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Sample records for common wild rice

  1. [Cloning and analyzing of rice blast resistance gene Pi-ta+ allele from Jinghong erect type of common wild rice (Oryza rufipogon Griff) in Yunnan].

    PubMed

    Geng, Xian-Sheng; Yang, Ming-Zhi; Huang, Xing-Qi; Cheng, Zai-Quan; Fu, Jian; Sun, Tao; Li, Jun

    2008-01-01

    A 4,672 bp DNA sequence including the whole coding region and partial non-coding region of rice blast resistance gene Pi-ta+ has been cloned from Jinghong erect type of common wild rice (Oryza rufipogon Griff) in Yunnan by polymerase chain reaction method. The coding region shares 99.86% and 98.78% identity with the corresponding regions of the reported cultivated rice Yashiro-mochi and Yuanjiang type of common wild rice respectively. There are 4 nucleotides difference in the coding region and 6 in intron of the cloned Pi-ta+ gene,compared with Pi-ta from Yashiro-mochi. Pi-ta+ gene in Jinghong erect type of common wild rice has been proved to be a rare existing Pi-ta+ allele, because there was a alanine rather than a serine at the position 918 within the predicted amino acid sequence of PITA. Pi-ta+ allele can cause disease resistance response to rice blast pathogens in plant cells. Differences in DNA sequence, deduced amino acid sequence and antibacterial spectrum may make the Pi-ta+ allele new resistant characteristics. Finding and cloning of Pi-ta+ allele from Jinghong erect type of common wild rice in Yunnan provides a basement for further utilization of the wild rice resources.

  2. Genetic-basis analysis of heterotic loci in Dongxiang common wild rice (Oryza rufipogon Griff.).

    PubMed

    Luo, Xiao-Jin; Xin, Xiao-Yun; Yang, Jin-Shui

    2012-04-01

    Heterosis is widely used in genetic crop improvement; however, the genetic basis of heterosis is incompletely understood. The use of whole-genome segregating populations poses a problem for establishing the genetic basis of heterosis, in that interactions often mask the effects of individual loci. However, introgression line (IL) populations permit the partitioning of heterosis into defined genomic regions, eliminating a major part of the genome-wide epistasis. In our previous study, based on mid-parental heterosis (HMP) value with single-point analysis, 42 heterotic loci (HLs) associated with six yield-related traits were detected in wild and cultivated rice using a set of 265 ILs of Dongxiang common wild rice (Oryza rufipogon Griff.). In this study, the genetic effects of HLs were determined as the combined effects of both additive and dominant gene actions, estimated from the performance values of testcross F1s and the dominance effects estimated from the HMP values of testcross F1s. We characterized the gene action type at each HL. Thirty-eight of the 42 HLs were over-dominant, and in the absence of epistasis, four HLs were dominant. Therefore, we favour that over-dominance is a major genetic basis of 'wild-cultivar' crosses at the single functional Mendelian locus level.

  3. [Drought resistance evaluation system for backcross lines of Dongxiang common wild rice (Oryza rufipogon Griff.)].

    PubMed

    Fu, Xue-Qin; He, Hao-Hua; Wen, Piao; Luo, Xiang-Dong; Xie, Jian-Kun

    2012-05-01

    A total of 79 rice materials containing Dongxiang wild rice (Oryza rufipogon Griff. ) backcross lines (Dwr)/Xie-qingzao B (Xqz B)//Xqz B and their parents were chosen as the test objects to study the relationships between the drought resistance of these materials and the 31 drought resistance indices at germinating stage, seedling stage, booting stage, and mature stage. The results showed that the drought resistance index or the drought resistance coefficient of these materials were significantly correlated to the relative germination energy (RGE) under 15% PEG-6000 drought stress, the germination drought resistance index (GDRI) and relative germination energy (RGE) under 20% PEG-6000 drought stress, and the relative value of maximum root length (MRL), seeding height (SH), fresh root mass (FRM), dry root mass (DRM), root relative water content (RRWC), wilting rate (WR), leaf soluble sugar content (LSSC), leaf proline content (LPC), leaf MDA content (LMDAC), leaf relative water content (LRWC), level of rolling leaf (RL), plant height (PH), tiller number per plant (TNP), productive tiller number per plant (PTNP), filled spikelets per panicle (FSP), panicle density (PD), seed setting rate (SR), and 1000-grain mass (TGM) under water stress. Through stepwise regression analysis, nine drought resistance indices including the RGE under 20% PEG-6000 drought stress and the relative values of DRM, RRWC, LSSC, LPC, LMDAC, ETNP, SR, and TGM under water stress were selected. Base on these indices and their partial correlation coefficients, the drought resistance evaluation equation (D value) and evaluation system were established, which could well assess the drought resistance of the Dongxiang common wild rice backcross lines at different growth stages.

  4. Identification of heterotic loci associated with yield-related traits in Chinese common wild rice (Oryza rufipogon Griff.).

    PubMed

    Luo, Xiaojin; Wu, Shuang; Tian, Feng; Xin, Xiaoyun; Zha, Xiaojun; Dong, Xianxin; Fu, Yongcai; Wang, Xiangkun; Yang, Jinshui; Sun, Chuanqing

    2011-07-01

    Many rice breeding programs have currently reached yield plateaus as a result of limited genetic variability in parental strains. Dongxiang common wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and serves as an important gene pool for the genetic improvement of rice cultivars. In this study, heterotic loci (HLs) associated with six yield-related traits were identified in wild and cultivated rice and investigated using a set of 265 introgression lines (ILs) of O. rufipogon Griff. in the background of the Indica high-yielding cultivar Guichao 2 (O. sativa L.). Forty-two HLs were detected by a single point analysis of mid-parent heterosis values from test cross F(1) offspring, and 30 (71.5%) of these HLs showed significantly positive effects, consistent with the superiority shown by the F(1) test cross population in the six yield-related traits under study. Genetic mapping of hsp11, a locus responsible for the number of spikelets per panicle, confirmed the utility of these HLs. The results indicate that favorable HLs capable of improving agronomic traits are available. The identification of HLs between wild rice and cultivated rice could lead to a new strategy for the application of heterosis in rice breeding.

  5. Genome wide re-sequencing of newly developed Rice Lines from common wild rice (Oryza rufipogon Griff.) for the identification of NBS-LRR genes.

    PubMed

    Liu, Wen; Ghouri, Fozia; Yu, Hang; Li, Xiang; Yu, Shuhong; Shahid, Muhammad Qasim; Liu, Xiangdong

    2017-01-01

    Common wild rice (Oryza rufipogon Griff.) is an important germplasm for rice breeding, which contains many resistance genes. Re-sequencing provides an unprecedented opportunity to explore the abundant useful genes at whole genome level. Here, we identified the nucleotide-binding site leucine-rich repeat (NBS-LRR) encoding genes by re-sequencing of two wild rice lines (i.e. Huaye 1 and Huaye 2) that were developed from common wild rice. We obtained 128 to 147 million reads with approximately 32.5-fold coverage depth, and uniquely covered more than 89.6% (> = 1 fold) of reference genomes. Two wild rice lines showed high SNP (single-nucleotide polymorphisms) variation rate in 12 chromosomes against the reference genomes of Nipponbare (japonica cultivar) and 93-11 (indica cultivar). InDels (insertion/deletion polymorphisms) count-length distribution exhibited normal distribution in the two lines, and most of the InDels were ranged from -5 to 5 bp. With reference to the Nipponbare genome sequence, we detected a total of 1,209,308 SNPs, 161,117 InDels and 4,192 SVs (structural variations) in Huaye 1, and 1,387,959 SNPs, 180,226 InDels and 5,305 SVs in Huaye 2. A total of 44.9% and 46.9% genes exhibited sequence variations in two wild rice lines compared to the Nipponbare and 93-11 reference genomes, respectively. Analysis of NBS-LRR mutant candidate genes showed that they were mainly distributed on chromosome 11, and NBS domain was more conserved than LRR domain in both wild rice lines. NBS genes depicted higher levels of genetic diversity in Huaye 1 than that found in Huaye 2. Furthermore, protein-protein interaction analysis showed that NBS genes mostly interacted with the cytochrome C protein (Os05g0420600, Os01g0885000 and BGIOSGA038922), while some NBS genes interacted with heat shock protein, DNA-binding activity, Phosphoinositide 3-kinase and a coiled coil region. We explored abundant NBS-LRR encoding genes in two common wild rice lines through genome wide re

  6. Construction of a bacterial artificial chromosome (BAC) library of common wild rice (Oryza rufipogon Griff.) for map-based cloning of genes selected during the domestication of rice.

    PubMed

    Li, Xianran; Tan, LuBin; Huang, Haiyan; Zhu, Zuofeng; Li, Chenji; Hu, Songnian; Sun, Chuanqing

    2008-03-01

    As a prerequisite for the map-based cloning of genes from common wild rice (Oryza rufipogon Griff.), which plays an important role in the domestication of cultivated rice (O. sativa L.), we constructed a median-insert size bacterial artificial chromosome (BAC) library of the common wild rice isolate, YJCWR, collected from Yuanjiang, Yunnan Province, China. The library consists of 52,992 clones, with an average insert size of 50 kb, and all clones were pooled into 46 three-dimensional super-pools to facilitate library screening through the PCR method. Seventeen candidate clones were isolated by five markers and some clones containing putative target regions were sequenced. Furthermore, in analyzing the sequences of YJCWR, a retrotransposon, SZ-55, that might contribute to the evolution of Oryza was found.

  7. De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data.

    PubMed

    Tian, Xin-Jie; Long, Yan; Wang, Jiao; Zhang, Jing-Wen; Wang, Yan-Yan; Li, Wei-Min; Peng, Yu-Fa; Yuan, Qian-Hua; Pei, Xin-Wu

    2015-01-01

    The perennial O. rufipogon (common wild rice), which is considered to be the ancestor of Asian cultivated rice species, contains many useful genetic resources, including drought resistance genes. However, few studies have identified the drought resistance and tissue-specific genes in common wild rice. In this study, transcriptome sequencing libraries were constructed, including drought-treated roots (DR) and control leaves (CL) and roots (CR). Using Illumina sequencing technology, we generated 16.75 million bases of high-quality sequence data for common wild rice and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 119,332 unigenes with an average length of 715 bp. A total of 88,813 distinct sequences (74.42% of unigenes) significantly matched known genes in the NCBI NT database. Differentially expressed gene (DEG) analysis showed that 3617 genes were up-regulated and 4171 genes were down-regulated in the CR library compared with the CL library. Among the DEGs, 535 genes were expressed in roots but not in shoots. A similar comparison between the DR and CR libraries showed that 1393 genes were up-regulated and 315 genes were down-regulated in the DR library compared with the CR library. Finally, 37 genes that were specifically expressed in roots were screened after comparing the DEGs identified in the above-described analyses. This study provides a transcriptome sequence resource for common wild rice plants and establishes a digital gene expression profile of wild rice plants under drought conditions using the assembled transcriptome data as a reference. Several tissue-specific and drought-stress-related candidate genes were identified, representing a fully characterized transcriptome and providing a valuable resource for genetic and genomic studies in plants.

  8. Identification of microRNAs in Response to Drought in Common Wild Rice (Oryza rufipogon Griff.) Shoots and Roots.

    PubMed

    Zhang, Jing-Wen; Long, Yan; Xue, Man-de; Xiao, Xing-Guo; Pei, Xin-Wu

    2017-01-01

    Drought is the most important factor that limits rice production in drought-prone environments. Plant microRNAs (miRNAs) are involved in biotic and abiotic stress responses. Common wild rice (Oryza rufipogon Griff.) contains abundant drought-resistant genes, which provide an opportunity to explore these excellent resources as contributors to improve rice resistance, productivity, and quality. In this study, we constructed four small RNA libraries, called CL and CR from PEG6000-free samples and DL and DR from PEG6000-treated samples, where 'R' indicates the root tissue and 'L' indicates the shoot tissue. A total of 200 miRNAs were identified to be differentially expressed under the drought-treated conditions (16% PEG6000 for 24 h), and the changes in the miRNA expression profile of the shoot were distinct from those of the root. At the miRNA level, 77 known miRNAs, which belong to 23 families, including 40 up-regulated and 37 down-regulated in the shoot, and 85 known miRNAs in 46 families, including 65 up-regulated and 20 down-regulated in the root, were identified as differentially expressed. In addition, we predicted 26 new miRNA candidates from the shoot and 43 from the root that were differentially expressed during the drought stress. The quantitative real-time PCR analysis results were consistent with high-throughput sequencing data. Moreover, 88 miRNAs that were differentially-expressed were predicted to match with 197 targets for drought-stress. Our results suggest that the miRNAs of O. rufipogon are responsive to drought stress. The differentially expressed miRNAs that are tissue-specific under drought conditions could play different roles in the regulation of the auxin pathway, the flowering pathway, the drought pathway, and lateral root formation. Thus, the present study provides an account of tissue-specific miRNAs that are involved in the drought adaption of O. rufipogon.

  9. Identification of microRNAs in Response to Drought in Common Wild Rice (Oryza rufipogon Griff.) Shoots and Roots

    PubMed Central

    Zhang, Jing-wen; Long, Yan; Xue, Man-de; Xiao, Xing-guo; Pei, Xin-wu

    2017-01-01

    Background Drought is the most important factor that limits rice production in drought-prone environments. Plant microRNAs (miRNAs) are involved in biotic and abiotic stress responses. Common wild rice (Oryza rufipogon Griff.) contains abundant drought-resistant genes, which provide an opportunity to explore these excellent resources as contributors to improve rice resistance, productivity, and quality. Results In this study, we constructed four small RNA libraries, called CL and CR from PEG6000-free samples and DL and DR from PEG6000-treated samples, where ‘R’ indicates the root tissue and ‘L’ indicates the shoot tissue. A total of 200 miRNAs were identified to be differentially expressed under the drought-treated conditions (16% PEG6000 for 24 h), and the changes in the miRNA expression profile of the shoot were distinct from those of the root. At the miRNA level, 77 known miRNAs, which belong to 23 families, including 40 up-regulated and 37 down-regulated in the shoot, and 85 known miRNAs in 46 families, including 65 up-regulated and 20 down-regulated in the root, were identified as differentially expressed. In addition, we predicted 26 new miRNA candidates from the shoot and 43 from the root that were differentially expressed during the drought stress. The quantitative real-time PCR analysis results were consistent with high-throughput sequencing data. Moreover, 88 miRNAs that were differentially-expressed were predicted to match with 197 targets for drought-stress. Conclusion Our results suggest that the miRNAs of O. rufipogon are responsive to drought stress. The differentially expressed miRNAs that are tissue-specific under drought conditions could play different roles in the regulation of the auxin pathway, the flowering pathway, the drought pathway, and lateral root formation. Thus, the present study provides an account of tissue-specific miRNAs that are involved in the drought adaption of O. rufipogon. PMID:28107426

  10. Identification and Functional Analysis of Flowering Related microRNAs in Common Wild Rice (Oryza rufipogon Griff.)

    PubMed Central

    Dong, Yibo; Yuan, Qianhua; Wang, Feng; Li, Weimin; Jiang, Ying; Jia, Shirong; Pei, XinWu

    2013-01-01

    Background MicroRNAs (miRNAs) is a class of non-coding RNAs involved in post- transcriptional control of gene expression, via degradation and/or translational inhibition. Six-hundred sixty-one rice miRNAs are known that are important in plant development. However, flowering-related miRNAs have not been characterized in Oryza rufipogon Griff. It was approved by supervision department of Guangdong wild rice protection. We analyzed flowering-related miRNAs in O. rufipogon using high-throughput sequencing (deep sequencing) to understand the changes that occurred during rice domestication, and to elucidate their functions in flowering. Results Three O. rufipogon sRNA libraries, two vegetative stage (CWR-V1 and CWR-V2) and one flowering stage (CWR-F2) were sequenced using Illumina deep sequencing. A total of 20,156,098, 21,531,511 and 20,995,942 high quality sRNA reads were obtained from CWR-V1, CWR-V2 and CWR-F2, respectively, of which 3,448,185, 4,265,048 and 2,833,527 reads matched known miRNAs. We identified 512 known rice miRNAs in 214 miRNA families and predicted 290 new miRNAs. Targeted functional annotation, GO and KEGG pathway analyses predicted that 187 miRNAs regulate expression of flowering-related genes. Differential expression analysis of flowering-related miRNAs showed that: expression of 95 miRNAs varied significantly between the libraries, 66 are flowering-related miRNAs, such as oru-miR97, oru-miR117, oru-miR135, oru-miR137, et al. 17 are early-flowering -related miRNAs, including osa-miR160f, osa-miR164d, osa-miR167d, osa-miR169a, osa-miR172b, oru-miR4, et al., induced during the floral transition. Real-time PCR revealed the same expression patterns as deep sequencing. miRNAs targets were confirmed for cleavage by 5′-RACE in vivo, and were negatively regulated by miRNAs. Conclusions This is the first investigation of flowering miRNAs in wild rice. The result indicates that variation in miRNAs occurred during rice domestication and lays a foundation

  11. Archeological evidence for utilizaton of wild rice.

    PubMed

    Johnson, E

    1969-01-17

    The use of wild rice during the late prehistoric period is suggested by charred wild rice grains associated with fire hearths and threshing pits in historically known, specialized harvesting sites. Similar wild rice grains imbedded in the clay lining of specialized threshing pits called "jig pots" confirms the prehistoric use.

  12. Unraveling the secrets of rice wild species

    USDA-ARS?s Scientific Manuscript database

    The rice wild species (Oryza spp.) genepool is a relatively untapped source of novel alleles for crop improvement. Several different accessions of rice wild species have been crossed as donor parents with several different Asian rice (O. sativa) cultivars, as the recurrent parent to develop mappi...

  13. Health-Promoting Compounds in Pigmented Thai and Wild Rice

    PubMed Central

    Melini, Valentina; Acquistucci, Rita

    2017-01-01

    Organic pigmented Thai rice and wild rice are commonly available in specialized Italian markets and food shops, and they are gaining popularity among consumers demanding healthy foods. Indeed, the typical colour of kernels, which is the unique characteristic of pigmented cereals, is due to the accumulation of pigments that are also responsible for a number of healthy effects. The aim of this study was to provide a portrait of two organic pigmented Thai rice varieties from Thailand and one wild rice variety from Canada, imported into Italy and at Italian consumers’ disposal. To this end, the proximate composition and the content of health-promoting compounds, such as carotenoids, anthocyanins and phenolic compounds, were determined in Thai and wild rice. Moreover, the effect of cooking on phytochemicals was assessed, in order to provide reliable data on the dietary intake of bioactive compounds by samples under investigation. Results show that studied samples have a content of phytochemicals higher than white rice and comparable to other cereals. The cooking process determined a decrease of bioactive compounds in all varieties under investigation. However, some samples were found more resistant to cooking stress, and some phytochemicals were little affected by this process. Therefore, pigmented Thai and wild rice may represent a valuable source of healthy compounds and an alternative to other wholesome foods required by consumers. PMID:28231088

  14. Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication.

    PubMed

    Zhang, Fantao; Xu, Tao; Mao, Linyong; Yan, Shuangyong; Chen, Xiwen; Wu, Zhenfeng; Chen, Rui; Luo, Xiangdong; Xie, Jiankun; Gao, Shan

    2016-04-26

    It is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetically elucidate the substantially phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level. Instead of comparing two assembled genomes, this study directly compared the Dongxiang wild rice (DXWR) Illumina sequencing reads with the Nipponbare (O. sativa) complete genome without assembly of the DXWR genome. Based on the results from the comparative genomics analysis, structural variations (SVs) between DXWR and Nipponbare were determined to locate deleted genes which could have been acquired by Nipponbare during rice domestication. To overcome the limit of the SV detection, the DXWR transcriptome was also sequenced and compared with the Nipponbare transcriptome to discover the genes which could have been lost in DXWR during domestication. Both 1591 Nipponbare-acquired genes and 206 DXWR-lost transcripts were further analyzed using annotations from multiple sources. The NGS data are available in the NCBI SRA database with ID SRP070627. These results help better understanding the domestication from wild rice to cultivated rice at the whole genome level and provide a genomic data resource for rice genetic research or breeding. One finding confirmed transposable elements contribute greatly to the genome evolution from wild rice to cultivated rice. Another finding suggested the photophosphorylation and oxidative phosphorylation system in cultivated rice could have adapted to environmental changes simultaneously during domestication.

  15. Maple Sugar Harvesting/Wild Rice Harvesting.

    ERIC Educational Resources Information Center

    Minneapolis Public Schools, MN.

    Comprised of two separate booklets, this resource unit assists elementary teachers in explaining how the Ojibwe people harvest maple sugar and wild rice. The first booklet explains the procedure of tapping the maple trees for sap, preparation for boiling the sap, and the three forms the sugar is made into (granulated, "molded," and…

  16. Molecular structures and properties of starches of Australian wild rice.

    PubMed

    Tikapunya, Tiparat; Zou, Wei; Yu, Wenwen; Powell, Prudence O; Fox, Glen P; Furtado, Agnelo; Henry, Robert J; Gilbert, Robert G

    2017-09-15

    Australian wild rices have significant genetic differences from domesticated rices, which might provide rices with different starch molecular structure and thus different functional properties. Molecular structure, gelatinization properties, and pasting behaviours of starch of three Australian wild rices (Oryza australiensis, taxa A (O. rufipogon like) and taxa B (O. meridionalis like)) were determined and compared to domesticated indica and japonica rice. These had higher amylose content, more shorter amylose chains and fewer short amylopectin chains, resulted in a high gelatinization temperature in these wild rices. Compared to domesticated japonica rice, taxa A had a lower pasting viscosity; taxa B had a similar pasting viscosity but lower final viscosity. The significantly different starch molecular structure from that of normal domesticated rices, and concomitantly different properties, suggest advantageous uses in products such as rice crackers or rice pudding, and a source of nutritionally-desirable slowly digestible starch. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Rubisco activity is associated with photosynthetic thermotolerance in a wild rice (Oryza meridionalis)

    USDA-ARS?s Scientific Manuscript database

    Oryza meridionalis is a wild species of rice, endemic to tropical Australia. It shares a significant genome homology with the common domesticated rice Oryza sativa. Exploiting the fact that the two species are highly related but O. meridionalis has superior heat tolerance, experiments were undertake...

  18. Nutritional constituents and health benefits of wild rice (Zizania spp.).

    PubMed

    Surendiran, Gangadaran; Alsaif, Maha; Kapourchali, Fatemeh Ramezani; Moghadasian, Mohammed H

    2014-04-01

    Wild rice (Zizania spp.) seems to have originated in North America and then dispersed into Eastern Asia and other parts of the world. Nutritional analysis shows that wild rice is rich in minerals, vitamins, protein, starch, dietary fiber, and various antioxidant phytochemicals, while it is low in fat. Wild rice has been recognized as a whole grain by the US Food and Drug Administration; in the North American marketplace it is currently sold as and considered to be a health-promoting food. Recent scientific studies have revealed antioxidant and lipid-lowering properties of wild rice, while others have documented cardiovascular benefits associated with the long-term consumption of wild rice in experimental settings. The present review article summarizes various features of wild rice and its cultivation, including its plantation, harvest, nutritional composition, and biological properties. While evidence for the cardiovascular benefits of wild rice consumption is accumulating, additional studies are warranted to determine the clinical benefits of regular consumption of wild rice.

  19. 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.

  20. 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.

  1. LABA1, a Domestication Gene Associated with Long, Barbed Awns in Wild Rice[OPEN

    PubMed Central

    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

    2015-01-01

    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. PMID:26082172

  2. 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.

