weibo; Li, Jing; Zhou, Fasong; Zhang, Qifa

    2014-01-01

    The advances in genotyping technology provide an opportunity to use genomic tools in crop breeding. As compared to field selections performed in conventional breeding programmes, genomics-based genotype screen can potentially reduce number of breeding cycles and more precisely integrate target genes for particular traits into an ideal genetic background. We developed a whole-genome single nucleotide polymorphism (SNP) array, RICE6K, based on Infinium technology, using representative SNPs selected from more than four million SNPs identified from resequencing data of more than 500 rice landraces. RICE6K contains 5102 SNP and insertion-deletion (InDel) markers, about 4500 of which were of high quality in the tested rice lines producing highly repeatable results. Forty-five functional markers that are located inside 28 characterized genes of important traits can be detected using RICE6K. The SNP markers are evenly distributed on the 12 chromosomes of rice with the average density of 12 SNPs per 1 Mb and can provide information for polymorphisms between indica and japonica subspecies as well as varieties within indica and japonica groups. Application tests of RICE6K showed that the array is suitable for rice germplasm fingerprinting, genotyping bulked segregating pools, seed authenticity check and genetic background selection. These results suggest that RICE6K provides an efficient and reliable genotyping tool for rice genomic breeding.

  18. Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.).

    PubMed

    Yan, Wen Gui; Li, Yong; Agrama, Hesham A; Luo, Dagang; Gao, Fangyuan; Lu, Xianjun; Ren, Guangjun

    2009-10-01

    Stigma and spikelet characteristics play an essential role in hybrid seed production. A mini-core of 90 accessions developed from USDA rice core collection was phenotyped in field grown for nine traits of stigma and spikelet and genotyped with 109 DNA markers, 108 SSRs plus an indel. Three major clusters were built upon Rogers' genetic distance, indicative of indicas, and temperate and tropical japonicas. A mixed linear model combining PC-matrix and K-matrix was adapted for mapping marker-trait associations. Resulting associations were adjusted using false discovery rate technique. We identified 34 marker-trait associations involving 22 SSR markers for eight traits. Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion. RM5_Chr1 played major role indicative of high regression with not only DStgE but also SStgE. Four markers were associated with spikelet length, three with width and seven with L/W ratio. Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 associated with all three correlated spikelet traits. The co-association should improve breeding efficiency because single marker could be used to assist breeding for multiple traits. Indica entry 1032 (cultivar 50638) and japonica entry 671 (cultivar Linia 84 Icar) with 80.65 and 75.17% of TStgE, respectively are recommended to breeder for improving stigma exsertion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-009-9290-y) contains supplementary material, which is available to authorized users.

  19. Variation in tolerance of rice to long-term stagnant flooding that submerges most of the shoot will aid in breeding tolerant cultivars

    PubMed Central

    Vergara, Georgina V.; Nugraha, Yudhistira; Esguerra, Manuel Q.; Mackill, David J.; Ismail, Abdelbagi M.

    2014-01-01

    Stagnant flooding (SF) is a major problem in rainfed lowlands where floodwater of 25–50 cm stagnates in the field for most of the season. We aimed to establish a system for phenotyping SF tolerance and identifying tolerant germplasm through screening of landraces. A total of 626 rice accessions were evaluated over 3 years under control conditions and two levels of SF. Floodwater was raised to 20 cm at 25 or 30 days after transplanting (DAT). In one trial, the depth was increased subsequently by 5 cm a week and in another (severe stress), it was increased to 40 cm at 37 DAT and to 50 cm at 42 DAT. In both trials, water depth was maintained at 50–60 cm until maturity. In all cases, no plant was completely submerged. Plant height, elongation rate and yield were measured at maturity. Genotypes best suited to SF showed moderate elongation of 1.3–2.3 cm day−1 under SF. In contrast, semi-dwarf and fast-elongating types performed poorly. Subsequent trials using 18 genotypes, including six pairs of near isogenic lines (NILs) with or without SUB1 showed that all SUB1 NILs were sensitive to SF. Five of the other six genotypes contained SUB1 and were SF tolerant, suggesting the possibility of combining tolerances to complete submergence (SUB1) and SF. Stem starch and soluble sugar concentrations were similar under control conditions among the 18 genotypes, but starch was depleted by 37 % under SF, with less depletion in tolerant genotypes. SUB1 NILs contained similar concentrations of starch and sugars under SF. We conclude that survival and yield under SF are dependent on moderate elongation, high tillering, lesser carbohydrate depletion and higher fertility. The tolerant genotypes identified here performed strongly in both wet and dry seasons and will be used to identify tolerance mechanisms and alleles for use in marker-assisted breeding. PMID:25202124

  20. Variation in tolerance of rice to long-term stagnant flooding that submerges most of the shoot will aid in breeding tolerant cultivars.

    PubMed

    Vergara, Georgina V; Nugraha, Yudhistira; Esguerra, Manuel Q; Mackill, David J; Ismail, Abdelbagi M

    2014-01-01

    Stagnant flooding (SF) is a major problem in rainfed lowlands where floodwater of 25-50 cm stagnates in the field for most of the season. We aimed to establish a system for phenotyping SF tolerance and identifying tolerant germplasm through screening of landraces. A total of 626 rice accessions were evaluated over 3 years under control conditions and two levels of SF. Floodwater was raised to 20 cm at 25 or 30 days after transplanting (DAT). In one trial, the depth was increased subsequently by 5 cm a week and in another (severe stress), it was increased to 40 cm at 37 DAT and to 50 cm at 42 DAT. In both trials, water depth was maintained at 50-60 cm until maturity. In all cases, no plant was completely submerged. Plant height, elongation rate and yield were measured at maturity. Genotypes best suited to SF showed moderate elongation of 1.3-2.3 cm day(-1) under SF. In contrast, semi-dwarf and fast-elongating types performed poorly. Subsequent trials using 18 genotypes, including six pairs of near isogenic lines (NILs) with or without SUB1 showed that all SUB1 NILs were sensitive to SF. Five of the other six genotypes contained SUB1 and were SF tolerant, suggesting the possibility of combining tolerances to complete submergence (SUB1) and SF. Stem starch and soluble sugar concentrations were similar under control conditions among the 18 genotypes, but starch was depleted by 37 % under SF, with less depletion in tolerant genotypes. SUB1 NILs contained similar concentrations of starch and sugars under SF. We conclude that survival and yield under SF are dependent on moderate elongation, high tillering, lesser carbohydrate depletion and higher fertility. The tolerant genotypes identified here performed strongly in both wet and dry seasons and will be used to identify tolerance mechanisms and alleles for use in marker-assisted breeding. PMID:25202124

  1. Effects of cooking methods and starch structures on starch hydrolysis rates of rice.

    PubMed

    Reed, Michael O; Ai, Yongfeng; Leutcher, Josh L; Jane, Jay-lin

    2013-07-01

    This study aimed to understand effects of different cooking methods, including steamed, pilaf, and traditional stir-fried, on starch hydrolysis rates of rice. Rice grains of 3 varieties, japonica, indica, and waxy, were used for the study. Rice starch was isolated from the grain and characterized. Amylose contents of starches from japonica, indica, and waxy rice were 13.5%, 18.0%, and 0.9%, respectively. The onset gelatinization temperature of indica starch (71.6 °C) was higher than that of the japonica and waxy starch (56.0 and 56.8 °C, respectively). The difference was attributed to longer amylopectin branch chains of the indica starch. Starch hydrolysis rates and resistant starch (RS) contents of the rice varieties differed after they were cooked using different methods. Stir-fried rice displayed the least starch hydrolysis rate followed by pilaf rice and steamed rice for each rice variety. RS contents of freshly steamed japonica, indica, and waxy rice were 0.7%, 6.6%, and 1.3%, respectively; those of rice pilaf were 12.1%, 13.2%, and 3.4%, respectively; and the stir-fried rice displayed the largest RS contents of 15.8%, 16.6%, and 12.1%, respectively. Mechanisms of the large RS contents of the stir-fried rice were studied. With the least starch hydrolysis rate and the largest RS content, stir-fried rice would be a desirable way of preparing rice for food to reduce postprandial blood glucose and insulin responses and to improve colon health of humans.

  2. PHIV-RootCell: a supervised image analysis tool for rice root anatomical parameter quantification

    PubMed Central

    Lartaud, Marc; Perin, Christophe; Courtois, Brigitte; Thomas, Emilie; Henry, Sophia; Bettembourg, Mathilde; Divol, Fanchon; Lanau, Nadege; Artus, Florence; Bureau, Charlotte; Verdeil, Jean-Luc; Sarah, Gautier; Guiderdoni, Emmanuel; Dievart, Anne

    2015-01-01

    We developed the PHIV-RootCell software to quantify anatomical traits of rice roots transverse section images. Combined with an efficient root sample processing method for image acquisition, this program permits supervised measurements of areas (those of whole root section, stele, cortex, and central metaxylem vessels), number of cell layers and number of cells per cell layer. The PHIV-RootCell toolset runs under ImageJ, an independent operating system that has a license-free status. To demonstrate the usefulness of PHIV-RootCell, we conducted a genetic diversity study and an analysis of salt stress responses of root anatomical parameters in rice (Oryza sativa L.). Using 16 cultivars, we showed that we could discriminate between some of the varieties even at the 6 day-olds stage, and that tropical japonica varieties had larger root sections due to an increase in cell number. We observed, as described previously, that root sections become enlarged under salt stress. However, our results show an increase in cell number in ground tissues (endodermis and cortex) but a decrease in external (peripheral) tissues (sclerenchyma, exodermis, and epidermis). Thus, the PHIV-RootCell program is a user-friendly tool that will be helpful for future genetic and physiological studies that investigate root anatomical trait variations. PMID:25646121

  3. Switchgrass cultivar EG1102

    DOEpatents

    Bouton, Joseph H; Wood, Donald T

    2012-11-20

    A switchgrass cultivar designated EG1102 is disclosed. The invention relates to the seeds of switchgrass cultivar EG1102, to the plants of switchgrass EG1102, to plant parts of switchgrass cultivar EG1102 and to methods for producing a switchgrass plant produced by crossing switchgrass cultivar EG1102 with itself or with another switchgrass variety. The invention also relates to methods for producing a switchgrass plant containing in its genetic material one or more transgenes and to the transgenic switchgrass plants and plant parts produced by those methods. This invention also relates to switchgrass cultivars or breeding cultivars and plant parts derived from switchgrass variety EG1102, to methods for producing other switchgrass cultivars, lines or plant parts derived from switchgrass cultivar EG1102 and to the switchgrass plants, varieties, and their parts derived from use of those methods. The invention further relates to hybrid switchgrass seeds, plants and plant parts produced by crossing the cultivar EG1102 with another switchgrass cultivar.

  4. Switchgrass cultivar EG1101

    DOEpatents

    Bouton, Joseph H; Wood, Donald T

    2012-11-27

    A switchgrass cultivar designated EG1101 is disclosed. Also disclosed are seeds of switchgrass cultivar EG1101, plants of switchgrass EG1101, plant parts of switchgrass cultivar EG1101 and methods for producing a switchgrass plant produced by crossing switchgrass cultivar EG1101 with itself or with another switchgrass variety. Methods are also described for producing a switchgrass plant containing in its genetic material one or more transgenes and to the transgenic switchgrass plants and plant parts produced by those methods. Switchgrass cultivars or breeding cultivars and plant parts derived from switchgrass variety EG1101, methods for producing other switchgrass cultivars, lines or plant parts derived from switchgrass cultivar EG1101 and the switchgrass plants, varieties, and their parts derived from use of those methods are described herein. Hybrid switchgrass seeds, plants and plant parts produced by crossing the cultivar EG1101 with another switchgrass cultivar are also described.

  5. SNP-assisted development of interspecific CSSLs in rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study is to generate six libraries of chromosome segment substitution lines (CSSLs) using three diverse accessions of the wild Oryza sativa progenitor species, O. rufipogon/O. nivara as donors, and two elite O. sativa cultivars, Cybonnet (tropical japonica) and IR64 (indica) as...

  6. Quantitative trait loci associated with functional stay-green SNU-SG1 in rice.

    PubMed

    Yoo, Soo-Cheul; Cho, Sung-Hwan; Zhang, Haitao; Paik, Hyo-Chung; Lee, Chung-Hee; Li, Jinjie; Yoo, Jeong-Hoon; Lee, Byun-Woo; Koh, Hee-Jong; Seo, Hak Soo; Paek, Nam-Chon

    2007-08-31

    During monocarpic senescence in higher plants, functional stay-green delays leaf yellowing, maintaining photosynthetic competence, whereas nonfunctional stay-green retains leaf greenness without sustaining photosynthetic activity. Thus, functional stay-green is considered a beneficial trait that can increase grain yield in cereal crops. A stay-green japonica rice 'SNU-SG1' had a good seed-setting rate and grain yield, indicating the presence of a functional stay-green genotype. SNU-SG1 was crossed with two regular cultivars to determine the inheritance mode and identify major QTLs conferring stay-green in SNU-SG1. For QTL analysis, linkage maps with 100 and 116 DNA marker loci were constructed using selective genotyping with F2 and RIL (recombinant inbred line) populations, respectively. Molecular marker-based QTL analyses with both populations revealed that the functional stay-green phenotype of SNU-SG1 is regulated by several major QTLs accounting for a large portion of the genetic variation. Three main-effect QTLs located on chromosomes 7 and 9 were detected in both populations and a number of epistatic-effect QTLs were also found. The amount of variation explained by several digenic interactions was larger than that explained by main-effect QTLs. Two main-effect QTLs on chromosome 9 can be considered the target loci that most influence the functional stay-green in SNU-SG1. The functional stay-green QTLs may help develop low-input high-yielding rice cultivars by QTL-marker-assisted breeding with SNU-SG1.

  7. Transgenic Bt Rice Does Not Challenge Host Preference of the Target Pest of Rice Leaffolder, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae)

    PubMed Central

    Sun, Xiao; Zhou, Wen; Liu, Hao; Zhang, Aijun; Ai, Chao-Ren; Zhou, Shuang-Shuang; Zhou, Chang-Xiang; Wang, Man-Qun

    2013-01-01

    Background Transgenic Bt rice line T2A-1 expresses a synthesized cry2A gene that shows high resistance to Lepidoptera pests, including Cnaphalocrocis medinalis (Guenée) (Lepidoptera: Pyralidae). Plant volatile orientation cues and the physical characteristics of the leaf surface play key roles in host location or host-plant acceptance of phytophagous insects. These volatile compounds and physical traits may become altered in Bt rice and it is not known whether this influences the behavior of C. medinalis when searching for oviposition sites. Results The results of electronic nose analysis showed that the Radar map of Bt rice cultivars was analogous to the non- Bt rice cultivars at each growing stage. PCA analysis was able to partly discriminate between some of the Bt vs. non-Bt rice sensors, but could not to separate Bt cultivars from non-Bt cultivars. The total ion chromatogram between Bt and non-Bt rice cultivars at the seedling, booting and tillering stages were similar and 25 main compounds were identified by GC-MS. For most compounds, there was no significant difference in compound quantities between Bt and non-Bt rice cultivars at equivalent growth stages. The densities of the tubercle papicles and the trichomes on the upper and lower surfaces were statistically equal in Bt and non-Bt rice. The target pest, C. medinalis, was attracted to host rice plants, but it could not distinguish between the transgenic and the isogenic rice lines. Conclusions There were no significant differences between the Bt rice line, T2A-1 and the non-Bt rice for volatiles produced or in its physical characteristics and there were no negative impacts on C. medinalis oviposition behavior. These results add to the mounting evidence that Bt rice has no negative impact on the target insect oviposition behavior. PMID:24244410

  8. Ingestion of Bt corn pollen containing Cry1Ab/2Aj or Cry1Ac does not harm Propylea japonica larvae

    PubMed Central

    Liu, Yanmin; Liu, Qingsong; Wang, Yanan; Chen, Xiuping; Song, Xinyuan; Romeis, Jörg; Li, Yunhe; Peng, Yufa

    2016-01-01

    Propylea japonica (Thunberg) (Coleoptera: Coccinellidae) is a prevalent pollen consumer in corn fields and is therefore exposed to insecticidal proteins contained in the pollen of insect-resistant transgenic corn cultivars expressing Cry proteins derived from Bacillus thuringiensis (Bt). In the present study, the potential effect of Cry1Ab/2Aj- or Cry1Ac-containing transgenic Bt corn pollen on the fitness of P. japonica larvae was evaluated. The results show that the larval developmental time was significantly shorter when P. japonica larvae were fed pollen from Bt corn cultivars rather than control pollen but that pupation rate, eclosion rate, and adult fresh weight were not significantly affected. In the feeding experiments, the stability of the Cry proteins in the food sources was confirmed. When Bt corn pollen passed through the gut of P. japonica, 23% of Cry1Ab/2Aj was digested. The results demonstrate that consumption of Bt corn pollen containing Cry1Ab/2Aj or Cry1Ac has no detrimental effect on P. japonica larvae; the shortened developmental time of larvae that consumed these proteins was likely attributable to unknown differences in the nutritional composition between the Bt-transgenic and control corn pollen. PMID:27005950

  9. Ingestion of Bt corn pollen containing Cry1Ab/2Aj or Cry1Ac does not harm Propylea japonica larvae.

    PubMed

    Liu, Yanmin; Liu, Qingsong; Wang, Yanan; Chen, Xiuping; Song, Xinyuan; Romeis, Jörg; Li, Yunhe; Peng, Yufa

    2016-01-01

    Propylea japonica (Thunberg) (Coleoptera: Coccinellidae) is a prevalent pollen consumer in corn fields and is therefore exposed to insecticidal proteins contained in the pollen of insect-resistant transgenic corn cultivars expressing Cry proteins derived from Bacillus thuringiensis (Bt). In the present study, the potential effect of Cry1Ab/2Aj- or Cry1Ac-containing transgenic Bt corn pollen on the fitness of P. japonica larvae was evaluated. The results show that the larval developmental time was significantly shorter when P. japonica larvae were fed pollen from Bt corn cultivars rather than control pollen but that pupation rate, eclosion rate, and adult fresh weight were not significantly affected. In the feeding experiments, the stability of the Cry proteins in the food sources was confirmed. When Bt corn pollen passed through the gut of P. japonica, 23% of Cry1Ab/2Aj was digested. The results demonstrate that consumption of Bt corn pollen containing Cry1Ab/2Aj or Cry1Ac has no detrimental effect on P. japonica larvae; the shortened developmental time of larvae that consumed these proteins was likely attributable to unknown differences in the nutritional composition between the Bt-transgenic and control corn pollen. PMID:27005950

  10. Root distribution and interactions between allelopathic rice and c4 grass weed species as determined by 13c isotope discrimination analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cultivars which carry allelopathic traits (traits that enable them to suppress weeds) could improve the economical management and sustainability of rice production. Interactions between roots of rice and weeds are thought to be modulated by the weed-suppressive activity of some rice cultivars, but ...

  11. A Novel Naturally Occurring Class I 5-Enolpyruvylshikimate-3-Phosphate Synthase from Janibacter sp. Confers High Glyphosate Tolerance to Rice

    PubMed Central

    Yi, Shu-yuan; Cui, Ying; Zhao, Yan; Liu, Zi-duo; Lin, Yong-jun; Zhou, Fei

    2016-01-01

    As glyphosate is a broad spectrum herbicide extensively used in agriculture worldwide, identification of new aroA genes with high level of glyphosate tolerance is essential for the development and breeding of transgenic glyphosate-tolerant crops. In this study, an aroA gene was cloned from a Janibacter sp. strain isolated from marine sediment (designated as aroAJ. sp). The purified aroAJ. sp enzyme has a Km value of 30 μM for PEP and 83 μM for S3P, and a significantly higher Ki value for glyphosate (373 μM) than aroAE. coli. AroAJ. sp is characterized as a novel and naturally occurring class I aroA enzyme with glyphosate tolerance. Furthermore, we show that aroAJ. sp can be used as an effective selectable marker in both japonica and indica rice cultivar. Transgenic rice lines were tested by herbicide bioassay and it was confirmed that they could tolerate up to 3360 g/ha glyphosate, a dosage four-fold that of the recommended agricultural application level. To our knowledge, it is the first report of a naturally occurring novel class I aroA gene which can be efficiently utilized to study and develop transgenic glyphosate-tolerant crops, and can facilitate a more economical and simplified weed control system. PMID:26754957

  12. Pathogenicity of Heterodera daverti, H. zeae, and Meloidogyne incognita on rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The reactions of five rice cultivars to the cyst nematodes Heterodera daverti and H. zeae and the root-knot nematode Meloidogyne incognita were determined in the greenhouse. The results showed that both H. daverti and H. zeae infected and reproduced successfully on some of the tested rice cultivars....

  13. Use of a Pollen-Based Diet to Expose the Ladybird Beetle Propylea japonica to Insecticidal Proteins

    PubMed Central

    Zhang, Xiaojie; Li, Yunhe; Romeis, Jörg; Yin, Xinming; Wu, Kongming; Peng, Yufa

    2014-01-01

    A rape seed pollen-based diet was developed and found to be suitable for use in a dietary exposure assay for Propylea japonica. Using the diet, we established and validated a dietary exposure assay by using the protease inhibitor E-64 as positive control. Dose-dependent responses were documented for all observed life-table parameters of P. japonica including survival, pupation and eclosion rates, development time and adult weight. Results suggested that the dietary assay can detect the effects of insecticidal compounds on the survival and development of P. japonica. Using the established dietary assay, we subsequently tested the toxicity of Cry1Ab, Cry1Ac and Cry1F proteins that are expressed by transgenic maize, cotton or rice plants to P. japonica larvae. The diet containing E-64 was included as a positive control. Survival and development of P. japonica larvae were not adversely affected when the diet contained purified Cry1Ab, Cry1Ac, or Cry1F at 500 µg/g diet representing a worst-case exposure scenario. In contrast, P. japonica larvae were adversely affected when the diet contained E-64. The bioactivity and stability of the Cry proteins in the diet and Cry protein uptake by the ladybird larvae were confirmed by bioassay with a Cry-sensitive insect species and by ELISA. The current study describes a suitable experimental system for assessing the potential effects of gut-active insecticidal compounds on ladybird beetle larvae. The experiments with the Cry proteins demonstrate that P. japonica larvae are not sensitive to Cry1Ab, Cry1Ac and Cry1F. PMID:24409328

  14. Use of a pollen-based diet to expose the ladybird beetle Propylea japonica to insecticidal proteins.

    PubMed

    Zhang, Xiaojie; Li, Yunhe; Romeis, Jörg; Yin, Xinming; Wu, Kongming; Peng, Yufa

    2014-01-01

    A rape seed pollen-based diet was developed and found to be suitable for use in a dietary exposure assay for Propylea japonica. Using the diet, we established and validated a dietary exposure assay by using the protease inhibitor E-64 as positive control. Dose-dependent responses were documented for all observed life-table parameters of P. japonica including survival, pupation and eclosion rates, development time and adult weight. Results suggested that the dietary assay can detect the effects of insecticidal compounds on the survival and development of P. japonica. Using the established dietary assay, we subsequently tested the toxicity of Cry1Ab, Cry1Ac and Cry1F proteins that are expressed by transgenic maize, cotton or rice plants to P. japonica larvae. The diet containing E-64 was included as a positive control. Survival and development of P. japonica larvae were not adversely affected when the diet contained purified Cry1Ab, Cry1Ac, or Cry1F at 500 µg/g diet representing a worst-case exposure scenario. In contrast, P. japonica larvae were adversely affected when the diet contained E-64. The bioactivity and stability of the Cry proteins in the diet and Cry protein uptake by the ladybird larvae were confirmed by bioassay with a Cry-sensitive insect species and by ELISA. The current study describes a suitable experimental system for assessing the potential effects of gut-active insecticidal compounds on ladybird beetle larvae. The experiments with the Cry proteins demonstrate that P. japonica larvae are not sensitive to Cry1Ab, Cry1Ac and Cry1F. PMID:24409328

  15. Use of a pollen-based diet to expose the ladybird beetle Propylea japonica to insecticidal proteins.

    PubMed

    Zhang, Xiaojie; Li, Yunhe; Romeis, Jörg; Yin, Xinming; Wu, Kongming; Peng, Yufa

    2014-01-01

    A rape seed pollen-based diet was developed and found to be suitable for use in a dietary exposure assay for Propylea japonica. Using the diet, we established and validated a dietary exposure assay by using the protease inhibitor E-64 as positive control. Dose-dependent responses were documented for all observed life-table parameters of P. japonica including survival, pupation and eclosion rates, development time and adult weight. Results suggested that the dietary assay can detect the effects of insecticidal compounds on the survival and development of P. japonica. Using the established dietary assay, we subsequently tested the toxicity of Cry1Ab, Cry1Ac and Cry1F proteins that are expressed by transgenic maize, cotton or rice plants to P. japonica larvae. The diet containing E-64 was included as a positive control. Survival and development of P. japonica larvae were not adversely affected when the diet contained purified Cry1Ab, Cry1Ac, or Cry1F at 500 µg/g diet representing a worst-case exposure scenario. In contrast, P. japonica larvae were adversely affected when the diet contained E-64. The bioactivity and stability of the Cry proteins in the diet and Cry protein uptake by the ladybird larvae were confirmed by bioassay with a Cry-sensitive insect species and by ELISA. The current study describes a suitable experimental system for assessing the potential effects of gut-active insecticidal compounds on ladybird beetle larvae. The experiments with the Cry proteins demonstrate that P. japonica larvae are not sensitive to Cry1Ab, Cry1Ac and Cry1F.

  16. Evolutionary and social consequences of introgression of nontransgenic herbicide resistance from rice to weedy rice in Brazil.

    PubMed

    Merotto, Aldo; Goulart, Ives C G R; Nunes, Anderson L; Kalsing, Augusto; Markus, Catarine; Menezes, Valmir G; Wander, Alcido E

    2016-08-01

    Several studies have expressed concerns about the effects of gene flow from transgenic herbicide-resistant crops to their wild relatives, but no major problems have been observed. This review describes a case study in which what has been feared in transgenics regarding gene flow has actually changed biodiversity and people's lives. Nontransgenic imidazolinone-resistant rice (IMI-rice) cultivars increased the rice grain yield by 50% in southern Brazil. This increase was beneficial for life quality of the farmers and also improved the regional economy. However, weedy rice resistant to imidazolinone herbicides started to evolve three years after the first use of IMI-rice cultivars. Population genetic studies indicate that the herbicide-resistant weedy rice was mainly originated from gene flow from resistant cultivars and distributed by seed migration. The problems related with herbicide-resistant weedy rice increased the production costs of rice that forced farmers to sell or rent their land. Gene flow from cultivated rice to weedy rice has proven to be a large agricultural, economic, and social constraint in the use of herbicide-resistant technologies in rice. This problem must be taken into account for the development of new transgenic or nontransgenic rice technologies.

  17. Evolutionary and social consequences of introgression of nontransgenic herbicide resistance from rice to weedy rice in Brazil.

    PubMed

    Merotto, Aldo; Goulart, Ives C G R; Nunes, Anderson L; Kalsing, Augusto; Markus, Catarine; Menezes, Valmir G; Wander, Alcido E

    2016-08-01

    Several studies have expressed concerns about the effects of gene flow from transgenic herbicide-resistant crops to their wild relatives, but no major problems have been observed. This review describes a case study in which what has been feared in transgenics regarding gene flow has actually changed biodiversity and people's lives. Nontransgenic imidazolinone-resistant rice (IMI-rice) cultivars increased the rice grain yield by 50% in southern Brazil. This increase was beneficial for life quality of the farmers and also improved the regional economy. However, weedy rice resistant to imidazolinone herbicides started to evolve three years after the first use of IMI-rice cultivars. Population genetic studies indicate that the herbicide-resistant weedy rice was mainly originated from gene flow from resistant cultivars and distributed by seed migration. The problems related with herbicide-resistant weedy rice increased the production costs of rice that forced farmers to sell or rent their land. Gene flow from cultivated rice to weedy rice has proven to be a large agricultural, economic, and social constraint in the use of herbicide-resistant technologies in rice. This problem must be taken into account for the development of new transgenic or nontransgenic rice technologies. PMID:27468302

  18. Rice Varieties in Archaic East Asia: Reduction of Its Diversity from Past to Present Times.

    PubMed

    Kumagai, Masahiko; Kanehara, Masaaki; Shoda, Shin'ya; Fujita, Saburo; Onuki, Shizuo; Ueda, Shintaroh; Wang, Li

    2016-10-01

    The Asian cultivated rice, Oryza sativa, is one of the most important crops feeding more than a third of global population. In spite of the studies for several decades, the origin and domestication history of rice varietal groups, japonica and indica, have not been fully unveiled. Genetic information of ancient rice remains is essential for direct and exclusive insight into the domestication history of rice. We performed ancient DNA analysis of 950- to 2,800-year-old rice remains excavated from Japan and Korea. We found the presence of both japonica- and indica-type varieties in the Yayoi period and the middle ages of Japan and the middle part of Korea Peninsula 2,000 years ago. It is popularly considered that japonica has been exclusively cultivated in northern part of East Asia including Japan and Korea. Our result disclosed unexpectedly wide diversity of rice varieties in archaic East Asia. The present results from ancient rice DNA reveal an exclusive insight for the domestication history of rice which is not provided as far as contemporary rice. PMID:27461246

  19. Polymorphism in rice amylases at an early stage of seed germination.

    PubMed

    Mitsunaga, S; Kawakami, O; Numata, T; Yamaguchi, J; Fukui, K; Mitsui, T

    2001-03-01

    A polymorphism in rice amylases at an early stage of seed germination is analyzed by zymogram. In non-glutinous cultivars of rice, alpha-amylase isozymes are mainly confirmed in germinating seeds. However, in glutinous cultivars, beta-amylase isozymes, which are not confirmed in nonglutinous cultivars, make up the major part of the total amylase activity and the expression of alpha-amylases are repressed. PMID:11330685

  20. Cytoplasmic-genetic male sterility gene provides direct evidence for some hybrid rice recently evolving into weedy rice.

