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Sample records for japonica rice cultivars

  1. Metabolic variation between japonica and indica rice cultivars as revealed by non-targeted metabolomics

    PubMed Central

    Hu, Chaoyang; Shi, Jianxin; Quan, Sheng; Cui, Bo; Kleessen, Sabrina; Nikoloski, Zoran; Tohge, Takayuki; Alexander, Danny; Guo, Lining; Lin, Hong; Wang, Jing; Cui, Xiao; Rao, Jun; Luo, Qian; Zhao, Xiangxiang; Fernie, Alisdair R.; Zhang, Dabing

    2014-01-01

    Seed metabolites are critically important both for plant development and human nutrition; however, the natural variation in their levels remains poorly characterized. Here we profiled 121 metabolites in mature seeds of a wide panel Oryza sativa japonica and indica cultivars, revealing correlations between the metabolic phenotype and geographic origin of the rice seeds. Moreover, japonica and indica subspecies differed significantly not only in the relative abundances of metabolites but also in their corresponding metabolic association networks. These findings provide important insights into metabolic adaptation in rice subgroups, bridging the gap between genome and phenome, and facilitating the identification of genetic control of metabolic properties that can serve as a basis for the future improvement of rice quality via metabolic engineering. PMID:24861081

  2. LSCHL4 from Japonica Cultivar, Which Is Allelic to NAL1, Increases Yield of Indica Super Rice 93-11

    PubMed Central

    Zhang, Guang-Heng; Li, Shu-Yu; Wang, Li; Ye, Wei-Jun; Zeng, Da-Li; Rao, Yu-Chun; Peng, You-Lin; Hu, Jiang; Yang, Yao-Long; Xu, Jie; Ren, De-Yong; Gao, Zhen-Yu; Zhu, Li; Dong, Guo-Jun; Hu, Xing-Ming; Yan, Mei-Xian; Guo, Long-Biao; Li, Chuan-You; Qian, Qian

    2014-01-01

    The basic premise of high yield in rice is to improve leaf photosynthetic efficiency and coordinate the source–sink relationship in rice plants. Quantitative trait loci (QTLs) related to morphological traits and chlorophyll content of rice leaves were detected at the stages of heading to maturity, and a major QTL (qLSCHL4) related to flag leaf shape and chlorophyll content was detected at both stages in recombinant inbred lines constructed using the indica rice cultivar 93-11 and the japonica rice cultivar Nipponbare. Map-based cloning and expression analysis showed that LSCHL4 is allelic to NAL1, a gene previously reported in narrow leaf mutant of rice. Overexpression lines transformed with vector carrying LSCHL4 from Nipponbare and a near-isogenic line of 93-11 (NIL-9311) had significantly increased leaf chlorophyll content, enlarged flag leaf size, and improved panicle type. The average yield of NIL-9311 was 18.70% higher than that of 93-11. These results indicate that LSCHL4 had a pleiotropic function. Exploring and pyramiding more high-yield alleles resembling LSCHL4 for super rice breeding provides an effective way to achieve new breakthroughs in raising rice yield and generate new ideas for solving the problem of global food safety. PMID:24795339

  3. 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...

  4. Characterization of Grain Quality and Starch Fine Structure of Two Japonica Rice (Oryza Sativa) Cultivars with Good Sensory Properties at Different Temperatures during the Filling Stage.

    PubMed

    Zhang, Changquan; Zhou, Lihui; Zhu, Zhengbin; Lu, Huwen; Zhou, Xingzhong; Qian, Yiting; Li, Qianfeng; Lu, Yan; Gu, Minghong; Liu, Qiaoquan

    2016-05-25

    Temperature during the growing season is a critical factor affecting grain quality. High temperatures at grain filling affect kernel development, resulting in reduced yield, increased chalkiness, reduced amylose content, and poor milling quality. Here, we investigated the grain quality and starch structure of two japonica rice cultivars with good sensory properties grown at different temperatures during the filling stage under natural field conditions. Compared to those grown under normal conditions, rice grains grown under hot conditions showed significantly reduced eating and cooking qualities, including a higher percentage of grains with chalkiness, lower protein and amylose contents, and higher pasting properties. Under hot conditions, rice starch contained reduced long-chain amylose (MW 10(7.1) to 10(7.4)) and significantly fewer short-chain amylopectin (DP 5-12) but more intermediate- (DP 13-34) and long- (DP 45-60) chain amylopectin than under normal conditions, as well as higher crystallinity and gelatinization properties.

  5. Utilization of weedy rice for development of japonica hybrid rice (Oryza sativa L.).

    PubMed

    Tang, Liang; Ma, Dian Rong; Xu, Zheng Jin; Deng, Hua Feng; Chen, Wen Fu; Yuan, Long Ping

    2011-05-01

    Two representative weedy rice lines, three typical japonica varieties and three typical indica varieties were used for 6 pairs of reciprocal crosses. The morphological traits of twelve F(1) hybrid lines, their parents and four elite cultivars were investigated for heterosis over mid-parent (HM), over parent (HP) and competitive heterosis (CH) analysis. Traits detected in weedy rice lines seemed larger than those in cultivars and excellent heterosis was produced in weedy rice crossing with japonica rice. Although weedy rice kept closer relationships with japonica rice compared to indica rice. But the heterosis of reciprocal crosses between weedy rice and japonica was closed to those of crosses between indica rice and japonica rice. In six of one hundred and eighteen weedy rice lines, the fertility restore gene for BT type cytoplasmic male sterility (BT-CMS) were detected. Weedy rice was very valuable germplasm resources with the abundant polymorphism. Meanwhile, the disadvantage, lodging, shattering and incompact plant type, should be modified by hybridization, backcross and multiple cross with japonica rice. Although it is difficult to use weedy rice directly, weedy rice may be available to breed both male sterile line and restorer line through improvement, developing japonica hybrid rice.

  6. 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...

  7. Differentiation of rice cultivar for grain arsenic content associated with soil and water management in rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Reduction of arsenic (As) in rice grains play an important role in improvement of food quality and minimization of any potential risk from dietary exposure. Twenty-one worldwide cultivars including both indica and japonica subspecies were grown under two water treatments, saturated soil and consiste...

  8. Golden Indica and Japonica rice lines amenable to deregulation.

    PubMed

    Hoa, Tran Thi Cuc; Al-Babili, Salim; Schaub, Patrick; Potrykus, Ingo; Beyer, Peter

    2003-09-01

    As an important step toward free access and, thus, impact of GoldenRice, a freedom-to-operate situation has been achieved for developing countries for the technology involved. Specifically, to carry the invention beyond its initial "proof-of-concept" status in a Japonica rice (Oryza sativa) cultivar, we report here on two transformed elite Indica varieties (IR64 and MTL250) plus one Japonica variety Taipei 309. Indica varieties are predominantly consumed in the areas with vitamin A deficiency. To conform with regulatory constraints, we changed the vector backbone, investigated the absence of beyond-border transfer, and relied on Agrobacterium tumefaciens-mediated transformation to obtain defined integration patterns. To avoid an antibiotic selection system, we now rely exclusively on phosphomannose isomerase as the selectable marker. Single integrations were given a preference to minimize potential epigenetic effects in subsequent generations. These novel lines, now in the T(3) generation, are highly valuable because they are expected to more readily receive approval for follow-up studies such as nutritional and risk assessments and for breeding approaches leading to locally adapted variety development.

  9. Important sensory properties differentiating premium rice cultivars.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In rice-consuming countries worldwide, specific cultivars are recognized as premium, “gold standard” cultivars, while others are recognized as being superior, but not the best. It has been difficult to ascertain whether preferences for premium rice cultivars are driven by discernable differences in...

  10. Sheath-blight resistance QTLs and in japonica rice germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sheath blight (SB), caused by Rhizoctonia solani, is one of the most serious diseases of cultivated rice (Oryza sativa L.) and genetic resistance is in demand by rice breeders. With the goal of resistance-QTL discovery in U. S. japonica breeding material, a set of 197 F1 doubled-haploid lines (DHLs)...

  11. Essential amino acids of starch synthase IIa differentiate amylopectin structure and starch quality between japonica and indica rice varieties.

    PubMed

    Nakamura, Yasunori; Francisco, Perigio B; Hosaka, Yuko; Sato, Aya; Sawada, Takayuki; Kubo, Akiko; Fujita, Naoko

    2005-05-01

    Four amino acids were variable between the 'active' indica-type and 'inactive' japonica-type soluble starch synthase IIa (SSIIa) of rice plants; Glu-88 and Gly-604 in SSIIa of indica-cultivars IR36 and Kasalath were replaced by Asp-88 and Ser-604, respectively, in both japonica cultivars Nipponbare and Kinmaze SSIIa, whereas Val-737 and Leu-781 in indica SSIIa were replaced by Met-737 in cv. Nipponbare and Phe-781 in cv. Kinmaze SSIIa, respectively. The SSIIa gene fragments shuffling experiments revealed that Val-737 and Leu-781 are essential not only for the optimal SSIIa activity, but also for the capacity to synthesize indica-type amylopectin. Surprisingly, however, a combination of Phe-781 and Gly-604 could restore about 44% of the SSIIa activity provided that Val-737 was conserved. The introduction of the 'active' indica-type SSIIa gene enabled the japonica-type cv. Kinmaze to synthesize indica-type amylopectin. The starch in the transformed japonica rice plants exhibited gelatinization-resistant properties that are characteristic of indica-rice starch. Transformed lines expressing different levels of the IR36 SSIIa protein produced a variety of starches with amylopectin chain-length distribution patterns that correlated well with their onset temperatures of gelatinization. The present study confirmed that the SSIIa activity determines the type of amylopectin structure of rice starch to be either the typical indica-type or japonica-type, by playing a specific role in the synthesis of the long B(1) chains by elongating short A and B(1) chains, notwithstanding the presence of functional two additional SSII genes, a single SSI gene, two SSIII genes, and two SSIV genes in rice plants.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. Development of casparian strip in rice cultivars

    PubMed Central

    Cai, Xia; Chen, Tong; Zhou, QingYuan; Xu, Lei; Qu, LeQing; Hua, XueJun

    2011-01-01

    The development of Casparian strips (CSs) on the endo- and exodermis and their chemical components in roots of three cultivars of rice (Oryza sativa) with different salt tolerance were compared using histochemistry and Fourier transform infrared (FTIR) spectroscopy. The development and deposition of suberin lamellae of CSs on the endo- and exodermis in the salt-tolerant cultivar Liaohan 109 was earlier than in the moderately tolerant cultivar Tianfeng 202 and the sensitive cultivar Nipponbare. The detection of chemical components indicated major contributions to the structure of the outer part from aliphatic suberin, lignin and cell wall proteins and carbohydrates to the rhizodermis, exodermis, sclerenchyma and one layer of cortical cells in series (OPR) and the endodermal Casparian strip. Moreover, the amounts of these major chemical components in the outer part of the Liaohan 109 root were higher than in Tianfeng 202 and Nipponbare, but there was no distinct difference in endodermal CSs among the three rice cultivars. The results suggest that the exodermis of the salt-tolerant cultivar Liaohan 109 functions as a barrier for resisting salt stress. PMID:21248477

  17. Study on creep properties of Japonica cooked rice and its relationship with rice chemical compositions and sensory evaluation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Creep properties of four varieties japonica cooked rice were tested using a Dynamic Mechanical Analyser (DMA Q800). The creep curve was described by Burgers model. The creep process of japonica cooked rice mainly consisted of retarded elastic deformation, epsilonR and viscous flow deformation, epsil...

  18. 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.

  19. 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.

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

    PubMed Central

    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

    2013-01-01

    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. PMID:24297875

  1. Characterization and Fine Mapping of a Blast Resistant Gene Pi-jnw1 from the japonica Rice Landrace Jiangnanwan

    PubMed Central

    Wang, Ruisen; Fang, Nengyan; Guan, Changhong; He, Wanwan; Bao, Yongmei; Zhang, Hongsheng

    2016-01-01

    Rice blast is a destructive disease caused by Magnaporthe oryzae, and it has a large impact on rice production worldwide. Compared with leaf blast resistance, our understanding of panicle blast resistance is limited. The japonica landrace Jiangnanwan from Taihu Lake region in China shows highly resistance to panicle and leaf blast. In this study, three generations (F2:5, F2:6, F2:7) consisting of 221 RILs (recombination inbreeding lines), developed from the cross of Jiangnanwan and Suyunuo, a susceptible-blast japonica variety, were evaluated for panicle blast resistance in the fields and leaf blast resistance in greenhouse in Nanjing in 2013, 2014 and 2015. A blast resistance gene Pi-jnw1 referring to panicle blast resistance and leaf blast resistance was identified in the three generations and located in the region of RM27273 and RM27381 in chromosome 11. The RIL18 line harboring Pi-jnw1 was selected to be backcrossed with Suyunuo to develop BC2F2 populations. According to the genotyping of 1,150 BC2F2 individuals and panicle blast and leaf blast resistance evaluation of 47 recombinants between RM27150 and RM27381, Pi-jnw1 was finally mapped to the 282 kb region between markers W28 and BS39. This study revealed that Jiangnanwan harboring a panicle blast and leaf blast resistance gene Pi-jnw1 could be a genetic source for breeding new rice cultivars with panicle blast resistance. PMID:28036378

  2. Characterization and Fine Mapping of a Blast Resistant Gene Pi-jnw1 from the japonica Rice Landrace Jiangnanwan.

    PubMed

    Wang, Ruisen; Fang, Nengyan; Guan, Changhong; He, Wanwan; Bao, Yongmei; Zhang, Hongsheng

    2016-01-01

    Rice blast is a destructive disease caused by Magnaporthe oryzae, and it has a large impact on rice production worldwide. Compared with leaf blast resistance, our understanding of panicle blast resistance is limited. The japonica landrace Jiangnanwan from Taihu Lake region in China shows highly resistance to panicle and leaf blast. In this study, three generations (F2:5, F2:6, F2:7) consisting of 221 RILs (recombination inbreeding lines), developed from the cross of Jiangnanwan and Suyunuo, a susceptible-blast japonica variety, were evaluated for panicle blast resistance in the fields and leaf blast resistance in greenhouse in Nanjing in 2013, 2014 and 2015. A blast resistance gene Pi-jnw1 referring to panicle blast resistance and leaf blast resistance was identified in the three generations and located in the region of RM27273 and RM27381 in chromosome 11. The RIL18 line harboring Pi-jnw1 was selected to be backcrossed with Suyunuo to develop BC2F2 populations. According to the genotyping of 1,150 BC2F2 individuals and panicle blast and leaf blast resistance evaluation of 47 recombinants between RM27150 and RM27381, Pi-jnw1 was finally mapped to the 282 kb region between markers W28 and BS39. This study revealed that Jiangnanwan harboring a panicle blast and leaf blast resistance gene Pi-jnw1 could be a genetic source for breeding new rice cultivars with panicle blast resistance.

  3. Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice.

    PubMed

    Yamanaka, Shinsuke; Nakamura, Ikuo; Watanabe, Kazuo N; Sato, Yo-Ichiro

    2004-05-01

    Common non-waxy ( Wx) rice cultivars contain two different alleles at the waxy locus, designated Wx(a) and Wx(b), which encode different levels of granule-bound starch synthases and are hence involved in the control of endosperm amylose content. The Wx(a) allele was predominant in non-waxy indica cultivars, whereas the Wx(b) allele was common to the non-waxy japonica variety. Recently, some of the molecular mechanisms underlying the differentiation of Wx(a) from Wx(b) have been characterized. One structural difference between these two alleles was shown to be due to alternative splicing caused by a single-base substitution (AG GT to AG TT) at a donor site of the first intron within the Wx gene. In the case of waxy ( wx) rice, it was not possible to distinguish whether the each wx allele was derived from Wx(a) or Wx(b) alleles by phenotypic analysis. However, we succeeded in developing a derived cleaved amplified polymorphic sequence (dCAPS) marker for the detection of the one-base splicing mutation without the need for sequencing. A mismatch primer was used to generate a restriction site in the Wx(a) allele (AGGT) but not in the Wx(b) allele (AGTT). Three hundred fifty-three waxy rice strains that are widely found in Asia were then employed for analysis using this dCAPS marker. Our findings suggested that waxy rice strains have both Wx(a)- and Wx(b)-derived alleles, but that the Wx(b)-derived allele was predominant, and its distribution was independent of indica- japonica differentiation. The wild relatives of cultivated rice all possessed the AGGT allele. It was concluded that the waxy mutations, and the corresponding rice cultivation, originated from japonica during the evolution and domestication process of rice and was preferentially selected by most Asian peoples.

  4. Characteristics and in vitro Anti-diabetic Properties of the Korean Rice Wine, Makgeolli Fermented with Laminaria japonica

    PubMed Central

    Choi, Jae-Suk; Seo, Hyo Ju; Lee, Yu-Ri; Kwon, Su-Jung; Moon, Sun Hwa; Park, Sun-Mee; Sohn, Jae Hak

    2014-01-01

    New in vitro anti-diabetes makgeolli was produced from rice by adding various quantities of Laminaria japonica, and the fermentation characteristics of the L. japonica makgeolli during the fermentation process were investigated. The contents of alcohol and reducing sugar, and viable count of yeast, of L. japonica makgeolli were not significantly changed when the proportion of L. japonica was increased. The total acid content decreased with an increase in L. japonica concentration; the pH and total bacterial cell count increased in proportion with the increase in L. japonica concentration. The L. japonica makgeolli contents of free sugars, such as fructose, glucose, and sucrose, and of organic acids, such as acetic acid, citric acid, succinic acid, and lactic acid, were altered during fermentation and showed various patterns. The effects of the quantity of L. japonica added on the acceptability and anti-diabetes activities of L. japonica makgeolli were also investigated. In a sensory evaluation, L. japonica makgeolli brewed by adding 2.5 or 5% L. japonica to the mash showed the best overall acceptability; the 12.5% L. japonica sample was least favored due to its seaweed flavor. L. japonica addition did not increase the peroxynitrite-scavenging activity of makgeolli. L. japonica makgeolli showed potent anti-diabetes activity, particularly that containing >7.5% L. japonica. Therefore, L. japonica makgeolli may represent a new functional makgeolli with anti-diabetes properties. PMID:25054108

  5. 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.

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

    PubMed Central

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

    2014-01-01

    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. PMID:24987304

  7. Soluble starch synthase I effects differences in amylopectin structure between indica and japonica rice varieties.

    PubMed

    Takemoto-Kuno, Yoko; Suzuki, Keitaro; Nakamura, Sumiko; Satoh, Hikaru; Ohtsubo, Keníchi

    2006-11-29

    The effect of soluble starch synthase I (SSI) on differences of amylopectin structure between the indica and japonica rice varieties was investigated. Native-PAGE/active staining analysis showed that the SSI activity of an indica rice variety, "Kasalath", was significantly lower than that of a japonica rice variety, "Nipponbare", and that the low activity in "Kasalath" was maintained during seed development. The result of northern blot analyses suggests that the low expression of SSI in "Kasalath" is controlled at the transcription levels of SSI mRNA. Chain length distribution of amylopectin in F3 endosperms derived from a cross between two varieties showed that not only SSIIa but also SSI regulated the population of short chains. These results indicate that the low activity of SSI gives rise to the decrease of short chains in amylopectin of indica rice varieties, suggesting that SSI effects the differences in physicochemical properties between two varieties.

  8. Development of Japonica mapping populations to validate GWAS in the rice diversity panel 1

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In order to validate associations identified in the Rice Diversity Panel 1 (RDP1) between SNP markers and 34 phenotypic traits, four bi-parental recombinant inbred line (RIL) populations were developed from Oryza sativa L. ssp. japonica accessions that were phenotypically and genotypically diverse. ...

  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. Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross

    PubMed Central

    Nagata, Kazufumi; Ando, Tsuyu; Nonoue, Yasunori; Mizubayashi, Tatsumi; Kitazawa, Noriyuki; Shomura, Ayahiko; Matsubara, Kazuki; Ono, Nozomi; Mizobuchi, Ritsuko; Shibaya, Taeko; Ogiso-Tanaka, Eri; Hori, Kiyosumi; Yano, Masahiro; Fukuoka, Shuichi

    2015-01-01

    Grain shape is an important trait for improving rice yield. A number of quantitative trait loci (QTLs) for this trait have been identified by using primary F2 mapping populations and recombinant inbred lines, in which QTLs with a small effect are harder to detect than they would be in advanced generations. In this study, we developed two advanced mapping populations (chromosome segment substitution lines [CSSLs] and BC4F2 lines consisting of more than 2000 individuals) in the genetic backgrounds of two improved cultivars: a japonica cultivar (Koshihikari) with short, round grains, and an indica cultivar (IR64) with long, slender grains. We compared the ability of these materials to reveal QTLs for grain shape with that of an F2 population. Only 8 QTLs for grain length or grain width were detected in the F2 population, versus 47 in the CSSL population and 65 in the BC4F2 population. These results strongly suggest that advanced mapping populations can reveal QTLs for agronomic traits under complicated genetic control, and that DNA markers linked with the QTLs are useful for choosing superior allelic combinations to enhance grain shape in the Koshihikari and IR64 genetic backgrounds. PMID:26366113

  11. 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

    2016-03-14

    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.

  12. 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

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

    PubMed Central

    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

    2016-01-01

    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. PMID:27246799

  14. 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.

  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. QTL analysis of percentage of grains with chalkiness in Japonica rice (Oryza sativa).

    PubMed

    Liu, X; Wang, Y; Wang, S W

    2012-03-22

    Appearance quality of rice grains is a major problem for rice production in many areas of the world. We conducted a molecular marker-based genetic analysis of percentage of grains with chalkiness (PGWC), which is a determining factor for appearance quality; it strongly affects milling, eating and cooking quality. An F(8) recombinant inbred line population, which consists of 261 lines derived from a cross between Koshihikari (Japonica) and C602 (Japonica), was used for QTL mapping. Three QTLs related to PGWC were detected on chromosomes 5, 8 and 10, together explaining 50.8% of the genetic variation. The 'Koshihikari' alleles qJPGC-5, qJPGC-8 and the 'C602' alleles at qJPGC-10 were associated with reduced PGWC. The QTL contributions to phenotypic variance were 18.2, 9.6 and 25%, respectively. These QTL markers for PGWC could be used for developing improved varieties.

  17. Gene expression profiling of flag leaves at the booting stage in the japonica hybrid rice Huayou14 and its parental lines by microarray.

    PubMed

    Huangwei, Chu; Fuan, Niu; Can, Cheng; Jihua, Zhou; Xinqi, Wang; Xiaojin, Luo; Qin, Yuan; Liming, Cao

    2015-09-01

    Gene expression profiling using microarray has contributed significantly to heterosis studies. Using the Affymetrix rice genome array, we investigated gene expression profiles in the flag leaves of the japonica hybrid rice Huayou14 and its parental cultivars Shen9A and Fan14 at the booting stage. A total of 2057 genes differentially expressed (fold change ≥2 or ≤0.5) between Huayou14 and its parents were identified. Functional classification of the differentially expressed genes by Gene Ontology (GO) analysis indicated the differentially expressed genes were significantly enriched in photosynthesis-related cellular component categories (e.g. photosystem Ⅰ, chloroplast membrane and chloroplast envelope), and biological process categories (e.g. chlorophyll catabolic, chlorophyll biosynthetic and carotenoid biosynthetic processes). These results suggest that the changes in the photosynthetic ability of the japonica hybrid rice Huayou14 may be related to heterosis. Metabolic pathway analysis indicated that differentially expressed genes were significantly enriched in photosynthesis-antenna proteins and starch and sucrose metabolic pathways, instead of photosynthesis and carbon fixation pathways as reported previously. These results suggest that different genes or metabolic pathways might contribute to the heterosis of different hybrid combinations.

  18. 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.

  19. 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

  20. A Novel Tiller Angle Gene, TAC3, together with TAC1 and D2 Largely Determine the Natural Variation of Tiller Angle in Rice Cultivars

    PubMed Central

    Dong, Haijiao; Zhao, Hu; Xie, Weibo; Han, Zhongmin; Li, Guangwei; Yao, Wen; Bai, Xufeng; Hu, Yong; Guo, Zilong; Lu, Kai; Yang, Lin; Xing, Yongzhong

    2016-01-01

    Tiller angle is one of the most important components of the ideal plant architecture that can greatly enhance rice grain yield. Understanding the genetic basis of tiller angle and mining favorable alleles will be helpful for breeding new plant-type varieties. Here, we performed genome-wide association studies (GWAS) to identify genes controlling tiller angle using 529 diverse accessions of Oryza sativa including 295 indica and 156 japonica accessions in two environments. We identified 7 common quantitative trait loci (QTLs), including the previously reported major gene Tiller Angle Control 1 (TAC1), in the two environments, 10 and 13 unique QTLs in Hainan and Wuhan, respectively. More QTLs were identified in indica than in japonica, and three major QTLs (qTA3, qTA1b/DWARF2 (D2) and qTA9c/TAC1) were fixed in japonica but segregating in indica, which explained the wider variation observed in indica compared with that in japonica. No common QTLs were identified between the indica and japonica subpopulations. Mutant analysis for the candidate gene of qTA3 on chromosome 3 indicated a novel gene, Tiller Angle Control 3 (TAC3), encoding a conserved hypothetical protein controlling tiller angle. TAC3 is preferentially expressed in the tiller base. The ebisu dwarf (d2) mutant exhibited a decreased tiller angle, in addition to its previously described abnormal phenotype. A nucleotide diversity analysis revealed that TAC3, D2 and TAC1 have been subjected to selection during japonica domestication. A haplotype analysis identified favorable alleles of TAC3, D2 and TAC1, which may be used for breeding plants with an ideal architecture. In conclusion, there is a diverse genetic basis for tiller angle between the two subpopulations, and it is the novel gene TAC3 together with TAC1, D2, and other newly identified genes in this study that controls tiller angle in rice cultivars. PMID:27814357

  1. 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

  2. Cropping system diversification for food production in Mindanao rubber plantations: a rice cultivar mixture and rice intercropped with mungbean

    PubMed Central

    Elazegui, Francisco; Duque, Jo-Anne Lynne Joy E.; Mundt, Christopher C.; Vera Cruz, Casiana M.

    2017-01-01

    Including food production in non-food systems, such as rubber plantations and biofuel or bioenergy crops, may contribute to household food security. We evaluated the potential for planting rice, mungbean, rice cultivar mixtures, and rice intercropped with mungbean in young rubber plantations in experiments in the Arakan Valley of Mindanao in the Philippines. Rice mixtures consisted of two- or three-row strips of cultivar Dinorado, a cultivar with higher value but lower yield, and high-yielding cultivar UPL Ri-5. Rice and mungbean intercropping treatments consisted of different combinations of two- or three-row strips of rice and mungbean. We used generalized linear mixed models to evaluate the yield of each crop alone and in the mixture or intercropping treatments. We also evaluated a land equivalent ratio for yield, along with weed biomass (where Ageratum conyzoides was particularly abundant), the severity of disease caused by Magnaporthe oryzae and Cochliobolus miyabeanus, and rice bug (Leptocorisa acuta) abundance. We analyzed the yield ranking of each cropping system across site-year combinations to determine mean relative performance and yield stability. When weighted by their relative economic value, UPL Ri-5 had the highest mean performance, but with decreasing performance in low-yielding environments. A rice and mungbean intercropping system had the second highest performance, tied with high-value Dinorado but without decreasing relative performance in low-yielding environments. Rice and mungbean intercropped with rubber have been adopted by farmers in the Arakan Valley. PMID:28194318

  3. Cropping system diversification for food production in Mindanao rubber plantations: a rice cultivar mixture and rice intercropped with mungbean.

    PubMed

    Hondrade, Rosa Fe; Hondrade, Edwin; Zheng, Lianqing; Elazegui, Francisco; Duque, Jo-Anne Lynne Joy E; Mundt, Christopher C; Vera Cruz, Casiana M; Garrett, Karen A

    2017-01-01

    Including food production in non-food systems, such as rubber plantations and biofuel or bioenergy crops, may contribute to household food security. We evaluated the potential for planting rice, mungbean, rice cultivar mixtures, and rice intercropped with mungbean in young rubber plantations in experiments in the Arakan Valley of Mindanao in the Philippines. Rice mixtures consisted of two- or three-row strips of cultivar Dinorado, a cultivar with higher value but lower yield, and high-yielding cultivar UPL Ri-5. Rice and mungbean intercropping treatments consisted of different combinations of two- or three-row strips of rice and mungbean. We used generalized linear mixed models to evaluate the yield of each crop alone and in the mixture or intercropping treatments. We also evaluated a land equivalent ratio for yield, along with weed biomass (where Ageratum conyzoides was particularly abundant), the severity of disease caused by Magnaporthe oryzae and Cochliobolus miyabeanus, and rice bug (Leptocorisa acuta) abundance. We analyzed the yield ranking of each cropping system across site-year combinations to determine mean relative performance and yield stability. When weighted by their relative economic value, UPL Ri-5 had the highest mean performance, but with decreasing performance in low-yielding environments. A rice and mungbean intercropping system had the second highest performance, tied with high-value Dinorado but without decreasing relative performance in low-yielding environments. Rice and mungbean intercropped with rubber have been adopted by farmers in the Arakan Valley.

  4. The contrasting responses of soil microorganisms in two rice cultivars to elevated ground-level ozone.

    PubMed

    Feng, Youzhi; Yu, Yongjie; Tang, Haoye; Zu, Qianhui; Zhu, Jianguo; Lin, Xiangui

    2015-02-01

    Although elevated ground-level O₃ has a species-specific impact on plant growth, the differences in soil biota responses to O₃ pollution among rice cultivars are rarely reported. Using O₃ Free-Air Concentration Enrichment, the responses of the rhizospheric bacterial communities in the O₃-tolerant (YD6) and the O₃-sensitive (IIY084) rice cultivars to O₃ pollution and their differences were assessed by pyrosequencing at rice tillering and anthesis stages. Elevated ground-level O₃ negatively influenced the bacterial community in cultivar YD6 at both rice growth stages by decreasing the bacterial phylogenetic diversities and response ratios. In contrast, in cultivar IIY084, the bacterial community responded positively at the rice tillering stage under O₃ pollution. However, several keystone bacterial guilds were consistently negatively affected by O₃ pollution in two rice cultivars. These findings indicate that continuously O₃ pollution would negatively influence rice agroecosystem and the crop cultivar is important in determining the soil biota responses to elevated O₃.

  5. Comparative proteomic analysis of methyl jasmonate-induced defense responses in different rice cultivars.

    PubMed

    Li, Yunfeng; Nie, Yanfang; Zhang, Zhihui; Ye, Zhijian; Zou, Xiaotao; Zhang, Lianhui; Wang, Zhenzhong

    2014-05-01

    Jasmonate is an important endogenous chemical signal that plays a role in modulation of plant defense responses. To understand its mechanisms in regulation of rice resistance against the fungal pathogen Magnaporthe oryzae, comparative phenotype and proteomic analyses were undertaken using two near-isogenic cultivars with different levels of disease resistance. Methyl-jasmonate (MeJA) treatment significantly enhanced the resistance against M. oryzae in both cultivars but the treated resistant cultivar maintained a higher level of resistance than the same treated susceptible cultivars. Proteomic analysis revealed 26 and 16 MeJA-modulated proteins in resistant and susceptible cultivars, respectively, and both cultivars shared a common set of 13 proteins. Cumulatively, a total of 29 unique MeJA-influenced proteins were identified with many of them known to be associated with plant defense response and ROS accumulation. Consistent with the findings of proteomic analysis, MeJA treatment increased ROS accumulation in both cultivars with the resistant cultivar showing higher levels of ROS production and cell membrane damage than the susceptible cultivar. Taken together, our data add a new insight into the mechanisms of overall MeJA-induced rice defense response and provide a molecular basis of using MeJA to enhance fungal disease resistance in resistant and susceptible rice cultivars.

  6. Outcrossing frequency and phenotypes of outcrosses based on flowering of red rice accessions and Clearfield cultivars in the Grand Prairie

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Outcrossing between Clearfield (CL) cultivars and red rice (RR) has been documented in experimental plots as well as in fields. The authors hypothesize that CL cultivars, red rice type, planting time, and flowering time of CL and RR influence the transfer of imazethapyr-resistance genes from CL rice...

  7. 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...

  8. Evaluation of the occluded carbon within husk phytoliths of 35 rice cultivars

    NASA Astrophysics Data System (ADS)

    Sun, Xing; Liu, Qin; Gu, Jie; Chen, Xiang; Zhu, Keya

    2016-12-01

    Rice is a well-known silicon accumulator. During its periods of growth, a great number of phytoliths are formed by taking up silica via the plant roots. Concurrently, carbon in those phytoliths is sequestrated by a mechanism of long-term biogeochemical processes within the plant. Phytolith occluded C (PhytOC) is very stable and can be retained in soil for longer than a millennium. In this study, we evaluated the carbon biosequestration within the phytoliths produced in rice seed husks of 35 rice cultivars, with the goal of finding rice cultivars with relatively higher phytolith carbon sequestration efficiencies. The results showed that the phytolith contents ranged from 71.6 mg•g‒1 to 150.1 mg•g‒1, and the PhytOC contents ranged from 6.4 mg•g‒1 to 38.4 mg•g‒1, suggesting that there was no direct correlation between the PhytOC content and the content of rice seed husk phytoliths ( R = 0.092, p>0.05). Of all rice cultivars, six showed a higher carbon sequestration efficiency in phytolith seed husks. Additionally, the carbon biosequestration within the rice seed husk phytoliths was approximately 0.45‒3.46 kg-e-CO2•ha‒1•yr‒1. These rates indicate that rice cultivars are a potential source of carbon biosequestration which could contribute to the global carbon cycle and climate change.

  9. 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.

  10. 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

  11. Whole-genome analysis revealed the positively selected genes during the differentiation of indica and temperate japonica rice.

    PubMed

    Sun, Xinli; Jia, Qi; Guo, Yuchun; Zheng, Xiujuan; Liang, Kangjing

    2015-01-01

    To investigate the selective pressures acting on the protein-coding genes during the differentiation of indica and japonica, all of the possible orthologous genes between the Nipponbare and 93-11 genomes were identified and compared with each other. Among these genes, 8,530 pairs had identical sequences, and 27,384 pairs shared more than 90% sequence identity. Only 2,678 pairs of genes displaying a Ka/Ks ratio significantly greater than one were revealed, and most of these genes contained only nonsynonymous sites. The genes without synonymous site were further analyzed with the SNP data of 1529 O. sativa and O. rufipogon accessions, and 1068 genes were identified to be under positive selection during the differentiation of indica and temperate japonica. The positively selected genes (PSGs) are unevenly distributed on 12 chromosomes, and the proteins encoded by the PSGs are dominant with binding, transferase and hydrolase activities, and especially enriched in the plant responses to stimuli, biological regulations, and transport processes. Meanwhile, the most PSGs of the known function and/or expression were involved in the regulation of biotic/abiotic stresses. The evidence of pervasive positive selection suggested that many factors drove the differentiation of indica and japonica, which has already started in wild rice but is much lower than in cultivated rice. Lower differentiation and less PSGs revealed between the Or-It and Or-IIIt wild rice groups implied that artificial selection provides greater contribution on the differentiation than natural selection. In addition, the phylogenetic tree constructed with positively selected sites showed that the japonica varieties exhibited more diversity than indica on differentiation, and Or-III of O. rufipogon exhibited more than Or-I.

  12. Variation of grain Cd and Zn concentrations of 110 hybrid rice cultivars grown in a low-Cd paddy soil.

    PubMed

    Shi, Jing; Li, Lianqing; Pan, Genxing

    2009-01-01

    Enhanced Cd uptake and Zn depletion in rice grains and high potential for food Cd exposure by the high-yielding hybrid cultivars of China had been addressed. A field experiment was conducted in 2006 to determine the difference in grain Cd and Zn between cultivars. Total 110 cultivars including super rice and common hybrid rice cultivars were grown on a single paddy soil (Entic Haplaquept) with a neutral reaction and low total Cd content. Grain Cd and Zn concentrations were determined with graphite atomic adsorption spectrophotometer (GFAAS) and flame atomic adsorption spectrophotometer (AAS) respectively. Wide variation of Cd content in grain was found in a range of 0.004-0.057 mg/kg, while the Zn content in a range of 10.25-30.06 mg/kg among the cultivars. Higher Cd but lower Zn concentration in grains of super rice cultivars was observed compared to the common hybrid ones. A highly significant positive linear correlation of grain Cd/Zn with grain Cd was found for super rice and common hybrid cultivars, meanwhile much higher slope for these hybrid cultivars than the reported non-hybrid cultivars was also observed. Using the limit value of the Chinese chemical guidelines for foods (MOHC and SSC, 2005), calculated potential risk of food Cd exposure with "Zn hungry" through diet intake was prominent with all the studied 110 hybrid rice cultivars, possessing high potential health problems for rice production in South China using the super rice cultivars. Breeding of genotypes of rice cultivars with low grain Cd and low Cd/Zn ratio is needed for rice production in acidic red soils where Cd bioavailability is prevalently high.

  13. Oviposition behavior of Diatraea saccharalis (Lepidoptera: Crambidae) on different rice cultivars in Louisiana.

    PubMed

    Hamm, Jason C; Sidhu, Jaspreet K; Stout, Michael J; Hummel, Natalie A; Reagan, Thomas E

    2012-06-01

    The sugarcane borer, Diatraea saccharalis (F.), is a pest of a variety of graminaceous crops in the southern United States, including sugarcane, maize, and rice in Louisiana. This study examined several aspects of D. saccharalis oviposition behavior on rice (Oryza sativa). The vertical distribution of egg masses on four phenological stages of rice in the field showed that D. saccharalis prefers to oviposit on the uppermost portions of rice plants, regardless of plant stage. In greenhouse choice experiments, females strongly preferred plants at the boot and panicle differentiation stages over plants at the tillering stage for oviposition. Greenhouse studies were also conducted to quantify the oviposition preference of D. saccharalis for different cultivars of. When plants were at the tillering stage, cultivars Cocodrie, Priscilla, Bengal, Cheniere, and CL161 were more preferred than cultivars Jupiter, XL723, and XP744. When plants reached the panicle initiation stage, cultivars Cocodrie, CL161, and Priscilla were more preferred than Bengal, Cheniere, Jupiter, XL723, and XP744. Females also oviposited significantly more egg masses on the adaxial surfaces of rice leaves than on the abaxial surfaces. These results will facilitate scouting and management of sugarcane borer and can be used as a foundation for the development of sugarcane borer resistant cultivars.

  14. Improving of Rice Blast Resistances in Japonica by Pyramiding Major R Genes.

    PubMed

    Xiao, Ning; Wu, Yunyu; Pan, Cunhong; Yu, Ling; Chen, Yu; Liu, Guangqing; Li, Yuhong; Zhang, Xiaoxiang; Wang, Zhiping; Dai, Zhengyuan; Liang, Chengzhi; Li, Aihong

    2016-01-01

    Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is a major constraint to rice production worldwide. In this study, we developed monogenic near-isogenic lines (NILs) NIL (Pi9), NIL (Pizt) , and NIL (Pi54) carrying genes Pi9, Pizt, and Pi54, respectively, by marker assisted backcross breeding using 07GY31 as the japonica genetic background with good agronomic traits. Polygene pyramid lines (PPLs) PPL (Pi9+Pi54) combining Pi9 with Pi54, and PPL (Pizt+Pi54) combining Pizt with Pi54 were then developed using corresponding NILs with genetic background recovery rates of more than 97%. Compared to 07GY31, the above NILs and PPLs exhibited significantly enhanced resistance frequencies (RFs) for both leaf and panicle blasts. RFs of both PPLs for leaf blast were somewhat higher than those of their own parental NILs, respectively, and PPL (Pizt)(+)(Pi54) exhibited higher RF for panicle blast than NIL (Pizt) and NIL (Pi54) (P < 0.001), hinting an additive effect on the resistance. However, PPL (Pi9+Pi54) exhibited lower RF for panicle blast than NIL (Pi9) (P < 0.001), failing to realize an additive effect. PPL (Pizt)(+)(Pi54) showed higher resistant level for panicle blast and better additive effects on the resistance than PPL (Pi9+Pi54). It was suggested that major R genes interacted with each other in a way more complex than additive effect in determining panicle blast resistance levels. Genotyping by sequencing analysis and extreme-phenotype genome-wide association study further confirmed the above results. Moreover, data showed that pyramiding multiple resistance genes did not affect the performance of basic agronomic traits. So the way to enhance levels of leaf and panicle blast resistances for rice breeding in this study is effective and may serve as a reference for breeders. Key Message: Resistant levels of rice blast is resulted from different combinations of major R genes, PPL (Pizt)(+)(Pi54) showed higher resistant level and better additive effects on

  15. Improving of Rice Blast Resistances in Japonica by Pyramiding Major R Genes

    PubMed Central

    Xiao, Ning; Wu, Yunyu; Pan, Cunhong; Yu, Ling; Chen, Yu; Liu, Guangqing; Li, Yuhong; Zhang, Xiaoxiang; Wang, Zhiping; Dai, Zhengyuan; Liang, Chengzhi; Li, Aihong

    2017-01-01

    Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is a major constraint to rice production worldwide. In this study, we developed monogenic near-isogenic lines (NILs) NILPi9, NILPizt, and NILPi54 carrying genes Pi9, Pizt, and Pi54, respectively, by marker assisted backcross breeding using 07GY31 as the japonica genetic background with good agronomic traits. Polygene pyramid lines (PPLs) PPLPi9+Pi54 combining Pi9 with Pi54, and PPLPizt+Pi54 combining Pizt with Pi54 were then developed using corresponding NILs with genetic background recovery rates of more than 97%. Compared to 07GY31, the above NILs and PPLs exhibited significantly enhanced resistance frequencies (RFs) for both leaf and panicle blasts. RFs of both PPLs for leaf blast were somewhat higher than those of their own parental NILs, respectively, and PPLPizt+Pi54 exhibited higher RF for panicle blast than NILPizt and NILPi54 (P < 0.001), hinting an additive effect on the resistance. However, PPLPi9+Pi54 exhibited lower RF for panicle blast than NILPi9 (P < 0.001), failing to realize an additive effect. PPLPizt+Pi54 showed higher resistant level for panicle blast and better additive effects on the resistance than PPLPi9+Pi54. It was suggested that major R genes interacted with each other in a way more complex than additive effect in determining panicle blast resistance levels. Genotyping by sequencing analysis and extreme-phenotype genome-wide association study further confirmed the above results. Moreover, data showed that pyramiding multiple resistance genes did not affect the performance of basic agronomic traits. So the way to enhance levels of leaf and panicle blast resistances for rice breeding in this study is effective and may serve as a reference for breeders. Key Message: Resistant levels of rice blast is resulted from different combinations of major R genes, PPLPizt+Pi54 showed higher resistant level and better additive effects on the panicle blast resistance than PPLPi9+Pi54. PMID

  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.

  17. 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

  18. Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.

    PubMed

    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.

  19. 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

  20. Effects of hydrostatic pressure/heat combinations on water uptake and gelatinization characteristics of japonica rice grains: a kinetic study.