  3. A walk on the wild side: Oryza species as source for rice abiotic stress tolerance

    PubMed Central

    Menguer, Paloma Koprovski; Sperotto, Raul Antonio; Ricachenevsky, Felipe Klein

    2017-01-01

    Abstract Oryza sativa, the common cultivated rice, is one of the most important crops for human consumption, but production is increasingly threatened by abiotic stresses. Although many efforts have resulted in breeding rice cultivars that are relatively tolerant to their local environments, climate changes and population increase are expected to soon call for new, fast generation of stress tolerant rice germplasm, and current within-species rice diversity might not be enough to overcome such needs. The Oryza genus contains other 23 wild species, with only Oryza glaberrima being also domesticated. Rice domestication was performed with a narrow genetic diversity, and the other Oryza species are a virtually untapped genetic resource for rice stress tolerance improvement. Here we review the origin of domesticated Oryza sativa from wild progenitors, the ecological and genomic diversity of the Oryza genus, and the stress tolerance variation observed for wild Oryza species, including the genetic basis underlying the tolerance mechanisms found. The summary provided here is important to indicate how we should move forward to unlock the full potential of these germplasms for rice improvement. PMID:28323300

  4. Fungicide sensitivity in the wild rice pathogen Bipolaris oryzae

    USDA-ARS?s Scientific Manuscript database

    In recent years the occurrence of fungal brown spot, caused by Bipolaris oryzae has increased in cultivated wild rice (Zizania palustris) paddies in spite of the use of fungicides. To implement an efficient integrated disease management system, we are exploring whether field isolates have developed ...

  5. 7 CFR 1412.62 - Fruit, vegetable, and wild rice acreage reporting violations.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 10 2014-01-01 2014-01-01 false Fruit, vegetable, and wild rice acreage reporting... Contract Violations and Reduction in Payments § 1412.62 Fruit, vegetable, and wild rice acreage reporting violations. (a)(1) If an acreage report of fruits, vegetables, or wild rice planted on base acreage of a farm...

  6. 7 CFR 1412.62 - Fruit, vegetable, and wild rice acreage reporting violations.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Fruit, vegetable, and wild rice acreage reporting... Contract Violations and Reduction in Payments § 1412.62 Fruit, vegetable, and wild rice acreage reporting violations. (a)(1) If an acreage report of fruits, vegetables, or wild rice planted on base acreage of a farm...

  7. 7 CFR 1412.62 - Fruit, vegetable, and wild rice acreage reporting violations.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 10 2011-01-01 2011-01-01 false Fruit, vegetable, and wild rice acreage reporting... Contract Violations and Reduction in Payments § 1412.62 Fruit, vegetable, and wild rice acreage reporting violations. (a)(1) If an acreage report of fruits, vegetables, or wild rice planted on base acreage of a farm...

  8. 7 CFR 1412.62 - Fruit, vegetable, and wild rice acreage reporting violations.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 10 2013-01-01 2013-01-01 false Fruit, vegetable, and wild rice acreage reporting... Contract Violations and Reduction in Payments § 1412.62 Fruit, vegetable, and wild rice acreage reporting violations. (a)(1) If an acreage report of fruits, vegetables, or wild rice planted on base acreage of a farm...

  9. 7 CFR 1412.62 - Fruit, vegetable, and wild rice acreage reporting violations.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 10 2012-01-01 2012-01-01 false Fruit, vegetable, and wild rice acreage reporting... Contract Violations and Reduction in Payments § 1412.62 Fruit, vegetable, and wild rice acreage reporting violations. (a)(1) If an acreage report of fruits, vegetables, or wild rice planted on base acreage of a farm...

  10. Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication.

    PubMed

    Wang, Yu; Bai, Xuefei; Yan, Chenghai; Gui, Yiejie; Wei, Xinghua; Zhu, Qian-Hao; Guo, Longbiao; Fan, Longjiang

    2012-11-01

    The lack of a MIRNA set and genome sequence of wild rice (Oryza rufipogon) has prevented us from determining the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O. rufipogon were sequenced by Illumina platform and the expression levels of microRNAs (miRNAs) were investigated by miRNA chips. A de novo O. rufipogon genome was assembled using c. 55× coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on c. 5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these, O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting a loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression differences between wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated that MIRNA genes, like protein-coding genes, might have been significantly shaped during rice domestication and could be one of the driving forces that contributed to rice domestication.

  11. Modern elite rice varieties of the 'Green Revolution' have retained a large introgression from wild rice around the Pi33 rice blast resistance locus.

    PubMed

    Ballini, Elsa; Berruyer, Romain; Morel, Jean-Benoît; Lebrun, Marc-Henri; Nottéghem, Jean-Loup; Tharreau, Didier

    2007-01-01

    During the breeding process of cultivated crops, resistance genes to pests and diseases are commonly introgressed from wild species. The size of these introgressions is predicted by theoretical models but has rarely been measured in cultivated varieties. By combining resistance tests with isogenic strains, genotyping and sequencing of different rice accessions, it was shown that, in the elite rice variety IR64, the resistance conferring allele of the rice blast resistance gene Pi33 was introgressed from the wild rice Oryza rufipogon (accession IRGC101508). Further characterization of this introgression revealed a large introgression at this locus in IR64 and the related variety IR36. The introgressed fragment represents approximately half of the short arm of rice chromosome 8. This is the first report of a large introgression in a cultivated variety of rice. Such a large introgression is likely to have been maintained during backcrossing only if a selection pressure was exerted on this genomic region. The possible traits that were selected are discussed.

  12. Heavy metals in wild rice from northern Wisconsin

    USGS Publications Warehouse

    Bennett, J.P.; Chiriboga, E.; Coleman, J.; Waller, D.M.

    2000-01-01

    Wild rice grain samples from various parts of the world have been found to have elevated concentrations of heavy metals, raising concern for potential effects on human health. It was hypothesized that wild rice from north-central Wisconsin could potentially have elevated concentrations of some heavy metals because of possible exposure to these elements from the atmosphere or from water and sediments. In addition, no studies of heavy metals in wild rice from Wisconsin had been performed, and a baseline study was needed for future comparisons. Wild rice plants were collected from four areas in Bayfield, Forest, Langlade, Oneida, Sawyer and Wood Counties in September, 1997 and 1998 and divided into four plant parts for elemental analyses: roots, stems, leaves and seeds. A total of 194 samples from 51 plants were analyzed across the localities, with an average of 49 samples per part depending on the element. Samples were cleaned of soil, wet digested, and analyzed by ICP for Ag, As, Cd, Cr, Cu, Hg, Mg, Pb, Se and Zn. Roots contained the highest concentrations of Ag, As, Cd, Cr, Hg, Pb, and Se. Copper was highest in both roots and seeds, while Zn was highest just in seeds. Magnesium was highest in leaves. Seed baseline ranges for the 10 elements were established using the 95% confidence intervals of the medians. Wild rice plants from northern Wisconsin had normal levels of the nutritional elements Cu, Mg and Zn in the seeds. Silver, Cd, Hg, Cr, and Se were very low in concentration or within normal limits for food plants. Arsenic and Pb, however, were elevated and could pose a problem for human health. The pathway for As, Hg and Pb to the plants could be atmospheric.

  13. Evaluation of genetic variation among wild rice populations in Cambodia

    PubMed Central

    Orn, Chhourn; Shishido, Rieko; Akimoto, Masahiro; Ishikawa, Ryo; Htun, Than Myint; Nonomura, Ken-Ichi; Koide, Yohei; Sarom, Men; Vang, Seng; Sophany, Sakhan; Makara, Ouk; Ishii, Takashige

    2015-01-01

    A total of 448 samples in five natural populations of wild rice (Oryza rufipogon) were collected in Cambodia. They were examined using 12 SSR and two chloroplast markers to evaluate the degree of variation among populations and the genetic structure within populations. In the two annual populations, the number of plants with homozygous alleles at all 12 SSR loci were high (66.3% and 79.5%), suggesting that these plants propagate mainly through self-pollination. In the three perennial populations, no individuals had all homozygous genotypes, but redundant genotypes resulted from clonal propagation were observed. Percentages of the redundant genotypes were highly varied (3.6%, 29.2% and 86.0%). This may be due to the different stable levels of environmental conditions. As for chloroplast genome, most of the wild plants showed the same chloroplast types as most Indica-type cultivars have. However, plants with different chloroplast types were maintained, even in the same population. In tropical Asian countries, many wild rice populations were observed under similar ecological conditions examined in this study. Therefore, the present results concerning population structure will be important to further elucidate genetic features of wild rice, and will also give strong clues to utilize and conserve wild natural genetic resources. PMID:26719746

  14. Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice.

    PubMed

    Brozynska, Marta; Copetti, Dario; Furtado, Agnelo; Wing, Rod A; Crayn, Darren; Fox, Glen; Ishikawa, Ryuji; Henry, Robert J

    2016-11-27

    The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.

  15. Molecular evolution of the Pi-ta gene resistant to rice blast in wild rice (Oryza rufipogon).

    PubMed

    Huang, Chun-Lin; Hwang, Shih-Ying; Chiang, Yu-Chung; Lin, Tsan-Piao

    2008-07-01

    Rice blast disease resistance to the fungal pathogen Magnaporthe grisea is triggered by a physical interaction between the protein products of the host R (resistance) gene, Pi-ta, and the pathogen Avr (avirulence) gene, AVR-pita. The genotype variation and resistant/susceptible phenotype at the Pi-ta locus of wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. sativa), was surveyed in 36 locations worldwide to study the molecular evolution and functional adaptation of the Pi-ta gene. The low nucleotide polymorphism of the Pi-ta gene of O. rufipogon was similar to that of O. sativa, but greatly differed from what has been reported for other O. rufipogon genes. The haplotypes can be subdivided into two divergent haplogroups named H1 and H2. H1 is derived from H2, with nearly no variation and at a low frequency. H2 is common and is the ancestral form. The leucine-rich repeat (LRR) domain has a high pi(non)/pi(syn) ratio, and the low polymorphism of the Pi-ta gene might have primarily been caused by recurrent selective sweep and constraint by other putative physiological functions. Meanwhile, we provide data to show that the amino acid Ala-918 of H1 in the LRR domain has a close relationship with the resistant phenotype. H1 might have recently arisen during rice domestication and may be associated with the scenario of a blast pathogen-host shift from Italian millet to rice.

  16. Development and Evaluation of Chromosome Segment Substitution Lines Carrying Overlapping Chromosome Segments of the Whole Wild Rice Genome

    PubMed Central

    Yang, Dewei; Ye, Xinfu; Zheng, Xianghua; Cheng, Chaoping; Ye, Ning; Huang, Fenghuang

    2016-01-01

    Common wild rice (Oryza rufipogon Griff.) represents an important resource for rice improvement. Genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segment substitution lines (CSSLs) are most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs). In this study, 146 CSSLs were produced; they were derived from the crossing and back-crossing of two rice cultivars: Dongnanihui 810 (Oryza sativa L.), an indica rice cultivar as the recipient, and ZhangPu wild rice, a wild rice cultivar as the donor. First, a physical map of the 146 CSSLs was constructed using 149 molecular markers. Based on this map, the total size of the 147 substituted segments in the population was 1145.65 Mb, or 3.04 times that of the rice genome. To further facilitate gene mapping, heterozygous chromosome segment substitution lines (HCSSLs) were also produced, which were heterozygous in the target regions. Second, a physical map of the 244 HCSSLs was produced using 149 molecular markers. Based on this map, the total length of substituted segments in the HCSSLs was 1683.75 Mb, or 4.47 times the total length of the rice genome. Third, using the 146 CSSLs, two QTLs for plant height, and one major QTL for apiculus coloration were identified. Using the two populations of HCSSLs, the qPa-6-2 gene was precisely mapped to an 88 kb region. These CSSLs and HCSSLs may, therefore, provide powerful tools for future whole genome large-scale gene discovery in wild rice, providing a foundation enabling the development of new rice varieties. This research will also facilitate fine mapping and cloning of quantitative trait genes, providing for the development of superior rice varieties. PMID:27933072

  17. Infanticide and cannibalism in wild common marmosets.

    PubMed

    Melo, L; Mendes Pontes, A R; Monteiro da Cruz, M A O

    2003-01-01

    Infanticide has been observed in many different species [1], including common marmosets [2-4], due to sexual selection, reproductive strategies or resource competition [3, 5, 6], which may ultimately lead to exploitation (cannibalism) [1, 7]. Wild callithrichids have a very flexible mating system, including monogamy, polygynandry, polyandry and polygyny [4, 8, 9], with Monteiro da Cruz [10] finding all these patterns within the same population. This results from the high degree of deforestation of their habitat [4], but non-monogamous groups cannot ensure successful rearing of infants, since helpers are crucial and should be present in high numbers [11]. In this study, we show for the first time that cannibalism can follow infanticide, and we hypothesise that it is a result of both competition for scarce resources and the need for animal protein, exacerbated by forest degradation.

  18. Bulliform Phytolith Research in Wild and Domesticated Rice Paddy Soil in South China

    PubMed Central

    Huan, Xiujia; Lu, Houyuan; Wang, Can; Tang, Xiangan; Zuo, Xinxin; Ge, Yong; He, Keyang

    2015-01-01

    Bulliform phytoliths play an important role in researching rice origins as they can be used to distinguish between wild and domesticated rice. Rice bulliform phytoliths are characterized by numerous small shallow fish-scale decorations on the lateral side. Previous studies have shown that domesticated rice has a larger number of these decorations than wild rice and that the number of decorations ≥9 is a useful feature for identifying domesticated rice. However, this standard was established based on limited samples of modern rice plants. In this study, we analyzed soil samples from both wild and domesticated rice paddies. Results showed that, in wild rice soil samples, the proportion of bulliform phytoliths with ≥9 decorations was 17.46% ± 8.29%, while in domesticated rice soil samples, the corresponding proportion was 63.70% ± 9.22%. This suggests that the proportion of phytoliths with ≥9 decorations can be adopted as a criterion for discriminating between wild and domesticated rice in prehistoric soil. This indicator will be of significance in improving the application of fish-scale decorations to research into rice origins and the rice domestication process. PMID:26488583

  19. Bulliform Phytolith Research in Wild and Domesticated Rice Paddy Soil in South China.

    PubMed

    Huan, Xiujia; Lu, Houyuan; Wang, Can; Tang, Xiangan; Zuo, Xinxin; Ge, Yong; He, Keyang

    2015-01-01

    Bulliform phytoliths play an important role in researching rice origins as they can be used to distinguish between wild and domesticated rice. Rice bulliform phytoliths are characterized by numerous small shallow fish-scale decorations on the lateral side. Previous studies have shown that domesticated rice has a larger number of these decorations than wild rice and that the number of decorations ≥9 is a useful feature for identifying domesticated rice. However, this standard was established based on limited samples of modern rice plants. In this study, we analyzed soil samples from both wild and domesticated rice paddies. Results showed that, in wild rice soil samples, the proportion of bulliform phytoliths with ≥9 decorations was 17.46% ± 8.29%, while in domesticated rice soil samples, the corresponding proportion was 63.70% ± 9.22%. This suggests that the proportion of phytoliths with ≥9 decorations can be adopted as a criterion for discriminating between wild and domesticated rice in prehistoric soil. This indicator will be of significance in improving the application of fish-scale decorations to research into rice origins and the rice domestication process.

  20. Endophytic Colonization and In Planta Nitrogen Fixation by a Herbaspirillum sp. Isolated from Wild Rice Species

    PubMed Central

    Elbeltagy, Adel; Nishioka, Kiyo; Sato, Tadashi; Suzuki, Hisa; Ye, Bin; Hamada, Toru; Isawa, Tsuyoshi; Mitsui, Hisayuki; Minamisawa, Kiwamu

    2001-01-01

    Nitrogen-fixing bacteria were isolated from the stems of wild and cultivated rice on a modified Rennie medium. Based on 16S ribosomal DNA (rDNA) sequences, the diazotrophic isolates were phylogenetically close to four genera: Herbaspirillum, Ideonella, Enterobacter, and Azospirillum. Phenotypic properties and signature sequences of 16S rDNA indicated that three isolates (B65, B501, and B512) belong to the Herbaspirillum genus. To examine whether Herbaspirillum sp. strain B501 isolated from wild rice, Oryza officinalis, endophytically colonizes rice plants, the gfp gene encoding green fluorescent protein (GFP) was introduced into the bacteria. Observations by fluorescence stereomicroscopy showed that the GFP-tagged bacteria colonized shoots and seeds of aseptically grown seedlings of the original wild rice after inoculation of the seeds. Conversely, for cultivated rice Oryza sativa, no GFP fluorescence was observed for shoots and only weak signals were observed for seeds. Observations by fluorescence and electron microscopy revealed that Herbaspirillum sp. strain B501 colonized mainly intercellular spaces in the leaves of wild rice. Colony counts of surface-sterilized rice seedlings inoculated with the GFP-tagged bacteria indicated significantly more bacterial populations inside the original wild rice than in cultivated rice varieties. Moreover, after bacterial inoculation, in planta nitrogen fixation in young seedlings of wild rice, O. officinalis, was detected by the acetylene reduction and 15N2 gas incorporation assays. Therefore, we conclude that Herbaspirillum sp. strain B501 is a diazotrophic endophyte compatible with wild rice, particularly O. officinalis. PMID:11679357

  1. Factors Affecting the Distribution of Wild Rice (Zizania palustris) and the Surrounding Macrophyte Community.

    NASA Astrophysics Data System (ADS)

    Pillsbury, R. W.; McGuire, M.

    2005-05-01

    A recent decline in wild rice wetlands is cause for concern due to its importance as a food source, refuge for wildlife, and cultural significance. Sixty wetlands in Wisconsin and Minnesota (USA) were sampled, with approximately equal numbers displaying dense, moderate and sparse wild rice production. Chemical, physical, and watershed parameters were measured as well as macrophyte densities. Data were analyzed using multivariate statistics (CCA). Moderate levels of phosphorus appear beneficial to the overall success of wild rice, while free-floating macrophytes show an overwhelming positive response to higher levels of P. The distribution of macrophytes bordering wild rice beds is correlated to pH,with Potamogeton robbinsii and filamentous green algae responding most strongly to its increase. Healthy stands of wild rice exhibit a narrow circum-neutral range of pH (6.1-8.0)which is significantly different from the greater range exhibited by sparse wild rice wetlands (6.5-8.5). This pattern was paralleled when considering depth which suggests that deeper wetlands may be more susceptible to wild rice loss. Management of existing wild rice wetlands should focus monitoring on pH, depth, phosphorus concentrations and shore development. We are currently using this data base to locate the best reintroduction sites for wild rice.

  2. Small brown planthopper resistance loci in wild rice (Oryza officinalis).

    PubMed

    Zhang, Weilin; Dong, Yan; Yang, Ling; Ma, Bojun; Ma, Rongrong; Huang, Fudeng; Wang, Changchun; Hu, Haitao; Li, Chunshou; Yan, Chengqi; Chen, Jianping

    2014-06-01

    Host-plant resistance is the most practical and economical approach to control the rice planthoppers. However, up to date, few rice germplasm accessions that are resistant to the all three kinds of planthoppers (1) brown planthopper (BPH; Nilaparvata lugens Stål), (2) the small brown planthopper (SBPH; Laodelphax striatellus Fallen), and (3) the whitebacked planthopper (WBPH, Sogatella furcifera Horvath) have been identified; consequently, the genetic basis for host-plant broad spectrum resistance to rice planthoppers in a single variety has been seldom studied. Here, one wild species, Oryza officinalis (Acc. HY018, 2n = 24, CC), was detected showing resistance to the all three kinds of planthoppers. Because resistance to WBPH and BPH in O. officinalis has previously been reported, the study mainly focused on its SBPH resistance. The SBPH resistance gene(s) was (were) introduced into cultivated rice via asymmetric somatic hybridization. Three QTLs for SBPH resistance detected by the SSST method were mapped and confirmed on chromosomes 3, 7, and 12, respectively. The allelic/non-allelic relationship and relative map positions of the three kinds of planthopper resistance genes in O. officinalis show that the SBPH, WBPH, and BPH resistance genes in O. officinalis were governed by multiple genes, but not by any major gene. The data on the genetics of host-plant broad spectrum resistance to planthoppers in a single accession suggested that the most ideally practical and economical approach for rice breeders is to screen the sources of broad spectrum resistance to planthoppers, but not to employ broad spectrum resistance gene for the management of planthoppers. Pyramiding these genes in a variety can be an effective way for the management of planthoppers.

  3. Studies on mineral nutrition and safety of wild rice (Oryza L.).

    PubMed

    Jiang, Shuli; Shi, Chunhai; Wu, Jianguo

    2009-01-01

    Mineral element contents of five wild rice were analyzed, including mineral nutrient elements such as phosphorus (P), potassium (K), calcium (Ca), sodium (Na), magnesium (Mg), iron (Fe), zinc (Zn), copper (Cu), manganese (Mn) and selenium (Se), and the potential toxic elements arsenic (As), mercury (Hg), lead (Pb) and cadmium (Cd). The results showed that the contents of K, Mg, Fe, Zn, Cu, Mn and Se in five wild rice materials were much higher than the cultivate variety Zhou 903 in both brown and milled rice. Wild rice also had lower potential toxic element contents of Hg, Pb and Cd compared with Zhou 903 in brown rice and milled rice, respectively. Among five wild rice samples, WR-3 from Uganda had the highest level of P, K, Ca, Na, Mg, Fe, Zn, Mn and Se, and the lowest contents of Hg, Pb and Cd.

  4. 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. © 2014 John Wiley & Sons Ltd.

  5. Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice.

    PubMed

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

    2016-12-01

    Understanding population structure of the wild progenitor of Asian cultivated rice (O. sativa), the Oryza rufipogon species complex (ORSC), is of interest to plant breeders and contributes to our understanding of rice domestication. A collection of 286 diverse ORSC accessions was evaluated for nuclear variation using genotyping-by-sequencing (113,739 SNPs) and for chloroplast variation using Sanger sequencing (25 polymorphic sites). Six wild subpopulations were identified, with 25 % of accessions classified as admixed. Three of the wild groups were genetically and geographically closely related to the O. sativa subpopulations, indica, aus and japonica, and carried O. sativa introgressions; the other three wild groups were genetically divergent, had unique chloroplast haplotypes, and were located at the geographical extremes of the species range. The genetic subpopulations were significantly correlated (r (2) = 0.562) with traditional species designations, O. rufipogon (perennial) and O. nivara (annual), differentiated based on morphology and life history. A wild diversity panel of 95 purified (inbred) accessions was developed for future genetic studies. Our results suggest that the cultivated aus subpopulation is most closely related to an annual wild relative, japonica to a perennial wild relative, and indica to an admixed population of diverse annual and perennial wild ancestors. Gene flow between ORSC and O. sativa is common in regions where rice is cultivated, threatening the identity and diversity of wild ORSC populations. The three geographically isolated ORSC populations harbor variation rarely seen in cultivated rice and provide a unique window into the genetic composition of ancient rice subpopulations.

  6. Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa

    PubMed Central

    Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania

    2016-01-01

    Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica. PMID:27077002

  7. Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa.

    PubMed

    Fuchs, Eric J; Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania; Arrieta-Espinoza, Griselda

    2016-01-01

    Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.

  8. Evaluation of Genetic Diversity and Development of a Core Collection of Wild Rice (Oryza rufipogon Griff.) Populations in China

    PubMed Central

    Bai, Lin; Lu, Zhenzhen; Chen, Yuhong; Jiang, Lan; Diao, Mengyang; Liu, Xiangdong; Lu, Yonggen

    2015-01-01

    Common wild rice (Oryza rufipogon Griff.), the progenitor of Asian cultivated rice (O. sativa L.), is endangered due to habitat loss. The objectives of this research were to evaluate the genetic diversity of wild rice species in isolated populations and to develop a core collection of representative genotypes for ex situ conservation. We collected 885 wild rice accessions from eight geographically distinct regions and transplanted these accessions in a protected conservation garden over a period of almost two decades. We evaluated these accessions for 13 morphological or phenological traits and genotyped them for 36 DNA markers evenly distributed on the 12 chromosomes. The coefficient of variation of quantitative traits was 0.56 and ranged from 0.37 to 1.06. SSR markers detected 206 different alleles with an average of 6 alleles per locus. The mean polymorphism information content (PIC) was 0.64 in all populations, indicating that the marker loci have a high level of polymorphism and genetic diversity in all populations. Phylogenetic analyses based on morphological and molecular data revealed remarkable differences in the genetic diversity of common wild rice populations. The results showed that the Zengcheng, Gaozhou, and Suixi populations possess higher levels of genetic diversity, whereas the Huilai and Boluo populations have lower levels of genetic diversity than do the other populations. Based on their genetic distance, 130 accessions were selected as a core collection that retained over 90% of the alleles at the 36 marker loci. This genetically diverse core collection will be a useful resource for genomic studies of rice and for initiatives aimed at developing rice with improved agronomic traits. PMID:26720755

  9. Evaluation of Genetic Diversity and Development of a Core Collection of Wild Rice (Oryza rufipogon Griff.) Populations in China.