    PubMed

    Zhang, Jingxu; Lu, Zuomei; Dai, Weimin; Song, Xiaoling; Peng, Yufa; Valverde, Bernal E; Qiang, Sheng

    2015-05-27

    Weedy rice infests paddy fields worldwide at an alarmingly increasing rate. There is substantial evidence indicating that many weedy rice forms originated from or are closely related to cultivated rice. There is suspicion that the outbreak of weedy rice in China may be related to widely grown hybrid rice due to its heterosis and the diversity of its progeny, but this notion remains unsupported by direct evidence. We screened weedy rice accessions by both genetic and molecular marker tests for the cytoplasmic male sterility (CMS) genes (Wild abortive, WA, and Boro type, BT) most widely used in the production of indica and japonica three-line hybrid rice as a diagnostic trait of direct parenthood. Sixteen weedy rice accessions of the 358 tested (4.5%) contained the CMS-WA gene; none contained the CMS-BT gene. These 16 accessions represent weedy rices recently evolved from maternal hybrid rice derivatives, given the primarily maternal inheritance of this trait. Our results provide key direct evidence that hybrid rice can be involved in the evolution of some weedy rice accessions, but is not a primary factor in the recent outbreak of weedy rice in China.

  1. Map-Based Cloning of Seed Dormancy1-2 Identified a Gibberellin Synthesis Gene Regulating the Development of Endosperm-Imposed Dormancy in Rice.

    PubMed

    Ye, Heng; Feng, Jiuhuan; Zhang, Lihua; Zhang, Jinfeng; Mispan, Muhamad S; Cao, Zhuanqin; Beighley, Donn H; Yang, Jianchang; Gu, Xing-You

    2015-11-01

    Natural variation in seed dormancy is controlled by multiple genes mapped as quantitative trait loci in major crop or model plants. This research aimed to clone and characterize the Seed Dormancy1-2 (qSD1-2) locus associated with endosperm-imposed dormancy and plant height in rice (Oryza sativa). qSD1-2 was delimited to a 20-kb region, which contains OsGA20ox2 and had an additive effect on germination. Naturally occurring or induced loss-of-function mutations of the gibberellin (GA) synthesis gene enhanced seed dormancy and also reduced plant height. Expression of this gene in seeds (including endospermic cells) during early development increased GA accumulation to promote tissue morphogenesis and maturation programs. The mutant allele prevalent in semidwarf cultivars reduced the seed GA content by up to 2-fold at the early stage, which decelerated tissue morphogenesis including endosperm cell differentiation, delayed abscisic acid accumulation by a shift in the temporal distribution pattern, and postponed dehydration, physiological maturity, and germinability development. As the endosperm of developing seeds dominates the moisture equilibrium and desiccation status of the embryo in cereal crops, qSD1-2 is proposed to control primary dormancy by a GA-regulated dehydration mechanism. Allelic distribution of OsGA20ox2, the rice Green Revolution gene, was associated with the indica and japonica subspeciation. However, this research provided no evidence that the primitive indica- and common japonica-specific alleles at the presumably domestication-related locus functionally differentiate in plant height and seed dormancy. Thus, the evolutionary mechanism of this agriculturally important gene remains open for discussion. PMID:26373662

  2. Accumulation of long-lived mRNAs associated with germination in embryos during seed development of rice.

    PubMed

    Sano, Naoto; Ono, Hanako; Murata, Kazumasa; Yamada, Tetsuya; Hirasawa, Tadashi; Kanekatsu, Motoki

    2015-07-01

    Mature dry seeds contain translatable mRNAs called long-lived mRNAs. Early studies have shown that protein synthesis during the initial phase of seed germination occurs from long-lived mRNAs, without de novo transcription. However, the gene expression systems that generate long-lived mRNAs in seeds are not well understood. To examine the accumulation of long-lived mRNAs in developing rice embryos, germination tests using the transcriptional inhibitor actinomycin D (Act D) were performed with the Japonica rice cultivar Nipponbare. Although over 70% of embryos at 10 days after flowering (DAF) germinated in the absence of the inhibitor, germination was remarkably impaired in embryos treated with Act D. In contrast, more than 70% of embryos at 20, 25, 30 and 40 DAF germinated in the presence of Act D. The same results were obtained when another cultivar, Koshihikari, was used, indicating that the long-lived mRNAs required for germination predominantly accumulate in embryos between 10 and 20 DAF during seed development. RNA-Seq identified 529 long-lived mRNA candidates, encoding proteins such as ABA, calcium ion and phospholipid signalling-related proteins, and HSP DNA J, increased from 10 to 20 DAF and were highly abundant in 40 DAF embryos of Nipponbare and Koshihikari. We also revealed that these long-lived mRNA candidates are clearly up-regulated in 10 DAF germinating embryos after imbibition, suggesting that the accumulation of these mRNAs in embryos is indispensable for the induction of germination. The findings presented here may facilitate in overcoming irregular seed germination or producing more vigorous seedlings.

  3. Accumulation of long-lived mRNAs associated with germination in embryos during seed development of rice

    PubMed Central

    Sano, Naoto; Ono, Hanako; Murata, Kazumasa; Yamada, Tetsuya; Hirasawa, Tadashi; Kanekatsu, Motoki

    2015-01-01

    Mature dry seeds contain translatable mRNAs called long-lived mRNAs. Early studies have shown that protein synthesis during the initial phase of seed germination occurs from long-lived mRNAs, without de novo transcription. However, the gene expression systems that generate long-lived mRNAs in seeds are not well understood. To examine the accumulation of long-lived mRNAs in developing rice embryos, germination tests using the transcriptional inhibitor actinomycin D (Act D) were performed with the Japonica rice cultivar Nipponbare. Although over 70% of embryos at 10 days after flowering (DAF) germinated in the absence of the inhibitor, germination was remarkably impaired in embryos treated with Act D. In contrast, more than 70% of embryos at 20, 25, 30 and 40 DAF germinated in the presence of Act D. The same results were obtained when another cultivar, Koshihikari, was used, indicating that the long-lived mRNAs required for germination predominantly accumulate in embryos between 10 and 20 DAF during seed development. RNA-Seq identified 529 long-lived mRNA candidates, encoding proteins such as ABA, calcium ion and phospholipid signalling-related proteins, and HSP DNA J, increased from 10 to 20 DAF and were highly abundant in 40 DAF embryos of Nipponbare and Koshihikari. We also revealed that these long-lived mRNA candidates are clearly up-regulated in 10 DAF germinating embryos after imbibition, suggesting that the accumulation of these mRNAs in embryos is indispensable for the induction of germination. The findings presented here may facilitate in overcoming irregular seed germination or producing more vigorous seedlings. PMID:25941326

  4. Migration, isolation and hybridization in island crop populations: the case of Madagascar rice.

    PubMed

    Mather, Kristie A; Molina, Jeanmaire; Flowers, Jonathan M; Rubinstein, Samara; Rauh, Brad L; Lawton-Rauh, Amy; Caicedo, Ana L; McNally, Kenneth L; Purugganan, Michael D

    2010-11-01

    Understanding how crop species spread and are introduced to new areas provides insights into the nature of species range expansions. The domesticated species Oryza sativa or Asian rice is one of the key domesticated crop species in the world. The island of Madagascar off the coast of East Africa was one of the last major Old World areas of introduction of rice after the domestication of this crop species and before extensive historical global trade in this crop. Asian rice was introduced in Madagascar from India, the Malay Peninsula and Indonesia approximately 800-1400 years ago. Studies of domestication traits characteristic of the two independently domesticated Asian rice subspecies, indica and tropical japonica, suggest two major waves of migrations into Madagascar. A population genetic analysis of rice in Madagascar using sequence data from 53 gene fragments provided insights into the dynamics of island founder events during the expansion of a crop species' geographic range and introduction to novel agro-ecological environments. We observed a significant decrease in genetic diversity in rice from Madagascar when compared to those in Asia, likely the result of a bottleneck on the island. We also found a high frequency of a unique indica type in Madagascar that shows clear population differentiation from most of the sampled Asian landraces, as well as differential exchange of alleles between Asia and Madagascar populations of the tropical japonica subspecies. Finally, despite partial reproductive isolation between japonica and indica, there was evidence of indica/japonica recombination resulting from their hybridization on the island.

  5. Association of Increased Grain Iron and Zinc Concentrations with Agro-morphological Traits of Biofortified Rice

    PubMed Central

    Moreno-Moyano, Laura T.; Bonneau, Julien P.; Sánchez-Palacios, José T.; Tohme, Joseph; Johnson, Alexander A. T.

    2016-01-01

    Biofortification of rice (Oryza sativa L.) with micronutrients is widely recognized as a sustainable strategy to alleviate human iron (Fe) and zinc (Zn) deficiencies in developing countries where rice is the staple food. Constitutive overexpression of the rice nicotianamine synthase (OsNAS) genes has been successfully implemented to increase Fe and Zn concentrations in unpolished and polished rice grain. Intensive research is now needed to couple this high-micronutrient trait with high grain yields. We investigated associations of increased grain Fe and Zn concentrations with agro-morphological traits of backcross twice second filial (BC2F2) transgenic progeny carrying OsNAS1 or OsNAS2 overexpression constructs under indica/japonica and japonica/japonica genetic backgrounds. Thirteen agro-morphological traits were evaluated in BC2F2 transgenic progeny grown under hydroponic conditions. Concentrations of eight mineral nutrients (Fe, Zn, copper, manganese, calcium, magnesium, potassium, and phosphorus) in roots, stems/sheaths, non-flag leaves, flag leaves, panicles, and grain were also determined. A distance-based linear model (DistLM) was utilized to extract plant tissue nutrient predictors accounting for the largest variation in agro-morphological traits differing between transgenic and non-transgenic progeny. Overall, the BC2F2 transgenic progeny contained up to 148% higher Fe and 336% higher Zn concentrations in unpolished grain compared to non-transgenic progeny. However, unpolished grain concentrations surpassing 23 μg Fe g-1 and 40 μg Zn g-1 in BC2F2 indica/japonica progeny, and 36 μg Fe g-1 and 56 μg Zn g1 in BC2F2 japonica/japonica progeny, were associated with significant reductions in grain yield. DistLM analyses identified grain-Zn and panicle-magnesium as the primary nutrient predictors associated with grain yield reductions in the indica/japonica and japonica/japonica background, respectively. We subsequently produced polished grain from high

  6. Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs.

    PubMed

    Cheng, Chaoyang; Motohashi, Reiko; Tsuchimoto, Suguru; Fukuta, Yoshimichi; Ohtsubo, Hisako; Ohtsubo, Eiichi

    2003-01-01

    The wild rice species Oryza rufipogon with wide intraspecific variation is thought to be the progenitor of the cultivated rice species Oryza sativa with two ecotypes, japonica and indica. To determine the origin of cultivated rice, subfamily members of the rice retroposon p-SINE1, which show insertion polymorphism in the O. sativa -O. rufipogon population, were identified and used to "bar code" each of 101 cultivated and wild rice strains based on the presence or absence of the p-SINE1 members at the respective loci. A phylogenetic tree constructed based on the bar codes given to the rice strains showed that O. sativa strains were classified into two groups corresponding to japonica and indica, whereas O. rufipogon strains were in four groups, in which annual O. rufipogon strains formed a single group, differing from the perennial O. rufipogon strains of the other three groups. Japonica strains were closely related to the O. rufipogon perennial strains of one group, and the indica strains were closely related to the O. rufipogon annual strains, indicating that O. sativa has been derived polyphyletically from O. rufipogon. The subfamily members of p-SINE1 constitute a powerful tool for studying the classification and relationship of rice strains, even when one has limited knowledge of morphology, taxonomy, physiology, and biochemistry of rice strains. PMID:12519908

  7. Xanthomonas oryzae pv. oryzae Type III Effector XopN Targets OsVOZ2 and a Putative Thiamine Synthase as a Virulence Factor in Rice

    PubMed Central

    Cheong, Hoon; Kim, Chi-Yeol; Jeon, Jong-Seong; Lee, Byoung-Moo; Sun Moon, Jae; Hwang, Ingyu

    2013-01-01

    Xanthomonasoryzae pv. oryzae (Xoo) is spread systemically through the xylem tissue and causes bacterial blight in rice. We evaluated the roles of Xanthomonas outer proteins (Xop) in the Xoo strain KXO85 in a Japonica-type rice cultivar, Dongjin. Five xop gene knockout mutants (xopQKXO85, xopXKXO85, xopP1KXO85, xopP2KXO85, and xopNKXO85) were generated by EZ-Tn5 mutagenesis, and their virulence was assessed in 3-month-old rice leaves. Among these mutants, the xopNKXO85 mutant appeared to be less virulent than the wild-type KXO85; however, the difference was not statistically significant. In contrast, the xopNKXO85 mutant exhibited significantly less virulence in flag leaves after flowering than the wild-type KXO85. These observations indicate that the roles of Xop in Xoo virulence are dependent on leaf stage. We chose the xopN gene for further characterization because the xopNKXO85 mutant showed the greatest influence on virulence. We confirmed that XopNKXO85 is translocated into rice cells, and its gene expression is positively regulated by HrpX. Two rice proteins, OsVOZ2 and a putative thiamine synthase (OsXNP), were identified as targets of XopNKXO85 by yeast two-hybrid screening. Interactions between XopNKXO85 and OsVOZ2 and OsXNP were further confirmed in planta by bimolecular fluorescence complementation and in vivo pull-down assays. To investigate the roles of OsVOZ2 in interactions between rice and Xoo, we evaluated the virulence of the wild-type KXO85 and xopNKXO85 mutant in the OsVOZ2 mutant line PFG_3A-07565 of Dongjin. The wild-type KXO85 and xopNKXO85 mutant were significantly less virulent in the mutant rice line. These results indicate that XopNKXO85 and OsVOZ2 play important roles both individually and together for Xoo virulence in rice. PMID:24019919

  8. A Missense Mutation in the Zinc Finger Domain of OsCESA7 Deleteriously Affects Cellulose Biosynthesis and Plant Growth in Rice.

    PubMed

    Wang, Daofeng; Qin, Yanling; Fang, Jingjing; Yuan, Shoujiang; Peng, Lixiang; Zhao, Jinfeng; Li, Xueyong

    2016-01-01

    Rice is a model plant species for the study of cellulose biosynthesis. We isolated a mutant, S1-24, from ethyl methanesulfonate (EMS)-treated plants of the japonica rice cultivar, Nipponbare. The mutant exhibited brittle culms and other pleiotropic phenotypes such as dwarfism and partial sterility. The brittle culms resulted from reduced mechanical strength due to a defect in thickening of the sclerenchyma cell wall and reduced cellulose content in the culms of the S1-24 mutant. Map-based gene cloning and a complementation assay showed that phenotypes of the S1-24 mutant were caused by a recessive point mutation in the OsCESA7 gene, which encodes cellulose synthase A subunit 7. The missense mutation changed the highly conserved C40 to Y in the zinc finger domain. The OsCESA7 gene is expressed predominantly in the culm at the mature stage, particularly in mechanical tissues such as vascular bundles and sclerenchyma cells, consistent with the brittle phenotype in the culm. These results indicate that OsCESA7 plays an important role in cellulose biosynthesis and plant growth. PMID:27092937

  9. Functional Inactivation of Putative Photosynthetic Electron Acceptor Ferredoxin C2 (FdC2) Induces Delayed Heading Date and Decreased Photosynthetic Rate in Rice.

    PubMed

    Zhao, Juan; Qiu, Zhennan; Ruan, Banpu; Kang, Shujing; He, Lei; Zhang, Sen; Dong, Guojun; Hu, Jiang; Zeng, Dali; Zhang, Guangheng; Gao, Zhenyu; Ren, Deyong; Hu, Xingming; Chen, Guang; Guo, Longbiao; Qian, Qian; Zhu, Li

    2015-01-01

    Ferredoxin (Fd) protein as unique electron acceptor, involved in a variety of fundamental metabolic and signaling processes, which is indispensable for plant growth. The molecular mechanisms of Fd such as regulation of electron partitioning, impact of photosynthetic rate and involvement in the carbon fixing remain elusive in rice. Here we reported a heading date delay and yellowish leaf 1 (hdy1) mutant derived from Japonica rice cultivar "Nipponbare" subjected to EMS treatment. In the paddy field, the hdy1 mutant appeared at a significantly late heading date and had yellow-green leaves during the whole growth stage. Further investigation indicated that the abnormal phenotype of hdy1 was connected with depressed pigment content and photosynthetic rate. Genetic analysis results showed that the hdy1 mutant phenotype was caused by a single recessive nuclear gene mutation. Map-based cloning revealed that OsHDY1 is located on chromosome 3 and encodes an ortholog of the AtFdC2 gene. Complementation and overexpression, transgenic plants exhibited the mutant phenotype including head date, leaf color and the transcription levels of the FdC2 were completely rescued by transformation with OsHDY1. Real-time PCR revealed that the expression product of OsHDY1 was detected in almost all of the organs except root, whereas highest expression levels were observed in seeding new leaves. The lower expression levels of HDY1 and content of iron were detected in hdy1 than WT's. The FdC2::GFP was detected in the chloroplasts of rice. Real-time PCR results showed that the expression of many photosynthetic electron transfer related genes in hdy1 were higher than WT. Our results suggest that OsFdC2 plays an important role in photosynthetic rate and development of heading date by regulating electron transfer and chlorophyll content in rice.

  10. Functional Inactivation of Putative Photosynthetic Electron Acceptor Ferredoxin C2 (FdC2) Induces Delayed Heading Date and Decreased Photosynthetic Rate in Rice.

    PubMed

    Zhao, Juan; Qiu, Zhennan; Ruan, Banpu; Kang, Shujing; He, Lei; Zhang, Sen; Dong, Guojun; Hu, Jiang; Zeng, Dali; Zhang, Guangheng; Gao, Zhenyu; Ren, Deyong; Hu, Xingming; Chen, Guang; Guo, Longbiao; Qian, Qian; Zhu, Li

    2015-01-01

    Ferredoxin (Fd) protein as unique electron acceptor, involved in a variety of fundamental metabolic and signaling processes, which is indispensable for plant growth. The molecular mechanisms of Fd such as regulation of electron partitioning, impact of photosynthetic rate and involvement in the carbon fixing remain elusive in rice. Here we reported a heading date delay and yellowish leaf 1 (hdy1) mutant derived from Japonica rice cultivar "Nipponbare" subjected to EMS treatment. In the paddy field, the hdy1 mutant appeared at a significantly late heading date and had yellow-green leaves during the whole growth stage. Further investigation indicated that the abnormal phenotype of hdy1 was connected with depressed pigment content and photosynthetic rate. Genetic analysis results showed that the hdy1 mutant phenotype was caused by a single recessive nuclear gene mutation. Map-based cloning revealed that OsHDY1 is located on chromosome 3 and encodes an ortholog of the AtFdC2 gene. Complementation and overexpression, transgenic plants exhibited the mutant phenotype including head date, leaf color and the transcription levels of the FdC2 were completely rescued by transformation with OsHDY1. Real-time PCR revealed that the expression product of OsHDY1 was detected in almost all of the organs except root, whereas highest expression levels were observed in seeding new leaves. The lower expression levels of HDY1 and content of iron were detected in hdy1 than WT's. The FdC2::GFP was detected in the chloroplasts of rice. Real-time PCR results showed that the expression of many photosynthetic electron transfer related genes in hdy1 were higher than WT. Our results suggest that OsFdC2 plays an important role in photosynthetic rate and development of heading date by regulating electron transfer and chlorophyll content in rice. PMID:26598971

  11. Loop Nucleotide Polymorphism in a Putative miRNA Precursor Associated with Seed Length in Rice (Oryza sativa L.)

    PubMed Central

    Wang, Chunming; Ye, Jian; Tang, Weijie; Liu, Zhiyi; Zhu, Chengsong; Wang, Maoqing; Wan, Jianmin

    2013-01-01

    The terminal loop region of primary miRNA transcripts is an important determinant controlling miRNA function in human, animals and plants. However, the effects of polymorphisms in loop region of miRNA precusors on phenotypic variation have not been reported, especially on agronomic traits in rice. From rice japonica variety Koshihikari and indica Guichao2, we isolated a precursor of putative miRNA osa-MIR2923a. We detected a GG/AA polymorphism in the loop structure from japonica and indica rice varieties, which was corresponding to japonica/indica rice differentiation. By using high-resolution melting (HRM) analysis, we measured the polymorphisms in a RIL (recombinant inbred lines) population derived from japonica variety Koshihikari and indica Guichao2. We found that the GG/AA polymorphism in the osa-MIR2923a loop was correlated to grain length and length-width ratio. We further found the significant association between seed length and GG/AA polymorphism in a population consisting of 72 rice landraces. Three targets were predicted, whose expressions showed significant differences between the two varieties. Our results suggested that the putative miRNA precursor and the three target genes could play functional roles for indica/japonica seed differentiation. PMID:23847440

  12. [EST-SSR identification of Lonicera japonica Thunb].

    PubMed

    Jiang, Chao; Yuan, Yuan; Liu, Gui-Ming; Huang, Lu-Qi; Wang, Xu-Min; Yu, Jun; Chen, Min

    2012-06-01

    Simple and effective methods are needed for the identification of Chinese medicinal material species and their variety. Lonicera japonica Thunb. is one of Chinese herbal medicines widely demanded. A total of 3 705 EST-SSRs of L. japonica and 2 818 EST-SSRs of L. japonica var. chinensis Thunb. were identified from EST database in our lab. In average, there was one EST-SSR per 4.05 kb in L. japonica ESTs and per 7.49 kb in L. japonica var. chinensis ESTs, separately. The identified SSRs in L. japonica were consisted of 51.98% dinucleotide and 34.61% trinucleotide repeats, while SSRs in L. japonica var. chinensis had 57.45% dinucleotide and 30.09% trinucleotide. The results reviewed that the classes AG/TC and GAG/TCT were predominant in the dinucleotide motifs and the trinucleotide motifs, respectively. Total 87 EST-SSRs were identified of significant difference between L. japonica and L. japonica var. chinensis. PCR products were obtained from 52 L. japonica samples in 13 out of 15 SSR markers tested. The polymorphism in L. japonica, L. japonica var. chinensis and other honeysuckles could be distinguished by three markers (jp.ssr4, jp.ssr64 and jp.ssr65) tested.

  13. Registration of 'Jazzman' aromatic long-grain rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Jazzman is a U.S.-bred Jasmine-type, soft-cooking aromatic long-grain rice cultivar (Oryza sativa L.) that is glabrous and has no seed dormancy. It was developed from a single cross using a modified pedigree breeding method at the Rice Research Station, Louisiana State University Agriculture Center,...

  14. Addressing the dilemmas of measuring amylose in rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Amylose content is a parameter that correlates with the cooking behaviour of rice. It is measured at the earliest possible stages of rice improvement programs to enable breeders to build the foundations of appropriate grain quality during cultivar development. Amylose is usually quantified by absorb...

  15. An active DNA transposon nDart causing leaf variegation and mutable dwarfism and its related elements in rice.

    PubMed

    Tsugane, Kazuo; Maekawa, Masahiko; Takagi, Kyoko; Takahara, Hiroyuki; Qian, Qian; Eun, Chang-Ho; Iida, Shigeru

    2006-01-01

    While characterized mutable alleles caused by DNA transposons have been abundant in maize since the discovery of Dissociation conferring variegation by Barbara McClintock, only a few mutable alleles have been described in rice even though the rice genome contains various transposons. Here, we show that a spontaneous mutable virescent allele, pyl-v, is caused by the disruption of the nuclear-coded essential chloroplast protease gene, OsClpP5, due to insertion of a 607-bp non-autonomous DNA transposon, non-autonomous DNA-based active rice transposon one (nDart1), belonging to the hAT superfamily. The transposition of nDart1 can be induced by crossing with a line containing an autonomous element, aDart, and stabilized by segregating out of aDart. We also identified a novel mutable dwarf allele thl-m caused by an insertion of nDart1. The japonica cultivar Nipponbare carries no aDart, although it contains epigenetically silenced Dart element(s), which can be activated by 5-azacytidine. Nipponbare bears four subgroups of about 3.6-kb Dart-like sequences, three of which contain potential transposase genes, and around 3.6-kb elements without an apparent transposase gene, as well as three subgroups of about 0.6-kb nDart1-related elements that are all internal deletions of the Dart-like sequences. Both nDart1 and 3.6-kb Dart-like elements were also present in indica varieties 93-11 and Kasalath. nDart1 appears to be the most active mutagen among nDart1-related elements contributing to generating natural variations. A candidate for an autonomous element, aDart, and a possible application of nDart1 for transposon tagging are discussed. PMID:16367953

  16. An active DNA transposon nDart causing leaf variegation and mutable dwarfism and its related elements in rice.

    PubMed

    Tsugane, Kazuo; Maekawa, Masahiko; Takagi, Kyoko; Takahara, Hiroyuki; Qian, Qian; Eun, Chang-Ho; Iida, Shigeru

    2006-01-01

    While characterized mutable alleles caused by DNA transposons have been abundant in maize since the discovery of Dissociation conferring variegation by Barbara McClintock, only a few mutable alleles have been described in rice even though the rice genome contains various transposons. Here, we show that a spontaneous mutable virescent allele, pyl-v, is caused by the disruption of the nuclear-coded essential chloroplast protease gene, OsClpP5, due to insertion of a 607-bp non-autonomous DNA transposon, non-autonomous DNA-based active rice transposon one (nDart1), belonging to the hAT superfamily. The transposition of nDart1 can be induced by crossing with a line containing an autonomous element, aDart, and stabilized by segregating out of aDart. We also identified a novel mutable dwarf allele thl-m caused by an insertion of nDart1. The japonica cultivar Nipponbare carries no aDart, although it contains epigenetically silenced Dart element(s), which can be activated by 5-azacytidine. Nipponbare bears four subgroups of about 3.6-kb Dart-like sequences, three of which contain potential transposase genes, and around 3.6-kb elements without an apparent transposase gene, as well as three subgroups of about 0.6-kb nDart1-related elements that are all internal deletions of the Dart-like sequences. Both nDart1 and 3.6-kb Dart-like elements were also present in indica varieties 93-11 and Kasalath. nDart1 appears to be the most active mutagen among nDart1-related elements contributing to generating natural variations. A candidate for an autonomous element, aDart, and a possible application of nDart1 for transposon tagging are discussed.

  17. Hop Cultivars and Breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pest management decision making in hops varies among cultivars. Historically, the primary objective of hop breeding programs has been to increase the yield or characteristics associated with either bittering (high alpha-acids) or aroma (unique volatile oil profiles) cultivars. Other factors consid...

  18. Selection Under Domestication: Evidence for a Sweep in the Rice Waxy Genomic Region

    PubMed Central

    Olsen, Kenneth M.; Caicedo, Ana L.; Polato, Nicholas; McClung, Anna; McCouch, Susan; Purugganan, Michael D.

    2006-01-01

    Rice (Oryza sativa) was cultivated by Asian Neolithic farmers >11,000 years ago, and different cultures have selected for divergent starch qualities in the rice grain during and after the domestication process. An intron 1 splice donor site mutation of the Waxy gene is responsible for the absence of amylose in glutinous rice varieties. This mutation appears to have also played an important role in the origin of low amylose, nonglutinous temperate japonica rice varieties, which form a primary component of Northeast Asian cuisines. Waxy DNA sequence analyses indicate that the splice donor mutation is prevalent in temperate japonica rice varieties, but rare or absent in tropical japonica, indica, aus, and aromatic varieties. Sequence analysis across a 500-kb genomic region centered on Waxy reveals patterns consistent with a selective sweep in the temperate japonicas associated with the mutation. The size of the selective sweep (>250 kb) indicates very strong selection in this region, with an inferred selection coefficient that is higher than similar estimates from maize domestication genes or wild species. These findings demonstrate that selection pressures associated with crop domestication regimes can exceed by one to two orders of magnitude those observed for genes under even strong selection in natural systems. PMID:16547098

  19. Viscoelastic Properties of Waxy and Non-Waxy Rice Flours, Their Fat and Protein-Free Starch, and the Microstructure of Their Cooked Kernels

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Physicochemistry and structural studies of two types of japonica rice, low amylose Calmochi-101 (CM101) and intermediate amylose M-202 (M202), were conducted to determine similarities and differences between the rices perhaps attributable to amylose content differences. The rheological behavior of ...

  20. A Putative Gene sbe3-rs for Resistant Starch Mutated from SBE3 for Starch Branching Enzyme in Rice (Oryza sativa L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Foods high in resistant starch (RS) are beneficial to prevent various diseases including diabetes, colon cancer, diarrhea and chronic renal or hepatic diseases. Elevated RS in rice is important for public health since rice is a staple food for half of the world’s population. A japonica mutant ‘Jiang...

  1. Arsenite stress variably stimulates pro-oxidant enzymes, anatomical deformities, photosynthetic pigment reduction, and antioxidants in arsenic-tolerant and sensitive rice seedlings.