    PubMed

    Huang, Shih-Li; Jao, Chia-Ling; Hsu, Kuo-Chiang

    2009-10-01

    The combination effects of pressure (200 to 500 MPa) and temperature (20, 40, and 50 degrees C) on the water uptake and gelatinization characteristics of japonica rice (Tainung 71) grains were investigated. Pressure greater than 200 MPa at all temperatures increased the moisture content and volume of rice grains; meanwhile, the increase content of rice grain volume showed a high correlation with that of moisture content (r(2)= 0.96). The highest degree of gelatinization of 73% was observed at 500 MPa and 50 degrees C for 120 min, while gelatinization did not occur at pressures below 300 MPa and temperatures of 20 and 40 degrees C. The rate of gelatinization followed the 1st-order kinetics at each temperature and pressure. The higher pressures and temperatures would result in higher values of rate constant k which could be correlated with both pressure and temperature by combining Arrhenius and Eyring models.

  1. 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 ...

  2. 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.

  3. Root transcriptome of two contrasting indica rice cultivars uncovers regulators of root development and physiological responses

    PubMed Central

    Singh, Alka; Kumar, Pramod; Gautam, Vibhav; Rengasamy, Balakrishnan; Adhikari, Bijan; Udayakumar, Makarla; Sarkar, Ananda K.

    2016-01-01

    The huge variation in root system architecture (RSA) among different rice (Oryza sativa) cultivars is conferred by their genetic makeup and different growth or climatic conditions. Unlike model plant Arabidopsis, the molecular basis of such variation in RSA is very poorly understood in rice. Cultivars with stable variation are valuable resources for identification of genes involved in RSA and related physiological traits. We have screened for RSA and identified two such indica rice cultivars, IR-64 (OsAS83) and IET-16348 (OsAS84), with stable contrasting RSA. OsAS84 produces robust RSA with more crown roots, lateral roots and root hairs than OsAS83. Using comparative root transcriptome analysis of these cultivars, we identified genes related to root development and different physiological responses like abiotic stress responses, hormone signaling, and nutrient acquisition or transport. The two cultivars differ in their response to salinity/dehydration stresses, phosphate/nitrogen deficiency, and different phytohormones. Differential expression of genes involved in salinity or dehydration response, nitrogen (N) transport, phosphate (Pi) starvation signaling, hormone signaling and root development underlies more resistance of OsAS84 towards abiotic stresses, Pi or N deficiency and its robust RSA. Thus our study uncovers gene-network involved in root development and abiotic stress responses in rice. PMID:28000793

  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. 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.

  6. 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.

  7. 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

  8. 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...

  9. Comparison of physical and chemical properties of medium-grain rice cultivars grown in California and Arkansas.

    PubMed

    Cameron, D K; Wang, Y-J; Moldenhauer, K A

    2008-03-01

    The physical attributes, chemical composition, and physicochemical properties of 2 medium-grain rice cultivars from Arkansas (Bengal, Medark) and from California (M202, M204) were compared when grown in their respective locations and grown together in Arkansas to better understand the impacts of heredity and environment on medium-grain rice quality. Variations existed in grain dimensions, particularly length distribution, among cultivars and between crop years. When grown separately, the Arkansas cultivars tended to have higher protein and lipid contents but lower amylose contents than the California cultivars. M204 contained a significantly higher apparent amylose content (21.0%) compared with the other 3 cultivars (14.3% to 16.4%). The Arkansas rice cultivars exhibited higher pasting and gelatinization temperatures and produced harder gels and less sticky cooked rice. However, when the 4 cultivars were grown together in Arkansas, differences in protein and amylose contents, gelatinization and pasting properties, and cooked rice texture decreased. This study demonstrated that genetics, location, and crop year all contributed to variations in rice chemical and physical characteristics.

  10. Adaptability of small brown planthopper to four rice cultivars using life table and population projection method

    PubMed Central

    Zheng, Xiao-Min; Tao, Yun-Li; Chi, Hsin; Wan, Fang-Hao; Chu, Dong

    2017-01-01

    In this study, we evaluated the adaptability of the small brown planthopper (SBPH), Laodelphax striatellus (Hemiptera: Delphacidae) to four rice cultivars including Shengdao13 (SD13), Shengdao14 (SD14), Shengdao15 (SD15), and Zixiangnuo (ZXN) using the age-stage, two-sex life table with a simplified method for recording egg production (i.e., every five days vs. daily). The intrinsic rate of increase (r) of the SBPH was the highest (0.1067 d−1) on cultivar SD15, which was similar to the rate on SD14 (0.1029 d−1), but was significantly higher than that occurring on ZXN (0.0897 d−1) and SD13 (0.0802 d−1). The differences of the finite rate of increase (λ) on the four rice cultivars were consistent with the r values. Population projection predicted an explosive population growth of the SBPH occurring in a relatively short time when reared on SD14 and SD15. These findings demonstrated that the SBPH can successfully survive on the four rice cultivars, although there were varying host adaptabilities. PMID:28205522

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

    PubMed

    Simmonds, Maegen B; Anders, Merle; Adviento-Borbe, Maria Arlene; van Kessel, Chris; McClung, Anna; Linquist, Bruce A

    2015-01-01

    An understanding of cultivar effects on field greenhouse gas (GHG) emissions in rice ( L.) systems is needed to improve the accuracy of predictive models used for estimating GHG emissions and to evaluate the GHG mitigation potential of different cultivars. We compared CH and NO emissions, global warming potential (GWP = NO + CH), yield-scaled GWP (GWP = GWP Mg grain), and plant growth characteristics of eight cultivars within four study sites in California and Arkansas. Nitrous oxide emissions were negligible (<10% of GWP) and were not different among cultivars. Seasonal CH emissions differed between cultivars by a factor of 2.1 and 1.4 at one California and one Arkansas site, respectively. Plant growth characteristics were generally not correlated with seasonal CH emissions; however, the strongest correlations were observed for shoot and total plant (root + shoot) biomass at heading ( = 0.60) at one California site and for grain at maturity ( = -0.95) at one Arkansas site. Although differences in GWP and GWP were observed, there were inconsistencies across sites, indicating the importance of the genotype × environment interaction. Overall, the cultivars with the lowest CH emissions, GWP, and GWP at the California and Arkansas sites were the lowest and highest yielding, respectively. These findings highlight the potential for breeding high-yielding cultivars with low GWP, the ideal scenario to achieve low GWP, but environmental conditions must also be considered.

  12. Search for cell-wall-degrading enzymes of world-wide rice grains by PCR and their effects on the palatability of rice.

    PubMed

    Nakamura, Sumiko; Machida, Keisuke; Ohtsubo, Ken'ichi

    2012-01-01

    Such rice cultivars as Japonica, Japonica-Indica hybrid, Javanica and Indica, were evaluated for their main chemical components (amylose content and protein content), pasting property of rice flour (consistency), physical property of the cooked rice grains (adhesion, L3), and enzyme activities (cellulase and xylanase). The amylose content, cellulase activity and xylanase activity showed significant positive or negative correlation with the pasting property (consistency) of rice flour (r = 0.89, r = 0.58, r = 0.70, respectively) and with the physical property of the cooked rice grains (adhesion, L3: r = -0.51, r = -0.61, r = -0.71, respectively) at the level of 1%. Endogenous xylanase and cellulase played important roles to determine the texture of the cooked rice grains similarly to the amylose content. Part of the DNA sequences of the α-glucosidase gene differed among the Japonica, Japonica-Indica hybrid and Indica subspecies. We found discriminative DNA bands appearing by PCR, corresponding to 1,4-β-xylanase and endo-1,4-β-glucanase 13 in the case of Indica rice, Indica-Japonica hybrid rice, and Javanica rice (non-Japonica subspecies). The equation for estimating the physical property (adhesion) of cooked rice grains by PCR was improved by adding novel primers related to the cell-wall-degrading enzymes.

  13. Expression of drought tolerance genes in tropical upland rice cultivars (Oryza sativa).

    PubMed

    Silveira, R D D; Abreu, F R M; Mamidi, S; McClean, P E; Vianello, R P; Lanna, A C; Carneiro, N P; Brondani, C

    2015-07-27

    Gene expression related to drought response in the leaf tissues of two Brazilian upland cultivars, the drought-tolerant Douradão and the drought-sensitive Primavera, was analyzed. RNA-seq identified 27,618 transcripts in the Douradão cultivar, with 24,090 (87.2%) homologous to the rice database, and 27,221 transcripts in the Primavera cultivar, with 23,663 (86.9%) homologous to the rice database. Gene-expression analysis between control and water-deficient treatments revealed 493 and 1154 differentially expressed genes in Douradão and Primavera cultivars, respectively. Genes exclusively expressed under drought were identified for Douradão, including two genes of particular interest coding for the protein peroxidase precursor, which is involved in three distinct metabolic pathways. Comparisons between the two drought-exposed cultivars revealed 2314 genes were differentially expressed (978 upregulated, 1336 downregulated in Douradão). Six genes distributed across 4 different transcription factor families (bHLH, MYB, NAC, and WRKY) were identified, all of which were upregulated in Douradão compared to Primavera during drought. Most of the genes identified in Douradão activate metabolic pathways responsible for production of secondary metabolites and genes coding for enzymatically active signaling receptors. Quantitative PCR validation showed that most gene expression was in agreement with computational prediction of these transcripts. The transcripts identified here will define molecular markers for identification of Cis-acting elements to search for allelic variants of these genes through analysis of polymorphic SNPs in GenBank accessions of upland rice, aiming to develop cultivars with the best combination of these alleles, resulting in materials with high yield potential in the event of drought during the reproductive phase.

  14. A comparison of nitrate transport in four different rice (Oryza sativa L.) cultivars.

    PubMed

    Fan, Xiaorong; Shen, Qirong; Ma, Zhengqiang; Zhu, Huilan; Yin, Xiaoming; Miller, Anthony J

    2005-09-01

    As rice can use both nitrate (NO(3)(-)) and ammonium (NH(4)(+)), we have tested the hypothesis that the shift in the pattern of cultivars grown in Jiangsu Province reflects the ability of the plants to exploit NO(3)(-) as a nitrogen (N) source. Four rice cultivars were grown in solution culture for comparison of their growth on NO(3)(-) and NH(4)(+) nitrogen sources. All four types of rice, Xian You 63 (XY63), Yang Dao 6 (YD), Nong Keng 57 (NK) and Si You 917 (SY917), grew well and produced similar amounts of shoot biomass with 1 mmol/L NH(4)(+) as the only N source. However, the roots of NK were significantly smaller in comparison with the other cultivars. When supplied with 1 mmol/L NO(3)(-), YD produced the greatest biomass; while NK achieved the lowest growth among the four cultivars. Electrophysiological measurements on root rhizodermal cells showed that the NO(3)(-)-elicited changes in membrane potential (Delta E(m)) of these four rice cultivars were significantly different when exposed to low external NO(3)(-) (<1 mmol/L); while they were very similar at high external NO(3)(-) (10 mmol/L). The root cell membrane potentials of YD and XY63 were more responsive to low external NO(3)(-) than those of NK and SY917. The Delta E(m) values for YD and XY63 rhizodermal cells were almost the same at both 0.1 mmol/L and 1 mmol/L NO(3)(-); while for the NK and SY917 the values became larger as the external NO(3)(-) increased. For YD cultivar, Delta E(m) was measured over a range of NO(3)(-) concentrations and a Michaelis-Menten fit to the data gave aK(m) value of 0.17 mmol/L. Net N(3)(-) uptake depletion kinetics were also compared and for some cultivars (YD and XY63) a single-phase uptake system with first order kinetics best fitted the data; while other cultivars (ND and SY917) showed a better fit to two uptake systems. These uptake systems had two affinity ranges: one had a similar K(m) in all the cultivars (0.2 mmol/L); the other much higher affinity system (0

  15. A comparison of nitrate transport in four different rice (Oryza sativa L.) cultivars.

    PubMed

    Fan, Xiaorong; Shen, Qirong; Ma, Zhengqiang; Zhu, Huilan; Yin, Xiaoming; Miller, Anthony J

    2005-12-01

    As rice can use both nitrate (NO3-) and ammonium (NH4+), we have tested the hypothesis that the shift in the pattern of cultivars grown in Jiangsu Province reflects the ability of the plants to exploit NO3- as a nitrogen (N) source. Four rice cultivars were grown in solution culture for comparison of their growth on NO3- and NH4+ nitrogen sources. All four types of rice, Xian You 63 (XY63), Yang Dao 6 (YD), Nong Keng 57 (NK) and Si You 917 (SY917), grew well and produced similar amounts of shoot biomass with 1 mmol/L NH4+ as the only N source. However, the roots of NK were significantly smaller in comparison with the other cultivars. When supplied with 1 mmol/L NO3-, YD produced the greatest biomass; while NK achieved the lowest growth among the four cultivars. Electrophysiological measurements on root rhizodermal cells showed that the NO3- -elicited changes in membrane potential (deltaEm) of these four rice cultivars were significantly different when exposed to low external NO3- (<1 mmol/L); while they were very similar at high external NO3- (10 mmol/L). The root cell membrane potentials of YD and XY63 were more responsive to low external NO3- than those of NK and SY917. The deltaEm values for YD and XY63 rhizodermal cells were almost the same at both 0.1 mmol/L and 1 mmol/L NO3-; while for the NK and SY917 the values became larger as the external NO3- increased. For YD cultivar, deltaEm was measured over a range of NO3- concentrations and a Michaelis-Menten fit to the data gave a Km value of 0.17 mmol/L. Net NO3- uptake depletion kinetics were also compared and for some cultivars (YD and XY63) a single-phase uptake system with first order kinetics best fitted the data; while other cultivars (ND and SY917) showed a better fit to two uptake systems. These uptake systems had two affinity ranges: one had a similar Km in all the cultivars (0.2 mmol/L); the other much higher affinity system (0.03 mmol/L) was only present in NK and SY917. The expression pattern of

  16. [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.

  17. 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.

  18. Effect of steam-cooking and parboiling on phenolics and antioxidant capacities of red and purple rice cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Red and purple rice cultivars contain high concentrations of phenolics, such as proanthocyanidins and anthocyanins, respectively. We investigated the effect of cooking processes on these antioxidants and antioxidant capacities of pigmented and common light-brown bran rice. The cooking processes incl...

  19. 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.

  20. Breeding of new rice cultivar 'Tohoku 194' with 'Sasanishiki'-type good eating quality of cooked rice.

    PubMed

    Nagano, Kuniaki; Sasaki, Kunihiko; Endo, Takashi

    2013-06-01

    Cooked rice of 'Sasanishiki' is soft and not as sticky as those of Japanese leading cultivars 'Koshihikari' and 'Hitomebore'. As a method for efficient selection of a breeding line having a good eating quality like that of 'Sasanishiki', the use of physical properties of cooked rice and cooking quality was examined. There were differences of physical properties of the surface layer, starch-iodine blue value per solid substance weight in cooking water and volume expansion of cooked rice between 'Sasanishiki' and 'Hitomebore', these properties being considered to be usable for the selection of breeding lines. Using these traits as selection targets, one line, named 'Tohoku 194', which has eating quality highly similar to that of 'Sasanishiki' and cold tolerance derived from 'Hitomebore', was selected from progeny of a cross between 'Sasanishiki' and 'Hitomebore'. An application for registration as a new variety has been submitted for 'Tohoku 194' under the Japanese Plant Variety Protection Act, and is expected to become a recommended cultivar in Miyagi Prefecture. 'Tohoku 194' may fulfill various demands of consumers and companies in the food industry.

  1. Evaluation of the Agronomic Performance of Atrazine-Tolerant Transgenic japonica Rice Parental Lines for Utilization in Hybrid Seed Production

    PubMed Central

    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. PMID:25275554

  2. Epistasis underlying female sterility detected in hybrid breakdown in a Japonica-Indica cross of rice (Oryza sativa L.).

    PubMed

    Kubo, Takahiko; Yoshimura, Atsushi

    2005-01-01

    Epistasis is considered to be a primary genetic basis of hybrid breakdown. We found novel epistatic genes causing hybrid breakdown in an intraspecific cross of cultivated rice (Oryza sativa L.). F2 progeny derived from a cross between a Japonica variety, Asominori, and an Indica variety, IR24, showed segregation of high sterility for seeds, even though the reciprocal F1 hybrids showed about 60% seed fertility. Backcross populations (BC3F2, BC3F3), obtained from repeated backcrossing with Asominori, showed the segregation of causal genes in a simple Mendelian fashion. Using these populations, we identified that this sterility was hybrid breakdown caused by interaction among three nuclear genes distributed on the both parental genomes. These new genes, designated as hsa1, hsa2, and hsa3, were found to be involved in female gamete development by histological examination. The Indica parent IR24 has a sterile allele, hsa1-IR, which was located at near RFLP marker G148 on chromosome 12, whereas the Japonica parent Asominori has two sterile alleles, hsa2-As on chromosome 8 (close to G104) and hsa3-As on chromosome 9 (close to RM285). Female gametes carrying the hsa1-IR, hsa2-As, and hsa3-As alleles aborted in hsa1-IR homozygous plant, leading to seed sterility and selective elimination of the specific allelic combination. This study provides direct evidence that hybrid breakdown is attributed to epistatic interaction of genes from both parents and suggests that complicated mechanisms has been developed for hybrid breakdown during the evolution of rice.

  3. 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.

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

    PubMed

    Wei, X D

    2016-07-29

    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.

  5. 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

  6. 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

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

    PubMed

    Zhang, Xiaohui; Yang, Sihai; Wang, Jiao; Jia, Yanxiao; Huang, Ju; Tan, Shengjun; Zhong, Yan; Wang, Ling; Gu, Longjiang; Chen, Jian-Qun; Pan, Qinghua; Bergelson, Joy; Tian, Dacheng

    2015-10-01

    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, the composite behavior of which is yet to be characterized? Here, we survey 332 NBS-LRR genes cloned from five resistant Oryza sativa (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.

  8. 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

  9. 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.

  10. Induction of Xa10-like genes in rice cultivar Nipponbare confers disease resistance to rice bacterial blight.

    PubMed

    Wang, Jun; Tian, Dongsheng; Gu, Keyu; Yang, Xiaobei; Wang, Lanlan; Zeng, Xuan; Yin, Zhongchao

    2017-03-17

    Bacterial blight of rice, caused by Xanthomonas oryzae pv. oryzae, is one of the most destructive bacterial diseases throughout the major rice growing regions in the world. The rice disease resistance (R) genes Xa10 confers race-specific disease resistance to X. oryzae pv. oryzae strains that deliver the corresponding transcription activator-like (TAL) effectors AvrXa10. Upon bacterial infection, AvrXa10 binds specifically to the effector binding element (EBE) in the promoter of the R gene and activates its expression. Xa10 encodes an executor R protein that triggers hypersensitive response and activates disease resistance. Rice cultivar Nipponbare carries two Xa10-like genes in its genome, of which one is the susceptible allele of the Xa23 gene, a Xa10-like TAL effector-dependent executor R gene isolated recently from rice cultivar CBB23. However, the function of the two Xa10-like genes in disease resistance to X. oryzae pv. oryzae strains has not been investigated. Here we designated the two Xa10-like genes as Xa10-Ni and Xa23-Ni and characterized their function for disease resistance to rice bacterial blight. Both Xa10-Ni and Xa23-Ni provided disease resistance to X. oryzae pv. oryzae strains that deliver the matching artificially designed TAL effectors (dTALEs). Transgenic rice plants containing Xa10-Ni and Xa23-Ni under the Xa10 promoter provided specific disease resistance to X. oryzae pv. oryzae strains that deliver AvrXa10. Xa10-Ni and Xa23-Ni knock-out mutants abolished dTALE-dependent disease resistance to X. oryzae pv. oryzae. Heterologous expression of Xa10-Ni and Xa23-Ni in Nicotiana benthamiana triggered cell death. The 19-amino acid residues at the N-terminal regions of XA10 or XA10-Ni are dispensable for their function in inducing cell death in N. benthamiana and the C-terminal regions of XA10, XA10-Ni and XA23-Ni are interchangeable among each other without affecting their function. Like XA10, both XA10-Ni and XA23-Ni locate to the endoplasmic

  11. Variation among conventional cultivars could be used as a criterion for environmental safety assessment of Bt rice on nontarget arthropods

    NASA Astrophysics Data System (ADS)

    Wang, Fang; Dang, Cong; Chang, Xuefei; Tian, Junce; Lu, Zengbin; Chen, Yang; Ye, Gongyin

    2017-02-01

    The current difficulty facing risk evaluations of Bacillus thuringiensis (Bt) crops on nontarget arthropods (NTAs) is the lack of criteria for determining what represents unacceptable risk. In this study, we investigated the biological parameters in the laboratory and field population abundance of Nilaparvata lugens (Hemiptera: Delphacidae) on two Bt rice lines and the non-Bt parent, together with 14 other conventional rice cultivars. Significant difference were found in nymphal duration and fecundity of N. lugens fed on Bt rice KMD2, as well as field population density on 12 October, compared with non-Bt parent. However, compared with the variation among conventional rice cultivars, the variation of each parameter between Bt rice and the non-Bt parent was much smaller, which can be easily seen from low-high bar graphs and also the coefficient of variation value (C.V). The variation among conventional cultivars is proposed to be used as a criterion for the safety assessment of Bt rice on NTAs, particularly when statistically significant differences in several parameters are found between Bt rice and its non-Bt parent. Coefficient of variation is suggested as a promising parameter for ecological risk judgement of IRGM rice on NTAs.

  12. Variation among conventional cultivars could be used as a criterion for environmental safety assessment of Bt rice on nontarget arthropods

    PubMed Central

    Wang, Fang; Dang, Cong; Chang, Xuefei; Tian, Junce; Lu, Zengbin; Chen, Yang; Ye, Gongyin

    2017-01-01

    The current difficulty facing risk evaluations of Bacillus thuringiensis (Bt) crops on nontarget arthropods (NTAs) is the lack of criteria for determining what represents unacceptable risk. In this study, we investigated the biological parameters in the laboratory and field population abundance of Nilaparvata lugens (Hemiptera: Delphacidae) on two Bt rice lines and the non-Bt parent, together with 14 other conventional rice cultivars. Significant difference were found in nymphal duration and fecundity of N. lugens fed on Bt rice KMD2, as well as field population density on 12 October, compared with non-Bt parent. However, compared with the variation among conventional rice cultivars, the variation of each parameter between Bt rice and the non-Bt parent was much smaller, which can be easily seen from low-high bar graphs and also the coefficient of variation value (C.V). The variation among conventional cultivars is proposed to be used as a criterion for the safety assessment of Bt rice on NTAs, particularly when statistically significant differences in several parameters are found between Bt rice and its non-Bt parent. Coefficient of variation is suggested as a promising parameter for ecological risk judgement of IRGM rice on NTAs. PMID:28167821

  13. Effect of gamma irradiation on physicochemical, functional and pasting properties of some locally-produced rice (Oryza spp) cultivars in Ghana

    NASA Astrophysics Data System (ADS)

    Ocloo, Fidelis C. K.; Owureku-Asare, Mavis; Agyei-Amponsah, Joyce; Agbemavor, Wisdom S. K.; Egblewogbe, Martin N. Y. H.; Apea-Bah, Franklin B.; Sarfo, Adjoa; Apatey, John; Doku, Henry; Ofori-Appiah, Dora; Ayeh, Ernestina

    2017-01-01

    Rice (Oryza sativa L.) is a staple crop in Ghana and much of West Africa, where it serves as an important convenience food for urban consumers. The objective of this study was to determine the effect of gamma irradiation as insect disinfestation technique on some physicochemical, functional and pasting properties of selected locally-produced rice cultivars in Ghana. Four local rice cultivars and an imported (commercial) type were purchased, cleaned and irradiated at doses of 0.0, 0.25, 0.50, 0.75, 1.0 and 1.5 kGy. The irradiated rice cultivars were milled and their physicochemical, functional and pasting properties determined. There were reductions in pH and swelling power, as well as increase in solubility of rice cultivars after gamma irradiation. Gamma irradiation did not change the XRD pattern of the rice cultivars. Gamma irradiation significantly (P<0.05) decreased peak time for BAL and VNT rice cultivars. Gamma irradiation significantly (P<0.05) decreased PV, HPV, BDV, FV and SBV for all the rice cultivars. This study shows that flours from gamma irradiated rice cultivars have potential in food formulations that require low viscosity.

  14. Genetic basis of multiple resistance to the brown planthopper (Nilaparvata lugens Stål) and the green rice leafhopper (Nephotettix cincticeps Uhler) in the rice cultivar ‘ASD7’ (Oryza sativa L. ssp. indica)

    PubMed Central

    Van Mai, Tan; Fujita, Daisuke; Matsumura, Masaya; Yoshimura, Atsushi; Yasui, Hideshi

    2015-01-01

    The rice cultivar ASD7 (Oryza sativa L. ssp. indica) is resistant to the brown planthopper (BPH; Nilaparvata lugens Stål) and the green leafhopper (Nephotettix virescens Distant). Here, we analyzed multiple genetic resistance to BPH and the green rice leafhopper (GRH; Nephotettix cincticeps Uhler). Using two independent F2 populations derived from a cross between ASD7 and Taichung 65 (Oryza sativa ssp. japonica), we detected two QTLs (qBPH6 and qBPH12) for resistance to BPH and one QTL (qGRH5) for resistance to GRH. Linkage analysis in BC2F3 populations revealed that qBPH12 controlled resistance to BPH and co-segregated with SSR markers RM28466 and RM7376 in plants homozygous for the ASD7 allele at qBPH6. Plants homozygous for the ASD7 alleles at both QTLs showed a much faster antibiosis response to BPH than plants homozygous at only one of these QTLs. It revealed that epistatic interaction between qBPH6 and qBPH12 is the basis of resistance to BPH in ASD7. In addition, qGRH5 controlled resistance to GRH and co-segregated with SSR markers RM6082 and RM3381. qGRH5 is identical to GRH1. Thus, we clarified the genetic basis of multiple resistance of ASD7 to BPH and GRH. PMID:26719745

  15. Genetic basis of multiple resistance to the brown planthopper (Nilaparvata lugens Stål) and the green rice leafhopper (Nephotettix cincticeps Uhler) in the rice cultivar 'ASD7' (Oryza sativa L. ssp. indica).

    PubMed

    Van Mai, Tan; Fujita, Daisuke; Matsumura, Masaya; Yoshimura, Atsushi; Yasui, Hideshi

    2015-12-01

    The rice cultivar ASD7 (Oryza sativa L. ssp. indica) is resistant to the brown planthopper (BPH; Nilaparvata lugens Stål) and the green leafhopper (Nephotettix virescens Distant). Here, we analyzed multiple genetic resistance to BPH and the green rice leafhopper (GRH; Nephotettix cincticeps Uhler). Using two independent F2 populations derived from a cross between ASD7 and Taichung 65 (Oryza sativa ssp. japonica), we detected two QTLs (qBPH6 and qBPH12) for resistance to BPH and one QTL (qGRH5) for resistance to GRH. Linkage analysis in BC2F3 populations revealed that qBPH12 controlled resistance to BPH and co-segregated with SSR markers RM28466 and RM7376 in plants homozygous for the ASD7 allele at qBPH6. Plants homozygous for the ASD7 alleles at both QTLs showed a much faster antibiosis response to BPH than plants homozygous at only one of these QTLs. It revealed that epistatic interaction between qBPH6 and qBPH12 is the basis of resistance to BPH in ASD7. In addition, qGRH5 controlled resistance to GRH and co-segregated with SSR markers RM6082 and RM3381. qGRH5 is identical to GRH1. Thus, we clarified the genetic basis of multiple resistance of ASD7 to BPH and GRH.

  16. Cultivars effect on the physical characteristics of rice (rough and milled) (Oryza Sativa L.) of temperate region of Kashmir (India).

    PubMed

    Bhat, Farhan M; Riar, Charanjit S

    2016-12-01

    The aim of present research was to evaluate physical and engineering properties of traditional paddy and rice cultivars native to temperate region of India. Length, width, thickness, equivalent diameter, surface area, aspect ratio, volume, bulk density, true density, porosity, thousand kernels weight, angle of repose and coefficient of friction were evaluated, which are required in designing of various post harvest operations and storage structures. The low bulk density of cultivars, Mushki budgi, Mushki tujan and Kaw kareed may be due to the presence of long awns possessed by these cultivars which were bulky and occupied more space. The wide variations were found in rice kernels with respect to colour, which determined the functional properties and energy requirement during polishing of these cultivars. Results indicated significant differences in the physical properties among various paddy and brown rice cultivars when compared with earlier reported results. Thousand kernel weight, width, arithmetic mean diameter and equivalent diameter showed significant positive correlations with spherecity, surface area, volume, true density, and angle of repose; but negatively correlated with bulk density. These desirable characteristics exploit agriculturists/institutions to preserve these races and encourage farmers to cultivate these cherished rice cultivars.

  17. [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.

  18. 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

  19. Volatile compounds from crabapple (Malus spp.) cultivars differing in susceptibility to the Japanese beetle (Popillia japonica Newman).

    PubMed

    Loughrin, J H; Potter, D A; Hamilton-Kemp, T R; Byers, M E

    1996-07-01

    The volatile compounds emitted by leaves of four crabapple cultivars susceptible to damage by Japanese beetles and four relatively resistant cultivars were examined. Twelve compounds, mostly terpene hydrocarbons, were identified from intact leaves. The terpenes (E)-β-ocimene, caryophylene, germacrene D and (E,E)-α-farnesene occurred in significantly higher levels in susceptible cultivars, whereas resistant cultivars produced greater amounts of (E)-4,8-dimethyl 1,3,7-nonatriene and linalool. The relative attractiveness of the cultivars as determined in a pitfall bioassay, however, was not related to their susceptibility to the Japanese beetle as previously determined by defoliation sustained in the field. The attractiveness of individual cultivars was found to be positiviely correlated with linalool as a percent of the total volatile blend emitted by leaves. This study and previous work suggest that variation in susceptibility of crabapple cultivars to defoliation by Japanese beetles is not due to the attractiveness of the individual cultivars but rather to nonvolatile components of susceptibility and/or resistance. A scenario for host location by the Japanese beetle is presented.

  20. Fine mapping and introgressing qFIS1-2, a major QTL for kernel fissure resistance in rice (Oryza sativa L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice (Oryza sativa L.) kernel fissuring increases breakage during milling and decreases the value of processed rice. This study employed molecular gene tagging methods to fine-map a fissure resistance (FR) locus in ‘Cybonnet’, a semidwarf tropical japonica cultivar, as well as transfer this trait to...

  1. 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.

  2. Pyramiding transgenic resistance in elite indica rice cultivars against the sheath blight and bacterial blight.

    PubMed

    Maruthasalam, S; Kalpana, K; Kumar, K K; Loganathan, M; Poovannan, K; Raja, J A J; Kokiladevi, E; Samiyappan, R; Sudhakar, D; Balasubramanian, P

    2007-06-01

    Elite indica rice cultivars were cotransformed with genes expressing a rice chitinase (chi11) and a thaumatin-like protein (tlp) conferring resistance to fungal pathogens and a serine-threonine kinase (Xa21) conferring bacterial blight resistance, through particle bombardment, with a view to pyramiding sheath blight and bacterial blight resistance. Molecular analyses of putative transgenic lines by polymerase chain reaction, Southern Blot hybridization, and Western Blotting revealed stable integration and expression of the transgenes in a few independent transgenic lines. Progeny analyses showed the stable inheritance of transgenes to their progeny. Coexpression of chitinase and thaumatin-like protein in the progenies of a transgenic Pusa Basmati1 line revealed an enhanced resistance to the sheath blight pathogen, Rhizoctonia solani, as compared to that in the lines expressing the individual genes. A transgenic Pusa Basmati1 line pyramided with chi11, tlp, and Xa21 showed an enhanced resistance to both sheath blight and bacterial blight.

  3. TOND1 confers tolerance to nitrogen deficiency in rice.

    PubMed

    Zhang, Yangjun; Tan, Lubin; Zhu, Zuofeng; Yuan, Lixing; Xie, Daoxin; Sun, Chuanqing

    2015-02-01

    Nitrogen (N), the most important mineral nutrient for plants, is critical to agricultural production systems. N deficiency severely affects rice growth and decreases rice yields. However, excessive use of N fertilizer has caused severe pollution to agricultural and ecological environments. The necessity of breeding of crops that require lower input of N fertilizer has been recognized. Here we identified a major quantitative trait locus on chromosome 12, Tolerance Of Nitrogen Deficiency 1 (TOND1), that confers tolerance to N deficiency in the indica cultivar Teqing. Sequence verification of 75 indica and 75 japonica cultivars from 18 countries and regions demonstrated that only 27.3% of cultivars (41 indica cultivars) contain TOND1, whereas 72.7% of cultivars, including the remaining 34 indica cultivars and all 75 japonica cultivars, do not harbor the TOND1 allele. Over-expression of TOND1 increased the tolerance to N deficiency in the TOND1-deficient rice cultivars. The identification of TOND1 provides a molecular basis for breeding rice varieties with improved grain yield despite decreased input of N fertilizers.

  4. 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

  5. Photosynthetic diffusional constraints affect yield in drought stressed rice cultivars during flowering.

    PubMed

    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 (g(m)) and not by stomatal conductance (g(s)). Mesophyll conductance declined during drought to differing extents among the cultivars; those varieties that maintained g(m) during water-deficit sustained A and yield to a greater extent. However, the variety with the highest g(m) 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 g(m) during optimal growth conditions and the capacity for g(m) 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.

  6. 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.

  7. Rice Seed Cultivar Identification Using Near-Infrared Hyperspectral Imaging and Multivariate Data Analysis

    PubMed Central

    Kong, Wenwen; Zhang, Chu; Liu, Fei; Nie, Pengcheng; He, Yong

    2013-01-01

    A near-infrared (NIR) hyperspectral imaging system was developed in this study. NIR hyperspectral imaging combined with multivariate data analysis was applied to identify rice seed cultivars. Spectral data was exacted from hyperspectral images. Along with Partial Least Squares Discriminant Analysis (PLS-DA), Soft Independent Modeling of Class Analogy (SIMCA), K-Nearest Neighbor Algorithm (KNN) and Support Vector Machine (SVM), a novel machine learning algorithm called Random Forest (RF) was applied in this study. Spectra from 1,039 nm to 1,612 nm were used as full spectra to build classification models. PLS-DA and KNN models obtained over 80% classification accuracy, and SIMCA, SVM and RF models obtained 100% classification accuracy in both the calibration and prediction set. Twelve optimal wavelengths were selected by weighted regression coefficients of the PLS-DA model. Based on optimal wavelengths, PLS-DA, KNN, SVM and RF models were built. All optimal wavelengths-based models (except PLS-DA) produced classification rates over 80%. The performances of full spectra-based models were better than optimal wavelengths-based models. The overall results indicated that hyperspectral imaging could be used for rice seed cultivar identification, and RF is an effective classification technique. PMID:23857260

  8. 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.

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

    PubMed

    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.

  10. A (1)H HR-MAS NMR-Based Metabolomic Study for Metabolic Characterization of Rice Grain from Various Oryza sativa L. Cultivars.

    PubMed

    Song, Eun-Hye; Kim, Hyun-Ju; Jeong, Jaesik; Chung, Hyun-Jung; Kim, Han-Yong; Bang, Eunjung; Hong, Young-Shick

    2016-04-20

    Rice grain metabolites are important for better understanding of the plant physiology of various rice cultivars and thus for developing rice cultivars aimed at providing diverse processed products. However, the variation of global metabolites in rice grains has rarely been explored. Here, we report the identification of intra- or intercellular metabolites in rice (Oryza sativa L.) grain powder using a (1)H high-resolution magic angle spinning (HR-MAS) NMR-based metabolomic approach. Compared with nonwaxy rice cultivars, marked accumulation of lipid metabolites such as fatty acids, phospholipids, and glycerophosphocholine in the grains of waxy rice cultivars demonstrated the distinct metabolic regulation and adaptation of each cultivar for effective growth during future germination, which may be reflected by high levels of glutamate, aspartate, asparagine, alanine, and sucrose. Therefore, this study provides important insights into the metabolic variations of diverse rice cultivars and their associations with environmental conditions and genetic backgrounds, with the aim of facilitating efficient development and the improvement of rice grain quality through inbreeding with genetic or chemical modification and mutation.

  11. H2O2 pretreated rice seedlings specifically reduces arsenate not arsenite: difference in nutrient uptake and antioxidant defense response in a contrasting pair of rice cultivars.

    PubMed

    Mallick, Shekhar; Kumar, Navin; Sinha, Sarita; Dubey, Arvind Kumar; Tripathi, Rudra Deo; Srivastav, Vivek

    2014-10-01

    The study investigated the reduction in metalloid uptake at equimolar concentrations (~53.3 μM) of As(III) and As(V) in contrasting pair of rice seedlings by pretreating with H2O2 (1.0 μM) and SA (1.0 mM). Results obtained from the contrasting pair (arsenic tolerant vs. sensitive) of rice seedlings (cv. Pant Dhan 11 and MTU 7029, respectively) shows that pretreatment of H2O2 and H2O2 + SA reduces As(V) uptake significantly in both the cultivars, while no reduction in the As(III) uptake. The higher growth inhibition, higher H2O2 and TBARS content in sensitive cultivar against As(III) and As(V) treatments along with higher As accumulation (~1.2 mg g(-1) dw) than in cv. P11, unravels the fundamental difference in the response between the sensitive and tolerant cultivar. In the H2O2 pretreated plants, the translocation of As increased in tolerant cultivar against AsIII, whereas, it decreased in sensitive cultivar both against AsIII and AsV. In both the cultivars translocation of Mn increased in the H2O2 pretreated plants against As(III), whereas, the translocation of Cu increased against As(V). In tolerant cultivar the translocation of Fe increased against As(V) with H2O2 pretreatment whereas, it decreased in the sensitive cultivar. In both the cultivars, Zn translocation increased against As(III) and decreased against As(V). The higher level of H2O2 and SOD (EC 1.15.1.1) activity in sensitive cultivar whereas, higher, APX (EC 1.11.1.11), GR (EC 1.6.4.2) and GST (EC 1.6.4.2) activity in tolerant cultivar, also demonstrated the differential anti-oxidative defence responses between the contrasting rice cultivars.

  12. 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.

  13. Proteomic profiling of rice embryos from a hybrid rice cultivar and its parental lines.

    PubMed

    Wang, Weiwei; Meng, Bo; Ge, Xiaomeng; Song, Shuhui; Yang, Yue; Yu, Xiaomin; Wang, Liguo; Hu, Songnian; Liu, Siqi; Yu, Jun

    2008-11-01

    Elite rice hybrids, when compared to their parental lines, exhibit increased yield and other favorable agronomical traits, such as pathogen- and water-stress resistances, which are described as heterosis, and the molecular mechanism of heterosis remains to be elucidated. Since genomic sequences of the paternal (9311) and maternal lines (P64S) of a major rice hybrid variety LYP9 (Liang-You-Pei-Jiu) were acquired recently, we performed a proteomic study on mature embryos of this hybrid triad based on 2-DE and MALDI-TOF MS analyses, and identified 54 differentially expressed proteins involved in major biological processes including nutrient reservoir, response to stress, and metabolism. We observed that most of the storage proteins exhibit overdominance and stress-induced proteins display additivity. We compared proteomic results with transcriptomic data generated from the same embryo samples and found 28 candidate heterosis-associated genes shared by the two datasets. We further traced back to their genomic structures including protein-coding and regulatory regions and found that most of these genes have multiple copies in rice genomes as paralogous genes. Based on alignment of coding and regulation regions, we found that most of the differentially expressed genes at both protein and RNA levels are recent gene duplicates (paralogous genes) with relative little difference in protein-coding regions between orthologous genes (between genes of the two parental genomes) as compared to regulatory regions that harbor numerous indels and base substitutions.

  14. A proteomic study of rice cultivar TNG67 and its high aroma mutant SA0420.

    PubMed

    Lin, Da-Gin; Chou, Szu-Yi; Wang, Arthur Z; Wang, Yi-Wen; Kuo, Shu-Ming; Lai, Chien-Chen; Chen, Liang-Jwu; Wang, Chang-Sheng

    2014-01-01

    Fragrance is a very important economic trait for rice cultivars. To identify the aroma genes in rice, we performed a proteomics analysis of aroma-related proteins between Tainung 67 (TNG67) and its high aroma mutant SA0420. Seventeen of the differentially identified proteins were close related with the aroma phenotype of SA0420. Among them, 9 were found in leaves and 8 were found in grains. One protein (L3) was identified as the chloroplastic glyceraldehyde-3-phosphate dehydrogenase B (OsGAPDHB) which was less abundant in SA0420 than TNG67. Sequence analysis demonstrated that this protein in SA0420 carries a P425S mutation in the C-terminal extension domain, which might hinder the formation of holoenzyme, thereby changing the profile of aroma compounds. The protein profile of OsGAPDHB showed only a weak correlation to its transcription profile. This result indicated that the reduction of OsGAPDHB in SA0420 is regulated by post-translational processes and can only be analyzed by proteomics approach. Transgenic lines suppressing OsGAPDHB through RNAi harbored more fragrance than TNG67 but less than SA0420. With betaine-aldehyde dehydrogenase as the only fragrance gene identified in rice to date, OsGAPDHB may serve as the second protein known to contribute to the aroma phenotype.

  15. 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.

  16. A proteomic analysis of salt stress response in seedlings of two African rice cultivars.

    PubMed

    Damaris, Rebecca Njeri; Li, Ming; Liu, Yanli; Chen, Xi; Murage, Hunja; Yang, Pingfang

    2016-11-01

    Salt stress is one of the key abiotic stresses threatening future agricultural production and natural ecosystems. This study investigates the salt stress response of two rice seedlings, which were screened from 28 Kenya rice cultivars. A proteomic analysis was carried out and Mapman bin codes employed in protein function categorization. Proteins in the redox, stress, and signaling categories were identified, and whose expression differed between the salt tolerant and the salt sensitive samples employed in the present study. 104 and 102 root proteins were observed as significantly altered during salt stress in the tolerant and sensitive samples, respectively and 13 proteins were commonly expressed. Among the 13 proteins, ketol-acid reductoisomerase protein was upregulated in both 1 and 3days of salt treatment in the tolerant sample, while it was down-regulated in both 1 and 3days of salt treatment in the sensitive sample. Actin-7, tubulin alpha, V-type proton ATPase, SOD (Cu-Zn), SOD (Mn), and pyruvate decarboxylase were among the observed salt-induced proteins. In general, this study improves our understanding about salt stress response mechanisms in rice.

  17. Odor-active compounds in cooked rice cultivars from Camargue (France) analyzed by GC-O and GC-MS.

    PubMed

    Maraval, Isabelle; Mestres, Christian; Pernin, Karine; Ribeyre, Fabienne; Boulanger, Renaud; Guichard, Elisabeth; Gunata, Ziya

    2008-07-09

    Volatile compounds of cooked rice from scented (Aychade, Fidji) and nonscented (Ruille) cultivars grown in the Camargue area in France were compared to that of a marketed Asian scented one (Thai) by gas chromatography-olfactometry (GC-O) and gas chromatography-mass spectrometry (GC-MS). GC-O analyses of the organic extracts resulted in the perception of 40 odorous compounds. Only two compounds, oct-1-en-3-one and 2-acetyl-1-pyrroline, were almost always perceived. Hierarchical cluster analysis showed that most of the difference between rice odors was linked to quantitative differences with only 11 compounds being specific to some of the rice. Sixty compounds were identified and quantified by GC-MS, including a few new odor-active components. Principal component analysis enabled us to differentiate scented cultivars from a nonscented one, and scented rice cultivars from Camargue from a Thai sample. Calculated odor-active values evidenced that the Thai sample odor differed from that of scented Camargue cultivars because of the degradation of lipids and of cinnamic acid compounds.