    PubMed

    Liu, Wen; Shahid, Muhammad Qasim; Bai, Lin; Lu, Zhenzhen; Chen, Yuhong; Jiang, Lan; Diao, Mengyang; Liu, Xiangdong; Lu, Yonggen

    2015-01-01

    Common wild rice (Oryza rufipogon Griff.), the progenitor of Asian cultivated rice (O. sativa L.), is endangered due to habitat loss. The objectives of this research were to evaluate the genetic diversity of wild rice species in isolated populations and to develop a core collection of representative genotypes for ex situ conservation. We collected 885 wild rice accessions from eight geographically distinct regions and transplanted these accessions in a protected conservation garden over a period of almost two decades. We evaluated these accessions for 13 morphological or phenological traits and genotyped them for 36 DNA markers evenly distributed on the 12 chromosomes. The coefficient of variation of quantitative traits was 0.56 and ranged from 0.37 to 1.06. SSR markers detected 206 different alleles with an average of 6 alleles per locus. The mean polymorphism information content (PIC) was 0.64 in all populations, indicating that the marker loci have a high level of polymorphism and genetic diversity in all populations. Phylogenetic analyses based on morphological and molecular data revealed remarkable differences in the genetic diversity of common wild rice populations. The results showed that the Zengcheng, Gaozhou, and Suixi populations possess higher levels of genetic diversity, whereas the Huilai and Boluo populations have lower levels of genetic diversity than do the other populations. Based on their genetic distance, 130 accessions were selected as a core collection that retained over 90% of the alleles at the 36 marker loci. This genetically diverse core collection will be a useful resource for genomic studies of rice and for initiatives aimed at developing rice with improved agronomic traits.

  10. WRKY transcription factor genes in wild rice Oryza nivara.

    PubMed

    Xu, Hengjian; Watanabe, Kenneth A; Zhang, Liyuan; Shen, Qingxi J

    2016-08-01

    The WRKY transcription factor family is one of the largest gene families involved in plant development and stress response. Although many WRKY genes have been studied in cultivated rice (Oryza sativa), the WRKY genes in the wild rice species Oryza nivara, the direct progenitor of O. sativa, have not been studied. O. nivara shows abundant genetic diversity and elite drought and disease resistance features. Herein, a total of 97 O. nivara WRKY (OnWRKY) genes were identified. RNA-sequencing demonstrates that OnWRKY genes were generally expressed at higher levels in the roots of 30-day-old plants. Bioinformatic analyses suggest that most of OnWRKY genes could be induced by salicylic acid, abscisic acid, and drought. Abundant potential MAPK phosphorylation sites in OnWRKYs suggest that activities of most OnWRKYs can be regulated by phosphorylation. Phylogenetic analyses of OnWRKYs support a novel hypothesis that ancient group IIc OnWRKYs were the original ancestors of only some group IIc and group III WRKYs. The analyses also offer strong support that group IIc OnWRKYs containing the HVE sequence in their zinc finger motifs were derived from group Ia WRKYs. This study provides a solid foundation for the study of the evolution and functions of WRKY genes in O. nivara. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  11. WRKY transcription factor genes in wild rice Oryza nivara

    PubMed Central

    Xu, Hengjian; Watanabe, Kenneth A.; Zhang, Liyuan; Shen, Qingxi J.

    2016-01-01

    The WRKY transcription factor family is one of the largest gene families involved in plant development and stress response. Although many WRKY genes have been studied in cultivated rice (Oryza sativa), the WRKY genes in the wild rice species Oryza nivara, the direct progenitor of O. sativa, have not been studied. O. nivara shows abundant genetic diversity and elite drought and disease resistance features. Herein, a total of 97 O. nivara WRKY (OnWRKY) genes were identified. RNA-sequencing demonstrates that OnWRKY genes were generally expressed at higher levels in the roots of 30-day-old plants. Bioinformatic analyses suggest that most of OnWRKY genes could be induced by salicylic acid, abscisic acid, and drought. Abundant potential MAPK phosphorylation sites in OnWRKYs suggest that activities of most OnWRKYs can be regulated by phosphorylation. Phylogenetic analyses of OnWRKYs support a novel hypothesis that ancient group IIc OnWRKYs were the original ancestors of only some group IIc and group III WRKYs. The analyses also offer strong support that group IIc OnWRKYs containing the HVE sequence in their zinc finger motifs were derived from group Ia WRKYs. This study provides a solid foundation for the study of the evolution and functions of WRKY genes in O. nivara. PMID:27345721

  12. Herbivory by resident geese: The loss and recovery of wild rice along the tidal Patuxent River

    USGS Publications Warehouse

    Haramis, G.M.; Kearns, G.D.

    2007-01-01

    Well known for a fall spectacle of maturing wild rice (Zizania aquatica) and migrant waterbirds, the tidal freshwater marshes of the Patuxent River, Maryland, USA, experienced a major decline in wild rice during the 1990s. We conducted experiments in 1999 and 2000 with fenced exclosures and discovered herbivory by resident Canada geese (Branta canadensis). Grazing by geese eliminated rice outside exclosures, whereas protected plants achieved greater size, density, and produced more panicles than rice occurring in natural stands. The observed loss of rice on the Patuxent River reflects both the sensitivity of this annual plant to herbivory and the destructive nature of an overabundance of resident geese on natural marsh vegetation. Recovery of rice followed 2 management actions: hunting removal of approximately 1,700 geese during a 4-year period and reestablishment of rice through a large-scale fencing and planting program.

  13. 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

  14. 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.

  15. Transcriptome Analysis of Salt Stress Responsiveness in the Seedlings of Dongxiang Wild Rice (Oryza rufipogon Griff.).

    PubMed

    Zhou, Yi; Yang, Ping; Cui, Fenglei; Zhang, Fantao; Luo, Xiangdong; Xie, Jiankun

    2016-01-01

    Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.), and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice.

  16. Transcriptome Analysis of Salt Stress Responsiveness in the Seedlings of Dongxiang Wild Rice (Oryza rufipogon Griff.)

    PubMed Central

    Zhou, Yi; Yang, Ping; Cui, Fenglei; Zhang, Fantao; Luo, Xiangdong; Xie, Jiankun

    2016-01-01

    Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.), and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice. PMID:26752408

  17. Rice production systems and avian influenza: Interactions between mixed-farming systems, poultry and wild birds

    USGS Publications Warehouse

    Muzaffar, S.B.; Takekawa, John Y.; Prosser, D.J.; Newman, S.H.; Xiao, X.

    2010-01-01

    Wild waterfowl are the reservoir for avian influenza viruses (AIVs), a family of RNA viruses that may cause mild sickness in waterbirds. Emergence of H5N1, a highly pathogenic avian influenza (HPAI) strain, causing severe disease and mortality in wild birds, poultry and humans, had raised concerns about the role of wild birds in possible transmission of the disease. In this review, the link between rice production systems, poultry production systems, and wild bird ecology is examined to assess the extent to which these interactions could contribute towards the persistence and evolution of HPAI H5N1. The rice (Oryza sativa) and poultry production systems in Asia described, and then migration and movements of wild birds discussed. Mixed farming systems in Asia and wild bird movement and migration patterns create opportunities for the persistence of low pathogenic AIVs in these systems. Nonetheless, there is no evidence of long-term persistence of HPAI viruses (including the H5N1 subtype) in the wild. There are still significant gaps in the understanding of how AIVs circulate in rice systems. A better understanding of persistence of AIVs in rice farms, particularly of poultry origins, is essential in limiting exchange of AIVs between mixed-farming systems, poultry and wild birds.

  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. Could abiotic stress tolerance in wild relatives of rice be used to improve Oryza sativa?

    PubMed

    Atwell, Brian J; Wang, Han; Scafaro, Andrew P

    2014-02-01

    Oryza sativa and Oryza glaberrima have been selected to acquire and partition resources efficiently as part of the process of domestication. However, genetic diversity in cultivated rice is limited compared to wild Oryza species, in spite of 120,000 genotypes being held in gene banks. By contrast, there is untapped diversity in the more than 20 wild species of Oryza, some having been collected from just a few coastal locations (e.g. Oryza schlechteri), while others are widely distributed (e.g. Oryza nivara and Oryza rufipogon). The extent of DNA sequence diversity and phenotypic variation is still being established in wild Oryza, with genetic barriers suggesting a vast range of morphologies and function even within species, such as has been demonstrated for Oryza meridionalis. With increasing climate variability and attempts to make more marginal land arable, abiotic and biotic stresses will be managed over the coming decades by tapping into the genetic diversity of wild relatives of O. sativa. To help create a more targeted approach to sourcing wild rice germplasm for abiotic stress tolerance, we have created a climate distribution map by plotting the natural occurrence of all Oryza species against corresponding temperature and moisture data. We then discuss interspecific variation in phenotype and its significance for rice, followed by a discussion of ways to integrate germplasm from wild relatives into domesticated rice. Crown Copyright © 2013. Published by Elsevier Ireland Ltd. All rights reserved.

  20. Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences.

    PubMed

    Wambugu, Peterson W; Brozynska, Marta; Furtado, Agnelo; Waters, Daniel L; Henry, Robert J

    2015-09-10

    Rice is the most important crop in the world, acting as the staple food for over half of the world's population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species, O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation.

  1. Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences

    PubMed Central

    Wambugu, Peterson W.; Brozynska, Marta; Furtado, Agnelo; Waters, Daniel L.; Henry, Robert J.

    2015-01-01

    Rice is the most important crop in the world, acting as the staple food for over half of the world’s population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species, O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation. PMID:26355750

  2. Mitochondrial Genome Analysis of Wild Rice (Oryza minuta) and Its Comparison with Other Related Species

    PubMed Central

    Asaf, Sajjad; Khan, Abdul Latif; Khan, Abdur Rahim; Waqas, Muhammad; Kang, Sang-Mo; Khan, Muhammad Aaqil; Shahzad, Raheem; Seo, Chang-Woo; Shin, Jae-Ho; Lee, In-Jung

    2016-01-01

    Oryza minuta (Poaceae family) is a tetraploid wild relative of cultivated rice with a BBCC genome. O. minuta has the potential to resist against various pathogenic diseases such as bacterial blight (BB), white backed planthopper (WBPH) and brown plant hopper (BPH). Here, we sequenced and annotated the complete mitochondrial genome of O. minuta. The mtDNA genome is 515,022 bp, containing 60 protein coding genes, 31 tRNA genes and two rRNA genes. The mitochondrial genome organization and the gene content at the nucleotide level are highly similar (89%) to that of O. rufipogon. Comparison with other related species revealed that most of the genes with known function are conserved among the Poaceae members. Similarly, O. minuta mt genome shared 24 protein-coding genes, 15 tRNA genes and 1 ribosomal RNA gene with other rice species (indica and japonica). The evolutionary relationship and phylogenetic analysis revealed that O. minuta is more closely related to O. rufipogon than to any other related species. Such studies are essential to understand the evolutionary divergence among species and analyze common gene pools to combat risks in the current scenario of a changing environment. PMID:27045847

  3. Expression profiling of common and specific defense responses of rice to Magnaporthe oryzae infection using deep sequencing technologies

    USDA-ARS?s Scientific Manuscript database

    Rice blast caused by Magnaporthe oryzae is a serious disease in rice production. Wild type Nipponbare and transgenic rice plants (carrying the Pi9 blast resistance gene) were challenged with the rice blast strain KJ201 to identify the early, mid and late host responses to M. oryzae infection at the ...

  4. Population Genetic Structure of Cochliobolus miyabeanus on Cultivated Wild Rice (Zizania palustris L.) in Minnesota

    USDA-ARS?s Scientific Manuscript database

    Cochliobolus miyabeanus (Bipolaris oryzae) is the causal agent of fungal brown spot (FBS) in wild rice (Zizania palustris L.), an aquatic grass, endemic in Minnesota, Wisconsin, and parts of Canada. Grain yield losses can reach up to 74% when the disease starts at the boot stage and continues until ...

  5. Variation in the nucleotide sequence of a prolamin gene family in wild rice.

    PubMed

    Barbier, P; Ishihama, A

    1990-07-01

    Variation in the DNA sequence of the 10 kDa prolamin gene family within the wild rice species Oryza rufipogon was probed using the direct sequencing of PCR-amplified genes. A comparison of the nucleotide and deduced amino-acid sequences of eight Asian strains of O. rufipogon and one strain of the related African species O. longistaminata is presented.

  6. 7 CFR 457.170 - Cultivated wild rice crop insurance provisions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... Cancellation date Termination date Mendocino, Glenn, Butte, and Sierra Counties, California; and all California... maximum price election for all the cultivated wild rice insured under this policy in the county. (b) The... cancellation date for counties with a February 28 cancellation date; and (b) June 30 preceding the cancellation...

  7. 7 CFR 457.170 - Cultivated wild rice crop insurance provisions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... Cancellation date Terminationdate Mendocino, Glenn, Butte, and Sierra Counties, California; and all California... maximum price election for all the cultivated wild rice insured under this policy in the county. (b) The... cancellation date for counties with a February 28 cancellation date; and (b) June 30 preceding the cancellation...

  8. 7 CFR 457.170 - Cultivated wild rice crop insurance provisions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Cancellation date Terminationdate Mendocino, Glenn, Butte, and Sierra Counties, California; and all California... maximum price election for all the cultivated wild rice insured under this policy in the county. (b) The... cancellation date for counties with a February 28 cancellation date; and (b) June 30 preceding the cancellation...

  9. 7 CFR 457.170 - Cultivated wild rice crop insurance provisions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Cancellation date Terminationdate Mendocino, Glenn, Butte, and Sierra Counties, California; and all California... maximum price election for all the cultivated wild rice insured under this policy in the county. (b) The... cancellation date for counties with a February 28 cancellation date; and (b) June 30 preceding the cancellation...

  10. 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.

  11. Inhibitory Effects of North American Wild Rice on Monocyte Adhesion and Inflammatory Modulators in LDL Receptor-Knockout Mice.

    PubMed

    Moghadasian, Mohammed H; Zhao, Ruozhi; Ghazzawi, Nora; Le, Khuong; Apea-Bah, Franklin B; Beta, Trust; Shen, Garry

    2017-09-25

    The present study examined the effects of wild rice on monocyte adhesion, inflammatory and fibrinolytic mediators in low-density lipoprotein receptor-knockout (LDLr-KO) mice. Male LDLr-KO mice received cholesterol (0.06%, w/w) supplemented diet with or without white rice or wild rice (60%, w/w) for 20 weeks. White rice significantly increased monocyte adhesion, abundances of monocyte chemoattractant protein-1, tissue necrosis factor-α, intracellular cell adhesion molecule-1, plasminogen activator inhibitor-1, urokinase plasminogen activator (uPA), and uPA receptor in aortae and hearts of LDLr-KO mice compared to control diet. Wild rice inhibited monocyte adhesion to aorta, atherosclerosis and the abundances of the inflammatory and fibrinolytic regulators in the cardiovascular tissue of LDLr-KO mice compared to white rice. White or wild rice did not significantly alter the levels of cholesterol, triglycerides, or antioxidant enzymes in plasma. The anti-atherosclerotic effect of wild rice may result from its inhibition on monocyte adhesion and inflammatory modulators in LDLr-KO mice.

  12. Ethnobotanical investigation of 'wild' food plants used by rice farmers in Kalasin, Northeast Thailand

    PubMed Central

    2011-01-01

    Background Wild food plants are a critical component in the subsistence system of rice farmers in Northeast Thailand. One of the important characteristics of wild plant foods among farming households is that the main collection locations are increasingly from anthropogenic ecosystems such as agricultural areas rather than pristine ecosystems. This paper provides selected results from a study of wild food conducted in several villages in Northeast Thailand. A complete botanical inventory of wild food plants from these communities and surrounding areas is provided including their diversity of growth forms, the different anthropogenic locations were these species grow and the multiplicity of uses they have. Methods Data was collected using focus groups and key informant interviews with women locally recognized as knowledgeable about contemporarily gathered plants. Plant species were identified by local taxonomists. Results A total of 87 wild food plants, belonging to 47 families were reported, mainly trees, herbs (terrestrial and aquatic) and climbers. Rice fields constitute the most important growth location where 70% of the plants are found, followed by secondary woody areas and home gardens. The majority of species (80%) can be found in multiple growth locations, which is partly explained by villagers moving selected species from one place to another and engaging in different degrees of management. Wild food plants have multiple edible parts varying from reproductive structures to vegetative organs. More than two thirds of species are reported as having diverse additional uses and more than half of them are also regarded as medicine. Conclusions This study shows the remarkable importance of anthropogenic areas in providing wild food plants. This is reflected in the great diversity of species found, contributing to the food and nutritional security of rice farmers in Northeast Thailand. PMID:22067578

  13. Ethnobotanical investigation of 'wild' food plants used by rice farmers in Kalasin, Northeast Thailand.

    PubMed

    Cruz-Garcia, Gisella S; Price, Lisa L

    2011-11-08

    Wild food plants are a critical component in the subsistence system of rice farmers in Northeast Thailand. One of the important characteristics of wild plant foods among farming households is that the main collection locations are increasingly from anthropogenic ecosystems such as agricultural areas rather than pristine ecosystems. This paper provides selected results from a study of wild food conducted in several villages in Northeast Thailand. A complete botanical inventory of wild food plants from these communities and surrounding areas is provided including their diversity of growth forms, the different anthropogenic locations were these species grow and the multiplicity of uses they have. Data was collected using focus groups and key informant interviews with women locally recognized as knowledgeable about contemporarily gathered plants. Plant species were identified by local taxonomists. A total of 87 wild food plants, belonging to 47 families were reported, mainly trees, herbs (terrestrial and aquatic) and climbers. Rice fields constitute the most important growth location where 70% of the plants are found, followed by secondary woody areas and home gardens. The majority of species (80%) can be found in multiple growth locations, which is partly explained by villagers moving selected species from one place to another and engaging in different degrees of management. Wild food plants have multiple edible parts varying from reproductive structures to vegetative organs. More than two thirds of species are reported as having diverse additional uses and more than half of them are also regarded as medicine. This study shows the remarkable importance of anthropogenic areas in providing wild food plants. This is reflected in the great diversity of species found, contributing to the food and nutritional security of rice farmers in Northeast Thailand.

  14. Sequence polymorphisms in wild, weedy, and cultivated rice suggest seed-shattering locus sh4 played a minor role in Asian rice domestication

    PubMed Central

    Zhu, Yongqing; Ellstrand, Norman C; Lu, Bao-Rong

    2012-01-01

    The predominant view regarding Asian rice domestication is that the initial origin of nonshattering involved a single gene of large effect, specifically, the sh4 locus via the evolutionary replacement of a dominant allele for shattering with a recessive allele for reduced shattering. Data have accumulated to challenge this hypothesis. Specifically, a few studies have reported occasional seed-shattering plants from populations of the wild progenitor of cultivated rice (Oryza rufipogon complex) being homozygous for the putative “nonshattering” sh4 alleles. We tested the sh4 hypothesis for the domestication of cultivated rice by obtaining genotypes and phenotypes for a diverse set of samples of wild, weedy, and cultivated rice accessions. The cultivars were fixed for the putative “nonshattering” allele and nonshattering phenotype, but wild rice accessions are highly polymorphic for the putative “nonshattering” allele (frequency ∼26%) with shattering phenotype. All weedy rice accessions are the “nonshattering” genotype at the sh4 locus but with shattering phenotype. These data challenge the widely accepted hypothesis that a single nucleotide mutation (“G”/“T”) of the sh4 locus is the major driving force for rice domestication. Instead, we hypothesize that unidentified shattering loci are responsible for the initial domestication of cultivated rice through reduced seed shattering. PMID:23139871

  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. Analysis of Rhizome Development in Oryza longistaminata, a Wild Rice Species.

    PubMed

    Yoshida, Akiko; Terada, Yasuhiko; Toriba, Taiyo; Kose, Katsumi; Ashikari, Motoyuki; Kyozuka, Junko

    2016-10-01

    Vegetative reproduction is a form of asexual propagation in plants. A wide range of plants develop rhizomes, modified stems that grow underground horizontally, as a means of vegetative reproduction. In rhizomatous species, despite their distinct developmental patterns, both rhizomes and aerial shoots derive from axillary buds. Therefore, it is of interest to understand the basis of rhizome initiation and development. Oryza longistaminata, a wild rice species, develops rhizomes. We analyzed bud initiation and growth of O. longistaminata rhizomes using various methods of morphological observation. We show that, unlike aerial shoot buds that contain a few leaves only, rhizome buds initiate several leaves and bend to grow at right angles to the original rhizome. Rhizomes are maintained in the juvenile phase irrespective of the developmental phase of the aerial shoot. Stem elongation and reproductive transition are tightly linked in the aerial shoots, but are uncoupled in the rhizome. Our findings indicate that developmental programs operate independently in the rhizomes and aerial shoots. Temporal modification of the developmental pathways that are common to rhizomes and aerial shoots may be the source of developmental plasticity. Furthermore, the creation of new developmental systems appears to be necessary for rhizome development.

  17. Phylogenetic relationships of annual and perennial wild rice: probing by direct DNA sequencing.

    PubMed

    Barbier, P; Morishima, H; Ishihama, A

    1991-05-01

    The phylogenetic relationships between Asian wild rice strains were analyzed by direct sequencing of PCR-amplified DNA fragments. The sequence of three introns located in the phytochrome gene was determined for eight strains of the Asian wild rice, Oryza rufipogon, and one strain of the related African species, Oryza longistaminata. The number of nucleotide substitutions per site between various strains within a single species, O. rufipogon, ranged between 0.0017 and 0.0050, while those between two related species, O. rufipogon and O. longistaminate, were 0.043-0.049 (23-26 within 532 bp). Taken together with the sequence differences of the 10-kDa prolamin gene, a model is proposed for the phylogenetic relationships and evolutionary history of annuals and perennials within O. rufipogon.

  18. Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice.

    PubMed

    Waters, Daniel L E; Nock, Catherine J; Ishikawa, Ryuji; Rice, Nicole; Henry, Robert J

    2012-01-01

    Cultivated rice (Oryza sativa) is an AA genome Oryza species that was most likely domesticated from wild populations of O. rufipogon in Asia. O. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. The chloroplast genome sequence of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (an Australian member of the genus very distant from O. sativa) was obtained by massively parallel sequencing and compared with the chloroplast genome sequence of domesticated O. sativa. Oryza australiensis differed in more than 850 sites single nucleotide polymorphism or indel from each of the other samples. The other wild rice species had only around 100 differences relative to cultivated rice. The chloroplast genomes of Australian O. rufipogon and O. meridionalis were closely related with only 32 differences. The Asian O. rufipogon chloroplast genome (with only 68 differences) was closer to O. sativa than the Australian taxa (both with more than 100 differences). The chloroplast sequences emphasize the genetic distinctness of the Australian populations and their potential as a source of novel rice germplasm. The Australian O. rufipogon may be a perennial form of O. meridionalis.

  19. Toxicity of sulfate and chloride to early life stages of wild rice (Zizania palustris).

    PubMed

    Fort, Douglas J; Mathis, Michael B; Walker, Rachel; Tuominen, Lindsey K; Hansel, Mike; Hall, Scott; Richards, Robin; Grattan, S R; Anderson, Kurt

    2014-12-01

    Despite the importance of wild rice (Zizania palustris) in the Great Lakes region of North America, its sensitivity to sulfate is not well understood. A 21-d hydroponic experiment was performed to determine the toxicity of sulfate to wild rice seeds and seedlings. Effects of 6 sulfate concentrations ranging from 10 mg/L to 5000 mg/L and of chloride salts at equivalent conductivity were evaluated to determine whether adverse effects were attributable to sulfate or to conductivity-related stress. Sulfate treatment decreased root length, shoot length, and leaf number, and increased phytotoxic effects at concentrations of 5000 mg/L relative to a 50 mg/L control. The time to 30% mesocotyl emergence decreased at 2500 mg/L sulfate, indicating a potential stimulatory effect. Sulfate exposures of ≤ 5000 mg/L had no effect on 5 additional end points. Multiple regression analysis indicated that most observed changes could be attributed to conductivity-related stress rather than sulfate per se, with the exception of shoot length and leaf number. Chloride was more toxic than sulfate, as determined by root length and phytotoxicity. In summary, sulfate concentrations below 5000 mg/L did not adversely affect early-life stage wild rice during a 21-d period, and effects at 5000 mg/L sulfate were attributable to conductivity-related stress rather than sulfate toxicity in 2 of 4 end points.