    PubMed

    Tripathi, Preeti; Singh, Rana Pratap; Sharma, Yogesh Kumar; Tripathi, Rudra Deo

    2015-07-01

    Contamination of arsenic (As) in rice (Oryza sativa L.) paddies and subsequent uptake by rice plants is a serious concern, because rice is a staple crop for millions of people. Identification of As toxicity and detoxification mechanisms in paddy rice cultivars would help to reduce As-associated risk. Arsenic tolerance and susceptibility mechanisms were investigated in 2 differential As-accumulating rice genotypes, Triguna and IET-4786, selected from initial screening of 52 rice cultivars as an As-tolerant and an As-sensitive cultivar, respectively, on the basis of root and shoot length during various arsenite (AsIII) exposures (0-50 μM). Indicators of oxidative stress, such as pro-oxidant enzymes (reduced nicotinamide adenine dinucleotide phosphate [NADPH] oxidase and ascorbate oxidase) and nitric oxide, were more numerous in the sensitive cultivar than in the tolerant cultivar. Arsenic-induced anatomical deformities were frequent in the sensitive cultivar, showing more distorted and flaccid root cells than the tolerant cultivar. Chlorophyll and carotenoid synthesis were inhibited in both cultivars, although the decline was more prominent in the sensitive cultivar at higher doses of As. Furthermore, the tolerant cultivar tolerated As stress by producing more antioxidants, such as proline, sustaining the ratio of ascorbate, dehydroascorbate, and glutathione peroxidase (GPX) activity as well as As detoxifying enzymes arsenate reductase, whereas these respective metabolic activities declined in sensitive cultivar, resulting in greater susceptibility to As toxicity. PMID:25683332

  2. Effects of Sophora japonica flowers (Huaihua) on cerebral infarction.

    PubMed

    Chen, Hsiang-Ni; Hsieh, Ching-Liang

    2010-01-01

    The dried flowers and buds of Sophora japonica are used as a medicinal herb in China, Japan and Korea to treat bleeding hemorrhoids and hematemesis. This article presents an overview of the effects of Sophora japonica on cerebral infarction based on literature searched from Medline, PubMed, Cochrane Library and the China National Knowledge Infrastructure (CNKI). Sophora japonica contains both anti-hemorrhagic and anti-hemostatic substances. Sophora japonica reduces cerebral infarction partly as a result of its anti-oxidative and anti-inflammatory activities. Previous studies found that Sophora japonica reduced the size of cerebral infarction and neurological deficits and reduced microglial activation, interleukin-1β release and number of apoptotic cells in ischemia-reperfusion injured Sprague-Dawley rats. Further study is required to determine the relationship between Sophora japonica-mediated reduction in cerebral infarction size and the effects of Sophora japonica on platelet aggregation and cardiovascular function. PMID:20875105

  3. Characterization of a new rice glutelin gene GluD-1 expressed in the starchy endosperm

    PubMed Central

    Kawakatsu, Taiji; Yamamoto, Masayuki P.; Hirose, Sakiko; Yano, Masahiro; Takaiwa, Fumio

    2008-01-01

    A new glutelin gene, designated GluD-1, has been discovered by comparing the seed storage proteins from 48 japonica and indica rice cultivars on SDS-PAGE gels. Evidence that GluD-1 is a member of the glutelin family was provided by Western blots using anti-glutelin antiserum and by mapping the gene to the chromosomal glutelin gene cluster. The limited GluD-1 size polymorphism among the rice varieties is due to amino acid substitutions rather than to post-transcriptional modification. GluD-1 is maximally expressed in the starchy endosperm starting at 5 d after flowering (DAF) and increasing through 30 DAF, a major difference from the other glutelins which are primarily expressed in the subaleurone from 10–16 DAF. Only about 0.2 kb of the GluD-1 promoter was sufficient to confer inner starchy endosperm-specific expression. The 0.2 kb truncated GluD-1 promoter contains a bifactorial endosperm box consisting of a truncated GCN4 motif (TGA(G/C)TCA) and AAAG Prolamin box (P box), and ACGT and AACA motifs as cis-regulatory elements. Gel retardation assays and trans-activation experiments indicated that the truncated GCN4 and P box are specifically recognized by RISBZ1 b-ZIP and RPBF Dof activators in vitro, respectively, and are synergistically transactivated, indicating that combinatorial interactions of these motifs are involved in essential endosperm-specific regulation. Furthermore, deviation from the cognate GCN4 motif alters tissue-specific expression in the inner starchy endosperm to include other endosperm tissues. PMID:18980953

  4. Rice brans, rice bran oils, and rice hulls: composition, food and industrial uses, and bioactivities in humans, animals, and cells.

    PubMed

    Friedman, Mendel

    2013-11-13

    Rice plants produce bioactive rice brans and hulls that have been reported to have numerous health-promoting effects in cells, animals, and humans. The main objective of this review is to consolidate and integrate the widely scattered information on the composition and the antioxidative, anti-inflammatory, and immunostimulating effects of rice brans from different rice cultivars, rice bran oils derived from rice brans, rice hulls, liquid rice hull smoke derived from rice hulls, and some of their bioactive compounds. As part of this effort, this paper also presents brief summaries on the preparation of health-promoting foods including bread, corn flakes, frankfurters, ice cream, noodles, pasta, tortillas, and zero-trans-fat shortening as well as industrial products such bioethanol and biodiesel fuels. Also covered are antibiotic, antiallergic, anticarcinogenic, antidiabetic, cardiovascular, allelochemical, and other beneficial effects and the mechanisms of the bioactivities. The results show that food-compatible and safe formulations with desirable nutritional and biological properties can be used to develop new multifunctional foods as well as bioethanol and biodiesel fuel. The overlapping aspects are expected to contribute to a better understanding of the potential impact of the described health-promoting potential of the rice-derived brans, oils, and hulls in food and medicine. Such an understanding will enhance nutrition and health and benefit the agricultural and industrial economies. PMID:24175575

  5. De novo Transcriptome Analysis of Rhizoctonia solani AG1 IA Strain Early Invasion in Zoysia japonica Root.

    PubMed

    Zhu, Chen; Ai, Lin; Wang, Li; Yin, Pingping; Liu, Chenglan; Li, Shanshan; Zeng, Huiming

    2016-01-01

    Zoysia japonica brown spot was caused by necrotrophic fungus Rhizoctonia solani invasion, which led to severe financial loss in city lawn and golf ground maintenance. However, little was known about the molecular mechanism of R. solani pathogenicity in Z. japonica. In this study we examined early stage interaction between R. solani AG1 IA strain and Z. japonica cultivar "Zenith" root by cell ultra-structure analysis, pathogenesis-related proteins assay and transcriptome analysis to explore molecular clues for AG1 IA strain pathogenicity in Z. japonica. No obvious cell structure damage was found in infected roots and most pathogenesis-related protein activities showedg a downward trend especially in 36 h post inoculation, which exhibits AG1 IA strain stealthy invasion characteristic. According to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database classification, most DEGs in infected "Zenith" roots dynamically changed especially in three aspects, signal transduction, gene translation, and protein synthesis. Total 3422 unigenes of "Zenith" root were predicted into 14 kinds of resistance (R) gene class. Potential fungal resistance related unigenes of "Zenith" root were involved in ligin biosynthesis, phytoalexin synthesis, oxidative burst, wax biosynthesis, while two down-regulated unigenes encoding leucine-rich repeat receptor protein kinase and subtilisin-like protease might be important for host-derived signal perception to AG1 IA strain invasion. According to Pathogen Host Interaction (PHI) database annotation, 1508 unigenes of AG1 IA strain were predicted and classified into 37 known pathogen species, in addition, unigenes encoding virulence, signaling, host stress tolerance, and potential effector were also predicted. This research uncovered transcriptional profiling during the early phase interaction between R. solani AG1 IA strain and Z. japonica, and will greatly help identify key pathogenicity of AG1 IA strain. PMID:27242730

  6. De novo Transcriptome Analysis of Rhizoctonia solani AG1 IA Strain Early Invasion in Zoysia japonica Root

    PubMed Central

    Zhu, Chen; Ai, Lin; Wang, Li; Yin, Pingping; Liu, Chenglan; Li, Shanshan; Zeng, Huiming

    2016-01-01

    Zoysia japonica brown spot was caused by necrotrophic fungus Rhizoctonia solani invasion, which led to severe financial loss in city lawn and golf ground maintenance. However, little was known about the molecular mechanism of R. solani pathogenicity in Z. japonica. In this study we examined early stage interaction between R. solani AG1 IA strain and Z. japonica cultivar “Zenith” root by cell ultra-structure analysis, pathogenesis-related proteins assay and transcriptome analysis to explore molecular clues for AG1 IA strain pathogenicity in Z. japonica. No obvious cell structure damage was found in infected roots and most pathogenesis-related protein activities showedg a downward trend especially in 36 h post inoculation, which exhibits AG1 IA strain stealthy invasion characteristic. According to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database classification, most DEGs in infected “Zenith” roots dynamically changed especially in three aspects, signal transduction, gene translation, and protein synthesis. Total 3422 unigenes of “Zenith” root were predicted into 14 kinds of resistance (R) gene class. Potential fungal resistance related unigenes of “Zenith” root were involved in ligin biosynthesis, phytoalexin synthesis, oxidative burst, wax biosynthesis, while two down-regulated unigenes encoding leucine-rich repeat receptor protein kinase and subtilisin-like protease might be important for host-derived signal perception to AG1 IA strain invasion. According to Pathogen Host Interaction (PHI) database annotation, 1508 unigenes of AG1 IA strain were predicted and classified into 37 known pathogen species, in addition, unigenes encoding virulence, signaling, host stress tolerance, and potential effector were also predicted. This research uncovered transcriptional profiling during the early phase interaction between R. solani AG1 IA strain and Z. japonica, and will greatly help identify key pathogenicity of AG1 IA strain

  7. De novo Transcriptome Analysis of Rhizoctonia solani AG1 IA Strain Early Invasion in Zoysia japonica Root.

    PubMed

    Zhu, Chen; Ai, Lin; Wang, Li; Yin, Pingping; Liu, Chenglan; Li, Shanshan; Zeng, Huiming

    2016-01-01

    Zoysia japonica brown spot was caused by necrotrophic fungus Rhizoctonia solani invasion, which led to severe financial loss in city lawn and golf ground maintenance. However, little was known about the molecular mechanism of R. solani pathogenicity in Z. japonica. In this study we examined early stage interaction between R. solani AG1 IA strain and Z. japonica cultivar "Zenith" root by cell ultra-structure analysis, pathogenesis-related proteins assay and transcriptome analysis to explore molecular clues for AG1 IA strain pathogenicity in Z. japonica. No obvious cell structure damage was found in infected roots and most pathogenesis-related protein activities showedg a downward trend especially in 36 h post inoculation, which exhibits AG1 IA strain stealthy invasion characteristic. According to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database classification, most DEGs in infected "Zenith" roots dynamically changed especially in three aspects, signal transduction, gene translation, and protein synthesis. Total 3422 unigenes of "Zenith" root were predicted into 14 kinds of resistance (R) gene class. Potential fungal resistance related unigenes of "Zenith" root were involved in ligin biosynthesis, phytoalexin synthesis, oxidative burst, wax biosynthesis, while two down-regulated unigenes encoding leucine-rich repeat receptor protein kinase and subtilisin-like protease might be important for host-derived signal perception to AG1 IA strain invasion. According to Pathogen Host Interaction (PHI) database annotation, 1508 unigenes of AG1 IA strain were predicted and classified into 37 known pathogen species, in addition, unigenes encoding virulence, signaling, host stress tolerance, and potential effector were also predicted. This research uncovered transcriptional profiling during the early phase interaction between R. solani AG1 IA strain and Z. japonica, and will greatly help identify key pathogenicity of AG1 IA strain.

  8. A flavonol tetraglycoside from Sophora japonica seeds.

    PubMed

    Wang, Jing-Hua; Lou, Feng-Chang; Wang, Ya-Lin; Tang, Yu-Ping

    2003-06-01

    A flavonol tetraglycoside, kaempferol 3-O-alpha-L-rhamnopyranosyl(1-->6)-beta-D-glucopyranosyl(1-->2)- beta-D-glucopyranoside-7-O-alpha-L rhamnopyranoside, together with nine known compounds were isolated from the seeds of Sophora japonica L. Their structures were elucidated on the basis of spectral and chemical evidence. PMID:12770599

  9. The Complex History of the Domestication of Rice

    PubMed Central

    Sweeney, Megan; McCouch, Susan

    2007-01-01

    Background Rice has been found in archaeological sites dating to 8000 bc, although the date of rice domestication is a matter of continuing debate. Two species of domesticated rice, Oryza sativa (Asian) and Oryza glaberrima (African) are grown globally. Numerous traits separate wild and domesticated rices including changes in: pericarp colour, dormancy, shattering, panicle architecture, tiller number, mating type and number and size of seeds. Scope Genetic studies using diverse methodologies have uncovered a deep population structure within domesticated rice. Two main groups, the indica and japonica subspecies, have been identified with several subpopulations existing within each group. The antiquity of the divide has been estimated at more than 100 000 years ago. This date far precedes domestication, supporting independent domestications of indica and japonica from pre-differentiated pools of the wild ancestor. Crosses between subspecies display sterility and segregate for domestication traits, indicating that different populations are fixed for different networks of alleles conditioning these traits. Numerous domestication QTLs have been identified in crosses between the subspecies and in crosses between wild and domesticated accessions of rice. Many of the QTLs cluster in the same genomic regions, suggesting that a single gene with pleiotropic effects or that closely linked clusters of genes underlie these QTL. Recently, several domestication loci have been cloned from rice, including the gene controlling pericarp colour and two loci for shattering. The distribution and evolutionary history of these genes gives insight into the domestication process and the relationship between the subspecies. Conclusions The evolutionary history of rice is complex, but recent work has shed light on the genetics of the transition from wild (O. rufipogon and O. nivara) to domesticated (O. sativa) rice. The types of genes involved and the geographic and genetic distribution of

  10. Archaeological and genetic insights into the origins of domesticated rice.

    PubMed

    Gross, Briana L; Zhao, Zhijun

    2014-04-29

    Rice (Oryza sativa) is one of the most important cereal grains in the world today and serves as a staple food source for more than half of the world's population. Research into when, where, and how rice was brought into cultivation and eventually domesticated, along with its development into a staple food source, is thus essential. These questions have been a point of nearly continuous research in both archaeology and genetics, and new information has continually come to light as theory, data acquisition, and analytical techniques have advanced over time. Here, we review the broad history of our scientific understanding of the rice domestication process from both an archaeological and genetic perspective and examine in detail the information that has come to light in both of these fields in the last 10 y. Current findings from genetics and archaeology are consistent with the domestication of O. sativa japonica in the Yangtze River valley of southern China. Interestingly, although it appears rice was cultivated in the area by as early 8000 BP, the key domestication trait of nonshattering was not fixed for another 1,000 y or perhaps longer. Rice was also cultivated in India as early as 5000 BP, but the domesticated indica subspecies currently appears to be a product of the introgression of favorable alleles from japonica. These findings are reshaping our understanding of rice domestication and also have implications for understanding the complex evolutionary process of plant domestication. PMID:24753573

  11. Functional properties as affected by laboratory-scale parboiling of rough rice and brown rice.

    PubMed

    Patindol, J; Newton, J; Wang, Y-J

    2008-10-01

    Rough rice (RR) is the conventional feedstock for parboiling. The use of brown rice (BR) instead of RR is gaining interest because it results in shorter processing time and lower energy requirement. This study compared the functional properties of milled parboiled rice under different parboiling conditions from RR and BR. Presoaked RR and BR from cultivars Bolivar, Cheniere, Dixiebelle, and Wells were parboiled under mild (20 min, 100 degrees C, 0 kPa) and severe (20 min, 120 degrees C, 98 kPa) laboratory-scale conditions. Head rice yield improved on the RR and BR samples subjected to severe parboiling and was comparable to that of a commercially parboiled sample. Mild parboiling of BR resulted in lower head rice yields. Parboiling generally resulted in decreased head rice whiteness, decreased apparent amylose, increased total lipid, and sparingly changed protein content. Under the same parboiling conditions, the extent of starch gelatinization was higher for BR compared to RR as manifested by some distinct differences in pasting and thermal properties. The cooking characteristics (water uptake ratio, leached materials, and volumetric expansion) and cooked rice texture (hardness and stickiness) of RR and BR subjected to severe parboiling were fairly comparable. Differences in parboiled rice functional properties due to cultivar effect were evident. PMID:19019108

  12. RNA-Seq analysis of urea nutrition responsive transcriptome of Oryza sativa elite indica cultivar RP Bio 226

    PubMed Central

    Reddy, Mettu Madhavi; Ulaganathan, Kandasamy

    2015-01-01

    Rice yield is greatly influenced by the nitrogen and rice varieties show variation in yield. For understanding the role of urea nutrition in the yield of elite indica rice cultivar RPBio-226, the urea responsive transcriptome was sequenced and analyzed. The raw reads and the Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GDKM00000000. The version described in this paper is the first version, GDKM01000000. PMID:26697348

  13. De Novo Transcriptome Analysis to Identify Anthocyanin Biosynthesis Genes Responsible for Tissue-Specific Pigmentation in Zoysiagrass (Zoysia japonica Steud.)

    PubMed Central

    Ahn, Jong Hwa; Kim, June-Sik; Kim, Seungill; Soh, Hye Yeon; Shin, Hosub; Jang, Hosung; Ryu, Ju Hyun; Kim, Ahyeong; Yun, Kil-Young; Kim, Shinje; Kim, Ki Sun; Choi, Doil; Huh, Jin Hoe

    2015-01-01

    Zoysiagrass (Zoysia japonica Steud.) is commonly found in temperate climate regions and widely used for lawns, in part, owing to its uniform green color. However, some zoysiagrass cultivars accumulate red to purple pigments in their spike and stolon tissues, thereby decreasing the aesthetic value. Here we analyzed the anthocyanin contents of two zoysiagrass cultivars ‘Anyang-jungji’ (AJ) and ‘Greenzoa’ (GZ) that produce spikes and stolons with purple and green colors, respectively, and revealed that cyanidin and petunidin were primarily accumulated in the pigmented tissues. In parallel, we performed a de novo transcriptome assembly and identified differentially expressed genes between the two cultivars. We found that two anthocyanin biosynthesis genes encoding anthocyanidin synthase (ANS) and dihydroflavonol 4-reductase (DFR) were preferentially upregulated in the purple AJ spike upon pigmentation. Both ANS and DFR genes were also highly expressed in other zoysiagrass cultivars with purple spikes and stolons, but their expression levels were significantly low in the cultivars with green tissues. We observed that recombinant ZjDFR1 and ZjANS1 proteins successfully catalyze the conversions of dihydroflavonols into leucoanthocyanidins and leucoanthocyanidins into anthocyanidins, respectively. These findings strongly suggest that upregulation of ANS and DFR is responsible for tissue-specific anthocyanin biosynthesis and differential pigmentation in zoysiagrass. The present study also demonstrates the feasibility of a de novo transcriptome analysis to identify the key genes associated with specific traits, even in the absence of reference genome information. PMID:25905914

  14. De Novo Transcriptome Analysis to Identify Anthocyanin Biosynthesis Genes Responsible for Tissue-Specific Pigmentation in Zoysiagrass (Zoysia japonica Steud.).

    PubMed

    Ahn, Jong Hwa; Kim, June-Sik; Kim, Seungill; Soh, Hye Yeon; Shin, Hosub; Jang, Hosung; Ryu, Ju Hyun; Kim, Ahyeong; Yun, Kil-Young; Kim, Shinje; Kim, Ki Sun; Choi, Doil; Huh, Jin Hoe

    2015-01-01

    Zoysiagrass (Zoysia japonica Steud.) is commonly found in temperate climate regions and widely used for lawns, in part, owing to its uniform green color. However, some zoysiagrass cultivars accumulate red to purple pigments in their spike and stolon tissues, thereby decreasing the aesthetic value. Here we analyzed the anthocyanin contents of two zoysiagrass cultivars 'Anyang-jungji' (AJ) and 'Greenzoa' (GZ) that produce spikes and stolons with purple and green colors, respectively, and revealed that cyanidin and petunidin were primarily accumulated in the pigmented tissues. In parallel, we performed a de novo transcriptome assembly and identified differentially expressed genes between the two cultivars. We found that two anthocyanin biosynthesis genes encoding anthocyanidin synthase (ANS) and dihydroflavonol 4-reductase (DFR) were preferentially upregulated in the purple AJ spike upon pigmentation. Both ANS and DFR genes were also highly expressed in other zoysiagrass cultivars with purple spikes and stolons, but their expression levels were significantly low in the cultivars with green tissues. We observed that recombinant ZjDFR1 and ZjANS1 proteins successfully catalyze the conversions of dihydroflavonols into leucoanthocyanidins and leucoanthocyanidins into anthocyanidins, respectively. These findings strongly suggest that upregulation of ANS and DFR is responsible for tissue-specific anthocyanin biosynthesis and differential pigmentation in zoysiagrass. The present study also demonstrates the feasibility of a de novo transcriptome analysis to identify the key genes associated with specific traits, even in the absence of reference genome information. PMID:25905914

  15. The roots of future rice harvests.

    PubMed

    Ahmadi, Nourollah; Audebert, Alain; Bennett, Malcolm J; Bishopp, Anthony; de Oliveira, Antonio Costa; Courtois, Brigitte; Diedhiou, Abdala; Diévart, Anne; Gantet, Pascal; Ghesquière, Alain; Guiderdoni, Emmanuel; Henry, Amelia; Inukai, Yoshiaki; Kochian, Leon; Laplaze, Laurent; Lucas, Mikael; Luu, Doan Trung; Manneh, Baboucarr; Mo, Xiaorong; Muthurajan, Raveendran; Périn, Christophe; Price, Adam; Robin, Sabariappan; Sentenac, Hervé; Sine, Bassirou; Uga, Yusaku; Véry, Anne Aliénor; Wissuwa, Matthias; Wu, Ping; Xu, Jian

    2014-12-01

    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 to be deeply affected by climate instability and resource scarcity in the coming decades, building rice cultivars harboring root systems that can maintain performance by capturing water and nutrient resources unevenly distributed is a major breeding target. Taking advantage of gathering a community of rice root biologists in a Global Rice Science Partnership workshop held in Montpellier, France, we present here the recent progresses accomplished in this area and focal points where an international network of laboratories should direct their efforts. PMID:26224558

  16. Variation in cooking and eating quality traits in Japanese rice germplasm accessions.

    PubMed

    Hori, Kiyosumi; Suzuki, Keitaro; Iijima, Ken; Ebana, Kaworu

    2016-03-01

    The eating quality of cooked rice is important and determines its market price and consumer acceptance. To comprehensively describe the variation of eating quality in 183 rice germplasm accessions, we evaluated 33 eating-quality traits including amylose and protein contents, pasting properties of rice flour, and texture of cooked rice grains. All eating-quality traits varied widely in the germplasm accessions. Principal-components analysis (PCA) revealed that allelic differences in the Wx gene explained the largest proportion of phenotypic variation of the eating-quality traits. In 146 accessions of non-glutinous temperate japonica rice, PCA revealed that protein content and surface texture of the cooked rice grains significantly explained phenotypic variations of the eating-quality traits. An allelic difference based on simple sequence repeats, which was located near a quantitative trait locus (QTL) on the short arm of chromosome 3, was associated with differences in the eating quality of non-glutinous temperate japonica rice. These results suggest that eating quality is controlled by genetic factors, including the Wx gene and the QTL on chromosome 3, in Japanese rice accessions. These genetic factors have been consciously selected for eating quality during rice breeding programs in Japan. PMID:27162502

  17. Variation in cooking and eating quality traits in Japanese rice germplasm accessions

    PubMed Central

    Hori, Kiyosumi; Suzuki, Keitaro; Iijima, Ken; Ebana, Kaworu

    2016-01-01

    The eating quality of cooked rice is important and determines its market price and consumer acceptance. To comprehensively describe the variation of eating quality in 183 rice germplasm accessions, we evaluated 33 eating-quality traits including amylose and protein contents, pasting properties of rice flour, and texture of cooked rice grains. All eating-quality traits varied widely in the germplasm accessions. Principal-components analysis (PCA) revealed that allelic differences in the Wx gene explained the largest proportion of phenotypic variation of the eating-quality traits. In 146 accessions of non-glutinous temperate japonica rice, PCA revealed that protein content and surface texture of the cooked rice grains significantly explained phenotypic variations of the eating-quality traits. An allelic difference based on simple sequence repeats, which was located near a quantitative trait locus (QTL) on the short arm of chromosome 3, was associated with differences in the eating quality of non-glutinous temperate japonica rice. These results suggest that eating quality is controlled by genetic factors, including the Wx gene and the QTL on chromosome 3, in Japanese rice accessions. These genetic factors have been consciously selected for eating quality during rice breeding programs in Japan. PMID:27162502

  18. Genetic control of inflorescence architecture during rice domestication.

    PubMed

    Zhu, Zuofeng; Tan, Lubin; Fu, Yongcai; Liu, Fengxia; Cai, Hongwei; Xie, Daoxin; Wu, Feng; Wu, Jianzhong; Matsumoto, Takashi; Sun, Chuanqing

    2013-01-01

    Inflorescence architecture is a key agronomical factor determining grain yield, and thus has been a major target of cereal crop domestication. Transition from a spread panicle typical of ancestral wild rice (Oryza rufipogon Griff.) to the compact panicle of present cultivars (O. sativa L.) was a crucial event in rice domestication. Here we show that the spread panicle architecture of wild rice is controlled by a dominant gene, OsLG1, a previously reported SBP-domain transcription factor that controls rice ligule development. Association analysis indicates that a single-nucleotide polymorphism-6 in the OsLG1 regulatory region led to a compact panicle architecture in cultivars during rice domestication. We speculate that the cis-regulatory mutation can fine-tune the spatial expression of the target gene, and that selection of cis-regulatory mutations might be an efficient strategy for crop domestication. PMID:23884108

  19. Genetic control of inflorescence architecture during rice domestication.

    PubMed

    Zhu, Zuofeng; Tan, Lubin; Fu, Yongcai; Liu, Fengxia; Cai, Hongwei; Xie, Daoxin; Wu, Feng; Wu, Jianzhong; Matsumoto, Takashi; Sun, Chuanqing

    2013-01-01

    Inflorescence architecture is a key agronomical factor determining grain yield, and thus has been a major target of cereal crop domestication. Transition from a spread panicle typical of ancestral wild rice (Oryza rufipogon Griff.) to the compact panicle of present cultivars (O. sativa L.) was a crucial event in rice domestication. Here we show that the spread panicle architecture of wild rice is controlled by a dominant gene, OsLG1, a previously reported SBP-domain transcription factor that controls rice ligule development. Association analysis indicates that a single-nucleotide polymorphism-6 in the OsLG1 regulatory region led to a compact panicle architecture in cultivars during rice domestication. We speculate that the cis-regulatory mutation can fine-tune the spatial expression of the target gene, and that selection of cis-regulatory mutations might be an efficient strategy for crop domestication.

  20. Gene limiting cadmium accumulation in rice.

    PubMed

    Ueno, Daisei; Yamaji, Naoki; Kono, Izumi; Huang, Chao Feng; Ando, Tsuyu; Yano, Masahiro; Ma, Jian Feng

    2010-09-21

    Intake of toxic cadmium (Cd) from rice caused Itai-itai disease in the past and it is still a threat for human health. Therefore, control of the accumulation of Cd from soil is an important food-safety issue, but the molecular mechanism for the control is unknown. Herein, we report a gene (OsHMA3) responsible for low Cd accumulation in rice that was isolated from a mapping population derived from a cross between a high and low Cd-accumulating cultivar. The gene encodes a transporter belonging to the P(1B)-type ATPase family, but shares low similarity with other members. Heterologous expression in yeast showed that the transporter from the low-Cd cultivar is functional, but the transporter from the high-Cd cultivar had lost its function, probably because of the single amino acid mutation. The transporter is mainly expressed in the tonoplast of root cells at a similar level in both the low and high Cd-accumulating cultivars. Overexpression of the functional gene from the low Cd-accumulating cultivar selectively decreased accumulation of Cd, but not other micronutrients in the grain. Our results indicated that OsHMA3 from the low Cd-accumulating cultivar limits translocation of Cd from the roots to the above-ground tissues by selectively sequestrating Cd into the root vacuoles.

  1. Manipulation of the rice L-galactose pathway: evaluation of the effects of transgene overexpression on ascorbate accumulation and abiotic stress tolerance.

    PubMed

    Zhang, Gui-Yun; Liu, Ru-Ru; Zhang, Chang-Quan; Tang, Ke-Xuan; Sun, Ming-Fa; Yan, Guo-Hong; Liu, Qiao-Quan

    2015-01-01

    Ascorbic acid (AsA) is the most abundant water-soluble antioxidant in plants, and it plays a crucial role in plant growth, development and abiotic stress tolerance. In the present study, six key Arabidopsis or rapeseed genes involved in AsA biosynthesis were constitutively overexpressed in an elite Japonica rice cultivar. These genes encoded the GDP-mannose pyrophosphorylase (GMP), GDP-mannose-3',5'-epimerase (GME), GDP-L-galactose phosphorylase (GGP), L-galactose-1-phosphate phosphatase (GPP), L-galactose dehydrogenase (GDH), and L-galactono-1,4-lactone dehydrogenase (GalLDH). The effects of transgene expression on rice leaf AsA accumulation were carefully evaluated. In homozygous transgenic seedlings, AtGGP transgenic lines had the highest AsA contents (2.55-fold greater than the empty vector transgenic control), followed by the AtGME and AtGDH transgenic lines. Moreover, with the exception of the AtGPP lines, the increased AsA content also provoked an increase in the redox state (AsA/DHA ratio). To evaluate salt tolerance, AtGGP and AtGME transgenic seedlings were exposed to salt stress for one week. The relative plant height, root length and fresh weight growth rates were significantly higher for the transgenic lines compared with the control plants. Altogether, our results suggest that GGP may be a key rate-limiting step in rice AsA biosynthesis, and the plants with elevated AsA contents demonstrated enhanced tolerance for salt stress.