  18. 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

  19. A map of rice genome variation reveals the origin of cultivated rice.

    PubMed

    Huang, Xuehui; Kurata, Nori; Wei, Xinghua; Wang, Zi-Xuan; Wang, Ahong; Zhao, Qiang; Zhao, Yan; Liu, Kunyan; Lu, Hengyun; Li, Wenjun; Guo, Yunli; Lu, Yiqi; Zhou, Congcong; Fan, Danlin; Weng, Qijun; Zhu, Chuanrang; Huang, Tao; Zhang, Lei; Wang, Yongchun; Feng, Lei; Furuumi, Hiroyasu; Kubo, Takahiko; Miyabayashi, Toshie; Yuan, Xiaoping; Xu, Qun; Dong, Guojun; Zhan, Qilin; Li, Canyang; Fujiyama, Asao; Toyoda, Atsushi; Lu, Tingting; Feng, Qi; Qian, Qian; Li, Jiayang; Han, Bin

    2012-10-25

    Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.

  20. Origin, dispersal, cultivation and variation of rice.

    PubMed

    Khush, G S

    1997-09-01

    There are two cultivated and twenty-one wild species of genus Oryza. O. sativa, the Asian cultivated rice is grown all over the world. The African cultivated rice, O. glaberrima is grown on a small scale in West Africa. The genus Oryza probably originated about 130 million years ago in Gondwanaland and different species got distributed into different continents with the breakup of Gondwanaland. The cultivated species originated from a common ancestor with AA genome. Perennial and annual ancestors of O. sativa are O. rufipogon and O. nivara and those of O. glaberrima are O. longistaminata, O. breviligulata and O. glaberrima probably domesticated in Niger river delta. Varieties of O. sativa are classified into six groups on the basis of genetic affinity. Widely known indica rices correspond to group I and japonicas to group VI. The so called javanica rices also belong to group VI and are designated as tropical japonicas in contrast to temperate japonicas grown in temperate climate. Indica and japonica rices had a polyphyletic origin. Indicas were probably domesticated in the foothills of Himalayas in Eastern India and japonicas somewhere in South China. The indica rices dispersed throughout the tropics and subtropics from India. The japonica rices moved northward from South China and became the temperate ecotype. They also moved southward to Southeast Asia and from there to West Africa and Brazil and became tropical ecotype. Rice is now grown between 55 degrees N and 36 degrees S latitudes. It is grown under diverse growing conditions such as irrigated, rainfed lowland, rainfed upland and floodprone ecosystems. Human selection and adaptation to diverse environments has resulted in numerous cultivars. It is estimated that about 120,000 varieties of rice exist in the world. After the establishment of International Rice Research Institute in 1960, rice varietal improvement was intensified and high yielding varieties were developed. These varieties are now planted to 70

  1. Ultraviolet B-sensitive rice cultivar deficient in cyclobutyl pyrimidine dimer repair

    SciTech Connect

    Hidema, Jun; Kumagai, Tadashi; Sutherland, J.C.; Sutherland, B.M.

    1997-01-01

    Repair of cyclobutyl pyrimidine dimers (CPDs) in DNA is essential in most organisms to prevent biological damage by ultraviolet (UV) light. In higher plants tested thus far, UV-sensitive strains had higher initial damage levels or deficient repair of nondimer DNA lesions but normal CPD repair. This suggested that CPDs might not be important for biological lesions. The photosynthetic apparatus has also been proposed as a critical target. We have analyzed CPD induction and repair in the UV-sensitive rice (Oryza sativa L.) cultivar Norin 1 and its close relative UV-resistant Sasanishiki using alkaline agarose gel electrophoresis. Norin 1 is deficient in cyclobutyl pyrimidine dimer photoreactivation and excision; thus, UV sensitivity correlates with deficient dimer repair. 38 refs., 3 figs.

  2. Taxonomy and phylogenetic position of Fomitiporia torreyae, a causal agent of trunk rot on Sanbu-sugi, a cultivar of Japanese cedar (Cryptomeria japonica) in Japan.

    PubMed

    Ota, Yuko; Hattori, Tsutomu; Nakamura, Hitoshi; Terashima, Yoshie; Lee, Su-See; Miyuki, Yurika; Sotome, Kozue

    2014-01-01

    Trunk rot poses a substantial threat to Sanbu-sugi, one of the most economically important cultivars of Japanese cedar (Cryptomeria japonica). The etiology of this disease, including its main agents, is incompletely known. This trunk rot was attributed to Fomitiporia (Phellinus) hartigii or F. (Phellinus) punctata. Here we phylogenetically analyzed DNA sequences of four markers from a set of strains isolated from trunk-rot symptoms and recovered a single, monophyletic clade, indicating that a single taxon is involved. This clade was identified as Fomitiporia torreyae, a species described from eastern China. This analysis also proved that trunk rot and/or dieback of other conifers and broadleaf trees, including Sawara cypress (Chamaecyparis pisifera), Japanese umbrella pine (Sciadopitys verticillata) and Japanese pear (Pyrus pyrifolia var. culta), were caused by the same species. The phylogenetic approach to Fomitiporia revealed that the F. torreyae clade was closely related to F. bannaensis but clearly distinct from F. punctata, which originally was thought to be the cause of trunk rot in Sanbu-sugi. Fomitiporia torreyae is redescribed on the basis of more than 40 specimens from multiple hosts from Japan and China. Fomitiporia juniperina comb. nov. is proposed.

  3. Analysis of drought-responsive signalling network in two contrasting rice cultivars using transcriptome-based approach

    PubMed Central

    Borah, Pratikshya; Sharma, Eshan; Kaur, Amarjot; Chandel, Girish; Mohapatra, Trilochan; Kapoor, Sanjay; Khurana, Jitendra P.

    2017-01-01

    Traditional cultivars of rice in India exhibit tolerance to drought stress due to their inherent genetic variations. Here we present comparative physiological and transcriptome analyses of two contrasting cultivars, drought tolerant Dhagaddeshi (DD) and susceptible IR20. Microarray analysis revealed several differentially expressed genes (DEGs) exclusively in DD as compared to IR20 seedlings exposed to 3 h drought stress. Physiologically, DD seedlings showed higher cell membrane stability and differential ABA accumulation in response to dehydration, coupled with rapid changes in gene expression. Detailed analyses of metabolic pathways enriched in expression data suggest interplay of ABA dependent along with secondary and redox metabolic networks that activate osmotic and detoxification signalling in DD. By co-localization of DEGs with QTLs from databases or published literature for physiological traits of DD and IR20, candidate genes were identified including those underlying major QTL qDTY1.1 in DD. Further, we identified previously uncharacterized genes from both DD and IR20 under drought conditions including OsWRKY51, OsVP1 and confirmed their expression by qPCR in multiple rice cultivars. OsFBK1 was also functionally validated in susceptible PB1 rice cultivar and Arabidopsis for providing drought tolerance. Some of the DEGs mapped to the known QTLs could thus, be of potential significance for marker-assisted breeding. PMID:28181537

  4. 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.

  5. [Influence of weeds in Echinochloa on growth and yield of rice].

    PubMed

    Zhang, Zi-Chang; Li, Yong-Feng; Zhang, Bin; Yang, Xia

    2014-11-01

    In order to investigate effects of different barnyardgrass species on growth and yiled of rice, two rice cultivars, Xinliangyou 6 hao (an indica hybrid cultivar) and Nanjing 46 (a japonica cultivar), were co-cultured with four barnyardgrass species grown at a density of six plants · m(-2) from 10 days after transplanting to maturity. The treatments were 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 result showed that barnyardgrass-induced reductions in grain yield of rice were obviously different among the four treatments. T1, T2 and T3 treatments reduced the grain yield of indicia cultivar by 19.2%, 10.8% and 21.9%, and the respective reductions in japonica cultivar were 39.7%, 25.3% and 47.3%, re- spectively. However, no significant difference was detected for T4 treatment. During rice co-culture with barnyardgrass, T1, T2 and T3 significantly reduced rice dry matter accumulation at maturity, flag leaf photosynthetic rate, root oxidation activity and the activity of adenosine triphosphate enzyme (ATPsse) in rice grains at the filling stage, and the magnitude of decrease was in the order of T3 > T1 > T2, while no significant difference was observed between T4 and CK. In addition, all treatments had no effects on the final tiller number and plant height of rice. It indicated that the negative effect of barnyardgrass on rice growth and yield differed among the four species of barnyardgrass, in the order of T3 > T1 > T2 > T4. Barnyardgrass reduced the flag leaf photosynthetic rate of rice, both root oxidation activity and ATPsse activity in grains, which resulted in the reduction in final productivity of rice when co-cultured with barnyardgrass.

  6. Different physiobiochemical and transcriptomic reactions of rice (Oryza sativa L.) cultivars differing in terms of salt sensitivity under salinity stress.

    PubMed

    Kordrostami, Mojtaba; Rabiei, Babak; Kumleh, Hassan Hassani

    2017-01-17

    Salinity stress is the most important and common environmental stresses throughout the world, including Iran. The aim of this study was to investigate the expression of several important genes involved in the salinity tolerance of the rice cultivars differing in salt sensitivity. In this research, the expression of four mitochondrial genes, H2O2, malondialdehyde (MDA), proline, sodium, potassium and superoxide dismutase (SOD), was measured in Iranian rice cultivars and two well-known international varieties as checks in response to 100 mM salt stress. The results show that the activity of SOD in the tolerant cultivars is much higher than in the susceptible ones under saline conditions (100 mM NaCl). The study of the gene expression in the tolerant and sensitive cultivars also showed that the expression of the genes increased in the early hours of the stress, with the exception of the OsGR1. Moreover, the amount of the expression in the tolerant cultivars was far more than the susceptible ones. The result of this study showed that the function of a set of antioxidant enzymes can lead to detoxification of the reactive oxygen species, so in order to better understand ROS scavengers, a comprehensive study on the antioxidant system should be conducted.

  7. Screening and Expression of a Silicon Transporter Gene (Lsi1) in Wild-Type Indica Rice Cultivars

    PubMed Central

    Abiri, Rambod; Kalhori, Nahid; Atabaki, Narges

    2017-01-01

    Silicon (Si) is one of the most prevalent elements in the soil. It is beneficial for plant growth and development, and it contributes to plant defense against different stresses. The Lsi1 gene encodes a Si transporter that was identified in a mutant Japonica rice variety. This gene was not identified in fourteen Malaysian rice varieties during screening. Then, a mutant version of Lsi1 was substituted for the native version in the three most common Malaysian rice varieties, MR219, MR220, and MR276, to evaluate the function of the transgene. Real-time PCR was used to explore the differential expression of Lsi1 in the three transgenic rice varieties. Silicon concentrations in the roots and leaves of transgenic plants were significantly higher than in wild-type plants. Transgenic varieties showed significant increases in the activities of the enzymes SOD, POD, APX, and CAT; photosynthesis; and chlorophyll content; however, the highest chlorophyll A and B levels were observed in transgenic MR276. Transgenic varieties have shown a stronger root and leaf structure, as well as hairier roots, compared to the wild-type plants. This suggests that Lsi1 plays a key role in rice, increasing the absorption and accumulation of Si, then alters antioxidant activities, and improves morphological properties. PMID:28191468

  8. Screening and Expression of a Silicon Transporter Gene (Lsi1) in Wild-Type Indica Rice Cultivars.

    PubMed

    Sahebi, Mahbod; Hanafi, Mohamed M; Rafii, M Y; Azizi, Parisa; Abiri, Rambod; Kalhori, Nahid; Atabaki, Narges

    2017-01-01

    Silicon (Si) is one of the most prevalent elements in the soil. It is beneficial for plant growth and development, and it contributes to plant defense against different stresses. The Lsi1 gene encodes a Si transporter that was identified in a mutant Japonica rice variety. This gene was not identified in fourteen Malaysian rice varieties during screening. Then, a mutant version of Lsi1 was substituted for the native version in the three most common Malaysian rice varieties, MR219, MR220, and MR276, to evaluate the function of the transgene. Real-time PCR was used to explore the differential expression of Lsi1 in the three transgenic rice varieties. Silicon concentrations in the roots and leaves of transgenic plants were significantly higher than in wild-type plants. Transgenic varieties showed significant increases in the activities of the enzymes SOD, POD, APX, and CAT; photosynthesis; and chlorophyll content; however, the highest chlorophyll A and B levels were observed in transgenic MR276. Transgenic varieties have shown a stronger root and leaf structure, as well as hairier roots, compared to the wild-type plants. This suggests that Lsi1 plays a key role in rice, increasing the absorption and accumulation of Si, then alters antioxidant activities, and improves morphological properties.

  9. Influence and interaction of iron and cadmium on photosynthesis and antioxidative enzymes in two rice cultivars.

    PubMed

    Liu, Houjun; Zhang, Chengxin; Wang, Junmei; Zhou, Chongjun; Feng, Huan; Mahajan, Manoj D; Han, Xiaori

    2017-03-01

    In this study, a soil pot experiment was conducted to investigate the changes in photosynthesis and antioxidative enzymes in two rice varieties (Shendao 6 and Shennong 265) supplied with iron (Fe), cadmium (Cd), and Fe and Cd together. The concentrations of Fe and Cd in the soil were 0, 1.0 g Fe·kg(-1) and 0, 2.0 mg Cd·kg(-1), respectively. Photosynthetic indices and antioxidative enzyme activities were recorded at different rice growth stages. At the early stage, Cd showed a transient stimulatory effect on the photosynthetic rate of Shennong 265. For Shendao 6, however, Cd showed a transient stimulatory effect on photosynthetic rate, intercellular CO2 concentration, stomatal conductance and transpiration efficiency. In addition, the results show that Cd can also enhance the superoxide dismutase (SOD) and peroxidase (POD) activities, but reduce the malondialdehyde (MDA) and soluble protein contents in the two rice cultivars. Subsequently, Cd starts to inhibit photosynthesis and SOD activity until the ripening stage, causing the lowest photosynthetic rate and SOD activity at this stage. In contrast, Fe alleviates the Cd-induced changes at earlier or later growth stage. Notably at the later growth stage, the results show that the interaction between Fe and Cd increases the SOD and catalase (CAT) activities, while decreasing the lipid peroxidation and promoting photosynthesis. As a result, it ultimately increases the biomass. The results from this study suggest that Fe (as Fe fertilizer) is a promising alternative for agricultural use to enhance the plant development and, simultaneously, to reduce Cd toxicity in extensively polluted soils.

  10. 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.

  11. Genetic dissection of seed storability using two different populations with a same parent rice cultivar N22

    PubMed Central

    Lin, Qiuyun; Wang, Wenyan; Ren, Yakun; Jiang, Yimei; Sun, Ailing; Qian, Ying; Zhang, Yifei; He, Niqing; Hang, Ngo Thi; Liu, Zhou; Li, Linfang; Liu, Linglong; Jiang, Ling; Wan, Jianmin

    2015-01-01

    Seed storability in rice (Oryza sativa L.) is an important agronomic trait. Two segregating populations with N22 (indica) as a common parent, viz. a set of 122 backcross-inbred lines (BILs) derived from the backcross Nanjing35 (japonica)/N22//Nanjing35 and another population comprising 189 recombinant inbred lines (RILs) from the cross of USSR5 (japonica) and N22, were studied to detect quantitative trait loci (QTL) controlling seed storability. Germination percentage (GP) was used to evaluate seed storability after aging treated under three different conditions, viz. natural, artificial and combined aging treatments. A total of seven QTLs were identified on chromosomes 1, 2, 5, 6 and 9. Among them, a major QTL, qSSn-9, was common in the two populations. In contrast, four QTLs (qSSnj-2-1, qSSn-2-2, qSSn-5 and qSSn-6) were detected in BILs and the QTL qSSn-1 was identified in RILs, which was a new QTL for seed storability. The N22-derived alleles increased the seed storability at all the loci except qSSnj-2-1. We also investigated the effect of QTLs using five selected lines with high storability from BILs and verified qSSn-5 with a near-isogenic line (NIL). These results provide an opportunity for pyramiding or map-based cloning major QTLs for seed storability in rice. PMID:26719744

  12. 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...

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. Studies on effect of temperature and time on textural and rheological properties of starch isolated from traditional rice cultivars of Kashmir (India).

    PubMed

    Bhat, Farhan M; Riar, Charanjit S

    2017-04-01

    In the present study, the effect of storage temperature and time on the textural and rheological properties of starch gels from seven different rice cultivars having higher amylose content than the hybrid rice varieties were evaluated. Water solubility and swelling power increased with every 10C increase in temperature due to granule swelling and solubilization of starch wherein the maximum solubility was found in starch of Koshkari rice cultivar (0.721 to 13.50) and swelling power in starch of Zag rice cultivar (3.688 to 10.806). However, syneresis in the analyzed rice starch gels had shown a fluctuating trend for each individual cultivar at different storage periods in which the cultivars Zag had shown the highest values of syneresis during storage (4.123 to 4.957%). In the texture profile analysis of starch gel of these cultivars, Mushki Budgi had the highest value of hardness (0.723N), gumminess (36.262) and chewiness (31.056). The turbidity values of gelatinized starch suspensions from different rice cultivars increased progressively during the first 4 days of storage followed by a decrease in the 5th day coupled with slight increase in the 6th day. The highest turbidity was found in Zag ranging from 1.47 to 1.67 during refrigerated storage after 6 days. The rheological analysis revealed that Zag indicated the highest value of TG' (76.96C) whereas cultivars Koshkari and Mushki Kandi had shown the lowest value of TG' (74.34C) upon heating cycle.

  18. 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...

  19. Abnormalities occurring during female gametophyte development result in the diversity of abnormal embryo sacs and leads to abnormal fertilization in indica/japonica hybrids in rice.

    PubMed

    Zeng, Yu-Xiang; Hu, Chao-Yue; Lu, Yong-Gen; Li, Jin-Quan; Liu, Xiang-Dong

    2009-01-01

    Embryo sac abortion is one of the major reasons for sterility in indica/japonica hybrids in rice. To clarify the causal mechanism of embryo sac abortion, we studied the female gametophyte development in two indica/japonica hybrids via an eosin B staining procedure for embryo sac scanning using confocal laser scanning microscope. Different types of abnormalities occurred during megasporogenesis and megagametogenesis were demonstrated. The earliest abnormality was observed in the megasporocyte. A lot of the chalazal-most megaspores were degenerated before the mono-nucleate embryo sac stage. Disordered positioning of nucleus and abnormal nucellus tissue were characteristics of the abnormal female gametes from the mono-nucleate to four-nucleate embryo sac stages. The abnormalities that occurred from the early stage of the eight-nucleate embryo sac development to the mature embryo sac stage were characterized by smaller sizes and wrinkled antipodals. Asynchronous nuclear migration, abnormal positioning of nucleus, and degeneration of egg apparatus were also found at the eight-nucleate embryo sac stage. The abnormalities that occurred during female gametophyte development resulted in five major types of abnormal embryo sacs. These abnormal embryo sacs led to abnormal fertilization. Hand pollination using normal pollens on the spikelets during anthesis showed that normal pollens could not exclude the effect of abnormal embryo sac on seed setting.

  20. Development of new rice cultivars for conventional and value-added markets

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice is a staple food crop for half of the world's population. The United States supplies about 10% of the rice that is the world market. US rice production is located in the mid-south and California, with half of the country's production located in Arkansas. Domestic rice consumption in the US has ...

  1. 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

  2. Diverse variation of reproductive barriers in three intraspecific rice crosses.

    PubMed Central

    Harushima, Yoshiaki; Nakagahra, Masahiro; Yano, Masahiro; Sasaki, Takuji; Kurata, Nori

    2002-01-01

    Reproductive barriers are thought to play an important role in the processes of speciation and differentiation. Asian rice cultivars, Oryza sativa, can be classified into two main types, Japonica and Indica, on the basis of several characteristics. The fertility of Japonica-Indica hybrids differs from one cross to another. Many genes involved in reproductive barriers (hybrid sterility, hybrid weakness, and gametophytic competition genes) have been reported in different Japonica-Indica crosses. To clarify the state of Japonica-Indica differentiation, all reproductive barriers causing deviation from Mendelian segregation ratios in F(2) populations were mapped and compared among three different Japonica-Indica crosses: Nipponbare/Kasalath (NK), Fl1084/Dao Ren Qiao (FD), and Fl1007/Kinandang puti (FK). Mapping of reproductive barriers was performed by regression analysis of allele frequencies of DNA markers covering the entire genome. Allele frequencies were explained by 33 reproductive barriers (15 gametophytic and 18 zygotic) in NK, 32 barriers (15 gametophytic and 17 zygotic) in FD, and 37 barriers (19 gametophytic and 18 zygotic) in FK. The number of reproductive barriers in the three crosses was similar; however, most of the barriers were mapped at different loci. Therefore, these reproductive barriers formed after Japonica-Indica differentiation. Considering the high genetic similarity within Japonica and Indica cultivars, the differences in the reproductive barriers of each cross were unexpectedly numerous. The reproductive barriers of Japonica-Indica hybrids likely evolved more rapidly than other genetic elements. One possible force responsible for such rapid evolution of the barriers may have been the domestication of rice. PMID:11805066

  3. 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

  4. 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.

  5. A three-season field study on the in-situ remediation of Cd-contaminated paddy soil using lime, two industrial by-products, and a low-Cd-accumulation rice cultivar.

    PubMed

    Yan-Bing, He; Dao-You, Huang; Qi-Hong, Zhu; Shuai, Wang; Shou-Long, Liu; Hai-Bo, He; Han-Hua, Zhu; Chao, Xu

    2017-02-01

    To mitigate the serious problem of Cd-contaminated paddy soil, we investigated the remediation potential of combining in-situ immobilization with a low-Cd-accumulation rice cultivar. A three-season field experiment compared the soil pH, available Cd and absorption of Cd by three rice cultivars with different Cd accumulation abilities grown in Cd-contaminated paddy soil amended with lime (L), slag (S), and bagasse (B) alone or in combination. The three amendments applied alone and in combination significantly increased soil pH, reduced available Cd and absorption of Cd by rice with no effect on grain yield. Among these, the LS and LSB treatments reduced the brown rice Cd content by 38.3-69.1% and 58.3-70.9%, respectively, during the three seasons. Combined with planting of a low-Cd-accumulation rice cultivar (Xiang Zaoxian 32) resulted in a Cd content in brown rice that met the contaminant limit (≤0.2mgkg(-1)). However, the grain yield of the low-Cd-accumulation rice cultivar was approximately 30% lower than the other two rice cultivars. Applying LS or LSB as amendments combined with planting a low-Cd-accumulation rice cultivar is recommended for the remediation of Cd-contaminated paddy soil. The selection and breeding of low-Cd-accumulation rice cultivars with high grain production requires further research.

  6. Methanotrophic bacteria associated to rice roots: the cultivar effect assessed by T-RFLP and microarray analysis.

    PubMed

    Lüke, Claudia; Bodrossy, Levente; Lupotto, Elisabetta; Frenzel, Peter

    2011-10-01

    Rice plants play a key role in regulating methane emissions from paddy fields by affecting both underlying processes: methane production and oxidation. Specific differences were reported for methane oxidation rates; however, studies on the bacterial communities involved are rare. Here, we analysed the methanotrophic community on the roots of 18 different rice cultivars by pmoA-based terminal restriction fragment length polymorphism (T-RFLP) and microarray analysis. Both techniques showed comparable and consistent results revealing a high diversity dominated by type II and type Ib methanotrophs. pmoA microarrays have been successfully used to study methane-oxidizing bacteria in various environments. However, the microarray's full potential resolving community structure has not been exploited yet. Here, we provide an example on how to include this information into multivariate statistics. The analysis revealed a rice cultivar effect on the methanotroph community composition that could be affiliated to the plant genotype. This effect became only significant by including the specific phylogenetic resolution provided by the microarray into the statistical analysis.

  7. 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.

  8. 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...

  9. 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...

  10. Assessing the impact of ambient ozone on growth and yield of a rice (Oryza sativa L.) and a wheat (Triticum aestivum L.) cultivar grown in the Yangtze Delta, China, using three rates of application of ethylenediurea (EDU).

    PubMed

    Wang, Xiaoke; Zheng, Qiwei; Yao, Fangfang; Chen, Zhan; Feng, Zhaozhong; Manning, W J

    2007-07-01

    Foliar applications of ethylenediurea (abbreviated as EDU) were made at 0, 150, 300 or 450 ppm to field-grown rice and wheat in the Yangtze Delta in China. Rice and wheat responded differently to ambient ozone and EDU applications. For wheat, some growth characteristics, such as yield, seed number per plant, seed set rate and harvest index, increased significantly at 300 ppm EDU treatment, while for rice no parameters measured were statistically different regarding EDU application. The reason may be that the wheat cultivar used may be more sensitive to ozone than the rice cultivar. EDU was effective in demonstrating ozone effects on the wheat cultivar, but not on the rice cultivar. Cultivar sensitivity might be an important consideration when assessing the effects of ambient ozone on plants.

  11. Bioengineered 'golden' indica rice cultivars with beta-carotene metabolism in the endosperm with hygromycin and mannose selection systems.

    PubMed

    Datta, Karabi; Baisakh, Niranjan; Oliva, Norman; Torrizo, Lina; Abrigo, Editha; Tan, Jing; Rai, Mayank; Rehana, Sayda; Al-Babili, Salim; Beyer, Peter; Potrykus, Ingo; Datta, Swapan K

    2003-03-01

    Vitamin-A deficiency (VAD) is a major malnutrition problem in South Asia, where indica rice is the staple food. Indica-type rice varieties feed more than 2 billion people. Hence, we introduced a combination of transgenes using the biolistic system of transformation enabling biosynthesis of provitamin A in the endosperm of several indica rice cultivars adapted to diverse ecosystems of different countries. The rice seed-specific glutelin promoter (Gt-1 P) was used to drive the expression of phytoene synthase (psy), while lycopene beta-cyclase (lcy) and phytoene desaturase (crtI), fused to the transit peptide sequence of the pea-Rubisco small subunit, were driven by the constitutive cauliflower mosaic virus promoter (CaMV35S P). Transgenic plants were recovered through selection with either CaMV35S P driven hph (hygromycin phosphotransferase) gene or cestrum yellow leaf curling virus promoter (CMP) driven pmi (phophomannose isomerase) gene. Molecular and biochemical analyses demonstrated stable integration and expression of the transgenes. The yellow colour of the polished rice grain evidenced the carotenoid accumulation in the endosperm. The colour intensity correlated with the estimated carotenoid content by spectrophotometric and HPLC analysis. Carotenoid level in cooked polished seeds was comparable (with minor loss of xanthophylls) to that in non-cooked seeds of the same transgenic line. The variable segregation pattern in T1 selfing generation indicated single to multiple loci insertion of the transgenes in the genome. This is the first report of using nonantibiotic pmi driven by a novel promoter in generating transgenic indica rice for possible future use in human nutrition.

  12. Single rice growth period was prolonged by cultivars shifts, but yield was damaged by climate change during 1981-2009 in China, and late rice was just opposite.

    PubMed

    Tao, Fulu; Zhang, Zhao; Shi, Wenjiao; Liu, Yujie; Xiao, Dengpan; Zhang, Shuai; Zhu, Zhu; Wang, Meng; Liu, Fengshan

    2013-10-01

    Based on the crop trial data during 1981-2009 at 57 agricultural experimental stations across the North Eastern China Plain (NECP) and the middle and lower reaches of Yangtze River (MLRYR), we investigated how major climate variables had changed and how the climate change had affected crop growth and yield in a setting in which agronomic management practices were taken based on actual weather. We found a significant warming trend during rice growing season, and a general decreasing trend in solar radiation (SRD) in the MLRYR during 1981-2009. Rice transplanting, heading, and maturity dates were generally advanced, but the heading and maturity dates of single rice in the MLRYR (YZ_SR) and NECP (NE_SR) were delayed. Climate warming had a negative impact on growth period lengths at about 80% of the investigated stations. Nevertheless, the actual growth period lengths of YZ_SR and NE_SR, as well as the actual length of reproductive growth period (RGP) of early rice in the MLRYR (YZ_ER), were generally prolonged due to adoption of cultivars with longer growth period to obtain higher yield. In contrast, the actual growth period length of late rice in the MLRYR (YZ_LR) was shortened by both climate warming and adoption of early mature cultivars to prevent cold damage and obtain higher yield. During 1981-2009, climate warming and decrease in SRD changed the yield of YZ_ER by -0.59 to 2.4%; climate warming during RGP increased the yield of YZ_LR by 8.38-9.56%; climate warming and decrease in SRD jointly reduced yield of YZ_SR by 7.14-9.68%; climate warming and increase in SRD jointly increased the yield of NE_SR by 1.01-3.29%. Our study suggests that rice production in China has been affected by climate change, yet at the same time changes in varieties continue to be the major factor driving yield and growing period trends.

  13. 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.

  14. [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.

  15. Fine mapping and identification of blast resistance gene Pi-hk1 in a broad-spectrum resistant japonica rice landrace.

    PubMed

    Wu, Yunyu; Bao, Yongmei; Xie, Liujie; Su, Yunyun; Chu, Ruizhen; He, Wanwan; Huang, Ji; Wang, Jianfei; Zhang, Hongsheng

    2013-11-01

    One Japonica rice landrace, Heikezijing, from the Taihu Lake region of China, exhibits broad-spectrum resistance to rice blast. As characterized in our previous research, a main-effect resistance (R) gene, Pi-hk1, in Heikezijing against five isolates (GD10-279a, JS2004-141-1, JS2004-185, JS90-78, and Hoku1) was roughly mapped on the long arm of chromosome 11. To fine map Pi-hk1, one recombinant inbred line (RIL), RIL72 (F2:8), from the cross between Heikezijing and blast-susceptible variety Suyunuo, was further crossed and backcrossed with Suyunuo to produce a BC1F2 population of 477 individuals. Inoculation experiments with the representative isolate Hoku 1 indicated that RIL72 carries a single dominant R gene for blast resistance. With the help of advanced BC1F3 (915 plants), BC1F4 (4,459 plants), and BC1F5 (2,000 plants) mapping populations, Pi-hk1 was finally mapped to a 107-kb region between molecular markers P3586 and ILP3, and co-segregated with the markers P4098, RM7654, and P4099. By sequence analysis of Heikezijing bacterial artificial chromosome clones covering Pi-hk1 region, 16 predicted genes were identified within this region, including three nucleotide-binding site leucine-rich repeat candidate genes. These results provide essential information for cloning of Pi-hk1 and its application in rice breeding for broad-spectrum blast resistance by marker-assisted selection.

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

    PubMed

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

    2014-10-01

    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.

  17. A new method for evaluation of the resistance to rice kernel cracking based on moisture absorption in brown rice under controlled conditions

    PubMed Central

    Hayashi, Takeshi; Kobayashi, Asako; Tomita, Katsura; Shimizu, Toyohiro

    2015-01-01

    We developed and evaluated the effectiveness of a new method to detect differences among rice cultivars in their resistance to kernel cracking. The method induces kernel cracking under laboratory controlled condition by moisture absorption to brown rice. The optimal moisture absorption conditions were determined using two japonica cultivars, ‘Nipponbare’ as a cracking-resistant cultivar and ‘Yamahikari’ as a cracking-susceptible cultivar: 12% initial moisture content of the brown rice, a temperature of 25°C, a duration of 5 h, and only a single absorption treatment. We then evaluated the effectiveness of these conditions using 12 japonica cultivars. The proportion of cracked kernels was significantly correlated with the mean 10-day maximum temperature after heading. In addition, the correlation between the proportions of cracked kernels in the 2 years of the study was higher than that for values obtained using the traditional late harvest method. The new moisture absorption method could stably evaluate the resistance to kernel cracking, and will help breeders to develop future cultivars with less cracking of the kernels. PMID:26719740

  18. 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.

  19. Arsenic concentrations in local aromatic and high-yielding hybrid rice cultivars and the potential health risk: a study in an arsenic hotspot.

    PubMed

    Sandhi, Arifin; Greger, Maria; Landberg, Tommy; Jacks, Gunnar; Bhattacharya, Prosun

    2017-04-01

    The presence of high levels of arsenic (As) in rice fields has negative effects on the health of those consuming rice as their subsistence food. This study determined the variation in total As concentration in local aromatic rice (LAR) (kalijira) and two high-yielding varieties (HYVs) (BRRI dhan 32 and BRRI dhan 28) grown in paddy fields in Matlab, Bangladesh, an As hotspot with elevated As levels in groundwater. Mature rice grain samples and soil samples were collected from different paddy fields, and the As concentrations in both the de-husked grains and the husks of the three rice cultivars were analysed to identify the safest of the three cultivars for human consumption. The results showed that the total As concentration was higher (0.09-0.21 mg As kg(-1)) in the de-husked grains of LAR than in the husks, while the opposite was found for the HYV rice. Moreover, the As concentration in soil samples was 2 to 5-fold higher for the LAR than for the HYVs, but the As accumulation factor (AF) was lower in the LAR (0.2-0.4%) than in the HYVs (0.9-1%). Thus, LAR can be considered the safest of the three cultivars for human consumption owing to its low AF value. Furthermore, due to the low AF, growing LAR instead of HYVs in soils with slightly elevated As levels could help improve the food safety level in the food chain.

  20. Does the upstream region possessing MULE-like sequence in rice upregulate PsbS1 gene expression?

    PubMed

    Nuruzzaman, Mohammed; Kanno, Tatsuo; Amada, Rika; Habu, Yoshiki; Kasajima, Ichiro; Ishikawa, Toshiki; Kawai-Yamada, Maki; Uchimiya, Hirofumi

    2014-01-01

    The genomic nucleotide sequences of japonica rice (Sasanishiki and Nipponbare) contained about 2.7-kb unique region at the point of 0.4-kb upstream of the OsPsbS1 gene. In this study, we found that japonica rice with a few exceptions possessing such DNA sequences [denoted to OsMULE-japonica specific sequence (JSS)] is distinct by the presence of Mutator-like-element (MULE). Such sequence was absent in most of indica cultivars and Oryza glaberrima. In OsMULE-JSS1, we noted the presence of possible target site duplication (TSD; CTTTTCCAG) and about 80-bp terminal inverted repeat (TIR) near TSD. We also found the enhancement ofOsPsbS1 mRNA accumulation by intensified light, which was not associated with the DNA methylation status in OsMULE/JSS. In addition, O. rufipogon, possible ancestor of modern rice cultivars was found to compose PsbS gene of either japonica (minor) or indica (major) type. Transient gene expression assay showed that the japonica type promoter elevated a reporter gene activity than indica type.

  1. Statistical inference of selection and divergence of the rice blast resistance gene Pi-ta.

    PubMed

    Amei, Amei; Lee, Seonghee; Mysore, Kirankumar S; Jia, Yulin

    2014-10-21

    The resistance gene Pi-ta has been effectively used to control rice blast disease, but some populations of cultivated and wild rice have evolved resistance. Insights into the evolutionary processes that led to this resistance during crop domestication may be inferred from the population history of domesticated and wild rice strains. In this study, we applied a recently developed statistical method, time-dependent Poisson random field model, to examine the evolution of the Pi-ta gene in cultivated and weedy rice. Our study suggests that the Pi-ta gene may have more recently introgressed into cultivated rice, indica and japonica, and U.S. weedy rice from the wild species, O. rufipogon. In addition, the Pi-ta gene is under positive selection in japonica, tropical japonica, U.S. cultivars and U.S. weedy rice. We also found that sequences of two domains of the Pi-ta gene, the nucleotide binding site and leucine-rich repeat domain, are highly conserved among all rice accessions examined. Our results provide a valuable analytical tool for understanding the evolution of disease resistance genes in crop plants.

  2. Fast recovery of transgenic submergence tolerant rice cultivars of North-East India by early co-cultivation of Agrobacterium with pre-cultured callus.

    PubMed

    Nguyen, Van Cuu; Nguyen, Van Khiem; Singh, Chongtham Henary; Devi, Guruaribam Shantibala; Reddy, Vanga Siva; Leelavathi, Sadhu

    2017-01-01

    Agro-climatic conditions of North-East India are very complex and rice cultivars present in the region have been adapted to grow under harsh environmental conditions. Germplasm present in the region is considered to possess several important and unique traits that are of importance in rice improvement programs. Genetic engineering is a powerful tool to introduce new traits into crop plants. However, not much information is available on the methods to introduce foreign genes into North-East rice cultivars. Therefore, the main objective of this study is to develop transformation procedures for fast recovery of transgenic plants from North-East rice cultivars. To achieve this objective, a systematic study was carried out to identify media components and culture conditions for efficient embryogenic callus induction from the mature seeds and differentiation of callus into plantlets from two North-East deep water rice cultivars, Taothabi and Khongan. Also, role of preculture of callus on Agrobacterium-mediated transformation was studied. Co-cultivation of Agrobacterium with 1-5 days precultured callus was found to result in high frequency of transformation. Detailed characterization of transgenic lines confirmed stable integration of transgenes and expression of reporter gfp gene. The whole process starting from callus induction to regenerating of transgenic rice plants that can be established in the soil was achieved in about 35-45 days. The procedures developed were found to be applicable to a popular variety IR 64. Therefore, methods developed in this study should be useful not only to introduce new traits quickly but also to validate the function(s) of several candidate gene(s) identified under the functional genomics of rice.

  3. Molecular mapping of the new blast resistance genes Pi47 and Pi48 in the durably resistant local rice cultivar Xiangzi 3150.

    PubMed

    Huang, Hongmei; Huang, Ling; Feng, Guangping; Wang, Suhua; Wang, Yue; Liu, Jinling; Jiang, Nan; Yan, Weiting; Xu, Lingchao; Sun, Pingyong; Li, Zhiqiang; Pan, Sujun; Liu, Xionglun; Xiao, Yinghui; Liu, Erming; Dai, Liangying; Wang, Guo-Liang

    2011-05-01

    The indica rice cultivar Xiangzi 3150 (XZ3150) confers a high level of resistance to 95% of the isolates of Magnaporthe oryzae (the agent of rice blast disease) collected in Hunan Province, China. To identify the resistance (R) gene(s) controlling the high level of resistance in this cultivar, we developed 286 F(9) recombinant inbred lines (RILs) from a cross between XZ3150 and the highly susceptible cultivar CO39. Inoculation of the RILs and an F(2) population from a cross between the two cultivars with the avirulent isolate 193-1-1 in the growth chamber indicated the presence of two dominant R genes in XZ3150. A linkage map with 134 polymorphic simple sequence repeat and single feature polymorphism markers was constructed with the genotype data of the 286 RILs. Composite interval mapping (CIM) using the results of 193-1-1 inoculation showed that two major R genes, designated Pi47 and Pi48, were located between RM206 and RM224 on chromosome 11, and between RM5364 and RM7102 on chromosome 12, respectively. Interestingly, the CIM analysis of the four resistant components of the RILs to the field blast population revealed that Pi47 and Pi48 were also the major genetic factors responsible for the field resistance in XZ3150. The DNA markers linked to the new R genes identified in this study should be useful for further fine mapping, gene cloning, and marker-aided breeding of blast-resistant rice cultivars.

  4. Threat to food security under current levels of ground level ozone: A case study for Indian cultivars of rice

    NASA Astrophysics Data System (ADS)

    Rai, Richa; Agrawal, Madhoolika; Agrawal, S. B.

    2010-11-01

    A higher ozone concentration in rural agricultural region poses threat to food production in developing countries. The present study was conducted to evaluate the growth, biomass accumulation and allocation pattern, quantitative and qualitative characteristics of grains for two tropical rice cultivars ( Oryza sativa L. cv NDR 97 and Saurabh 950) at ambient O 3 concentrations at a rural site in the Indo Gangetic plains of India. Percent inhibition in number of leaves was higher for NDR 97, but in leaf area for Saurabh 950 grown in non filtered chambers (NFCs) compared to filtered chambers (FCs). Higher inhibition in root biomass was recorded in Saurabh 950 and in leaf and standing dead biomass for NDR 97. During vegetative phase, relative growth rate showed more percent inhibition in Saurabh 950, but at reproductive phase in NDR 97. Net assimilation rate showed higher values for Saurabh 950 than NDR 97 in NFCs but percent inhibition in leaf area ratio was higher for former than latter cultivar in NFCs. The ozone resistance was higher in NDR 97 during vegetative phase, but in Saurabh 950 at reproductive phase. Number of grains was higher in NDR 97 than Saurabh 950, but test weight and weight of grains m -2 showed reverse trends. Concentrations of starch, protein, P, N, Ca, Mg and K decreased, while reducing and total soluble sugar increased in grains of both the cultivars in NFCs compared to FCs. The study concluded that under ambient condition of O 3 exposure, the two cultivars responded differently. Saurabh 950 favoured biomass translocation priority towards ear in reproductive phase and hence showed higher resistivity due to maintenance of higher test weight. NDR 97, however, showed better growth during vegetative period, but could not allocate efficiently to developing ears, hence higher number of unfilled grains in NFCs led lower test weight.

  5. 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.

  6. Variations between the photosynthetic properties of elite and landrace Chinese rice cultivars revealed by simultaneous measurements of 820 nm transmission signal and chlorophyll a fluorescence induction.

    PubMed

    Hamdani, Saber; Qu, Mingnan; Xin, Chang-Peng; Li, Ming; Chu, Chengcai; Govindjee; Zhu, Xin-Guang

    2015-04-01

    The difference between the photosynthetic properties of elite and landrace Chinese rice cultivars was studied, using chlorophyll a fluorescence induction (mostly a monitor of Photosystem II activity) and I820 transmission signal (mostly a monitor of Photosystem I activity) to identify potential photosynthetic features differentiating these two groups, which show different degrees of artificial selection and grain yields. A higher fluorescence (related to PSII) IP rise phase and a lower P700(+) (related to PSI) accumulation were observed in the elite cultivars as compared to the landraces. Using these data, together with simulation data from a kinetic model of fluorescence induction, we show that the high IP rise phase and the low P700(+) accumulation can be a result of transient block on electron transfer and traffic jam on the electron acceptor side of PSI under a high [NADPH]/[NADP(+)] ratio. Considering that the ferredoxin NADP(+) reductase (FNR) transcript levels of XS134 (a representative elite cultivars) remains unaffected during the first few minutes of light/dark transition compared to Q4145 (a representative landrace cultivars), which shows a strong decline during the same time range, we propose that the FNR of elite cultivars may take more time to be inactivated in darkness. During this time the FNR enzyme can continue to reduce NADP(+) molecules, leading to initially high [NADPH]/[NADP(+)] ratio during OJIP transient. These data suggested a potential artificial selection of FNR during the breeding process of these examined elite rice cultivars.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous studies suggest that the intraspecific variability of rice yield response to rising carbon dioxide concentration, [CO2], could serve as a basis of selection to improve genotypes for future high CO2 conditions. However, assessment of responses to elevated [CO2] must consider air temperature,...