  20. Differential analyses of major allergen proteins in wild-type rice and rice producing a fragment of anti-rotavirus antibody.

    PubMed

    Yuki, Yoshikazu; Kurokawa, Shiho; Kozuka-Hata, Hiroko; Tokuhara, Daisuke; Mejima, Mio; Kuroda, Masaharu; Oyama, Masaaki; Nishimaki-Mogami, Tomoko; Teshima, Reiko; Kiyono, Hiroshi

    2016-04-01

    To develop oral antibody therapy against rotavirus infection, we previously produced a recombinant fragment of llama heavy-chain antibody to rotavirus (ARP1) in rice seeds (MucoRice-ARP1). We intend to use a purification-free rice powder for clinical application but needed to check whether MucoRice-ARP1 had increased levels of known allergen proteins. For this purpose, we used two-dimensional fluorescence difference gel electrophoresis to compare the allergen protein levels in MucoRice-ARP1 and wild-type rice. We detected no notable differences, except in the levels of α-amylase/trypsin inhibitor-like family proteins. Because by this approach we could not completely separate ARP1 from the proteins of this family, we confirmed the absence of changes in the levels of these allergens by using shotgun mass spectrometry as well as immunoblot. By using immunoelectron microscopy, we also showed that RAG2, a member of the α-amylase/trypsin inhibitor-like protein family, was relocated from protein bodies II to the plasma membrane or cell wall in MucoRice-ARP1 seed. The relocation did not affect the level of RAG2. We demonstrated that most of the known rice allergens were not considerably upregulated by the genetic modification in MucoRice-ARP1. Our data suggest that MucoRice-ARP1 is a potentially safe oral antibody for clinical application.

  1. Ultrastructure of Oryza glumaepatula, a wild rice species endemic of tropical America.

    PubMed

    Sánchez, Ethel; Espinoza, Ana M

    2005-01-01

    Orv'za gluniaepatula is a perennial wild rice species, endemic to tropical America, previously known as the Latin American race of Orrza rufipogon. In Costa Rica, it is found in the northern region of the country, mainly in the wetland of the Medio Queso River, Los Chiles, Alajuela. It is diploid, of AA type genome and because of its genetic relatedness to cultivated rice it is included in the O. saliva complex. We describe the ultrastructure of leaf blade, spikelet, ligule and auricles. Special emphasis is given to those traits of major taxonomic value for O. glumaepatula and to those characters that distinguish this species from O. rufipogon and O. sativa. O. glumaepatula has a leaf blade covered with tombstone-shaped, oblong and spheroid epicuticular wax papillae. It has diamond-shaped stomata surrounded by spherical papillae, rows of zipper-like silica cells, bulky prickle trichomes of ca. 40 microm in length and small hirsute trichomes of ca. 32 tpm in length. The central vein is covered with large, globular papillae of ca. 146 microm in length, a characteristic that distinguishes this species from O. rufipogon and O. sativa. The border of the leaf blade exhibits a row of even-sized bulky prickle trichomes of ca. 42.5 microm in length. Auricles have attenuated trichomes of ca. 5.5 mm in length on the edges and small bicellular trichomes of 120 microm in length on the surface. The ligule has a large number of short attenuated trichomes on its surface of 100 microm in length. These latter two traits have important taxonomic value since they were found in O. glumaepatula but not found in O. sativa or in O. rufipogon. The spikelet has the typical morphology of the Oryza genus. Fertile lemmas have abundant spines, a trait shared with O. rufipogon but not with O. sativa. The sterile lemmas are wing-shaped with serrated borders, a characteristic that distinguishes this species from O. rufipogon and O. sativa. All the ultrastructure characters observed in O

  2. Growth promotion and inhibition of the Amazonian wild rice species Oryza grandiglumis to survive flooding.

    PubMed

    Okishio, Takuma; Sasayama, Daisuke; Hirano, Tatsuya; Akimoto, Masahiro; Itoh, Kazuyuki; Azuma, Tetsushi

    2014-09-01

    In Asian cultivated rice (Oryza sativa), distinct mechanisms to survive flooding are activated in two groups of varieties. Submergence-tolerant rice varieties possessing the SUBMERGENCE1A (SUB1A) gene display reduced growth during flash floods at the seedling stage and resume growth after the flood recedes, whereas deepwater rice varieties possessing the SNORKEL1 (SK1) and SNORKEL2 (SK2) genes display enhanced growth based on internodal elongation during prolonged submergence at the mature stage. In this study, we investigated the occurrence of these growth responses to submergence in the wild rice species Oryza grandiglumis, which is native to the Amazon floodplains. When subjected to gradual submergence, adult plants of O. grandiglumis accessions showed enhanced internodal elongation with rising water level and their growth response closely resembled that of deepwater varieties of O. sativa with high floating capacity. On the other hand, when subjected to complete submergence, seedlings of O. grandiglumis accessions displayed reduced shoot growth and resumed normal growth after desubmergence, similar to the response of submergence-tolerant varieties of O. sativa. Neither SUB1A nor the SK genes were detected in the O. grandiglumis accessions. These results indicate that the O. grandiglumis accessions are capable of adapting successfully to flooding by activating two contrasting mechanisms as the situation demands and that each mechanism of adaptation to flooding is not mediated by SUB1A or the SK genes.

  3. Water resources of the Wild Rice River watershed, northwestern Minnesota

    USGS Publications Warehouse

    Winter, Thomas C.; Bidwell, L.E.; Maclay, Robert W.

    1970-01-01

    The area of the watershed is about 2,600 square miles and includes most of Mahnomen and Norman Counties and parts of Becker, Clay, Clearwater, and Polk Counties. The population of the area is about 37,000 people of which about 70 percent live on farms. The economy is based principally on farming. The area of lake clay and silt is used mostly for raising sugar beets and wheat; and potatoes are grown largely on the sandy soils. In the western part of the morainal area small grain, dairy, and cattle farming is the most common. The eastern part of the morainal area is important for forest products and recreation. Industries in the area are small and are based on agricultural processing and service.

  4. Analysis of common canopy vegetation indices for indicating leaf nitrogen accumulations in wheat and rice

    NASA Astrophysics Data System (ADS)

    Zhu, Yan; Yao, Xia; Tian, YongChao; Liu, XiaoJun; Cao, WeiXing

    2008-02-01

    The common spectra wavebands and vegetation indices (VI) were identified for indicating leaf nitrogen accumulation (LNA), and the quantitative relationships of LNA to canopy reflectance spectra were determined in both wheat ( Triticum aestivum L.) and rice ( Oryza sativa L.). The 810 and 870 nm are two common spectral wavebands indicating LNA in both wheat and rice. Among all ratio vegetation indices (RVI), difference vegetation indices (DVI) and normalized difference vegetation indices (NDVI) of 16 wavebands from the MSR16 radiometer, RVI (870, 660) and RVI (810, 660) were most highly correlated to LNA in both wheat and rice. In addition, the relations between VIs and LNA gave better results than relations between single wavebands and LNA in both wheat and rice. Thus LNA in both wheat and rice could be indicated with common VIs, but separate regression equations are better for LNA monitoring.

  5. UVB sensitivity and cyclobutane pyrimidine dimer (CPD) photolyase genotypes in cultivated and wild rice species.

    PubMed

    Iwamatsu, Yutaka; Aoki, Chizuru; Takahashi, Masaaki; Teranishi, Mika; Ding, Yuanying; Sun, Chuanqing; Kumagai, Tadashi; Hidema, Jun

    2008-03-01

    We investigated the UVB-sensitivity in 12 rice strains belonging to two cultivated species (O. sativa and O. glaberrima) and three wild species (O. barthii, O. meridionalis and O. rufipogon) of rice possessing the AA genome, while focusing on the CPD photolyase activity and the genotypes of CPD photolyase. Although the UVB sensitivity, CPD photolyase activity, and CPD photolyase genotype varied widely among these rice species, the sensitivity to UVB radiation depended on the activity of the CPD photolyase, regardless of grass shape, habitat, or species. The rice strains examined here clearly divided into three groups based on the CPD photolyase activity, and the activity of the strains greatly depended on amino acid residues at positions 126 and 296, with the exception of the W1299 strain (O. meridionalis). The amino acid residues 126 and 296 of CPD photolyase in Sasanishiki strain (O. sativa), which showed higher enzymatic activity and more resistance to UVB, were glutamine (Gln) and Gln, respectively. An amino acid change at position 126 from Gln to arginine ("Nori"-type) in the photolyase led to a reduction of enzymatic activity. Additionally, an amino acid change at position 296 from Gln to histidine led to a further reduction in activity. The activity of the W1299 strain, which possesses a "Nori"-type CPD photolyase, was the highest among the strains examined here, and was similar to that of the Sasanishiki. The CPD photolyase of the W1299 contains ten amino acid substitutions, compared to Sasanishiki. The alterations in amino acid residues in the W1299 CPD photolyase compensated for the reduction in activity caused by the amino acid substitutions at positions 126. Knowledge of the activity of different CPD photolyase genotypes will be useful in developing improved rice cultivars.

  6. Effects of different treatments of fly ash and mining soil on growth and antioxidant protection of Indian wild rice.

    PubMed

    Bisoi, Sidhanta Sekhar; Mishra, Swati S; Barik, Jijnasa; Panda, Debabrata

    2017-05-04

    The aim of the present study was investigation of the effects of fly ash and mining soil on growth and antioxidant protection of two cultivars of Indian wild rice (Oryza nivara and Oryza rufipogon) for possible phytoremediation and restoration of metal-contaminated site. In this study, Indian wild rice showed significant changes in germination, growth, and biochemical parameters after exposure to different ratio of fly ash and mining soil with garden soil. There was significant reduction of germination, fresh weight, dry weight, leaf chlorophyll content, leaf area, Special Analysis Device Chlorophyll (SPAD) Index, proteins, and activities of antioxidant enzymes in both cultivars of the wild rice grown in 100% fly ash and mining soil compared to the plants grown in 100% garden soil. Results from this study showed that in both cultivars of wild rice, all growth and antioxidant parameters increased when grown in 50% fly ash and mining soil. Taken together, Indian wild rice has the capacity to tolerate 50% of fly ash and mining soil, and can be considered as a good candidate for possible phytoremediation of contaminated soils.

  7. Toxicity of sulfide to early life-stages of wild rice (Zizania palustris).

    PubMed

    Fort, Douglas J; Todhunter, Kevin; Fort, Troy D; Mathis, Michael B; Walker, Rachel; Hansel, Mike; Hall, Scott; Richards, Robin; Anderson, Kurt

    2017-02-07

    Wild rice (Zizania palustris) sensitivity to sulfide is not well understood. Since sulfate in surface waters is reduced to sulfide by anaerobic bacteria in sediments and historical information indicated that 10 mg/L sulfate in Minnesota surface water reduced Z. palustris abundance, the Minnesota Pollution Control Agency (MPCA) established 10 mg/L sulfate as a water quality criterion in 1973. A 21-day daily-renewal hydroponic study was conducted to evaluate sulfide toxicity to wild rice and the potential mitigation of sulfide toxicity by Fe. The hydroponic design used hypoxic test media for seed and root exposure and aerobic headspace for the vegetative portion of the plant. Test concentrations were 0.3, 1.6, 3.1, 7.8, and 12.5 mg/L sulfide in test media with 0.8, 2.8, and 10.8 mg/L total Fe used to evaluate the impact of iron on sulfide toxicity. Visual assessments (i.e., no plants harvested) of seed activation, mesocotyl emergence, seedling survival, and phytoxicity were conducted 10 days following dark-phase exposure. Each treatment was also evaluated for time to 30% emergence (ET30), total plant biomass, root and shoot lengths, and signs of phytotoxicity at study conclusion (21 days). Results from this study indicated that exposure of developing wild rice to sulfide at ≥3.1 mg sulfide/L in the presence of 0.8 mg/L iron reduced mesocotyl emergence. Sulfide toxicity was mitigated by the addition of iron at 2.8 and 10.8 mg /L relative to the control value of 0.8 mg Fe/L, demonstrating the importance of iron in mitigating sulfide toxicity to wild rice. Ultimately, determination of site-specific sulfate criteria that consider factors that alter toxicity, including sediment Fe and organic carbon, are necessary. This article is protected by copyright. All rights reserved.

  8. Evolutionary dynamics and structure of the rice blast resistance locus Pi-ta in wild, cultivated, and US weedy rice

    USDA-ARS?s Scientific Manuscript database

    The Pi-ta gene in rice has been used to control rice blast pathogen, Magnaporthe oryza, in rice growing areas worldwide for decades. To understand the evolutionary process and natural selection of Pi-ta during rice domestication, we first examined sequences of the genomic region of Pi-ta in geograph...

  9. Jasmonic acid and salicylic acid activate a common defense system in rice

    PubMed Central

    Tamaoki, Daisuke; Seo, Shigemi; Yamada, Shoko; Kano, Akihito; Miyamoto, Ayumi; Shishido, Hodaka; Miyoshi, Seika; Taniguchi, Shiduku; Akimitsu, Kazuya; Gomi, Kenji

    2013-01-01

    Jasmonic acid (JA) and salicylic acid (SA) play important roles in plant defense systems. JA and SA signaling pathways interact antagonistically in dicotyledonous plants, but, the status of crosstalk between JA and SA signaling is unknown in monocots. Our rice microarray analysis showed that more than half of the genes upregulated by the SA analog BTH are also upregulated by JA, suggesting that a major portion of the SA-upregulated genes are regulated by JA-dependent signaling in rice. A common defense system that is activated by both JA and SA is thus proposed which plays an important role in pathogen defense responses in rice. PMID:23518581

  10. Jasmonic acid and salicylic acid activate a common defense system in rice.

    PubMed

    Tamaoki, Daisuke; Seo, Shigemi; Yamada, Shoko; Kano, Akihito; Miyamoto, Ayumi; Shishido, Hodaka; Miyoshi, Seika; Taniguchi, Shiduku; Akimitsu, Kazuya; Gomi, Kenji

    2013-06-01

    Jasmonic acid (JA) and salicylic acid (SA) play important roles in plant defense systems. JA and SA signaling pathways interact antagonistically in dicotyledonous plants, but, the status of crosstalk between JA and SA signaling is unknown in monocots. Our rice microarray analysis showed that more than half of the genes upregulated by the SA analog BTH are also upregulated by JA, suggesting that a major portion of the SA-upregulated genes are regulated by JA-dependent signaling in rice. A common defense system that is activated by both JA and SA is thus proposed which plays an important role in pathogen defense responses in rice.

  11. Analysis of koi herpesvirus latency in wild common carp and ornamental koi in Oregon, USA.

    PubMed

    Xu, Jia-Rong; Bently, Jennifer; Beck, Linda; Reed, Aimee; Miller-Morgan, Tim; Heidel, Jerry R; Kent, Michael L; Rockey, Daniel D; Jin, Ling

    2013-02-01

    Koi herpesvirus (KHV) infection is associated with high mortalities in both common carp (Cyprinus carpio carpio) and koi carp (Cyprinus carpio koi) worldwide. Although acute infection has been reported in both domestic and wild common carp, the status of KHV latent infection is largely unknown in wild common carp. To investigate whether KHV latency is present in wild common carp, the distribution of KHV latent infection was investigated in two geographically distinct populations of wild common carp in Oregon, as well as in koi from an Oregon-based commercial supplier. Latent KHV infection was demonstrated in white blood cells from each of these populations. Although KHV isolated from acute infections has two distinct genetic groups, Asian and European, KHV detected in wild carp has not been genetically characterized. DNA sequences from ORF 25 to 26 that are unique between Asian and European were investigated in this study. KHV from captive koi and some wild common carp were found to have ORF-25-26 sequences similar to KHV-J (Asian), while the majority of KHV DNA detected in wild common carp has similarity to KHV-U/-I (European). In addition, DNA sequences from IL-10, and TNFR were sequenced and compared with no differences found, which suggests immune suppressor genes of KHV are conserved between KHV in wild common carp and koi, and is consistent with KHV-U, -I, -J.

  12. Signatures of adaptation in the weedy rice genome

    USDA-ARS?s Scientific Manuscript database

    Weedy rice is a common problem of by product of domestication that has evolved multiple times from cultivated and wild rice relatives. Here we use whole genome sequences to examine the origin and adaptation of the two major US weedy red rice strains, with a comparison to Chinese weedy red rice. We f...

  13. Arteriviruses, Pegiviruses, and Lentiviruses Are Common among Wild African Monkeys

    PubMed Central

    Bailey, Adam L.; Lauck, Michael; Ghai, Ria R.; Nelson, Chase W.; Heimbruch, Katelyn; Hughes, Austin L.; Goldberg, Tony L.; Jasinska, Anna J.; Freimer, Nelson B.; Apetrei, Cristian

    2016-01-01

    ABSTRACT Nonhuman primates (NHPs) are a historically important source of zoonotic viruses and are a gold-standard model for research on many human pathogens. However, with the exception of simian immunodeficiency virus (SIV) (family Retroviridae), the blood-borne viruses harbored by these animals in the wild remain incompletely characterized. Here, we report the discovery and characterization of two novel simian pegiviruses (family Flaviviridae) and two novel simian arteriviruses (family Arteriviridae) in wild African green monkeys from Zambia (malbroucks [Chlorocebus cynosuros]) and South Africa (vervet monkeys [Chlorocebus pygerythrus]). We examine several aspects of infection, including viral load, genetic diversity, evolution, and geographic distribution, as well as host factors such as age, sex, and plasma cytokines. In combination with previous efforts to characterize blood-borne RNA viruses in wild primates across sub-Saharan Africa, these discoveries demonstrate that in addition to SIV, simian pegiviruses and simian arteriviruses are widespread and prevalent among many African cercopithecoid (i.e., Old World) monkeys. IMPORTANCE Primates are an important source of viruses that infect humans and serve as an important laboratory model of human virus infection. Here, we discover two new viruses in African green monkeys from Zambia and South Africa. In combination with previous virus discovery efforts, this finding suggests that these virus types are widespread among African monkeys. Our analysis suggests that one of these virus types, the simian arteriviruses, may have the potential to jump between different primate species and cause disease. In contrast, the other virus type, the pegiviruses, are thought to reduce the disease caused by human immunodeficiency virus (HIV) in humans. However, we did not observe a similar protective effect in SIV-infected African monkeys coinfected with pegiviruses, possibly because SIV causes little to no disease in these hosts

  14. Characterization of seeds of selected wild species of rice (Oryza) stored under high temperature and humidity conditions.

    PubMed

    Das, Smruti; Nayak, Monalisa; Patra, B C; Ramakrishnan, B; Krishnan, P

    2010-06-01

    Wild progenitors of rice (Oryza) are an invaluable resource for restoring genetic diversity and incorporating useful traits back into cultivars. Studies were conducted to characterize the biochemical changes, including SDS-PAGE banding pattern of storage proteins in seeds of six wild species (Oryza alta, O. grandiglumis, O. meridionalis, O. nivara, O. officinalis and O. rhizomatis) of rice stored under high temperature (45 degrees C) and humidity (approixmately 100%) for 15 days, which facilitated accelerated deterioration. Under the treated conditions, seeds of different wild rice species showed decrease in per cent germination and concentrations of protein and starch, but increase in conductivity of leachate and content of sugar. The SDS-PAGE analysis of seed proteins showed that not only the total number of bands, but also their intensity in terms of thickness differed for each species under storage. The total number of bands ranged from 11 to 22, but none of the species showed all the bands. Similarity index for protein bands between the control and treated seeds was observed to be least in O. rhizomatis and O. alta, while the indices were 0.7 and 0.625 for O. officinalis and O. nivara, respectively. This study clearly showed that seed deterioration led to distinctive biochemical changes, including the presence or absence as well as altered levels of intensity of proteins. Hence, SDS-PAGE protein banding pattern can be used effectively to characterize deterioration of seeds of different wild species of rice.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  16. Research on the ultrafast fluorescence property of thylakoid membranes of the wild-type and mutant rice

    NASA Astrophysics Data System (ADS)

    Ren, Zhao-Yu; Xu, Xiao-Ming; Wang, Shui-Cai; Xin, Yue-Yong; He, Jun-Fang; Hou, Xun

    2003-10-01

    A high yielding rice variety mutant (Oryza sativa L., Zhenhui 249) with low chlorophyll b (Chl b) has been discovered in natural fields. It has a quality character controlled by a pair of recessive genes (nuclear gene). The partial loss of Chl b in content affects the efficiency of light harvest in a light harvest complex (LHC), thus producing the difference of the exciting energy transfer and the efficiency of photochemistry conversion between the mutant and wild-type rice in photosynthetic unit. The efficiency of utilizing light energy is higher in the mutant than that in the wild-type rice relatively. For further discussion of the above-mentioned difference and learning about the mechanism of the increase in the photochemical efficiency of the mutant, the pico-second resolution fluorescence spectrum measurement with delay-frame-scanning single photon counting technique is adopted. Thylakoid membranes of the mutant and the wild-type rice are excited by an Ar+ laser with a pulse width of 120 ps, repetition rate of 4 MHz and wavelength of 514 nm. Compared with the time and spectrum property of exciting fluorescence, conclusions of those ultrafast dynamic experiments are: 1) The speeds of the exciting energy transferred in photo-system I are faster than that in photo-system II in both samples. 2) The speeds of the exciting energy transfer of mutant sample are faster than those of the wild-type. This might be one of the major reasons why the efficiency of photosynthesis is higher in mutant than that in the wild-type rice.

  17. Anatomical root variations in response to water deficit: wild and domesticated common bean (Phaseolus vulgaris L).

    PubMed

    Peña-Valdivia, Cecilia B; Sánchez-Urdaneta, Adriana B; Rangel, Joel Meza; Muñoz, Juana Juárez; García-Nava, Rodolfo; Velázquez, Raquel Celis

    2010-01-01

    Root anatomical responses to water deficit are diverse and regulation of water uptake strongly depends on plant anatomy. The ancestors of common bean (Phaseolus vulgaris L.) cultivars are the wild common beans. Because wild beans adapt and survive well in the natural environment, it is hypothesized that wild common bean roots are less affected than those of domesticated beans at low substrate water potential (ψW). A wild common bean accession from Chihuahua Mexico and cv. Bayomex were studied. Seedlings with a mean root length between 3 and 4 cm were maintained for 24 h in vermiculite at ψW of -0.03 (well hydrated), -0.65, -1.48 and -2.35 MPa (partially dry). Ten anatomical characteristics of differentiation and cell division in root regions were evaluated. Thickness of epidermis and protoderm diminished similarly in wild and domesticated beans growing at low substrate ψW (between -0.65 and -2.35 MPa). At the same time, parenchymatic cell area diminished by 71 % in the domesticated variety, but by only 32 % in the wild bean at -2.35 MPa. The number of cells in the cortex and the thickness of the xylem wall increased in both wild and domesticated beans at low substrate ψW; nevertheless, the effect was significantly lower in the wild bean. The number of xylem vessels increased in the cultivar (up to 40 %) while in the wild bean it decreased (up to 33 %). The diameter of xylem vessels and transverse root area diminished (15 and 57 %, respectively) in the cultivar, but in the wild common bean were not affected. Anatomical root characteristics and their modifications in both differentiation and cell division in root regions demonstrated that the wild bean reacted quite differently to substrate ψW than the domesticated common bean.

  18. 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.