  2. In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches.

    PubMed

    Lorieux, Mathias; Blein, Mélisande; Lozano, Jaime; Bouniol, Mathieu; Droc, Gaétan; Diévart, Anne; Périn, Christophe; Mieulet, Delphine; Lanau, Nadège; Bès, Martine; Rouvière, Claire; Gay, Céline; Piffanelli, Pietro; Larmande, Pierre; Michel, Corinne; Barnola, Isabelle; Biderre-Petit, Corinne; Sallaud, Christophe; Perez, Pascual; Bourgis, Fabienne; Ghesquière, Alain; Gantet, Pascal; Tohme, Joe; Morel, Jean Benoit; Guiderdoni, Emmanuel

    2012-06-01

    We report here the molecular and phenotypic features of a library of 31,562 insertion lines generated in the model japonica cultivar Nipponbare of rice (Oryza sativa L.), called Oryza Tag Line (OTL). Sixteen thousand eight hundred and fourteen T-DNA and 12,410 Tos17 discrete insertion sites have been characterized in these lines. We estimate that 8686 predicted gene intervals--i.e. one-fourth to one-fifth of the estimated rice nontransposable element gene complement--are interrupted by sequence-indexed T-DNA (6563 genes) and/or Tos17 (2755 genes) inserts. Six hundred and forty-three genes are interrupted by both T-DNA and Tos17 inserts. High quality of the sequence indexation of the T2 seed samples was ascertained by several approaches. Field evaluation under agronomic conditions of 27,832 OTL has revealed that 18.2% exhibit at least one morphophysiological alteration in the T1 progeny plants. Screening 10,000 lines for altered response to inoculation by the fungal pathogen Magnaporthe oryzae allowed to observe 71 lines (0.7%) developing spontaneous lesions simulating disease mutants and 43 lines (0.4%) exhibiting an enhanced disease resistance or susceptibility. We show here that at least 3.5% (four of 114) of these alterations are tagged by the mutagens. The presence of allelic series of sequence-indexed mutations in a gene among OTL that exhibit a convergent phenotype clearly increases the chance of establishing a linkage between alterations and inserts. This convergence approach is illustrated by the identification of the rice ortholog of AtPHO2, the disruption of which causes a lesion-mimic phenotype owing to an over-accumulation of phosphate, in nine lines bearing allelic insertions. PMID:22369597

  3. In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches.

    PubMed

    Lorieux, Mathias; Blein, Mélisande; Lozano, Jaime; Bouniol, Mathieu; Droc, Gaétan; Diévart, Anne; Périn, Christophe; Mieulet, Delphine; Lanau, Nadège; Bès, Martine; Rouvière, Claire; Gay, Céline; Piffanelli, Pietro; Larmande, Pierre; Michel, Corinne; Barnola, Isabelle; Biderre-Petit, Corinne; Sallaud, Christophe; Perez, Pascual; Bourgis, Fabienne; Ghesquière, Alain; Gantet, Pascal; Tohme, Joe; Morel, Jean Benoit; Guiderdoni, Emmanuel

    2012-06-01

    We report here the molecular and phenotypic features of a library of 31,562 insertion lines generated in the model japonica cultivar Nipponbare of rice (Oryza sativa L.), called Oryza Tag Line (OTL). Sixteen thousand eight hundred and fourteen T-DNA and 12,410 Tos17 discrete insertion sites have been characterized in these lines. We estimate that 8686 predicted gene intervals--i.e. one-fourth to one-fifth of the estimated rice nontransposable element gene complement--are interrupted by sequence-indexed T-DNA (6563 genes) and/or Tos17 (2755 genes) inserts. Six hundred and forty-three genes are interrupted by both T-DNA and Tos17 inserts. High quality of the sequence indexation of the T2 seed samples was ascertained by several approaches. Field evaluation under agronomic conditions of 27,832 OTL has revealed that 18.2% exhibit at least one morphophysiological alteration in the T1 progeny plants. Screening 10,000 lines for altered response to inoculation by the fungal pathogen Magnaporthe oryzae allowed to observe 71 lines (0.7%) developing spontaneous lesions simulating disease mutants and 43 lines (0.4%) exhibiting an enhanced disease resistance or susceptibility. We show here that at least 3.5% (four of 114) of these alterations are tagged by the mutagens. The presence of allelic series of sequence-indexed mutations in a gene among OTL that exhibit a convergent phenotype clearly increases the chance of establishing a linkage between alterations and inserts. This convergence approach is illustrated by the identification of the rice ortholog of AtPHO2, the disruption of which causes a lesion-mimic phenotype owing to an over-accumulation of phosphate, in nine lines bearing allelic insertions.

  4. Restricting the above ground sink corrects the root/shoot ratio and substantially boosts the yield potential per panicle in field-grown rice (Oryza sativa L.).

    PubMed

    Nada, Reham M; Abogadallah, Gaber M

    2016-04-01

    Rice has shallow, weak roots, but it is unknown how much increase in yield potential could be achieved if the root/shoot ratio is corrected. Removing all tillers except the main one, in a japonica (Sakha 101) and an indica (IR64) rice cultivar, instantly increased the root/shoot ratio from 0.21 to 1.16 in Sakha 101 and from 0.16 to 1.46 in IR64. Over 30 days after detillering, the root/shoot ratios of the detillered plants decreased to 0.49 in Sakha 101 and 0.46 in IR64 but remained significantly higher than in the controls. The detillered plants showed two- or fourfold increase in the main tiller fresh weight, as a consequence of more positive midday leaf relative water content (RWC), and consistently higher rates of stomatal conductance and photosynthesis, but not transpiration, compared with the controls. The enhanced photosynthesis in Sakha 101 after detillering resulted from both improved water status and higher Rubisco contents whereas in IR64, increasing the Rubisco content did not contribute to improving photosynthesis. Detillering did not increase the carbohydrate contents of leaves but prevented starch depletion at the end of grain filling. The leaf protein content during vegetative and reproductive stages, the grain filling rate, the number of filled grains per panicle were greatly improved, bringing about 38.3 and 35.9% increase in the harvested grain dry weight per panicle in Sakha 101 and IR64, respectively. We provide evidence that improving the root performance by increasing the root/shoot ratio would eliminate the current limitations to photosynthesis and growth in rice. PMID:26296302

  5. Manipulation of the Rice L-Galactose Pathway: Evaluation of the Effects of Transgene Overexpression on Ascorbate Accumulation and Abiotic Stress Tolerance

    PubMed Central

    Zhang, Gui-Yun; Liu, Ru-Ru; Zhang, Chang-Quan; Tang, Ke-Xuan; Sun, Ming-Fa; Yan, Guo-Hong; Liu, Qiao-Quan

    2015-01-01

    Ascorbic acid (AsA) is the most abundant water-soluble antioxidant in plants, and it plays a crucial role in plant growth, development and abiotic stress tolerance. In the present study, six key Arabidopsis or rapeseed genes involved in AsA biosynthesis were constitutively overexpressed in an elite Japonica rice cultivar. These genes encoded the GDP-mannose pyrophosphorylase (GMP), GDP-mannose-3',5'-epimerase (GME), GDP-L-galactose phosphorylase (GGP), L-galactose-1-phosphate phosphatase (GPP), L-galactose dehydrogenase (GDH), and L-galactono-1,4-lactone dehydrogenase (GalLDH). The effects of transgene expression on rice leaf AsA accumulation were carefully evaluated. In homozygous transgenic seedlings, AtGGP transgenic lines had the highest AsA contents (2.55-fold greater than the empty vector transgenic control), followed by the AtGME and AtGDH transgenic lines. Moreover, with the exception of the AtGPP lines, the increased AsA content also provoked an increase in the redox state (AsA/DHA ratio). To evaluate salt tolerance, AtGGP and AtGME transgenic seedlings were exposed to salt stress for one week. The relative plant height, root length and fresh weight growth rates were significantly higher for the transgenic lines compared with the control plants. Altogether, our results suggest that GGP may be a key rate-limiting step in rice AsA biosynthesis, and the plants with elevated AsA contents demonstrated enhanced tolerance for salt stress. PMID:25938231

  6. Restricting the above ground sink corrects the root/shoot ratio and substantially boosts the yield potential per panicle in field-grown rice (Oryza sativa L.).

    PubMed

    Nada, Reham M; Abogadallah, Gaber M

    2016-04-01

    Rice has shallow, weak roots, but it is unknown how much increase in yield potential could be achieved if the root/shoot ratio is corrected. Removing all tillers except the main one, in a japonica (Sakha 101) and an indica (IR64) rice cultivar, instantly increased the root/shoot ratio from 0.21 to 1.16 in Sakha 101 and from 0.16 to 1.46 in IR64. Over 30 days after detillering, the root/shoot ratios of the detillered plants decreased to 0.49 in Sakha 101 and 0.46 in IR64 but remained significantly higher than in the controls. The detillered plants showed two- or fourfold increase in the main tiller fresh weight, as a consequence of more positive midday leaf relative water content (RWC), and consistently higher rates of stomatal conductance and photosynthesis, but not transpiration, compared with the controls. The enhanced photosynthesis in Sakha 101 after detillering resulted from both improved water status and higher Rubisco contents whereas in IR64, increasing the Rubisco content did not contribute to improving photosynthesis. Detillering did not increase the carbohydrate contents of leaves but prevented starch depletion at the end of grain filling. The leaf protein content during vegetative and reproductive stages, the grain filling rate, the number of filled grains per panicle were greatly improved, bringing about 38.3 and 35.9% increase in the harvested grain dry weight per panicle in Sakha 101 and IR64, respectively. We provide evidence that improving the root performance by increasing the root/shoot ratio would eliminate the current limitations to photosynthesis and growth in rice.

  7. Polishing and parboiling effect on the nutritional and technological properties of pigmented rice.

    PubMed

    Paiva, Flávia Fernandes; Vanier, Nathan Levien; Berrios, Jose De J; Pinto, Vânia Zanella; Wood, Delilah; Williams, Tina; Pan, James; Elias, Moacir Cardoso

    2016-01-15

    This study aims to evaluate the effects of polishing and parboiling on proximate composition, structure, phenolic compounds, antioxidant activity, cooking time and hardness of IAC-600 black rice cultivar and MPB-10 red rice lineage. Proximate analysis and light micrographs revealed higher migration of red rice proteins than black rice proteins to the endosperm as a result of parboiling. Parboiling reduced the ash content of red rice while no difference was determined in black rice. Gelatinized starch granules from both genotypes showed similar appearance. There was a decrease in relative crystallinity on both black and red rice subjected to parboiling, which was an indicative of crystallites disruption. Polishing removed more than 90% of free phenolics for both genotypes, while parboiling allowed the partial preservation of free phenolics content in polished rice. Parboiling induced an increase in the cooking time of red rice, but a decrease in the cooking time of black rice. PMID:26258708

  8. [Major domestication traits in Asian rice].

    PubMed

    Ou, Shu-Jun; Wang, Hong-Ru; Chu, Cheng-Cai

    2012-11-01

    Rice (Oryza sativa L.) is an excellent model plant in elucidation of cereal domestication. Loss of seed shattering, weakened dormancy, and changes in plant architecture were thought to be three key events in the rice domestication and creating the high-yield, uniform-germinating, and densely-planting modern rice. Loss of shattering is considered to be the direct morphological evidence for identifying domesticated rice. Two major shattering QTLs, Sh4 and qSH1, have displayed different domestication histories. Weakened seed dormancy is essential for synchronous germination in agricultural production. Genes Sdr4, qSD7-1, and qSD12 impose a global and complementary adaptation strategies in controlling seed dormancy. The prostate growth habit of wild rice is an adaptation to disturbed habitats, while the erect growth habit of rice cultivars meet the needs of compact planting, and such a plant architecture is mainly controlled by PROG1. The outcrossing habit of wild rice promotes propagation of domestication genes among different populations, while the self-pollinating habit of cultivated rice facilitates fixation of domestication genes. Currently, the researches on rice domestication mainly focus on individual genes or multiple neutral markers, and much less attention has been paid to the evolution of network controlling domestication traits. With the progress in functional genomics research, the molecular mechanism of domestication traits is emerging. Rice domestication researches based on network will be more comprehensive and better reflect rice domestica-tion process. Here, we reviewed most progresses in molecular mechanisms of rice domestication traits, in order to provide the new insights for rice domestication and molecular breeding.

  9. Effect of hydrothermal processing on antioxidant contents and capacities in pigmented rice (Oryza sativa L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Purple and red bran rice cultivars (Oryza sativa L.) are rich sources of antioxidants including lipophilic antioxidants (vitamin E homologues and '-oryzanol), soluble phenolics (including anthocyanidins and proanthocyanidins), and cell-wall-bound phenolics. This study investigated impacts of hydroth...

  10. Mitochondrial genome of Japanese angel shark Squatina japonica (Chondrichthyes: Squatinidae).

    PubMed

    Chai, Aihong; Yamaguchi, Atsuko; Furumitsu, Keisuke; Zhang, Jie

    2016-01-01

    Squatina japonica belonging to the monogenetic family Squatinidae is endemic to the Northwest Pacific. The complete mitochondrial genome sequence of S. japonica is 16,689 bp long and comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. The base composition of the genome is 31.10% A, 31.04% T, 24.42% C, and 13.43% G. The geographic clade and phylogenetic relationship of S. japonica are ambiguous. Therefore, studying the complete mitochondrial genome of S. japonica is highly important to understand the aforementioned aspect and to analyze the conservation genetics in the genus Squatina.

  11. Rice antioxidants: phenolic acids, flavonoids, anthocyanins, proanthocyanidins, tocopherols, tocotrienols, γ-oryzanol, and phytic acid

    PubMed Central

    Goufo, Piebiep; Trindade, Henrique

    2014-01-01

    Epidemiological studies suggested that the low incidence of certain chronic diseases in rice-consuming regions of the world might be associated with the antioxidant compound contents of rice. The molecules with antioxidant activity contained in rice include phenolic acids, flavonoids, anthocyanins, proanthocyanidins, tocopherols, tocotrienols, γ-oryzanol, and phytic acid. This review provides information on the contents of these compounds in rice using a food composition database built from compiling data from 316 papers. The database provides access to information that would have otherwise remained hidden in the literature. For example, among the four types of rice ranked by color, black rice varieties emerged as those exhibiting the highest antioxidant activities, followed by purple, red, and brown rice varieties. Furthermore, insoluble compounds appear to constitute the major fraction of phenolic acids and proanthocyanidins in rice, but not of flavonoids and anthocyanins. It is clear that to maximize the intake of antioxidant compounds, rice should be preferentially consumed in the form of bran or as whole grain. With respect to breeding, japonica rice varieties were found to be richer in antioxidant compounds compared with indica rice varieties. Overall, rice grain fractions appear to be rich sources of antioxidant compounds. However, on a whole grain basis and with the exception of γ-oryzanol and anthocyanins, the contents of antioxidants in other cereals appear to be higher than those in rice. PMID:24804068

  12. The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication.

    PubMed

    Wang, Hongru; Xu, Xun; Vieira, Filipe Garrett; Xiao, Yunhua; Li, Zhikang; Wang, Jun; Nielsen, Rasmus; Chu, Chengcai

    2016-07-01

    Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in humans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice (Oryza sativa L.), which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5× and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SNPs in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice, japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.

  13. Rice methylmercury exposure and mitigation: a comprehensive review.

    PubMed

    Rothenberg, Sarah E; Windham-Myers, Lisamarie; Creswell, Joel E

    2014-08-01

    Rice cultivation practices from field preparation to post-harvest transform rice paddies into hot spots for microbial mercury methylation, converting less-toxic inorganic mercury to more-toxic methylmercury, which is likely translocated to rice grain. This review includes 51 studies reporting rice total mercury and/or methylmercury concentrations, based on rice (Orzya sativa) cultivated or purchased in 15 countries. Not surprisingly, both rice total mercury and methylmercury levels were significantly higher in polluted sites compared to non-polluted sites (Wilcoxon rank sum, p<0.001). However, rice percent methylmercury (of total mercury) did not differ statistically between polluted and non-polluted sites (Wilcoxon rank sum, p=0.35), suggesting comparable mercury methylation rates in paddy soil across these sites and/or similar accumulation of mercury species for these rice cultivars. Studies characterizing the effects of rice cultivation under more aerobic conditions were reviewed to determine the mitigation potential of this practice. Rice management practices utilizing alternating wetting and drying (instead of continuous flooding) caused soil methylmercury levels to spike, resulting in a strong methylmercury pulse after fields were dried and reflooded; however, it is uncertain whether this led to increased translocation of methylmercury from paddy soil to rice grain. Due to the potential health risks, it is advisable to investigate this issue further, and to develop separate water management strategies for mercury polluted and non-polluted sites, in order to minimize methylmercury exposure through rice ingestion.

  14. Rice methylmercury exposure and mitigation: a comprehensive review

    USGS Publications Warehouse

    Rothenberg, Sarah E.; Windham-Myers, Lisamarie; Creswell, Joel E.

    2014-01-01

    Rice cultivation practices from field preparation to post-harvest transform rice paddies into hot spots for microbial mercury methylation, converting less-toxic inorganic mercury to more-toxic methylmercury, which is likely translocated to rice grain. This review includes 51 studies reporting rice total mercury and/or methylmercury concentrations, based on rice (Orzya sativa) cultivated or purchased in 15 countries. Not surprisingly, both rice total mercury and methylmercury levels were significantly higher in polluted sites compared to non-polluted sites (Wilcoxon rank sum, p<0.001). However, rice percent methylmercury (of total mercury) did not differ statistically between polluted and non-polluted sites (Wilcoxon rank sum, p=0.35), suggesting comparable mercury methylation rates in paddy soil across these sites and/or similar accumulation of mercury species for these rice cultivars. Studies characterizing the effects of rice cultivation under more aerobic conditions were reviewed to determine the mitigation potential of this practice. Rice management practices utilizing alternating wetting and drying (instead of continuous flooding) caused soil methylmercury levels to spike, resulting in a strong methylmercury pulse after fields were dried and reflooded; however, it is uncertain whether this led to increased translocation of methylmercury from paddy soil to rice grain. Due to the potential health risks, it is advisable to investigate this issue further, and to develop separate water management strategies for mercury polluted and non-polluted sites, in order to minimize methylmercury exposure through rice ingestion.

  15. Rice Methylmercury Exposure and Mitigation: A Comprehensive Review

    PubMed Central

    Rothenberg, Sarah E.; Windham-Myers, Lisamarie; Creswell, Joel E.

    2014-01-01

    Rice cultivation practices from field preparation to post-harvest transform rice paddies into hot spots for microbial mercury methylation, converting less-toxic inorganic mercury to more-toxic methylmercury, which is likely translocated to rice grain. This review includes 51 studies reporting rice total mercury and/or methylmercury concentrations, based on rice cultivated or purchased in 15 countries. Not surprisingly, both rice total mercury and methylmercury levels were significantly higher in polluted sites compared to non-polluted sites (Wilcoxon rank sum, p<0.001). However, rice percent methylmercury (of total mercury) did not differ statistically between polluted and non-polluted sites (Wilcoxon rank sum, p=0.35), suggesting comparable mercury methylation rates in paddy soil across these sites and/or similar accumulation of mercury species for these rice cultivars. Studies characterizing the effect of rice cultivation under more aerobic conditions were reviewed to determine the mitigation potential of this practice. Rice management practices utilizing alternating wetting and drying (instead of continuous flooding) caused soil methylmercury levels to spike, resulting in a strong methylmercury pulse after fields were dried and reflooded; however, it is uncertain whether this led to increased translocation of methylmercury from paddy soil to rice grain. Due to the potential health risks, it is advisable to investigate this issue further, and to develop separate water management strategies for mercury polluted and non-polluted sites, which minimize methylmercury exposure through rice ingestion. PMID:24972509

  16. Rice methylmercury exposure and mitigation: a comprehensive review.

    PubMed

    Rothenberg, Sarah E; Windham-Myers, Lisamarie; Creswell, Joel E

    2014-08-01

    Rice cultivation practices from field preparation to post-harvest transform rice paddies into hot spots for microbial mercury methylation, converting less-toxic inorganic mercury to more-toxic methylmercury, which is likely translocated to rice grain. This review includes 51 studies reporting rice total mercury and/or methylmercury concentrations, based on rice (Orzya sativa) cultivated or purchased in 15 countries. Not surprisingly, both rice total mercury and methylmercury levels were significantly higher in polluted sites compared to non-polluted sites (Wilcoxon rank sum, p<0.001). However, rice percent methylmercury (of total mercury) did not differ statistically between polluted and non-polluted sites (Wilcoxon rank sum, p=0.35), suggesting comparable mercury methylation rates in paddy soil across these sites and/or similar accumulation of mercury species for these rice cultivars. Studies characterizing the effects of rice cultivation under more aerobic conditions were reviewed to determine the mitigation potential of this practice. Rice management practices utilizing alternating wetting and drying (instead of continuous flooding) caused soil methylmercury levels to spike, resulting in a strong methylmercury pulse after fields were dried and reflooded; however, it is uncertain whether this led to increased translocation of methylmercury from paddy soil to rice grain. Due to the potential health risks, it is advisable to investigate this issue further, and to develop separate water management strategies for mercury polluted and non-polluted sites, in order to minimize methylmercury exposure through rice ingestion. PMID:24972509

  17. RiceCAP: Development of molecular markers associated with long grain milling yield

    Technology Transfer Automated Retrieval System (TEKTRAN)

    U.S. rice breeders are focused on developing new cultivars that have high yield and high milling quality. Using traditional breeding methods, it takes approximately ten years to develop a new cultivar. Development of molecular markers that are closely linked to traits of economic value will increase...

  18. Lonicerae Japonicae Flos and Lonicerae Flos: A Systematic Pharmacology Review

    PubMed Central

    Li, Yujie; Cai, Weiyan; Weng, Xiaogang; Li, Qi; Wang, Yajie; Chen, Ying; Zhang, Wei; Yang, Qing; Guo, Yan; Zhu, Xiaoxin; Wang, Hainan

    2015-01-01

    Lonicerae japonicae flos, a widely used traditional Chinese medicine (TCM), has been used for several thousand years in China. Chinese Pharmacopeia once included Lonicerae japonicae flos of Caprifoliaceae family and plants of the same species named Lonicerae flos in general in the same group. Chinese Pharmacopeia (2005 Edition) lists Lonicerae japonicae flos and Lonicerae flos under different categories, although they have the similar history of efficacy. In this study, we research ancient books of TCM, 4 main databases of Chinese academic journals, and MEDLINE/PubMed to verify the origins and effects of Lonicerae japonicae flos and Lonicerae flos in traditional medicine and systematically summarized the research data in light of modern pharmacology and toxicology. Our results show that Lonicerae japonicae flos and Lonicerae flos are similar pharmacologically, but they also differ significantly in certain aspects. A comprehensive systematic review and a standard comparative pharmacological study of Lonicerae japonicae flos and Lonicerae flos as well as other species of Lonicerae flos support their clinical safety and application. Our study provides evidence supporting separate listing of Lonicerae japonicae flos and Lonicerae flos in Chinese Pharmacopeia as well as references for revision of relevant pharmacopeial records dealing with traditional efficacy of Lonicerae japonicae flos and Lonicerae flos. PMID:26257818

  19. Arsenic biotransformation and volatilization in transgenic rice.

    PubMed

    Meng, Xiang-Yan; Qin, Jie; Wang, Li-Hong; Duan, Gui-Lan; Sun, Guo-Xin; Wu, Hui-Lan; Chu, Cheng-Cai; Ling, Hong-Qing; Rosen, Barry P; Zhu, Yong-Guan

    2011-07-01

    • Biotransformation of arsenic includes oxidation, reduction, methylation, and conversion to more complex organic arsenicals. Members of the class of arsenite (As(III)) S-adenosylmethyltransferase enzymes catalyze As(III) methylation to a variety of mono-, di-, and trimethylated species, some of which are less toxic than As(III) itself. However, no methyltransferase gene has been identified in plants. • Here, an arsM gene from the soil bacterium Rhodopseudomonas palustris was expressed in Japonica rice (Oryza sativa) cv Nipponbare, and the transgenic rice produced methylated arsenic species, which were measured by inductively coupled plasma mass spectrometry (ICP-MS) and high-performance liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICP-MS). • Both monomethylarsenate (MAs(V)) and dimethylarsenate (DMAs(V)) were detected in the roots and shoots of transgenic rice. After 12 d exposure to As(III), the transgenic rice gave off 10-fold greater volatile arsenicals. • The present study demonstrates that expression of an arsM gene in rice induces arsenic methylation and volatilization, theoretically providing a potential stratagem for phytoremediation. PMID:21517874

  20. [Bioinformatics analysis of DNA demethylase genes in Lonicera japonica Thunb].

    PubMed

    Qi, Lin-jie; Yuan, Yuan; Wu, Chong; Huang, Lu-qi; Chen, Ping

    2015-03-01

    The DNA demethylase genes are widespread in plants. Four DNA demethylase genes (LJDME1, LJDME2, LJDME3 and LJDME4) were obtained from transcriptome dataset of Lonicera japonica Thunb by using bioinformatics methods and the proteins' physicochemical properties they encoded were predicted. The phylogenetic tree showed that the four DNA demethylase genes and Arabidopsis thaliana DME had a close relationship. The result of gene expression model showed that four DNA demethylase genes were different between species. The expression levels of LJDME1 and LJDME2 were even more higher in Lonicera japonica var. chinensis than those in L. japonica. LJDME] and LJDME2 maybe regulate the active compounds of L. japonica. This study aims to lay a foundation for further understanding of the function of DNA demethylase genes in L. japonica.

  1. [Yield formation of different single-season rice (Oryza sativa L. ) types and its relationships with meteorological factors in Yunnan Province of Southwest China].

    PubMed

    Zhong, Chu; Zhu, Ying-Mo; Zhu, Yong; Zhu, Bin; Zhang, Mao-Song; Xu, Meng-Ying

    2013-10-01

    By using the 1994-2010 observation data of paddy rice growth period and yield from 14 agro-meteorological stations at different altitudes in Yunnan Province, this paper studied the rice yield formation and the effects of meteorological factors on low-yield rice yield components. According to the systematic cluster analysis of rice yield components and the rice types at the 14 stations, the rice was divided into 4 types, i. e., low-yield japonica rice, low-yield indica rice, high-yield japonica rice, and high-yield indica rice. The analysis of the yield components of the 4 rice types showed that there was a significant positive correlation between the spikelet number per square meter (sqm) and the rice yield. The yield of low-yield japonica was mainly affected by the seed setting rate and the spikelet number per sqm. For the other three rice types, the spikelet number per sqm had greater effects on the rice yield. The low-yield japonica rice was mainly affected by low temperature. At booting stage, low temperature decreased the spikelet number and the productive panicle number of unit sqm. At booting and flowering stages, low temperature increased the empty grain rate, and the effects of average temperature, average maximum temperature, and cold accumulated temperature were greater. At pre-milk stage, low temperature increased the unfilled grain rate, and meanwhile, decreased the 1000-grain mass. The yield components of low-yield indica rice were obviously affected by multiple meteorological factors. A certain degree of warming at tillering and jointing stages was not beneficial to the increase of productive panicle number per sqm of low-yield indica rice, but the more sunshine hours and the greater average diurnal temperature range at tillering stage was beneficial to the increase of the productive panicle number per sqm. There was a parabolic relationship between the temperature and sunshine hours at tillering and jointing stages and the spikelet number per

  2. [Yield formation of different single-season rice (Oryza sativa L. ) types and its relationships with meteorological factors in Yunnan Province of Southwest China].

    PubMed

    Zhong, Chu; Zhu, Ying-Mo; Zhu, Yong; Zhu, Bin; Zhang, Mao-Song; Xu, Meng-Ying

    2013-10-01

    By using the 1994-2010 observation data of paddy rice growth period and yield from 14 agro-meteorological stations at different altitudes in Yunnan Province, this paper studied the rice yield formation and the effects of meteorological factors on low-yield rice yield components. According to the systematic cluster analysis of rice yield components and the rice types at the 14 stations, the rice was divided into 4 types, i. e., low-yield japonica rice, low-yield indica rice, high-yield japonica rice, and high-yield indica rice. The analysis of the yield components of the 4 rice types showed that there was a significant positive correlation between the spikelet number per square meter (sqm) and the rice yield. The yield of low-yield japonica was mainly affected by the seed setting rate and the spikelet number per sqm. For the other three rice types, the spikelet number per sqm had greater effects on the rice yield. The low-yield japonica rice was mainly affected by low temperature. At booting stage, low temperature decreased the spikelet number and the productive panicle number of unit sqm. At booting and flowering stages, low temperature increased the empty grain rate, and the effects of average temperature, average maximum temperature, and cold accumulated temperature were greater. At pre-milk stage, low temperature increased the unfilled grain rate, and meanwhile, decreased the 1000-grain mass. The yield components of low-yield indica rice were obviously affected by multiple meteorological factors. A certain degree of warming at tillering and jointing stages was not beneficial to the increase of productive panicle number per sqm of low-yield indica rice, but the more sunshine hours and the greater average diurnal temperature range at tillering stage was beneficial to the increase of the productive panicle number per sqm. There was a parabolic relationship between the temperature and sunshine hours at tillering and jointing stages and the spikelet number per

  3. Combined herbicide and saline stress differentially modulates hormonal regulation and antioxidant defense system in Oryza sativa cultivars.

    PubMed

    Islam, Faisal; Ali, Basharat; Wang, Jian; Farooq, Muhammad A; Gill, Rafaqat A; Ali, Shafaqat; Wang, Danying; Zhou, Weijun

    2016-10-01

    Plants are simultaneously exposed to a combination of biotic and abiotic stresses in field conditions. Crops respond to the combined stress in a unique way which cannot be understood by extrapolating the results of individual stress. In the present study, effects of individual and combined stress of herbicide (2,4-dichlorophenoxyacetic acid) and salinity (NaCl) on two Oryza sativa cultivars (ZJ 88 and XS 134) were investigated. Both herbicide and saline stress affected the plant growth differentially and produced oxidative stress in rice cultivars. Interestingly, the combination of herbicide and salinity showed a significant protection to both rice cultivars by reducing ROS (H2O2, O2(-)) and lipid peroxidation through modulation of enzymatic (SOD, POD, CAT and APX) and non-enzymatic (TSP, sugars, phenolic and proline) antioxidants. In addition, active regulation of transcript levels of genes encoding Na(+) and K(+) (OsHKT1;5, OsLti6a,b, OsHKT2;1, OsSOS1, OsCNGC1, OsNHX1 and OsAKT1) transporter proteins reduced sodium and enhanced potassium accumulation under combined stress, resulted a better growth and ionic homeostasis in both rice cultivars. The production of ABA and IAA was significantly higher in cultivar XS 134 compared to cultivar ZJ 88 under control conditions. However, combined herbicide and saline stress enhanced the accumulation of phytohormones (IAA and ABA) and transcription of ethylene in cultivar ZJ 88, which might be one of the factors responsible for poor salt tolerance in sensitive cultivar. These findings indicated that herbicide application under saline stress confers tolerance to salinity in rice cultivars, likely by reducing oxidative damage, modulating mineral absorption, upgradation of antioxidant defense and by dynamic regulation of key genes involved in Na(+) and K(+) homeostasis in plants. PMID:27258572

  4. Combined herbicide and saline stress differentially modulates hormonal regulation and antioxidant defense system in Oryza sativa cultivars.