  8. [Comparison on submergence tolerance of different type rice at tillering stage in lower reaches of Yangtze River].

    PubMed

    Ming, Liu; Yan, Li; Gui-hua, Guo; Hai-yan, Liu; Gang-hua, Li; Shao-hua, Wang; Zheng-hui, Liu; Yan-feng, Ding

    2015-05-01

    The agronomic traits, physiological characteristics and yield traits of 9 rice varieties popularized in lower reaches of Yangtze River were investigated under submergence stress at the tillering stage. The differences of environmental adaptability to submergence stress for conventional japonica rice, indica hybrid rice and hybrid japonica rice, were also analyzed and compared. The results showed that the stem and the upper three leaves under submergence stress were elongated compared with the control. And the elongation of the different varieties was shown as, hybrid japonica rice > indica hybrid rice > conventional japonica rice. As to the numbers of tillers and green leaves, and the aboveground dry mass, the reduction of indica hybrid rice was all between hybrid japonica rice and conventional japonica rice. The damage of hybrid japonica was the lightest. The content of MDA in the leaves of conventional japonica rice increased, while the activities of SOD and CAT decreased. However, the performances of hybrid japonica rice and indica hybrid rice were opposite with conventional japonica rice. The yield loss of conventional japonica rice was significantly higher than those of the other types of rice. These results suggested that the submergence tolerance ability of hybrid japonica rice is superior to indica hybrid rice, and the submergence tolerance ability of conventional japonica rice is the weakest.

  9. Natural leaf senescence: probed by chlorophyll fluorescence, CO2 photosynthetic rate and antioxidant enzyme activities during grain filling in different rice cultivars.

    PubMed

    Panda, Debabrata; Sarkar, Ramani Kumar

    2013-01-01

    Natural leaf senescence was investigated in four rainfed lowland rice cultivars, FR 13A (tolerant to submergence), Sabita and Sarala (adapted to medium depth, 0-50 cm stagnant flooding) and Dengi (conventional farmers' cultivar). Changes in the levels of pigment content, CO2 photosynthetic rate, photosystem II photochemistry and anti-oxidant enzyme activities of flag leaves during grain-filling stage were investigated. Chlorophyll content, photochemical efficiency of photosystem II and CO2 photosynthetic rate decreased significantly with the progress of grain-filling. Likely, the activities of antioxidant enzymes namely, superoxide dismutase, catalase, guaiacol peroxidase and ascorbate peroxidase decreased with progress of grain-filling. A substantial difference was observed among the four cultivars for the sustainability index (SI) of different photosynthetic parameters and antioxidant enzyme activities; SIs of those parameters, in general, were lower in low yielding cultivar FR 13A compared to the other three cultivars. Among the four cultivars Sabita gave maximum grain yield. Yet, SI of Pn was greater in Sarala and Dengi compared to the Sabita. SIs of electron transport (ETo/CS), maximal photochemical efficiency (Fv/Fm), area above Fo and Fm, catalase and ascorbate peroxidase were also greater in Sarala and Dengi. The data showed that among the different Chl a fluorescence parameters, PI could be used with greater accuracy to distinguish slow and fast senescence rice cultivars during grain-filling period. It was concluded that maintaining the vitality of rice plants during grain-filling gave guarantee to synthesize carbohydrate, however greater yield could be realized provided superior yield attributing parameters are present.

  10. 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...

  11. Auxin distribution is differentially affected by nitrate in roots of two rice cultivars differing in responsiveness to nitrogen

    PubMed Central

    Song, Wenjing; Sun, Huwei; Li, Jiao; Gong, Xianpo; Huang, Shuangjie; Zhu, Xudong; Zhang, Yali; Xu, Guohua

    2013-01-01

    Background and Aims Although ammonium (NH4+) is the preferred form of nitrogen over nitrate (NO3−) for rice (Oryza sativa), lateral root (LR) growth in roots is enhanced by partial NO3− nutrition (PNN). The roles of auxin distribution and polar transport in LR formation in response to localized NO3− availability are not known. Methods Time-course studies in a split-root experimental system were used to investigate LR development patterns, auxin distribution, polar auxin transport and expression of auxin transporter genes in LR zones in response to localized PNN in ‘Nanguang’ and ‘Elio’ rice cultivars, which show high and low responsiveness to NO3−, respectively. Patterns of auxin distribution and the effects of polar auxin transport inhibitors were also examined in DR5::GUS transgenic plants. Key Results Initiation of LRs was enhanced by PNN after 7 d cultivation in ‘Nanguang’ but not in ‘Elio’. Auxin concentration in the roots of ‘Nanguang’ increased by approx. 24 % after 5 d cultivation with PNN compared with NH4+ as the sole nitrogen source, but no difference was observed in ‘Elio’. More auxin flux into the LR zone in ‘Nanguang’ roots was observed in response to NO3− compared with NH4+ treatment. A greater number of auxin influx and efflux transporter genes showed increased expression in the LR zone in response to PNN in ‘Nanguang’ than in ‘Elio’. Conclusions The results indicate that higher NO3− responsiveness is associated with greater auxin accumulation in the LR zone and is strongly related to a higher rate of LR initiation in the cultivar ‘Nanguang’. PMID:24095838

  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. Effect of salinity stress on growth and carbohydrate metabolism in three rice (Oryza sativa L.) cultivars differing in salinity tolerance.

    PubMed

    Pattanagul, Wattana; Thitisaksakul, Maysaya

    2008-10-01

    Rice seedlings cv. Khao Dawk Mali 105 (salt-sensitive), Luang Anan (moderately salt-tolerant) and Pokkali (salt-tolerant) were exposed to 0, 50, 100 and 150 mM NaCI for 9 d. Salinity stress caused reduction in leaf relative water contents in all cultivars. Shoot length of cv. Pokkali was least affected by salinity stress whereas increased root length in response to salinity stress was apparent in cvs. Khao Dawk Mali 105 and Luang Anan. Increased salinity level also caused reduction in fresh and dry weights in cvs. Khao Dawk Mali 105 and Luang Anan, but had no effect in cv. Pokkali except at 150 mM. Accumulation of total soluble sugars and sucrose in mature leaves were observed in cv. Khao Dawk Mali 105 exposed to high level of salinity whereas their concentrations in cvs. Luang Anan and Pokkali remained the same as control plants. Accumulation of sucrose in cv. Khao Dawk Mali 105 was suggested to be resulted from the alteration of photosynthate partitioning since the activities of sucrose phosphate synthase were not affected by salinity in this cultivar. On the contrary, salinity stress induced an accumulation of starch in cv. Pokkali. It is suggested that partitioning sugars into starch may involve in salinity tolerance by avoiding metabolic alterations.

  14. Genetic variation for traits associated with domestication identified in a cultivated rice, Nipponbare (Oryza sativa ssp. japonica) x ancestral rice, O. nivara, mapping population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Oryza nivara, the progenitor of cultivated rice, O. sativa, has been the source of novel alleles for resistance to biotic and abiotic stresses, as well as for yield improvement. Many of these alleles were lost during the domestication process. To determine the molecular changes that occurred during ...

  15. Effect of gamma irradiation on starch viscosity and physicochemical properties of different rice

    NASA Astrophysics Data System (ADS)

    Wu, Dianxing; Shu, Qingyao; Wang, Zhonghua; Xia, Yingwu

    2002-08-01

    Three types of rice cultivars (indica, japonica and hybrid rice) with similar intermediate apparent amylose content (AAC) as well as early indica rice cultivars with different amounts of AAC were selected for studying the effects of gamma irradiation on starch viscosity, physicochemical properties and starch granule structure. Four major parameters of RVA profile, that was determined by a rapid visco analyser (RVA, Model-3D), peak viscosity, hot pasting viscosity, cool pasting viscosity, and setback viscosity, were considerably decreased with increasing dose levels. Gamma irradiation reduced the amylose contents in the cultivars with low AAC, intermediate AAC, and glutinous rice, but had no effects on the high AAC cultivar. No visible changes in gelatinization temperature were detected after irradiation, but the peak time was reduced with the dose levels. Gel consistency was significantly increased in the tested cultivars, especially in the high AAC indica rice. The starch granules were somewhat deformed by gamma irradiation. These results suggested that it is promising to use gamma irradiation to improve rice eating or cooking quality.

  16. Selenium Fortification of an Italian Rice Cultivar via Foliar Fertilization with Sodium Selenate and Its Effects on Human Serum Selenium Levels and on Erythrocyte Glutathione Peroxidase Activity

    PubMed Central

    Giacosa, Attilio; Faliva, Milena Anna; Perna, Simone; Minoia, Claudio; Ronchi, Anna; Rondanelli, Mariangela

    2014-01-01

    Selenium food fortification could be a cost-effective strategy to counteract the inadequacy of selenium intake among the Italian population. In this study, the effect of foliar fertilization with sodium selenate of an Italian rice cultivar and the increase of serum selenium and of erythrocyte glutathione peroxidase (GPx) activity after intake of fortified rice, have been evaluated. The effect of foliar fertilization with sodium selenate (50 g Se/ha) vs. water was studied. Moreover, in a randomized, double-blind study, 10 healthy women supplemented their usual diet with a daily dose of 80 g of Se-enriched-rice and 10 matched-women with 80 g of regular rice. Before, after 5 and 20 days of supplementation, serum Se and GPx-activity were evaluated. The mean selenium content in Se-enriched-rice was 1.64 ± 0.28 μg/g, while in regular rice it was 0.36 ± 0.15 μg/g (p < 0.001). A significant increase of serum Se and GPx-activity was observed only in the intervention group and only after 20 days. The results show that selenium fortification of rice can be achieved with foliar fertilization with sodium selenate and that the 20 days intake of this Se-enriched-rice increases the serum selenium levels and GPx-activity. PMID:24667132

  17. Selenium fortification of an Italian rice cultivar via foliar fertilization with sodium selenate and its effects on human serum selenium levels and on erythrocyte glutathione peroxidase activity.

    PubMed

    Giacosa, Attilio; Faliva, Milena Anna; Perna, Simone; Minoia, Claudio; Ronchi, Anna; Rondanelli, Mariangela

    2014-03-24

    Selenium food fortification could be a cost-effective strategy to counteract the inadequacy of selenium intake among the Italian population. In this study, the effect of foliar fertilization with sodium selenate of an Italian rice cultivar and the increase of serum selenium and of erythrocyte glutathione peroxidase (GPx) activity after intake of fortified rice, have been evaluated. The effect of foliar fertilization with sodium selenate (50 g Se/ha) vs. water was studied. Moreover, in a randomized, double-blind study, 10 healthy women supplemented their usual diet with a daily dose of 80 g of Se-enriched-rice and 10 matched-women with 80 g of regular rice. Before, after 5 and 20 days of supplementation, serum Se and GPx-activity were evaluated. The mean selenium content in Se-enriched-rice was 1.64 ± 0.28 μg/g, while in regular rice it was 0.36 ± 0.15 μg/g (p < 0.001). A significant increase of serum Se and GPx-activity was observed only in the intervention group and only after 20 days. The results show that selenium fortification of rice can be achieved with foliar fertilization with sodium selenate and that the 20 days intake of this Se-enriched-rice increases the serum selenium levels and GPx-activity.

  18. 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.

  19. Synchronism of Leaf and Tiller Emergence Relative to Position and to Main Stem Development Stage in a Rice Cultivar

    PubMed Central

    JAFFUEL, SYLVIE; DAUZAT, JEAN

    2004-01-01

    • Background and Aims Tillering is an essential factor when estimating yield, but investigations rarely include both the temporal and spatial changes that occur in tillers. This study analyses the morphology and development dynamics of each tiller, based on its topological location, the timing of appearance and main stem development stage. • Methods An indica cultivar of rice, ‘Ir64’, glasshouse-grown (25/20 °C, 12 h photoperiod), was used to examine the emergence, phenology and morphology of each axis starting at the third leaf stage up to heading. • Key Results Little variability was observed in the structural and morphological characteristics of the tillers, and the rice population appeared to be hierarchical. Blade length initially increased with leaf rank and then decreased sharply for the last three leaves. The number of phytomers per axis decreased with branching order and rank. An analysis of plant dynamics showed synchronous emergence of the leaves on the main stem and on the tillers up to flowering. Axillary bud development into tillers depended on their topological location and plant developmental stage. • Conclusions The timing and frequency of flowering tillers complied with rules of priority depending on their order, rank and emergence time. Precise description of plant topology in grasses is a useful tool that can be used to quantify growth events and predict tillering in terms of location, structure and fate according to growing conditions. PMID:15601682

  20. Development of genome-wide PCR-based markers from insertion, deletion and single nucleotide polymorphisms for closely related Japanese rice cultivars and identification of QTLs for the appearance of cooked rice and polished rice

    PubMed Central

    Kinoshita, Noriko; Takano, Sho; Shimoda, Naomi; Takamure, Itsuro; Sato, Takashi; Kato, Kiyoaki

    2016-01-01

    Appearance of rice grain is an important property, affecting its acceptance by consumers. Moreover, appearance is a complex characteristic involving many components, including glossiness and whiteness. The genetic bases for the glossiness of cooked rice and the whiteness of polished rice (WPR) were determined using 133 recombinant inbred lines (RILs) derived from a cross between two closely related cultivars from Hokkaido, Joiku462, with high glossiness and whiteness, and Yukihikari, an ancestor of Joiku462 with low glossiness and whiteness. Analyses identified 167 genome-wide InDel markers, five cleaved amplified polymorphic sequences (CAPS) and eight derived CAPS markers differentiating the parental lines. The glossiness area (GLA) and glossiness strength (GLS) of cooked rice and WPR were determined for RILs in two locations, Pippu and Sapporo, Hokkaido. Four QTLs were detected. qGLA10 and qGLS9 were detected on chromosomes 10 and 9, respectively, with both being significant at both geographic locations. qWPR1 on chromosome 1 was significant at Pippu, and qWPR4 on chromosome 4 was significant at Sapporo. The Joiku462 alleles at all QTLs increased each trait. The PCR-based markers flanking these four QTLs may be useful for improvement of GLA, GLS and WPR. PMID:28163590

  1. Heat and chilling induced disruption of redox homeostasis and its regulation by hydrogen peroxide in germinating rice seeds (Oryza sativa L., Cultivar Ratna).

    PubMed

    Bhattacharjee, Soumen

    2013-04-01

    Extremes of temperature (both heat and chilling) during early inbibitional phase of germination caused disruption of redox-homeostasis by increasing accumulation of reactive oxygen species (superoxide and hydrogen peroxide) and significant reduction of antioxidative defense (assessed in terms of total thiol content and activities of superoxide dismutase, catalase, ascorbate peroxidase and glutathione reductase) in germinating tissues of rice (Oryza sativa L., cultivar Ratna). Imbibitional heat and chilling stress also induced oxidative damage to newly assembled membrane system by aggravating membrane lipid peroxidation and protein oxidation [measured in terms of thiobarbituric acid reactive substances (TBARS), free carbonyl content (C = O groups) and membrane protein thiol level (MPTL)]. Treatment with standardized low titer hydrogen peroxide during early imbibitional phase of germination caused significant reversal in oxidative damages to the newly assembled membrane system imposed by heat and chilling stress [evident from the data of TBARS, C = O, MPTL, ROS accumulation, membrane permeability status, membrane injury index and oxidative stress index] in seedlings of experimental rice cultivar. Imbibitional H2O2 pretreatment also caused up-regulation of antioxidative defense (activities of superoxide dismutase, catalase, ascorbate peroxidase, glutathione reductase and total thiol content) in the heat and chilling stress-raised rice seedlings. When the parameters of early growth performances were assessed (in terms of relative growth index, biomass accumulation, relative germination performance, mean daily germination, T50 value), it clearly exhibited significant improvement of early growth performances of the experimental rice cultivar. The result proposes that an 'inductive pulse' of H2O2 is required to switch on some stress acclimatory metabolism through which plant restores redox homeostasis and prevents or repairs oxidative damages to newly assembled membrane

  2. 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.

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

    PubMed Central

    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

  4. Non-destructive Assessment of Plant Nitrogen Parameters Using Leaf Chlorophyll Measurements in Rice.

    PubMed

    Ata-Ul-Karim, Syed Tahir; Cao, Qiang; Zhu, Yan; Tang, Liang; Rehmani, Muhammad Ishaq Asif; Cao, Weixing

    2016-01-01

    Non-destructive assessment of plant nitrogen (N) status is essential for efficient crop production and N management in intensive rice (Oryza sativa L.) cropping systems. Chlorophyll meter (SPAD-502) has been widely used as a rapid, non-destructive and cost-effective diagnostic tool for in-season assessment of crop N status. The present study was intended to establish the quantitative relationships between chlorophyll meters readings, plant N concentration (PNC), N nutrition index (NNI), accumulated N deficit (AND), and N requirement (NR), as well as to compare the stability of these relationships at different vegetative growth stages in Japonica and Indica rice cultivars. Seven multi-locational field experiments using varied N rates and seven rice cultivars were conducted in east China. The results showed that the PNC and chlorophyll meters readings increased with increasing N application rates across the cultivars, growing seasons, and sites. The PNC and chlorophyll meters readings under varied N rates ranged from 2.29 to 3.21, 1.06 to 1.82 and 37.10 to 45.4 and 37.30 to 46.6, respectively, at TL and HD stages for Japonica rice cultivars, while they ranged from 2.25 to 3.23, 1.34 to 1.91 and 35.6 to 43.3 and 37.3 to 45.5 for Indica rice cultivars, respectively. The quantitative relationships between chlorophyll meters readings, PNC, NNI, AND, and NR established at different crop growth stages in two rice ecotypes, were highly significant with R(2) values ranging from 0.69 to 0.93 and 0.71 to 0.86 for Japonica and Indica rice, respectively. The strongest relationships were observed for AND and NR at panicle initiation and booting stages in both rice ecotypes. The validation of the relationships developed in the present study with an independent data exhibited a solid model performance and confirmed their robustness as a reliable and rapid diagnostic tool for in-season estimation of plant N parameters for sustainable N management in rice. The results of this study

  5. Non-destructive Assessment of Plant Nitrogen Parameters Using Leaf Chlorophyll Measurements in Rice

    PubMed Central

    Ata-Ul-Karim, Syed Tahir; Cao, Qiang; Zhu, Yan; Tang, Liang; Rehmani, Muhammad Ishaq Asif; Cao, Weixing

    2016-01-01

    Non-destructive assessment of plant nitrogen (N) status is essential for efficient crop production and N management in intensive rice (Oryza sativa L.) cropping systems. Chlorophyll meter (SPAD-502) has been widely used as a rapid, non-destructive and cost-effective diagnostic tool for in-season assessment of crop N status. The present study was intended to establish the quantitative relationships between chlorophyll meters readings, plant N concentration (PNC), N nutrition index (NNI), accumulated N deficit (AND), and N requirement (NR), as well as to compare the stability of these relationships at different vegetative growth stages in Japonica and Indica rice cultivars. Seven multi-locational field experiments using varied N rates and seven rice cultivars were conducted in east China. The results showed that the PNC and chlorophyll meters readings increased with increasing N application rates across the cultivars, growing seasons, and sites. The PNC and chlorophyll meters readings under varied N rates ranged from 2.29 to 3.21, 1.06 to 1.82 and 37.10 to 45.4 and 37.30 to 46.6, respectively, at TL and HD stages for Japonica rice cultivars, while they ranged from 2.25 to 3.23, 1.34 to 1.91 and 35.6 to 43.3 and 37.3 to 45.5 for Indica rice cultivars, respectively. The quantitative relationships between chlorophyll meters readings, PNC, NNI, AND, and NR established at different crop growth stages in two rice ecotypes, were highly significant with R2 values ranging from 0.69 to 0.93 and 0.71 to 0.86 for Japonica and Indica rice, respectively. The strongest relationships were observed for AND and NR at panicle initiation and booting stages in both rice ecotypes. The validation of the relationships developed in the present study with an independent data exhibited a solid model performance and confirmed their robustness as a reliable and rapid diagnostic tool for in-season estimation of plant N parameters for sustainable N management in rice. The results of this study

  6. Time-series RNA-seq analysis package (TRAP) and its application to the analysis of rice, Oryza sativa L. ssp. Japonica, upon drought stress.

    PubMed

    Jo, Kyuri; Kwon, Hawk-Bin; Kim, Sun

    2014-06-01

    Measuring expression levels of genes at the whole genome level can be useful for many purposes, especially for revealing biological pathways underlying specific phenotype conditions. When gene expression is measured over a time period, we have opportunities to understand how organisms react to stress conditions over time. Thus many biologists routinely measure whole genome level gene expressions at multiple time points. However, there are several technical difficulties for analyzing such whole genome expression data. In addition, these days gene expression data is often measured by using RNA-sequencing rather than microarray technologies and then analysis of expression data is much more complicated since the analysis process should start with mapping short reads and produce differentially activated pathways and also possibly interactions among pathways. In addition, many useful tools for analyzing microarray gene expression data are not applicable for the RNA-seq data. Thus a comprehensive package for analyzing time series transcriptome data is much needed. In this article, we present a comprehensive package, Time-series RNA-seq Analysis Package (TRAP), integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment. In addition to implementing useful algorithms that are not available for RNA-seq data, we extended existing pathway analysis methods, ORA and SPIA, for time series analysis and estimates statistical values for combined dataset by an advanced metric. TRAP also produces visual summary of pathway interactions. Gene expression change labeling, a practical clustering method used in TRAP, enables more accurate interpretation of the data when combined with pathway analysis. We applied our methods on a real dataset for the analysis of rice (Oryza sativa L. Japonica nipponbare) upon drought stress. The result

  7. Two evolutionary histories in the genome of rice: the roles of domestication genes.

    PubMed

    He, Ziwen; Zhai, Weiwei; Wen, Haijun; Tang, Tian; Wang, Yu; Lu, Xuemei; Greenberg, Anthony J; Hudson, Richard R; Wu, Chung-I; Shi, Suhua

    2011-06-01

    Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice taxa (about 22 each from Oryza sativa indica, O. sativa japonica, and O. rufipogon) for whole-genome sequencing. In the search for the signature of selection, we focus on low diversity regions (LDRs) shared by both cultivars. We found that the genealogical histories of these overlapping LDRs are distinct from the genomic background. While indica and japonica genomes generally appear to be of independent origin, many overlapping LDRs may have originated only once, as a result of selection and subsequent introgression. Interestingly, many such LDRs contain only one candidate gene of rice domestication, and several known domestication genes have indeed been "rediscovered" by this approach. In summary, we identified 13 additional candidate genes of domestication.

  8. 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...

  9. 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

  10. Quantitative trait loci analysis for rice seed vigor during the germination stage.

    PubMed

    Wang, Zhou-fei; Wang, Jian-fei; Bao, Yong-mei; Wang, Fu-hua; Zhang, Hong-sheng

    2010-12-01

    Seed vigor is an important characteristic of seed quality, and rice cultivars with strong seed vigor are desirable in direct-sowing rice production for optimum stand establishment. In the present study, the quantitative trait loci (QTLs) of three traits for rice seed vigor during the germination stage, including germination rate, final germination percentage, and germination index, were investigated using one recombinant inbred line (RIL) population derived from a cross between japonica Daguandao and indica IR28, and using the multiple interval mapping (MIM) approach. The results show that indica rice presented stronger seed vigor during the germination stage than japonica rice. A total of ten QTLs, and at least five novel alleles, were detected to control rice seed vigor, and the amount of variation (R(2)) explained by an individual QTL ranged from 7.5% to 68.5%, with three major QTLs with R(2)>20%. Most of the QTLs detected here are likely to coincide with QTLs for seed weight, seed size, or seed dormancy, suggesting that the rice seed vigor might be correlated with seed weight, seed size, and seed dormancy. At least five QTLs are novel alleles with no previous reports of seed vigor genes in rice, and those major or minor QTLs could be used to significantly improve the seed vigor by marker-assisted selection (MAS) in rice.

  11. Quantitative trait loci analysis for rice seed vigor during the germination stage*

    PubMed Central

    Wang, Zhou-fei; Wang, Jian-fei; Bao, Yong-mei; Wang, Fu-hua; Zhang, Hong-sheng

    2010-01-01

    Seed vigor is an important characteristic of seed quality, and rice cultivars with strong seed vigor are desirable in direct-sowing rice production for optimum stand establishment. In the present study, the quantitative trait loci (QTLs) of three traits for rice seed vigor during the germination stage, including germination rate, final germination percentage, and germination index, were investigated using one recombinant inbred line (RIL) population derived from a cross between japonica Daguandao and indica IR28, and using the multiple interval mapping (MIM) approach. The results show that indica rice presented stronger seed vigor during the germination stage than japonica rice. A total of ten QTLs, and at least five novel alleles, were detected to control rice seed vigor, and the amount of variation (R 2) explained by an individual QTL ranged from 7.5% to 68.5%, with three major QTLs with R 2>20%. Most of the QTLs detected here are likely to coincide with QTLs for seed weight, seed size, or seed dormancy, suggesting that the rice seed vigor might be correlated with seed weight, seed size, and seed dormancy. At least five QTLs are novel alleles with no previous reports of seed vigor genes in rice, and those major or minor QTLs could be used to significantly improve the seed vigor by marker-assisted selection (MAS) in rice. PMID:21121075

  12. 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.

  13. Variation in grain arsenic assessed in a diverse panel of rice (Oryza sativa) grown in multiple sites.

    PubMed

    Norton, Gareth J; Pinson, Shannon R M; Alexander, Jill; McKay, Susan; Hansen, Helle; Duan, Gui-Lan; Rafiqul Islam, M; Islam, Shofiqul; Stroud, Jacqueline L; Zhao, Fang-Jie; McGrath, Steve P; Zhu, Yong-Guan; Lahner, Brett; Yakubova, Elena; Guerinot, Mary Lou; Tarpley, Lee; Eizenga, Georgia C; Salt, David E; Meharg, Andrew A; Price, Adam H

    2012-02-01

    • Inorganic arsenic (As(i) ) in rice (Oryza sativa) grains is a possible threat to human health, with risk being strongly linked to total dietary rice consumption and consumed rice As(i) content. This study aimed to identify the range and stability of genetic variation in grain arsenic (As) in rice. • Six field trials were conducted (one each in Bangladesh and China, two in Arkansas, USA over 2 yr, and two in Texas, USA comparing flooded and nonflood treatments) on a large number of common rice cultivars (c. 300) representing genetic diversity among international rice cultivars. • Within each field there was a 3-34 fold range in grain As concentration which varied between rice subpopulations. Importantly, As(i) correlated strongly with total As among a subset of 40 cultivars harvested in Bangladesh and China. • Genetic variation at all field sites was a large determining factor for grain As concentration, indicating that cultivars low in grain As could be developed through breeding. The temperate japonicas exhibited lower grain As compared with other subpopulations. Effects for year, location and flooding management were also statistically significant, suggesting that breeding strategies must take into account environmental factors.

  14. Identification of a new locus conferring antixenosis to the brown planthopper in rice cultivar Swarnalata (Oryza sativa L.).

    PubMed

    Qiu, Y F; Cheng, L; Liu, F; Li, R B

    2013-08-29

    The brown planthopper [Nilaparvata lugens (Stål); BPH] has caused severe damage to rice production. The identification of resistance genes and the development of BPH-resistant varieties are economical and effective ways to manage this pest. Using an F2 population from a cross between the Indica cultivars 93-11 and Swarnalata, we mapped the Qbph-8 locus to a 7.3-cM region on chromosome 8 in two tests, flanked by the markers RM339 and RM515. In this population, Qbph-8 explained 7.7 and 6.6% of the phenotypic variance of BPH preference in both tests. In the BPH host choice test, the average number of settled BPHs on the Qbph-8 plants was less than that on the 93-11 plants over the 24- to 120-h observation period. Furthermore, less BPH insects were observed on the BPH6+Qbph-8 plant compared with the BPH6 plant or Qbph-8 plant, indicating a stronger antixenotic effect shown in the gene pyramiding plants. Hence, this locus can be pyramided with other BPH resistance genes and applied to breed-resistant varieties, which possibly can improve the resistance level and durable resistance to the BPH.

  15. 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.

  16. Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs

    PubMed Central

    Cardoso, Catarina; Zhang, Yanxia; Jamil, Muhammad; Hepworth, Jo; Charnikhova, Tatsiana; Dimkpa, Stanley O. N.; Meharg, Caroline; Wright, Mark H.; Liu, Junwei; Meng, Xiangbing; Wang, Yonghong; Li, Jiayang; McCouch, Susan R.; Leyser, Ottoline; Price, Adam H.; Bouwmeester, Harro J.; Ruyter-Spira, Carolien

    2014-01-01

    Rice (Oryza sativa) cultivar Azucena—belonging to the Japonica subspecies—exudes high strigolactone (SL) levels and induces high germination of the root parasitic plant Striga hermonthica. Consistent with the fact that SLs also inhibit shoot branching, Azucena is a low-tillering variety. In contrast, Bala, an Indica cultivar, is a low-SL producer, stimulates less Striga germination, and is highly tillered. Using a Bala × Azucena F6 population, a major quantitative trait loci—qSLB1.1—for the exudation of SL, tillering, and induction of Striga germination was detected on chromosome 1. Sequence analysis of the corresponding locus revealed a rearrangement of a 51- to 59-kbp stretch between 28.9 and 29 Mbp in the Bala genome, resulting in the deletion of two cytochrome P450 genes—SLB1 and SLB2—with high homology to the Arabidopsis SL biosynthesis gene, MAX1. Both rice genes rescue the Arabidopsis max1-1 highly branched mutant phenotype and increase the production of the SL, ent-2′-epi-5-deoxystrigol, when overexpressed in Bala. Furthermore, analysis of this region in 367 cultivars of the publicly available Rice Diversity Panel population shows that the rearrangement at this locus is a recurrent natural trait associated with the Indica/Japonica divide in rice. PMID:24464483

  17. Evaluation of Host-Plant Resistance of Selected Rice Genotypes to the Rice Water Weevil (Coleoptera: Curculionidae).

    PubMed

    Vyavhare, Suhas S; Gealy, David R; Way, Michael O; Tabien, Rodante E; Pearson, Rebecca A

    2016-08-30

    The rice water weevil, Lissorhoptrus oryzophilus Kuschel, is the most important insect pest of rice in the United States. Management of L. oryzophilus mainly depends upon the use of insecticides due to the lack of effective alternative management tactics. A 3-yr field study was conducted to determine if difference exists among rice genotypes and cultivars of inbred tropical japonica subspecies commercially grown in the southern United States [Cocodrie (PI 606331), CL171, and CL151 (PI 654463)] and the germplasm lines of indica subspecies adapted to tropical climates of Asia [WC 4644 (PI 312777), TNI (PI 495830), Rondo (PI 615022), 4612 (PI 615039), TeQing (PI 536047), and 4593 (PI 615031)] for resistance to L. oryzophilus Experiments were established as a split-plot design with cultivars as main plots and insecticide treatment as subplots. No significant differences were observed in number of L. oryzophilus larvae recovered across cultivars and genotypes, indicating no significant variation in their preference to L. oryzophilus oviposition. Insecticide treatment had a significant impact on L. oryzophilus larval density. However, grain yield did not vary significantly between treated and untreated plots for any of the cultivars and genotypes. The amount of yield loss in response to L. oryzophilus infestation did not vary significantly across genotypes and cultivars, indicating no variation among these genotypes for resistance to L. oryzophilus.

  18. Evaluation of Host-Plant Resistance of Selected Rice Genotypes to the Rice Water Weevil (Coleoptera: Curculionidae).

    PubMed

    Vyavhare, Suhas S; Gealy, David R; Way, Michael O; Tabien, Rodante E; Pearson, Rebecca A

    2016-12-01

    The rice water weevil, Lissorhoptrus oryzophilus Kuschel, is the most important insect pest of rice in the United States. Management of L. oryzophilus mainly depends upon the use of insecticides due to the lack of effective alternative management tactics. A 3-yr field study was conducted to determine if difference exists among rice genotypes and cultivars of inbred tropical japonica subspecies commercially grown in the southern United States [Cocodrie (PI 606331), CL171, and CL151 (PI 654463)] and the germplasm lines of indica subspecies adapted to tropical climates of Asia [WC 4644 (PI 312777), TNI (PI 495830), Rondo (PI 615022), 4612 (PI 615039), TeQing (PI 536047), and 4593 (PI 615031)] for resistance to L. oryzophilus Experiments were established as a split-plot design with cultivars as main plots and insecticide treatment as subplots. No significant differences were observed in number of L. oryzophilus larvae recovered across cultivars and genotypes, indicating no significant variation in their preference to L. oryzophilus oviposition. Insecticide treatment had a significant impact on L. oryzophilus larval density. However, grain yield did not vary significantly between treated and untreated plots for any of the cultivars and genotypes. The amount of yield loss in response to L. oryzophilus infestation did not vary significantly across genotypes and cultivars, indicating no variation among these genotypes for resistance to L. oryzophilus.

  19. STV11 encodes a sulphotransferase and confers durable resistance to rice stripe virus.

    PubMed

    Wang, Qi; Liu, Yuqiang; He, Jun; Zheng, Xiaoming; Hu, Jinlong; Liu, Yanling; Dai, Huimin; Zhang, Yingxin; Wang, Baoxiang; Wu, Weixun; Gao, He; Zhang, Yunhui; Tao, Xiaorong; Deng, Huafeng; Yuan, Dingyang; Jiang, Ling; Zhang, Xin; Guo, Xiuping; Cheng, Xianian; Wu, Chuanyin; Wang, Haiyang; Yuan, Longping; Wan, Jianmin

    2014-09-09

    Rice stripe virus (RSV) causes one of the most serious viral diseases of rice (Oryza sativa L.), but the molecular basis of RSV resistance has remained elusive. Here we show that the resistant allele of rice STV11 (STV11-R) encodes a sulfotransferase (OsSOT1) catalysing the conversion of salicylic acid (SA) into sulphonated SA (SSA), whereas the gene product encoded by the susceptible allele STV11-S loses this activity. Sequence analyses suggest that the STV11-R and STV11-S alleles were predifferentiated in different geographic populations of wild rice, Oryza rufipogon, and remained prevalent in cultivated indica and japonica rice varieties, respectively. Introgression of the STV11-R allele into susceptible cultivars or heterologous transfer of STV11-R into tobacco plants confers effective resistance against RSV. Our results shed new insights into plant viral defense mechanisms and suggest effective means of breeding RSV-resistant crops using molecular marker-assisted selection or genetic engineering.

  20. Collection and comparative analysis of 1888 full-length cDNAs from wild rice Oryza rufipogon Griff. W1943.

    PubMed

    Lu, Tingting; Yu, Shuliang; Fan, Danlin; Mu, Jie; Shangguan, Yingying; Wang, Zixuan; Minobe, Yuzo; Lin, Zhixin; Han, Bin

    2008-10-01

    A huge amount of cDNA and EST resources have been developed for cultivated rice species Oryza sativa; however, only few cDNA resources are available for wild rice species. In this study, we isolated and completely sequenced 1888 putative full-length cDNA (FLcDNA) clones from wild rice Oryza rufipogon Griff. W1943 for comparative analysis between wild and cultivated rice species. Two cDNA libraries were constructed from 3-week-old leaf samples under either normal or cold-treated conditions. Homology searching of these cDNA sequences revealed that >96.8% of the wild rice cDNAs were matched to the cultivated rice O. sativa ssp. japonica cv. Nipponbare genome sequence. However, <22% of them were fully matched to the cv. Nipponbare genome sequence. The comparative analysis showed that O. rufipogon W1943 had greater similarity to O. sativa ssp. japonica than to ssp. indica cultivars. In addition, 17 novel rice cDNAs were identified, and 41 putative tissue-specific expression genes were defined through searching the rice massively parallel signature-sequencing database. In conclusion, these FLcDNA clones are a resource for further function verification and could be broadly utilized in rice biological studies.

  1. Putrescine differently influences the effect of salt stress on polyamine metabolism and ethylene synthesis in rice cultivars differing in salt resistance.

    PubMed

    Quinet, Muriel; Ndayiragije, Alexis; Lefèvre, Isabelle; Lambillotte, Béatrice; Dupont-Gillain, Christine C; Lutts, Stanley

    2010-06-01

    Effects of salt stress on polyamine metabolism and ethylene production were examined in two rice (Oryza sativa L.) cultivars [I Kong Pao (IKP), salt sensitive; and Pokkali, salt resistant] grown for 5 d and 12 d in nutrient solution in the presence or absence of putrescine (1 mM) and 0, 50, and 100 mM NaCl. The salt-sensitive (IKP) and salt-resistant (Pokkali) cultivars differ not only in their mean levels of putrescine, but also in the physiological functions assumed by this molecule in stressed tissues. Salt stress increased the proportion of conjugated putrescine in salt-resistant Pokkali and decreased it in the salt-sensitive IKP, suggesting a possible protective function in response to NaCl. Activities of the enzymes ornithine decarboxylase (ODC; EC 4.1.1.17) and arginine decarboxylase (ADC; EC 4.1.1.19) involved in putrescine synthesis were higher in salt-resistant Pokkali than in salt-sensitive IKP. Both enzymes were involved in the response to salt stress. Salt stress also increased diamine oxidase (DAO; 1.4.3.6) and polyamine oxidase (PAO EC 1.5.3.11) activities in the roots of salt-resistant Pokkali and in the shoots of salt-sensitive IKP. Gene expression followed by reverse transcription-PCR suggested that putrescine could have a post-translational impact on genes coding for ADC (ADCa) and ODC (ODCa and ODCb) but could induce a transcriptional activation of genes coding for PAO (PAOb) mainly in the shoot of salt-stressed plants. The salt-resistant cultivar Pokkali produced higher amounts of ethylene than the salt-sensitive cultivar IKP, and exogenous putrescine increased ethylene synthesis in both cultivars, suggesting no direct antagonism between polyamine and ethylene pathways in rice.

  2. Putrescine differently influences the effect of salt stress on polyamine metabolism and ethylene synthesis in rice cultivars differing in salt resistance

    PubMed Central

    Quinet, Muriel; Lefèvre, Isabelle; Lambillotte, Béatrice; Dupont-Gillain, Christine C.; Lutts, Stanley

    2010-01-01

    Effects of salt stress on polyamine metabolism and ethylene production were examined in two rice (Oryza sativa L.) cultivars [I Kong Pao (IKP), salt sensitive; and Pokkali, salt resistant] grown for 5 d and 12 d in nutrient solution in the presence or absence of putrescine (1 mM) and 0, 50, and 100 mM NaCl. The salt-sensitive (IKP) and salt-resistant (Pokkali) cultivars differ not only in their mean levels of putrescine, but also in the physiological functions assumed by this molecule in stressed tissues. Salt stress increased the proportion of conjugated putrescine in salt-resistant Pokkali and decreased it in the salt-sensitive IKP, suggesting a possible protective function in response to NaCl. Activities of the enzymes ornithine decarboxylase (ODC; EC 4.1.1.17) and arginine decarboxylase (ADC; EC 4.1.1.19) involved in putrescine synthesis were higher in salt-resistant Pokkali than in salt-sensitive IKP. Both enzymes were involved in the response to salt stress. Salt stress also increased diamine oxidase (DAO; 1.4.3.6) and polyamine oxidase (PAO EC 1.5.3.11) activities in the roots of salt-resistant Pokkali and in the shoots of salt-sensitive IKP. Gene expression followed by reverse transcription-PCR suggested that putrescine could have a post-translational impact on genes coding for ADC (ADCa) and ODC (ODCa and ODCb) but could induce a transcriptional activation of genes coding for PAO (PAOb) mainly in the shoot of salt-stressed plants. The salt-resistant cultivar Pokkali produced higher amounts of ethylene than the salt-sensitive cultivar IKP, and exogenous putrescine increased ethylene synthesis in both cultivars, suggesting no direct antagonism between polyamine and ethylene pathways in rice. PMID:20472577

  3. 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.

  4. Molecular analysis of an additional case of hybrid sterility in rice (Oryza sativa L.).

    PubMed

    Zhao, Z G; Zhu, S S; Zhang, Y H; Bian, X F; Wang, Y; Jiang, L; Liu, X; Chen, L M; Liu, S J; Zhang, W W; Ikehashi, H; Wan, J M

    2011-03-01

    Hybrid sterility hinders the exploitation of the heterosis displayed by japonica × indica rice hybrids. The variation in pollen semi-sterility observed among hybrids between the japonica recipient cultivar and each of two sets of chromosome segment substitution lines involving introgression from an indica cultivar was due to a factor on chromosome 5 known to harbor the gene S24. S24 was fine mapped to a 42 kb segment by analyzing a large F(2) population bred from the cross S24-NIL × Asominori, while the semi-sterility shown by the F(1) hybrid was ascribable to mitotic failure at the early bicellular pollen stage. Interestingly, two other pollen sterility genes (f5-Du and Sb) map to the same region (Li et al. in Chin Sci Bull 51:675-680, 2006; Wang et al. in Theor Appl Genet 112:382-387, 2006), allowing a search for candidate genes in the 6.4 kb overlap between the three genes. By sequencing the overlapped fragment in wild rice, indica cultivars and japonica cultivars, a protein ankyrin-3 encoded by the ORF2 was identified as the molecular base for S24. A cultivar Dular was found to have a hybrid-sterility-neutral allele, S24-n, in which an insertion of 30 bp was confirmed. Thus, it was possible to add one more case of molecular bases for the hybrid sterility. No gamete abortion is caused on heterozygous maternal genotype with an impaired sequence from the hybrid-sterility-neutral genotype. This result will be useful in understanding of wide compatibility in rice breeding.

  5. 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

    2008-12-02

    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.

  6. Comparative analysis of microRNA profiles of rice anthers between cool-sensitive and cool-tolerant cultivars under cool-temperature stress.

    PubMed

    Maeda, Shunsuke; Sakazono, Satomi; Masuko-Suzuki, Hiromi; Taguchi, Midori; Yamamura, Kaori; Nagano, Kuniaki; Endo, Takashi; Saeki, Kenichi; Osaka, Masaaki; Nabemoto, Moe; Ito, Kana; Kudo, Toru; Kobayashi, Masaaki; Kawagishi, Mizuho; Fujita, Kotomi; Nanjo, Hikaru; Shindo, Tomoe; Yano, Kentaro; Suzuki, Go; Suwabe, Keita; Watanabe, Masao

    2016-10-13

    Plants subjected to abiotic stress can regulate gene expression post-transcriptionally by means of small RNAs such as microRNAs. Cool-temperature stress causes abnormal tapetum hypertrophy in rice anthers, leading to pollen sterility. As a first step toward understanding the molecular mechanisms of cool tolerance in developing anthers of rice, we report here a comprehensive comparative analysis of microRNAs between cool-sensitive Sasanishiki and cool-tolerant Hitomebore cultivars. High-throughput Illumina sequencing revealed 241 known and 46 novel microRNAs. Interestingly, 15 of these microRNAs accumulated differentially in the two cultivars at the uninucleate microspore stage under cool conditions. Inverse correlations between expression patterns of microRNAs and their target genes were confirmed by quantitative RT-PCR analysis, and cleavage sites of some of the target genes were determined by 5' RNA ligase-mediated RACE experiments. Thus, our data are useful resources to elucidate microRNA-mediated mechanism(s) of cool tolerance in rice anthers at the booting stage.