  19. The Complete Chloroplast Genome of Wild Rice (Oryza minuta) and Its Comparison to Related Species

    PubMed Central

    Asaf, Sajjad; Waqas, Muhammad; Khan, Abdul L.; Khan, Muhammad A.; Kang, Sang-Mo; Imran, Qari M.; Shahzad, Raheem; Bilal, Saqib; Yun, Byung-Wook; Lee, In-Jung

    2017-01-01

    Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites. The genomic organization, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. Approximately 30 forward, 28 tandem and 20 palindromic repeats were detected in the O. minuta cp genome. Comparison of the complete O. minuta cp genome with another eleven Oryza species showed a high degree of sequence similarity and relatively high divergence of intergenic spacers. Phylogenetic analyses were conducted based on the complete genome sequence, 65 shared genes and matK gene showed same topologies and O. minuta forms a single clade with parental O. punctata. Thus, the complete O. minuta cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny. PMID:28326093

  20. 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

  1. Rice: a common and severe cause of food protein-induced enterocolitis syndrome.

    PubMed

    Mehr, S S; Kakakios, A M; Kemp, A S

    2009-03-01

    To examine and compare the characteristics of food protein-induced enterocolitis syndrome (FPIES) caused by rice and cow's milk/soy. Retrospective study of children presenting with FPIES to the Children's Hospital at Westmead, NSW, Australia, over a 16-year period. There were 14 children with 26 episodes of rice FPIES compared with 17 children with 30 episodes of cow's milk (n = 10) or soy (n = 7) FPIES. Children with rice FPIES were more likely to have FPIES caused by other foods (36%) than children with FPIES caused by cow's milk/soy (0%). Rice caused more episodes of FPIES before a correct diagnosis was made (median 4 (range 1-4) vs median 2 (range 1-4)) and triggered more severe reactions with higher rates of intravenous fluid resuscitation (42% vs 17%) than reactions caused by cow's milk/soy. This study highlights the emerging importance of rice, a food commonly thought to be "hypoallergenic", as a significant trigger of FPIES. Paediatricians should be aware that rice not only has the potential to cause FPIES, but that such reactions tend be more severe than those caused by cow's milk/soy.

  2. A Tribal Story Written in Silica: Using Phytoliths to Research the Effects of Mining on Past Wild Rice (Zizania palustris) Abundance in Sandy Lake, Minnesota

    NASA Astrophysics Data System (ADS)

    Clarke, I. R.; Jones, M. A.; Yost, C. L.; Drake, C.; Ladwig, J. L.; Myrbo, A.; Howes, T.

    2014-12-01

    Wild rice (Zizania palustris, manoomin) is an emergent aquatic plant that grows annually in the northern Great Lakes region of North America. This region is also rich in iron ore deposits and correspondingly has an extensive history of mining activities. Wild rice no longer grows in some areas where it was previously abundant. Sandy Lake, located in St. Louis County on federally protected lands that are ceded territory of the Fond du Lac Band of Lake Superior Chippewa in Minnesota and downstream of the nearby U.S. Steel Minntac mine, was selected as a test site. This lake has a history of ricing activities by the Ojibwe (Chippewa) People, for whom manoomin has cultural importance. Lake cores were taken on June 17, 2014 by LacCore and FDLRM staff and samples were obtained. This project used phytolith analysis to answer the question of past wild rice presence and abundance in Sandy Lake. Phytoliths are microscopic opal silica deposits produced in some plants. Zizania palustris produces phytolith morphotypes that are unequivocally diagnostic of this species in this region. Microscopic slides were prepared and analyzed for wild rice phytoliths. Concentration values ranged from 25 to 4379 phytoliths per cm3/year, and wild rice accumulation figures ranged from 7 to 789 phytoliths/cm2/year, the maximum values of which occurred in the 1920s and generally declined to the current lowest levels observed. Mining has likely impacted wild rice populations by causing increased sulfate levels and possibly contributing to higher lake levels.

  3. Mechanisms of resistance in wild riceOryza brachyantha to rice leaffolderCnaphalocrocis medinalis (Guenée) (Lepidoptera: Pyralidae).

    PubMed

    Ramachandran, R; Khan, Z R

    1991-01-01

    A wild rice,Oryza brachyantha, was rated as highly resistant to rice leaffolder,Cnaphalocrocis medinalis (Guenée), while its F1 hybrid from a cross with a high-yielding, leaffolder-susceptible rice, IR31917-45-3-2, was rated resistant in a standard screening test. In comparison with IR31917-45-3-2,O. brachyantha and the F1 hybrid were unsuitable for oviposition, survival, and growth ofC. medinalis. However, growth and survival of larvae in artificial diets containing lyophilized leaf powder of IR31917-45-3-2 andO. brachyantha were comparable. Studies on the feeding and settling preference of the larval stages suggested that the mechanism of resistance ofO. brachyantha is that of antixenosis type. Olfactometer tests with first-instar larvae and electroantennogram responses of adults indicated a lack or low levels of volatile attractants inO. brachyantha and the F1 hybrid in comparison with IR31917-45-3-2. Bioassays of sequential solvent extracts of these plants indicated that larval preference for IR31917-45-3-2 and nonpreference forO. brachyantha and the F1 hybrid were due partly to chemical factors present in hexane and methylene chloride extractables. Closer arrangement of silica cells in the epidermal layer ofO. brachyantha and a higher mandibular wear in larvae reared onO. brachyantha suggested that physical resistance due to silica may be an additional cause of resistance. It was hypothesized that the high levels of resistance observed inO. brachyantha may be due to an additive or synergistic action of the absence of attractants or feeding stimulants, the presence of deterrents, and the physical resistance offered by silica. The significance of these results to a successful wide hybridization program aimed at transferring resistance factors from wild rice to cultivated rice is discussed.

  4. Lowered Diversity and Increased Inbreeding Depression within Peripheral Populations of Wild Rice Oryza rufipogon

    PubMed Central

    Gao, Li-Zhi; Gao, Cheng-Wen

    2016-01-01

    Background The distribution of genetic variability from the interior towards the periphery of a species’ range is of great interest to evolutionary biologists. Although it has been long presumed that population genetic variation should decrease as a species’ range is approached, results of empirical investigations still remain ambiguous. Knowledge regarding patterns of genetic variability as well as affected factors is particularly not conclusive in plants. Methodology/Principal Findings To determine genetic divergence in peripheral populations of the wild rice Oryza rufipogon Griff. from China, genetic diversity and population structure were studied in five northern & northeastern peripheral and 16 central populations using six microsatellite loci. We found that populations resided at peripheries of the species possessed markedly decreased microsatellite diversity than those located in its center. Population size was observed to be positively correlated with microsatellite diversity. Moreover, there are significantly positive correlations between levels of microsatellite diversity and distances from the northern and northeastern periphery of this species. To investigate genetic structure and heterozygosity variation between generations of O. rufipogon, a total of 2382 progeny seeds from 186 maternal families were further assayed from three peripheral and central populations, respectively. Peripheral populations exhibited significantly lower levels of heterozygosities than central populations for both seed and maternal generations. In comparisons with maternal samples, significantly low observed heterozygosity (HO) and high heterozygote deficit within populations (FIS) values were detected in seed samples from both peripheral and central populations. Significantly lower observed heterozygosity (HO) and higher FIS values were further observed in peripheral populations than those in central populations for seed samples. The results indicate an excess of

  5. The biosynthesis, structure and gelatinization properties of starches from wild and cultivated African rice species (Oryza barthii and Oryza glaberrima).

    PubMed

    Wang, Kai; Wambugu, Peterson W; Zhang, Bin; Wu, Alex Chi; Henry, Robert J; Gilbert, Robert G

    2015-09-20

    The molecular structure and gelatinization properties of starches from domesticated African rice (Oryza glaberrima) and its wild progenitor (Oryza barthii) are determined and comparison made with Asian domesticated rice (Oryza sativa), the commonest commercial rice. This suggests possible enzymatic processes contributing to the unique traits of the African varieties. These have similar starch structures, including smaller amylose molecules, but larger amounts of amylose chains across the whole amylose chain-length distribution, and higher amylose contents, than O. sativa. They also show a higher proportion of two- and three-lamellae spanning amylopectin branch chains (degree of polymerization 34-100) than O. sativa, which contributes to their higher gelatinization temperatures. Fitting amylopectin chain-length distribution with a biosynthesis-based mathematical model suggests that the reason for this difference might be because O. glaberrima and O. barthii have more active SSIIIa and/or less active SBEIIb enzymes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Flood Control Wild Rice River - South Branch and Felton Ditch, Minnesota.

    DTIC Science & Technology

    1974-09-01

    common inhabitants are the thirteen-lined ground squirrel, pocket gopher , striped skunk, meadow vole, killdeer, red-tailed hawk and mourning dove...tridecemlineatv Gray squirrel 1 Sciurus carolinensis Fox squirrel 1R Sciurus niger Red squirrel 3 Tamiasciurus hudsonicus Plains pocket gopher 2...NUMBER 01 r. RECIPIENTS CATALOG NUMBER 4. TITLE (and Subtle) S. TYPE OF REPORT a PERIOD COVERED FLOOD CONTROL WILD RIVE RIVER-SOUTH BRANCH- Final AND

  7. 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.

  8. Drought stress-induced compositional changes in tolerant transgenic rice and its wild type.

    PubMed

    Nam, Kyong-Hee; Kim, Do-Young; Shin, Hee Jae; Nam, Ki Jung; An, Joo Hee; Pack, In-Soon; Park, Jung-Ho; Jeong, Soon-Chun; Kim, Ho Bang; Kim, Chang-Gi

    2014-06-15

    Comparing well-watered versus deficit conditions, we evaluated the chemical composition of grains harvested from wild-type (WT) and drought-tolerant, transgenic rice (Oryza sativa L.). The latter had been developed by inserting AtCYP78A7, which encodes a cytochrome P450 protein. Two transgenic Lines, '10B-5' and '18A-4', and the 'Hwayoung' WT were grown under a rainout shelter. After the harvested grains were polished, their levels of key components, including proximates, amino acids, fatty acids, minerals and vitamins were analysed to determine the effect of watering system and genotype. Drought treatment significantly influenced the levels of some nutritional components in both transgenic and WT grains. In particular, the amounts of lignoceric acid and copper in the WT decreased by 12.6% and 39.5%, respectively, by drought stress, whereas those of copper and potassium in the transgenics rose by 88.1-113.3% and 10.4-11.9%, respectively, under water-deficit conditions.

  9. Ultrastructure of the wild rice Oryza grandiglumis (Gramineae) in Costa Rica.

    PubMed

    Sánchez, Ethel; Quesada, Tania; Espinoza, Ana M

    2006-06-01

    Oryza grandiglumis is a wild species of rice endemic to tropical America. This species was first found in 1998 in the wetlands of Caño Negro, located in the northern part of Costa Rica. Twenty five plants of O. grandiglumis were processed for scanning electron microscope. An ultrastructural description of the leaf blade, ligule, auricles, spikelet and caryopsis, with an emphasis on structures of taxonomic value. The leaf blade has a characteristic cuticular wax pattern, composed of dense rod-like structures, and is surrounded by papillae, zipper-like silica cells, abundant bulky prickle trichomes, and hooked trichomes. The blade's edge has three rows of hooked prickle trichomes of various sizes. The auricles wrapped the culm, with long attenuated trichomes at the edges; the base was surrounded by oblong cells. The ligule is a blunt membrane covered by short prickle trichomes. Spikelet morphology is characteristic of the Poaceae family, but the sterile lemmas were nearly as long as the fertile lemmas, and they have an unique crown-like structure of lignified spines between the rachilla and the fertile lemmas. Comparison with Brazilian specimens of O. grandiglumis revealed little differences in the ultrastructural characteristics.

  10. Preimpoundment water quality of the Wild Rice River, Norman County, Minnesota

    USGS Publications Warehouse

    Tornes, L.H.

    1980-01-01

    Water samples have been collected at two sites on the Wild Rice River since September 1974 to establish baseline water-quality characteristics before construction of a reservoir for recreation and flood control near Twin Valley, Minn. A decline in water quality between the sites is shown by mean total phosphorus concentrations, which increase from 0.06 to 0.10 milligram per liter downstream, and mean turbidity, which increases from 12 to 24 units downstream. Phosphorus and ammonia concentrations, as high as 0.31 and 2.7 milligrams per liter, respectively, could be the result of domestic waste input to the river upstream from Hendrum. Biochemical oxygen demand concentrations were significantly higher during spring runoff than during the rest of the year. Four out of 90 bacteria samples taken at Twin Valley indicate the presence of human fecal material, though bacteria densities do not exceed recommendations of the U.S. Environmental Protection Agency for public-water supplies. The dominace of organic-pollution tolerant phytoplankton in 49 out of 78 samples also indicates degradation of the river quality at Twin Valley. Nutrient concentrations at Twin Valley have no apparent effect on phytoplankton concentrations. None of the consitituents sampled were found to exceed recommended concentrations for public-water supplies.

  11. Genetic architecture for the adaptive origin of annual wild rice, oryza nivara.

    PubMed

    Grillo, Michael A; Li, Changbao; Fowlkes, Angela M; Briggeman, Trevor M; Zhou, Ailing; Schemske, Douglas W; Sang, Tao

    2009-04-01

    The wild progenitors of cultivated rice, Oryza nivara and Oryza rufipogon, provide an experimental system for characterizing the genetic basis of adaptation. The evolution of annual O. nivara from a perennial ancestor resembling its sister species, O. rufipogon, was associated with an ecological shift from persistently wet to seasonally dry habitats. Here we report a quantitative trait locus (QTL) analysis of phenotypic differentiation in life history, mating system, and flowering time between O. nivara and O. rufipogon. The exponential distribution of effect sizes of QTL fits the prediction of a recently proposed population genetic model of adaptation. More than 80% of QTL alleles of O. nivara acted in the same direction of phenotypic evolution, suggesting that they were fixed under directional selection. The loss of photoperiod sensitivity, which might be essential to the survival of the ancestral populations of O. nivara in the new environment, was controlled by QTL of relatively large effect. Mating system evolution from cross- to self-fertilization through the modification of panicle and floral morphology was controlled by QTL of small-to-moderate effect. The lack of segregation of the recessive annual habit in the F(2) mapping populations suggested that the evolution of annual from perennial life form had a complex genetic basis. The study captured the genetic architecture for the adaptive origin of O. nivara and provides a foundation for rigorous experimental tests of population genetic theories of adaptation.

  12. Fine mapping and characterization of BPH27, a brown planthopper resistance gene from wild rice (Oryza rufipogon Griff.).

    PubMed

    Huang, D; Qiu, Y; Zhang, Y; Huang, F; Meng, J; Wei, S; Li, R; Chen, B

    2013-01-01

    The brown planthopper (Nilaparvata lugens Stål; BPH) is one of the most serious rice pests worldwide. Growing resistant varieties is the most effective way to manage this insect, and wild rice species are a valuable source of resistance genes for developing resistant cultivars. BPH27 derived from an accession of Guangxi wild rice, Oryza rufipogon Griff. (Accession no. 2183, hereafter named GX2183), was primarily mapped to a 17-cM region on the long arm of the chromosome four. In this study, fine mapping of BPH27 was conducted using two BC(1)F(2) populations derived from introgression lines of GX2183. Insect resistance was evaluated in the BC(1)F(2) populations with 6,010 individual offsprings, and 346 resistance extremes were obtained and employed for fine mapping of BPH27. High-resolution linkage analysis defined the BPH27 locus to an 86.3-kb region in Nipponbare. Regarding the sequence information of rice cultivars, Nipponbare and 93-11, all predicted open reading frames (ORFs) in the fine-mapping region have been annotated as 11 types of proteins, and three ORFs encode disease-related proteins. Moreover, the average BPH numbers showed significant differences in 96-120 h after release in comparisons between the preliminary near-isogenic lines (pre-NILs, lines harboring resistance genes) and BaiR54. BPH growth and development were inhibited and survival rates were lower in the pre-NIL plants compared with the recurrent parent BaiR54. The pre-NIL exhibited 50.7% reductions in population growth rates (PGR) compared to BaiR54. The new development in fine mapping of BPH27 will facilitate the efforts to clone this important resistant gene and to use it in BPH-resistance rice breeding.

  13. Selection pressures have driven population differentiation of domesticated and wild common carp (Cyprinus carpio L.).

    PubMed

    Xu, L H; Wang, C H; Wang, J; Dong, Z J; Ma, Y Q; Yang, X X

    2012-09-12

    Selection pressures are the principle evolutionary forces for the genetic differentiation of populations. Recent changes in selection pressures on mitochondrial DNA and microsatellite have been described in a wide variety of organisms. The common carp (Cyprinus carpio) has experienced strong selection pressure, in particular artificial selection, during its domestication. However, the contribution and extent of artificial selection in driving genome-wide population differentiation remain unclear. We investigated the genetic differentiation of 4 domesticated strains (Xingguo red common carp, Glass red common carp, Purse red common carp, and Jian common carp, which have been generated by artificial selection since 1970s) and 2 wild populations (Shishou section in Hubei and Yangzhou section in Jiangsu of the Yangtze River) of common carp in China by sequencing the mitochondrial DNA D-loop and by genotyping 10 microsatellite loci. It was found that the domesticated strains exhibited linkage disequilibrium within the population and less genetic variability, higher inbreeding coefficients (F(IS) = 0.101 vs 0.038), and higher genetic differentiation (F(ST) = 0.087 vs 0.001) than the wild populations, which indicates strong selection pressures in the process of domestication. Of the 10 loci, 5 appeared to be under positive directional selection in the domesticated strains, and all 10 loci in wild populations were potentially under balancing selection. We conclude that strong selection pressures, artificial selection in particular, have caused genetic differentiation between populations of domesticated and wild common carp.

  14. Coordination of Leaf Photosynthesis, Transpiration, and Structural Traits in Rice and Wild Relatives (Genus Oryza).

    PubMed

    Giuliani, Rita; Koteyeva, Nuria; Voznesenskaya, Elena; Evans, Marc A; Cousins, Asaph B; Edwards, Gerald E

    2013-07-01

    The genus Oryza, which includes rice (Oryza sativa and Oryza glaberrima) and wild relatives, is a useful genus to study leaf properties in order to identify structural features that control CO(2) access to chloroplasts, photosynthesis, water use efficiency, and drought tolerance. Traits, 26 structural and 17 functional, associated with photosynthesis and transpiration were quantified on 24 accessions (representatives of 17 species and eight genomes). Hypotheses of associations within, and between, structure, photosynthesis, and transpiration were tested. Two main clusters of positively interrelated leaf traits were identified: in the first cluster were structural features, leaf thickness (Thick(leaf)), mesophyll (M) cell surface area exposed to intercellular air space per unit of leaf surface area (S(mes)), and M cell size; a second group included functional traits, net photosynthetic rate, transpiration rate, M conductance to CO(2) diffusion (g(m)), stomatal conductance to gas diffusion (g(s)), and the g(m)/g(s) ratio.While net photosynthetic rate was positively correlated with gm, neither was significantly linked with any individual structural traits. The results suggest that changes in gm depend on covariations of multiple leaf (S(mes)) and M cell (including cell wall thickness) structural traits. There was an inverse relationship between Thick(leaf) and transpiration rate and a significant positive association between Thick(leaf) and leaf transpiration efficiency. Interestingly, high g(m) together with high g(m)/g(s) and a low S(mes)/g(m) ratio (M resistance to CO(2) diffusion per unit of cell surface area exposed to intercellular air space) appear to be ideal for supporting leaf photosynthesis while preserving water; in addition, thick M cell walls may be beneficial for plant drought tolerance.

  15. Ultrastructural morphologic description of the wild rice species Oryza latifolia (Poaceae) in Costa Rica.

    PubMed

    Sánchez, Ethel; Montiel, Mayra; Espinoza, Ana M

    2003-06-01

    The wild rice species Oryza latifolia is endemic to Tropical America, allotetraploid and has a CCDD genome type. It belongs to the officinalis group of the genus Oryza. This species is widely distributed throughout the lowlands of Costa Rica and it is found on different life zones, having great morphologic diversity. The purpose of this research is to perform a morphologic description of O. latifolia samples of three Costa Rican localities (Carara, Liberia and Cañas) and to see if the phenotypic diversity of the species is reflected at the ultra-structure level. Structures such as the leaf blade, ligule, auricles and spikelet were analyzed. Leaf blade morphology of the specimens from the three localities is characterized by the presence of diamond-shaped stomata with papillae, zipper-like rows of silica cells; a variety of evenly distributed epicuticular wax papillae and bulky prickle trichomes. The central vein of the leaf blade from the Cañas populations is glabrous, while those from Carara and Liberia have abundant papillae. There are also differences among the borders of the leaf blade between these locations. Cañas and Liberia present alternating large and small prickle trichomes ca. 81 and 150 microns, while Carara exhibits even sized prickle trichomes of ca. 93 microns. Auricles from Cañas are rectangular and present long trichomes along the surface ca. 1.5 mm, while those of Liberia and Carara wrap the culm and exhibit trichomes only in the borders. The ligule from the plants of Carara has an acute distal tip, while that of Cañas and Liberia is blunt. The Liberia spikelet has large lignified spines while Cañas and Carara show flexible trichomes.

  16. Are common symbiosis genes required for endophytic rice-rhizobial interactions?

    PubMed

    Chen, Caiyan; Zhu, Hongyan

    2013-09-01

    Legume plants are able to establish root nodule symbioses with nitrogen-fixing bacteria, called rhizobia. Recent studies revealed that the root nodule symbiosis has co-opted the signaling pathway that mediates the ancestral mycorrhizal symbiosis that occurs in most land plants. Despite being unable to induce nodulation, rhizobia have been shown to be able to infect and colonize the roots of non-legumes such as rice. One fascinating question is whether establishment of such associations requires the common symbiosis (Sym) genes that are essential for infection of plant cells by mycorrhizal fungi and rhizobia in legumes. Here, we demonstrated that the common Sym genes are not required for endophytic colonization of rice roots by nitrogen-fixing rhizobia.

  17. Allelic diversification at the C (OsC1) locus of wild and cultivated rice: nucleotide changes associated with phenotypes.

    PubMed

    Saitoh, Kumi; Onishi, Kazumitsu; Mikami, Ichiho; Thidar, Khin; Sano, Yoshio

    2004-10-01

    Divergent phenotypes are often detected in domesticated plants despite the existence of invariant phenotypes in their wild forms. One such example in rice is the occurrence of varying degrees of apiculus coloration due to anthocyanin pigmentation, which was previously reported to be caused by a series of alleles at the C locus. The present study reveals, on the basis of comparison of its maps, that the C gene appears to be the rice homolog (OsC1) of maize C1, which belongs to the group of R2R3-Myb factors. Two different types of deletions causing a frameshift were detected in the third exon, and both of the deleted nucleotides corresponded to the positions of putative base-contacting residues, suggesting that the Indica and Japonica types carry loss-of-function mutations with independent origins. In addition, replacement substitutions were frequently detected in OsC1 of strains carrying the previously defined C alleles. Molecular population analysis revealed that 17 haplotypes were found in 39 wild and cultivated rices, and the haplotypes of most cultivated forms could be classified into one of three distinct groups, with few shared haplotypes among taxa, including Indica and Japonica types. The genealogy of the OsC1 gene suggests that allelic diversification causing phenotypic change might have resulted from mutations in the coding region rather than from recombination between preexisting alleles. The McDonald and Kreitman test revealed that the changes in amino acids might be associated with selective forces acting on the lineage of group A whose haplotypes were carried by most Asian cultivated forms. The results regarding a significant implication for genetic diversity in landraces of rice are also discussed.

  18. A Dichotomous Key for the Identification of Common British Wild Flower Families

    ERIC Educational Resources Information Center

    Wood, Piers

    2004-01-01

    This article argues the need for, and provides, a dichotomous single access key for the identification of common British wild flower families. A minimum of technical vocabulary is used while at the same time retaining most of the recent botanical names of families. The key provides a user-friendly opportunity for school pupils to become familiar…

  19. A Dichotomous Key for the Identification of Common British Wild Flower Families

    ERIC Educational Resources Information Center

    Wood, Piers

    2004-01-01

    This article argues the need for, and provides, a dichotomous single access key for the identification of common British wild flower families. A minimum of technical vocabulary is used while at the same time retaining most of the recent botanical names of families. The key provides a user-friendly opportunity for school pupils to become familiar…

  20. Analysis of suspended-sediment concentrations and radioisotope levels in the Wild Rice River basin, northwestern Minnesota, 1973-98

    USGS Publications Warehouse

    Brigham, Mark E.; McCullough, Carolyn J.; Wilkinson, Philip M.