    PubMed

    Islam, Faisal; Ali, Basharat; Wang, Jian; Farooq, Muhammad A; Gill, Rafaqat A; Ali, Shafaqat; Wang, Danying; Zhou, Weijun

    2016-10-01

    Plants are simultaneously exposed to a combination of biotic and abiotic stresses in field conditions. Crops respond to the combined stress in a unique way which cannot be understood by extrapolating the results of individual stress. In the present study, effects of individual and combined stress of herbicide (2,4-dichlorophenoxyacetic acid) and salinity (NaCl) on two Oryza sativa cultivars (ZJ 88 and XS 134) were investigated. Both herbicide and saline stress affected the plant growth differentially and produced oxidative stress in rice cultivars. Interestingly, the combination of herbicide and salinity showed a significant protection to both rice cultivars by reducing ROS (H2O2, O2(-)) and lipid peroxidation through modulation of enzymatic (SOD, POD, CAT and APX) and non-enzymatic (TSP, sugars, phenolic and proline) antioxidants. In addition, active regulation of transcript levels of genes encoding Na(+) and K(+) (OsHKT1;5, OsLti6a,b, OsHKT2;1, OsSOS1, OsCNGC1, OsNHX1 and OsAKT1) transporter proteins reduced sodium and enhanced potassium accumulation under combined stress, resulted a better growth and ionic homeostasis in both rice cultivars. The production of ABA and IAA was significantly higher in cultivar XS 134 compared to cultivar ZJ 88 under control conditions. However, combined herbicide and saline stress enhanced the accumulation of phytohormones (IAA and ABA) and transcription of ethylene in cultivar ZJ 88, which might be one of the factors responsible for poor salt tolerance in sensitive cultivar. These findings indicated that herbicide application under saline stress confers tolerance to salinity in rice cultivars, likely by reducing oxidative damage, modulating mineral absorption, upgradation of antioxidant defense and by dynamic regulation of key genes involved in Na(+) and K(+) homeostasis in plants.

  5. Hybrid male sterility in rice is due to epistatic interactions with a pollen killer locus.

    PubMed

    Kubo, Takahiko; Yoshimura, Atsushi; Kurata, Nori

    2011-11-01

    In intraspecific crosses between cultivated rice (Oryza sativa) subspecies indica and japonica, the hybrid male sterility gene S24 causes the selective abortion of male gametes carrying the japonica allele (S24-j) via an allelic interaction in the heterozygous hybrids. In this study, we first examined whether male sterility is due solely to the single locus S24. An analysis of near-isogenic lines (NIL-F(1)) showed different phenotypes for S24 in different genetic backgrounds. The S24 heterozygote with the japonica genetic background showed male semisterility, but no sterility was found in heterozygotes with the indica background. This result indicates that S24 is regulated epistatically. A QTL analysis of a BC(2)F(1) population revealed a novel sterility locus that interacts with S24 and is found on rice chromosome 2. The locus was named Epistatic Factor for S24 (EFS). Further genetic analyses revealed that S24 causes male sterility when in combination with the homozygous japonica EFS allele (efs-j). The results suggest that efs-j is a recessive sporophytic allele, while the indica allele (EFS-i) can dominantly counteract the pollen sterility caused by S24 heterozygosity. In summary, our results demonstrate that an additional epistatic locus is an essential element in the hybrid sterility caused by allelic interaction at a single locus in rice. This finding provides a significant contribution to our understanding of the complex molecular mechanisms underlying hybrid sterility and microsporogenesis.

  6. Hybrid sterility in plant: stories from rice.

    PubMed

    Ouyang, Yidan; Liu, Yao-Guang; Zhang, Qifa

    2010-04-01

    Hybrid sterility is the most common form of postzygotic reproductive isolation in plants. The best-known example is perhaps the hybrid sterility between indica and japonica subspecies of Asian cultivated rice (Oryza sativa L.). Major progress has been reported recently in rice in identifying and cloning hybrid sterility genes at two loci regulating female and male fertility, respectively. Genetic analyses and molecular characterization of these genes, together with the results from other model organisms especially Drosophila, have advanced the understanding of the processes underlying reproductive isolation and speciation. These findings also have significant implications for crop genetic improvement, by providing the feasibility and strategies for overcoming intersubspecific hybrid sterility thus allowing the development of intersubspecific hybrids.

  7. Analysis of rice PDR-like ABC transporter genes in sheath blight resistance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sheath blight caused by Rhizoctonia solani is one of the most damaging diseases of rice worldwide. To understand the molecular mechanism of resistance, we identified 450 differentially expressed genes in a resistant rice cultivar Jasmine 85 after R. solani infection with a combination of DNA microar...

  8. Polishing and parboiling effect on the nutritional and technological properties of pigmented rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study aims to evaluate the effects of polishing and parboiling on proximate composition, structure, phenolic compounds, antioxidant activity, cooking time and hardness of IAC-600 black rice cultivar and MPB-10 red rice lineage. Proximate analysis and light micrographs revealed higher migration ...

  9. Using Genetic Markers to Track the Origin, Distribution, and Renaissance of Carolina Gold Rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Carolina Gold was the first rice cultivar to be successfully commercialized in North America and was highly responsible for the establishment and growth of the British colonies along the southeast US coast. Although by the late 1800's, rice production had moved to the other regions of the country, C...

  10. Inoculation and scoring methods for rice sheath blight disease.

    PubMed

    Jia, Yulin; Liu, Guangjie; Park, Dong-Soo; Yang, Yinong

    2013-01-01

    Sheath blight disease of rice caused by the soilborne fungal pathogen Rhizoctonia solani has been a major disease of rice with a serious threat to stable rice production worldwide. Although various cultural practices have been used to manage the disease, it is advantageous and important to screen rice germplasm and identify resistant rice cultivars for more effective disease control. Recent advances in methods for the fungal inoculation and disease evaluation have enabled a better measurement of host resistance by minimizing confounding factors from plant architectures and environmental conditions. This chapter introduces five such methods: (1) detached leaf method; (2) micro-chamber method; (3) mist-chamber method; (4) parafilm sachet method; and (5) aluminum foil method. These methods are useful for screening and evaluating disease reactions of rice germplasm and facilitating the genetic mapping of disease resistance genes.

  11. Loss of a 1.6 Mb chromosome in Pyricularia oryzae harboring two alleles of AvrPik leads to acquisition of virulence to rice cultivars containing resistance alleles at the Pik locus.

    PubMed

    Kusaba, Motoaki; Mochida, Taiga; Naridomi, Takeshi; Fujita, Yoshikatsu; Chuma, Izumi; Tosa, Yukio

    2014-11-01

    A small and extra chromosome of 1.6 Mb was previously identified in a Pyricularia oryzae strain, 84R-62B. To understand a role of the 1.6 Mb chromosome in the pathogenic changeability of P. oryzae, we performed experiments designed to characterize the 1.6 Mb chromosome in the present study. A gene family encoding secreted protein Pex31s in P. oryzae consists of five homologs, Pex31-A to -E. Among them, Pex31-A and -D are known to be recognized by Pik-m and Pik/Pik-m/Pik-p, respectively. In the present study, we identified Pex31-A and -D in the genome of 84R-62B. Segregation analyses using an F1 population between 84R-62B and another rice blast strain, Y93-245c-2, revealed a strong linkage between the two homologs and the 1.6 Mb chromosome of 84R-62B. A CHEF-Southern analysis revealed an association between the 1.6 Mb chromosome and the homologs, indicating that both homologs are located on the 1.6 Mb chromosome of 84R-62B. The loss of the 1.6 Mb chromosome was observed in subcultures of a F1 progeny, F1-327. These subcultures concomitantly acquired virulence on Pik, Pik-m, and Pik-p. The present study is the first report showing that loss of a small and extra chromosome leads to pathogenic mutation of P. oryzae and may provide a new insight into the mechanisms generating pathogenic variation of this fungus. PMID:25056242

  12. Isoflavone tetraglycosides from Sophora japonica Leaves.

    PubMed

    Tang, Yuping; Yang, Ruolin; Duan, Jin-Ao; Shang, Erxin; Su, Shulan; Zhu, Min; Qian, Dawei

    2008-03-01

    Two new isoflavone tetraglycosides ( 1 and 2) and six known compounds were isolated from the leaves of Sophora japonica. The new glycosides are genistein 7- O-beta- d-glucopyranoside-4'- O-(6'''- O-alpha- l-rhamnopyranosyl)-beta-sophoroside ( 1) and genistein 7- O-alpha- l-rhamnopyranoside-4'- O-(6'''- O-alpha- l-rhamnopyranosyl)-beta-sophoroside ( 2). The structures of compounds 1 and 2 were established primarily by NMR experiments and chemical methods, and they are the first reported naturally occurring isoflavone glycosides with four attached sugar residues. PMID:18047294

  13. Comparison on cellular mechanisms of iron and cadmium accumulation in rice: prospects for cultivating Fe-rich but Cd-free rice.

    PubMed

    Gao, Lei; Chang, Jiadong; Chen, Ruijie; Li, Hubo; Lu, Hongfei; Tao, Longxing; Xiong, Jie

    2016-12-01

    Iron (Fe) is essential for rice growth and humans consuming as their staple food but is often deficient because of insoluble Fe(III) in soil for rice growth and limited assimilation for human bodies, while cadmium (Cd) is non-essential and toxic for rice growth and humans if accumulating at high levels. Over-accumulated Cd can cause damage to human bodies. Selecting and breeding Fe-rich but Cd-free rice cultivars are ambitious, challenging and meaningful tasks for researchers. Although evidences show that the mechanisms of Fe/Cd uptake and accumulation in rice are common to some extent as a result of similar entry routes within rice, an increasing number of researchers have discovered distinct mechanisms between Fe/Cd uptake and accumulation in rice. This comprehensive review systematically elaborates and compares cellular mechanisms of Fe/Cd uptake and accumulation in rice, respectively. Mechanisms for maintaining Fe homeostasis and Cd detoxicification are also elucidated. Then, effects of different fertilizer management on Fe/Cd accumulation in rice are discussed. Finally, this review enumerates various approaches for reducing grain Cd accumulation and enhancing Fe content in rice. In summary, understanding of discrepant cellular mechanisms of Fe/Cd accumulation in rice provides guidance for cultivating Fe-fortified rice and has paved the way to develop rice that are tolerant to Cd stress, aiming at breeding Fe-rich but Cd-free rice.

  14. Comparison on cellular mechanisms of iron and cadmium accumulation in rice: prospects for cultivating Fe-rich but Cd-free rice.

    PubMed

    Gao, Lei; Chang, Jiadong; Chen, Ruijie; Li, Hubo; Lu, Hongfei; Tao, Longxing; Xiong, Jie

    2016-12-01

    Iron (Fe) is essential for rice growth and humans consuming as their staple food but is often deficient because of insoluble Fe(III) in soil for rice growth and limited assimilation for human bodies, while cadmium (Cd) is non-essential and toxic for rice growth and humans if accumulating at high levels. Over-accumulated Cd can cause damage to human bodies. Selecting and breeding Fe-rich but Cd-free rice cultivars are ambitious, challenging and meaningful tasks for researchers. Although evidences show that the mechanisms of Fe/Cd uptake and accumulation in rice are common to some extent as a result of similar entry routes within rice, an increasing number of researchers have discovered distinct mechanisms between Fe/Cd uptake and accumulation in rice. This comprehensive review systematically elaborates and compares cellular mechanisms of Fe/Cd uptake and accumulation in rice, respectively. Mechanisms for maintaining Fe homeostasis and Cd detoxicification are also elucidated. Then, effects of different fertilizer management on Fe/Cd accumulation in rice are discussed. Finally, this review enumerates various approaches for reducing grain Cd accumulation and enhancing Fe content in rice. In summary, understanding of discrepant cellular mechanisms of Fe/Cd accumulation in rice provides guidance for cultivating Fe-fortified rice and has paved the way to develop rice that are tolerant to Cd stress, aiming at breeding Fe-rich but Cd-free rice. PMID:27502932

  15. Application of a rotation system to oilseed rape and rice fields in Cd-contaminated agricultural land to ensure food safety.

    PubMed

    Yu, Lingling; Zhu, Junyan; Huang, Qingqing; Su, Dechun; Jiang, Rongfeng; Li, Huafen

    2014-10-01

    This field experiment analyzed the phytoremediation effects of oilseed rape in moderately cadmium (Cd)-contaminated farmland and the food safety of successive rice in an oilseed rape-rice rotation system. Two oilseed rape cultivars accumulated Cd at different rates. The rapeseed cultivar Zhucang Huazi exhibited high Cd accumulation rates, higher than the legal limit for human consumption (0.2mgkg(-1)); Cd concentrations in the cultivar Chuanyou II-93 were all below the maximum allowed level. Planting oilseed rape increased the uptake of Cd by the successive rice crop compared with a previous fallow treatment. Most Cd concentrations of brown rice were below the maximum allowed level. The phytoextraction efficiency was lower in the moderately Cd-contaminated soil in field experiments. The results suggest screening rice cultivars with lower Cd accumulation can assure the food safety; the mobilization of heavy metals by roots of different plant species should be considered during crop rotation to assure food safety.

  16. A biochar application protects rice pollen from high-temperature stress.

    PubMed

    Fahad, Shah; Hussain, Saddam; Saud, Shah; Tanveer, Mohsin; Bajwa, Ali Ahsan; Hassan, Shah; Shah, Adnan Noor; Ullah, Abid; Wu, Chao; Khan, Faheem Ahmed; Shah, Farooq; Ullah, Sami; Chen, Yajun; Huang, Jianliang

    2015-11-01

    The influences of high temperature and fertilization with biochar and phosphorus (P) on the pollen characteristics of two rice cultivars (IR-64 and Huanghuazhan) were examined in controlled growth chambers. Temperature treatments included high daytime temperature (HDT), high nighttime temperature (HNT) and ambient temperature (AT). The fertilization treatments were control, biochar alone, P alone and biochar + P. High temperature severely reduced pollen fertility, anther dehiscence, pollen retention and pollen germination of both rice cultivars, with HNT more destructive than HDT. The Huanghuazhan cultivar performed better than IR-64 under high temperature, with higher pollen fertility, better anther dehiscence and greater pollen retention and germination rates. In both cultivars, the pollen of plants treated with biochar + P were more resistant to heat induced stress. Further studies are needed to test the ability of biochar to ameliorate the effects of different abiotic stresses in rice and other crops.

  17. [Effect of HCO3- on root growth and nutrient absorption of different rice genotypes].

    PubMed

    Xu, X; Yang, X; Yang, Y

    2001-08-01

    Solution culture experiments with Zn-inefficient cultivar (IR26) and the Zn-efficient cultivar (IR8192-31-2) were conducted to study the effect of HCO3- on the root growth and nutrient absorption of different rice cultivars. The results showed that HCO3- strongly inhibited the root growth of Zn-inefficient cultivar especially at low Zn concentration. In contrast, that of Zn-efficient cultivar was slightly stimulated by HCO3- at low Zn concentration. HCO3- not only inhibited Zn absorption of Zn-inefficient cultivar, but also inhibited its absorption of Fe, Mn, Cu, implying that there was no specific inhibition of HCO3- on Zn absorption. These results demonstrated that the inhibition of root growth by HCO3- was likely to be the initial action of HCO3- in inducing Zn deficiency in lowland rice. With treatment of bicarbonate, Zn concentrations in upper and lower leaves of the Zn-efficient cultivar and their ratios were higher than those of the Zn-inefficient cultivar. The results showed that the Zn-efficient cultivar could transport more zinc from lower leaves to upper leaves, which might be-one of mechanisms that the Zn-efficient cultivar adapted to zinc deficiency in calcareous soil.

  18. Genome-wide DNA polymorphism in the indica rice varieties RGD-7S and Taifeng B as revealed by whole genome re-sequencing.

    PubMed

    Fu, Chong-Yun; Liu, Wu-Ge; Liu, Di-Lin; Li, Ji-Hua; Zhu, Man-Shan; Liao, Yi-Long; Liu, Zhen-Rong; Zeng, Xue-Qin; Wang, Feng

    2016-03-01

    Next-generation sequencing technologies provide opportunities to further understand genetic variation, even within closely related cultivars. We performed whole genome resequencing of two elite indica rice varieties, RGD-7S and Taifeng B, whose F1 progeny showed hybrid weakness and hybrid vigor when grown in the early- and late-cropping seasons, respectively. Approximately 150 million 100-bp pair-end reads were generated, which covered ∼86% of the rice (Oryza sativa L. japonica 'Nipponbare') reference genome. A total of 2,758,740 polymorphic sites including 2,408,845 SNPs and 349,895 InDels were detected in RGD-7S and Taifeng B, respectively. Applying stringent parameters, we identified 961,791 SNPs and 46,640 InDels between RGD-7S and Taifeng B (RGD-7S/Taifeng B). The density of DNA polymorphisms was 256.8 SNPs and 12.5 InDels per 100 kb for RGD-7S/Taifeng B. Copy number variations (CNVs) were also investigated. In RGD-7S, 1989 of 2727 CNVs were overlapped in 218 genes, and 1231 of 2010 CNVs were annotated in 175 genes in Taifeng B. In addition, we verified a subset of InDels in the interval of hybrid weakness genes, Hw3 and Hw4, and obtained some polymorphic InDel markers, which will provide a sound foundation for cloning hybrid weakness genes. Analysis of genomic variations will also contribute to understanding the genetic basis of hybrid weakness and heterosis.

  19. Over-expression of PsGPD, a mushroom glyceraldehyde-3-phosphate dehydrogenase gene, enhances salt tolerance in rice plants.

    PubMed

    Cho, Jung-Il; Lim, Hye-Min; Siddiqui, Zamin Shaheed; Park, Sung-Han; Kim, A-Ram; Kwon, Taek-Ryoun; Lee, Seong-Kon; Park, Soo-Chul; Jeong, Mi-Jeong; Lee, Gang-Seob

    2014-08-01

    Transgenic potatoes expressing glyceraldehyde-3-phosphate dehydrogenase (GPD), isolated from the oyster mushroom, Pleurotus sajor-caju, had increased tolerance to salt stress (Jeong et al. Biochem Biophys Res Commun 278:192-196, 2000). To examine the physiological mechanisms enhancing salt tolerance in GPD-transgenic rice plants, the salt tolerance of five GPD transgenic rice lines (T1-T5) derived from Dongjin rice cultivar were evaluated in a fixed 150 mM saline environment in comparison to two known wild-type rice cultivars, Dongjin (salt sensitive) and Pokali (salt tolerant). Transgenic lines, T2, T3, and T5, had a substantial increase in biomass and relative water content compared to Dongjin. Stomatal conductance and osmotic potential were higher in the GPD transgenic lines and were similar to those in Pokali. The results are discussed based on the comparative physiological response of GPD transgenic lines with those of the salt-sensitive and salt-tolerant rice cultivars.

  20. Crystallization and preliminary X-ray crystallographic studies of dehydroascorbate reductase (DHAR) from Oryza sativa L. japonica

    PubMed Central

    Do, Hackwon; Kim, Il-Sup; Kim, Young-Saeng; Shin, Sun-Young; Kim, Jin-Ju; Mok, Ji-Eun; Park, Seong-Im; Wi, Ah Ram; Park, Hyun; Kim, Han-Woo; Yoon, Ho-Sung; Lee, Jun Hyuck

    2014-01-01

    Dehydroascorbate reductase from Oryza sativa L. japonica (OsDHAR), a key enzyme in the regeneration of vitamin C, maintains reduced pools of ascorbic acid to detoxify reactive oxygen species. In previous studies, the overexpression of OsDHAR in transgenic rice increased grain yield and biomass as well as the amount of ascorbate, suggesting that ascorbate levels are directly associated with crop production in rice. Hence, it has been speculated that the increased level of antioxidants generated by OsDHAR protects rice from oxidative damage and increases the yield of rice grains. However, the crystal structure and detailed mechanisms of this important enzyme need to be further elucidated. In this study, recombinant OsDHAR protein was purified and crystallized using the sitting-drop vapour-diffusion method at pH 8.0 and 298 K. Plate-shaped crystals were obtained using 0.15 M potassium bromide, 30%(w/v) PEG MME 2000 as a precipitant, and the crystals diffracted to a resolution of 1.9 Å on beamline 5C at the Pohang Accelerator Laboratory. The X-ray diffraction data indicated that the crystal contained one OsDHAR molecule in the asymmetric unit and belonged to space group P21 with unit-cell parameters a = 47.03, b = 48.38, c = 51.83 Å, β = 107.41°. PMID:24915093

  1. Comparative evaluation of three different extraction methods for rice (Oryza sativa L.) genomic DNA.

    PubMed

    Sagi, Naoki; Monma, Kimio; Ibe, Akihiro; Kamata, Kunihiro

    2009-04-01

    Recently, more immediate and precise cultivar-identifying methods targeting the specific and/or introduced gene(s) have been put into practical use for various rice cultivars. However trustworthy and innovative the biotechnological analyses may be, DNA purity and quality do have unpredictable influences upon the identification. Extraction methods of rice DNA have hardly ever been compared in a comprehensive manner. In this study, we investigated extraction characteristics of three methods by using 10 rice cultivars and then examined template availability of rice DNAs thereby extracted. An UV spectrophotometric study with a view toward methods revealed three different facts: The Isoplant II kit method with inhibitor absorption yielded the most DNAs, the Takara kit method with magnetic trapping produced the best DNAs free from contaminative proteins, and the enzymatic digestion method exclusively with enzymatic digestions prepared the best DNAs free from contaminative polysaccharides. Moreover, with a view toward cultivars, an insignificant difference in yield was not entirely bore out, and some difference in cultivar might cause significant difference in yield; however, no significant difference in purity was found among the cultivars used. On the other hand, electrophoretic images of the DNAs from the same cultivars showed considerable differences in quality among the methods. Furthermore, the DNA extracts from certain brands of rice proved really available for cultivar identification by using polymerase chain reaction (PCR) related to sequence-tagged sites. Therefore, this study suggested that these extraction methods may be used as the situation demands and that the DNAs thereby extracted might work successfully even in cultivar-identifying PCRs.

  2. Does morphological and anatomical plasticity during the vegetative stage make wheat more tolerant of water deficit stress than rice?

    PubMed

    Kadam, Niteen N; Yin, Xinyou; Bindraban, Prem S; Struik, Paul C; Jagadish, Krishna S V

    2015-04-01

    Water scarcity and the increasing severity of water deficit stress are major challenges to sustaining irrigated rice (Oryza sativa) production. Despite the technologies developed to reduce the water requirement, rice growth is seriously constrained under water deficit stress compared with other dryland cereals such as wheat (Triticum aestivum). We exposed rice cultivars with contrasting responses to water deficit stress and wheat cultivars well adapted to water-limited conditions to the same moisture stress during vegetative growth to unravel the whole-plant (shoot and root morphology) and organ/tissue (root anatomy) responses. Wheat cultivars followed a water-conserving strategy by reducing specific leaf area and developing thicker roots and moderate tillering. In contrast, rice 'IR64' and 'Apo' adopted a rapid water acquisition strategy through thinner roots under water deficit stress. Root diameter, stele and xylem diameter, and xylem number were more responsive and varied with different positions along the nodal root under water deficit stress in wheat, whereas they were relatively conserved in rice cultivars. Increased metaxylem diameter and lower metaxylem number near the root tips and exactly the opposite phenomena at the root-shoot junction facilitated the efficient use of available soil moisture in wheat. Tolerant rice 'Nagina 22' had an advantage in root morphological and anatomical attributes over cultivars IR64 and Apo but lacked plasticity, unlike wheat cultivars exposed to water deficit stress. The key traits determining the adaptation of wheat to dryland conditions have been summarized and discussed.

  3. Research Progress on Chemical Constituents of Lonicerae japonicae flos.

    PubMed

    Wang, Lingna; Jiang, Qiu; Hu, Jinghong; Zhang, Yongqing; Li, Jia

    2016-01-01

    Lonicerae japonicae flos is commonly used in traditional Chinese medicine for thousands of years with confirmed curative effects. Except for medicine, it is also used in healthy food, cosmetics, and soft beverages for its specific activities. Therefore, the chemical constituents, mainly including organic acids, flavonoids, iridoids, triterpenoids, and volatile oils, have been well studied by many scholars in recent years and a comprehensive and systematic review on chemical constituents of Lonicerae japonicae flos is indispensable. This paper aims at reviewing the chemical components of LJF in recent years through searching for the literatures both at home and abroad. Our results show that 212 components have been isolated from Lonicerae japonicae flos, including 27 flavonoids, 40 organic acids, 83 iridoids, 17 triterpenoids, and 45 other compounds, which could lay a foundation for the further application of Lonicerae japonicae flos.

  4. Research Progress on Chemical Constituents of Lonicerae japonicae flos

    PubMed Central

    Wang, Lingna; Jiang, Qiu; Hu, Jinghong; Zhang, Yongqing; Li, Jia

    2016-01-01

    Lonicerae japonicae flos is commonly used in traditional Chinese medicine for thousands of years with confirmed curative effects. Except for medicine, it is also used in healthy food, cosmetics, and soft beverages for its specific activities. Therefore, the chemical constituents, mainly including organic acids, flavonoids, iridoids, triterpenoids, and volatile oils, have been well studied by many scholars in recent years and a comprehensive and systematic review on chemical constituents of Lonicerae japonicae flos is indispensable. This paper aims at reviewing the chemical components of LJF in recent years through searching for the literatures both at home and abroad. Our results show that 212 components have been isolated from Lonicerae japonicae flos, including 27 flavonoids, 40 organic acids, 83 iridoids, 17 triterpenoids, and 45 other compounds, which could lay a foundation for the further application of Lonicerae japonicae flos. PMID:27403439

  5. Complete mitochondrial genome of Anguilla japonica (Anguilliformes, Anguillidae).

    PubMed

    Zhang, Shuo; Huang, Lin; Luo, Ling; Wang, Qinglin

    2016-01-01

    The complete mitochondrial genome of Anguilla japonica have been determined in this study. The gene composition, arrangement and transcriptional orientation in A. japonica mitogenome were identical to those of most vertebrates. The complete mitogenome of A. japonica was 16,615 bp in size wih 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region. Two start codon patterns and three stop codon patterns were found in protein-coding genes. Only the tRNA-Ser2 could not fold into a typical clover-leaf secondary structure for lacking the dihydrouridine arm. Sequences alignment results suggest that the complete mitogenome of A. japonica is an efficient tool to study molecular phylogenetics, biogeography and adaptive evolution of this lineage. PMID:25010074

  6. Cultivar evaluation for hoop house grown onions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Oklahoma onions are produced for the fresh market using a combination of short and intermediate day cultivars. Recently developed hoop house transplant production techniques enable local production of cultivars not available as transplants elsewhere. Several new intermediate cultivars have product...

  7. Immunosuppressive activities of fucoidan from Laminaria japonica

    NASA Astrophysics Data System (ADS)

    Zhang, Quanbin; Li, Zhien; Zhou, Gefei; Niu, Xizhen; Zhang, Hong

    2003-12-01

    Effects of fucoidan from Laminaria japonica on 2,4-dinitrochlorobenzene induced delayed-type hypersensitivity (DTH) reaction and the serum levels of IgG, IgM, complement C3 and C4 were investigated in the present study. Results showed that oral administration of fucoidan at dose of 150 and 300 mg/(kg· d) for 9 days before the hapten challenge significantly inhibited 2,4-dinitrochlorobenzene induced delayed-type hypersensitivity reaction; and also inhibited the humoral immunity. Serum C3 and C4 levels were markedly reduced by fucoidan at dose of 150 and 300 mg/kg; and serum IgG and IgM levels were reduced by fucoidan at dose of 300mg/kg. The inhibitory effects of fucoidan on delayed-type hypersensitivity suggested that it may be potential medication for chronic inflammatory diseases in the future.

  8. A transformation model for Laminaria Japonica (Phaeophyta, Laminariales)

    NASA Astrophysics Data System (ADS)

    Qin, Song; Jiang, Peng; Li, Xin-Ping; Wang, Xi-Hua; Zeng, Cheng-Kui

    1998-03-01

    A genetic transformation model for the seaweed Laminaria japonica mainly includes the following aspects: 1. The method to introduce foreign genes into the kelp, L. japonica Biolistic bombardment has been proved to be an effective method to bombard foreign DNA through cell walls into intact cells of both sporophytes and gametophytes. The expression of cat and lacZ was detected in regenerated sporophytes, which suggests that this method could induce random integration of foreign genes. Promoters to drive gene expression

  9. Association mapping of starch physicochemical properties with starch biosynthesizing genes in waxy rice (Oryza sativa L.).

    PubMed

    Xu, Feifei; Zhang, Gan; Tong, Chuan; Sun, Xiao; Corke, Harold; Sun, Mei; Bao, Jinsong

    2013-10-23

    Waxy (glutinous) rice is widely used in traditional foods, and understanding the genetic bases of its diverse physicochemical properties will contribute to breeding of new waxy rice with unique qualities. The objective of this study was to investigate the genetic relationship between the starch biosynthesis related genes and the physicochemical properties of waxy rice using association mapping. A total of 36 molecular markers representing 18 genes were used to genotype 50 waxy rice accessions for which starch properties were previously available. Most of the starch properties differed between high and low gelatinization temperature (GT) groups, whereas most traits were similar between the low-GT indica rice and low-GT japonica rice, suggesting GT was the main determinant of the starch quality of waxy rice. Association mapping indicated that the starch properties of waxy rice were mainly controlled by starch synthase IIa (SSIIa or SSII-3, a major gene responsible for the gelatinization temperature) and SSI. It was found that gene-gene interactions were also important for the genetic control of starch properties of waxy rice. This study suggests that application of the functional SNPs of SSIIa in molecular breeding may facilitate quality improvement of waxy rice.

  10. Reducing arsenic accumulation in rice grain through iron oxide amendment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this research, we investigated the accumulation of arsenic (As), selenium (Se), molybdenum (Mo), and cadmium (Cd) in rice grain under different soil conditions in standard straighthead-resistant and straighthead-susceptible cultivars, Zhe 733 and Cocodrie, respectively. Results demonstrated that,...