  7. An optical interferometric technique for assessing ozone induced damage and recovery under cumulative exposures for a Japanese rice cultivar.

    PubMed

    Thilakarathne, Bodhipaksha Lalith Sanjaya; Rajagopalan, Uma Maheswari; Kadono, Hirofumi; Yonekura, Tetsushi

    2014-01-01

    Exposure to ozone (O3) causes reduction both in the growth and yield of rice (Oriza sativa L.). Commonly used Chlorophyll fluorescent measurements are not sensitive enough for short term exposure of O3 aiming an immediate assessments. Such a conventional method typically needs exposure over a few days to detect the influence. As an alternative method, we proposed a novel non-invasive, robust, real-time, optical Statistical Interferometric Technique (SIT) to measure growth at an accuracy of 0.1 nm with a commonly consumed Japanese rice cultivar, Koshihikari. In the present study, we have conducted a repetitive O3 exposure experiment for three days under three different concentrations of 0 nl l(-1) (control), 120 nl l(-1), and 240 nl l(-1), to investigate the damage and recovery strengths. As a measure to assess the effect and recovery from three consecutive day exposures of O3, we measured the elongation rate (nm mm(-1) sec(-1)) every 5.5 sec for 7 hours, and it revealed nanometric elongation rate fluctuations or Nanometric Intrinsic Fluctuations (NIF). Comparing the standard deviation (SD) of normalized nanometric intrinsic fluctuations (NNIF), which was normalized by that before the exposure, we found that drastic reductions under both 120 nl l(-1) and 240 nl l(-1) O3 concentrations. Reduction percentages were large under high O3 concentration of 240 nl l(-1) indicating the possibility of irreversible effect. However exposure to 120 nl l(-1) of O3 showed recovery on the 2(nd) and 3(rd) days. While SIT did reveal immediate effect based on an observation for a few hours, the visible foliar effect could be observed only after a week. Hence, the technique could provide a way for fast assessment of effect and recovery due to cumulative exposure of O3 and hence the tolerance as well as the vitality of plant.

  8. 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

  9. Water deficit and aluminum interactive effects on generation of reactive oxygen species and responses of antioxidative enzymes in the seedlings of two rice cultivars differing in stress tolerance.

    PubMed

    Pandey, Poonam; Srivastava, Rajneesh Kumar; Rajpoot, Ritika; Rani, Anjana; Pandey, Akhilesh Kumar; Dubey, R S

    2016-01-01

    Aluminum (Al) is a major constraint to crop productivity in acid soils, whereas water deficit severely limits crop production in arid and semi-arid regions of the world. The objective of the present study was to examine the effects of both stresses, Al excess and water deficit, individually and in combination on the production of the reactive oxygen species (ROS) superoxide anion (O2˙(-)), hydrogen peroxide (H2O2), hydroxyl radical, and lipid peroxidation and the activity of antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), and guaiacol peroxidase (GPX) in the seedlings of two rice (Oryza sativa L.) cvs. Malviya-36 (sensitive to water deficit and Al) and Vandana (tolerant to water deficit and Al). When 15-day grown seedlings were exposed to water deficit (created with 15% polyethylene glycol, PEG-6000) or Al (1 mM AlCl3) treatment or both treatments together for 24-72 h, the lengths and fresh weights of root/shoot declined in the seedlings of the sensitive cultivar, whereas in the tolerant seedlings, either little or insignificant decline in these parameters was observed due to the treatments. Biochemical determinations and histochemical studies revealed that under a similar level of water deficit, Al, or combined treatment, seedlings of sensitive cultivar showed a higher level of production of O2˙(-), H2O2, hydroxyl radical, and lipid peroxides compared to the tolerant seedlings. Seedlings of tolerant cultivars, both in roots and shoots, had constitutively higher activity levels of antioxidative enzymes SOD, CAT, and GPX and showed a greater increase in activity under water deficit or Al treatment alone or in combination compared to the similarly treated seedlings of sensitive cultivar. Our results suggest that a lower constitutive level of ROS and a high antioxidative enzyme capacity are associated with tolerance to both water deficit and Al excess in rice seedlings.

  10. 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.

  11. 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

  12. 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.

  13. Involvement of ASR genes in aluminium tolerance mechanisms in rice.

    PubMed

    Arenhart, Rafael Augusto; Lima, Julio César de; Pedron, Marcelo; Carvalho, Fabricio E L; Silveira, Joaquim Albenisio Gomes da; Rosa, Silvia Barcelos; Caverzan, Andreia; Andrade, Claudia M B; Schünemann, Mariana; Margis, Rogério; Margis-Pinheiro, Márcia

    2013-01-01

    Among cereal crops, rice is considered the most tolerant to aluminium (Al). However, variability among rice genotypes leads to remarkable differences in the degree of Al tolerance for distinct cultivars. A number of studies have demonstrated that rice plants achieve Al tolerance through an unknown mechanism that is independent of root tip Al exclusion. We have analysed expression changes of the rice ASR gene family as a function of Al treatment. The gene ASR5 was differentially regulated in the Al-tolerant rice ssp. Japonica cv. Nipponbare. However, ASR5 expression did not respond to Al exposure in Indica cv. Taim rice roots, which are highly Al sensitive. Transgenic plants carrying RNAi constructs that targeted the ASR genes were obtained, and increased Al susceptibility was observed in T1 plants. Embryogenic calli of transgenic rice carrying an ASR5-green fluorescent protein fusion revealed that ASR5 was localized in both the nucleus and cytoplasm. Using a proteomic approach to compare non-transformed and ASR-RNAi plants, a total of 41 proteins with contrasting expression patterns were identified. We suggest that the ASR5 protein acts as a transcription factor to regulate the expression of different genes that collectively protect rice cells from Al-induced stress responses.

  14. Genetic relationships in a germplasm collection of Camellia japonica and Camellia oleifera using SSR analysis.

    PubMed

    Zhao, Y; Ruan, C J; Ding, G J; Mopper, S

    2017-02-16

    Camellia japonica produces different color and bigger flowers, widely being used for gardening green in southern China. However, cultivars were introduced from different regions, but their origin and pedigree information is either not available poorly documented, causing problems in authentication. Many low-yield trees in Camellia oleifera forests have been used as stocks for grafting C. japonica. However, the survival rate of grafts between these two species is related to genetic relationship between stock of C. oleifera and scion of C. japonica. We used simple sequence repeat (SSR) markers to genotype 41 C. japonica cultivars from different regions, as well as nine genotypes of C. oleifera in China. Twenty-one SSR markers generated 438 alleles, with an average of 20.85 alleles per locus. All alleles were used to generate Dice coefficients between two genotypes of all genotypes of these two species. Cluster analysis based on SSR data clustered genotypes showed clustering of genotypes into groups that agreed well with their taxonomic classification and geographic origin. Cultivar 'Damaonao' was a large tree with flowers of composite color, and showed the most genetic distance from other C. japonica cultivars and C. oleifera genotypes in the cluster analysis. The cultivars of C. japonica are distinct from genotypes of C. oleifera. The results for cultivars of C. japonica also revealed the presence of different cultivars with the same name, and identical cultivars but with a different name. SSR profiles can improve C. japonica germplasm management, and provide potential determine correlations between genetic relationship and graft compatibility among scions of C. japonica and genotypes of C. oleifera.

  15. 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.

  16. Structural determination of elicitors in Sogatella furcifera (Horváth) that induce Japonica rice plant varieties (Oryza sativa L.) to produce an ovicidal substance against S. furcifera eggs.

    PubMed

    Yang, Jeong-Oh; Nakayama, Naoya; Toda, Kyohei; Tebayashi, Shinichi; Kim, Chul-Sa

    2014-01-01

    Certain Japonica rice plant varieties (Oryza sativa L.) show resistance to the eggs of the white backed planthopper (Sogatella furcifera Horváth) by the formation of watery lesions and production of benzyl benzoate, an active ovicidal compound. Benzyl benzoate results in high ovicidal activity of S. furcifera eggs and reduces egg hatchability. The production of benzyl benzoate by the rice plants is only induced by an unknown elicitor(s) from the female S. furcifera. Therefore, we tried to isolate and identify these elicitors. An active 80% MeOH extract of S. furcifera was separated on a reverse-phase ODS MPLC, and the elicitor(s) was eluted in 100% MeOH and 100% EtOH fractions. Further separation of the active 100% MeOH fraction using a HPLC led to the isolation of four active compounds. The structures of each compound were determined by using NMR, LC-MS, and GC-MS spectra. The compounds were 1,2-dilinoleoyl-sn-glycero-3-phosphocholine, 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine, 1-palmitoyl-2-oleoyl-X-glycero-3-phosphoethanolamine, and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine.

  17. 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...

  18. 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

  19. Use of the Rice Diversity Panel 1 to map traits important for rice improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ‘Rice Diversity Panel 1’ (RDP1) is composed of 421 diverse Oryza sativa accessions from 79 countries, including indica and aus which belong to the Indica varietal group, and tropical japonica, temperate japonica, and aromatic (Group V) which comprise the Japonica varietal group. This panel was ...

  20. The durably resistant rice cultivar Digu activates defence gene expression before the full maturation of Magnaporthe oryzae appressorium.

    PubMed

    Li, Weitao; Liu, Ya; Wang, Jing; He, Min; Zhou, Xiaogang; Yang, Chao; Yuan, Can; Wang, Jichun; Chern, Mawsheng; Yin, Junjie; Chen, Weilan; Ma, Bingtian; Wang, Yuping; Qin, Peng; Li, Shigui; Ronald, Pamela; Chen, Xuewei

    2016-04-01

    Rice blast caused by the fungal pathogen Magnaporthe oryzae is one of the most destructive diseases worldwide. Although the rice-M. oryzae interaction has been studied extensively, the early molecular events that occur in rice before full maturation of the appressorium during M. oryzae invasion are unknown. Here, we report a comparative transcriptomics analysis of the durably resistant rice variety Digu and the susceptible rice variety Lijiangxintuanheigu (LTH) in response to infection by M. oryzae (5, 10 and 20 h post-inoculation, prior to full development of the appressorium). We found that the transcriptional responses differed significantly between these two rice varieties. Gene ontology and pathway analyses revealed that many biological processes, including extracellular recognition and biosynthesis of antioxidants, terpenes and hormones, were specifically activated in Digu shortly after infection. Forty-eight genes encoding receptor kinases (RKs) were significantly differentially regulated by M. oryzae infection in Digu. One of these genes, LOC_Os08g10300, encoding a leucine-rich repeat RK from the LRR VIII-2 subfamily, conferred enhanced resistance to M. oryzae when overexpressed in rice. Our study reveals that a multitude of molecular events occur in the durably resistant rice Digu before the full maturation of the appressorium after M. oryzae infection and that membrane-associated RKs play important roles in the early response.

  1. Evaluation of seedling cold tolerance in rice cultivars: a comparison of visual ratings and quantitative indicators of physiological changes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice (Oryza sativa L.) is sensitive to prolonged exposure to low temperature, which at the seedling stage can result in significant chilling injury and mortality. The objective of this study was to quantify physiological and biochemical changes in rice seedlings undergoing chilling stress and compar...

  2. [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.

  3. Identification of neutral genes at pollen sterility loci Sd and Se of cultivated rice (Oryza sativa) with wild rice (O. rufipogon) origin.

    PubMed

    Liu, B; Li, J Q; Liu, X D; Shahid, M Q; Shi, L G; Lu, Y G

    2011-10-31

    Pollen sterility is one of the main hindrances against the utilization of strong intersubspecific (indica-japonica) heterosis in rice. We looked for neutral alleles at known pollen sterility loci Sd and Se that could overcome this pollen sterility characteristic. Taichung 65, a typical japonica cultivar, and its near isogenic lines E7 and E8 for pollen sterility loci Sd and Se were employed as tester lines for crossing with 13 accessions of wild rice (O. rufipogon). Pollen fertility and genotypic segregations of the molecular markers tightly linked with Sd and Se loci were analyzed in the paired F(1)s and F(2) populations. One accession of wild rice (GZW054) had high pollen fertility in the paired F(1)s between Taichung 65 and E7 or E8. Genotypic segregations of the molecular markers tightly linked with Sd and Se loci fit the expected Mendelian ratio (1:2:1), and non-significances were shown among the mean pollen fertilities with the maternal, parental, and heterozygous genotypes of each molecular markers tightly linked with Sd and Se loci. Evidentially, it indicated that the alleles of Sd and Se loci for GZW054 did not interact with those of Taichung 65 and its near isogenic lines, and, thus were identified as neutral alleles Sd(n) and Se(n). These neutral genes could become important germplasm resources for overcoming pollen sterility in indica-japonica hybrids, making utilization of strong heterosis in such hybrids viable.

  4. Homologous expression of cytosolic dehydroascorbate reductase increases grain yield and biomass under paddy field conditions in transgenic rice (Oryza sativa L. japonica).

    PubMed

    Kim, Young-Saeng; Kim, Il-Sup; Bae, Mi-Jung; Choe, Yong-Hoe; Kim, Yul-Ho; Park, Hyang-Mi; Kang, Hong-Gyu; Yoon, Ho-Sung

    2013-06-01

    Dehydroascorbate reductase (DHAR, EC 1.8.5.1) maintains redox pools of ascorbate (AsA) by recycling oxidized AsA to reduced AsA. To investigate whether DHAR affects rice yield under normal environmental conditions, cDNA-encoding DHAR (OsDHAR1) was isolated from rice and used to develop OsDHAR1-overexpressing transgenic rice plants, under the regulation of a maize ubiquitin promoter. Incorporation and expression of the transgene in transgenic rice plants was confirmed by genomic polymerase chain reaction (PCR), semi-quantitative reverse transcription PCR (RT-PCR), western blot, and enzyme activity. The expression levels were at least twofold higher in transgenic (TG) rice plants than in control wild-type (WT) rice plants. In addition, OsDHAR1-overexpression in seven-independent homologous transgenic plants, as compared to WT plants, increased photosynthetic capacity and antioxidant enzyme activities under paddy field conditions, which led to an improved AsA pool and redox homeostasis. Furthermore, OsDHAR1 overexpression significantly improved grain yield and biomass due to the increase of culm and root weights and to enhance panicle and spikelet numbers in the same seven independent TG rice plants during the farming season (2010 and 2011) in South Korea. The OsDHAR protein contained the redox-active site (Cys20), as well as the conserved GSH-binding region, GSH-binding motif, glutathione-S-transferase (GST) N-terminal domain, C-terminal domain interface, and GST C-terminal domain. Therefore, our results indicate that OsDHAR1 overexpression, capable of functioning in AsA recycling, and protein folding increases environmental adaptation to paddy field conditions by the improving AsA pool and redox homeostasis, which enhances rice grain yield and biomass.

  5. 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.

  6. Do the rich always become richer? Characterizing the leaf physiological response of the high-yielding rice cultivar Takanari to free-air CO2 enrichment.

    PubMed

    Chen, Charles P; Sakai, Hidemitsu; Tokida, Takeshi; Usui, Yasuhiro; Nakamura, Hirofumi; Hasegawa, Toshihiro

    2014-02-01

    The development of crops which are well suited to growth under future environmental conditions such as higher atmospheric CO2 concentrations ([CO2]) is essential to meeting the challenge of ensuring food security in the face of the growing human population and changing climate. A high-yielding indica rice variety (Oryza sativa L. cv. Takanari) has been recently identified as a potential candidate for such breeding, due to its high productivity in present [CO2]. To test if it could further increase its productivity under elevated [CO2] (eCO2), Takanari was grown in the paddy field under season-long free-air CO2 enrichment (FACE, approximately 200 µmol mol(-1) above ambient [CO2]) and its leaf physiology was compared with the representative japonica variety 'Koshihikari'. Takanari showed consistently higher midday photosynthesis and stomatal conductance than Koshihikari under both ambient and FACE growth conditions over 2 years. Maximum ribulose-1,5-bisphosphate carboxylation and electron transport rates were higher for Takanari at the mid-grain filling stage in both years. Mesophyll conductance was higher in Takanari than in Koshihikari at the late grain-filling stage. In contrast to Koshihikari, Takanari grown under FACE conditions showed no decrease in total leaf nitrogen on an area basis relative to ambient-grown plants. Chl content was higher in Takanari than in Koshihikari at the same leaf nitrogen level. These results indicate that Takanari maintains its superiority over Koshihikari in regards to its leaf-level productivity when grown in elevated [CO2] and it may be a valuable resource for rice breeding programs which seek to increase crop productivity under current and future [CO2].

  7. 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...

  8. 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.

  9. Evaluation of physiological and biochemical responses of two rice (Oryza sativa L.) cultivars to ambient air pollution using open top chambers at a rural site in India.

    PubMed

    Rai, Richa; Agrawal, Madhoolika

    2008-12-15

    Air pollutant concentrations are rising in India, causing potential threats to crop production. As air pollutants are known to interfere with physiological processes, this study was conducted to assess the relative responses of physiological and biochemical characteristics of two cultivars of rice (Oryza sativa L. cv. Saurabh 950 and NDR 97) leading to variable yield responses. Twelve hour monitoring of ambient concentrations of SO2, NO2 and O3 in filtered chambers (FCs), non-filtered chambers (NFCs) and open plots (OPs) showed that O3 was the main pollutant at the experimental site. Ozone concentrations often exceeded 40 ppb during anthesis but not during the vegetative growth period. Photosynthetic rate (Ps), stomatal conductance (g(s)) and Fv/Fm ratio, superoxide dismutase (SOD) and peroxidase (POD) activities and photosynthetic pigments, ascorbic acid, total phenolics and protein contents were assessed at different developmental stages and yield of grains were quantified. Lipid peroxidation, SOD and POD activities, ascorbic acid and total phenolics were higher, whereas Ps, g(s), Fv/Fm ratio and contents of protein and photosynthetic pigment were lower in plants of NFCs as compared to FCs. Yield decreased significantly in both cultivars grown in NFCs. NDR 97 showed less reductions in physiological characteristics, photosynthetic pigments and protein, but a greater increase in the antioxidative defense system as compared to Saurabh 950. Yield reduction was higher in NDR 97 than in Saurabh 950. This suggested that NDR 97 utilized more photosynthate in maintaining the metabolic machinery against O3 stress leading to lower translocation of photosynthate to reproductive parts. The study concluded that under natural field conditions, physiological and biochemical responses of plants varied with pollutant concentrations leading to different translocation strategies in plants, modifying their yield responses. NDR 97, a fast growing and high yielding cultivar was more

  10. Biochemical and molecular characteristics of leaf photosynthesis and relative seed yield of two contrasting rice cultivars in response to elevated [CO₂].

    PubMed

    Zhu, Chunwu; Zhu, Jianguo; Cao, Jing; Jiang, Qian; Liu, Gang; Ziska, Lewis H

    2014-11-01

    Understanding the basis for intraspecific yield variability may be important in elucidating biological mechanisms that are associated with superior yield performance in response to projected increases in carbon dioxide concentration, [CO₂]. Using a free-air CO₂ enrichment (FACE) facility, two rice lines, S63 and W14, which differed consistently in their enhancement of seed yield when grown at elevated [CO₂] in multiple field trials, were examined. To determine if the different cultivar responses were linked to changes in photosynthetic characteristics at elevated [CO₂], spatial and temporal changes in photosynthetic stimulation and the occurrence of down-regulation, or acclimation, in relation to panicle sink development were quantified for the uppermost canopy leaves. Changes in photosynthetic capacity were determined by quantifying changes in the sink:source ratio, leaf nitrogen (N) content, the concentration and mRNA expression of the large Rubisco subunit, and changes in V c,max, the maximum ribulose bisphosphate (RuBP)-saturated rate of carboxylation. For the W14 cultivar, significant reductions in photosynthesis at the elevated, relative to ambient [CO₂], signalling photosynthetic acclimation, were observed following panicle initiation. The observance of photosynthetic acclimation was consistent with significant reductions in N, Rubisco content and expression, and V c,max. In contrast, for the cultivar S63, elevated [CO₂] resulted in increased spikelet number and grain weight, increased sink:source ratios, and continued stimulation of photosynthesis up to grain maturity. Overall, these data suggest that the greater response of the S63 line to elevated [CO₂] may be associated with enhanced carbon sinks relative to sources, and the ability to maintain photosynthetic capacity during grain development.

  11. 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.

  12. Using an Active-Optical Sensor to Develop an Optimal NDVI Dynamic Model for High-Yield Rice Production (Yangtze, China).

    PubMed

    Liu, Xiaojun; Ferguson, Richard B; Zheng, Hengbiao; Cao, Qiang; Tian, Yongchao; Cao, Weixing; Zhu, Yan

    2017-03-24

    The successful development of an optimal canopy vegetation index dynamic model for obtaining higher yield can offer a technical approach for real-time and nondestructive diagnosis of rice (Oryza sativa L) growth and nitrogen (N) nutrition status. In this study, multiple rice cultivars and N treatments of experimental plots were carried out to obtain: normalized difference vegetation index (NDVI), leaf area index (LAI), above-ground dry matter (DM), and grain yield (GY) data. The quantitative relationships between NDVI and these growth indices (e.g., LAI, DM and GY) were analyzed, showing positive correlations. Using the normalized modeling method, an appropriate NDVI simulation model of rice was established based on the normalized NDVI (RNDVI) and relative accumulative growing degree days (RAGDD). The NDVI dynamic model for high-yield production in rice can be expressed by a double logistic model: RNDVI = ( 1 + e - 15.2829 × ( R A G D D i - 0.1944 ) ) - 1 - ( 1 + e - 11.6517 × ( R A G D D i - 1.0267 ) ) - 1 (R2 = 0.8577**), which can be used to accurately predict canopy NDVI dynamic changes during the entire growth period. Considering variation among rice cultivars, we constructed two relative NDVI (RNDVI) dynamic models for Japonica and Indica rice types, with R2 reaching 0.8764** and 0.8874**, respectively. Furthermore, independent experimental data were used to validate the RNDVI dynamic models. The results showed that during the entire growth period, the accuracy (k), precision (R2), and standard deviation of RNDVI dynamic models for the Japonica and Indica cultivars were 0.9991, 1.0170; 0.9084**, 0.8030**; and 0.0232, 0.0170, respectively. These results indicated that RNDVI dynamic models could accurately reflect crop growth and predict dynamic changes in high-yield crop populations, providing a rapid approach for monitoring rice growth status.

  13. 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

  14. Genetic enhancement of host plant-resistance of the Lalat cultivar of rice against bacterial blight employing marker-assisted selection.

    PubMed

    Dokku, Prasad; Das, K M; Rao, G J N

    2013-08-01

    To incorporate durable resistance against bacterial blight, a major disease rice, three resistance genes, xa 5, xa13 and Xa21, from IRBB 60 were transferred through marker-assisted backcrossing using RG 556, RG 136 and pTA248 markers linked to the three genes to supplement the Xa4 gene present in Lalat, a popular rice cultivar. Effective selection enabled the transfer in three back-crosses and a generation of selfing and background selection employing morphological and grain quality traits and molecular markers, led to >90 % recovery of the recurrent parental genome. The gene pyramids exhibited high levels of resistance against the pathogen in multi-location evaluation trials conducted over several locations of bacterial blight in India. IL-2 (CRMAS2621-7-1), a gene pyramid, was identified as being promising for several endemic regions of bacterial blight and was released as Improved Lalat in one of the identified regions. The success of the study demonstrates the vast potential of marker-assisted selection for gene stacking and recovery of the parental genome with high precision.

  15. 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.

  16. Effect of early planting on weed suppression activity of indica and commercial U.S. rice cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Indica and commercial cultivars can suppress barnyardgrass when drill-seeded into ‘warm’ soils and grown under flood-irrigation in Arkansas. Because early planting is popular with growers and considered to improve productivity and flexibility, weed suppression tests were planted in the field on Apr...

  17. The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication.

    PubMed

    Lu, Jian; Tang, Tian; Tang, Hua; Huang, Jianzi; Shi, Suhua; Wu, Chung-I

    2006-03-01

    The extent of molecular differentiation between domesticated animals or plants and their wild relatives is postulated to be small. The availability of the complete genome sequences of two subspecies of the Asian rice, Oryza sativa (indica and japonica) and their wild relatives have provided an unprecedented opportunity to study divergence following domestication. We observed significantly more amino acid substitutions during rice domestication than can be expected from a comparison among wild species. This excess is disproportionately larger for the more radical kinds of amino acid changes (e.g. Cys<-->Tyr). We estimate that approximately a quarter of the amino acid differences between rice cultivars are deleterious, not accountable by the relaxation of selective constraints. This excess is negatively correlated with the rate of recombination, suggesting that 'hitchhiking' has occurred. We hypothesize that during domestication artificial selection increased the frequency of many deleterious mutations.

  18. 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

  19. Selective bactericidal potential of rice (Oryza sativa L. var. japonica) hull extract on Microcystis strains in comparison with green algae and zooplankton.

    PubMed

    Park, Myung-Hwan; Kim, Baik-Ho; Chung, Ill-Min; Hwang, Soon-Jin

    2009-07-01

    We examined the selective inhibitory potential of rice hull extract on the toxic cyanobacterium Microcystis aeruginosa, in comparison with inhibitory effects on two green algae (Ankistrodesmus convolutus and Scenedesmus quadricauda) and a zooplankton (Daphnia magna) species. The inhibitory effect of rice hull extract, measured by algal growth or zooplankton survival using four different concentrations of extract (1, 10, 100 and 1000 microg L(-1)), was highest on Microcystis strains (average: 98%, range: 95%-99%), followed by D. magna (average: 22%, range: 10%-47%), A. convolutus (average: 20%, range: 16%-24%), and S. quadricauda (average: 8%, range: 0%-15%). Rice hull extract had only a small effect on the growth of the green algae and Daphnia, particularly in the range 1-100 microg L(-1), and the inhibitory effect was somewhat diminished even at the 1,000 microg L(-1) level, at the end of the experimental period, especially for Daphnia. Our study indicates that rice hull extract has a strong specific algicide potential when used to combat M. aeruginosa.

  20. 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.

  1. 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.

  2. Greenhouse validation of yield component transgressive variation effects of wild Oryza species introgressions in an elite US rice cultivar

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A number of global studies have been conducted which have shown that the wild ancestral species, Oryza rufipogon, possesses beneficial alleles that can be used to improve cultivated rice, O. sativa, for biotic and abiotic stress tolerance as well as yield. Introgression lines (IL) were developed thr...

  3. Gene tree discordance of wild and cultivated Asian rice deciphered by genome-wide sequence comparison.

    PubMed

    Yang, Ching-chia; Sakai, Hiroaki; Numa, Hisataka; Itoh, Takeshi

    2011-05-15

    Although a large number of genes are expected to correctly solve a phylogenetic relationship, inconsistent gene tree topologies have been observed. This conflicting evidence in gene tree topologies, known as gene tree discordance, becomes increasingly important as advanced sequencing technologies produce an enormous amount of sequence information for phylogenomic studies among closely related species. Here, we aim to characterize the gene tree discordance of the Asian cultivated rice Oryza sativa and its progenitor, O. rufipogon, which will be an ideal case study of gene tree discordance. Using genome and cDNA sequences of O. sativa and O. rufipogon, we have conducted the first in-depth analyses of gene tree discordance in Asian rice. Our comparison of full-length cDNA sequences of O. rufipogon with the genome sequences of the japonica and indica cultivars of O. sativa revealed that 60% of the gene trees showed a topology consistent with the expected one, whereas the remaining genes supported significantly different topologies. Moreover, the proportions of the topologies deviated significantly from expectation, suggesting at least one hybridization event between the two subgroups of O. sativa, japonica and indica. In fact, a genome-wide alignment between japonica and indica indicated that significant portions of the indica genome are derived from japonica. In addition, literature concerning the pedigree of the indica cultivar strongly supported the hybridization hypothesis. Our molecular evolutionary analyses deciphered complicated evolutionary processes in closely related species. They also demonstrated the importance of gene tree discordance in the era of high-speed DNA sequencing.

  4. Strain-dependent effects of inoculation of Lactobacillus plantarum subsp. plantarum on fermentation quality of paddy rice (Oryza sativa L. subsp. japonica) silage.

    PubMed

    Tohno, Masanori; Kobayashi, Hisami; Tajima, Kiyoshi; Uegaki, Ryuichi

    2012-12-01

    Paddy rice has been of particular interest as a forage crop in Japan. In this study, the isolated strains TO1000, TO1001, TO1002, and TO1003 were characterized by phenotypic and genotypic approaches. These strains were identified as Lactobacillus plantarum subsp. plantarum by species-specific PCR. Phenotypic characteristics varied among different strains of the same subspecies, and the strains represented unique and diverse phenotypes related to fermentation factors, such as carbohydrate assimilation and range of pH and temperature allowing growth. PCR analysis revealed that the patterns of presence/absence of known plantaricin genes differed in a strain-specific manner. Using these strains as inoculants for preparation of whole crop paddy rice silage, fermentation quality was significantly improved, as shown by lower pH, higher lactic acid content, and inhibition of the growth of undesirable microorganisms such as molds, coliform bacteria, and clostridia, after 30 and 60 days of storage, with effectiveness differing from strain to strain. These observations suggest that suitable candidates for bacterial inoculants in silage preparation should be screened at the strain level. Strain TO1002 may be useful for producing silage inoculants for the production of well-preserved whole crop paddy rice silage.

  5. Geographic description of genetic diversity and genetic relationships in the USDA Rice World Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Asian cultivated rice (Oryza sativa L.) is structured into five genetic groups, indica, AUS, tropical japonica, temperate japonica and aromatic. Genetic characterization of a global rice collection could help better serve the global research community. Collecting worldwide rice germplasm started in ...

  6. Genetic structure associated with diversity and geographic distribution in the USDA rice world collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Asian cultivated rice (Oryza sativa L.) is structured into five genetic groups, indica, AUS, tropical japonica, temperate japonica and aromatic. Genetic characterization of a global rice collection could help better serve the global research community. Collecting worldwide rice germplasm started in ...

  7. Changes in root hydraulic conductivity facilitate the overall hydraulic response of rice (Oryza sativa L.) cultivars to salt and osmotic stress.

    PubMed

    Meng, Delong; Fricke, Wieland

    2017-04-01

    The aim of the present work was to assess the significance of changes in root AQP gene expression and hydraulic conductivity (Lp) in the regulation of water balance in two hydroponically-grown rice cultivars (Azucena, Bala) which differ in root morphology, stomatal regulation and aquaporin (AQP) isoform expression. Plants were exposed to NaCl (25 mM, 50 mM) and osmotic stress (5%, 10% PEG6000). Root Lp was determined for exuding root systems (osmotic forces driving water uptake; 'exudation Lp') and transpiring plants (hydrostatic forces dominating; 'transpiration-Lp'). Gene expression was analysed by qPCR. Stress treatments caused a consistent and significant decrease in plant growth, transpirational water loss, stomatal conductance, shoot-to-root surface area ratio and root Lp. Comparison of exudation-with transpiration-Lp supported a significant contribution of AQP-facilitated water flow to root water uptake. Changes in root Lp in response to treatments were correlated much stronger with root morphological characteristics, such as the number of main and lateral roots, surface area ratio of root to shoot and plant transpiration rate than with AQP gene expression. Changes in root Lp, involving AQP function, form an integral part of the plant hydraulic response to stress and facilitate changes in the root-to-shoot surface area ratio, transpiration and stomatal conductance.

  8. Adapting rice anther culture to gene transformation and RNA interference.

    PubMed

    Chen, Caiyan; Xiao, Han; Zhang, Wenli; Wang, Aiju; Xia, Zhihui; Li, Xiaobing; Zhai, Wenxue; Cheng, Zhukuan; Zhu, Lihuang

    2006-10-01

    Anther culture offers a rapid method of generating homozygous lines for breeding program and genetic analysis. To produce homozygous transgenic lines of rice (Oryza sativa L.) in one step, we developed an efficient protocol of anther-callus-based transformation mediated by Agrobacterium after optimizing several factors influencing efficient transformation, including callus induction and Agrobacterium density for co-cultivation. Using this protocol, we obtained 145 independent green transformants from five cultivars of japonica rice by transformation with a binary vector pCXK1301 bearing the rice gene, Xa21 for resistance to bacterial blight, of which 140 were further confirmed by PCR and Southern hybridization analysis, including haploids (32.1%), diploids (62.1%) and mixoploids (7.5%). Fifteen diploids were found to be doubled haploids, which accounted for 10.7% of the total positive lines. Finally, by including 28 from colchicine induced or spontaneous diploidization of haploids later after transformation, a total of 43 doubled haploids (30.7%) of Xa21 transgenic lines were obtained. We also generated two RNAi transgenic haploids of the rice OsMADS2 gene, a putative redundant gene of OsMADS4 based on their sequence similarity, to investigate its possible roles in rice flower development by this method. Flowers from the two OsMADS2 RNAi transgenic haploids displayed obvious homeotic alternations, in which lodicules were transformed into palea/lemma-like tissues, whereas identities of other floral organs were maintained. The phenotypic alternations were proved to result from specific transcriptional suppression of OsMADS2 gene by the introduced RNAi transgene. The results confirmed that OsMADS2 is involved in lodicule development of rice flower and functionally redundant with OsMADS4 gene. Our results demonstrated that rice anther culture could be adapted to gene transformation and RNAi analysis in rice.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. Natural variation of rice blast resistance gene Pi-d2

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Studying natural variation of rice resistance (R) genes in cultivated and wild rice relatives can predict resistance stability to rice blast fungus. In the present study, the protein coding regions of rice R gene Pi-d2 in 35 rice accessions of subgroups, aus (AUS), indica (IND), temperate japonica (...

  14. 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

  15. 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.

  16. 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...

  17. 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...

  18. Red rice (Oryza sativa L.) emergence characteristics and influence on rice (O. sativa) yield at different planting dates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cultivated rice yield losses due to red rice infestation vary by cultivar, red rice density, and duration of interference. The competition effects of red rice could be influenced further by emergence characteristics, red rice biotype, and planting time of cultivated rice. We aimed to characterize th...

  19. 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.

  20. 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

  1. 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

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

    PubMed

    Kanapeckas, Kimberly L; Vigueira, Cynthia C; Ortiz, Aida; Gettler, Kyle A; Burgos, Nilda R; Fischer, Albert J; Lawton-Rauh, Amy L

    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

  3. 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...

  4. Natural variation in OsPRR37 regulates heading date and contributes to rice cultivation at a wide range of latitudes.

    PubMed

    Koo, Bon-Hyuk; Yoo, Soo-Cheul; Park, Joon-Woo; Kwon, Choon-Tak; Lee, Byoung-Doo; An, Gynheung; Zhang, Zhanying; Li, Jinjie; Li, Zichao; Paek, Nam-Chon

    2013-11-01

    Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus (QTL) mapping and candidate gene analysis using whole-genome re-sequencing, we found that Oryza sativa Pseudo-Response Regulator37 (OsPRR37; hereafter PRR37) is responsible for the Early heading7-2 (EH7-2)/Heading date2 (Hd2) QTL which was identified from a cross of late-heading rice 'Milyang23 (M23)' and early-heading rice 'H143'. H143 contains a missense mutation of an invariantly conserved amino acid in the CCT (CONSTANS, CO-like, and TOC1) domain of PRR37 protein. In the world rice collection, different types of nonfunctional PRR37 alleles were found in many European and Asian rice cultivars. Notably, the japonica varieties harboring nonfunctional alleles of both Ghd7/Hd4 and PRR37/Hd2 flower extremely early under natural long-day conditions, and are adapted to the northernmost regions of rice cultivation, up to 53° N latitude. Genetic analysis revealed that the effects of PRR37 and Ghd7 alleles on heading date are additive, and PRR37 down-regulates Hd3a expression to suppress flowering under long-day conditions. Our results demonstrate that natural variations in PRR37/Hd2 and Ghd7/Hd4 have contributed to the expansion of rice cultivation to temperate and cooler regions.

  5. Identification of a Genetic Factor Required for High γ-Isoform Concentration in Rice Vitamin E.

    PubMed

    Sekine, Daisuke; Murata, Kazumasa; Kimura, Toshiyuki; Nakagawa, Kiyotaka; Miyazawa, Teruo

    2016-12-14

    The γ-isoforms of tocopherols (Tc) and tocotrienols (T3) possess high biological activities in comparison to the α-isoforms. The concentrations of Tc and T3 isoforms in rice (Oriza sativa) was cultivar-dependent. Using chromosome segment substitution lines (CSSLs) and near isogenic lines (NILs) of indica cultivar "Kasalath" in a japonica cultivar "Koshihikari" genetic background, the Kasalath genomic segment on chromosome 2 was determined to be responsible for the high γ-isoform concentration: γ-tocopherol methyltransferase (γ-TMT) was identified as a candidate gene. An amino acid substitution in the coding region and several nucleotide polymorphisms, including an insertion of 10 base pairs in the promoter region, were identified. Gene expression analysis revealed that low expression levels of the γ-TMT gene in Kasalath were not associated with the γ-isoform concentration. Genetic variations in the coding region of the γ-TMT gene may play a major role in determining the γ-isoform concentration. This information could be used to breed rice with a high γ-isoform content.

  6. Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes.

    PubMed

    Mizuta, Yoko; Harushima, Yoshiaki; Kurata, Nori

    2010-11-23

    Genetic incompatibility is a barrier contributing to species isolation and is caused by genetic interactions. We made a whole genome survey of two-way interacting loci acting within the gametophyte or zygote using independence tests of marker segregations in an F(2) population from an intersubspecific cross between O. sativa subspecies indica and japonica. We detected only one reproducible interaction, and identified paralogous hybrid incompatibility genes, DOPPELGANGER1 (DPL1) and DOPPELGANGER2 (DPL2), by positional cloning. Independent disruptions of DPL1 and DPL2 occurred in indica and japonica, respectively. DPLs encode highly conserved, plant-specific small proteins (∼10 kDa) and are highly expressed in mature anther. Pollen carrying two defective DPL alleles became nonfunctional and did not germinate, suggesting an essential role for DPLs in pollen germination. Although rice has many duplicated genes resulting from ancient whole genome duplication, the origin of this gene duplication was in recent small-scale gene duplication, occurring after Oryza-Brachypodium differentiation. Comparative analyses suggested the geographic and phylogenetic distribution of these two defective alleles, showing that loss-of-function mutations of DPL1 genes emerged multiple times in indica and its wild ancestor, O. rufipogon, and that the DPL2 gene defect is specific to japonica cultivars.

  7. Mapping QTL main and interaction influences on milling quality in elite US rice germplasm.

    PubMed

    Nelson, J C; McClung, A M; Fjellstrom, R G; Moldenhauer, K A K; Boza, E; Jodari, F; Oard, J H; Linscombe, S; Scheffler, B E; Yeater, K M

    2011-02-01

    Rice (Oryza sativa L.) head-rice yield (HR) is a key export and domestic quality trait whose genetic control is poorly understood. With the goal of identifying genomic regions influencing HR, quantitative-trait-locus (QTL) mapping was carried out for quality-related traits in recombinant inbred lines (RILs) derived from crosses of common parent Cypress, a high-HR US japonica cultivar, with RT0034, a low-HR indica line (129 RILs) and LaGrue, a low-HR japonica cultivar (298 RILs), grown in two US locations in 2005-2007. Early heading increased HR in the Louisiana (LA) but not the Arkansas (AR) location. Fitting QTL-mapping models to separate QTL main and QTL × environment interaction (QEI) effects and identify epistatic interactions revealed six main-effect HR QTLs in the two crosses, at four of which Cypress contributed the increasing allele. Multi-QTL models accounted for 0.36 of genetic and 0.21 of genetic × environment interaction of HR in MY1, and corresponding proportions of 0.25 and 0.37 in MY2. The greater HR advantage of Cypress in LA than in AR corresponded to a genomewide pattern of opposition of HR-increasing QTL effects by AR-specific effects, suggesting a selection strategy for improving this cultivar for AR. Treating year-location combinations as independent environments resulted in underestimation of QEI effects, evidently owing to lower variation among years within location than between location. Identification of robust HR QTLs in elite long-grain germplasm is suggested to require more detailed attention to the interaction of plant and grain development parameters with environmental conditions than has been given to date.

  8. 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...

  9. 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.

  10. Cooked rice texture and rice flour pasting properties; impacted by rice temperature during milling.

    PubMed

    Saleh, Mohammed; Meullenet, Jean-Francois

    2015-03-01

    Rice milling plays a key factor in determining rice quality and value. Therefore accurate quality assessments are critical to the rice industry. This study was undertaken to assess the effect of exposing rice to elevated temperatures during milling, on cooked rice texture and rice flour pasting properties. Two long (Cybonnett and Francis) and one medium (Jupiter) rice (oryzae sativa L.) cultivars were milled using McGill laboratory mill for 30 and 40 s after warmed up the mill before milling. Four different milling temperatures per milling duration were achieved. Cooked rice texture properties were assessed using a uniaxial compression test and rice flour pasting properties measured using a TA-2000 rheometer. Results of this study showed that exposure of rice to high temperatures during milling significantly decreased cooked rice firmness. An increase in milled rice temperature after milling from 10.0 to 13.3 °C resulted in a 5.4 and 8.1 N decrease in cooked rice firmness. Although not always significant, the increase in milled rice temperature during milling resulted in an increase in cooked rice stickiness. The increase in milling temperature also showed significant increase in rice flour pasting properties. Changes in rice functional characteristics were attributed to the changes occurring to rice chemical constituents due to temperature exposure as indicated by the increase in rice protein hydrophobicity. Proteins are known to affect rice starch water holding capacity and other starch gelatinization properties.

  11. Mapping and validation of quantitative trait loci associated with tiller production in rice (Oryza sativa L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice has two main subspecies under world-wide production; the indica rices, grown primarily in tropical rice-growing regions, tiller profusely compared to the japonica rices which are grown in temperate and subtropical regions, including the U.S. All breeders seek to increase yield potential by opt...

  12. 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...

  13. Effect of the interaction between light and touch stimuli on inducing curling seminal roots in rice seedlings

    PubMed Central

    Kang, Chia-Hao; Chen, Hsiang-Wen

    2011-01-01

    Root development is sensitive to environmental stimuli. We have recently reported that the light signal could promote the helical growth of seminal roots and drive the wavy root morphology in rice (Oryza sativa L.) young seedlings. The light-stimulated wavy roots were mostly performed in indica-type rice varieties (e.g., Taichung Native 1; TCN1) but not in japonica rice (e.g., Tainung 67; TNG67). Here, we demonstrated that the light-driven circumutation trajectory of TCN1 seminal roots could be changed if the seedling roots were grown in the medium containing high concentration of Phytagel. The data showed the root morphology would be modulated from wavy to curling when the Phytagel concentration was increased to 2%. However, the touch-stimulated curling root phenotype could not be performed in dark. In addition, the touch-induced curling roots were not appeared in the TNG67 rice cultivar. Although touch stimuli could not induce wavy/curling root phenotype in dark, it could modify the light-promoted helical growth to conduct curling roots in TCN1 rice seedlings. Thus, it was suggested that there is a crosstalk mechanism between touching-induced root curling and light-stimulated root waving. PMID:21912213

  14. 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

    2013-01-02

    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.