    2001-01-01

    We examined historical suspended-sediment data and activities of fallout radioisotopes (lead-210 [210Pb], cesium-137 [137Cs], and beryllium-7 [7Be]) associated with suspended sediments and source-area sediments (cultivated soils, bank material, and reference soils) in the Wild Rice River Basin, a tributary to the Red River of the North, to better understand sources of suspended sediment to streams in the region. Multiple linear regression analysis of suspended-sediment concentrations from the Wild Rice River at Twin Valley, Minnesota indicated significant relations between suspended-sediment concentrations and streamflow. Flow-adjusted sediment concentrations tended to be slightly higher in spring than summer-autumn. No temporal trends in concentration were observed during 1973-98. The fallout radioisotopes were nearly always detectable in suspended sediments during spring-summer 1998. Mean 210Pb and 7Be activities in suspended sediment and surficial, cultivated soils were similar, perhaps indicating little dilution of suspended sediment from low-isotopic-activity bank sediments. In contrast, mean 137Cs activities in suspended sediment indicated a mixture of sediment originating from eroded soils and from eroded bank material, with bank material being a somewhat more important source upstream of Twin Valley, Minnesota; and approximately equal fractions of bank material and surficial soils contributing to the suspended load downstream at Hendrum, Minnesota. This study indicates that, to be effective, efforts to reduce sediment loading to the Wild Rice River should include measures to control soil erosion from cultivated fields.

  1. Transcriptome analysis confers a complex disease resistance network in wild rice Oryza meyeriana against Xanthomonas oryzae pv. oryzae.

    PubMed

    Cheng, Xiao-Jie; He, Bin; Chen, Lin; Xiao, Su-Qin; Fu, Jian; Chen, Yue; Yu, Teng-Qiong; Cheng, Zai-Quan; Feng, Hong

    2016-12-01

    Rice bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the devastating diseases of rice. It is well established that the wild rice Oryza meyeriana is immune to BB. In this study, the transcriptomic analysis was carried out by RNA sequencing of O. meyeriana leaves, inoculated with Xoo to understand the transcriptional responses and interaction between the host and pathogen. Totally, 57,313 unitranscripts were de novo assembled from 58.7 Gb clean reads and 14,143 unitranscripts were identified after Xoo inoculation. The significant metabolic pathways related to the disease resistance enriched by KEGG, were revealed to plant-pathogen interaction, phytohormone signaling, ubiquitin mediated proteolysis, and phenylpropanoid biosynthesis. Further, many disease resistance genes were also identified to be differentially expressed in response to Xoo infection. Conclusively, the present study indicated that the induced innate immunity comprise the basal defence frontier of O. meyeriana against Xoo infection. And then, the resistance genes are activated. Simultaneously, the other signaling transduction pathways like phytohormones and ubiquitin mediated proteolysis may contribute to the disease defence through modulation of the disease-related genes or pathways. This could be an useful information for further investigating the molecular mechanism associated with disease resistance in O. meyeriana.

  2. Transcriptome analysis confers a complex disease resistance network in wild rice Oryza meyeriana against Xanthomonas oryzae pv. oryzae

    PubMed Central

    Cheng, Xiao-Jie; He, Bin; Chen, Lin; Xiao, Su-qin; Fu, Jian; Chen, Yue; Yu, Teng-qiong; Cheng, Zai-Quan; Feng, Hong

    2016-01-01

    Rice bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the devastating diseases of rice. It is well established that the wild rice Oryza meyeriana is immune to BB. In this study, the transcriptomic analysis was carried out by RNA sequencing of O. meyeriana leaves, inoculated with Xoo to understand the transcriptional responses and interaction between the host and pathogen. Totally, 57,313 unitranscripts were de novo assembled from 58.7 Gb clean reads and 14,143 unitranscripts were identified after Xoo inoculation. The significant metabolic pathways related to the disease resistance enriched by KEGG, were revealed to plant-pathogen interaction, phytohormone signaling, ubiquitin mediated proteolysis, and phenylpropanoid biosynthesis. Further, many disease resistance genes were also identified to be differentially expressed in response to Xoo infection. Conclusively, the present study indicated that the induced innate immunity comprise the basal defence frontier of O. meyeriana against Xoo infection. And then, the resistance genes are activated. Simultaneously, the other signaling transduction pathways like phytohormones and ubiquitin mediated proteolysis may contribute to the disease defence through modulation of the disease-related genes or pathways. This could be an useful information for further investigating the molecular mechanism associated with disease resistance in O. meyeriana. PMID:27905546

  3. Genetic signature of rice domestication shown by a variety of genes.

    PubMed

    Zhang, Yuanli; Wang, Jiao; Zhang, Xiaohui; Chen, Jian-Qun; Tian, Dacheng; Yang, Sihai

    2009-04-01

    Cultivated rice was domesticated from common wild rice. However, little is known about genetic adaptation under domestication. We investigated the nucleotide variation of both cultivated rice and its wild progenitors at 22 R-gene and 10 non-R-gene loci. A significant regression was observed between wild rice and rice cultivars in their polymorphic levels, particularly in their nonsynonymous substitutions (theta ( a )). Our data also showed that a similar proportion (approximately 60%) of nucleotide variation in wild rice was retained in cultivated rice in both R-genes and non-R-genes. Interestingly, the slope always was >1 and the intercept always >0 in linear regressions when a cultivar's polymorphism was x-axis. The slope and intercept values can provide a basis by which to estimate the founder effect and the strength of artificial direct selection. A larger founder effect than previously reported and a strong direct-selection effect were shown in rice genes. In addition, two-directional selection was commonly found in differentiated genes between indica and japonica rice subspecies. This kind of selection may explain the mosaic origins of indica and japonica rice subspecies. Furthermore, in most R-genes, no significant differentiation between cultivated and wild rice was detected. We found evidence for genetic introgression from wild rice, which may have played an important role during the domestication of rice R-genes.

  4. Long-term balancing selection at the Phosphorus Starvation Tolerance 1 (PSTOL1) locus in wild, domesticated and weedy rice (Oryza).

    PubMed

    Vigueira, Cynthia C; Small, Linda L; Olsen, Kenneth M

    2016-04-22

    The ability to grow in phosphorus-depleted soils is an important trait for rice cultivation in many world regions, especially in the tropics. The Phosphorus Starvation Tolerance 1 (PSTOL1) gene has been identified as underlying the ability of some cultivated rice varieties to grow under low-phosphorus conditions; however, the gene is absent from other varieties. We assessed PSTOL1 presence/absence in a geographically diverse sample of wild, domesticated and weedy rice and sequenced the gene in samples where it is present. We find that the presence/absence polymorphism spans cultivated, weedy and wild Asian rice groups. For the subset of samples that carry PSTOL1, haplotype sequences suggest long-term selective maintenance of functional alleles, but with repeated evolution of loss-of-function alleles through premature stops and frameshift mutations. The loss-of-function alleles have evolved convergently in multiple rice species and cultivated rice varieties. Greenhouse assessments of plant growth under low- and high-phosphorus conditions did not reveal significant associations with PSTOL1 genotype variation; however, the striking signature of balancing selection at this locus suggests that further phenotypic characterizations of PSTOL1 allelic variants is warranted and may be useful for crop improvement. These findings suggest balancing selection for both functional and non-functional PSTOL1 alleles that predates and transcends Asian rice domestication, a pattern that may reflect fitness tradeoffs associated with geographical variation in soil phosphorus content.

  5. Insight into the salt tolerance factors of a wild halophytic rice, Porteresia coarctata: a physiological and proteomic approach.

    PubMed

    Sengupta, Sonali; Majumder, Arun Lahiri

    2009-03-01

    Salinity poses a serious threat to yield performance of cultivated rice in South Asian countries. To understand the mechanism of salt-tolerance of the wild halophytic rice, Porteresia coarctata in contrast to the salt-sensitive domesticated rice Oryza sativa, we have compared P. coarctata with the domesticated O. sativa rice varieties under salinity stress with respect to several physiological parameters and changes in leaf protein expression. P. coarctata showed a better growth performance and biomass under salinity stress. Relative water content was conserved in Porteresia during stress and sodium ion accumulation in leaves was comparatively lesser. Scanning electron microscopy revealed presence of two types of salt hairs on two leaf surfaces, each showing a different behaviour under stress. High salt stress for prolonged period also revealed accumulation of extruded NaCl crystals on leaf surface. Changes induced in leaf proteins were studied by two-dimensional gel electrophoresis and subsequent quantitative image analysis. Out of more than 700 protein spots reproducibly detected and analyzed, 60% spots showed significant changes under salinity. Many proteins showed steady patterns of up- or downregulation in response to salinity stress. Twenty protein spots were analyzed by MALDI-TOF, leading to identification of 16 proteins involved in osmolyte synthesis, photosystem functioning, RubisCO activation, cell wall synthesis and chaperone functions. We hypothesize that some of these proteins confer a physiological advantage on Porteresia under salinity, and suggest a pattern of salt tolerance strategies operative in salt-marsh grasses. In addition, such proteins may turn out to be potential targets for recombinant cloning and introgression in salt-sensitive plants.

  6. Memory, transmission and persistence of alternative foraging techniques in wild common marmosets

    PubMed Central

    Gunhold, Tina; Massen, Jorg J.M.; Schiel, Nicola; Souto, Antonio; Bugnyar, Thomas

    2014-01-01

    Experimental studies on traditions in animals have focused almost entirely on the initial transmission phase in captive populations. We conducted an open diffusion field experiment with 13 groups of wild common marmosets, Callithrix jacchus. Seven groups contained individuals that were already familiar with the task (‘push or pull’ box) and thus served as potential models for naïve individuals. Additionally, in four groups one individual was trained for one of the two possible techniques and in two control groups no skilled individuals were present. First, we investigated whether experienced individuals would remember how to solve the task even after 2 years without exposure and whether they would still prefer their learned technique. Second, we tested whether naïve individuals would learn socially from their skilled family members and, more importantly, whether they would use the same technique. Third, we conducted several test blocks to see whether the individual and/or group behaviour would persist over time. Our results show that wild common marmosets were able to memorize, learn socially and maintain preferences of foraging techniques. This field experiment thus reveals a promising approach to studying social learning in the wild and provides the basis for long-term studies on tradition formation. PMID:24910466

  7. Severity of Bovine Tuberculosis Is Associated with Co-Infection with Common Pathogens in Wild Boar

    PubMed Central

    Risco, David; Serrano, Emmanuel; Fernández-Llario, Pedro; Cuesta, Jesús M.; Gonçalves, Pilar; García-Jiménez, Waldo L.; Martínez, Remigio; Cerrato, Rosario; Velarde, Roser; Gómez, Luis; Segalés, Joaquím; Hermoso de Mendoza, Javier

    2014-01-01

    Co-infections with parasites or viruses drive tuberculosis dynamics in humans, but little is known about their effects in other non-human hosts. This work aims to investigate the relationship between Mycobacterium bovis infection and other pathogens in wild boar (Sus scrofa), a recognized reservoir of bovine tuberculosis (bTB) in Mediterranean ecosystems. For this purpose, it has been assessed whether contacts with common concomitant pathogens are associated with the development of severe bTB lesions in 165 wild boar from mid-western Spain. The presence of bTB lesions affecting only one anatomic location (cervical lymph nodes), or more severe patterns affecting more than one location (mainly cervical lymph nodes and lungs), was assessed in infected animals. In addition, the existence of contacts with other pathogens such as porcine circovirus type 2 (PCV2), Aujeszky's disease virus (ADV), swine influenza virus, porcine reproductive and respiratory syndrome virus, Mycoplasma hyopneumoniae, Actinobacillus pleuropneumoniae, Haemophilus parasuis and Metastrongylus spp, was evaluated by means of serological, microbiological and parasitological techniques. The existence of contacts with a structured community of pathogens in wild boar infected by M. bovis was statistically investigated by null models. Association between this community of pathogens and bTB severity was examined using a Partial Least Squares regression approach. Results showed that adult wild boar infected by M. bovis had contacted with some specific, non-random pathogen combinations. Contact with PCV2, ADV and infection by Metastrongylus spp, was positively correlated to tuberculosis severity. Therefore, measures against these concomitant pathogens such as vaccination or deworming, might be useful in tuberculosis control programmes in the wild boar. However, given the unexpected consequences of altering any community of organisms, further research should evaluate the impact of such measures under

  8. Severity of bovine tuberculosis is associated with co-infection with common pathogens in wild boar.

    PubMed

    Risco, David; Serrano, Emmanuel; Fernández-Llario, Pedro; Cuesta, Jesús M; Gonçalves, Pilar; García-Jiménez, Waldo L; Martínez, Remigio; Cerrato, Rosario; Velarde, Roser; Gómez, Luis; Segalés, Joaquím; Hermoso de Mendoza, Javier

    2014-01-01

    Co-infections with parasites or viruses drive tuberculosis dynamics in humans, but little is known about their effects in other non-human hosts. This work aims to investigate the relationship between Mycobacterium bovis infection and other pathogens in wild boar (Sus scrofa), a recognized reservoir of bovine tuberculosis (bTB) in Mediterranean ecosystems. For this purpose, it has been assessed whether contacts with common concomitant pathogens are associated with the development of severe bTB lesions in 165 wild boar from mid-western Spain. The presence of bTB lesions affecting only one anatomic location (cervical lymph nodes), or more severe patterns affecting more than one location (mainly cervical lymph nodes and lungs), was assessed in infected animals. In addition, the existence of contacts with other pathogens such as porcine circovirus type 2 (PCV2), Aujeszky's disease virus (ADV), swine influenza virus, porcine reproductive and respiratory syndrome virus, Mycoplasma hyopneumoniae, Actinobacillus pleuropneumoniae, Haemophilus parasuis and Metastrongylus spp, was evaluated by means of serological, microbiological and parasitological techniques. The existence of contacts with a structured community of pathogens in wild boar infected by M. bovis was statistically investigated by null models. Association between this community of pathogens and bTB severity was examined using a Partial Least Squares regression approach. Results showed that adult wild boar infected by M. bovis had contacted with some specific, non-random pathogen combinations. Contact with PCV2, ADV and infection by Metastrongylus spp, was positively correlated to tuberculosis severity. Therefore, measures against these concomitant pathogens such as vaccination or deworming, might be useful in tuberculosis control programmes in the wild boar. However, given the unexpected consequences of altering any community of organisms, further research should evaluate the impact of such measures under

  9. Transitions in photoperiodic flowering are common and involve few loci in wild sunflowers (Helianthus; Asteraceae).

    PubMed

    Henry, Lucas P; Watson, Ray H B; Blackman, Benjamin K

    2014-10-01

    • Evolutionary changes in how flowering time responds to photoperiod cues have been instrumental in expanding the geographic range of agricultural production for many crop species. Locally adaptive natural variation in photoperiod response present in wild relatives of crop plants could be leveraged to further improve the present and future climatic ranges of cultivation or to increase region-specific yields. Previous work has demonstrated ample variability in photoperiod response among wild populations of the common sunflower, Helianthus annuus. Here, we characterize patterns of photoperiod response variation throughout the genus and examine the genetic architecture of intraspecific divergence.• The requirement of short day lengths for floral induction was characterized for a phylogenetically dispersed sample of Helianthus species. In addition, flowering time was assessed under short days and long days for a population of F3 individuals derived from crosses between day-neutral and short-day, wild H. annuus parents.• An obligate requirement for short-day induced flowering has evolved repeatedly in Helianthus, and this character was correlated with geographic ranges restricted to the southern United States. Parental flowering times under long days were recovered in high proportion in the F3 generation.• Together, these findings (1) reveal that substantial variation in the nature of flowering time responses to photoperiod cues has arisen during the evolution of wild sunflowers and (2) suggest these transitions may be largely characterized by simple genetic architectures. Thus, introgression of wild alleles may be a tractable means of genetically tailoring sunflower cultivars for climate-specific production. © 2014 Botanical Society of America, Inc.

  10. A 400-year phytolith-based reconstruction of wild rice (Zizania palustris) abundance from Mud Lake core sediments, Fond du Lac Band of Lake Superior Chippewa Reservation, Minnesota, USA.

    NASA Astrophysics Data System (ADS)

    Munoz, R.; Caylor, E.; Yost, C. L.; Drake, C.; Ladwig, J. L.; Myrbo, A.; Howes, T.

    2014-12-01

    Wild rice (Zizania palustris L.) is an aquatic grass with spiritual and subsistence significance to Native people of the Great Lakes region of North America. Mud Lake (Mashkiigwaagamaag), located on the Fond du Lac Band of Lake Superior Chippewa Reservation in Carlton County, Minnesota, USA, once supported an extensive population of wild rice (manoomin). However, early 20th century attempts to ditch and drain surrounding wetlands for landuse intensification severely altered the natural hydrological system that supports wild rice. Fond du Lac Resource Management (FDLRM) technicians are currently working to increase the wild rice population in Mud Lake. As part of these efforts, this phytolith study was undertaken to better understand how wild rice abundance has fluctuated over the past 400 years, with particular emphasis on the 19th and 20th centuries. Phytoliths are microscopic opal silica plant remains that are incorporated into soils and lake sediments after the plant-parts that contain them decay. Wild rice produces phytolith morphotypes that are unequivocally diagnostic. Mud Lake core MNMN-MUD11-1C-1P-1 (46°43'38.39"N, 92°42'2.45"W) was piston cored by LacCore (National Lacustrine Core Facility) and FDLRM technicians on 24 May 2011. Initial core descriptions, multi-sensor core logging, phytolith sampling and phytolith extractions were completed during the summer of 2014 at LacCore. Wild rice phytolith identification and quantification was conducted on twelve samples using brightfield microscopy at 400x magnification. Wild rice phytolith concentration values ranged from 68 to 2,300 phytoliths/cm3. Wild rice accumulation rates ranged from 9 to 383 phytoliths/ cm2/yr, peaking in 1952 AD. Wild rice abundance in Mud Lake appears to be influenced by a complex set of variables that include anthropogenic disturbance, climatic events and aquatic plant community succession.

  11. Characterization of Salinity Tolerance of Transgenic Rice Lines Harboring HsCBL8 of Wild Barley (Hordeum spontanum) Line from Qinghai-Tibet Plateau

    PubMed Central

    Guo, Wanli; Chen, Tianlong; Hussain, Nazim; Zhang, Guoping; Jiang, Lixi

    2016-01-01

    Rice is more sensitive to salinity, particularly at its early vegetative and later productive stages. Wild plants growing in harsh environments such as wild barley from Qinghai-Tibet Plateau adapt to the adverse environment with allelic variations at the loci responsible for stressful environment, which could be used for rice genetic improvement. In this study, we overexpressed HsCBL8 encoding a calcium-sensor calcineurin B-like (CBL) protein in rice. The gene was isolated from XZ166, a wild-barley (Hordeum spontanum) line originated from Qinghai-Tibet Plateau. We found that XZ166 responded to high NaCl concentration (200 mM) with more HsCBL8 transcripts than CM72, a cultivated barley line known for salinity tolerance. XZ166 is significantly different from CM72 with nucleotide sequences at HsCBL8. The overexpression of HsCBL8 in rice resulted in significant improvement of water protection in vivo and plasma membrane, more proline accumulation, and a reduction of overall Na+ uptake but little change in K+ concentration in the plant tissues. Notably, HsCBL8 did not act on some genes downstream of the rice CBL family genes, suggesting an interesting interaction between HsCBL8 and unknown factors to be further investigated. PMID:27891136

  12. Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L.

    PubMed Central

    Mamidi, S; Rossi, M; Moghaddam, S M; Annam, D; Lee, R; Papa, R; McClean, P E

    2013-01-01

    Wild common bean (Phaseolus vulgaris L.) is distributed throughout the Americas from Mexico to northern Argentina. Within this range, the species is divided into two gene pools (Andean and Middle American) along a latitudinal gradient. The diversity of 24 wild common bean genotypes from throughout the geographic range of the species was described by using sequence data from 13 loci. An isolation–migration model was evaluated using a coalescent analysis to estimate multiple demographic parameters. Using a Bayesian approach, Andean and Middle American subpopulations with high percentage of parentages were observed. Over all loci, the Middle American gene pool was more diverse than the Andean gene pool (πsil=0.0089 vs 0.0068). The two subpopulations were strongly genetically differentiated over all loci (Fst=0.29). It is estimated that the two current wild gene pools diverged from a common ancestor ∼111 000 years ago. Subsequently, each gene pool underwent a bottleneck immediately after divergence and lasted ∼40 000 years. The Middle American bottleneck population size was ∼46% of the ancestral population size, whereas the Andean was 26%. Continuous asymmetric gene flow was detected between the two gene pools with a larger number of migrants entering Middle American gene pool from the Andean gene pool. These results suggest that because of the complex population structure associated with the ancestral divergence, subsequent bottlenecks in each gene pool, gene pool-specific domestication and intense selection within each gene pool by breeders; association mapping would best be practised within each common bean gene pool. PMID:23169559

  13. Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L.

    PubMed

    Mamidi, S; Rossi, M; Moghaddam, S M; Annam, D; Lee, R; Papa, R; McClean, P E

    2013-03-01

    Wild common bean (Phaseolus vulgaris L.) is distributed throughout the Americas from Mexico to northern Argentina. Within this range, the species is divided into two gene pools (Andean and Middle American) along a latitudinal gradient. The diversity of 24 wild common bean genotypes from throughout the geographic range of the species was described by using sequence data from 13 loci. An isolation-migration model was evaluated using a coalescent analysis to estimate multiple demographic parameters. Using a Bayesian approach, Andean and Middle American subpopulations with high percentage of parentages were observed. Over all loci, the Middle American gene pool was more diverse than the Andean gene pool (π(sil)=0.0089 vs 0.0068). The two subpopulations were strongly genetically differentiated over all loci (F(st)=0.29). It is estimated that the two current wild gene pools diverged from a common ancestor ∼111 000 years ago. Subsequently, each gene pool underwent a bottleneck immediately after divergence and lasted ∼40 000 years. The Middle American bottleneck population size was ∼46% of the ancestral population size, whereas the Andean was 26%. Continuous asymmetric gene flow was detected between the two gene pools with a larger number of migrants entering Middle American gene pool from the Andean gene pool. These results suggest that because of the complex population structure associated with the ancestral divergence, subsequent bottlenecks in each gene pool, gene pool-specific domestication and intense selection within each gene pool by breeders; association mapping would best be practised within each common bean gene pool.