  11. Registration of "Rex" Southern Long-Grain Rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ‘Rex’ (Oryza sativa L.) (Reg. No. CV-136, PI 661111) is a conventional, southern, long-grain rice cultivar developed at the Mississippi Agricultural and Forestry Experiment Station, Delta Research and Extension Center, Stoneville, MS, and officially released in February 2010. Rex is a semidwarf cult...

  12. Model biases in rice phenology under warmer climates

    NASA Astrophysics Data System (ADS)

    Zhang, Tianyi; Li, Tao; Yang, Xiaoguang; Simelton, Elisabeth

    2016-06-01

    Climate-induced crop yields model projections are constrained by the accuracy of the phenology simulation in crop models. Here, we use phenology observations from 775 trials with 19 rice cultivars in 5 Asian countries to compare the performance of four rice phenology models (growing-degree-day (GDD), exponential, beta and bilinear models) when applied to warmer climates. For a given cultivar, the difference in growing season temperature (GST) varied between 2.2 and 8.2 °C in different trials, which allowed us to calibrate the models for lower GST and validate under higher GST, with three calibration experiments. The results show that in warmer climates the bilinear and beta phenology models resulted in gradually increasing bias for phenology predication and double yield bias per percent increase in phenology simulation bias, while the GDD and exponential models maintained a comparatively constant bias. The phenology biases were primarily attributed to varying phenological patterns to temperature in models, rather than on the size of the calibration dataset. Additionally, results suggest that model simulations based on multiple cultivars provide better predictability than using one cultivar. Therefore, to accurately capture climate change impacts on rice phenology, we recommend simulations based on multiple cultivars using the GDD and exponential phenology models.

  13. Model biases in rice phenology under warmer climates.

    PubMed

    Zhang, Tianyi; Li, Tao; Yang, Xiaoguang; Simelton, Elisabeth

    2016-01-01

    Climate-induced crop yields model projections are constrained by the accuracy of the phenology simulation in crop models. Here, we use phenology observations from 775 trials with 19 rice cultivars in 5 Asian countries to compare the performance of four rice phenology models (growing-degree-day (GDD), exponential, beta and bilinear models) when applied to warmer climates. For a given cultivar, the difference in growing season temperature (GST) varied between 2.2 and 8.2 °C in different trials, which allowed us to calibrate the models for lower GST and validate under higher GST, with three calibration experiments. The results show that in warmer climates the bilinear and beta phenology models resulted in gradually increasing bias for phenology predication and double yield bias per percent increase in phenology simulation bias, while the GDD and exponential models maintained a comparatively constant bias. The phenology biases were primarily attributed to varying phenological patterns to temperature in models, rather than on the size of the calibration dataset. Additionally, results suggest that model simulations based on multiple cultivars provide better predictability than using one cultivar. Therefore, to accurately capture climate change impacts on rice phenology, we recommend simulations based on multiple cultivars using the GDD and exponential phenology models. PMID:27273847

  14. Model biases in rice phenology under warmer climates.

    PubMed

    Zhang, Tianyi; Li, Tao; Yang, Xiaoguang; Simelton, Elisabeth

    2016-06-07

    Climate-induced crop yields model projections are constrained by the accuracy of the phenology simulation in crop models. Here, we use phenology observations from 775 trials with 19 rice cultivars in 5 Asian countries to compare the performance of four rice phenology models (growing-degree-day (GDD), exponential, beta and bilinear models) when applied to warmer climates. For a given cultivar, the difference in growing season temperature (GST) varied between 2.2 and 8.2 °C in different trials, which allowed us to calibrate the models for lower GST and validate under higher GST, with three calibration experiments. The results show that in warmer climates the bilinear and beta phenology models resulted in gradually increasing bias for phenology predication and double yield bias per percent increase in phenology simulation bias, while the GDD and exponential models maintained a comparatively constant bias. The phenology biases were primarily attributed to varying phenological patterns to temperature in models, rather than on the size of the calibration dataset. Additionally, results suggest that model simulations based on multiple cultivars provide better predictability than using one cultivar. Therefore, to accurately capture climate change impacts on rice phenology, we recommend simulations based on multiple cultivars using the GDD and exponential phenology models.

  15. Model biases in rice phenology under warmer climates

    PubMed Central

    Zhang, Tianyi; Li, Tao; Yang, Xiaoguang; Simelton, Elisabeth

    2016-01-01

    Climate-induced crop yields model projections are constrained by the accuracy of the phenology simulation in crop models. Here, we use phenology observations from 775 trials with 19 rice cultivars in 5 Asian countries to compare the performance of four rice phenology models (growing-degree-day (GDD), exponential, beta and bilinear models) when applied to warmer climates. For a given cultivar, the difference in growing season temperature (GST) varied between 2.2 and 8.2 °C in different trials, which allowed us to calibrate the models for lower GST and validate under higher GST, with three calibration experiments. The results show that in warmer climates the bilinear and beta phenology models resulted in gradually increasing bias for phenology predication and double yield bias per percent increase in phenology simulation bias, while the GDD and exponential models maintained a comparatively constant bias. The phenology biases were primarily attributed to varying phenological patterns to temperature in models, rather than on the size of the calibration dataset. Additionally, results suggest that model simulations based on multiple cultivars provide better predictability than using one cultivar. Therefore, to accurately capture climate change impacts on rice phenology, we recommend simulations based on multiple cultivars using the GDD and exponential phenology models. PMID:27273847

  16. Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping.

    PubMed

    Shinada, Hiroshi; Yamamoto, Toshio; Sato, Hirokazu; Yamamoto, Eiji; Hori, Kiyosumi; Yonemaru, Junichi; Sato, Takashi; Fujino, Kenji

    2015-12-01

    Plant breeding programs aim to develop cultivars with high adaptability to the specific conditions in a local region. As a result, unique genes and gene combinations have been accumulated in local elite breeding populations during the long history of plant breeding. Genetic analyses on such genes and combinations may be useful for developing new cultivars with more-desirable agronomic traits. Here, we attempted to detect quantitative trait loci (QTL) for rice blast resistance (BR) using a local breeding rice population from Hokkaido, Japan. Using genotyping data on single nucleotide polymorphisms and simple sequence repeat markers distributed throughout the whole genomic region, we detected genetic regions associated with phenotypic variation in BR by a genome-wide association mapping study (GWAS). An additional association analysis using other breeding cultivars verified the effect and inheritance of the associated region. Furthermore, the existence of a gene for BR in the associated region was confirmed by QTL mapping. The results from these studies enabled us to estimate potential of the Hokkaido rice population as a gene pool for improving BR. The results of this study could be useful for developing novel cultivars with vigorous BR in rice breeding programs.

  17. Cold Treatment Breaks Dormancy but Jeopardizes Flower Quality in Camellia japonica L.

    PubMed

    Berruti, Andrea; Christiaens, Annelies; Keyser, Ellen De; Labeke, Marie-Christine Van; Scariot, Valentina

    2015-01-01

    Camellia japonica L. is an evergreen shrub whose cultivars are of great ornamental value. In autumn, after flower bud differentiation, dormancy is initiated. As in many other spring flowering woody ornamentals, winter low temperatures promote dormancy release of both flower and vegetative buds. However, warm spells during late autumn and winter can lead to unfulfilled chilling requirements leading to erratic and delayed flowering. We hypothesized that storing plants at no light and low temperature could favor dormancy breaking and lead to early and synchronized flowering in response to forcing conditions in C. japonica 'Nuccio's Pearl'. Plants with fully developed floral primordia were stored at dark, 7°C, and RH > 90% for up to 8 weeks. To monitor endodormancy release during the storage, we evaluated the content of abscisic acid (ABA) in flower buds and the expression profiles of five putative genes related to dormancy and cold acclimation metabolism in leaves and flower buds. In addition, the expression of four anthocyanin biosynthesis pathway genes was profiled in flower buds to assess the effect of the treatment on flower pigment biosynthesis. At 0, 4, 6, and 8 weeks of cold treatment, 10 plants were transferred to the greenhouse and forced to flower. Forced plant flower qualities and growth were observed. The ABA content and the expression profiles of two dormancy-related genes (CjARP and CjDEH) suggested that dormancy breaking occurred after 6-8 weeks of cold treatment. Overall, plants treated for 6-8 weeks showed earlier vegetative sprouting, enhanced, and homogeneous flowering with reduced forcing time. Prolonged cold treatments also reduced flower size and longevity, anthocyanin content, and pigment biosynthesis-related gene transcripts. In conclusion, the cold treatment had a promotive effect on dormancy breaking but caused severe drawbacks on flower quality. PMID:26617623

  18. Cold Treatment Breaks Dormancy but Jeopardizes Flower Quality in Camellia japonica L.

    PubMed Central

    Berruti, Andrea; Christiaens, Annelies; Keyser, Ellen De; Labeke, Marie-Christine Van; Scariot, Valentina

    2015-01-01

    Camellia japonica L. is an evergreen shrub whose cultivars are of great ornamental value. In autumn, after flower bud differentiation, dormancy is initiated. As in many other spring flowering woody ornamentals, winter low temperatures promote dormancy release of both flower and vegetative buds. However, warm spells during late autumn and winter can lead to unfulfilled chilling requirements leading to erratic and delayed flowering. We hypothesized that storing plants at no light and low temperature could favor dormancy breaking and lead to early and synchronized flowering in response to forcing conditions in C. japonica ‘Nuccio’s Pearl’. Plants with fully developed floral primordia were stored at dark, 7°C, and RH > 90% for up to 8 weeks. To monitor endodormancy release during the storage, we evaluated the content of abscisic acid (ABA) in flower buds and the expression profiles of five putative genes related to dormancy and cold acclimation metabolism in leaves and flower buds. In addition, the expression of four anthocyanin biosynthesis pathway genes was profiled in flower buds to assess the effect of the treatment on flower pigment biosynthesis. At 0, 4, 6, and 8 weeks of cold treatment, 10 plants were transferred to the greenhouse and forced to flower. Forced plant flower qualities and growth were observed. The ABA content and the expression profiles of two dormancy-related genes (CjARP and CjDEH) suggested that dormancy breaking occurred after 6–8 weeks of cold treatment. Overall, plants treated for 6–8 weeks showed earlier vegetative sprouting, enhanced, and homogeneous flowering with reduced forcing time. Prolonged cold treatments also reduced flower size and longevity, anthocyanin content, and pigment biosynthesis-related gene transcripts. In conclusion, the cold treatment had a promotive effect on dormancy breaking but caused severe drawbacks on flower quality. PMID:26617623

  19. The effect of fertilization on cesium concentration of rice grown in a paddy field in Fukushima Prefecture in 2011 and 2012.

    PubMed

    Ohmori, Yoshihiro; Kajikawa, Masataka; Nishida, Sho; Tanaka, Nobuhiro; Kobayashi, Natsuko I; Tanoi, Keitaro; Furukawa, Jun; Fujiwara, Toru

    2014-01-01

    After the accident of the Fukushima 1 nuclear power plant in March 2011, radioactive cesium was released and paddy field in a wide area of Fukushima Prefecture was contaminated. To reduce radioactive Cs uptake by rice, it is important to understand factors that affect Cs uptake in rice. Here we describe our study in 2011 and 2012 to investigate Cs concentration in two rice cultivars, Koshihikari and Hitomebore, the top two cultivars in Fukushima prefecture, grown under different fertilizer conditions in the contaminated paddy field. Our study demonstrated that high nitrogen and low potassium conditions increase Cs concentrations both in straw and brown rice.

  20. Genetic analysis of genetic basis of a physiological disorder "straighthead’’ in rice (Oryza sativa L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Straighthead is a physiological disorder in rice that causes yield losses and is a serious threat to rice production worldwide. Identification of QTL conferring resistance will help develop resistant cultivars for straighthead control. We conducted linkage mapping to identify QTL involved with strai...

  1. RESPONSE OF OXIDATIVE STRESS DEFENSE SYSTEMS IN RICE (ORYZA SATIVA) LEAVES WITH SUPPLEMENTAL UV-B RADIATION

    EPA Science Inventory

    The impact of elevated ultraviolet-B radiation (UV-B, 280-320 nm) on membrane systems and lipid peroxidation, and possible involvement of active oxygen radicals was investigated in leaves of two UV-B susceptible rice cultivars (Oryza sativa L. cvs IR74 and Dular). Rice seedlings ...

  2. Molecular evolution of shattering loci in U.S. weedy rice

    PubMed Central

    Thurber, Carrie S.; Reagon, Michael; Gross, Briana L.; Olsen, Kenneth M.; Jia, Yulin; Caicedo, Ana L.

    2010-01-01

    Cultivated rice fields worldwide are plagued with weedy rice, a conspecific weed of cultivated rice (Oryza sativa L.). The persistence of weedy rice has been attributed, in part, to its ability to shatter (disperse) seed prior to crop harvesting. In the United States, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. Here, we investigate the shattering phenotype in a collection of U.S. weedy rice accessions, as well as wild and cultivated relatives. We find that all U.S. weedy rice groups shatter seeds easily, despite multiple origins, and in contrast to a decrease in shattering ability seen in cultivated groups. We assessed allelic identity and diversity at the major shattering locus, sh4, in weedy rice; we find that all cultivated and weedy rice, regardless of population, share similar haplotypes at sh4, and all contain a single derived mutation associated with decreased seed shattering. Our data constitute the strongest evidence to date of an evolution of weeds from domesticated backgrounds. The combination of a shared cultivar sh4 allele and a highly shattering phenotype, suggests that U.S. weedy rice have re-acquired the shattering trait after divergence from their progenitors through alternative genetic mechanisms. PMID:20584132

  3. Determination of resistance spectra of the Pi-ta and Pi-k genes to US races of Magnaporthe oryzae causing rice blast in a recombinant inbred line population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Resistance (R) genes to ten common races of Magnaporthe oryzae were mapped using an F10 recombinant inbred line population of a cross of a tropical japonica cultivar Katy with a breeding line RU9101001. Katy was found to confer resistance to all common races IA-45, IB-1, IB-45, IB-49, IB-54, IC-17,...

  4. Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice

    PubMed Central

    Ueda, Yoshiaki; Frindte, Katharina; Knief, Claudia; Ashrafuzzaman, Md; Frei, Michael

    2016-01-01

    Microbes constitute a vital part of the plant holobiont. They establish plant-microbe or microbe-microbe associations, forming a unique microbiota with each plant species and under different environmental conditions. These microbial communities have to adapt to diverse environmental conditions, such as geographical location, climate conditions and soil types, and are subjected to changes in their surrounding environment. Elevated ozone concentration is one of the most important aspects of global change, but its effect on microbial communities living on plant surfaces has barely been investigated. In the current study, we aimed at elucidating the potential effect of elevated ozone concentrations on the phyllosphere (aerial part of the plant) and rhizoplane (surface of the root) microbiota by adopting next-generation 16S rRNA amplicon sequencing. A standard japonica rice cultivar Nipponbare and an ozone-tolerant breeding line L81 (Nipponbare background) were pre-grown in a greenhouse for 10 weeks and then exposed to ozone at 85 ppb for 7 h daily for 30 days in open top chambers. Microbial cells were collected from the phyllosphere and rhizoplane separately. The treatment or different genotypes did not affect various diversity indices. On the other hand, the relative abundance of some bacterial taxa were significantly affected in the rhizoplane community of ozone-treated plants. A significant effect of ozone was detected by homogeneity of molecular variance analysis in the phyllosphere, meaning that the community from ozone-treated phyllosphere samples was more variable than those from control plants. In addition, a weak treatment effect was observed by clustering samples based on the Yue and Clayton and weighted UniFrac distance matrices among samples. We therefore conclude that the elevated ozone concentrations affected the bacterial community structure of the phyllosphere and the rhizosplane as a whole, even though this effect was rather weak and did not lead to

  5. Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice.

    PubMed

    Ueda, Yoshiaki; Frindte, Katharina; Knief, Claudia; Ashrafuzzaman, Md; Frei, Michael

    2016-01-01

    Microbes constitute a vital part of the plant holobiont. They establish plant-microbe or microbe-microbe associations, forming a unique microbiota with each plant species and under different environmental conditions. These microbial communities have to adapt to diverse environmental conditions, such as geographical location, climate conditions and soil types, and are subjected to changes in their surrounding environment. Elevated ozone concentration is one of the most important aspects of global change, but its effect on microbial communities living on plant surfaces has barely been investigated. In the current study, we aimed at elucidating the potential effect of elevated ozone concentrations on the phyllosphere (aerial part of the plant) and rhizoplane (surface of the root) microbiota by adopting next-generation 16S rRNA amplicon sequencing. A standard japonica rice cultivar Nipponbare and an ozone-tolerant breeding line L81 (Nipponbare background) were pre-grown in a greenhouse for 10 weeks and then exposed to ozone at 85 ppb for 7 h daily for 30 days in open top chambers. Microbial cells were collected from the phyllosphere and rhizoplane separately. The treatment or different genotypes did not affect various diversity indices. On the other hand, the relative abundance of some bacterial taxa were significantly affected in the rhizoplane community of ozone-treated plants. A significant effect of ozone was detected by homogeneity of molecular variance analysis in the phyllosphere, meaning that the community from ozone-treated phyllosphere samples was more variable than those from control plants. In addition, a weak treatment effect was observed by clustering samples based on the Yue and Clayton and weighted UniFrac distance matrices among samples. We therefore conclude that the elevated ozone concentrations affected the bacterial community structure of the phyllosphere and the rhizosplane as a whole, even though this effect was rather weak and did not lead to

  6. Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice.

    PubMed

    Ueda, Yoshiaki; Frindte, Katharina; Knief, Claudia; Ashrafuzzaman, Md; Frei, Michael

    2016-01-01

    Microbes constitute a vital part of the plant holobiont. They establish plant-microbe or microbe-microbe associations, forming a unique microbiota with each plant species and under different environmental conditions. These microbial communities have to adapt to diverse environmental conditions, such as geographical location, climate conditions and soil types, and are subjected to changes in their surrounding environment. Elevated ozone concentration is one of the most important aspects of global change, but its effect on microbial communities living on plant surfaces has barely been investigated. In the current study, we aimed at elucidating the potential effect of elevated ozone concentrations on the phyllosphere (aerial part of the plant) and rhizoplane (surface of the root) microbiota by adopting next-generation 16S rRNA amplicon sequencing. A standard japonica rice cultivar Nipponbare and an ozone-tolerant breeding line L81 (Nipponbare background) were pre-grown in a greenhouse for 10 weeks and then exposed to ozone at 85 ppb for 7 h daily for 30 days in open top chambers. Microbial cells were collected from the phyllosphere and rhizoplane separately. The treatment or different genotypes did not affect various diversity indices. On the other hand, the relative abundance of some bacterial taxa were significantly affected in the rhizoplane community of ozone-treated plants. A significant effect of ozone was detected by homogeneity of molecular variance analysis in the phyllosphere, meaning that the community from ozone-treated phyllosphere samples was more variable than those from control plants. In addition, a weak treatment effect was observed by clustering samples based on the Yue and Clayton and weighted UniFrac distance matrices among samples. We therefore conclude that the elevated ozone concentrations affected the bacterial community structure of the phyllosphere and the rhizosplane as a whole, even though this effect was rather weak and did not lead to

  7. Arsenic uptake by rice is influenced by microbe-mediated arsenic redox changes in the rhizosphere.

    PubMed

    Jia, Yan; Huang, Hai; Chen, Zheng; Zhu, Yong-Guan

    2014-01-21

    Arsenic (As) uptake by rice is largely determined by As speciation, which is strongly influenced by microbial activities. However, little is known about interactions between root and rhizosphere microbes, particularly on arsenic oxidation and reduction. In this study, two rice cultivars with different radial oxygen loss (ROL) ability were used to investigate the impact of microbially mediated As redox changes in the rhizosphere on As uptake. Results showed that the cultivar with higher ROL (Yangdao) had lower As uptake than that with lower ROL (Nongken). The enhancement of the rhizospheric effect on the abundance of the arsenite (As(III)) oxidase gene (aroA-like) was greater than on the arsenate (As(V)) reductase gene (arsC), and As(V) respiratory reductase gene (arrA), resulting in As oxidation and sequestration in the rhizosphere, particularly for cultivar Yangdao. The community of As(III)-oxidizing bacteria in the rhizosphere was dominated by α-Proteobacteria and β-Proteobacteria and was influenced by rhizospheric effects, rice straw application, growth stage, and cultivar. Application of rice straw into the soil increased As release and accumulation into rice plants. These results highlighted that uptake of As by rice is influenced by microbial processes, especially As oxidation in the rhizosphere, and these processes are influenced by root ROL and organic matter application. PMID:24383760

  8. Arsenic accumulation and speciation in rice grains influenced by arsenic phytotoxicity and rice genotypes grown in arsenic-elevated paddy soils.

    PubMed

    Syu, Chien-Hui; Huang, Chia-Chen; Jiang, Pei-Yu; Lee, Chia-Hsing; Lee, Dar-Yuan

    2015-04-01

    Rice consumption is a major route of As exposure to human for the population of worldwide. This study investigates the effect of phytotoxicity and rice genotypes on the content and speciation of As in rice grains grown in different levels of As-elevated paddy soils from Taiwan. Three levels of As-elevated soils and six rice genotypes commonly planted in Taiwan were used for this study. The results indicate that As contents in grains of rice is not proportional to soil As concentrations and they were equal or higher in indica genotypes than japonica genotypes used in this study. It was also found that the As phytotoxicity not only reducing the grain yields but also the As concentrations in grain of rice. The predominant As species found in rice grains were dimethylarsinic acid (DMA) and arsenite. The concentrations of DMA increased with total As concentrations, wherggeas the arsenite remained in a narrow range from 0.1 to 0.3 mg kg(-1). Because of the lower toxicity of DMA than inorganic As species, the health risks may not be increased through consumption of rice even when total As content in the grains is increased. PMID:25577320

  9. Dietary supplementation of germinated pigmented rice (Oryza sativa L.) lowers dyslipidemia risk in ovariectomized Sprague–Dawley rats

    PubMed Central

    Lo, Lara Marie Pangan; Kang, Mi Young; Yi, Seong Joon; Chung, Soo Im

    2016-01-01

    Background In the recent years, cases of elderly women suffering from metabolic diseases such as dyslipidemias brought about by hormonal imbalance after menopause are continuously increasing. In this regard, a continuous and escalating demand to develop a more functional and highly nutritional food product as an adjunct supplement that can help alleviate these diseases is still being sought. Objective This study investigated the effects of germinated blackish-purple rice cultivars Keunnunjami, Superjami, and reddish-brown cultivar Superhongmi in the lipid metabolism of ovariectomized Sprague–Dawley rats. Method The animals were randomly divided into nine groups (n=5) and were supplemented with either non-germinated or germinated rice for 9 weeks. Then the plasma, liver, and fat samples were collected for the lipid metabolism effects analyses. Results Animals fed with germinated rice cultivars had improved lipid profile levels relative to the groups supplemented with non-germinated rice cultivars. The germinated rice groups, Keununjami and Superjami in particular, showed a low total cholesterol levels, high levels of high-density lipoproteins-cholesterol, high fecal lipid output, low hepatic lipid values, and low hepatic adipocyte accumulation. There was also an increase in the rate of lipolysis and decrease in lipogenesis based on the lipid-regulating enzyme activity profiles obtained for the groups that fed on germinated rice. Also, results revealed that pigmented rice cultivars had superior effects in improving the lipid metabolism relative to the non-pigmented normal brown rice variety. Conclusion Based on the results, this study suggests that germinated pigmented rice consumption can confer better lipid metabolism than ordinary white rice and constitutes as an effective functional food in alleviating the risk of having dyslipidemias like those suffering from menopausal co-morbidities. PMID:27032671

  10. Rapid quantitative analysis of adulterant Lonicera species in preparations of Lonicerae Japonicae Flos.

    PubMed

    Zhang, Xiao; Guo, Qing; Yu, Boyang

    2015-12-01

    Lonicerae Japonicae Flos is often adulterated with Lonicerae Flos, which is derived from the other four Lonicera species, in both the crude drug and Lonicerae Japonicae Flos preparations. We proposed a methodology for the quantitative analysis of adulterant Lonicerae Flos in Lonicerae Japonicae Flos preparations. Taking macranthoidins A, B, dipsacoside B (saponins), sweroside (iridoids), and luteolin-7-O-d-glucoside (flavonoids) as markers, a method of ultra high performance liquid chromatography with triple quadrupole mass spectrometry was employed to determine their amounts in Lonicerae Flos, Lonicerae Japonicae Flos, and Lonicerae Japonicae Flos preparations. The proportion of adulterant Lonicerae Flos in Lonicerae Japonicae Flos preparations was estimated based on the saponin contents of Lonicerae Japonicae Flos and Lonicerae Flos. All analytes separated under isocratic elution in 12 min with acceptable linearity, precision, repeatability, and accuracy. Lonicerae Japonicae Flos was easily distinguished from Lonicerae Flos by the total amount of saponins (0.067 and > 45.8 mg/g for Lonicerae Japonicae Flos and Lonicerae Flos, respectively). Eighteen of twenty one Lonicerae Japonicae Flos preparation samples were adulterated with Lonicerae Flos in proportions of 11.3-100%. The developed ultra high performance liquid chromatography with triple quadrupole mass spectrometry method could be used for the identification of Lonicerae Japonicae Flos and the four species of Lonicerae Flos and for the analysis of Lonicerae Japonicae Flos preparations adulterated with Lonicerae Flos. PMID:26420337

  11. Responses of super rice (Oryza sativa L.) to different planting methods for grain yield and nitrogen-use efficiency in the single cropping season.

    PubMed

    Chen, Song; Wang, Danying; Xu, Chunmei; Ji, Chenglin; Zhang, Xiaoguo; Zhao, Xia; Zhang, Xiufu; Chauhan, Bhagirath Singh

    2014-01-01

    To break the yield ceiling of rice production, a super rice project was developed in 1996 to breed rice varieties with super high yield. A two-year experiment was conducted to evaluate yield and nitrogen (N)-use response of super rice to different planting methods in the single cropping season. A total of 17 rice varieties, including 13 super rice and four non-super checks (CK), were grown under three N levels [0 (N0), 150 (N150), and 225 (N225) kg ha-1] and two planting methods [transplanting (TP) and direct-seeding in wet conditions (WDS)]. Grain yield under WDS (7.69 t ha-1) was generally lower than TP (8.58 t ha-1). However, grain yield under different planting methods was affected by N rates as well as variety groups. In both years, there was no difference in grain yield between super and CK varieties at N150, irrespective of planting methods. However, grain yield difference was dramatic in japonica groups at N225, that is, there was an 11.3% and 14.1% average increase in super rice than in CK varieties in WDS and TP, respectively. This suggests that high N input contributes to narrowing the yield gap in super rice varieties, which also indicates that super rice was bred for high fertility conditions. In the japonica group, more N was accumulated in super rice than in CK at N225, but no difference was found between super and CK varieties at N0 and N150. Similar results were also found for N agronomic efficiency. The results suggest that super rice varieties have an advantage for N-use efficiency when high N is applied. The response of super rice was greater under TP than under WDS. The results suggest that the need to further improve agronomic and other management practices to achieve high yield and N-use efficiency for super rice varieties in WDS.

  12. Cellulitis in Japanese quail (Coturnix coturnix japonica).

    PubMed

    Burns, Karen E; Otalora, Raul; Glisson, John R; Hofacre, Charles L

    2003-01-01

    A case of cellulitis was observed in Japanese quail (Coturnix coturnix japonica) reared for commercial meat production. This condition in Japanese quail has not been reported in the literature. This incident was the first, and to date only, occurrence of cellulitis in this processing plant. The cellulitis lesions were localized to the subcutis overlying the breast and inner thigh. Carcasses of processed birds and live birds from the affected farm were presented to the Poultry Diagnostic and Research Center, University of Georgia. Escherichia coli was cultured from the lesion. The affected live birds displayed lameness and had osteomyelitis. Pasteurella multocida serotype 3,4 was cultured from the liver and bone marrow of affected birds. Approximately 4.61% of the processed carcasses from the flock were condemned because of cellulitis. This represented a 10fold increase from the typical condemnation rate. Further investigation revealed birds were placed in higher than normal density; therefore, we theorize that the concurrent pasteurellosis and increased placement density resulted in the cellulitis condition. PMID:12713180

  13. Flowers of Inula japonica Attenuate Inflammatory Responses

    PubMed Central

    Choi, Jeon Hyeun; Park, Young Na; Li, Ying; Jin, Mei Hua; Lee, Jiean; Lee, Younju; Son, Jong Keun; Chang, Hyeun Wook

    2010-01-01

    Background The flowers of Inula japonica (Inulae Flos) have long been used in traditional medicine for the treatment of inflammatory diseases. In the present study, we investigated the anti-inflammatory properties of Inulae Flos Extract (IFE). Methods The anti-inflammatory effects of IFE against nitric oxide (NO), PGE2, TNF-α, and IL-6 release, as well as NF-κB and MAP kinase activation were evaluated in RAW 264.7 cells. Results IFE inhibited the production of NO and the expression of inducible nitric oxide synthase (iNOS) in LPS-stimulated RAW264.7 cells. In addition, IFE reduced the release of pro-inflammatory cytokines, such as TNF-α and IL-6. Furthermore, IFE inhibited the NF-κB activation induced by LPS, which was associated with the abrogation of IκB-α degradation and subsequent decreases in nuclear p65 and p50 levels. Moreover, the phosphorylation of ERK, JNK, and p38 MAP kinases in LPS-stimulated RAW 264.7 cells was suppressed by IFE in a dose-dependent manner. Conclusion These results suggest that the anti-inflammation activities of IFE might be attributed to the inhibition of NO, iNOS and cytokine expression through the down-regulation of NF-κB activation via suppression of IκBα and MAP kinase phosphorylation in macrophages. PMID:21165243

  14. Vaccines and diagnostics for zoonotic schistosomiasis japonica.

    PubMed

    You, Hong; McManus, Donald P

    2015-02-01

    Schistosomiasis is one of the most prevalent, insidious and serious of the tropical parasitic diseases. Although the effective anthelmintic drug, praziquantel, is widely available and cheap, it does not protect against re-infection, drug-resistant schistosome may evolve and mass drug administration programmes based around praziquantel are probably unsustainable long term. Whereas protective anti-schistosome vaccines are not yet available, the zoonotic nature of Schistosoma japonicum provides a novel approach for developing a transmission-blocking veterinary vaccine in domestic animals, especially bovines, which are major reservoir hosts, being responsible for up to 90% of environmental egg contamination in China and the Philippines. However, a greater knowledge of schistosome immunology is required to understand the processes associated with anti-schistosome protective immunity and to reinforce the rationale for vaccine development against schistosomiasis japonica. Importantly as well, improved diagnostic tests, with high specificity and sensitivity, which are simple, rapid and able to diagnose light S. japonicum infections, are required to determine the extent of transmission interruption and the complete elimination of schistosomiasis following control efforts. This article discusses aspects of the host immune response in schistosomiasis, the current status of vaccine development against S. japonicum and reviews approaches for diagnosing and detecting schistosome infections in mammalian hosts.