  15. Gene targeting by the TAL effector PthXo2 reveals cryptic resistance gene for bacterial blight of rice.

    PubMed

    Zhou, Junhui; Peng, Zhao; Long, Juying; Sosso, Davide; Liu, Bo; Eom, Joon-Seob; Huang, Sheng; Liu, Sanzhen; Vera Cruz, Casiana; Frommer, Wolf B; White, Frank F; Yang, Bing

    2015-05-01

    Bacterial blight of rice is caused by the γ-proteobacterium Xanthomonas oryzae pv. oryzae, which utilizes a group of type III TAL (transcription activator-like) effectors to induce host gene expression and condition host susceptibility. Five SWEET genes are functionally redundant to support bacterial disease, but only two were experimentally proven targets of natural TAL effectors. Here, we report the identification of the sucrose transporter gene OsSWEET13 as the disease-susceptibility gene for PthXo2 and the existence of cryptic recessive resistance to PthXo2-dependent X. oryzae pv. oryzae due to promoter variations of OsSWEET13 in japonica rice. PthXo2-containing strains induce OsSWEET13 in indica rice IR24 due to the presence of an unpredicted and undescribed effector binding site not present in the alleles in japonica rice Nipponbare and Kitaake. The specificity of effector-associated gene induction and disease susceptibility is attributable to a single nucleotide polymorphism (SNP), which is also found in a polymorphic allele of OsSWEET13 known as the recessive resistance gene xa25 from the rice cultivar Minghui 63. The mutation of OsSWEET13 with CRISPR/Cas9 technology further corroborates the requirement of OsSWEET13 expression for the state of PthXo2-dependent disease susceptibility to X. oryzae pv. oryzae. Gene profiling of a collection of 104 strains revealed OsSWEET13 induction by 42 isolates of X. oryzae pv. oryzae. Heterologous expression of OsSWEET13 in Nicotiana benthamiana leaf cells elevates sucrose concentrations in the apoplasm. The results corroborate a model whereby X. oryzae pv. oryzae enhances the release of sucrose from host cells in order to exploit the host resources.

  16. Effects of manganese oxide-modified biochar composites on arsenic speciation and accumulation in an indica rice (Oryza sativa L.) cultivar.

    PubMed

    Yu, Zhihong; Qiu, Weiwen; Wang, Fei; Lei, Ming; Wang, Di; Song, Zhengguo

    2017-02-01

    A pot experiment was used to investigate arsenic (As) speciation and accumulation in rice, as well as its concentration in both heavily contaminated and moderately contaminated soils amended with manganese oxide-modified biochar composites (MBC) and biochar alone (BC). In heavily As-contaminated soil, application of BC and MBC improved the weight of above-ground part and rice root, whereas in moderately As-contaminated soil, the application of MBC and low rate BC amendment increased rice root, grain weight and the biomass of the plant. Arsenic reduction in different parts of rice grown in MBC-amended soils was greater than that in plants cultivated in BC-amended soils. Such reduction can be attributed to the oxidation of arsenite, As(III), to arsenate, As(V), by Mn-oxides, which also had a strong adsorptive capacity for As(V). MBC amended to As-contaminated soil had a positive effect on amino acids. The Fe and Mn levels in the iron-manganese plaque that formed on the rice root surface differed among the treatments. MBC addition significantly increased Mn content (p < 0.05); the application of 2.0% MBC increased Mn content 36- and 10-fold compared to the control in heavily and moderately As-contaminated soils, respectively. The results indicate that application of Mn oxide-modified biochar to As-contaminated paddy soil could effectively remediate contaminated soil and reduce As accumulation in edible parts of rice.

  17. 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

  18. 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.

  19. 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.

  20. Differential expression of the microRNAs in superior and inferior spikelets in rice (Oryza sativa).

    PubMed

    Peng, Ting; Lv, Qiang; Zhang, Jing; Li, Junzhou; Du, Yanxiu; Zhao, Quanzhi

    2011-10-01

    MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. This work investigated miRNAs in rice (Oryza sativa), an important food crop. High-throughput sequencing technology was used to reveal expression differences in miRNAs between superior and inferior spikelets in rice (japonica cultivar Xinfeng 2) at 18 d after fertilization. Totals of 351 and 312 known miRNAs were obtained from the superior and inferior spikelets, respectively. Analysis of the expression profiles of these miRNAs showed that 189 miRNAs were differentially expressed between superior spikelets and inferior spikelets. In addition, 43 novel miRNAs were identified mostly by the accumulation of miRNA*s expressed differentially between the superior and inferior spikelets. Further analysis with bioinformatics software and comparison with existing databases showed that these differentially expressed miRNAs may individually participate in regulating hormone metabolism, carbohydrate metabolic pathways, and cell division during rice grain development. The results indicate that the slow grain-filling and low grain weight of rice inferior spikelets are attributed partly to differences in expression and function between superior and inferior spikelet miRNAs.

  1. Detection of DNA polymerase λ activity during seed germination and enhancement after salinity stress and dehydration in the plumules of indica rice (Oryza sativa L.

    PubMed

    Sihi, Sayantani; Bakshi, Sankar; Sengupta, Dibyendu Narayan

    2015-02-01

    DNA polymerase λ (DNA pol λ) is the only reported X-family DNA polymerases in plants and has been shown to play a significant role in dry quiescent seeds, growth, development and nuclear DNA repair. cDNA for DNA pol λ has been reported in Arabidopsis and japonica rice cultivar and has been characterized from E. coli expressed protein, but very little is known about its activity at protein level in plants. The enzymatic activity of DNA pol λ was studied in dry, imbibed and during different germination stages of indica rice IR-8 (salt sensitive) by in-gel activity assay to determine its physiological role in important stages of growth and development. The upstream sequence was also analyzed using plantCARE database and was found to contain several cis-acting elements, including light responsive elements, dehydration responsive elements, Myb binding sites, etc. Hence, 4-day-old germinating seedlings of IR29, a salt-sensitive, but high yielding indica rice cultivar and Nonabokra, a salt-tolerant, but low yielding cultivar were treated with water (control) or 250 mM NaCl or 20% polyethyleneglycol-6000 for 4 and 8 h. The protein was analyzed by in vitro DNA pol λ activity assay, in-gel activity assay and Western blot analysis. DNA pol λ was not detected in dry seeds, but enhanced after imbibition and detectable from low level to high level during subsequent germination steps. Both salinity and dehydration stress led to the enhancement of the activity and protein level of DNA pol λ, as compared to control tissues. This is the first evidence of the salinity or dehydration stress induced enhancement of DNA pol λ activity in the plumules of rice (Oryza sativa L.) cultivars.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa.

    PubMed

    Londo, Jason P; Chiang, Yu-Chung; Hung, Kuo-Hsiang; Chiang, Tzen-Yuh; Schaal, Barbara A

    2006-06-20

    Cultivated rice, Oryza sativa L., represents the world's most important staple food crop, feeding more than half of the human population. Despite this essential role in world agriculture, the history of cultivated rice's domestication from its wild ancestor, Oryza rufipogon, remains unclear. In this study, DNA sequence variation in three gene regions is examined in a phylogeographic approach to investigate the domestication of cultivated rice. Results indicate that India and Indochina may represent the ancestral center of diversity for O. rufipogon. Additionally, the data suggest that cultivated rice was domesticated at least twice from different O. rufipogon populations and that the products of these two independent domestication events are the two major rice varieties, Oryza sativa indica and Oryza sativa japonica. Based on this geographical analysis, O. sativa indica was domesticated within a region south of the Himalaya mountain range, likely eastern India, Myanmar, and Thailand, whereas O. sativa japonica was domesticated from wild rice in southern China.

  7. Aluminum triggers broad changes in microRNA expression in rice roots.

    PubMed

    Lima, J C; Arenhart, R A; Margis-Pinheiro, M; Margis, R

    2011-11-10

    MicroRNAs are small 21-nucleotide RNA molecules with regulatory roles in development and in response to stress. Expression of some plant miRNAs has been specifically associated with responses to abiotic stresses caused by cold, light, iron, and copper ions. In acid soils, aluminum solubility increases, thereby causing severe damage to plants. Although physiological aspects of aluminum toxicity in plants have been well characterized, the molecular mediators are not fully elucidated. There have been no reports about miRNA responses to aluminum stress. Modulation of miRNA expression may constitute a key element to explain the mechanisms implicated in aluminum toxicity and tolerance. We examined the expression of at least one miRNA member from each miRNA family in rice roots of Oryza sativa spp indica cv. Embrapa Taim and Oryza sativa spp japonica cv. Nipponbare under high concentrations of aluminum. Forty-six miRNA families were effectively detected by quantitative PCR. Among these, 13 were down-regulated and six were up-regulated in roots of the Nipponbare cultivar after 8 h of aluminum treatment. In roots of the Embrapa Taim cultivar, five miRNAs were down-regulated and three were up-regulated. Analyses of their putative targets suggest that these rice miRNAs are involved in the regulation of various metabolic pathways in response to high concentrations of aluminum.

  8. 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

  9. Dissecting Rice Polyamine Metabolism under Controlled Long-Term Drought Stress

    PubMed Central

    Do, Phuc Thi; Degenkolbe, Thomas; Erban, Alexander; Heyer, Arnd G.; Kopka, Joachim; Köhl, Karin I.; Hincha, Dirk K.; Zuther, Ellen

    2013-01-01

    A selection of 21 rice cultivars (Oryza sativa L. ssp. indica and japonica) was characterized under moderate long-term drought stress by comprehensive physiological analyses and determination of the contents of polyamines and selected metabolites directly related to polyamine metabolism. To investigate the potential regulation of polyamine biosynthesis at the transcriptional level, the expression of 21 genes encoding enzymes involved in these pathways were analyzed by qRT-PCR. Analysis of the genomic loci revealed that 11 of these genes were located in drought-related QTL regions, in agreement with a proposed role of polyamine metabolism in rice drought tolerance. The cultivars differed widely in their drought tolerance and parameters such as biomass and photosynthetic quantum yield were significantly affected by drought treatment. Under optimal irrigation free putrescine was the predominant polyamine followed by free spermidine and spermine. When exposed to drought putrescine levels decreased markedly and spermine became predominant in all cultivars. There were no correlations between polyamine contents and drought tolerance. GC-MS analysis revealed drought-induced changes of the levels of ornithine/arginine (substrate), substrates of polyamine synthesis, proline, product of a competing pathway and GABA, a potential degradation product. Gene expression analysis indicated that ADC-dependent polyamine biosynthesis responded much more strongly to drought than the ODC-dependent pathway. Nevertheless the fold change in transcript abundance of ODC1 under drought stress was linearly correlated with the drought tolerance of the cultivars. Combining metabolite and gene expression data, we propose a model of the coordinate adjustment of polyamine biosynthesis for the accumulation of spermine under drought conditions. PMID:23577102

  10. Identification of broad spectrum rice blast resistance genes with IRRI Rice monogenic lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice blast disease, caused by the fungus Magnaporthe oryzae, is the most destructive rice disease worldwide. This disease is managed with a combination of the use of resistant cultivars, application of fungicides, and improved cultural practices. Among them, the use of resistant cultivars is the mos...

  11. 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.

  12. Rice Morphogenesis and Plant Architecture: Measurement, Specification and the Reconstruction of Structural Development by 3D Architectural Modelling

    PubMed Central

    WATANABE, TOMONARI; HANAN, JIM S.; ROOM, PETER M.; HASEGAWA, TOSHIHIRO; NAKAGAWA, HIROSHI; TAKAHASHI, WATARU

    2005-01-01

    • Background and Aims The morphogenesis and architecture of a rice plant, Oryza sativa, are critical factors in the yield equation, but they are not well studied because of the lack of appropriate tools for 3D measurement. The architecture of rice plants is characterized by a large number of tillers and leaves. The aims of this study were to specify rice plant architecture and to find appropriate functions to represent the 3D growth across all growth stages. • Methods A japonica type rice, ‘Namaga’, was grown in pots under outdoor conditions. A 3D digitizer was used to measure the rice plant structure at intervals from the young seedling stage to maturity. The L-system formalism was applied to create ‘3D virtual rice’ plants, incorporating models of phenological development and leaf emergence period as a function of temperature and photoperiod, which were used to determine the timing of tiller emergence. • Key Results The relationships between the nodal positions and leaf lengths, leaf angles and tiller angles were analysed and used to determine growth functions for the models. The ‘3D virtual rice’ reproduces the structural development of isolated plants and provides a good estimation of the tillering process, and of the accumulation of leaves. • Conclusions The results indicated that the ‘3D virtual rice’ has a possibility to demonstrate the differences in the structure and development between cultivars and under different environmental conditions. Future work, necessary to reflect both cultivar and environmental effects on the model performance, and to link with physiological models, is proposed in the discussion. PMID:15820987

  13. OsMYB511 encodes a MYB domain transcription activator early regulated by abiotic stress in rice.

    PubMed

    Huang, P; Chen, H; Mu, R; Yuan, X; Zhang, H S; Huang, J

    2015-08-14

    The MYB-domain proteins exist universally across diverse organisms and regulate numerous processes during the plant life cycle. In the present research, a full-length MYB gene OsMYB511 was identified from rice seedlings through microarray data. Induction of OsMYB511 by cold stress was dramatic in japonica cultivar Jiucaiqing as compared to indica IR26. In addition to cold, OsMYB511 was also markedly induced by osmotic stress, high temperature, and exogenous ABA, suggesting that OsMYB511 is a multiple-stress responsive gene in rice. Tissue-specific expression analysis indicated that OsMYB511 was highly expressed in rice panicles at earlier development stage. Interestingly, OsMYB511 expression is fully subjected to circadian rhythm regulation. The subcellular localization and yeast hybrid assay suggested that OsMYB511 is nucleus-localized transcription activator. Deletion analysis suggested that trans-activation activity of OsMYB511 relied on its C-terminus. Co-expression analysis revealed additional 2 MYB genes co-expressed with OsMYB511, implying that these MYB genes might coordinately regulate stress responses in rice.

  14. Effects of Delaying Transplanting on Agronomic Traits and Grain Yield of Rice under Mechanical Transplantation Pattern

    PubMed Central

    Liu, Qihua; Wu, Xiu; Ma, Jiaqing; Chen, Bocong; Xin, Caiyun

    2015-01-01

    A delay in the mechanical transplantation (MT) of rice seedlings frequently occurs in Huanghuai wheat-rice rotation cropping districts of China, due to the late harvest of wheat, the poor weather conditions and the insufficiency of transplanters, missing the optimum transplanting time and causing seedlings to age. To identify how delaying transplanting rice affects the agronomic characteristics including the growth duration, photosynthetic productivity and dry matter remobilization efficiency and the grain yield under mechanical transplanting pattern, an experiment with a split-plot design was conducted over two consecutive years. The main plot includes two types of cultivation: mechanical transplanting and artificial transplanting (AT). The subplot comprises four japonica rice cultivars. The results indicate that the rice jointing, booting, heading and maturity stages were postponed under MT when using AT as a control. The tiller occurrence number, dry matter weight per tiller, accumulative dry matter for the population, leaf area index, crop growth rate, photosynthetic potential, and dry matter remobilization efficiency of the leaf under MT significantly decreased compared to those under AT. In contrast, the reduction rate of the leaf area during the heading-maturity stage was markedly enhanced under MT. The numbers of effective panicles and filled grains per panicle and the grain yield significantly decreased under MT. A significant correlation was observed between the dry matter production, remobilization and distribution characteristics and the grain yield. We infer that, as with rice from old seedlings, the decrease in the tiller occurrence, the photosynthetic productivity and the assimilate remobilization efficiency may be important agronomic traits that are responsible for the reduced grain yield under MT. PMID:25875607

  15. Analysis of nucleotide diversity among alleles of the major bacterial blight resistance gene Xa27 in cultivars of rice (Oryza sativa) and its wild relatives.

    PubMed

    Bimolata, Waikhom; Kumar, Anirudh; Sundaram, Raman Meenakshi; Laha, Gouri Shankar; Qureshi, Insaf Ahmed; Reddy, Gajjala Ashok; Ghazi, Irfan Ahmad

    2013-08-01

    Xa27 is one of the important R-genes, effective against bacterial blight disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Using natural population of Oryza, we analyzed the sequence variation in the functionally important domains of Xa27 across the Oryza species. DNA sequences of Xa27 alleles from 27 rice accessions revealed higher nucleotide diversity among the reported R-genes of rice. Sequence polymorphism analysis revealed synonymous and non-synonymous mutations in addition to a number of InDels in non-coding regions of the gene. High sequence variation was observed in the promoter region including the 5'UTR with 'π' value 0.00916 and 'θ w ' = 0.01785. Comparative analysis of the identified Xa27 alleles with that of IRBB27 and IR24 indicated the operation of both positive selection (Ka/Ks > 1) and neutral selection (Ka/Ks ≈ 0). The genetic distances of alleles of the gene from Oryza nivara were nearer to IRBB27 as compared to IR24. We also found the presence of conserved and null UPT (upregulated by transcriptional activator) box in the isolated alleles. Considerable amino acid polymorphism was localized in the trans-membrane domain for which the functional significance is yet to be elucidated. However, the absence of functional UPT box in all the alleles except IRBB27 suggests the maintenance of single resistant allele throughout the natural population.

  16. Development of the recombinant inbred line population of tropical japonica Lemont crossed with indica Jasmine 85

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A recombinant inbred line (RIL) population of rice is routinely used in studying agronomically important genes, and is particularly useful for analyzing quantitative trait loci (QTL) since phenotypes can be assessed over years. Jasmine 85, a midseason aromatic long-grain indica rice cultivar develo...

  17. Identification of the rice blast resistance gene Pib in the National Small Grains Collection.

    PubMed

    Roychowdhury, M; Jia, Y; Jia, M H; Fjellstrom, R; Cartwright, R D

    2012-07-01

    The Pib gene in rice confers resistance to a wide range of races of the rice blast pathogen, Magnaporthe oryzae, including race IE1k that overcomes Pita, another broad-spectrum resistance gene. In this study, the presence of Pib was determined in 164 rice germplasm accessions from a core subset of the National Small Grains Collection utilizing DNA markers and pathogenicity assays. The presence of Pib was evaluated with two simple sequence repeat (SSR) markers and a dominant marker (Pib-dom) derived from the Pib gene sequence. Pathogenicity assays using two avirulent races (IE1k and IB1) and a virulent race (IB54) were performed to verify the resistance responses of accessions. Of the 164 accessions evaluated, 109 contained the Pib gene as determined using both SSR markers and pathogenicity assays, albeit different haplotypes were detected. The remaining 52 germplasm accessions were different in their responses to the blast races IB54, IE1k, and IB1, thus indicating the presence of R gene(s) other than Pib. The accessions characterized in this study could be used for marker-assisted breeding to improve blast resistance in indica and japonica cultivars worldwide.

  18. Agronomic traits and gene containment capability of cleistogamous rice lines with the superwoman1-cleistogamy mutation

    PubMed Central

    Ohmori, Shinnosuke; Tabuchi, Hiroaki; Yatou, Osamu; Yoshida, Hitoshi

    2012-01-01

    Pollen-mediated transgene flow is a major concern for the production of genetically modified (GM) rice. Cleistogamy is a useful tool for preventing this form of gene flow. We previously identified the cleistogamous rice mutant superwoman1-cleistogamy (spw1-cls) and determined its molecular genetic mechanism. In the present study, we cultivated spw1-cls over five years to examine effects of cleistogamy on agronomic traits. Simultaneously, we cultivated cleistogamous backcross lines created by continuous backcrossing with “Yumeaoba” (a japonica cultivar) as the recurrent parent and by application of a DNA marker. In these experimental cultivations, spw1-cls and its backcross lines showed almost equal or slightly lower, but acceptable, agronomic traits compared with each control line. We also conducted natural crossing tests in paddy fields to assess the gene containment capability of spw1-cls. In a series of field experiments, there was no natural crossing between spw1-cls (pollen donor) and pollen recipient lines, but the wild-type donor and recipient lines were crossed. Thus, the cleistogamy of the spw1-cls mutation is able to inhibit natural crossing effectively, without significant loss of commercial benefits, such as yield. We conclude that spw1-cls cleistogamy is a practical tool for gene containment in GM rice cultivation. PMID:23136523

  19. 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

  20. 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.

  1. Shewanella japonica sp. nov.

    PubMed

    Ivanova, E P; Sawabe, T; Gorshkova, N M; Svetashev, V I; Mikhailov, V V; Nicolau, D V; Christen, R

    2001-05-01

    Two strains of agar-digesting bacteria, KMM 3299T and KMM 3300, respectively isolated from sea water and the mussel Protothaca jedoensis, have been characterized. Based on sequencing of the 16S rRNA gene, KMM 3299T showed the highest similarity (93-95%) to members of the genus Shewanella. The G+C contents of the DNAs of these strains were 43-44 mol%. The level of DNA homology between the two strains was conspecific (95%), indicating that they represent a distinct genospecies. These organisms were non-pigmented, Gram-negative, polarly flagellated, facultatively anaerobic, mesophilic, neutrophilic and able to degrade a wide range of high molecular mass polymers, including alginate, carrageenan, laminaran and agar. The novel organisms were susceptible to gentamycin, carbenicillin, lincomycin and oleandomycin. The predominant cellular fatty acids were i-15:0, 16:0, 16:1(n-7), 18:1(n-7). Eicosapentaenoic acid, 20:5(n-3), was detected in the two isolates at levels of 1-8%, depending on the temperature of cultivation. Phylogenetic evidence, together with phenotypic characteristics, showed that the two isolates studied constitute a novel species of the genus Shewanella. The name Shewanella japonica is proposed; the type strain is KMM 3299T(= LMG 19691T = CIP 106860T).

  2. 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...

  3. 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...

  4. 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-...

  5. [Effects of relatively high temperature at grain-filling stage on rice grain's starch viscosity profile and magnesium and potassium contents].

    PubMed

    Zhang, Guo-Fa; Wang, Shao-Hua; You, Juan; Zhang, Yan-Xia; Wang, Qiang-Sheng; Ding, Yan-Feng

    2008-09-01

    With rice cultivars Yangdao 6 (Indica) and Wuyujing 3 (Japonica) as test materials, the effects of relatively high temperature (RHT, mean temperature 30 degrees C) at grain-filling stage (GFS) on the starch viscosity profile and magnesium (Mg) and potassium (K) contents of rice grain were studied in a phytotron. Four temperature treatments were installed, i.e., RHT at whole GFS, RHT at early GFS and optimum temperature at later GFS, optimum temperature at early GFS and RHT at later GFS, and optimum temperature (CK, mean temperature 23 degrees C) at whole GFS. The results showed that RHT at GFS significantly influenced the characteristic values of rice grain' s starch viscosity profile, e.g., the values of gelatinization temperature, final viscosity, consistency, and setback increased, while those of peak viscosity, hot viscosity, and breakdown decreased, with Yangdao 6 and Wuyujing 3 followed the similar pattern. The RHT increased the contents of Mg, K, and N, especially of K, resulting in a marked decrease of Mg/K and Mg/(N * AC * K) in the grain. The grain's amylase content (AC) of the two cultivars showed contrasting in response to temperature treatments. Wuyujing 3 performed decrease, while Yangdao 6 exhibited increase in AC values. The RHT at whole GFS affected the starch viscosity profile and the Mg and K contents most greatly, followed by the RHT at early GFS, and the RHT at later GFS. The period within 20 days after flowering was the key period during which temperature affected the grain's starch viscosity profile and Mg and K contents. The Mg/K and Mg/ (N * AC * K) in rice grain significant correlated with the characteristic values of starch viscosity profile, which could be used as the reference indices of rice eating quality.

  6. 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.

  7. 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

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

    PubMed

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

    2016-02-01

    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.

  9. 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

  10. 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 Varieties1[W][OPEN

    PubMed Central

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

    2014-01-01

    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. PMID:24520156

  11. 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.

  12. Root distribution and potential interactions between allelopathic rice, sprangletop (Leptochloa spp.), and barnyardgrass (Echinochloa crus-galli) based on 13C isotope discrimination analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 understo...

  13. Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups

    PubMed Central

    Parida, Swarup Kumar; Dalal, Vivek; Singh, Ashok Kumar; Singh, Nagendra Kumar; Mohapatra, Trilochan

    2009-01-01

    Background Completely sequenced plant genomes provide scope for designing a large number of microsatellite markers, which are useful in various aspects of crop breeding and genetic analysis. With the objective of developing genic but non-coding microsatellite (GNMS) markers for the rice (Oryza sativa L.) genome, we characterized the frequency and relative distribution of microsatellite repeat-motifs in 18,935 predicted protein coding genes including 14,308 putative promoter sequences. Results We identified 19,555 perfect GNMS repeats with densities ranging from 306.7/Mb in chromosome 1 to 450/Mb in chromosome 12 with an average of 357.5 GNMS per Mb. The average microsatellite density was maximum in the 5' untranslated regions (UTRs) followed by those in introns, promoters, 3'UTRs and minimum in the coding sequences (CDS). Primers were designed for 17,966 (92%) GNMS repeats, including 4,288 (94%) hypervariable class I types, which were bin-mapped on the rice genome. The GNMS markers were most polymorphic in the intronic region (73.3%) followed by markers in the promoter region (53.3%) and least in the CDS (26.6%). The robust polymerase chain reaction (PCR) amplification efficiency and high polymorphic potential of GNMS markers over genic coding and random genomic microsatellite markers suggest their immediate use in efficient genotyping applications in rice. A set of these markers could assess genetic diversity and establish phylogenetic relationships among domesticated rice cultivar groups. We also demonstrated the usefulness of orthologous and paralogous conserved non-coding microsatellite (CNMS) markers, identified in the putative rice promoter sequences, for comparative physical mapping and understanding of evolutionary and gene regulatory complexities among rice and other members of the grass family. The divergence between long-grained aromatics and subspecies japonica was estimated to be more recent (0.004 Mya) compared to short-grained aromatics from japonica

  14. Genome-wide identification and analysis of rice genes preferentially expressed in pollen at an early developmental stage.

    PubMed

    Nguyen, Tien Dung; Moon, Sunok; Nguyen, Van Ngoc Tuyet; Gho, Yunsil; Chandran, Anil Kumar Nalini; Soh, Moon-Soo; Song, Jong Tae; An, Gynheung; Oh, Sung Aeong; Park, Soon Ki; Jung, Ki-Hong

    2016-09-01

    Microspore production using endogenous developmental programs has not been well studied. The main limitation is the difficulty in identifying genes preferentially expressed in pollen grains at early stages. To overcome this limitation, we collected transcriptome data from anthers and microspore/pollen and performed meta-expression analysis. Subsequently, we identified 410 genes showing preferential expression patterns in early developing pollen samples of both japonica and indica cultivars. The expression patterns of these genes are distinguishable from genes showing pollen mother cell or tapetum-preferred expression patterns. Gene Ontology enrichment and MapMan analyses indicated that microspores in rice are closely linked with protein degradation, nucleotide metabolism, and DNA biosynthesis and regulation, while the pollen mother cell or tapetum are strongly associated with cell wall metabolism, lipid metabolism, secondary metabolism, and RNA biosynthesis and regulation. We also generated transgenic lines under the control of the promoters of eight microspore-preferred genes and confirmed the preferred expression patterns in plants using the GUS reporting system. Furthermore, cis-regulatory element analysis revealed that pollen specific elements such as POLLEN1LELAT52, and 5659BOXLELAT5659 were commonly identified in the promoter regions of eight rice genes with more frequency than estimation. Our study will provide new sights on early pollen development in rice, a model crop plant.

  15. Characterization and gene cloning of the rice (Oryza sativa L.) dwarf and narrow-leaf mutant dnl3.

    PubMed

    Shi, L; Wei, X J; Adedze, Y M N; Sheng, Z H; Tang, S Q; Hu, P S; Wang, J L

    2016-09-16

    The dwarf and narrow-leaf rice (Oryza sativa L.) mutant dnl3 was isolated from the Japonica cultivar Zhonghua 11 (wild-type). dnl3 exhibited pleiotropic developmental defects. The narrow-leaf phenotype resulted from a marked reduction in the number of vascular bundles, while the dwarf stature was caused by the formation of foreshortened internodes and a reduced number of parenchyma cells. The suggestion that cell division is impaired in the mutant was consistent with the transcriptional behavior of various genes associated with cell division. The mutant was less responsive to exogenously supplied gibberellic acid than the wild-type, and profiling the transcription of genes involved in gibberellin synthesis and response revealed that a lesion in the mutant affected gibberellin signal transduction. The dnl3 phenotype was inherited as a single-dominant gene, mapping within a 19.1-kb region of chromosome 12, which was found to harbor three open reading frames. Resequencing the open reading frames revealed that the mutant carried an allele at one of the three genes that differed from the wild-type sequence by 2-bp deletions; this gene encoded a cellulose synthase-like D4 (CSLD4) protein. Therefore, OsCSLD4 is a candidate gene for DNL3. DNL3 was expressed in all of the rice organs tested at the heading stage, particularly in the leaves, roots, and culms. These results suggest that DNL3 plays important roles in rice leaf morphogenesis and vegetative development.

  16. 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

  17. Molecular phylogenomic study and the role of exogenous spermidine in the metabolic adjustment of endogenous polyamine in two rice cultivars under salt stress.

    PubMed

    Saha, Jayita; Giri, Kalyan

    2017-04-20

    Compelling evidences anticipated the well acclamation of involvement of exogenous and endogenous polyamines (PAs) in conferring salt tolerance in plants. Intracellular PA's anabolism and catabolism should have contributed to maintain endogenous PAs homeostasis to induce stress signal networks. In this report, the evolutionary study has been conducted to reveal the phylogenetic relationship of genes encoding enzymes of the anabolic and catabolic pathway of PAs among the five plant lineages including green algae, moss, lycophyte, dicot and monocot along with their respective exon-intron structural patterns. Our results indicated that natural selection pressure had considerable influence on the ancestral PA metabolic pathway coding genes of land plants. PA metabolic genes have undergone gradual evolution by duplication and diversification process leading to subsequent structural modification through exon-intron gain and loss events to acquire specific function under environmental stress conditions. We have illuminated on the potential regulation of both the pathways by investigating the real-time expression analyses of PA metabolic pathway related enzyme coding genes at the transcriptional level in root and shoot tissues of two indica rice varieties, namely IR 36 (salt sensitive) and Nonabokra (salt-tolerant) in response to salinity in presence or absence of exogenous spermidine (Spd) treatment. Additionally, we have performed tissue specific quantification of the intracellular PAs and tried to draw probable connection between the PA metabolic pathway activation and endogenous PAs accumulation. Our results successfully enlighten the fact that how exogenous Spd in presence or absence of salt stress adjust the intracellular PA pathways to equilibrate the cellular PAs that would have been attributed to plant salt tolerance.

  18. Efficient in vitro plant regeneration through leaf base derived callus cultures of abiotic stress sensitive popular Asian Indica rice cultivar IR 64 (Oryza sativa L.).

    PubMed

    Mohana Priya, A; Karutha Pandian, S; Ramesh, M

    2011-12-01

    A simple and efficient protocol has been developed for high frequency plant regeneration through callus cultures derived from leaf bases of abiotic stress sensitive Asian indica rice variety IR 64. Leaf base segments (4-5 mm diameter) were obtained from 6-day-old dark grown seedlings germinated on halfstrength Murashige and Skoog medium and cultured on MS medium supplemented with different concentrations of 2,4-Dichlorophenoxyacetic acid (2.2-18 μM) and Kinetin (0.2-1.7 μM). Among the various combinations, 13.5 μM 2,4-D and 1.3 μM Kn resulted in high callus induction frequency (87.5%) with a maximum fresh weight of 0.22 g per segment. The regeneration frequency was 75.5% with multiple shoots within 3 weeks of transfer on MS medium supplemented with 13.3 μM 6-benzylamino purine and 8 μM Naphthaleneacetic acid. The shoots readily rooted on half-strength MS medium without any hormonal supplements. In vitro regenerated plantlets with multiple shoots and roots were transferred to sterile soil and vermiculite mix and maintained in shade house for 30 days. Complete plantlets were then transferred to nursery and acclimatized to the external environment until seed set. RAPD profile reveals monomorphism and thus confirming the genetic stability of the regenerated plants. This method has the potential for both direct as well as indirect method of transformation for the production of genetically modified plants.

  19. Pathogen effectors and plant immunity determine specialization of the blast fungus to rice subspecies

    PubMed Central

    Liao, Jingjing; Huang, Huichuan; Meusnier, Isabelle; Adreit, Henri; Ducasse, Aurélie; Bonnot, François; Pan, Lei; He, Xiahong; Kroj, Thomas; Fournier, Elisabeth; Tharreau, Didier; Gladieux, Pierre; Morel, Jean-Benoit

    2016-01-01

    Understanding how fungi specialize on their plant host is crucial for developing sustainable disease control. A traditional, centuries-old rice agro-system of the Yuanyang terraces was used as a model to show that virulence effectors of the rice blast fungus Magnaporthe oryzaeh play a key role in its specialization on locally grown indica or japonica local rice subspecies. Our results have indicated that major differences in several components of basal immunity and effector-triggered immunity of the japonica and indica rice varieties are associated with specialization of M. oryzae. These differences thus play a key role in determining M. oryzae host specificity and may limit the spread of the pathogen within the Yuanyang agro-system. Specifically, the AVR-Pia effector has been identified as a possible determinant of the specialization of M. oryzae to local japonica rice. DOI: http://dx.doi.org/10.7554/eLife.19377.001 PMID:28008850

  20. Marker-free transgenic (MFT) near-isogenic introgression lines (NIILs) of 'golden' indica rice (cv. IR64) with accumulation of provitamin A in the endosperm tissue.

    PubMed

    Baisakh, Niranjan; Rehana, Sayda; Rai, Mayank; Oliva, Norman; Tan, Jing; Mackill, David J; Khush, Gurdev S; Datta, Karabi; Datta, Swapan K

    2006-07-01

    We have developed near-isogenic introgression lines (NIILs) of an elite indica rice cultivar (IR64) with the genes for beta-carotene biosynthesis from dihaploid (DH) derivatives of golden japonica rice (cv. T309). A careful analysis of the DH lines indicated the integration of the genes of interest [phytoene synthase (psy) and phytoene desaturase (crtI)] and the selectable marker gene (hygromycin phosphotransferase, hph) in two unlinked loci. During subsequent crossing, progenies could be obtained carrying only the locus with psy and crtI, which was segregated independently from the locus containing the hph gene during meiotic segregation. The NIILs (BC(2)F(2)) showed maximum similarity with the recurrent parent cultivar IR64. Further, progenies of two NIILs were devoid of any fragments beyond the left or right border, including the chloramphenicol acetyltransferase (cat) antibiotic resistance gene of the transformation vector. Spectrophotometric readings showed the accumulation of up to 1.06 microg total carotenoids, including beta-carotene, in 1 g of the endosperm. The accumulation of beta-carotene was also evident from the clearly visible yellow colour of the polished seeds.

  1. Relationship of cooked rice nutritionally-important starch fractions with other physicochemical properties.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sixteen rice cultivars representing 5 cytosine-thymine repeat (CTn) microsatellite genetic marker groups were analyzed for their cooked rice nutritionally-important starch fractions (rapidly digestible, slowly digestible, and resistant starch), basic grain quality indices (apparent amylose, crude pr...

  2. 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.

  3. A putative gene sbe3-rs for resistant starch mutated from SBE3 for starch branching enzyme in rice (Oryza sativa L.).

    PubMed

    Yang, Ruifang; Sun, Chunlong; Bai, Jianjiang; Luo, Zhixiang; Shi, Biao; Zhang, Jianming; Yan, Wengui; Piao, Zhongze

    2012-01-01

    Foods high in resistant starch (RS) are beneficial to prevent various diseases including diabetes, colon cancers, 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 population. A japonica mutant 'Jiangtangdao 1' (RS = 11.67%) was crossed with an indica cultivar 'Miyang 23' (RS = 0.41%). The mutant sbe3-rs that explained 60.4% of RS variation was mapped between RM6611 and RM13366 on chromosome 2 (LOD = 36) using 178 F(2) plants genotyped with 106 genome-wide polymorphic SSR markers. Using 656 plants from four F(3:4) families, sbe3-rs was fine mapped to a 573.3 Kb region between InDel 2 and InDel 6 using one STS, five SSRs and seven InDel markers. SBE3 which codes for starch branching enzyme was identified as a candidate gene within the putative region. Nine pairs of primers covering 22 exons were designed to sequence genomic DNA of the wild type for SBE3 and the mutant for sbe3-rs comparatively. Sequence analysis identified a missense mutation site where Leu-599 of the wild was changed to Pro-599 of the mutant in the SBE3 coding region. Because the point mutation resulted in the loss of a restriction enzyme site, sbe3-rs was not digested by a CAPS marker for SpeI site while SBE3 was. Co-segregation of the digestion pattern with RS content among 178 F(2) plants further supported sbe3-rs responsible for RS in rice. As a result, the CAPS marker could be used in marker-assisted breeding to develop rice cultivars with elevated RS which is otherwise difficult to accurately assess in crops. Transgenic technology should be employed for a definitive conclusion of the sbe3-rs.

  4. Tryptophan Enhancement of Somatic Embryogenesis in Rice 1

    PubMed Central

    Siriwardana, Sunitha; Nabors, Murray W.

    1983-01-01

    Cereal embryos can produce two types of callus. One type, termed “embryogenic,” consists of small meristematic-like cells and gives rise to many plants by somatic embryogenesis if placed on a suitable regeneration medium. The other is termed “nonembryogenic” and consists of long tubular cells which gives rise to few or no plants. High concentrations of tryptophan increased the formation of embryogenic callus in three rice cultivars (Oryza sativa L. Calrose 76, Pokkali, and IR 36) but not in four others (Mahsuri, Bg 400-1, H4, and Giza 159). The best concentration of tryptophan for Pokkali and Calrose 76 was 100 micrograms per milliliter, and for IR 36, 50 micrograms per milliliter. Indoleacetic acid at 100 micrograms per milliliter promoted an effect similar to that of tryptophan on Calrose 76. The difference between japonica (Calrose 76, Giza 159) and indica (Pokkali, IR 36) varieties is not the causal factor for the difference in response to tryptophan. Kinetin does not appear to be a requirement for embryogenic callus formation in Calrose 76. Plant regeneration from Calrose 76 embryogenic callus occurred at low levels in media containing no hormones. 6-benzyladenine, or 2,3,5-triiodobenzoic acid but not indoleacetic acid at 0.1 to 0.5 micrograms per milliliter significantly increased regeneration. Images Fig. 1 PMID:16663163

  5. A novel gene, Pi40(t), linked to the DNA markers derived from NBS-LRR motifs confers broad spectrum of blast resistance in rice.

    PubMed

    Jeung, J U; Kim, B R; Cho, Y C; Han, S S; Moon, H P; Lee, Y T; Jena, K K

    2007-11-01

    Rice blast disease caused by Magnaporthe grisea is a continuous threat to stable rice production worldwide. In a modernized agricultural system, the development of varieties with broad-spectrum and durable resistance to blast disease is essential for increased rice production and sustainability. In this study, a new gene is identified in the introgression line IR65482-4-136-2-2 that has inherited the resistance gene from an EE genome wild Oryza species, O. australiensis (Acc. 100882). Genetic and molecular analysis localized a major resistance gene, Pi40(t), on the short arm of chromosome 6, where four blast resistance genes (Piz, Piz-5, Piz-t, and Pi9) were also identified, flanked by the markers S2539 and RM3330. Through e-Landing, 14 BAC/PAC clones within the 1.81-Mb equivalent virtual contig were identified on Rice Pseudomolecule3. Highly stringent primer sets designed for 6 NBS-LRR motifs located within PAC clone P0649C11 facilitated high-resolution mapping of the new resistance gene, Pi40(t). Following association analysis and detailed haplotyping approaches, a DNA marker, 9871.T7E2b, was identified to be linked to the Pi40(t) gene at the 70 Kb chromosomal region, and differentiated the Pi40(t) gene from the LTH monogenic differential lines possessing genes Piz, Piz-5, Piz-t, and Pi-9. Pi40(t) was validated using the most virulent isolates of Korea as well as the Philippines, suggesting a broad spectrum for the resistance gene. Marker-assisted selection (MAS) and pathotyping of BC progenies having two japonica cultivar genetic backgrounds further supported the potential of the resistance gene in rice breeding. Our study based on new gene identification strategies provides insight into novel genetic resources for blast resistance as well as future studies on cloning and functional analysis of a blast resistance gene useful for rice improvement.

  6. Population genomics identifies the origin and signatures of selection of Korean weedy rice.

    PubMed

    He, Qiang; Kim, Kyu-Won; Park, Yong-Jin

    2017-03-01

    Weedy rice is the same biological species as cultivated rice (Oryza sativa); it is also a noxious weed infesting rice fields worldwide. Its formation and population-selective or -adaptive signatures are poorly understood. In this study, we investigated the phylogenetics, population structure and signatures of selection of Korean weedy rice by determining the whole genomes of 30 weedy rice, 30 landrace rice and ten wild rice samples. The phylogenetic tree and results of ancestry inference study clearly showed that the genetic distance of Korean weedy rice was far from the wild rice and near with cultivated rice. Furthermore, 537 genes showed evidence of recent positive or divergent selection, consistent with some adaptive traits. This study indicates that Korean weedy rice originated from hybridization of modern indica/indica or japonica/japonica rather than wild rice. Moreover, weedy rice is not only a notorious weed in rice fields, but also contains many untapped valuable traits or haplotypes that may be a useful genetic resource for improving cultivated rice.

  7. Using the rice diversity panel 1 to develop novel germplasm for breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Rice Diversity Project aims to explore the relationship between genotypic and phenotypic variation in a panel of rice (Oryza sativa) landraces, elite cultivars, and wild ancestors to utilize this broad range of natural variation in rice improvement. The ‘Rice Diversity Panel 1’ (RDP1) is compose...

  8. Genetic diversity and phylogeny of Japanese sake-brewing rice as revealed by AFLP and nuclear and chloroplast SSR markers.

    PubMed

    Hashimoto, Z; Mori, N; Kawamura, M; Ishii, T; Yoshida, S; Ikegami, M; Takumi, S; Nakamura, C

    2004-11-01

    Japanese rice ( Oryza sativa L.) cultivars that are strictly used for the brewing of sake (Japanese rice wine) represent a unique and traditional group. These cultivars are characterized by common traits such as large grain size with low protein content and a large, central white-core structure. To understand the genetic diversity and phylogenetic characteristics of sake-brewing rice, we performed amplified fragment length polymorphism and simple sequence repeat analyses, using 95 cultivars of local and modern sake-brewing rice together with 76 cultivars of local and modern cooking rice. Our analysis of both nuclear and chloroplast genome polymorphisms showed that the genetic diversity in sake-brewing rice cultivars was much smaller than the diversity found in cooking rice cultivars. Interestingly, the genetic diversity within the modern sake-brewing cultivars was about twofold higher than the diversity within the local sake-brewing cultivars, which was in contrast to the cooking cultivars. This is most likely due to introgression of the modern cooking cultivars into the modern sake-brewing cultivars through breeding practices. Cluster analysis and chloroplast haplotype analysis suggested that the local sake-brewing cultivars originated monophyletically in the western regions of Japan. Analysis of variance tests showed that several markers were significantly associated with sake-brewing traits, particularly with the large white-core structure.