  14. Genome-Wide Analysis of Polycistronic MicroRNAs in Cultivated and Wild Rice

    PubMed Central

    Baldrich, Patricia; Hsing, Yue-Ie Caroline; San Segundo, Blanca

    2016-01-01

    MicroRNAs (miRNAs) are small noncoding RNAs that direct posttranscriptional gene silencing in eukaryotes. They are frequently clustered in the genomes of animals and can be independently transcribed or simultaneously transcribed into single polycistronic transcripts. Only a few miRNA clusters have been described in plants, and most of them are generated from independent transcriptional units. Here, we used a combination of bioinformatic tools and experimental analyses to discover new polycistronic miRNAs in rice. A genome-wide analysis of clustering patterns of MIRNA loci in the rice genome was carried out using a criterion of 3 kb as the maximal distance between two miRNAs. This analysis revealed 28 loci with the ability to form the typical hairpin structure of miRNA precursors in which 2 or more mature miRNAs mapped along the same structure. RT-PCR provided evidence for the polycistronic nature of seven miRNA precursors containing homologous or nonhomologous miRNA species. Polycistronic miRNAs and candidate polycistronic miRNAs are located across different rice chromosomes, except chromosome 12, and resided in both duplicated and nonduplicated chromosomal regions. Finally, most polycistronic and candidate polycistronic miRNAs showed a pattern of conservation in the genome of rice species with an AA genome. The diversity in the organization of MIR genes that are transcribed as polycistrons suggests a versatile mechanism for the control of gene expression in different biological processes and supports additional levels of complexity in miRNA functioning in plants. PMID:27190137

  15. Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice

    PubMed Central

    Piegu, Benoit; Guyot, Romain; Picault, Nathalie; Roulin, Anne; Saniyal, Abhijit; Kim, Hyeran; Collura, Kristi; Brar, Darshan S.; Jackson, Scott; Wing, Rod A.; Panaud, Olivier

    2006-01-01

    Retrotransposons are the main components of eukaryotic genomes, representing up to 80% of some large plant genomes. These mobile elements transpose via a “copy and paste” mechanism, thus increasing their copy number while active. Their accumulation is now accepted as the main factor of genome size increase in higher eukaryotes, besides polyploidy. However, the dynamics of this process are poorly understood. In this study, we show that Oryza australiensis, a wild relative of the Asian cultivated rice O. sativa, has undergone recent bursts of three LTR-retrotransposon families. This genome has accumulated more than 90,000 retrotransposon copies during the last three million years, leading to a rapid twofold increase of its size. In addition, phenetic analyses of these retrotransposons clearly confirm that the genomic bursts occurred posterior to the radiation of the species. This provides direct evidence of retrotransposon-mediated variation of genome size within a plant genus. PMID:16963705

  16. Greenhouse gas emissions, irrigation water use, and arsenic concentrations; a common thread in rice water management

    USDA-ARS?s Scientific Manuscript database

    Rice has historically been grown as a flooded crop in the United States. As competition for water resources has grown, there is interest in reducing water use in rice production so as to maintain a viable and sustainable rice industry into the future. An irrigation study was established in 2011 at ...

  17. Alteration of leaf metabolism in Bt-transgenic rice (Oryza sativa L.) and its wild type under insecticide stress.

    PubMed

    Zhou, Jia; Zhang, Lei; Chang, Yuwei; Lu, Xin; Zhu, Zhen; Xu, Guowang

    2012-08-03

    Insecticide is always used to control the damage from pests, while the potential influence on plants is rarely known. Time-course metabolic changes of wild and Bacillus thuringiensis (Bt) transgenic rice (Oryza sativa L.) plants after insecticide treatment were investigated by using gas chromatography-mass spectrometry (GC-MS). A combined statistical strategy of 2-way ANOVA and multivariate analyses (principal component analysis and hierarchal cluster analysis) was performed to find the stress-associated effects. The results reveal that a wide range of metabolites were dynamically varied in both varieties as a response to insecticide, in multiple metabolic pathways, such as biosynthesis and metabolism of amino acids, carbohydrates, fatty acids, TCA cycle, and the shikimate/phenylpropanoid pathway, and most of the changes were correlated with the exposure time and dependent on the variety. A set of stress defenses were activated, including phytohormone signaling pathway, antioxidant defense system, shikimate-mediated secondary metabolism, and so on. In particular, insecticide led to much stronger regulations of signaling molecules (salicylate and the precursor of jasmonate) and antioxidants (α-tocopherol and dehydroascorbate/ascorbate) in Bt-transgenic variety at the early stage. Our results demonstrated that the Bt-transgenic rice had a more acute and drastic response to insecticide stress than its non-transgenic counterpart in antioxidant system and signaling regulation.

  18. Distribution, genetic diversity and potential spatiotemporal scale of alien gene flow in crop wild relatives of rice (Oryza spp.) in Colombia.

    PubMed

    Thomas, Evert; Tovar, Eduardo; Villafañe, Carolina; Bocanegra, José Leonardo; Moreno, Rodrigo

    2017-12-01

    Crop wild relatives (CWRs) of rice hold important traits that can contribute to enhancing the ability of cultivated rice (Oryza sativa and O. glaberrima) to produce higher yields, cope with the effects of climate change, and resist attacks of pests and diseases, among others. However, the genetic resources of these species remain dramatically understudied, putting at risk their future availability from in situ and ex situ sources. Here we assess the distribution of genetic diversity of the four rice CWRs known to occur in Colombia (O. glumaepatula, O. alta, O. grandiglumis, and O. latifolia). Furthermore, we estimated the degree of overlap between areas with suitable habitat for cultivated and wild rice, both under current and predicted future climate conditions to assess the potential spatiotemporal scale of potential gene flow from GM rice to its CWRs. Our findings suggest that part of the observed genetic diversity and structure, at least of the most exhaustively sampled species, may be explained by their glacial and post-glacial range dynamics. Furthermore, in assessing the expected impact of climate change and the potential spatiotemporal scale of gene flow between populations of CWRs and GM rice we find significant overlap between present and future suitable areas for cultivated rice and its four CWRs. Climate change is expected to have relatively limited negative effects on the rice CWRs, with three species showing opportunities to expand their distribution ranges in the future. Given (i) the sparse presence of CWR populations in protected areas (ii) the strong suitability overlap between cultivated rice and its four CWRs; and (iii) the complexity of managing and regulating areas to prevent alien gene flow, the first priority should be to establish representative ex situ collections for all CWR species, which currently do not exist. In the absence of studies under field conditions on the scale and extent of gene flow between cultivated rice and its Colombian

  19. qEMF3, a novel QTL for the early-morning flowering trait from wild rice, Oryza officinalis, to mitigate heat stress damage at flowering in rice, O. sativa

    PubMed Central

    Hirabayashi, Hideyuki; Sasaki, Kazuhiro; Kambe, Takashi; Gannaban, Ritchel B.; Miras, Monaliza A.; Mendioro, Merlyn S.; Simon, Eliza V.; Lumanglas, Patrick D.; Fujita, Daisuke; Takemoto-Kuno, Yoko; Takeuchi, Yoshinobu; Kaji, Ryota; Kondo, Motohiko; Kobayashi, Nobuya; Ogawa, Tsugufumi; Ando, Ikuo; Jagadish, Krishna S. V.; Ishimaru, Tsutomu

    2015-01-01

    A decline in rice (Oryza sativa L.) production caused by heat stress is one of the biggest concerns resulting from future climate change. Rice spikelets are most susceptible to heat stress at flowering. The early-morning flowering (EMF) trait mitigates heat-induced spikelet sterility at the flowering stage by escaping heat stress during the daytime. We attempted to develop near-isogenic lines (NILs) for EMF in the indica-type genetic background by exploiting the EMF locus from wild rice, O. officinalis (CC genome). A stable quantitative trait locus (QTL) for flower opening time (FOT) was detected on chromosome 3. A QTL was designated as qEMF3 and it shifted FOT by 1.5–2.0h earlier for cv. Nanjing 11 in temperate Japan and cv. IR64 in the Philippine tropics. NILs for EMF mitigated heat-induced spikelet sterility under elevated temperature conditions completing flower opening before reaching 35°C, a general threshold value leading to spikelet sterility. Quantification of FOT of cultivars popular in the tropics and subtropics did not reveal the EMF trait in any of the cultivars tested, suggesting that qEMF3 has the potential to advance FOT of currently popular cultivars to escape heat stress at flowering under future hotter climates. This is the first report to examine rice with the EMF trait through marker-assisted breeding using wild rice as a genetic resource. PMID:25534925

  20. DNA polymorphism in the SUPERWOMAN1 (SPW1) locus of the wild rice Oryza rufipogon and its related species.

    PubMed

    Teranishi, Chika; Yoshida, Kentaro; Miyashita, Naohiko T

    2008-10-01

    The level and pattern of nucleotide variation in the SUPERWOMAN1(SPW1) locus of the wild rice Oriza rufipogon and its related species were analyzed. SPW1 is orthologous to APETELA3(AP3) in Arabidopsis thaliana. The estimated level of nucleotide variation for the entire region (pi = 0.0046) was intermediate among those for other genes of O. rufipogon, although the estimates varied considerably among the SPW1 domains. Complicated haplotype structure was detected, resulting in a high proportion of significant linkage disequilibrium. Deviation from the neutrality was not detected. However, purifying selection was suggested by lack of replacement variation in the MADS-box and I-domain regions, which function as DNA-binding domain. On the other hand, an excess of drastic amino acid changes was detected in the C-domain, as in the AP3 region of A. thaliana. Taken together, these results imply that different types of natural selection are acting among different domains of a single protein. In the phylogenetic tree, O. sativa strains were included in the same cluster of O. rufipogon, supporting the hypothesis that O. rufipogon is the wild ancestor of O. sativa.

  1. Validation of yield enhancing QTLs from a low-yielding wild ancestor of rice

    USDA-ARS?s Scientific Manuscript database

    A set of introgression lines (ILs) containing chromosomal segments from O. rufipogon (IRGC 105491), a wild relative of O. sativa, in the genetic background of an elite U.S. variety, cv. Jefferson, was developed to confirm the performance of six yield-enhancing quantitative trait loci (QTLs). Fifty B...

  2. Video demonstrations seed alternative problem-solving techniques in wild common marmosets.

    PubMed

    Gunhold, Tina; Whiten, Andrew; Bugnyar, Thomas

    2014-09-01

    Studies of social learning and tradition formation under field conditions have recently gained momentum, but suffer from the limited control of socio-ecological factors thought to be responsible for transmission patterns. The use of artificial visual stimuli is a potentially powerful tool to overcome some of these problems. Here, in a field experiment, we used video images of unfamiliar conspecifics performing virtual demonstrations of foraging techniques. We tested 12 family groups of wild common marmosets. Six groups received video demonstrations (footage of conspecifics either pulling a drawer open or pushing a lid upwards, in an 'artificial fruit'); the other six groups served as controls (exposed to a static image of a conspecific next to the fruit). Subjects in video groups were more manipulative and successful in opening the fruit than controls; they were also more likely to use the technique they had witnessed and thus could serve as live models for other family members. To our knowledge, this is the first study that used video demonstrations in the wild and demonstrated the potent force of social learning, even from unfamiliar conspecifics, under field conditions.

  3. Antimicrobial resistance profiles of Escherichia coli from common European wild bird species.

    PubMed

    Guenther, Sebastian; Grobbel, Mirjam; Lübke-Becker, Antina; Goedecke, Andreas; Friedrich, Nicole D; Wieler, Lothar H; Ewers, Christa

    2010-07-29

    The emergence and spread of multiresistant bacteria in natural environments constitute a serious impact on animal and human health. To gain more insight into the role of wild birds as carriers and reservoir of multiresistant Escherichia coli we tested a broad spectrum of common European bird species for the occurrence of E. coli strains and their antimicrobial resistance by minimal inhibitory concentration testing and PCR analysis of several resistance genes. Nine of the 187 E. coli isolates (4.8%) exhibited multiresistant phenotypes including resistances against beta-lactams, aminoglycosides, fluoroquinolones, tetracyclines and sulfonamides. By comparing avian E. coli resistance frequencies with frequencies known for E. coli isolated from livestock and companion animals analogous profiles were identified. Multiresistant E. coli strains were isolated from synanthropic avian species as well as from birds of prey, waterfowl and passerines. By that, all these avian hosts are suggested to represent a considerable reservoir of resistant E. coli strains. Consequently wild birds might constitute a potential hazard to human and animal health by transmitting multiresistant strains to waterways and other environmental sources via their faecal deposits.

  4. 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.

  5. Effects of excess copper on growth of wild rice (Zizania palustris) seedlings tested in reconstituted and natural waters.

    PubMed

    Nimmo, Del Wayne R; Preul, Michael A; Castle, Carla J; Self, James R; Pillsbury, Robert W; Bergey, Elizabeth A

    2003-10-01

    Dissolved copper was toxic to wild rice (Zizania palustris) seedlings when exposed in water from the seed collection site of Swamp Creek, Crandon, Wisconsin, USA, and in laboratory-prepared artificial or reconstituted water. Seeds for the study were harvested, then held through a portion of dormancy, in Swamp Creek. After 60 days they were shipped to a laboratory, chilled, and tested with copper after germination. The end point of the tests was net gain in wet weight of the seedlings; additionally, a pronounced reduction in root development was observed. Using measured concentrations, the lowest no-observable-effect concentration (NOEC) in our study was 37 microg/liter in Swamp Creek water and the lowest-observable-effect concentration (LOEC) was 59 microg/liter. However, it appeared that there was a point at which concentrations of copper above 400 microg/liter did not result in any measurable effect or exhibit a definitive dose-response. Because the results in Swamp Creek water were more relevant to the possibility of local metals additions and the association of reduced seedling growth by copper was more powerful in this water, we derived an equation to express the relationship between copper concentration and toxicity for Swamp Creek water. As an example, we would expect a 3.0% reduction in seedling growth at 5.0 microg/liter copper. Seedling roots were particularly affected and the resultant plants may be less well anchored and more susceptible to dislodging than plants not exposed to copper. Further refinement of the methodology may be used to address effects of other contaminants impacting rice beds in North America.

  6. Chemical components with health implications in wild and cultivated Mexican common bean seeds (Phaseolus vulgaris L.).

    PubMed

    Díaz-Batalla, Luis; Widholm, Jack M; Fahey, George C; Castaño-Tostado, Eduardo; Paredes-López, Octavio

    2006-03-22

    Common bean effects on health have been related to its dietary fiber content and other active compounds. This study assessed the content of flavonoids, coumestrol, phenolic acids, galactooligosaccharides, and phytic acid in wild and cultivated Mexican common bean seeds (raw and cooked) and that of flavonoids, coumestrol, and phenolic acids in germinated bean seeds. The presence of isoflavones in raw bean seeds was not confirmed by the UV spectra. Quercetin, kaempferol, p-coumaric acid, ferulic acid, p-hydroxybenzoic acid, and vanillic acid mean contents were 10.9, 52.3, 10.1, 9.6, 5.4, and 18.2 microg/g, respectively; raffinose, stachyose, verbascose, and phytic acid mean contents were 8.5, 56.3, 5.5, and 11.5 mg/g, respectively, in raw seeds. All compounds were affected by autoclaving, and germination resulted in a de novo synthesis of flavonols, phytoestrogens, and phenolic acids. The impact on health of common bean seed is affected by dietary burden, specific compounds content, and processing. On the other hand, germinated bean seed or beans sprouts may be sources of antioxidants and phytoestrogens.

  7. Identity, Diversity, and Molecular Phylogeny of the Endophytic Mycobiota in the Roots of Rare Wild Rice (Oryza granulate) from a Nature Reserve in Yunnan, China▿ †

    PubMed Central

    Yuan, Zhi-lin; Zhang, Chu-long; Lin, Fu-cheng; Kubicek, Christian P.

    2010-01-01

    Rice (Oryza sativa L.) is, on a global scale, one of the most important food crops. Although endophytic fungi and bacteria associated with rice have been investigated, little is known about the endophytic fungi of wild rice (Oryza granulate) in China. Here we studied the root endophytic mycobiota residing in roots of O. granulate by the use of an integrated approach consisting of microscopy, cultivation, ecological indices, and direct PCR. Microscopy confirmed the ubiquitousness of dark septate endophytes (DSEs) and sclerotium-like structures in root tissues. Isolations from 204 root segments from 15 wild rice plants yielded 58 isolates, for which 31 internal transcribed spacer (ITS)-based genotypes were recorded. The best BLAST match indicated that 34.5% of all taxa encountered may represent hitherto undescribed species. Most of the fungi were isolated with a very low frequency. Calculation of ecological indices and estimation of taxon accumulation curves indicated a high diversity of fungal species. A culture-independent approach was also performed to analyze the endophytic fungal community. Three individual clone libraries were constructed. Using a threshold of 90% similarity, 35 potentially different sequences (phylotypes) were found among 186 positive clones. Phylogenetic analysis showed that frequently detected clones were classified as Basidiomycota, and 60.2% of total analyzed clones were affiliated with unknown taxa. Exophiala, Cladophialophora, Harpophora, Periconia macrospinosa, and the Ceratobasidium/Rhizoctonia complex may act as potential DSE groups. A comparison of the fungal communities characterized by the two approaches demonstrated distinctive fungal groups, and only a few taxa overlapped. Our findings indicate a complex and rich endophytic fungal consortium in wild rice roots, thus offering a potential bioresource for establishing a novel model of plant-fungal mutualistic interactions. PMID:20038691

  8. Rice Bran Amendment Suppresses Potato Common Scab by Increasing Antagonistic Bacterial Community Levels in the Rhizosphere.

    PubMed

    Tomihama, Tsuyoshi; Nishi, Yatsuka; Mori, Kiyofumi; Shirao, Tsukasa; Iida, Toshiya; Uzuhashi, Shihomi; Ohkuma, Moriya; Ikeda, Seishi

    2016-07-01

    Potato common scab (PCS), caused by pathogenic Streptomyces spp., is a serious disease in potato production worldwide. Cultural practices, such as optimizing the soil pH and irrigation, are recommended but it is often difficult to establish stable disease reductions using these methods. Traditionally, local farmers in southwest Japan have amended soils with rice bran (RB) to suppress PCS. However, the scientific mechanism underlying disease suppression by RB has not been elucidated. The present study showed that RB amendment reduced PCS by repressing the pathogenic Streptomyces population in young tubers. Amplicon sequencing analyses of 16S ribosomal RNA genes from the rhizosphere microbiome revealed that RB amendment dramatically changed bacterial composition and led to an increase in the relative abundance of gram-positive bacteria such as Streptomyces spp., and this was negatively correlated with PCS disease severity. Most actinomycete isolates derived from the RB-amended soil showed antagonistic activity against pathogenic Streptomyces scabiei and S. turgidiscabies on R2A medium. Some of the Streptomyces isolates suppressed PCS when they were inoculated onto potato plants in a field experiment. These results suggest that RB amendment increases the levels of antagonistic bacteria against PCS pathogens in the potato rhizosphere.

  9. Contribution of individual phenolics to antioxidant activity and in vitro digestibility of wild rices (Zizania aquatica L.).

    PubMed

    Sumczynski, Daniela; Kotásková, Eva; Orsavová, Jana; Valášek, Pavel

    2017-03-01

    Zizania aquatica L. was analysed for total flavonoids, phenolics and HPLC profile in both free and bound phenolic fractions. The highest content of flavonoids (378-455mgRE/kg) was detected in bound fractions, while the highest polyphenols content (1061-2988mgGAE/kg) was determined in free fractions. Additionally, predominant phenolics were identified. To understand the contribution of individual phenolics to an antioxidant activity their mutual correlations were evaluated. Regarding free flavonoids, the main contributors to an antioxidant activity (r>0.7111) were epigallocatechin, epicatechin and rutin; while epicatechin, quercetin and rutin were the main contributors in bound fractions (r>0.6868). Concerning free phenolic acids, the main contributors to an antioxidant activity (r>0.7585) were ferulic, vanillic, ellagic, sinapic and syringic acids; while caffeic, sinapic, syringic, o-coumaric, p-hydroxy benzoic, vanillic, protocatechuic, gallic and cinnamic acids were the main contributors in bound fractions of wild rice (r>0.6538). Finally, in vitro organic matter and dry matter digestibility were assessed.

  10. A vacuolar antiporter is differentially regulated in leaves and roots of the halophytic wild rice Porteresia coarctata (Roxb.) Tateoka.

    PubMed

    Kizhakkedath, Praseetha; Jegadeeson, Vidya; Venkataraman, Gayatri; Parida, Ajay

    2015-06-01

    Vacuolar NHX-type antiporters play a role in Na(+)/K(+) uptake that contributes to growth, nutrition and development. Under salt/osmotic stress they mediate the vacuolar compartmentalization of K(+)/Na(+), thereby preventing toxic Na(+)K(+) ratios in the cytosol. Porteresia coarctata (Roxb.) Tateoka, a mangrove associate, is a distant wild relative of cultivated rice and is saline as well as submergence tolerant. A vacuolar NHX homolog isolated from a P. coarctata cDNA library (PcNHX1) shows 96 % identity (nucleotide level) to OsNHX1. Diurnal PcNHX1 expression in leaves was found to be largely unaltered, though damped by salinity. PcNHX1 promoter directed GUS expression is phloem-specific in leaves, stem and roots of transgenic plants in the absence of stress. Under NaCl stress, GUS expression was also seen in the epidermal and sub-epidermal layers (mesophyll, guard cells and trichomes) of leaves, root tip. The salinity in the rhizosphere of P. coarctata varies considerably due to diurnal/semi-diurnal tidal inundation. The diurnal expression of PcNHX1 in leaves and salinity induced expression in roots may have evolved in response to dynamic changes in salinity of in the P. coarctata rhizosphere. Despite high sequence conservation between OsNHX1 and PcNHX1, the distinctive expression pattern of PcNHX1 exemplifies how variation in expression is fine tuned to suit the halophytic growth habitat of a plant.

  11. Ethylene is not involved in adaptive responses to flooding in the Amazonian wild rice species Oryza grandiglumis.

    PubMed

    Okishio, Takuma; Sasayama, Daisuke; Hirano, Tatsuya; Akimoto, Masahiro; Itoh, Kazuyuki; Azuma, Tetsushi

    2015-02-01

    The Amazonian wild rice Oryza grandiglumis has two contrasting adaptation mechanisms to flooding submergence: a quiescence response to complete submergence at the seedling stage and an escape response based on internodal elongation to partial submergence at the mature stage. We investigated possible factors that trigger these responses. In stem segments excised from mature O. grandiglumis plants, complete submergence only slightly promoted internodal elongation with increased ethylene levels in the internodes, while partial submergence substantially promoted internodal elongation without increased ethylene levels in the internodes. Incubation of non-submerged stem segments under a continuous flow of humidified ethylene-free air promoted internodal elongation to the same extent as that observed for partially submerged segments. Applied ethylene had little effect on the internodal elongation of non-submerged segments irrespective of humidity conditions. These results indicate that the enhanced internodal elongation of submerged O. grandiglumis plants is not triggered by ethylene accumulated during submergence but by the moist surroundings provided by submergence. The growth of shoots in O. grandiglumis seedlings was not promoted by ethylene or complete submergence, as is the case in O. sativa cultivars possessing the submergence-tolerant gene SUB1A. However, because the genome of O. grandiglumis lacks the SUB1A gene, the quiescence response of O. grandiglumis seedlings to complete submergence may be regulated by a mechanism distinct from that involved in the response of submergence-tolerant O. sativa cultivars.

  12. Molecular relationships between Australian annual wild rice, Oryza meridionalis, and two related perennial forms

    PubMed Central

    2013-01-01

    Background The perennial, Oryza rufipogon distributed from Asia to Australia and the annual O. meridionalis indigenous to Australia are AA genome species in the Oryza. However, recent research has demonstrated that the Australian AA genome perennial populations have maternal genomes more closely related to those of O. meridionalis than to those found in Asian populations of O. rufipogon suggesting that the Australian perennials may represent a new distinct gene pool for rice. Results Analysis of an Oryza core collection covering AA genome species from Asia to Oceania revealed that some Oceania perennials had organellar genomes closely related to that of O meridionalis (meridionalis-type). O. rufipogon accessions from New Guinea carried either the meridionalis-type or rufirpogon-type (like O. rufipogon) organellar genomes. Australian perennials carried only the meridionalis-type organellar genomes when accompanied by the rufipogon-type nuclear genome. New accessions were collected to better characterize the Australian perennials, and their life histories (annual or perennial) were confirmed by field observations. All of the material collected carried only meridionalis-type organellar genomes. However, there were two distinct perennial groups. One of them carried an rufipogon-type nuclear genome similar to the Australian O. rufipogon in the core collection and the other carried an meridionalis-type nuclear genome not represented in the existing collection. Morphologically the rufipogon-type shared similarity with Asian O. rufipogon. The meridionalis-type showed some similarities to O. meridionalis such as the short anthers usually characteristic of annual populations. However, the meridionalis-type perennial was readily distinguished from O. meridionalis by the presence of a larger lemma and higher number of spikelets. Conclusion Analysis of current accessions clearly indicated that there are two distinct types of Australian perennials. Both of them differed

  13. Nanda-gikendaasowin Naawij Gaa-izhiwebakin Manoomini-zaaga'iganiing: Core-based research by Native students on wild rice lakes in northern Minnesota

    NASA Astrophysics Data System (ADS)

    Myrbo, A.; Howes, T.; Defoe, R.; Dalbotten, D. M.; Pellerin, H.; McEathron, M.; Ito, E.