  15. Wild rice, hypoallergenic rice--immunologic comparison.

    PubMed

    Yum, Hye-Yung; Lee, Kyung Eun; Choi, Sung Youn; Yang, Hea Sun; Sohn, Myung Hyun; Kim, Kyu-Earn; Lee, Sang-Il

    2006-01-01

    Rice is a cereal that is mainly produced and widely consumed in Asian countries including Korea. Several reports have suggested a role of IgE-mediated hypersensitivity in asthma and eczema associated with ingestion or inhalation of rice. In Japan, hypoallergenic rices are used for a substitute of common rice in some atopic patients. We performed this study to identify major allergens of rice and changed allergenicity in cooked and hypoallergenic rice. We purified crude extracts from a variety of rice and analyzed their protein distributions by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Based on UniCAP test and skin-prick test, we selected sera with high sensitivity and analyzed specific IgE binding to rice by immunoblotting. In addition, the inhibition rate among some rice was determined by enzyme linked immunosorbent assay and CAP test. As the result of this study, rice with various origins and polishing levels had no difference in protein band pattern. After cooking, it was difficult to detect protein bands distributed in raw rice; and, even through IgE immunoblot analysis, it was impossible to differentiate between wild and hypoallergenic rice. In addition, both wild and hypoallergenic rice still had IgE binding activity on their remaining protein bands. In conclusion, almost all proteins of rice were excluded or weakened in the process of boiling and IgE binding activity still remained even in hypoallergenic rice.

  16. Isolation and identification of an allelopathic phenylethylamine in rice.

    PubMed

    Le Thi, Ho; Lin, Chung-Ho; Smeda, Reid J; Leigh, Nathan D; Wycoff, Wei G; Fritschi, Felix B

    2014-12-01

    Allelopathy is the process whereby an organic chemical (allelochemical) released from one plant influences the growth and development of other plants. Allelochemicals produced by specific rice (Oryza sativa L.) cultivars have potential to manage barnyard grass (Echinochloa crus-galli L.), a major yield-limiting weed species in rice production systems in Asia and North America. In this study, isolation and identification of an allelopathic compound, N-trans-cinnamoyltyramine (NTCT), in a Vietnamese rice cultivar 'OM 5930' was accomplished through bioassay-guided purification using reversed-phase liquid chromatography coupled with spectroscopic techniques, including tandem mass spectrometry, high resolution mass spectrometry, as well as one-dimensional and two-dimensional (1)H NMR and (13)C NMR spectroscopy. The identified compound, NTCT is considered a β-phenylethylamine. NTCT inhibited root and hypocotyl growth of cress (Lepidium sativum L.), barnyard grass and red sprangletop (Leptochloa chinensis L. Nees) at concentrations as low as 0.24 μM. The ED50 (concentration required for 50% inhibition) of NTCT on barnyard grass root and hypocotyl elongation were 1.35 and 1.85 μM, respectively. Results further demonstrated that mortality of barnyard grass and red sprangletop seedlings was >80% at a concentration of 2.4 μM of NTCT. By 20 days after transplanting, 0.425 nmol of NTCT per OM 5930 rice seedling was released into the culture solution. With concentrations of 42 μg g(-1) fresh weight, production of NTCT in intact rice plants can be considered high. These findings suggest that developing plants of Vietnamese rice cultivar OM 5930 release NTCT and may be utilized to suppress barnyard grass in rice fields. The potency of NTCT may encourage development of this compound as a bio-herbicide. PMID:25212867

  17. [Effects of free-air CO2 enrichment (FACE) on yield formation in rice (Oryza sativa)].

    PubMed

    Huang, Jianye; Yang, Hongjian; Dong, Guichun; Wang, Yulong; Zhu, Jianguo; Yang, Lianxian; Shan, Yuhua

    2002-10-01

    Effect of Free-Air CO2 enrichment (FACE, 200 mumol.mol-1 higher than CK) on rice yield and its components under field condition were studied with a Japonica variety 99-15. Results showed that FACE treatment had no obvious effect on plant height and number of leaves on main stem, but could quicken growth process of rice, shorten the whole growth duration. Increment of nitrogen application rate could weaken the effect of FACE on whole growth duration. The number of tillers and panicles, and fulfilled-grain percentage increased significantly under FACE treatment, whereas spikelets per panicle decreased. FACE treatment could significantly increase grain yield of rice, especially when higher rate of nitrogen fertilizer was applied. Increasing spikelets per panicle and spikelets per unit area under FACE treatment would result in marked increment of rice yield. Increasing nitrogen application rate was an important approach to increase spikelets per panicle and spikelets per unit area under FACE treatment.

  18. Mutation effect of high altitude balloon flight on rice and green pepper seeds.

    PubMed

    Li, J; Wang, P; Han, D; Chen, F; Deng, L; Guo, Y

    1997-04-01

    Dry seeds of rice and green pepper were carried in the basket of a high altitude balloon to 30-40 km for 8 h. The treated seeds were planted on the ground and characters of these seeds and their progenies, such as development, fruiting, disease resistance were observed. The results showed that the SP2 generation of the treated rice showed strong mutation. A Japonica male fertility restorer rice line was found out. It could be hybridized with sterile line of Indica rice, and their progeny had strong hybrid vigor, high setting percentage and good plumpness of grain. Disease resistance, high-yield, big-fruit and high vitamin C content strains were selected from the progenies of treated green pepper seeds. The above results indicated that the special conditions in high altitude could produce a variety of mutations and most of them are hereditable. Therefore, high altitude balloon flight can be used as a new method of mutation breeding. PMID:11539903

  19. Allele Distributions at Hybrid Incompatibility Loci Facilitate the Potential for Gene Flow between Cultivated and Weedy Rice in the US

    PubMed Central

    Craig, Stephanie M.; Reagon, Michael; Resnick, Lauren E.; Caicedo, Ana L.

    2014-01-01

    The accumulation of independent mutations over time in two populations often leads to reproductive isolation. Reproductive isolation between diverging populations may be reinforced by barriers that occur either pre- or postzygotically. Hybrid sterility is the most common form of postzygotic isolation in plants. Four postzygotic sterility loci, comprising three hybrid sterility systems (Sa, s5, DPL), have been recently identified in Oryza sativa. These loci explain, in part, the limited hybridization that occurs between the domesticated cultivated rice varieties, O. sativa spp. japonica and O. sativa spp. indica. In the United States, cultivated fields of japonica rice are often invaded by conspecific weeds that have been shown to be of indica origin. Crop-weed hybrids have been identified in crop fields, but at low frequencies. Here we examined the possible role of these hybrid incompatibility loci in the interaction between cultivated and weedy rice. We identified a novel allele at Sa that seemingly prevents loss of fertility in hybrids. Additionally, we found wide-compatibility type alleles at strikingly high frequencies at the Sa and s5 loci in weed groups, and a general lack of incompatible alleles between crops and weeds at the DPL loci. Our results suggest that weedy individuals, particularly those of the SH and BRH groups, should be able to freely hybridize with the local japonica crop, and that prezygotic factors, such as differences in flowering time, have been more important in limiting weed-crop gene flow in the past. As the selective landscape for weedy rice changes due to increased use of herbicide resistant strains of cultivated rice, the genetic barriers that hinder indica-japonica hybridization cannot be counted on to limit the flow of favorable crop genes into weeds. PMID:24489758

  20. Biological control of Xanthomonas Oryzae pv. Oryzae causing rice bacterial blight disease by Streptomyces toxytricini VN08-A-12, isolated from soil and leaf-litter samples in Vietnam.

    PubMed

    Van Hop, Duong; Phuong Hoa, Phan Thi; Quang, Nguyen Duc; Ton, Phan Huu; Ha, Trinh Hoang; Van Hung, Nguyen; Van, Nguyen Thi; Van Hai, Tong; Kim Quy, Nguyen Thi; Anh Dao, Nguyen Thi; Thi Thom, Vu

    2014-01-01

    A total of 2690 actinomycete strains were screened as potential biological control agents in controlling rice bacterial blight (BB) in Vietnam. From these microorganisms, seventeen actinomycete strains were found to be capable of inhibiting all 10 major Xoo races isolated from Xoo-infected rice leaves. One strain, namely VN08-A-12, contained effective characteristics in selectively inhibiting all 10 races in vitro, but did not inhibit most of the other tested microorganisms. Therefore, VN08-A-12 was subsequently selected for rice field trials for two seasons on two rice cultivars SS1 and KD18. Results showed VN08-A-12 was not only able to reduce Xoo lesion lengths in the two rice cultivars (lesion length reduction of up to 38.3%), but it also significantly reduced Xoo-related yield loss in infected rice cultivars from the field (yield loss reduction of up to 43.2%). Interestingly, the culture of this strain also increased the rice yield in healthy rice cultivars (from 2.66% to 16.98% for SS1 and from 3.11% to 5.94% for KD18 cultivar). The strain VN08-A-12 was shown to be identical to Streptomyces toxytricini. To our knowledge, this is the first study reporting S. toxytricini as a beneficial biological agent for the control of BB in rice.

  1. Biological control of Xanthomonas Oryzae pv. Oryzae causing rice bacterial blight disease by Streptomyces toxytricini VN08-A-12, isolated from soil and leaf-litter samples in Vietnam.

    PubMed

    Van Hop, Duong; Phuong Hoa, Phan Thi; Quang, Nguyen Duc; Ton, Phan Huu; Ha, Trinh Hoang; Van Hung, Nguyen; Van, Nguyen Thi; Van Hai, Tong; Kim Quy, Nguyen Thi; Anh Dao, Nguyen Thi; Thi Thom, Vu

    2014-01-01

    A total of 2690 actinomycete strains were screened as potential biological control agents in controlling rice bacterial blight (BB) in Vietnam. From these microorganisms, seventeen actinomycete strains were found to be capable of inhibiting all 10 major Xoo races isolated from Xoo-infected rice leaves. One strain, namely VN08-A-12, contained effective characteristics in selectively inhibiting all 10 races in vitro, but did not inhibit most of the other tested microorganisms. Therefore, VN08-A-12 was subsequently selected for rice field trials for two seasons on two rice cultivars SS1 and KD18. Results showed VN08-A-12 was not only able to reduce Xoo lesion lengths in the two rice cultivars (lesion length reduction of up to 38.3%), but it also significantly reduced Xoo-related yield loss in infected rice cultivars from the field (yield loss reduction of up to 43.2%). Interestingly, the culture of this strain also increased the rice yield in healthy rice cultivars (from 2.66% to 16.98% for SS1 and from 3.11% to 5.94% for KD18 cultivar). The strain VN08-A-12 was shown to be identical to Streptomyces toxytricini. To our knowledge, this is the first study reporting S. toxytricini as a beneficial biological agent for the control of BB in rice. PMID:25252641

  2. Comparison between rice husk ash grown in different regions for stabilizing fly ash from a solid waste incinerator.

    PubMed

    Benassi, L; Bosio, A; Dalipi, R; Borgese, L; Rodella, N; Pasquali, M; Depero, L E; Bergese, P; Bontempi, E

    2015-08-15

    The Stabilization of heavy metals from municipal solid waste incineration (MSWI) fly ash by rice husk ash (RHA) is under intense study as an effective strategy to recover and reuse industrial and agricultural waste together. We compare the metal entrapment performances of RHA from different Asian rice sources – namely from Japonica rice grown in Italy and Indica rice grown in India – Physicochemical and morphological characterization of the final stabilized material show that the same thermal treatment may result in marked structural differences in the silica contained in the two RHA. Remarkably, one of them displays a crystalline silica content, although obtained by a thermal treatment below 800 °C. We also find that the presence of an alkali metal ion (potassium) in the rice husk plays a crucial role in the attainment of the final silica phase. These physicochemical differences are mirrored by different stabilization yields by the two RHA. PMID:26063517

  3. Involvement of multiple types of dehydrins in the freezing response in loquat (Eriobotrya japonica).

    PubMed

    Xu, Hongxia; Yang, Yong; Xie, Li; Li, Xiaoying; Feng, Chao; Chen, Junwei; Xu, Changjie

    2014-01-01

    Dehydrins (DHNs) are a family of plant proteins typically induced in response to stress conditions that cause cellular dehydration, such as low temperatures, high salinity, and drought. Loquat (Eriobotrya japonica) is a perennial fruit crop that blossoms during winter. Loquat fruitlets are frequently injured by freezing. To evaluate the role of the EjDHNs in freezing resistance in loquat fruitlets, two cultivars of loquat, the freezing-sensitive 'Ninghaibai' (FS-NHB) and the freezing-tolerant 'Jiajiao' (FT-JJ), were analyzed under induced freezing stress. Freezing stress led to obvious accumulation of reactive oxygen species and considerable lipid peroxidation in membranes during the treatment period. Both these phenomena were more pronounced in 'FS-NHB' than in 'FS-JJ.' Immunogold labeling of dehydrin protein was performed. DHN proteins were found to be concentrated mainly in the vicinity of the plasma membrane, and the density of the immunogold labeling was significantly higher after freezing treatment, especially in the more freezing-tolerant cultivar 'FT-JJ.' Seven DHNs, showing four different structure types, were obtained from loquat fruitlets and used to study the characteristics of different EjDHN proteins. These DHN proteins are all highly hydrophilic, but they differ significantly in size, ranging from 188 to 475 amino acids, and in biochemical properties, such as theoretical pI, aliphatic index, and instability index. Freezing treatment resulted in up-regulation of the expression levels of all seven EjDHNs, regardless of structure type. The accumulation of the transcripts of these EjDHN genes was much more pronounced in 'FT-JJ' than in 'FS-NHB.' Altogether, this study provides evidence that EjDHNs are involved in the cryoprotection of the plasma membrane during freeze-induced dehydration in loquat fruitlets.

  4. Mechanisms controlling arsenic uptake in rice grown in mining impacted regions in South China.

    PubMed

    Li, Junhui; Dong, Fei; Lu, Ying; Yan, Qiuyan; Shim, Hojae

    2014-01-01

    Foods produced on soils impacted by Pb-Zn mining activities are a potential health risk due to plant uptake of the arsenic (As) associated with such mining. A field survey was undertaken in two Pb-Zn mining-impacted paddy fields in Guangdong Province, China to assess As accumulation and translocation, as well as other factors influencing As in twelve commonly grown rice cultivars. The results showed that grain As concentrations in all the surveyed rice failed national food standards, irrespective of As speciation. Among the 12 rice cultivars, "SY-89" and "DY-162" had the least As in rice grain. No significant difference for As concentration in grain was observed between the rice grown in the two areas that differed significantly for soil As levels, suggesting that the amount of As contamination in the soil is not necessarily the overriding factor controlling the As content in the rice grain. The iron and manganese plaque on the root surface curtailed As accumulation in rice roots. Based on our results, the accumulation of As within rice plants was strongly associated with such soil properties such as silicon, phosphorus, organic matter, pH, and clay content. Understanding the factors and mechanisms controlling As uptake is important to develop mitigation measures that can reduce the amount of As accumulated in rice grains produced on contaminated soils. PMID:25251438

  5. Mechanisms Controlling Arsenic Uptake in Rice Grown in Mining Impacted Regions in South China

    PubMed Central

    Lu, Ying; Yan, Qiuyan; Shim, Hojae

    2014-01-01

    Foods produced on soils impacted by Pb-Zn mining activities are a potential health risk due to plant uptake of the arsenic (As) associated with such mining. A field survey was undertaken in two Pb-Zn mining-impacted paddy fields in Guangdong Province, China to assess As accumulation and translocation, as well as other factors influencing As in twelve commonly grown rice cultivars. The results showed that grain As concentrations in all the surveyed rice failed national food standards, irrespective of As speciation. Among the 12 rice cultivars, “SY-89” and “DY-162” had the least As in rice grain. No significant difference for As concentration in grain was observed between the rice grown in the two areas that differed significantly for soil As levels, suggesting that the amount of As contamination in the soil is not necessarily the overriding factor controlling the As content in the rice grain. The iron and manganese plaque on the root surface curtailed As accumulation in rice roots. Based on our results, the accumulation of As within rice plants was strongly associated with such soil properties such as silicon, phosphorus, organic matter, pH, and clay content. Understanding the factors and mechanisms controlling As uptake is important to develop mitigation measures that can reduce the amount of As accumulated in rice grains produced on contaminated soils. PMID:25251438

  6. Mechanisms controlling arsenic uptake in rice grown in mining impacted regions in South China.

    PubMed

    Li, Junhui; Dong, Fei; Lu, Ying; Yan, Qiuyan; Shim, Hojae

    2014-01-01

    Foods produced on soils impacted by Pb-Zn mining activities are a potential health risk due to plant uptake of the arsenic (As) associated with such mining. A field survey was undertaken in two Pb-Zn mining-impacted paddy fields in Guangdong Province, China to assess As accumulation and translocation, as well as other factors influencing As in twelve commonly grown rice cultivars. The results showed that grain As concentrations in all the surveyed rice failed national food standards, irrespective of As speciation. Among the 12 rice cultivars, "SY-89" and "DY-162" had the least As in rice grain. No significant difference for As concentration in grain was observed between the rice grown in the two areas that differed significantly for soil As levels, suggesting that the amount of As contamination in the soil is not necessarily the overriding factor controlling the As content in the rice grain. The iron and manganese plaque on the root surface curtailed As accumulation in rice roots. Based on our results, the accumulation of As within rice plants was strongly associated with such soil properties such as silicon, phosphorus, organic matter, pH, and clay content. Understanding the factors and mechanisms controlling As uptake is important to develop mitigation measures that can reduce the amount of As accumulated in rice grains produced on contaminated soils.

  7. The extraction of pigments from fresh Laminaria japonica

    NASA Astrophysics Data System (ADS)

    Yang, Liqun; Li, Pengcheng; Fan, Shoujin

    2008-05-01

    The pigments in Laminaria japonica was extracted with six organic solvents and analyzed in spectroscopy analysis. The extractions conditions were screened by an orthogonal test and the quantity of extracted pigments was determined spectroscopically. The results show that: (1) among the six organic solvents, acetone was the most effective one for the extraction; (2) the optimum extraction conditions were as follows: the ratio of S/M (solvent volume/ material weight) was 30 ml/g; fresh seaweed was extracted 2 times in 2 h; (3) the average total content of pigments was 1.85 mg/g (calculated with dry L. japonica).

  8. Genetic diversity of loquat germplasm (Eriobotrya japonica (Thunb) Lindl) assessed by SSR markers.

    PubMed

    Soriano, José Miguel; Romero, Carlos; Vilanova, Santiago; Llácer, Gerardo; Badenes, María Luisa

    2005-02-01

    Genetic relationships among 40 loquat (Eriobotrya japonica (Thunb) Lindl) accessions that originated from different countries and that are part of the germplasm collection of the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were evaluated using microsatellites. Thirty primer pairs flanking microsatellites previously identified in Malus x domestica (Borkh.) were assayed. Thirteen of them amplified polymorphic products and unambiguously distinguished 34 genotypes from the 40 accessions analyzed. Six accessions showing identical marker patterns were Spanish local varieties thought to have been derived from 'Algerie' by a mutational process very common in loquat species. A total of 39 alleles were detected in the population studied, with a mean value of 2.4 alleles per locus. The expected and observed heterozygosities were 0.46 and 51% on average, respectively, leading to a negative value of the Wright's fixation index (-0.20). The values of these parameters indicate a smaller degree of genetic diversity in the set of loquat accessions analyzed than in other members of the Rosaceae family. Unweighted pair-group method (UPGMA) cluster analysis, based on Nei's genetic distance, generally grouped genotypes according to their geographic origins and pedigrees. The high number of alleles and the high expected heterozygosity detected with SSR markers developed in Malus x domestica (Borkh.) make them a suitable tool for loquat cultivar identification, confirming microsatellite marker transportability among genera in the Rosaceae family.

  9. Reducing arsenic accumulation in rice grain through iron oxide amendment.

    PubMed

    Farrow, Eric M; Wang, Jianmin; Burken, Joel G; Shi, Honglan; Yan, Wengui; Yang, John; Hua, Bin; Deng, Baolin

    2015-08-01

    Effects of soil-arsenic (As), phosphorus and iron oxide on As accumulation in rice grain were investigated. Cultivars that have significantly different sensitivity to As, straighthead-resistant Zhe 733 and straighthead-susceptible Cocodrie, were used to represent different cultivar varieties. The grain accumulation of other elements of concern, selenium (Se), molybdenum (Mo), and cadmium (Cd) was also monitored. Results demonstrated that high soil-As not only resulted in high grain-As, but could also result in high grain-Se, and Zhe 733 had significantly less grain-As than Cocodrie did. However, soil-As did not impact grain-Mo and Cd. Among all elements monitored, iron oxide amendment significantly reduced grain-As for both cultivars, while the phosphate application only reduced grain-Se for Zhe 733. Results also indicated that cultivar type significantly impacted grain accumulation of all monitored trace elements. Therefore, applying iron oxide to As-contaminated land, in addition to choosing appropriate rice cultivar, can effectively reduce the grain accumulation of As. PMID:25910688

  10. Overexpression of acetylcholinesterase gene in rice results in enhancement of shoot gravitropism.

    PubMed

    Yamamoto, Kosuke; Shida, Satoshi; Honda, Yoshihiro; Shono, Mariko; Miyake, Hiroshi; Oguri, Suguru; Sakamoto, Hikaru; Momonoki, Yoshie S

    2015-09-25

    Acetylcholine (ACh), a known neurotransmitter in animals and acetylcholinesterase (AChE) exists widely in plants, although its role in plant signal transduction is unclear. We previously reported AChE in Zea mays L. might be related to gravitropism based on pharmacological study using an AChE inhibitor. Here we clearly demonstrate plant AChE play an important role as a positive regulator in the gravity response of plants based on a genetic study. First, the gene encoding a second component of the ACh-mediated signal transduction system, AChE was cloned from rice, Oryza sativa L. ssp. Japonica cv. Nipponbare. The rice AChE shared high homology with maize, siratro and Salicornia AChEs. Similar to animal and other plant AChEs, the rice AChE hydrolyzed acetylthiocholine and propionylthiocholine, but not butyrylthiocholine. Thus, the rice AChE might be characterized as an AChE (E.C.3.1.1.7). Similar to maize and siratro AChEs, the rice AChE exhibited low sensitivity to the AChE inhibitor, neostigmine bromide, compared with the electric eel AChE. Next, the functionality of rice AChE was proved by overexpression in rice plants. The rice AChE was localized in extracellular spaces of rice plants. Further, the rice AChE mRNA and its activity were mainly detected during early developmental stages (2 d-10 d after sowing). Finally, by comparing AChE up-regulated plants with wild-type, we found that AChE overexpression causes an enhanced gravitropic response. This result clearly suggests that the function of the rice AChE relate to positive regulation of gravitropic response in rice seedlings. PMID:26277389

  11. Developmental characteristics and aluminum resistance of root border cells in rice seedlings.

    PubMed

    Cai, MiaoZhen; Zhang, ShuNa; Xing, ChengHua; Wang, FangMei; Ning, Wang; Lei, Zhu

    2011-05-01

    The developmental characteristics of root border cells (RBCs) and their role in protection of root apices of rice seedling from Al toxicity were evaluated in two rice (Oryza sativa L.) cultivars differing in Al tolerance. Root elongation and RBCs viability were used as indicators for Al effects. The formation of RBCs and the emergence of the root tip occurred almost simultaneously. Treatment of the root with Al inhibited root elongation and increased Al accumulation in the root tips. Physical removal of RBCs from root tips resulted in a more severe inhibition of root elongation and a higher Al accumulation in the root tips. These effects were more pronounced in the Al-sensitive rice cultivar (II You 6216) than that in the Al-tolerant rice cultivar (II You 838). The relative viability of attached and detached RBCs decreased with increasing Al concentrations. Al also induced a thicker mucilage layer surrounding attached RBCs of both cultivars, and detached RBCs did not. Maintaining the abundant live RBCs encapsulated root tip and enhancing their mucilage secretion, appear to be important in alleviating Al toxicity and in allowing exclusion of Al from the rice root apex.

  12. Method of creating starch-like ultra-fine rice flour and effect of spray drying on formation of free fatty acid.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice flour from long, medium, and short grain cultivars were processed by passing a 32% rice flour slurry through a microfluidizer at 100 MPa, and spray dryer at three different outlet temperatures, OT (50°C, 80°C, and 115°C). Spray drying conditions were controlled by the flow-rate of the slurry ...

  13. Identification of up-regulated genes in flag leaves during rice grain filling and characterization of OsNAC5, a new ABA-dependent transcription factor

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice is a poor source of essential micronutrients such as iron and zinc. To help clarify the molecular mechanisms that regulate the mobilization of metals from leaves to developing seeds, we conducted suppression subtractive hybridization analysis in flag leaves of two rice cultivars. Flag leaves ar...

  14. Analysis of the Structure of the AVR1-CO39 Avirulence Locus in Virulent Rice-Infecting Isolates of Magnaporthe grisea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The AVR1-CO39 gene that came from a Magnaporthe grisea isolate from weeping lovegrass controls avirulence on the rice cultivar CO39. AVR1-CO39 was not present in the genome of the rice-infecting M. grisea isolate Guy11 from French Guyana, suggesting that the gene had been deleted. Molecular analysis...

  15. Analysis of genetic and molecular identity among field isolates of the rice blast fungus with an international differential system, rep-PCR and DNA sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Pi-ta gene deployed in the Southern US rice germplasm is effective in preventing the infection by strains of Magnaporthe oryzae isolates that carry the avirulence gene AVR-Pita1. In the present study, a total of 169 isolates from rice (Oryza sativa) cultivars, with and without Pi-ta, were analyz...

  16. Laminaria japonica Extract, an Inhibitor of Clavibater michiganense Subsp. Sepedonicum

    PubMed Central

    Cai, Jin; Feng, Jia; Xie, Shulian; Wang, Feipeng; Xu, Qiufeng

    2014-01-01

    Bacterial ring rot of potato is one of the most serious potato plant and tuber diseases. Laminaria japonica extract was investigated for its antimicrobial activity against Clavibater michiganense subsp. sepedonicum (Spieckermann & Kotthoff) Davis et al., the causative agent of bacterial ring rot of potato. The results showed that the optimum extraction conditions of antimicrobial substances from L. japonica were an extraction temperature of 80°C, an extraction time of 12 h, and a solid to liquid ratio of 1∶25. Active compounds of L. japonica were isolated by solvent partition, thin layer chromatography (TLC) and column chromatography. All nineteen fractionations had antimicrobial activities against C. michiganense subsp. sepedonicum, while Fractionation three (Fr.3) had the highest (P<0.05) antimicrobial activity. Chemical composition analysis identified a total of 26 components in Fr.3. The main constituents of Fr.3 were alkanes (80.97%), esters (5.24%), acids (4.87%) and alcohols (2.21%). Antimicrobial activity of Fr.3 against C. michiganense subsp. sepedonicum could be attributed to its ability to damage the cell wall and cell membrane, induce the production of reactive oxygen species (ROS), increase cytosolic Ca2+ concentration, inhibit the glycolytic pathway (EMP) and tricarboxylic acid (TCA) cycle, inhibit protein and nucleic acid synthesis, and disrupt the normal cycle of DNA replication. These findings indicate that L. japonica extracts have potential for inhibiting C. michiganense subsp. sepedonicum. PMID:24714388

  17. Biosorption of heavy metals onto nonliving Laminaria japonica.

    PubMed

    Xiao, Jun; Chikanori, Miyamoto; Yu, Ke-Feng; Hideshi, Seki; Hideo, Maruyama; He, Pei-Min

    2012-01-01

    In this paper, study of the biosorption of Cd(2+) and Pb(2+) by nonliving Laminaria japonica in a batch adsorption system is described. The content of acidic sites and the dissociation constant of carboxylic acid functional groups (metal-binding site) of L. japonica were experimentally determined by conductometric and potentiometric titrations and theoretically predicated by using monodentate and bidentate binding models. The models are based on the monodentate or bidentate binding reactions of bivalent metal ions to acidic sites. The acidic site content and carboxylic acid dissociation constants determined are 1.25 and 0.18 mmol L(-1), respectively. The results showed that the bidentate adsorption model fits well the biosorption of bivalent metal ions onto L. japonica with the bidentate binding constants for Cd(2+) and Pb(2+) being 5.72 × 10(3) and 6.24 × 10(4) L mol(-1), respectively. The adsorption process of L. japonica followed the pseudo-second-order kinetics. PMID:22466601

  18. Response of rice genotype to straighthead disease as influenced by arsenic level and water management practices in soil.