  9. 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.

  10. 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.

  11. Production and heterosis analysis of rice (Oryza sativa L.) autotetraploid hybrids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It is hard to achieve good seed set in hybrid rice between cultivarsof the same Oyrza sataiva L sub-species, and even harder in hybrids between the two rice sub-species, indica and japonica. The wider cross has greater hybrid vigor or heterosis. Cytoplasmic male sterile (CMS) system used widely and ...

  12. Identification of Genomic Regions and the Isoamylase Gene for Reduced Grain Chalkiness in Rice

    PubMed Central

    Sun, Wenqian; Zhou, Qiaoling; Yao, Yue; Qiu, Xianjin; Xie, Kun; Yu, Sibin

    2015-01-01

    Grain chalkiness is an important grain quality related to starch granules in the endosperm. A high percentage of grain chalkiness is a major problem because it diminishes grain quality in rice. Here, we report quantitative trait loci identification for grain chalkiness using high-throughput single nucleotide polymorphism genotyping of a chromosomal segment substitution line population in which each line carried one or a few introduced japonica cultivar Nipponbare segments in the genetic background of the indica cultivar ZS97. Ten quantitative trait loci regions were commonly identified for the percentage of grain chalkiness and the degree of endosperm chalkiness. The allelic effects at nine of these quantitative trait loci reduced grain chalkiness. Furthermore, a quantitative trait locus (qPGC8-2) on chromosome 8 was validated in a chromosomal segment substitution line–derived segregation population, and had a stable effect on chalkiness in a multiple-environment evaluation of the near-isogenic lines. Residing on the qPGC8-2 region, the isoamylase gene (ISA1) was preferentially expressed in the endosperm and revealed some nucleotide polymorphisms between two varieties, Nipponbare and ZS97. Transgenic lines with suppression of ISA1 by RNA interference produced grains with 20% more chalkiness than the control. The results support that the gene may underlie qPGC8-2 for grain chalkiness. The multiple-environment trials of the near-isogenic lines also show that combination of the favorable alleles such as the ISA1 gene for low chalkiness and the GS3 gene for long grains considerably improved grain quality of ZS97, which proves useful for grain quality improvement in rice breeding programs. PMID:25790260

  13. 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

  14. Characterization of rice blast resistance gene Pi61(t) in rice germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Identification of resistance (R) genes to races of Magnaporthe oryzae in rice germplasm is essential for the development of rice cultivars with long lasting blast resistance. In the present study, one major quantitative trait locus, qPi93-3, was fine mapped using a recombinant inbred line (RIL), F8 ...

  15. 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

  16. 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

    2016-03-23

    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.

  17. 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 ...

  18. An evolutionarily conserved gene, FUWA, plays a role in determining panicle architecture, grain shape and grain weight in rice.

    PubMed

    Chen, Jun; Gao, He; Zheng, Xiao-Ming; Jin, Mingna; Weng, Jian-Feng; Ma, Jin; Ren, Yulong; Zhou, Kunneng; Wang, Qi; Wang, Jie; Wang, Jiu-Lin; Zhang, Xin; Cheng, Zhijun; Wu, Chuanyin; Wang, Haiyang; Wan, Jian-Min

    2015-08-01

    Plant breeding relies on creation of novel allelic combinations for desired traits. Identification and utilization of beneficial alleles, rare alleles and evolutionarily conserved genes in the germplasm (referred to as 'hidden' genes) provide an effective approach to achieve this goal. Here we show that a chemically induced null mutation in an evolutionarily conserved gene, FUWA, alters multiple important agronomic traits in rice, including panicle architecture, grain shape and grain weight. FUWA encodes an NHL domain-containing protein, with preferential expression in the root meristem, shoot apical meristem and inflorescences, where it restricts excessive cell division. Sequence analysis revealed that FUWA has undergone a bottleneck effect, and become fixed in landraces and modern cultivars during domestication and breeding. We further confirm a highly conserved role of FUWA homologs in determining panicle architecture and grain development in rice, maize and sorghum through genetic transformation. Strikingly, knockdown of the FUWA transcription level by RNA interference results in an erect panicle and increased grain size in both indica and japonica genetic backgrounds. This study illustrates an approach to create new germplasm with improved agronomic traits for crop breeding by tapping into evolutionary conserved genes.

  19. 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

  20. A Novel Naturally Occurring Class I 5-Enolpyruvylshikimate-3-Phosphate Synthase from Janibacter sp. Confers High Glyphosate Tolerance to Rice.

    PubMed

    Yi, Shu-yuan; Cui, Ying; Zhao, Yan; Liu, Zi-duo; Lin, Yong-jun; Zhou, Fei

    2016-01-12

    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.

  1. 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.

  2. 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....

  3. 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.

  4. A relative resistance Ratio for Evaluation of Stem Borer Susceptibility Among Sugarcane Cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Mexican rice borer, Eoreuma loftini (Dyar), is a major pest of sugarcane in Louisiana and Texas. Cultivar resistance to E. loftini was evaluated in commercial and experimental sugarcane cultivars in four replicated field studies between 2009 and 2012. A relative resistance ratio was developed t...

  5. A gene block causing cross-incompatibility hidden in wild and cultivated rice.

    PubMed Central

    Matsubara, Kazuki; Khin-Thidar; Sano, Yoshio

    2003-01-01

    Unidirectional cross-incompatibility was detected in advanced generations of backcrossing between wild (Oryza rufipogon) and cultivated (O. sativa) rice strains. The near-isogenic line (NIL) of T65wx (Japonica type) carrying an alien segment of chromosome 6 from a wild strain gave a reduced seed setting only when crossed with T65wx as the male. Cytological observations showed that abortion of hybrid seeds occurred as a consequence of a failure of early endosperm development followed by abnormalities in embryo development. The genetic basis of cross-incompatibility reactions in the female and male was investigated by testcrosses using recombinant inbred lines (RILs) that were established through dissecting the introgressed segments of wild and cultivated (Indica type) strains. The results revealed that the cross-incompatibility reaction was controlled by Cif in the female and by cim in the male. When the female plant with Cif was crossed with the male plant with cim, a failure of early endosperm development was observed in the hybrid zygotes. Among cultivars of O. sativa, cim was distributed predominantly in the Japonica type but not in the Indica type. In addition, a dominant suppressor, Su-Cif, which changes the reaction in the female from incompatible to compatible was proposed to present near the centromere of chromosome 6 of the Indica type. Further, the death of young F(1) zygotes was controlled by the parental genotypes rather than by the genotype of the hybrid zygote itself since all three genes acted sporophytically, which strongly suggests an involvement of parent-of-origin effects. We discuss the results in relation to the origin of a crossing barrier as well as their maintenance within the primary gene pool. PMID:14504241

  6. Head rice rate measurement based on concave point matching

    NASA Astrophysics Data System (ADS)

    Yao, Yuan; Wu, Wei; Yang, Tianle; Liu, Tao; Chen, Wen; Chen, Chen; Li, Rui; Zhou, Tong; Sun, Chengming; Zhou, Yue; Li, Xinlu

    2017-01-01

    Head rice rate is an important factor affecting rice quality. In this study, an inflection point detection-based technology was applied to measure the head rice rate by combining a vibrator and a conveyor belt for bulk grain image acquisition. The edge center mode proportion method (ECMP) was applied for concave points matching in which concave matching and separation was performed with collaborative constraint conditions followed by rice length calculation with a minimum enclosing rectangle (MER) to identify the head rice. Finally, the head rice rate was calculated using the sum area of head rice to the overall coverage of rice. Results showed that bulk grain image acquisition can be realized with test equipment, and the accuracy rate of separation of both indica rice and japonica rice exceeded 95%. An increase in the number of rice did not significantly affect ECMP and MER. High accuracy can be ensured with MER to calculate head rice rate by narrowing down its relative error between real values less than 3%. The test results show that the method is reliable as a reference for head rice rate calculation studies.

  7. Head rice rate measurement based on concave point matching

    PubMed Central

    Yao, Yuan; Wu, Wei; Yang, Tianle; Liu, Tao; Chen, Wen; Chen, Chen; Li, Rui; Zhou, Tong; Sun, Chengming; Zhou, Yue; Li, Xinlu

    2017-01-01

    Head rice rate is an important factor affecting rice quality. In this study, an inflection point detection-based technology was applied to measure the head rice rate by combining a vibrator and a conveyor belt for bulk grain image acquisition. The edge center mode proportion method (ECMP) was applied for concave points matching in which concave matching and separation was performed with collaborative constraint conditions followed by rice length calculation with a minimum enclosing rectangle (MER) to identify the head rice. Finally, the head rice rate was calculated using the sum area of head rice to the overall coverage of rice. Results showed that bulk grain image acquisition can be realized with test equipment, and the accuracy rate of separation of both indica rice and japonica rice exceeded 95%. An increase in the number of rice did not significantly affect ECMP and MER. High accuracy can be ensured with MER to calculate head rice rate by narrowing down its relative error between real values less than 3%. The test results show that the method is reliable as a reference for head rice rate calculation studies. PMID:28128315

  8. Impacts of seeding rate on interactions between rice and rice water weevils.

    PubMed

    Stout, M J; Harrell, D; Tindall, K V; Bond, J

    2009-10-01

    The rice water weevil, Lissorhoptrus oryzophilus Kuschel, is the most widely distributed and destructive early season insect pest of rice, Oryza sativa L., in the United States. Economic losses result primarily from feeding by the larval stage of this insect on the roots of flooded rice plants. Prior studies suggest that infestations of rice water weevil larvae are more severe at low plant densities. Moreover, because feeding by the rice water weevil reduces rice plant tillering, a process particularly important to yield at low seeding rates, infestations by weevil larvae may have a greater impact on rice yields when rice is seeded at low rates. In total, six experiments were conducted over a 3-yr period in Louisiana and Missouri to investigate the impacts of rice seeding rate on levels of infestations by, and yield losses from, the rice water weevil. An inverse relationship between seeding rate and densities of rice water weevil larvae and pupae on a per area basis was found in two of the six experiments. Furthermore, in two of the three experiments conducted with 'Bengal' (a susceptible cultivar) in Louisiana, percentages of yield loss were significantly higher at lower seeding rates than at higher seeding rates. Overall, these results indicate that rice sown at low rates is more vulnerable to infestation by rice water weevils and more susceptible to yield losses from weevil injury. The significance of these findings in light of recent trends toward the use of lower seeding rates in drill-seeded rice is discussed.

  9. Cytoplasmic-genetic male sterility gene provides direct evidence for some hybrid rice recently evolving into weedy rice

    PubMed Central

    Zhang, Jingxu; Lu, Zuomei; Dai, Weimin; Song, Xiaoling; Peng, Yufa; Valverde, Bernal E.; Qiang, Sheng

    2015-01-01

    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. PMID:26012494

  10. 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.

  11. Map-Based Cloning of Seed Dormancy1-2 Identified a Gibberellin Synthesis Gene Regulating the Development of Endosperm-Imposed Dormancy in Rice1

    PubMed Central

    Ye, Heng; Feng, Jiuhuan; Zhang, Lihua; Zhang, Jinfeng; Mispan, Muhamad S.; Cao, Zhuanqin; Beighley, Donn H.; Yang, Jianchang; Gu, Xing-You

    2015-01-01

    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

  12. 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

  13. 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.

  14. 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.

  15. A killer-protector system regulates both hybrid sterility and segregation distortion in rice.

    PubMed

    Yang, Jiangyi; Zhao, Xiaobo; Cheng, Ke; Du, Hongyi; Ouyang, Yidan; Chen, Jiongjiong; Qiu, Shuqing; Huang, Jianyan; Jiang, Yunhe; Jiang, Liwen; Ding, Jihua; Wang, Jia; Xu, Caiguo; Li, Xianghua; Zhang, Qifa

    2012-09-14

    Hybrid sterility is a major form of postzygotic reproductive isolation that restricts gene flow between populations. Cultivated rice (Oryza sativa L.) consists of two subspecies, indica and japonica; inter-subspecific hybrids are usually sterile. We show that a killer-protector system at the S5 locus encoded by three tightly linked genes [Open Reading Frame 3 (ORF3) to ORF5] regulates fertility in indica-japonica hybrids. During female sporogenesis, the action of ORF5+ (killer) and ORF4+ (partner) causes endoplasmic reticulum (ER) stress. ORF3+ (protector) prevents ER stress and produces normal gametes, but ORF3- cannot prevent ER stress, resulting in premature programmed cell death and leads to embryo-sac abortion. Preferential transmission of ORF3+ gametes results in segregation distortion in the progeny. These results add to our understanding of differences between indica and japonica rice and may aid in rice genetic improvement.

  16. [HPLC-FPS establishment of Iris japonica Thunb].

    PubMed

    Zhang, Jin-zhuan; Luo, Ai-qin; Liu, Li-wen; Fang, Min; Deng, Yu-lin

    2006-09-01

    Samples extracted from the root of Iris japonica Thunb were analyzed and the optimal HPLC chromatographic conditions was confirmed. Through analyzing the chromatography, the HPLC-FPS of Iris japonica Thunb was established.

  17. Amplifying the benefits of agroecology by using the right cultivars.

    PubMed

    Noguera, D; Laossi, K-R; Lavelle, P; De Carvalho, M H Cruz; Asakawa, N; Botero, C; Barot, S

    2011-10-01

    Tropical soils are particularly vulnerable to fertility losses due to their low capacity to retain organic matter and mineral nutrients. This urges the development of new agricultural practices to manage mineral nutrients and organic matter in a more sustainable way while relying less on fertilizer inputs. Two methods pertaining to ecological engineering and agroecology have been tested with some success: (1) the addition of biochar to the soil, and (2) the maintenance of higher earthworm densities. However, modern crop varieties have been selected to be adapted to agricultural practices and to the soil conditions they lead to and common cultivars might not be adapted to new practices. Using rice as a model plant, we compared the responsiveness to biochar and earthworms of five rice cultivars with contrasted selection histories. These cultivars had contrasted responsivenesses to earthworms, biochar, and the combination of both. The mean relative increase in grain biomass, among all treatments and cultivars, was 94% and 32%, respectively, with and without fertilization. Choosing the best combination of cultivar and treatment led to a more than fourfold increase in this mean benefit (a 437% and a 353% relative increase in grain biomass, respectively, with and without fertilization). Besides, the more rustic cultivar, a local landrace adapted to diverse and difficult conditions, responded the best to earthworms in terms of total biomass, while a modern common cultivar responded the best in term of grain biomass. This suggests that cultivars could be selected to amplify the benefit of biochar- and earthworm-based practices. Overall, selecting new cultivars interacting more closely with soil organisms and soil heterogeneity could increase agriculture sustainability, fostering the positive feedback loop between soils and plants that has evolved in natural ecosystems.

  18. 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

  19. Rice growth monitoring using simulated compact polarimetric C band SAR

    NASA Astrophysics Data System (ADS)

    Yang, Zhi; Li, Kun; Liu, Long; Shao, Yun; Brisco, Brian; Li, Weiguo

    2014-12-01

    In this study, a set of nine compact polarimetric (CP) images were simulated from polarimetric RADARSAT-2 data acquired over a test site containing two types of rice field in Jiangsu province, China. The types of rice field in the test site were (1) transplanted hybrid rice fields, and (2) direct-sown japonica rice fields. Both types have different yields and phenological stages. As a first step, the two types of rice field were distinguished with 94% and 86% accuracy respectively through analyzing CP synthetic aperture radar (SAR) observations and their behavior in terms of scattering mechanisms during the rice growth season. The focus was then on phenology retrieval for each type of rice field. A decision tree (DT) algorithm was built to fulfill the precise retrieval of rice phenological stages, in which seven phenological stages were discriminated. The key criterion for each phenological stage was composed of 1-4 CP parameters, some of which were first used for rice phenology retrieval and found to be very sensitive to rice phenological changes. The retrieval results were verified at parcel level for a set of 12 stands of rice and up to nine observation dates per stand. This gave an accuracy of 88-95%. Throughout the phenology retrieval process, only simulated CP data were used, without any auxiliary data. These results demonstrate the potential of CP SAR for rice growth monitoring applications.

  20. Analysis of the genetic diversity of Lonicera japonica Thumb. using inter-simple sequence repeat markers.

    PubMed

    He, H Y; Zhang, D; Qing, H; Yang, Y

    2017-01-23

    Inter-simple sequence repeats (ISSRs) were used to analyze the genetic diversity of 21 accessions obtained from four provinces in China, Shandong, Henan, Hebei, and Sichuan. A total of 272 scored bands were generated using the eight primers previously screened across 21 accessions, of which 267 were polymorphic (98.16%). Genetic similarity coefficients varied from 0.4816 to 0.9118, with an average of 0.6337. The UPGMA dendrogram grouped 21 accessions into two main clusters. Cluster A comprised four Lonicera macranthoides Hand. Mazz. accessions, of which J10 was found to be from Sichuan, and J17, J18, and J19 were found to be from Shandong. Cluster B comprised 17 Lonicera japonica Thumb. accessions, divided into the wild accession J16 and the other 16 cultivars. The results of the principal component analysis were comparable to the cluster analysis. Therefore, the ISSR markers could be effectively used to distinguish interspecific and intraspecific variations, which may facilitate identification of Lonicera japonica cultivars for planting, medicinal use, and germplasm conservation.

  1. Conserved and novel heat stress-responsive microRNAs were identified by deep sequencing in Saccharina japonica (Laminariales, Phaeophyta).

    PubMed

    Liu, Fuli; Wang, Wenjun; Sun, Xiutao; Liang, Zhourui; Wang, Feijiu

    2015-07-01

    As a temperate-cold species, Saccharina japonica often suffers heat stress when it is transplanted to temperate and subtropical zones. Study the heat stress response and resistance mechanism of Saccharina is of great significance for understanding the acclimation to heat stress under domestication as well as for breeding new cultivars with heat stress resistance. In this study, we identified a set of heat stress-responsive miRNAs and analysed their regulation during the heat stress response. CO (control) and heat stress (HS) sRNA libraries were constructed and sequenced. Forty-nine known miRNAs and 75 novel miRNAs were identified, of which seven known and 25 novel miRNAs were expressed differentially under heat stress. Quantitative PCR of six selected miRNAs confirmed that these loci were responsive to heat stress. Thirty-nine and 712 genes were predicted to be targeted by the seven known miRNAs and 25 novel miRNAs, respectively. Gene function and pathway analyses showed that these genes probably play important roles in S. japonica heat stress tolerance. The miRNAs identified represent the first set of heat-responsive miRNAs identified from S. japonica, and their identification can help elucidate the heat stress response and resistance mechanisms in S. japonica.

  2. Identification and linkage analysis of a new rice bacterial blight resistance gene from XM14, a mutant line from IR24

    PubMed Central

    Busungu, Constantine; Taura, Satoru; Sakagami, Jun-Ichi; Ichitani, Katsuyuki

    2016-01-01

    Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is a chief factor limiting rice productivity worldwide. XM14, a rice mutant line resistant to Xoo, has been obtained by treating IR24, which is susceptible to six Philippine Xoo races and six Japanese Xoo races, with N-methyl-N-nitrosourea. XM14 showed resistance to six Japanese Xoo races. The F2 population from XM14 × IR24 clearly showed 1 resistant : 3 susceptible segregation, suggesting control of resistance by a recessive gene. The approximate chromosomal location of the resistance gene was determined using 10 plants with shortest lesion length in the F2 population from XM14 × Koshihikari, which is susceptible to Japanese Xoo races. DNA marker-assisted analysis revealed that the gene was located on chromosome 3. IAS16 line carries IR24 genetic background with a Japonica cultivar Asominori segment of chromosome 3, on which the resistance gene locus was thought to be located. The F2 population from IAS16 × XM14 showed a discrete distribution. Linkage analysis indicated that the gene is located around the centromeric region. The resistance gene in XM14 was a new gene, named XA42. This gene is expected to be useful for resistance breeding programs and for genetic analysis of Xoo resistance. PMID:27795689

  3. Identification and linkage analysis of a new rice bacterial blight resistance gene from XM14, a mutant line from IR24.

    PubMed

    Busungu, Constantine; Taura, Satoru; Sakagami, Jun-Ichi; Ichitani, Katsuyuki

    2016-09-01

    Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is a chief factor limiting rice productivity worldwide. XM14, a rice mutant line resistant to Xoo, has been obtained by treating IR24, which is susceptible to six Philippine Xoo races and six Japanese Xoo races, with N-methyl-N-nitrosourea. XM14 showed resistance to six Japanese Xoo races. The F2 population from XM14 × IR24 clearly showed 1 resistant : 3 susceptible segregation, suggesting control of resistance by a recessive gene. The approximate chromosomal location of the resistance gene was determined using 10 plants with shortest lesion length in the F2 population from XM14 × Koshihikari, which is susceptible to Japanese Xoo races. DNA marker-assisted analysis revealed that the gene was located on chromosome 3. IAS16 line carries IR24 genetic background with a Japonica cultivar Asominori segment of chromosome 3, on which the resistance gene locus was thought to be located. The F2 population from IAS16 × XM14 showed a discrete distribution. Linkage analysis indicated that the gene is located around the centromeric region. The resistance gene in XM14 was a new gene, named XA42. This gene is expected to be useful for resistance breeding programs and for genetic analysis of Xoo resistance.

  4. [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.

  5. Development of strategies to manage rice blast disease in the USA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice blast disease has been a serious threat to stable rice production in the southern USA. Blast disease has been causing yield losses for decades. Severity of blast epidemics has been always influenced by a combination of the following three factors: 1) rice cultivars deployed with different comb...

  6. Low pH-induced changes of antioxidant enzyme and ATPase activities in the roots of rice (Oryza sativa L.) seedlings.

    PubMed

    Zhang, Yi-Kai; Zhu, De-Feng; Zhang, Yu-Ping; Chen, Hui-Zhe; Xiang, Jing; Lin, Xian-Qing

    2015-01-01

    Soil acidification is the main problem in the current rice production. Here, the effects of low pH on the root growth, reactive oxygen species metabolism, plasma membrane functions, and the transcript levels of the related genes were investigated in rice seedlings (Oryza sativa L.) in a hydroponic system at pH 3.5, 4.5, and 5.5. There were two hybrid rice cultivars in this trial, including Yongyou 12 (YY12, a japonica hybrid) and Zhongzheyou 1 (ZZY1, an indica hybrid). Higher H+ activity markedly decreased root length, the proportion of fine roots, and dry matter production, but induced a significant accumulation of hydrogen peroxide (H2O2), and led to serious lipid peroxidation in the roots of the two varieties. The transcript levels of copper/zinc superoxide dismutase 1 (Cu/Zn SOD1), copper/zinc superoxide dismutase 2 (Cu/Zn SOD2), catalase A (CATA) and catalase B (CATB) genes in YY12 and ZZY1 roots were significantly down-regulated after low pH exposure for two weeks. Meanwhile, a significant decrease was observed in the expression of the P-type Ca2+-ATPases in roots at pH 3.5. The activities of antioxidant enzymes (SOD, CAT) and plasma membrane (PM) Ca2+-ATPase in the two varieties were dramatically inhibited by strong rhizosphere acidification. However, the expression levels of ascorbate peroxidase 1 (APX1) and PM H+-ATPase isoform 7 were up-regulated under H+ stress compared with the control. Significantly higher activities of APX and PM H+-ATPase could contribute to the adaptation of rice roots to low pH.

  7. 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.

  8. Genetic mapping of a QTL controlling source-sink size and heading date in rice.

    PubMed

    Zhan, Xiaodeng; Sun, Bin; Lin, Zechuan; Gao, Zhiqiang; Yu, Ping; Liu, Qunen; Shen, Xihong; Zhang, Yingxin; Chen, Daibo; Cheng, Shihua; Cao, Liyong

    2015-10-25

    Source size, sink size and heading date (HD) are three important classes of traits that determine the productivity of rice. In this study, a set of recombinant inbred lines (RILs) derived from the cross between an elite indica line Big Grain1 (BG1) and a japonica line Xiaolijing (XLJ) were used to map quantitative trait loci (QTLs) for source-sink size and heading date. Totally, thirty-one QTLs for source size, twenty-two for sink size, four for heading date and seven QTL clusters which included QTLs for multiple traits were identified in three environmental trials. Thirty QTLs could be consistently detected in at least two trials and generally located in the clusters. Using a set of BC4F2 lines, the QTL cluster in C5-1-C5-2 on chromosome 5 was validated to be a major QTL pleiotropically affecting heading date, source size (flag leaf area) and panicle type (neck length of panicle, primary branching number and the ratio of secondary branching number to primary branching number), and was narrowed down to a 309.52Kb region. QTL clusters described above have a large effect on source-sink size and/or heading date, therefore they should be good resources to improve the adaptability and high yield potential of cultivars genetically.

  9. 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,...

  10. 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...

  11. Natural variation in the glucose content of dilute sulfuric acid-pretreated rice straw liquid hydrolysates: implications for bioethanol production.

    PubMed

    Goda, Takashi; Teramura, Hiroshi; Suehiro, Miki; Kanamaru, Kengo; Kawaguchi, Hideo; Ogino, Chiaki; Kondo, Akihiko; Yamasaki, Masanori

    2016-05-01

    Rice straw is a promising resource for bioethanol production. Because the glucose content of pretreatment liquid hydrolysates is highly correlated with ethanol yield, the selection of appropriate rice cultivars is essential. The glucose content in liquid hydrolysates of pretreated rice straws of 208 diverse cultivars was evaluated in natural field in 2013 and 2014 using a novel high-throughput system. The glucose content of the rice straw samples varied across cultivars and was affected by environmental factors such as temperature and solar radiation. Several high-quality cultivars exhibiting high glucose content in both years were identified. The results of this study can aid in development of novel rice cultivars suitable as both feedstocks for bioethanol production and cooking.

  12. RAPD-based genetic diversities and correlation with morphological traits in Camellia (Theaceae) cultivars in China.

    PubMed

    Wang, X F; Zheng, H Y; Zheng, W H; Ao, C Q; Jin, H Y; Zhao, L H; Li, N; Jia, L R

    2011-05-10

    Camellia is an economically important ornamental plant that has many uses, such as in beverages, foods and medicines. We examined 15 Camellia cultivars in Wenzhou, China, using RAPD markers and measurements of three traits (petal color, flower diameter, blooming period). PCR amplification with 15 random primers produced 1935 bands, observed at 88 amplification loci; 77% of the amplified loci were polymorphic, with a mean of 4.5 polymorphic loci per primer. The similarity coefficient ranged from 0.5419 to 0.7933 among the 15 samples; the lowest value was between Manao (C. reticulata) and Feibai FR (C. japonica), and the largest value was between Chidan (C. japonica) and Yuanyang FG (C. japonica). Cluster analysis divided the 15 cultivars into two groups at the similarity coefficient of 0.65. A correlation was found between RAPD markers and petal color in the first group. No correlation was found between RAPD markers and the other traits (flower diameter, blooming period). This study provides information useful for the identification, classification, phylogenesis, and breeding of Camellia cultivars.

  13. 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

  14. An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice

    PubMed Central

    Daware, Anurag; Das, Sweta; Srivastava, Rishi; Badoni, Saurabh; Singh, Ashok K.; Agarwal, Pinky; Parida, Swarup K.; Tyagi, Akhilesh K.

    2016-01-01

    Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus, and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16–74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7–8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region (OsqGW5.1) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis-regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse

  15. An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice.

    PubMed

    Daware, Anurag; Das, Sweta; Srivastava, Rishi; Badoni, Saurabh; Singh, Ashok K; Agarwal, Pinky; Parida, Swarup K; Tyagi, Akhilesh K

    2016-01-01

    Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus, and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16-74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7-8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region (OsqGW5.1) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis-regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse cultivar

  16. 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...

  17. 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 ...

  18. 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.

  19. 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...

  20. The regulatory network mediated by circadian clock genes is related to heterosis in rice.

    PubMed

    Shen, Guojing; Hu, Wei; Zhang, Bo; Xing, Yongzhong

    2015-03-01

    Exploitation of heterosis in rice (Oryza sativa L.) has contributed greatly to global food security. In this study, we generated three sets of reciprocal F1 hybrids of indica and japonica subspecies to evaluate the relationship between yield heterosis and the circadian clock. There were no differences in trait performance or heterosis between the reciprocal hybrids, indicating no maternal effects on heterosis. The indica-indica and indica-japonica reciprocal F1 hybrids exhibited pronounced heterosis for chlorophyll and starch content in leaves and for grain yield/biomass. In contrast, the japonica-japonica F1 hybrids showed low heterosis. The three circadian clock genes investigated expressed in an above-high-parent pattern (AHP) at seedling stage in all the hybrids. The five genes downstream of the circadian clock, and involved in chlorophyll and starch metabolic pathways, were expressed in AHP in hybrids with strong better-parent heterosis (BPH). Similarly, three of these five genes in the japonica-japonica F1 hybrids showing low BPH were expressed in positive overdominance, but the other two genes were expressed in additive or negative overdominance. These results indicated that the expression patterns of circadian clock genes and their downstream genes are associated with heterosis, which suggests that the circadian rhythm pathway may be related to heterosis in rice.

  1. 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.

  2. 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

  3. Gene flow from transgenic rice to red rice (Oryza sativa L.) in the field.

    PubMed

    Busconi, M; Baldi, G; Lorenzoni, C; Fogher, C

    2014-01-01

    In this study, we simulate a transgenic rice crop highly infested with red rice to examine transgene transfer from a transgenic line (A2504) resistant to glufosinate ammonium to cohabitant red rice. The red rice was sown along with the transgenic line at the highest density found in naturally infested crops in the region. Agricultural practices similar to those used to control red rice infestation in northern Italy rice fields were used to reproduce the local rice production system. During the first 2 years, the field was treated with herbicide at the appropriate time; in the first year the dosage of herbicide was three times the recommended amount. In this first year, detectable red rice plants that escaped herbicide treatment were manually removed. Nevertheless, two herbicide-resistant hybrid plants (named 101 and 104) were identified in the experimental field during the second year of cultivation. Phenotypic and molecular characterisation suggests the hybrid nature of these two plants, deriving from crossing events involving A2504, respectively, with red rice (plant 101) and the buffer cultivar Gladio (plant 104). The progeny of two subsequent generations of the two plants were examined and the presence of the transgene detected, indicating stable transfer of the transgene across generations. In conclusion, despite control methods, red rice progeny tolerant to the herbicide can be expected following use of transgenic rice and, consequently, difficulties in controlling this weed with chemicals will emerge in a relatively short time.

  4. Archaeological and genetic insights into the origins of domesticated rice

    PubMed Central

    Gross, Briana L.; Zhao, Zhijun

    2014-01-01

    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

  5. 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.

  6. 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

  7. The relationship between translucency of rice grain and gelatinization of starch in the grain during cooking.

    PubMed

    He, G; Suzuki, H

    1987-08-01

    The soaked and nonsoaked rice grains were cooked by the excess water method and the steamer method, and subjected to Ranghino's test, X-ray diffraction, and microscopic observation. The starch granules in the nonsoaked rice were gelatinized at the same time as the grains became translucent during cooking. However, when the grains of medium amylose varieties and waxy rice were presoaked, the starch granules were not fully gelatinized in the translucent grains cooked for Ranghino's cooking time. The gelatinization of starch granules proceeded faster in the soaked rice and by the excess water method than that in the nonsoaked rice and by the steamer method. The cooking time and gelatinization time correlated negatively with the water content after soaking, and positively with the amylose content in the rice grains. The japonica rices were gelatinized fully in less than 20 min when the amount of water added for cooking was adequate.

  8. 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

  9. 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.

  10. Rice, indica (Oryza sativa L.).

    PubMed

    Hiei, Yukoh; Ishida, Yuji; Komari, Toshihiko

    2015-01-01

    Indica varieties, which are generally recalcitrant to tissue culture and transformation, occupy 80 % of rice cultivation area in the world. Therefore, transformation method for indica rice must be improved greatly so that global rice production would take full advantage of cutting-edge biotechnology. An efficient protocol for indica transformation mediated by Agrobacterium tumefaciens is hereby described. Immature embryos collected from plants in a greenhouse are cocultivated with A. tumefaciens after pretreatment with heat and centrifuging. The protocol was successfully tested in many elite indica cultivars such as IR8, IR24, IR58025B, IR64, IR72, Suweon 258, and Nanjing 11, yielding between 5 and 15 of independent transgenic plants per immature embryo. The use of immature embryos is recommended because gene transfer to them could be much more efficient and much less genotype dependent than gene transfer to callus.

  11. Registration of the "Rice Diversity Panel I' Genome-Wide Association Mapping Studies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Rice Diversity Panel (RDP) is a collection of 409 O. sativa accessions (GSOR301001 through GSOR301422) representing the five subpopulations: aromatic (Group V) composed of 15 accessions; aus (59) and indica (90) which compose the Indica subspecies; tropical (104) and temperate (108) japonica whi...

  12. Microsatellite markers reveal multiple origins for Italian weedy rice

    PubMed Central

    Grimm, Annabelle; Fogliatto, Silvia; Nick, Peter; Ferrero, Aldo; Vidotto, Francesco

    2013-01-01

    Weedy rice (Oryza sativa L.) is one of the major issues of rice cultivation worldwide. In Italy, it infests about 70% of the total rice area. Different Weedy Rice populations can be distinguished based on variable morphological and physiological traits; however, little is known about genetic differentiation and origin of Italian weedy rice populations. The objective of this study was to genetically and morphologically characterize and compare different Italian weedy rice populations selected on the basis of different phenotypes. The main Italian rice territory was divided into 10 geographical areas in which 40 weedy rice populations were collected and grouped according to the awn traits. All the individuals of the populations were morphologically characterized according to plant and seed traits. Genetic characterization was performed using 19 SSR markers on all the collected accessions, and several rice cultivars, including some very old (late 19th century), nowadays are no longer cultivated. ANOVA showed that morphological plant and seed traits were significantly affected by the collection area and awnedness group. The importance of the awn morphology was also reflected in the Bayesian clustering where, despite a relatively low genetic diversity, the clusters displayed different awn types. An UPGMA dendrogram confirmed the clusters detected in STRUCTURE analysis and also revealed a grouping of certain old cultivars with the weedy rice, suggesting a common origin. PMID:24363904

  13. Development of a microarray for two rice subspecies: characterization and validation of gene expression in rice tissues

    PubMed Central

    2014-01-01

    Background Rice is one of the major crop species in the world helping to sustain approximately half of the global population’s diet especially in Asia. However, due to the impact of extreme climate change and global warming, rice crop production and yields may be adversely affected resulting in a world food crisis. Researchers have been keen to understand the effects of drought, temperature and other environmental stress factors on rice plant growth and development. Gene expression microarray technology represents a key strategy for the identification of genes and their associated expression patterns in response to stress. Here, we report on the development of the rice OneArray® microarray platform which is suitable for two major rice subspecies, japonica and indica. Results The rice OneArray® 60-mer, oligonucleotide microarray consists of a total of 21,179 probes covering 20,806 genes of japonica and 13,683 genes of indica. Through a validation study, total RNA isolated from rice shoots and roots were used for comparison of gene expression profiles via microarray examination. The results were submitted to NCBI’s Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE50844 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50844). A list of significantly differentially expressed genes was generated; 438 shoot-specific genes were identified among 3,138 up-regulated genes, and 463 root-specific genes were found among 3,845 down-regulated genes. GO enrichment analysis demonstrates these results are in agreement with the known physiological processes of the different organs/tissues. Furthermore, qRT-PCR validation was performed on 66 genes, and found to significantly correlate with the microarray results (R = 0.95, p < 0.001***). Conclusion The rice OneArray® 22 K microarray, the first rice microarray, covering both japonica and indica subspecies was designed and validated in a comprehensive study of gene expression in

  14. Planting geometry as a pre-screening technique for identifying CO2 responsive rice genotypes: a case study of panicle number.

    PubMed

    Shimono, Hiroyuki; Ozaki, Youhei; Jagadish, Krishna S V; Sakai, Hidemitsu; Usui, Yasuhiro; Hasegawa, Toshihiro; Kumagai, Etsushi; Nakano, Hiroshi; Yoshinaga, Satoshi

    2014-11-01

    Identifying CO(2) responsive genotypes is a major target for enhancing crop productivity under future global elevated atmospheric CO(2) concentration ([CO(2)]). However, [CO(2)]-fumigation facilities are extremely expensive and are not easily accessible, and are limited in space for large-scale screening. Hence, reliable donors for initiating [CO(2)]-responsive breeding programs are not in place for crops, including rice. We propose a simple and novel phenotyping method for identifying [CO(2)]-responsive genotypes, and quantify the responsiveness to low planting density over 4-year trials across both temperate and tropical conditions. Panicle number per plant is the key determinant of grain yield and hence was the focus trait across all our trials. In temperate climate, a 3-season field screening using 127 diverse rice genotypes and employing two planting densities (normal and low density) was conducted. Two japonica genotypes were selected based on their higher responsiveness to low planting density as candidates for validating the proposed phenotyping protocol as a pre-screen for [CO(2)]-responsiveness. The approach using the two selected candidates and three standard genotypes was confirmed using a free-air CO(2) enrichment facility and temperature gradient chambers under elevated [CO(2)]. In tropical climate, we grew three rice cultivars, previously identified for their [CO(2)]-responsiveness, at two planting densities. The experiments provided confirmation that responsiveness to low planting density was correlated with that of [CO(2)]-responsiveness across both the temperate and tropical conditions. The planting density would be useful pre-screening method for testing large panels of diverse germplasm at low cost complemented by available CO(2) -control facilities for final validation of candidates from the pre-screens.

  15. 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.

  16. Changes in the thermal dissipation and the electron flow in the water-water cycle in rice grown under conditions of physiologically low temperature.

    PubMed

    Hirotsu, Naoki; Makino, Amane; Ushio, Ayuko; Mae, Tadahiko

    2004-05-01

    Effects of low temperature on chlorophyll (Chl) fluorescence, gas exchange rate, the amounts of xanthophyll cycle pigments (Xp) and the activities of several antioxidant enzymes were examined in the 8th leaf of two rice (Oryza sativa L.) cultivars (japonica and indica types) and rbcS antisense rice. All plants were grown hydroponically at 25/20 degrees C (day/night), and then exposed to 20/17 degrees C (day/night) after full expansion of the 8th leaf, or exposed to either 20/17 degrees C or 15/13 degrees C (day/night) during the expansion of the 8th leaf. All plants exposed to low temperatures showed a decrease in CO(2) assimilation rate without photoinhibition, and increases in the fraction of thermal dissipation in PSII, and in the electron flux through the water-water cycle (WWC) were observed. Although the increase of thermal dissipation was associated with increases in the ratio of carotenoids to Chl, the ratio of Xp to carotenoids and the de-epoxidation state of Xp, the increase of the electron flux of WWC was not accompanied by an increase in the activities of antioxidant enzymes. Such photoprotective responses did not differ between during and after full expansion of the leaf, and did not differ among the three genotypes. Quantitative analyses on the dissipation of excess light energy showed that thermal dissipation makes a larger contribution than WWC. Thus, although low temperature led to a decrease in CO(2) assimilation, rice potentially coped with the excess light energy by increasing the thermal dissipation and the electron flux of WWC under low temperature irrespective of leaf development and genotypes.

  17. 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

  18. RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression

    PubMed Central

    Liu, Wei-Ting; Yang, Chia-Chun; Chen, Rong-Kuen; Jwo, Woei-Shyuan; Wu, Chih-Wen; Ting, Wen-Yen; Shung, Dah-Pyng; Liu, Chun-Chi; Chen, Jeremy J.W.

    2016-01-01

    MicroRNAs (miRNAs) are known to play critical roles in plant development and stress-response regulation, and they frequently display multi-targeting characteristics. The control of defined rice phenotypes occurs through multiple genes; however, evidence demonstrating the relationship between agronomic traits and miRNA expression profiles is lacking. In this study, we investigated eight yield-related traits in 187 local rice cultivars and profiled the expression levels of 193 miRNAs in these cultivars using microarray analyses. By integrating the miRBase database, the rice annotation project database, and the miRanda and psRNATarget web servers, we constructed a database (RiceATM) that can be employed to investigate the association between rice agronomic traits and miRNA expression. The functions of this platform include phenotype selection, sample grouping, microarray data pretreatment, statistical analysis and target gene predictions. To demonstrate the utility of RiceATM, we used the database to identify four miRNAs associated with the heading date and validated their expression trends in the cultivars with early or late heading date by real-time PCR. RiceATM is a useful tool for researchers seeking to characterize the role of certain miRNAs for a specific phenotype and discover potential biomarkers for breeding or functional studies. Database URL: http://syslab3.nchu.edu.tw/rice/ PMID:28025342

  19. 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.

  20. Production of biodiesel from carbon sources of macroalgae, Laminaria japonica.

    PubMed

    Xu, Xu; Kim, Ji Young; Oh, Yu Ri; Park, Jong Moon

    2014-10-01

    As aquatic biomass which is called "the third generation biomass", Laminaria japonica (also known as Saccharina japonica) consists of mannitol and alginate which are the main polysaccharides of algal carbohydrates. In this study, oleaginous yeast (Cryptococcus curvatus) was used to produce lipid from carbon sources derived from Laminaria japonica. Volatile fatty acids (VFAs) were produced by fermentation of alginate extracted from L. japonica. Thereafter, mannitol was mixed with VFAs to culture the oleaginous yeast. The highest lipid content was 48.30%. The composition of the fatty acids was similar to vegetable oils. This is the first confirmation of the feasibility of using macroalgae as a carbon source for biodiesel production.

  1. 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...

  2. Rice antioxidants: phenolic acids, flavonoids, anthocyanins, proanthocyanidins, tocopherols, tocotrienols, γ-oryzanol, and phytic acid.

    PubMed

    Goufo, Piebiep; Trindade, Henrique

    2014-03-01

    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.

  3. Cultivated and weedy rice interactions and the domestication process.

    PubMed

    Lawton-Rauh, Amy; Burgos, Nilda

    2010-08-01

    Examining the targets of selection in crop species and their wild and weedy relatives sheds light on the evolutionary processes underlying differentiation of cultivars from progenitor lineages. On one hand, human-mediated directional selection in crops favours traits associated with the streamlining of controllable and predictable monoculture practices alongside selection for desired trait values. On the other hand, natural selection in wild and especially weedy relatives presumably favours trait values that increase the probability of escaping eradication. Gene flow between crops and wild species may also counter human-mediated selection, promoting the evolution and persistence of weedy forms. In this issue, two studies from a group of collaborators examine diversity and divergence patterns of genes underlying two traits associated with red rice (Oryza sp.), the conspecific relative of cultivated rice (Oryza sativa) that is a non-native weed (see Fig. 1). In the first study by Gross et al. (2010), genetic variation in the major gene underlying the hallmark red pigmentation characterizing most weedy rice (Rc) is found to have a pattern consistent with non-reversion from U.S. cultivated rice (i.e. the cultivar did not 'go feral'). This suggests that U.S. weedy rice is not an escaped lineage derived from U.S. cultivated rice populations; weedy rice likely differentiated prior to the selective sweep occurred in this gene within cultivated rice populations. Using the major seed shattering locus sh4 gene and the neighbouring genomic region, Thurber et al. (2010) track the molecular evolutionary history of the high shattering phenotype, a trait contributing dramatically to the success of crop selection in cultivated rice as well as the persistence and expansion of weedy red rice. In this study, the shared fixation of a sh4 mutation in both cultivated rice and weedy rice indicates that weedy rice arose subsequent to the strong selective sweep leading to significant

  4. Spread of herbicide-resistant weedy rice (red rice, Oryza sativa L.) after 5 years of Clearfield rice cultivation in Italy.

    PubMed

    Busconi, M; Rossi, D; Lorenzoni, C; Baldi, G; Fogher, C

    2012-09-01

    The weedy relative of cultivated rice, red rice, can invade and severely infest rice fields, as reported by rice farmers throughout the world. Because of its close genetic relationship to commercial rice, red rice has proven difficult to control. Clearfield (Cl) varieties, which are resistant to the inhibiting herbicides in the chemical group AHAS (acetohydroxyacid synthase), provide a highly efficient opportunity to control red rice infestations. In order to reduce the risk of herbicide resistance spreading from cultivated rice to red rice, stewardship guidelines are regularly released. In Italy, the cultivation of Cl cultivars started in 2006. In 2010, surveillance of the possible escape of herbicide resistance was carried out; 168 red rice plants were sampled in 16 fields from six locations containing Cl and traditional cultivars. A first subsample of 119 plants was analysed after herbicide treatment and the resistance was found in 62 plants. Of these 119 plants, 78 plants were randomly selected and analysed at the level of the AHAS gene to search for the Cl mutation determining the resistant genotype: the Cl mutation was present in all the resistant plants. Nuclear and chloroplast microsatellite markers revealed a high correlation between genetic similarity and herbicide resistance. The results clearly show that Cl herbicide-resistant red rice plants are present in the field, having genetic relationships with the Cl variety. Finding plants homozygous for the mutation suggests that the crossing event occurred relatively recently and that these plants are in the F2 or later generations. These observations raise the possibility that Cl red rice is already within the cultivated rice seed supply.

  5. Arsenic accumulation and speciation in rice grown in arsanilic acid-elevated paddy soil.

    PubMed

    Geng, Anjing; Wang, Xu; Wu, Lishu; Wang, Fuhua; Chen, Yan; Yang, Hui; Zhang, Zhan; Zhao, Xiaoli

    2017-03-01

    P-arsanilic acid (AsA) is a emerging but less concerned contaminant used in animal feeding operations, for it can be degraded to more toxic metabolites after being excreted by animals. Rice is the staple food in many parts of the world, and also more efficient in accumulating arsenic (As) compared to other cereals. However, the uptake and transformation of AsA by rice is unclear. This study aimed to evaluate the potential risk of using AsA as a feed additive and using the AsA contaminated animal manure as a fertilizer. Five rice cultivars were grown in soil containing 100mg AsA/kg soil, after harvest, As species and their concentrations in different tissues were determined. Total As concentration of the hybrid rice cultivar was more than conventional rice cultivars for whole rice plant. For rice organs, the highest As concentration was found in roots. AsA could be absorbed by rice, partly degraded and converted to arsenite, monomethylarsonic acid, dimethylarsinic acid, arsenate. The number of As species and their concentrations in each cultivar were related to their genotypes. The soil containing 100mg AsA/kg or more is unsuitable for growing rice. The use of AsA and the disposal of animal manure requires detailed attention.

  6. The role of aquaporin RWC3 in drought avoidance in rice.

    PubMed

    Lian, Hong-Li; Yu, Xin; Ye, Qin; Ding, Xiaodong; Kitagawa, Yoshichika; Kwak, Sang-Soo; Su, Wei-Ai; Tang, Zhang-Cheng; Ding, Xiao-Song

    2004-04-01

    Although the discovery of aquaporins in plants has resulted in a paradigm shift in the understanding of plant water relations, the relationship between aquaporins and drought resistance still remains elusive. From an agronomic viewpoint, upland rice is traditionally considered as showing drought avoidance. In the investigation of different morphological and physiological responses of upland rice (Oryza sativa L. spp indica cv. Zhonghan 3) and lowland rice (O. sativa L. spp japonica cv. Xiushui 63) to water deficit, we observed young leaf rolling and the remarkable decline of cumulative transpiration in the upland rice. The expression of water channel protein RWC3 mRNA was increased in upland rice at the early response (up to 4 h) to the 20% polyethylene glycol (PEG) 6000 treatment, whereas there was no significant expression changes in lowland rice. Protein levels were increased in upland rice and decreased in lowland rice at 10 h after the water deficit. The up-regulation of RWC3 in upland rice fits well with the knowledge that upland rice adopts the mechanism of drought avoidance. The physiological significance of this RWC3 up-regulation was then explored with the over-expression of RWC3 in transgenic lowland rice (O. sativa L. spp japonica cv. Zhonghua 11) controlled by a stress-inducible SWPA2 promoter. Compared to the wild-type plant, the transgenic lowland rice exhibited higher root osmotic hydraulic conductivity (Lp), leaf water potential and relative cumulative transpiration at the end of 10 h PEG treatment. These results indicated that RWC3 probably played a role in drought avoidance in rice.

  7. Rice domestication: histories and mysteries.

    PubMed

    Gross, Briana L

    2012-09-01

    Domesticated rice (Oryza sativa) is one of the world's most important food crops, culturally, nutritionally and economically (Khush 1997). Thus, it is no surprise that there is intense curiosity about its genetic and geographical origins, its response to selection under domestication, and the genetic structure of its wild relative, Oryza rufipogon. Studies of Oryza attempting to answer these questions have accompanied each stage of the development of molecular markers, starting with allozymes and continuing to genome sequencing. While many of these studies have been restricted to small sample sizes, in terms of either the number of markers used or the number and distribution of the accessions, costs are now low enough that researchers are including large numbers of molecular markers and accessions. How will these studies relate to previous findings and long-held assumptions about rice domestication and evolution? If the paper in this issue of Molecular Ecology (Huang et al. 2012) is any indication, there will be some considerable surprises in store. In this study, a geographically and genomically thorough sampling of O. rufipogon and O. sativa revealed two genetically distinct groups of wild rice and also indicated that only one of these groups appears to be related to domesticated rice. While this fits well with previous studies indicating that there are genetic subdivisions within O. rufipogon, it stands in contrast to previous findings that the two major varieties of O. sativa (indica and japonica) were domesticated from two (or more) subpopulations of wild rice.

  8. Comparative transcriptome profiling of the early response to Magnaporthe oryzae in durable resistant vs susceptible rice (Oryza sativa L.) genotypes.

    PubMed

    Bagnaresi, Paolo; Biselli, Chiara; Orrù, Luigi; Urso, Simona; Crispino, Laura; Abbruscato, Pamela; Piffanelli, Pietro; Lupotto, Elisabetta; Cattivelli, Luigi; Valè, Giampiero

    2012-01-01

    Durable resistance to blast, the most significant fungal disease of rice, represents an agronomically relevant character. Gigante Vercelli (GV) and Vialone Nano (VN) are two old temperate japonica Italian rice cultivars with contrasting response to blast infection: GV displays durable and broad resistance while VN is highly susceptible. RNA-seq was used to dissect the early molecular processes deployed during the resistance response of GV at 24 h after blast inoculation. Differential gene expression analysis identified 1,070 and 1,484 modulated genes, of which 726 and 699 were up regulated in response to infection in GV and VN, respectively. Gene ontology (GO) enrichment analyses revealed a set of GO terms enriched in both varieties but, despite this commonality, the gene sets contributing to common GO enriched terms were dissimilar. The expression patterns of genes grouped in GV-specific enriched GO terms were examined in detail including at the transcript isoform level. GV exhibited a dramatic up-regulation of genes encoding diterpene phytoalexin biosynthetic enzymes, flavin-containing monooxygenase, class I chitinase and glycosyl hydrolase 17. The sensitivity and high dynamic range of RNA-seq allowed the identification of genes critically involved in conferring GV resistance during the early steps of defence perception-signalling. These included chitin oligosaccharides sensing factors, wall associated kinases, MAPK cascades and WRKY transcription factors. Candidate genes with expression patterns consistent with a potential role as GV-specific functional resistance (R) gene(s) were also identified. This first application of RNA-seq to dissect durable blast resistance supports a crucial role of the prompt induction of a battery of responses including defence-related genes as well as members of gene families involved in signalling and pathogen-related gene expression regulation.

  9. 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.

  10. 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.

  11. 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

  12. Contribution of momilactone A and B to rice allelopathy.

    PubMed

    Kato-Noguchi, Hisashi; Hasegawa, Morifumi; Ino, Takeshi; Ota, Katsumi; Kujime, Hiroya

    2010-07-01

    Eight cultivars of rice (Oryza sativa L.) inhibited shoot and root growth of Echinochloa crus-galli when co-cultured with rice seedlings in a bioassay medium. Momilactone A and B were found in the bioassay medium of all rice cultivars, and concentrations of momilactone A and B in the medium were 0.21-1.5 and 0.66-3.8 micromol/L, respectively, indicating that all rice cultivars may secrete momilactone A and B into the medium. Exogenously applied momilactone A and B inhibited the growth of shoots and roots of E. crus-galli at concentrations greater than 30 and 1 micromol/L, respectively. The concentrations required for 50% growth inhibition of E. crus-galli shoots and roots, respectively, were 146 and 91 micromol/L for momilactone A and 6.5 and 6.9 micromol/L for momilactone B. Considering the growth inhibitory activity and concentrations found in the bioassay medium, momilactone A may have caused only 0.8-2.2% of the observed growth inhibition of E. crus-galli roots and shoots by rice. However, momilactone B in the medium was estimated to be able to cause 59-82% of the observed growth inhibition of E. crus-galli roots and shoots by the rice seedlings. In addition, the concentrations of momilactone B in the medium reflected the observed differences in the growth inhibition of E. crus-galli by the eight rice cultivars investigated. This suggests that the allelopathic activity of rice may depend primarily on the secretion level of momilactone B. Therefore, momilactone B may play a very important role in rice allelopathy.

  13. 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

  14. [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.

  15. Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice.

    PubMed

    Tong, Wei; He, Qiang; Park, Yong-Jin

    2017-03-03

    Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level.

  16. Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice

    PubMed Central

    Tong, Wei; He, Qiang; Park, Yong-Jin

    2017-01-01

    Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level. PMID:28256554

  17. Toward a Cytological Characterization of the Rice Genome

    PubMed Central

    Cheng, Zhukuan; Buell, C. Robin; Wing, Rod A.; Gu, Minghong; Jiang, Jiming

    2001-01-01

    Rice (Oryza sativa L.) will be the first major crop, as well as the first monocot plant species, to be completely sequenced. Integration of DNA sequence-based maps with cytological maps will be essential to fully characterize the rice genome. We have isolated a set of 24 chromosomal arm-specific bacterial artificial chromosomes to facilitate rice chromosome identification. A standardized rice karyotype was constructed using meiotic pachytene chromosomes of O. sativa spp. japonica rice var. Nipponbare. This karyotype is anchored by centromere-specific and chromosomal arm-specific cytological landmarks and is fully integrated with the most saturated rice genetic linkage maps in which Nipponbare was used as one of the mapping parents. An ideogram depicting the distribution of heterochromatin in the rice genome was developed based on the patterns of 4',6-diamidino-2-phenylindole staining of the Nipponbare pachytene chromosomes. The majority of the heterochromatin is distributed in the pericentric regions with some rice chromosomes containing a significantly higher proportion of heterochromatin than other chromosomes. We showed that pachytene chromosome-based fluorescence in situ hybridization analysis is the most effective approach to integrate DNA sequences with euchromatic and heterochromatic features. PMID:11731505

  18. The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species.

    PubMed

    Wing, Rod A; Ammiraju, Jetty S S; Luo, Meizhong; Kim, Hyeran; Yu, Yeisoo; Kudrna, Dave; Goicoechea, Jose L; Wang, Wenming; Nelson, Will; Rao, Kiran; Brar, Darshan; Mackill, Dave J; Han, Bin; Soderlund, Cari; Stein, Lincoln; SanMiguel, Phillip; Jackson, Scott

    2005-09-01

    The wild species of the genus Oryza offer enormous potential to make a significant impact on agricultural productivity of the cultivated rice species Oryza sativa and Oryza glaberrima. To unlock the genetic potential of wild rice we have initiated a project entitled the 'Oryza Map Alignment Project' (OMAP) with the ultimate goal of constructing and aligning BAC/STC based physical maps of 11 wild and one cultivated rice species to the International Rice Genome Sequencing Project's finished reference genome--O. sativa ssp. japonica c. v. Nipponbare. The 11 wild rice species comprise nine different genome types and include six diploid genomes (AA, BB, CC, EE, FF and GG) and four tetrapliod genomes (BBCC, CCDD, HHKK and HHJJ) with broad geographical distribution and ecological adaptation. In this paper we describe our strategy to construct robust physical maps of all 12 rice species with an emphasis on the AA diploid O. nivara--thought to be the progenitor of modern cultivated rice.

  19. [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

  20. 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.

  1. 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...

  2. 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 ...

  3. Analysis of the effectiveness of the rice blast resistance gene Pi-ta

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The casual agent of rice blast, Magnaporthe oryzae, continues to remain a serious threat for rice production and in general for the world food supply. The most economically and environmentally viable strategy to control this pathogen is the development of cultivars which possess major resistance gen...

  4. 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...

  5. 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.

  6. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The domestication of Asian rice (Oryza sativa) was a complex process and substantial ambiguity remains regarding the timing, number, and locations of domestication events. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests at least two independent domesticati...

  7. High resolution genotyping by restriction enzyme-phased sequencing of advanced backcross lines of rice exhibiting differential cold stress recovery

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Advanced backcross rice lines MIb 4853-9 and 6885-2 harbor major seedling cold tolerance QTL qCTS4 and qCTS12 from the temperate japonica M202 in the genetic background of the indica IR50. Previous studies have shown that these lines exhibit the same tolerance, based on visual ratings, under constan...

  8. Residues of thiamethoxam and chlorantraniliprole in rice grain.

    PubMed

    Teló, Gustavo Mack; Senseman, Scott Allen; Marchesan, Enio; Camargo, Edinalvo Rabaioli; Jones, Trevor; McCauley, Garry

    2015-03-04

    Thiamethoxam and chlorantraniliprole insecticides have been important tools for controlling pests in rice. However, food safety issues related to pesticide residues are important to consider with a food crop such as rice. Therefore, the objective of this study was to analyze thiamethoxam and chlorantraniliprole residues in rice hull, bran, and polished rice grains. The study was conducted during the 2012 cropping season at the Texas A&M Agrilife Research, David R. Wintermann Rice Research Station, near Eagle Lake, TX, USA. Rice was planted on May 5, 2012, using the cultivar 'Presidio'. Pesticide applications were performed at 5, 15, 25, and 35 days after flowering (DAF) using 1 and 2 times the recommended rate of 30 g active ingredient (ai) ha(-1) for thiamethoxam and 30 g ai ha(-1) for chlorantraniliprole. Sequentially, two treatments using the insecticides at recommended rate were applied at 5 and 25 DAF and at 5, 25, and 35 DAF. Insecticide residues were analyzed in different sample fractions: rice hull, bran, and polished rice grains. The samples were subjected to extraction using an accelerated solvent extraction (ASE) technique. Sample aliquots were analyzed using ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), with a limit of quantification (LOQ) of 5 × 10(-5) mg kg(-1). Residues of thiamethoxam and chlorantraniliprole were detected in rice hull, bran, and polished rice grains, and the quantified values were greater in hull and in rice bran.

  9. [Selection behavior of Cuscuta japonica on their hosts].

    PubMed

    Hu, Fei; Kong, Chuihua; Zhang, Chaoxian; Liang, Wenju; Wang, Peng

    2005-02-01

    A field investigation on the selection behavior of Cuscuta japonica on their hosts showed that among the test plant communities, the number of coiling, the time of haustorium occurring, and the rate of coiling of C. japonica on hosts followed the order of B. papyrifera, W. chinensis, I. cairica, and L. camara; but the length of the elongation of C. japonica growing tips from coiling to haustorium occurring was with the order of L. camara, I. cairica, W. chinensis, and B. papyrifera. Furthermore, the growing tips of C. japonica coiled 3 circles in left direction on all selected hosts in 12 hrs, but grew away after contacting PVC rods within 24 hrs. The host diversity of C. japonic was beneficial to the survival of both C. japonica and its hosts. The selection behavior of C. japonica on their hosts had no correlation with the total N contents of different hosts. It could be postulated that the secondary metabolites of hosts made a contribution to the selection behavior of C. japonica on their hosts.

  10. 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.

  11. Critical Importance of alpha-glucosidase contained in rice kernel for alcohol fermentation of rice polish.

    PubMed

    Iwata, Hiroshi; Suzuki, Toshiaki; Takahashi, Kazuhide; Aramaki, Isao

    2002-01-01

    In our previous study, we proposed a new alcoholic beverage called nuka-sake, which is made from uncooked rice polish without any enzyme source such as koji. In nuka-sake brewing, the uncooked rice polish serves not only as the fermentation material but also as the enzyme source. In the present study, the results of both laboratory-scale nuka-sake brewing runs with various grades of rice polish and analysis of amylolitic enzyme distribution in rice polish suggested that alpha-glucosidase (EC 3.2.1.20) is a key enzyme of parallel fermentation in nuka-sake brewing. Miglitol, a specific inhibitor of alpha-glucosidase, strongly inhibited glucose production from rice polish. To obtain further evidence regarding the contribution of alpha-glucosidase, this enzyme was purified from rice grain kernels (Yamadanishiki cultivar) and supplied for both rice polish saccharification and nuka-sake brewing. The purified alpha-glucosidase promoted both glucose production from rice polish and alcohol fermentation in nuka-sake brewing. Based on these results, it was considered that the alpha-glucosidase contained in rice polish plays an important role in glucose production. This role may be a rate-limiting factor for parallel fermentation in nuka-sake brewing. Moreover, oligosaccarides accumulated during the saccharification of uncooked rice polish, implying the contribution of not only alpha-glucosidase but also alpha-amylase (EC 3.2.1.1). Through this result, it can be speculated that the starch contained in rice polish will be decomposed to glucose as a result of the action of alpha-glucosidase and alpha-amylase contained in rice polish.

  12. Balance between a higher degree of heterosis and increased reproductive isolation: a strategic design for breeding inter-subspecific hybrid rice.

    PubMed

    Dan, Zhiwu; Liu, Ping; Huang, Wenchao; Zhou, Wei; Yao, Guoxin; Hu, Jun; Zhu, Renshan; Lu, Baorong; Zhu, Yingguo

    2014-01-01

    The application of heterosis (hybrid vigor) has brought great success to plant breeding, particularly of hybrid rice, achieving significant yield increases. Attempts to explore the heterosis of inter-subspecific hybrids between indica and japonica rice, which result in even greater yield increases, have greatly increased in the past decades. However, because of the reduced seed setting rate in F1 hybrids as a result of increased reproductive isolation, the application of inter-subspecific hybrids in rice has slowed. Understanding the balance between heterosis and the reproductive isolation of inter-subspecific hybrids will facilitate the strategic design of inter-subspecific hybrid breeding. In this study, five indica and seven japonica rice varieties were chosen as the parental lines of a complete diallel mating design. Data from six group traits from all of the hybrids and inbred lines were collected. We found that the grain weight per plant, grain number per panicle, tiller per plant, thousand grain weight and plant height, which reflected increased heterosis, were associated with the genetic divergence index (GDI) of the parents. Meanwhile, owing to the reduced seed setting rate, which was also associated with the parents' GDI, the grain production of the hybrids was negatively affected. After analyzing the relationships between the GDI of indica-japonica parents and the grain weight per plant of the F1 hybrids, an ideal GDI value (0.37) for the two indica-japonica parents that could provide an optimal balance between the inter-subspecific heterosis and reproductive isolation was proposed. Our findings will help in the strategic design of an inter-subspecific hybrid rice breeding program by identifying the ideal indica and japonica parents for a hybrid combination to achieve hybrid rice with an optimal yield. This strategic design of an inter-subspecific hybrid rice breeding program will be time saving and cost effective.

  13. Elongated phytoglycogen chain length in transgenic rice endosperm expressing active starch synthase IIa affects the altered solubility and crystallinity of the storage α-glucan

    PubMed Central

    Fujita, Naoko; Toyosawa, Yoshiko; Utsumi, Yoshinori

    2012-01-01

    The relationship between the solubility, crystallinity, and length of the unit chains of plant storage α-glucan was investigated by manipulating the chain length of α-glucans accumulated in a rice mutant. Transgenic lines were produced by introducing a cDNA for starch synthase IIa (SSIIa) from an indica cultivar (SSIIa I, coding for active SSIIa) into an isoamylase1 (ISA1)-deficient mutant (isa1) that was derived from a japonica cultivar (bearing inactive SSIIa proteins). The water-soluble fraction accounted for >95% of the total α-glucan in the isa1 mutant, whereas it was only 35–70% in the transgenic SSIIa I /isa1 lines. Thus, the α-glucans from the SSIIa I /isa1 lines were fractionated into soluble and insoluble fractions prior to the following characterizations. X-ray diffraction analysis revealed a weak B-type crystallinity for the α-glucans of the insoluble fraction, while no crystallinity was confirmed for α-glucans in isa1. Concerning the degree of polymerization (DP) ≤30, the chain lengths of these α-glucans differed significantly in the order of SSIIa I /isa1 insoluble > SSIIa I /isa1 soluble > α-glucans in isa1. The amount of long chains with DP ≥33 was higher in the insoluble fraction α-glucans than in the other two α-glucans. No difference was observed in the chain length distributions of the β-amylase limit dextrins among these α-glucans. These results suggest that in the SSIIa I /isa1 transgenic lines, the unit chains of α-glucans were elongated by SSIIaI, whereas the expression of SSIIaI did not affect the branch positions. Thus, the observed insolubility and crystallinity of the insoluble fraction can be attributed to the elongated length of the outer chains due to SSIIaI. PMID:23048127

  14. AVR1-CO39 is a predominant locus governing the broad avirulence of Magnaporthe oryzae 2539 on cultivated rice (Oryza sativa L.).

    PubMed

    Zheng, Yan; Zheng, Wenhui; Lin, Fucheng; Zhang, Ying; Yi, Yunping; Wang, Baohua; Lu, Guodong; Wang, Zonghua; Wu, Weiren

    2011-01-01

    Magnaporthe oryzae 2539 was previously found to be avirulent to most rice cultivars and, therefore, was assumed to carry many avirulence (AVR) genes. However, only one AVR gene, AVR1-CO39, which corresponds to a resistance (R) gene Pi-CO39(t) in rice cv. CO39, has been found from 2539 thus far. In order to identify more AVR genes, we isolated 228 progeny strains from a cross between 2539 and Guy11, an M. oryzae strain with strong virulence on rice, and inoculated these strains onto 23 rice accessions (22 individual cultivars and a mixture of 14 cultivars) that are all resistant to 2539 but susceptible to Guy11. Unexpectedly, the experimental results indicated that the avirulence of 2539 on these rice cultivars appeared to be controlled only by the AVR1-CO39 locus. Consistent with this result, we further found that all except one of the rice cultivars were resistant to two transformed Guy11 strains carrying a 1.05-kb fragment containing the AVR1-CO39 gene from 2539. These results suggest that AVR1-CO39 is a predominant locus controlling the broad avirulence of 2539 on cultivated rice. Based on the results of this study and other previous studies, we infer that AVR1-CO39 is a species-wise rather than a cultivar-wise host-specific AVR locus of M. oryzae for rice.

  15. Study on Analysis of Variance on the indigenous wild and cultivated rice species of Manipur Valley

    NASA Astrophysics Data System (ADS)

    Medhabati, K.; Rohinikumar, M.; Rajiv Das, K.; Henary, Ch.; Dikash, Th.

    2012-10-01

    The analysis of variance revealed considerable variation among the cultivars and the wild species for yield and other quantitative characters in both the years of investigation. The highly significant differences among the cultivars in year wise and pooled analysis of variance for all the 12 characters reveal that there are enough genetic variabilities for all the characters studied. The existence of genetic variability is of paramount importance for starting a judicious plant breeding programme. Since introduced high yielding rice cultivars usually do not perform well. Improvement of indigenous cultivars is a clear choice for increase of rice production. The genetic variability of 37 rice germplasms in 12 agronomic characters estimated in the present study can be used in breeding programme

  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. Grain-filling problem in 'super' rice.

    PubMed

    Yang, Jianchang; Zhang, Jianhua

    2010-01-01

    Modern rice (Oryza sativa L.) cultivars, especially the newly bred 'super' rice, have numerous spikelets on a panicle with a large yield capacity. However, these cultivars often fail to achieve their high yield potential due to poor grain-filling of later-flowering inferior spikelets (in contrast to the earlier-flowering superior spikelets). Conventional thinking to explain the poor grain-filling is the consequence of carbon limitation. Recent studies, however, have shown that carbohydrate supply should not be the major problem because they have adequate sucrose at their initial grain-filling stage. The low activities of key enzymes in carbon metabolism may contribute to the poor grain-filling. Proper field practices, such as moderate soil drying during mid- and late grain-filling stages, could solve some problems in poor grain-filling. Further studies are needed by molecular approaches to investigate the signal transport, the hormonal action, the gene expressions, and the biochemical processes in inferior spikelets.

  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. 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

  1. 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.

  2. 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

  3. 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,...

  4. Breeding Jasmine-Type Aromatic Rice for Southern United States

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the United States, over 70% of imported rice that currently makes up the 12% of domestic consumption is Jasmine, primarily from Thailand. Development of improved Jasmine-type cultivar with similar specialty characteristics (aroma, texture, and flavor) to those imports and with competitive grain a...

  5. 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.

  6. Detection of bacterial blight resistance genes in basmati rice landraces.

    PubMed

    Ullah, I; Jamil, S; Iqbal, M Z; Shaheen, H L; Hasni, S M; Jabeen, S; Mehmood, A; Akhter, M

    2012-07-20

    Aromatic basmati rice is vulnerable to bacterial blight disease. Genes conferring resistance to bacterial blight have been identified in coarse rice; however, their incorporation into basmati varieties compromises the prized basmati aroma. We identified bacterial blight resistance genes Xa4, xa5, Xa7, and xa13 in 52 basmati landraces and five basmati cultivars using PCR markers. The Xa7 gene was found to be the most prevalent among the cultivars and landraces. The cultivars Basmati-385 and Basmati-2000 also contained the Xa4 gene; however, xa5 and xa13 were confined to landraces only. Ten landraces were found to have multiple resistance genes. Landraces Basmati-106, Basmati-189 and Basmati-208 contained Xa4 and Xa7 genes. Whereas, landraces Basmati-122, Basmati-427, Basmati-433 were observed to have xa5 and Xa7 genes. Landraces Basmati-48, Basmati-51A, Basmati-334, and Basmati-370A possessed Xa7 and xa13 genes. The use of landraces containing recessive genes xa5 and xa13 as donor parents in hybridization with cultivars Basmati-385 and Basmati-2000, which contain the genes Xa4 and Xa7, will expedite efforts to develop bacterial blight-resistant basmati rice cultivars through marker assisted selection, based on a pyramiding approach, without compromising aroma and grain quality.

  7. Comparison of different critical nitrogen dilution curves for nitrogen diagnosis in rice

    NASA Astrophysics Data System (ADS)

    Ata-Ul-Karim, Syed Tahir; Zhu, Yan; Liu, Xiaojun; Cao, Qiang; Tian, Yongchao; Cao, Weixing

    2017-03-01

    The critical nitrogen (N) dilution curve is a suitable analytical tool for in-season estimation of N status to implement precision N management. This study was undertaken for a comprehensive comparison of N dilution curves in Japonica and Indica rice to investigate, whether a single curve can be used for both rice ecotypes and to determine the most robust plant index for assessing N status in rice ecotypes. The different N dilution curves were developed based on plant dry matter (PDM), leaf area index (LAI), leaf dry matter (LDM) and stem dry matter (SDM) for N diagnosis in Japonica and Indica rice. The comparison of N dilution curves of two rice ecotypes showed non-significant differences, therefore a single/unified curve can be used to assess plant N status for precision N management in both rice ecotypes. The relationships between PDM based, with LAI, LDM, and SDM based N nutrition index, accumulated N deficit and N requirement, indicated that leaf based approaches could be used as substitutes for PDM approach. The lower coefficient b values of LDM based curve (due to efficient physiological N use in leaves) implied that LDM was the most appropriate approach for developing N curve as compared to other approaches.

  8. Comparison of different critical nitrogen dilution curves for nitrogen diagnosis in rice

    PubMed Central

    Ata-Ul-Karim, Syed Tahir; Zhu, Yan; Liu, Xiaojun; Cao, Qiang; Tian, Yongchao; Cao, Weixing

    2017-01-01

    The critical nitrogen (N) dilution curve is a suitable analytical tool for in-season estimation of N status to implement precision N management. This study was undertaken for a comprehensive comparison of N dilution curves in Japonica and Indica rice to investigate, whether a single curve can be used for both rice ecotypes and to determine the most robust plant index for assessing N status in rice ecotypes. The different N dilution curves were developed based on plant dry matter (PDM), leaf area index (LAI), leaf dry matter (LDM) and stem dry matter (SDM) for N diagnosis in Japonica and Indica rice. The comparison of N dilution curves of two rice ecotypes showed non-significant differences, therefore a single/unified curve can be used to assess plant N status for precision N management in both rice ecotypes. The relationships between PDM based, with LAI, LDM, and SDM based N nutrition index, accumulated N deficit and N requirement, indicated that leaf based approaches could be used as substitutes for PDM approach. The lower coefficient b values of LDM based curve (due to efficient physiological N use in leaves) implied that LDM was the most appropriate approach for developing N curve as compared to other approaches. PMID:28262685

  9. The Birth of a Black Rice Gene and Its Local Spread by Introgression

    PubMed Central

    Oikawa, Tetsuo; Maeda, Hiroaki; Oguchi, Taichi; Yamaguchi, Takuya; Tanabe, Noriko; Ebana, Kaworu; Yano, Masahiro; Izawa, Takeshi

    2015-01-01

    The origin and spread of novel agronomic traits during crop domestication are complex events in plant evolution. Wild rice (Oryza rufipogon) has red grains due to the accumulation of proanthocyanidins, whereas most cultivated rice (Oryza sativa) varieties have white grains induced by a defective allele in the Rc basic helix-loop-helix (bHLH) gene. Although the events surrounding the origin and spread of black rice traits remain unknown, varieties with black grains due to anthocyanin accumulation are distributed in various locations throughout Asia. Here, we show that the black grain trait originated from ectopic expression of the Kala4 bHLH gene due to rearrangement in the promoter region. Both the Rc and Kala4 genes activate upstream flavonol biosynthesis genes, such as chalcone synthase and dihydroflavonol-4-reductase, and downstream genes, such as leucoanthocyanidin reductase and leucoanthocyanidin dioxygenase, to produce the respective specific pigments. Genome analysis of 21 black rice varieties as well as red- and white-grained landraces demonstrated that black rice arose in tropical japonica and its subsequent spread to the indica subspecies can be attributed to the causal alleles of Kala4. The relatively small size of genomic fragments of tropical japonica origin in some indica varieties indicates that refined introgression must have occurred by natural crossbreeding in the course of evolution of the black trait in rice. PMID:26362607

  10. Selection and breeding of plant cultivars to minimize cadmium accumulation.

    PubMed

    Grant, C A; Clarke, J M; Duguid, S; Chaney, R L

    2008-02-15

    Natural variation occurs in the uptake and distribution of essential and nonessential trace elements among crop species and among cultivars within species. Such variation can be responsible for trace element deficiencies and toxicities, which in turn can affect the quality of food. Plant breeding can be an important tool to both increase the concentration of desirable trace elements and reduce that of potentially harmful trace elements such as cadmium (Cd). Selection programs for a low-Cd content of various crops, including durum wheat, sunflower, rice and soybean have been established and low-Cd durum wheat cultivars and sunflower hybrids have been developed. In durum wheat (Triticum turgidum L. var durum), low-Cd concentration is controlled by a single dominant gene. The trait is highly heritable, and incorporation of the low-Cd allele can help to reduce the average grain Cd to levels below proposed international limits. The allele for low-Cd concentration does not appear to affect major economic traits and should not cause problems when incorporated into durum cultivars. The cost of Cd selection in a breeding program is initially large both in terms of Cd determination and reduced progress towards development of other economic traits, but declines as more breeding lines in the program carry the low-Cd trait and are utilized in new crosses. Production of low-Cd crop cultivars can be used as a tool to reduce the risk of movement of Cd into the human diet.

  11. 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.

  12. 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

  13. 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...

  14. Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga.

    PubMed

    Arbelaez, Juan D; Moreno, Laura T; Singh, Namrata; Tung, Chih-Wei; Maron, Lyza G; Ospina, Yolima; Martinez, César P; Grenier, Cécile; Lorieux, Mathias; McCouch, Susan

    Two populations of interspecific introgression lines (ILs) in a common recurrent parent were developed for use in pre-breeding and QTL mapping. The ILs were derived from crosses between cv Curinga, a tropical japonica upland cultivar, and two different wild donors, Oryza meridionalis Ng. accession (W2112) and Oryza rufipogon Griff. accession (IRGC 105491). The lines were genotyped using genotyping-by-sequencing (GBS) and SSRs. The 32 Curinga/O. meridionalis ILs contain 76.73 % of the donor genome in individual introgressed segments, and each line has an average of 94.9 % recurrent parent genome. The 48 Curinga/O. rufipogon ILs collectively contain 97.6 % of the donor genome with an average of 89.9 % recurrent parent genome per line. To confirm that these populations were segregating for traits of interest, they were phenotyped for pericarp color in the greenhouse and for four agronomic traits-days to flowering, plant height, number of tillers, and number of panicles-in an upland field environment. Seeds from these IL libraries and the accompanying GBS datasets are publicly available and represent valuable genetic resources for exploring the genetics and breeding potential of rice wild relatives.

  15. 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.

  16. Disease reactions of IRRI near-isogenic rice lines to U.S. isolates of Magnaporthe oryzae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice blast, caused by Magnaporthe oryzae, is a destructive disease of rice. The use of resistant cultivars is the most effective way to manage this disease. However, to be effective, it is necessary to know how the isolates of the pathogen within a population respond to specific resistance genes. Tw...

  17. 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 ...

  18. 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...

  19. 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

  20. Mitigation of arsenic accumulation in rice with water management and silicon fertilization.

    PubMed

    Li, R Y; Stroud, J L; Ma, J F; McGrath, S P; Zhao, F J

    2009-05-15

    Rice represents a major route of As exposure in populations that depend on a rice diet. Practical measures are needed to mitigate the problem of excessive As accumulation in paddy rice. Two potential mitigation methods, management of the water regime and Si fertilization, were investigated under greenhouse conditions. Growing rice aerobically during the entire rice growth duration resulted in the leastAs accumulation. Maintaining aerobic conditions during either vegetative or reproductive stage of rice growth also decreased As accumulation in rice straw and grain significantly compared with rice grown under flooded conditions. The effect of water management regimes was consistent with the observed effect of flooding-induced arsenite mobilization in the soil solution. Aerobic treatments increased the percentage of inorganic As in grain, but the concentrations of inorganic As remained lower than in the flooded rice. Silicon fertilization decreased the total As concentration in straw and grain by 78 and 16%, respectively, even though Si addition increased As concentration in the soil solution. Silicon also significantly influenced As speciation in rice grain and husk by enhancing methylation. Silicon decreased the inorganic As concentration in grain by 59% while increasing the concentration of dimethylarsinic acid (DMA) by 33%. There were also significant differences between two rice genotypes in grain As speciation. This study demonstrated that water management Si fertilization, and selection of rice cultivars are effective measures that can be used to reduce As accumulation in rice.

  1. Impact of phytic acid on nutrient bioaccessibility and antioxidant properties of dehusked rice.

    PubMed

    Lee, H H; Loh, S P; Bong, C F J; Sarbini, S R; Yiu, P H

    2015-12-01

    Whole grains consumption promotes health benefits, but demonstrates controversial impacts from phytic acid in meeting requirements of good health. Therefore, this study was aimed to determine the nutrient bioaccessibility and antioxidant properties of rice cultivars named "Adan" or "Bario" and deduce the nutritional impact of phytic acid. Majority of the dehusked rice in the collection showed an acceptable level of in-vitro starch digestibility and in-vitro protein digestibility, but were poor in antioxidant properties and bioaccessibility of minerals (Ca, Fe and Zn). The drawbacks identified in the rice cultivars were due to relatively high phytic acid content (2420.6 ± 94.6 mg/100 g) and low phenolic content (152.39 ± 18.84 μg GAE/g). The relationship between phytic acid content and mineral bioaccessibility was strongest in calcium (r = 0.60), followed by iron (r = 0.40) and zinc (r = 0.27). Phytic acid content did not significantly correlate with in-vitro starch digestibility and in-vitro protein digestibility but showed a weak relationship with antioxidant properties. These suggest that phytic acid could significantly impair the mineral bioaccessibility of dehusked rice, and also act as an important antioxidant in non-pigmented rice. Bario rice cultivars offered dehusked rice with wide range of in-vitro digestibility of starch and protein, and also pigmented rice as a good source of antioxidants. However, there is a need to reduce phytic acid content in dehusked rice for improved mineral bioaccessibility among Bario rice cultivars.

  2. Genome re-sequencing and bioinformatics analysis of a nutraceutical rice.

    PubMed

    Lin, Juncheng; Cheng, Zuxin; Xu, Ming; Huang, Zhiwei; Yang, Zhijian; Huang, Xinying; Zheng, Jingui; Lin, Tongxiang

    2015-06-01

    The genomes of two rice cultivars, Nipponbare and 93-11, have been well studied. However, there is little available genetic information about nutraceutical rice cultivars. To remedy this situation, the present study aimed to provide a basic genetic landscape of nutraceutical rice. The genome of Black-1, a black pericarp rice containing higher levels of anthocyanins, flavonoids, and a more potent antioxidant capacity, was sequenced at ≥30 × coverage using Solexa sequencing technology. The complete sequences of Black-1 genome shared more consensus sequences with indica cultivar 93-11 than with Nipponbare. With reference to the 93-11 genome, Black-1 contained 675,207 single-nucleotide polymorphisms, 43,130 insertions and deletions (1-5 bp), 1,770 copy number variations, and 10,911 presence/absence variations. These variations were observed to reside preferentially in Myb domains, NB-ARC domains and kinase domains, providing clues to the diversity of biological functions or secondary metabolisms in this cultivar. Intriguingly, 496 unique genes were identified by comparing it with the genomes of these two rice varieties; among the genes, 119 genes participate in the biosynthesis of secondary metabolites. Furthermore, several unique genes were predicted to be involved in the anthocyanins synthesis pathway. The genome-wide landscape of Black-1 uncovered by this study represents a valuable resource for further studies and for breeding nutraceutical rice varieties.

  3. 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.

  4. Pyrolysis characteristics and kinetics of the alga Saccharina japonica.

    PubMed

    Kim, Seung-Soo; Ly, Hoang Vu; Choi, Gyeong-Ho; Kim, Jinsoo; Woo, Hee Chul

    2012-11-01

    Saccharina japonica can be converted to bio-oil, gas, and char through pyrolysis. In this study, the pyrolysis characteristics of S. japonica were investigated using a thermogravimetric analyzer. Most of the materials decomposed between 200°C and 350°C at heating rates of 10-20°C/min. The apparent activation energy increased from 102.5kJmol(-1) to 269.7kJmol(-1) with increasing pyrolysis conversion. The kinetic parameters of S. japonica pyrolysis were determined using nonlinear least-squares regression of the experimental data assuming first-order kinetics. The kinetic rate constants indicated that the predominant reaction pathway was B (bio-oil) to C (gas; C(1)-C(4)), rather than A (S. japonica) to B (bio-oil) and/or to C (gas; C(1)-C(4)). The proposed lumped kinetics of S. japonica pyrolysis offers a guide for the scale-up of the process at the research and industrial level.

  5. 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

  6. 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.

  7. Comparative transcriptome analysis of two rice varieties in response to rice stripe virus and small brown planthoppers during early interaction.

    PubMed

    Zheng, Wenjing; Ma, Li; Zhao, Jiaming; Li, Zhiqiang; Sun, Fuyu; Lu, Xiaochun

    2013-01-01

    Rice stripe, a virus disease, transmitted by a small brown planthopper (SBPH), has greatly reduced production of japonica rice in East Asia, especially in China. Although we have made great progress in mapping resistance genes, little is known about the mechanism of resistance. By de novo transcriptome assembling, we gained sufficient transcript data to analyze changes in gene expression of early interaction in response to SBPH and RSV infection in rice. Respectively 648 and 937 DEGs were detected from the disease-resistant (Liaonong 979) and the susceptible (Fengjin) varieties, most of which were up-regulated. We found 37 genes related to insect resistance, which mainly included genes for jasmonate-induced protein, TIFY protein, lipoxygenase, as well as trypsin inhibitor genes and transcription factor genes. In the interaction process between RSV and rice, 87 genes were thought to be related to RSV resistance; these primarily included 12 peroxidase biosynthesis genes, 12 LRR receptor-like protein kinase genes, 6 genes coding pathogenesis-related proteins, 4 glycine-rich cell wall structural protein genes, 2 xyloglucan hydrolase genes and a cellulose synthase. The results indicate that the rice-pathogen interaction happened both in disease-resistant and susceptible varieties, and some genes related to JA biosynthesis played key roles in the interaction between SBPHs and rice. When rice was infected by RSV a hypersensitive reaction (HR) in the disease-resistant variety was suppressed, which resulted from an increase in peroxidase expression and down-regulation of LRR receptor-like protein kinase and pathogenesis-related proteins, while, the changes of peroxidase biosynthesis, glycine-rich cell wall structural protein, cellulose synthase and xyloglucan endotransglucosylase/hydrolase could lead to the strengthening of physical barriers of rice, which may be an important resistance mechanism to RSV in rice.

  8. [Temperature differences of air-rice plant under different irrigated water depths at spiking stage].

    PubMed

    Zhang, Bin; Zheng, Jian-chu; Huang, Shan; Tian, Yun-lu; Peng, Lan; Bian, Xin-min; Zhang, Wei-jian

    2008-01-01

    With rice cultivars Yangdao 6, Yangjing 9538 and Wuxiangjing 14 as test materials, field experiment was conducted to study the effects of 3 irrigated water depths (0 cm, 2-4 cm, and > 10 cm) on the temperature of different parts of rice plant at spiking stage. The results showed that from 10:30 to 15:00 on sunny days, irrigated water depth on paddy field had significant effects on the temperature of field surface, middle part of rice plant, and rice spike. The higher the water depth on field surface, the lower the temperature of rice plant and rice spike. At the water level > 10 cm, the average temperature differences between air and the rice spike, middle part of rice plant and field surface of these three cultivars were 1.37, 2.98 and 4.12 degrees C higher than those at the water depth of 0 cm, and 0.67, 1.59 and 2.17 degrees C higher than those at the water depth of 2-4 cm, respectively. In addition, the temperature differences were 0.71, 1.39 and 1.95 degrees C higher at the water depth of 2-4 cm than those at the water depth of 0 cm, respectively. Obvious temperature differences of air-rice plant were also observed among the three rice