    PubMed

    Hua, Bin; Yan, Wengui; Yang, John

    2013-01-01

    Arsenic (As) uptake by rice plants and the straighthead disease induced by As-based herbicide are of environmental concerns. Bioavailability or mobility of inorganic As in soil has been reported to be significantly influenced by soil minerals such as iron (hydr) oxide; however, the interactions of organic As such as monosodium methanearsonate (MSMA) with soil minerals are little studied, thus largely unknown. In an effort to minimize the As uptake by rice and determine rice cultivar response to soil MSMA level, a field experiment was conducted on three rice cultivars grown in both MSMA-treated and -untreated soils under continuous or intermittent flood water management practices. Results indicated that the grain yield and the occurrence of straighthead disease were cultivar-dependent and influenced by soil As level and water management practices. Straighthead-resistant cultivars yielded more and had lower grain As than the susceptible ones. Elevated soil As with continuous flood management significantly reduced the grain yield of susceptible cultivars by >89% due to substantially increased straighthead, which were induced by increased As content in grains. Yield reduction by MSMA treatment could be partially mitigated with intermittent flood water practice. The As accumulation was found to be associated with soil iron redox transformation influenced by the water management. This study demonstrates that the selection of less As-susceptible cultivars and intermittent flood water practice could be effective means to lower the As accumulation in grains and minimize the occurrence of the As-induced straighthead symptom and yield reduction. PMID:23183123

  19. Development of formulae for estimating amylose content, amylopectin chain length distribution, and resistant starch content based on the iodine absorption curve of rice starch.

    PubMed

    Nakamura, Sumiko; Satoh, Hikaru; Ohtsubo, Ken'ichi

    2015-01-01

    Not only amylose but also amylopectin greatly affects the gelatinization properties of rice starch and the quality of cooked rice grains. We here characterized the starches of 32 rice cultivars and evaluated the relationship between their iodine absorption curve, apparent amylose content (AAC), pasting property, resistant starch (RS) content, and chain length distribution of amylopectin. We found that the iodine absorption curve differed among the various sample rice cultivars. Using the wavelength at which absorbance becomes maximum on iodine staining of starch (λmax), we propose a novel index, "new λmax" (AAC/(λmax of sample rice starches-λmax of glutinous rice starch)). We developed the novel estimation formulae for AAC, RS contents, and amylopectin fractions with the use of λmax and "new λmax." These formulae would lead to the improved method for estimating starch properties using an easy and rapid iodine colorimetric method.

  20. Variation in arsenic speciation and concentration in paddy rice related to dietary exposure.

    PubMed

    Williams, P N; Price, A H; Raab, A; Hossain, S A; Feldmann, J; Meharg, A A

    2005-08-01

    Ingestion of drinking water is not the only elevated source of arsenic to the diet in the Bengal Delta. Even at background levels, the arsenic in rice contributes considerably to arsenic ingestion in subsistence rice diets. We set out to survey As speciation in different rice varieties from different parts of the globe to understand the contribution of rice to arsenic exposure. Pot experiments were utilized to ascertain whether growing rice on As contaminated soil affected speciation and whether genetic variation accounted for uptake and speciation. USA long grain rice had the highest mean arsenic level in the grain at 0.26 microg As g(-1) (n = 7), and the highest grain arsenic value of the survey at 0.40 microg As g(-1). The mean arsenic level of Bangladeshi rice was 0.13 microg As g(-1) (n = 15). The main As species detected in the rice extract were AsIII, DMAV, and AsV. In European, Bangladeshi, and Indian rice 64 +/- 1% (n = 7), 80 +/- 3% (n = 11), and 81 +/- 4% (n = 15), respectively, of the recovered arsenic was found to be inorganic. In contrast, DMAV was the predominant species in rice from the USA, with only 42 +/- 5% (n = 12) of the arsenic being inorganic. Pot experiments show that the proportions of DMAV in the grain are significantly dependent on rice cultivar (p = 0.026) and that plant nutrient status is effected by arsenic exposure. PMID:16124284

  1. Manganese-induced regulations in growth, yield formation, quality characters, rice aroma and enzyme involved in 2-acetyl-1-pyrroline biosynthesis in fragrant rice.

    PubMed

    Li, Meijuan; Ashraf, Umair; Tian, Hua; Mo, Zhaowen; Pan, Shenggang; Anjum, Shakeel Ahmad; Duan, Meiyang; Tang, Xiangru

    2016-06-01

    Micro-nutrient application is essential for normal plant growth while a little is known about manganese (Mn)-induced regulations in morpho-physiological attributes, aroma formation and enzyme involved in 2-acetyl-1-pyrroline (2-AP) biosynthesis in aromatic rice. Present study aimed to examine the influence of four levels of Mn i.e., Mn1 (100 mg MnSO4 pot(-1)), Mn2 (150 mg MnSO4 pot(-1)), Mn3 (200 mg MnSO4 pot(-1)), and Mn4 (250 mg MnSO4 pot(-1)) on the growth, yield formation, quality characters, rice aroma and enzyme involved in 2-acetyl-1-pyrroline biosynthesis in two fragrant rice cultivars i.e., Meixiangzhan and Nongxiang 18. Pots without Mn application were served as control (Ck). Each pot contained 15 kg of soil. Effects on agronomic characters, quality attributes, 2-AP contents and enzymes involved in 2-AP biosynthesis have been studied in early and late season rice. Results depicted that Mn improved rice growth, yield and related characters, and some quality attributes significantly. It further up-regulated proline, pyrroline-5-carboxylic acid (P5C) (precursors of 2-AP), soluble proteins and activities of proline dehydrogenase (ProDH), Δ(1) pyrroline-5-carboxylic acid synthetase (P5CS) ornithine aminotransferase (OAT) that led to enhanced 2-AP production in rice grains. Moreover, higher Mn levels resulted in increased grain Mn contents in both rice cultivars. Along with growth and yield improvement, Mn application significantly improved rice aromatic contents. Overall, Nongxiang 18 accumulated more 2-AP contents than Meixiangzhan in both seasons under Mn application. This study further explored the importance of Mn in rice aroma formation and signifies that micro-nutrients can play significant roles in rice aroma synthesis; however, intensive studies at molecular levels are still needed to understand the exact mechanisms of Mn to improve rice aroma formation. PMID:26995311

  2. A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement

    PubMed Central

    2014-01-01

    Background The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant. Results We used an integrated approach to compare the transcriptome, proteome and metabolome of the rhizome to other tissues of red rice. 116 Gb of transcriptome sequence was obtained from various tissues and used to identify rhizome-specific and preferentially expressed genes, including transcription factors and hormone metabolism and stress response-related genes. Proteomics and metabolomics approaches identified 41 proteins and more than 100 primary metabolites and plant hormones with rhizome preferential accumulation. Of particular interest was the identification of a large number of gene transcripts from Magnaportha oryzae, the fungus that causes rice blast disease in cultivated rice, even though the red rice plants showed no sign of disease. Conclusions A significant set of genes, proteins and metabolites appear to be specifically or preferentially expressed in the rhizome of O. longistaminata. The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease. PMID:24521476

  3. Metabolite Profiling of Diverse Rice Germplasm and Identification of Conserved Metabolic Markers of Rice Roots in Response to Long-Term Mild Salinity Stress

    PubMed Central

    Nam, Myung Hee; Bang, Eunjung; Kwon, Taek Yun; Kim, Yuran; Kim, Eun Hee; Cho, Kyungwon; Park, Woong June; Kim, Beom-Gi; Yoon, In Sun

    2015-01-01

    The sensitivity of rice to salt stress greatly depends on growth stages, organ types and cultivars. Especially, the roots of young rice seedlings are highly salt-sensitive organs that limit plant growth, even under mild soil salinity conditions. In an attempt to identify metabolic markers of rice roots responding to salt stress, metabolite profiling was performed by 1H-NMR spectroscopy in 38 rice genotypes that varied in biomass accumulation under long-term mild salinity condition. Multivariate statistical analysis showed separation of the control and salt-treated rice roots and rice genotypes with differential growth potential. By quantitative analyses of 1H-NMR data, five conserved salt-responsive metabolic markers of rice roots were identified. Sucrose, allantoin and glutamate accumulated by salt stress, whereas the levels of glutamine and alanine decreased. A positive correlation of metabolite changes with growth potential and salt tolerance of rice genotypes was observed for allantoin and glutamine. Adjustment of nitrogen metabolism in rice roots is likely to be closely related to maintain the growth potential and increase the stress tolerance of rice. PMID:26378525

  4. Evaluation of the impacts of different nuclear DNA content in the hull, endosperm, and embryo of rice seeds on GM rice quantification.

    PubMed

    Liu, Donger; Shen, Jie; Yang, Litao; Zhang, Dabing

    2010-04-28

    Rice (Oryza sativa) is a main staple food in the world, and several genetically modified (GM) rice events have been approved for commercialization. To accurately quantify GM contents in rice derived products, we have evaluated the variation of seed DNA density and nuclear DNA content in the hull, endosperm, and embryo of rice seeds from 19 cultivars, as well as their impacts on GM rice quantification. Rice endosperm DNA accounts for 73.71% of total seed DNA, whereas the hull and embryo DNAs account for 3.98% and 22.31%, respectively. Two formulas were established to describe the relationship between GM content on the basis of weight ratio (GM(wt)%) and that on the basis of haploid genome copy number ratio (GM(hg)%) for the samples containing heterozygous GM rice seeds. These two equations were well confirmed in quantification of the heterozygous GM rice TT51-1 seeds containing the GM allele from a female parent or that from a male parent. This work is useful for accurate quantification of GM rice using reference materials containing the heterozygous GM rice seed powder.

  5. Cadmium stress in rice: toxic effects, tolerance mechanisms, and management: a critical review.

    PubMed

    Rizwan, Muhammad; Ali, Shafaqat; Adrees, Muhammad; Rizvi, Hina; Zia-Ur-Rehman, Muhammad; Hannan, Fakhir; Qayyum, Muhammad Farooq; Hafeez, Farhan; Ok, Yong Sik

    2016-09-01

    Cadmium (Cd) is one of the main pollutants in paddy fields, and its accumulation in rice (Oryza sativa L.) and subsequent transfer to food chain is a global environmental issue. This paper reviews the toxic effects, tolerance mechanisms, and management of Cd in a rice paddy. Cadmium toxicity decreases seed germination, growth, mineral nutrients, photosynthesis, and grain yield. It also causes oxidative stress and genotoxicity in rice. Plant response to Cd toxicity varies with cultivars, growth condition, and duration of Cd exposure. Under Cd stress, stimulation of antioxidant defense system, osmoregulation, ion homeostasis, and over production of signaling molecules are important tolerance mechanisms in rice. Several strategies have been proposed for the management of Cd-contaminated paddy soils. One such approach is the exogenous application of hormones, osmolytes, and signaling molecules. Moreover, Cd uptake and toxicity in rice can be decreased by proper application of essential nutrients such as nitrogen, zinc, iron, and selenium in Cd-contaminated soils. In addition, several inorganic (liming and silicon) and organic (compost and biochar) amendments have been applied in the soils to reduce Cd stress in rice. Selection of low Cd-accumulating rice cultivars, crop rotation, water management, and exogenous application of microbes could be a reasonable approach to alleviate Cd toxicity in rice. To draw a sound conclusion, long-term field trials are still required, including risks and benefit analysis for various management strategies. PMID:26996904

  6. Cadmium stress in rice: toxic effects, tolerance mechanisms, and management: a critical review.

    PubMed

    Rizwan, Muhammad; Ali, Shafaqat; Adrees, Muhammad; Rizvi, Hina; Zia-Ur-Rehman, Muhammad; Hannan, Fakhir; Qayyum, Muhammad Farooq; Hafeez, Farhan; Ok, Yong Sik

    2016-09-01

    Cadmium (Cd) is one of the main pollutants in paddy fields, and its accumulation in rice (Oryza sativa L.) and subsequent transfer to food chain is a global environmental issue. This paper reviews the toxic effects, tolerance mechanisms, and management of Cd in a rice paddy. Cadmium toxicity decreases seed germination, growth, mineral nutrients, photosynthesis, and grain yield. It also causes oxidative stress and genotoxicity in rice. Plant response to Cd toxicity varies with cultivars, growth condition, and duration of Cd exposure. Under Cd stress, stimulation of antioxidant defense system, osmoregulation, ion homeostasis, and over production of signaling molecules are important tolerance mechanisms in rice. Several strategies have been proposed for the management of Cd-contaminated paddy soils. One such approach is the exogenous application of hormones, osmolytes, and signaling molecules. Moreover, Cd uptake and toxicity in rice can be decreased by proper application of essential nutrients such as nitrogen, zinc, iron, and selenium in Cd-contaminated soils. In addition, several inorganic (liming and silicon) and organic (compost and biochar) amendments have been applied in the soils to reduce Cd stress in rice. Selection of low Cd-accumulating rice cultivars, crop rotation, water management, and exogenous application of microbes could be a reasonable approach to alleviate Cd toxicity in rice. To draw a sound conclusion, long-term field trials are still required, including risks and benefit analysis for various management strategies.

  7. Root distribution and potential interactions between allelopathic rice, sprangletop (Leptochloa spp.), and barnyardgrass (Echinochloa crus-galli) based on ¹³C isotope discrimination analysis.

    PubMed

    Gealy, David; Moldenhauer, Karen; Duke, Sara

    2013-02-01

    Weed-suppressive rice cultivars hold promise for improved and more economical weed management in rice. Interactions between roots of rice and weeds are thought to be modulated by the weed-suppressive activity of some rice cultivars, but these phenomena are difficult to measure and not well understood. Thus, above-ground productivity, weed suppression, and root distribution of 11 rice cultivars and two weed species were evaluated in a drill-seeded, flood-irrigated system at Stuttgart, Arkansas, USA in a two-year study. The allelopathic cultivars, PI 312777 and Taichung Native 1 (TN-1), three other weed-suppressive cultivars, three indica-derived breeding selections, and three non-suppressive commercial cultivars were evaluated in field plots infested with barnyardgrass (Echinochloa crus-galli (L.) Beauv.) or bearded sprangletop (sprangletop, Leptochloa fusca (L.) Kunth var. fascicularis (Lam.) N. Snow). The allelopathic cultivars produced more tillers and suppressed both weed species to a greater extent than did the breeding selections or the non-suppressive cultivars. (13)C isotope discrimination analysis of mixed root samples to a depth of 15 cm revealed that the allelopathic cultivars typically produced a greater fraction of their total root mass in the surface 0-5 cm of soil depth compared to the breeding selections or the non-suppressive cultivars, which tended to distribute their roots more evenly throughout the soil profile. These trends in root mass distribution were apparent at both early (pre-flood) and late-season stages in weed-free and weed-infested plots. Cultivar productivity and root distribution generally responded similarly to competition with the two weed species, but barnyardgrass reduced rice yield and root mass more than did sprangletop. These findings demonstrate for the first time that roots of the allelopathic cultivars PI 312777 and TN-1 explore the upper soil profile more thoroughly than do non-suppressive cultivars under weed

  8. Effects of Lonicera japonica Thunb. on Type 2 Diabetes via PPAR-γ Activation in Rats.

    PubMed

    Han, Jae Min; Kim, Mi Hye; Choi, You Yeon; Lee, Haesu; Hong, Jongki; Yang, Woong Mo

    2015-10-01

    Lonicera japonica Thunb. (Caprifoliaceae) is a traditional herbal medicine and has been used to treat diabetic symptoms. Notwithstanding its use, the scientific basis on anti-diabetic properties of L. japonica is not yet established. This study is designed to investigate anti-diabetic effects of L. japonica in type 2 diabetic rats. L. japonica was orally administered at the dose of 100 mg/kg in high-fat diet-fed and low-dose streptozotocin-induced rats. After the treatment of 4 weeks, L. japonica reduced high blood glucose level and homeostatic model assessment of insulin resistance in diabetic rats. In addition, body weight and food intake were restored by the L. japonica treatment. In the histopathologic examination, the amelioration of damaged β-islet in pancreas was observed in L. japonica-treated diabetic rats. The administration of L. japonica elevated peroxisome proliferator-activated receptor gamma and insulin receptor subunit-1 protein expressions. The results demonstrated that L. japonica had anti-diabetic effects in type 2 diabetic rats via the peroxisome proliferator-activated receptor gamma regulatory action of L. japonica as a potential mechanism.

  9. Effects of Lonicera japonica Thunb. on Type 2 Diabetes via PPAR-γ Activation in Rats.

    PubMed

    Han, Jae Min; Kim, Mi Hye; Choi, You Yeon; Lee, Haesu; Hong, Jongki; Yang, Woong Mo

    2015-10-01

    Lonicera japonica Thunb. (Caprifoliaceae) is a traditional herbal medicine and has been used to treat diabetic symptoms. Notwithstanding its use, the scientific basis on anti-diabetic properties of L. japonica is not yet established. This study is designed to investigate anti-diabetic effects of L. japonica in type 2 diabetic rats. L. japonica was orally administered at the dose of 100 mg/kg in high-fat diet-fed and low-dose streptozotocin-induced rats. After the treatment of 4 weeks, L. japonica reduced high blood glucose level and homeostatic model assessment of insulin resistance in diabetic rats. In addition, body weight and food intake were restored by the L. japonica treatment. In the histopathologic examination, the amelioration of damaged β-islet in pancreas was observed in L. japonica-treated diabetic rats. The administration of L. japonica elevated peroxisome proliferator-activated receptor gamma and insulin receptor subunit-1 protein expressions. The results demonstrated that L. japonica had anti-diabetic effects in type 2 diabetic rats via the peroxisome proliferator-activated receptor gamma regulatory action of L. japonica as a potential mechanism. PMID:26174209

  10. Application of resistance gene analog markers to analyses of genetic structure and diversity in rice.

    PubMed

    Ren, Juansheng; Yu, Yuchao; Gao, Fangyuan; Zeng, Lihua; Lu, Xianjun; Wu, Xianting; Yan, Wengui; Ren, Guangjun

    2013-07-01

    Plant disease resistance gene analog (RGA) markers were designed according to the conserved sequence of known RGAs and used to map resistance genes. We used genome-wide RGA markers for genetic analyses of structure and diversity in a global rice germplasm collection. Of the 472 RGA markers, 138 were polymorphic and these were applied to 178 entries selected from the USDA rice core collection. Results from the RGA markers were similar between two methods, UPGMA and STRUCTURE. Additionally, the results from RGA markers in our study were agreeable with those previously reported from SSR markers, including cluster of ancestral classification, genetic diversity estimates, genetic relatedness, and cluster of geographic origins. These results suggest that RGA markers are applicable for analyses of genetic structure and diversity in rice. However, unlike SSR markers, the RGA markers failed to differentiate temperate japonica, tropical japonica, and aromatic subgroups. The restricted way for developing RGA markers from the cDNA sequence might limit the polymorphism of RGA markers in the genome, thus limiting the discriminatory power in comparison with SSR markers. Genetic differentiation obtained using RGA markers may be useful for defining genetic diversity of a suite of random R genes in plants, as many studies show a differentiation of resistance to a wide array of pathogens. They could also help to characterize the genetic structure and geographic distribution in crops, including rice, wheat, barley, and banana.

  11. Application of resistance gene analog markers to analyses of genetic structure and diversity in rice.

    PubMed

    Ren, Juansheng; Yu, Yuchao; Gao, Fangyuan; Zeng, Lihua; Lu, Xianjun; Wu, Xianting; Yan, Wengui; Ren, Guangjun

    2013-07-01

    Plant disease resistance gene analog (RGA) markers were designed according to the conserved sequence of known RGAs and used to map resistance genes. We used genome-wide RGA markers for genetic analyses of structure and diversity in a global rice germplasm collection. Of the 472 RGA markers, 138 were polymorphic and these were applied to 178 entries selected from the USDA rice core collection. Results from the RGA markers were similar between two methods, UPGMA and STRUCTURE. Additionally, the results from RGA markers in our study were agreeable with those previously reported from SSR markers, including cluster of ancestral classification, genetic diversity estimates, genetic relatedness, and cluster of geographic origins. These results suggest that RGA markers are applicable for analyses of genetic structure and diversity in rice. However, unlike SSR markers, the RGA markers failed to differentiate temperate japonica, tropical japonica, and aromatic subgroups. The restricted way for developing RGA markers from the cDNA sequence might limit the polymorphism of RGA markers in the genome, thus limiting the discriminatory power in comparison with SSR markers. Genetic differentiation obtained using RGA markers may be useful for defining genetic diversity of a suite of random R genes in plants, as many studies show a differentiation of resistance to a wide array of pathogens. They could also help to characterize the genetic structure and geographic distribution in crops, including rice, wheat, barley, and banana. PMID:24099390

  12. Morphology based field rice density detection from rice transplant stage to rice jointing stage

    NASA Astrophysics Data System (ADS)

    Bai, X. D.; Cao, Z. G.; Wang, Y.; Ye, M. N.; Yu, Z. H.; Li, Y. N.

    2013-10-01

    Rice yield estimation is an important aspect in the agriculture research field. For the rice yield estimation, rice density is one of its useful factors. In this paper, we propose a new method to automatically detect the rice density from the rice transplanting stage to rice jointing stage. It devotes to detect rice planting density by image low-level features of the rice image sequences taken in the fields. Moreover, a rice jointing stage automatic detection method is proposed so as to terminate the rice density detection algorithm. The validities of the proposed rice density detection method and the rice jointing stage automatic detection method are proved in the experiment.

  13. Extensive Microsatellite Variation in Rice Induced by Introgression from Wild Rice (Zizania latifolia Griseb.)

    PubMed Central

    Dong, Zhenying; Wang, Hongyan; Dong, Yuzhu; Wang, Yongming; Liu, Wei; Miao, Gaojian; Lin, Xiuyun; Wang, Daqing; Liu, Bao

    2013-01-01

    Background It is widely accepted that interspecific hybridization may induce genomic instability in the resultant hybrids. However, few studies have been performed on the genomic analysis of homoploid hybrids and introgression lines. We have reported previously that by introgressive hybridization, a set of introgression lines between rice (Oryza sativa L.) and wild rice (Zizania latifolia Griseb.) was successfully generated, and which have led to the release of several cultivars. Methodology Using 96 microsatellite markers located in the nuclear and organelle genomes of rice, we investigated microsatellite stability in three typical introgression lines. Expression of a set of mismatch repair (MMR) genes and microsatellite-containing genes was also analyzed. Results/Conclusions Compared with the recipient rice cultivar (Matsumae), 55 of the 96 microsatellite loci revealed variation in one or more of the introgression lines, and 58.2% of the altered alleles were shared by at least two lines, indicating that most of the alterations had occurred in the early stages of introgression before their further differentiation. 73.9% of the non-shared variations were detected only in one introgression line, i.e. RZ2. Sequence alignment showed that the variations included substitutions and indels that occurred both within the repeat tracts and in the flanking regions. Interestingly, expression of a set of MMR genes altered dramatically in the introgression lines relative to their rice parent, suggesting participation of the MMR system in the generation of microsatellite variants. Some of the altered microsatellite loci are concordant with changed expression of the genes harboring them, suggesting their possible cis-regulatory roles in controlling gene expression. Because these genes bear meaningful homology to known-functional proteins, we conclude that the introgression-induced extensive variation of microsatellites may have contributed to the novel phenotypes in the

  14. Overexpression of Arabidopsis and rice stress genes' inducible transcription factor confers drought and salinity tolerance to rice.

    PubMed

    Datta, Karabi; Baisakh, Niranjan; Ganguly, Moumita; Krishnan, Sellapan; Yamaguchi Shinozaki, Kazuko; Datta, Swapan K

    2012-06-01

    Rice yield is greatly affected by environmental stresses such as drought and salinity. In response to the challenge of producing rice plants tolerant to these stresses, we introduced cDNA encoding the transcription factors DREB1A and DREB1B under the control of the stress inducible rd29 promoter. Two different indica rice cultivars were used, BR29, an improved commercially cultivated variety from Bangladesh and IR68899B, an IRRI bred maintainer line for hybrid rice. Agrobacterium mediated transformation of BR29 was done independently with DREB1A isolated from rice and Arabidopsis and DREB1B isolated from rice, whereas biolistic transformation was done with rice- DREB1B in the case of IR68899B. Initial genetic integration was confirmed by PCR and Southern blot analysis. Salinity tolerance was assayed in very young seedlings. Drought stress tests were found to be more reliable when they were carried out at the pre-flowering booting stage. RNA gel blot analysis as well as quantitative PCR analysis was performed to estimate the transcription level under stressed and unstressed conditions. Agronomic performance studies were done with stressed and unstressed plants to compare the yield losses due to dehydration and salt loading stresses. Noticeably enhanced tolerance to dehydration was observed in the plants transformed with DREB1A isolated from Arabidopsis while DREB1B was found to be more effective for salt tolerance.

  15. Rice Molecular Breeding Laboratories in the Genomics Era: Current Status and Future Considerations

    PubMed Central

    Collard, Bert C. Y.; Vera Cruz, Casiana M.; McNally, Kenneth L.; Virk, Parminder S.; Mackill, David J.

    2008-01-01

    Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information—coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools—provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to “bridge the application gap” between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs. PMID:18528527

  16. Structural understanding of the recycling of oxidized ascorbate by dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica

    PubMed Central

    Do, Hackwon; Kim, Il-Sup; Jeon, Byoung Wook; Lee, Chang Woo; Park, Ae Kyung; Wi, Ah Ram; Shin, Seung Chul; Park, Hyun; Kim, Young-Saeng; Yoon, Ho-Sung; Kim, Han-Woo; Lee, Jun Hyuck

    2016-01-01

    Dehydroascorbate reductase (DHAR) is a key enzyme involved in the recycling of ascorbate, which catalyses the glutathione (GSH)-dependent reduction of oxidized ascorbate (dehydroascorbate, DHA). As a result, DHAR regenerates a pool of reduced ascorbate and detoxifies reactive oxygen species (ROS). In previous experiments involving transgenic rice, we observed that overexpression of DHAR enhanced grain yield and biomass. Since the structure of DHAR is not available, the enzymatic mechanism is not well-understood and remains poorly characterized. To elucidate the molecular basis of DHAR catalysis, we determined the crystal structures of DHAR from Oryza sativa L. japonica (OsDHAR) in the native, ascorbate-bound, and GSH-bound forms and refined their resolutions to 1.9, 1.7, and 1.7 Å, respectively. These complex structures provide the first information regarding the location of the ascorbate and GSH binding sites and their interacting residues. The location of the ascorbate-binding site overlaps with the GSH-binding site, suggesting a ping-pong kinetic mechanism for electron transfer at the common Cys20 active site. Our structural information and mutagenesis data provide useful insights into the reaction mechanism of OsDHAR against ROS-induced oxidative stress in rice. PMID:26775680

  17. [Bioinformatics analysis and expressed level of histone methyltransferase genes in Lonicera japonica].

    PubMed

    Qi, Lin-jie; Yuan, Yuan; Huang, Lu-qi; Long, Ping; Zha, Liang-ping; Wang, Yao-long

    2015-06-01

    Twenty-three histone methyltransferase genes were obtained from transcriptome dataset of Lonicera japonica. The nucleotide and proteins characteristics, subcellular localization, senior structural domains and conservative forecasting were analyzed. The result of phylogenetic tree showed that 23 histone methyltransferases were mainly divided into two groups: lysine methyltransferase and arginine methyltransferases. The result of gene expression showed that 23 histone methyltransferases showed preference in terms of interspecies and organs. They were more expressed in buds of L. japonica than in L. japonica var. chinensis and lower in leaves of L. japonica than in L. japonica var. chinensis. Eight genes were specific expressed in flower. These results provided basis for further understanding the function of histone methyltransferase and epigenetic regulation of active ingredients of L. japonica. PMID:26552158

  18. Sensitivity of tomato cultivars to sulfur dioxide

    SciTech Connect

    Howe, T.K.; Woltz, S.S.

    1982-04-01

    The sensitivity of 26 cultivars of tomato (Lycopersicon esculentum Mill.) were compared at 2 concentrations of SO/sub 2/in specially designed exposure greenhouses. Cultivars studied included fresh market, processing, and specialty types. Insensitive and sensitive cultivars were identified by assessment of acute SO/sub 2/-induced foliar necrosis. Cultivars found to be insensitive to SO/sub 2/ included: 'Ace', 'Bonanza', 'Heinz 1350', 'Tarquinia Tondino', and 'VF 145-B 7879'. Cultivars found to be sensitive to SO/sub 2/ included: 'Bellarina', 'Chico III', 'Flora-Dade', 'Red Cherry Large' 'Sub-Arctic Delight', and 'Vetomold. 10 figures, 1 table.

  19. Characterization of High-Value Bioactives in Some Selected Varieties of Pakistani Rice (Oryza sativa L.)

    PubMed Central

    Zubair, Muhammad; Anwar, Farooq; Ashraf, Muhammad; Uddin, Md. Kamal

    2012-01-01

    The present study reports the composition and variation of fatty acids, sterols, tocopherols and γ-oryzanol among selected varieties namely Basmati Super, Basmati 515, Basmati 198, Basmati 385, Basmati 2000, Basmati 370, Basmati Pak, KSK-139, KS-282 and Irri-6 of Pakistani rice (Oryza sativa L). Oil content extracted with n-hexane from different varieties of brown rice seed (unpolished rice) ranged from 1.92% to 2.72%. Total fatty acid contents among rice varieties tested varied between 18240 and 25840 mg/kg brown rice seed. The rice tested mainly contained oleic (6841–10952 mg/kg) linoleic (5453–7874 mg/kg) and palmitic acid (3613–5489 mg/kg). The amounts of total phytosterols (GC and GC-MS analysis), with main contribution from β-sitosterol (445–656 mg/kg), campesterol (116–242 mg/kg), Δ5-avenasterol (89–178 mg/kg) and stigmasterol (75–180 mg/kg) were established to be 739.4 to 1330.4 mg/kg rice seed. The content of α-, γ- and δ-tocopherols as analyzed by HPLC varied from 39.0–76.1, 21.6–28.1 and 6.5–16.5 mg/kg rice seed, respectively. The amounts of different γ-oryzanol components (HPLC data), identified as cycloartenyl ferulate, 24-methylene cycloartanyl ferulate, campesteryl ferulate and β-sitosteryl ferulate, were in the range of 65.5–103.6, 140.2–183.1, 29.8–45.5 and 8.6–10.4 mg/kg rice seed, respectively. Overall, the concentration of these bioactives was higher in the Basmati rice cultivars showing their functional food superiority. In conclusion, the tested varieties of Pakistani rice, especially the Basmati cultivars, can provide best ingredients for functional foods. PMID:22605998

  20. Herbicide-induced anthocyanin accumulation in transgenic rice by expression of rice OSB2 under the control of rice CYP72A21 promoter.

    PubMed

    Hirose, Sakiko; Kawahigashi, Hiroyuki; Tagiri, Akem