    2011-12-01

    Little is known about how local and global environmental changes affect the habitat of wild rice (manoomin in Ojibwe; Zizania sp.). Using transects of sediment cores from wild rice lakes on the Fond du Lac Band of Lake Superior Chippewa Reservation (FDL) in Minnesota, undergraduate student researchers are working to reconstruct the lakes' ecological history in order to better manage future change. Reservation Resource Management personnel and University science mentors work together to develop research questions and mentor small groups of college-age students during short (two-week) and long (ten-week) summer internships. Cores are collected during the winter from the frozen lake surface with "Lake Teams" of mainly Native junior high and high school students attending weekend science camps, who also visit LacCore (the National Lacustrine Core Facility) in Minneapolis to conduct initial core description and basic analyses. At the same time as the Fond du Lac Band gains information about the long-term history and variability of the Reservation's lakes, young Native people are exposed to primary research, natural resources management and academia as occupations, and scientists as people. Scientific results, as well as the results of program evaluation, show clearly that this approach has so far been successful and eye-opening for both students and mentors. Lead-210 dated records of the past ~150 years cover the period of European settlement, logging, and the massive ditching of FDL lakes to convert wetlands to agricultural land. Phytolith, pollen, plant macrofossil, and diatom studies by interns, as well as sediment composition and mass accumulation rate data, show anthropogenic lake level and vegetation fluctuations associated with these activities. Earlier in the record (~10,000 years to ~100 years before present), the natural and slow processes of lake infilling and encroachment of shallow-water vegetation are the dominant processes controlling the ecology of the

  14. qEMF3, a novel QTL for the early-morning flowering trait from wild rice, Oryza officinalis, to mitigate heat stress damage at flowering in rice, O. sativa.

    PubMed

    Hirabayashi, Hideyuki; Sasaki, Kazuhiro; Kambe, Takashi; Gannaban, Ritchel B; Miras, Monaliza A; Mendioro, Merlyn S; Simon, Eliza V; Lumanglas, Patrick D; Fujita, Daisuke; Takemoto-Kuno, Yoko; Takeuchi, Yoshinobu; Kaji, Ryota; Kondo, Motohiko; Kobayashi, Nobuya; Ogawa, Tsugufumi; Ando, Ikuo; Jagadish, Krishna S V; Ishimaru, Tsutomu

    2015-03-01

    A decline in rice (Oryza sativa L.) production caused by heat stress is one of the biggest concerns resulting from future climate change. Rice spikelets are most susceptible to heat stress at flowering. The early-morning flowering (EMF) trait mitigates heat-induced spikelet sterility at the flowering stage by escaping heat stress during the daytime. We attempted to develop near-isogenic lines (NILs) for EMF in the indica-type genetic background by exploiting the EMF locus from wild rice, O. officinalis (CC genome). A stable quantitative trait locus (QTL) for flower opening time (FOT) was detected on chromosome 3. A QTL was designated as qEMF3 and it shifted FOT by 1.5-2.0 h earlier for cv. Nanjing 11 in temperate Japan and cv. IR64 in the Philippine tropics. NILs for EMF mitigated heat-induced spikelet sterility under elevated temperature conditions completing flower opening before reaching 35°C, a general threshold value leading to spikelet sterility. Quantification of FOT of cultivars popular in the tropics and subtropics did not reveal the EMF trait in any of the cultivars tested, suggesting that qEMF3 has the potential to advance FOT of currently popular cultivars to escape heat stress at flowering under future hotter climates. This is the first report to examine rice with the EMF trait through marker-assisted breeding using wild rice as a genetic resource. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  15. Ranid Herpesvirus 3 and Proliferative Dermatitis in Free-Ranging Wild Common Frogs (Rana Temporaria).

    PubMed

    Origgi, F C; Schmidt, B R; Lohmann, P; Otten, P; Akdesir, E; Gaschen, V; Aguilar-Bultet, L; Wahli, T; Sattler, U; Stoffel, M H

    2017-07-01

    Amphibian pathogens are of current interest as contributors to the global decline of amphibians. However, compared with chytrid fungi and ranaviruses, herpesviruses have received relatively little attention. Two ranid herpesviruses have been described: namely, Ranid herpesvirus 1 (RHV1) and Ranid herpesvirus 2 (RHV2). This article describes the discovery and partial characterization of a novel virus tentatively named Ranid herpesvirus 3 (RHV3), a candidate member of the genus Batrachovirus in the family Alloherpesviridae. RHV3 infection in wild common frogs (Rana temporaria) was associated with severe multifocal epidermal hyperplasia, dermal edema, a minor inflammatory response, and variable mucous gland degeneration. Intranuclear inclusions were numerous in the affected epidermis together with unique extracellular aggregates of herpesvirus-like particles. The RHV3-associated skin disease has features similar to those of a condition recognized in European frogs for the last 20 years and whose cause has remained elusive. The genome of RHV3 shares most of the features of the Alloherpesviruses. The characterization of this presumptive pathogen may be of value for amphibian conservation and for a better understanding of the biology of Alloherpesviruses.

  16. Characterization of rhizobia isolates obtained from nodules of wild genotypes of common bean.

    PubMed

    Cardoso, Aline Assis; Andraus, Michel de Paula; Borba, Tereza Cristina de Oliveira; Martin-Didonet, Claudia Cristina Garcia; Ferreira, Enderson Petrônio de Brito

    This study aimed to evaluate the tolerance to salinity and temperature, the genetic diversity and the symbiotic efficiency of rhizobia isolates obtained from wild genotypes of common bean cultivated in soil samples from the States of Goiás, Minas Gerais and Paraná. The isolates were subjected to different NaCl concentrations (0%, 1%, 2%, 4% and 6%) at different temperatures (28°C, 33°C, 38°C, 43°C and 48°C). Genotypic characterization was performed based on BOX-PCR, REP-PCR markers and 16S rRNA sequencing. An evaluation of symbiotic efficiency was carried out under greenhouse conditions in autoclaved Leonard jars. Among 98 isolates about 45% of them and Rhizobium freirei PRF81 showed a high tolerance to temperature, while 24 isolates and Rhizobium tropici CIAT899 were able to use all of the carbon sources studied. Clustering analysis based on the ability to use carbon sources and on the tolerance to salinity and temperature grouped 49 isolates, R. tropici CIAT899 and R. tropici H12 with a similarity level of 76%. Based on genotypic characterization, 65% of the isolates showed an approximately 66% similarity with R. tropici CIAT899 and R. tropici H12. About 20% of the isolates showed symbiotic efficiency similar to or better than the best Rhizobium reference strain (R. tropici CIAT899). Phylogenetic analysis of the 16S rRNA revealed that two efficient isolates (ALSG5A1 and JPrG6A8) belong to the group of strains used as commercial inoculant for common bean in Brazil and must be assayed in field experiments.

  17. A novel blast resistance gene, Pi54rh cloned from wild species of rice, Oryza rhizomatis confers broad spectrum resistance to Magnaporthe oryzae.

    PubMed

    Das, Alok; Soubam, D; Singh, P K; Thakur, S; Singh, N K; Sharma, T R

    2012-06-01

    The dominant rice blast resistance gene, Pi54 confers resistance to Magnaporthe oryzae in different parts of India. In our effort to identify more effective forms of this gene, we isolated an orthologue of Pi54 named as Pi54rh from the blast-resistant wild species of rice, Oryza rhizomatis, using allele mining approach and validated by complementation. The Pi54rh belongs to CC-NBS-LRR family of disease resistance genes with a unique Zinc finger (C(3)H type) domain. The 1,447 bp Pi54rh transcript comprises of 101 bp 5'-UTR, 1,083 bp coding region and 263 bp 3'-UTR, driven by pathogen inducible promoter. We showed the extracellular localization of Pi54rh protein and the presence of glycosylation, myristoylation and phosphorylation sites which implicates its role in signal transduction process. This is in contrast to other blast resistance genes that are predicted to be intracellular NBS-LRR-type resistance proteins. The Pi54rh was found to express constitutively at basal level in the leaves, but upregulates 3.8-fold at 96 h post-inoculation with the pathogen. Functional validation of cloned Pi54rh gene using complementation test showed high degree of resistance to seven isolates of M. oryzae collected from different geographical locations of India. In this study, for the first time, we demonstrated that a rice blast resistance gene Pi54rh cloned from wild species of rice provides broad spectrum resistance to M. oryzae hence can be used in rice improvement breeding programme.

  18. Oral administration of hydrolyzed rice bran prevents the common cold syndrome in the elderly based on its immunomodulatory action.

    PubMed

    Maeda, Hiroaki; Ichihashi, Kenichi; Fujii, Takako; Omura, Kazunobu; Zhu, Xia; Anazawa, Mari; Tazawa, Kenji

    2004-01-01

    The preventive effect of Hydrolyzed Rice Bran against the common cold syndrome was examined in elderly people. Arabinoxylan derivatives of Hydrolyzed Rice Bran (HRB) were prepared from water-soluble rice bran through partial processing using a carbohydrate complex. Using the water-soluble Rice Bran (RB) as a control, a cross over double-blind study was conducted on both substances over a 6-week administration period. Fifty elderly people aged from 70 to 95 years participated in the study and the comparative data from 36 participants were analyzed. There were no withdrawals from in the study due to the side effects of the experimental foods. Symptoms were observed and scored. The total symptom score for the RB treatment group was three times higher than that for the HRB treatment group. The average duration of symptoms was 2.6 days for RB whereas it was only 1.2 days for HRB. Furthermore, some immunomodulatory action was observed in laboratory tests. HRB was shown to be useful in reducing the physical stress associated with acute respiratory tract infection.

  19. Functionality of chemically modified waxy, partial waxy and wild-type starches from common wheat

    USDA-ARS?s Scientific Manuscript database

    Waxy wheat (Triticum aestivum L.) starch contains little or no amylose. Partial waxy wheats have amylose concentrations intermediate between those of waxy and wild-type (normal) starches. A factorial design was used to compare waxy, wild-type, partial waxy, and blends (10 and 17% amylose) of waxy an...

  20. Characterization of N2-fixing plant growth promoting endophytic and epiphytic bacterial community of Indian cultivated and wild rice (Oryza spp.) genotypes.

    PubMed

    Banik, Avishek; Mukhopadhaya, Subhra Kanti; Dangar, Tushar Kanti

    2016-03-01

    The diversity of endophytic and epiphytic diazotrophs in different parts of rice plants has specificity to the niche (i.e. leaf, stem and root) of different genotypes and nutrient availability of the organ. Inoculation of the indigenous, polyvalent diazotrophs can facilitate and sustain production of non-leguminous crops like rice. Therefore, N2-fixing plant growth promoting bacteria (PGPB) were isolated from different parts of three Indian cultivated [Oryza sativa L. var. Sabita (semi deep/deep water)/Swarna (rain fed shallow lowland)/Swarna-Sub1(submergence tolerant)] and a wild (O. eichingeri) rice genotypes which respond differentially to nitrogenous fertilizers. Thirty-five isolates from four rice genotypes were categorized based on acetylene reduction assay on nitrogenase activity, biochemical tests, BIOLOG and 16S rRNA gene sequencing. The bacteria produced 9.36-155.83 nmole C2H4 mg(-1) dry bacteria h(-1) and among them nitrogenase activity of 11 potent isolates was complemented by nifH-sequence analysis. Phylogenetic analysis based on 16S rDNA sequencing divided them into five groups (shared 95-100 % sequence homology with type strains) belonging to five classes-alpha (Ancylobacter, Azorhizobium, Azospirillum, Rhizobium, Bradyrhizobium, Sinorhizobium, Novosphingobium, spp.), beta (Burkholderia sp.), gamma (Acinetobacter, Aeromonas, Azotobacter, Enterobacter, Klebsiella, Pantoea, Pseudomonas, Stenotrophomonas spp.) Proteobacteria, Bacilli (Bacillus, Paenibacillus spp.) and Actinobacteria (Microbacterium sp.). Besides, all bacterial strains possessed the intrinsic PGP traits of like indole (0.44-7.4 µg ml(-1)), ammonia (0.18-6 mmol ml(-1)), nitrite (0.01-3.4 mol ml(-1)), and siderophore (from 0.16-0.57 μmol ml(-1)) production. Inoculation of rice (cv. Swarna) seedlings with selected isolates had a positive impact on plant growth parameters like shoot and root elongation which was correlated with in vitro PGP attributes. The results indicated that the

  1. Ectopic expression of ubiquitin-conjugating enzyme gene from wild rice, OgUBC1, confers resistance against UV-B radiation and Botrytis infection in Arabidopsis thaliana

    SciTech Connect

    Jeon, En Hee; Pak, Jung Hun; Kim, Mi Jin; Kim, Hye Jeong; Shin, Sang Hyun; Lee, Jai Heon; Kim, Doh Hoon; Oh, Ju Sung; Oh, Boung-Jun; Jung, Ho Won; Chung, Young Soo

    2012-10-19

    Highlights: Black-Right-Pointing-Pointer We isolated a novel E2 ubiquitin-conjugating enzyme from leaves of wild rice plants. Black-Right-Pointing-Pointer The OgUBC1 was highly expressed in leaves treated with SA and UV-B radiation. Black-Right-Pointing-Pointer The recombinant OgUBC1 has an enzymatic activity of E2 in vitro. Black-Right-Pointing-Pointer The OgUBC1 could protect disruption of plant cells by UV-B radiation. Black-Right-Pointing-Pointer OgUBC1 confers disease resistance and UV-B tolerance in transgenic Arabidopsis plants. -- Abstract: A previously unidentified gene encoding ubiquitin-conjugating enzyme was isolated from leaves of wild rice plant treated with wounding and microbe-associated molecular patterns. The OgUBC1 gene was composed of 148 amino acids and contained a typical active site and 21 ubiquitin thioester intermediate interaction residues and 4 E3 interaction residues. Both exogenous application of salicylic acid and UV-B irradiation triggered expression of OgUBC1 in leaves of wild rice. Recombinant OgUBC1 proteins bound to ubiquitins in vitro, proposing that the protein might act as E2 enzyme in planta. Heterologous expression of the OgUBC1 in Arabidopsis thaliana protected plants from cellular damage caused by an excess of UV-B radiation. A stable expression of chalcone synthase gene was detected in leaves of OgUBC1-expressing Arabidopsis, resulting in producing higher amounts of anthocyanin than those in wild-type Col-0 plants. Additionally, both pathogenesis-related gene1 and 5 were transcribed in the transgenic Arabidopsis in the absence of pathogen infection. The OgUBC1-expressing plants were resistant to the infection of Botrytis cinerea. Taken together, we suggested that the OgUBC1 is involved in ubiquitination process important for cellular response against biotic and abiotic stresses in plants.

  2. Identification of Novel and Conserved miRNAs from Extreme Halophyte, Oryza coarctata, a Wild Relative of Rice

    PubMed Central

    Mondal, Tapan Kumar; Ganie, Showkat Ahmad; Debnath, Ananda Bhusan

    2015-01-01

    Oryza coarctata, a halophyte and wild relative of rice, is grown normally in saline water. MicroRNAs (miRNAs) are non-coding RNAs that play pivotal roles in every domain of life including stress response. There are very few reports on the discovery of salt-responsive miRNAs from halophytes. In this study, two small RNA libraries, one each from the control and salt-treated (450 mM NaCl for 24 h) leaves of O. coarctata were sequenced, which yielded 338 known and 95 novel miRNAs. Additionally, we used publicly available transcriptomics data of O. coarctata which led to the discovery of additional 48 conserved miRNAs along with their pre-miRNA sequences through in silico analysis. In total, 36 known and 7 novel miRNAs were up-regulated whereas, 12 known and 7 novel miRNAs were down-regulated under salinity stress. Further, 233 and 154 target genes were predicted for 48 known and 14 novel differentially regulated miRNAs respectively. These targets with the help of gene ontology analysis were found to be involved in several important biological processes that could be involved in salinity tolerance. Relative expression trends of majority of the miRNAs as detected by real time-PCR as well as predicted by Illumina sequencing were found to be coherent. Additionally, expression of most of the target genes was negatively correlated with their corresponding miRNAs. Thus, the present study provides an account of miRNA-target networking that is involved in salinity adaption of O. coarctata. PMID:26506249

  3. Coordination of Leaf Photosynthesis, Transpiration, and Structural Traits in Rice and Wild Relatives (Genus Oryza)1[W][OA

    PubMed Central

    Giuliani, Rita; Koteyeva, Nuria; Voznesenskaya, Elena; Evans, Marc A.; Cousins, Asaph B.; Edwards, Gerald E.

    2013-01-01

    The genus Oryza, which includes rice (Oryza sativa and Oryza glaberrima) and wild relatives, is a useful genus to study leaf properties in order to identify structural features that control CO2 access to chloroplasts, photosynthesis, water use efficiency, and drought tolerance. Traits, 26 structural and 17 functional, associated with photosynthesis and transpiration were quantified on 24 accessions (representatives of 17 species and eight genomes). Hypotheses of associations within, and between, structure, photosynthesis, and transpiration were tested. Two main clusters of positively interrelated leaf traits were identified: in the first cluster were structural features, leaf thickness (Thickleaf), mesophyll (M) cell surface area exposed to intercellular air space per unit of leaf surface area (Smes), and M cell size; a second group included functional traits, net photosynthetic rate, transpiration rate, M conductance to CO2 diffusion (gm), stomatal conductance to gas diffusion (gs), and the gm/gs ratio. While net photosynthetic rate was positively correlated with gm, neither was significantly linked with any individual structural traits. The results suggest that changes in gm depend on covariations of multiple leaf (Smes) and M cell (including cell wall thickness) structural traits. There was an inverse relationship between Thickleaf and transpiration rate and a significant positive association between Thickleaf and leaf transpiration efficiency. Interestingly, high gm together with high gm/gs and a low Smes/gm ratio (M resistance to CO2 diffusion per unit of cell surface area exposed to intercellular air space) appear to be ideal for supporting leaf photosynthesis while preserving water; in addition, thick M cell walls may be beneficial for plant drought tolerance. PMID:23669746

  4. [Index screening and comprehensive evaluation of phenotypic traits of low nitrogen tolerance using BILs population derived from Dongxiang wild rice (Oryza rufipogon Griff)].

    PubMed

    Hu, Biao-lin; Li, Xia; Wan, Yong; Qiu, Zai-hui; Nie, Yuan-yuan; Xie, Jian-kun

    2015-08-01

    To identify the low nitrogen tolerance of Dongxiang wild rice (DXWR) and its progenies, ten phenotypic traits including plant height (PH), heading day (HD), panicle length (PL), number of effective tillers per plant (NETP), number of filled grains per panicle (NFGP), number of grains per panicle (NGP), grain density (GD), spikelet fertility (SF), 1000-grain mass (TGM) and grain yield per plant (GYP) were studied under normal and low nitrogen treatments, using backcross inbred lines (BILs) of Xieqingzao B//DXWR/Xieqingzao B in BC1 F12. Comprehensive evaluation on the low nitrogen tolerance of the BILs population was conducted using principal component analysis and the subordinate function. The evaluation results indicated that the low nitrogen tolerance of the line 116, 143 and 157 was the strongest, which could be served as the intermediate materials for genetic studies on the low nitrogen tolerance of DXWR and breeding for the low nitrogen tolerance in rice. The optimal regression equation of the low nitrogen tolerance in rice was established using stepwise regression analysis. The relative values of five traits including PH, NGP, SF, TGM and GYP were screened out and could be used as comprehensive evaluation indices for the low nitrogen tolerance in the whole growth stage. Therefore, more attention should be paid to the relative values of these five traits, especially for NGP and GYP, in the genetic improvement of the low nitrogen tolerance in rice.

  5. Markers for Ongoing or Previous Hepatitis E Virus Infection Are as Common in Wild Ungulates as in Humans in Sweden

    PubMed Central

    Roth, Anette; Lin, Jay; Magnius, Lars; Karlsson, Marie; Belák, Sándór; Widén, Frederik; Norder, Heléne

    2016-01-01

    Hepatitis E virus (HEV) is a human pathogen with zoonotic spread, infecting both domestic and wild animals. About 17% of the Swedish population is immune to HEV, but few cases are reported annually, indicating that most infections are subclinical. However, clinical hepatitis E may also be overlooked. For identified cases, the source of infection is mostly unknown. In order to identify whether HEV may be spread from wild game, the prevalence of markers for past and/or ongoing infection was investigated in sera and stool samples collected from 260 hunted Swedish wild ungulates. HEV markers were found in 43 (17%) of the animals. The most commonly infected animal was moose (Alces alces) with 19 out of 69 animals (28%) showing HEV markers, followed by wild boar (Sus scrofa) with 21 out of 139 animals (15%), roe deer (Capreolus capreolus) with 2 out of 30 animals, red deer (Cervus elaphus) with 1 out of 15 animals, and fallow deer (Dama dama) 0 out of 7 animals. Partial open reading frame 1 (ORF1) of the viral genomes from the animals were sequenced and compared with those from 14 endemic human cases. Phylogenetic analysis revealed that three humans were infected with HEV strains similar to those from wild boar. These results indicate that wild animals may be a source of transmission to humans and could be an unrecognized public health concern. PMID:27657108

  6. Recent and Projected Increases in Atmospheric CO2 Concentration Can Enhance Gene Flow between Wild and Genetically Altered Rice (Oryza sativa)

    PubMed Central

    Ziska, Lewis H.; Gealy, David R.; Tomecek, Martha B.; Jackson, Aaron K.; Black, Howard L.

    2012-01-01

    Although recent and projected increases in atmospheric carbon dioxide can alter plant phenological development, these changes have not been quantified in terms of floral outcrossing rates or gene transfer. Could differential phenological development in response to rising CO2 between genetically modified crops and wild, weedy relatives increase the spread of novel genes, potentially altering evolutionary fitness? Here we show that increasing CO2 from an early 20th century concentration (300 µmol mol−1) to current (400 µmol mol−1) and projected, mid-21st century (600 µmol mol−1) values, enhanced the flow of genes from wild, weedy rice to the genetically altered, herbicide resistant, cultivated population, with outcrossing increasing from 0.22% to 0.71% from 300 to 600 µmol mol−1. The increase in outcrossing and gene transfer was associated with differential increases in plant height, as well as greater tiller and panicle production in the wild, relative to the cultivated population. In addition, increasing CO2 also resulted in a greater synchronicity in flowering times between the two populations. The observed changes reported here resulted in a subsequent increase in rice dedomestication and a greater number of weedy, herbicide-resistant hybrid progeny. Overall, these data suggest that differential phenological responses to rising atmospheric CO2 could result in enhanced flow of novel genes and greater success of feral plant species in agroecosystems. PMID:22649533

  7. A genetic resource for early-morning flowering trait of wild rice Oryza officinalis to mitigate high temperature-induced spikelet sterility at anthesis

    PubMed Central

    Ishimaru, Tsutomu; Hirabayashi, Hideyuki; Ida, Masashi; Takai, Toshiyuki; San-Oh, Yumiko A.; Yoshinaga, Satoshi; Ando, Ikuo; Ogawa, Tsugufumi; Kondo, Motohiko

    2010-01-01

    Background and Aims High temperatures over 32–36 °C at anthesis induce spikelet sterility in rice. The use of a germplasm with an early-morning flowering (EMF) trait has been hypothesized as a way of avoiding this problem. In this study, the effect of the EMF trait on avoiding high temperature-induced sterility at anthesis by flowering at a cooler temperature in the early morning was evaluated. Methods The EMF trait was introgressed from wild rice (Oryza officinalis) into the rice cultivar ‘Koshihikari’ (O. sativa). First, spikelets of the EMF line and Koshihikari were subjected to rising temperatures during the daytime in the greenhouse to test for differences in spikelet sterility. Secondly, spikelets of both plants were exposed to 26, 34 and 38 °C at anthesis and to 38 °C beginning at least 1 h after flowering, in the growth chambers at 70 % relative humidity, to test for differences in tolerance to high temperatures. Key Results Spikelets of the EMF line started and completed flowering a few hours earlier than Koshihikari. In a greenhouse experiment, spikelets of Koshihikari opened after the air temperature reached 35 °C, but those of the EMF line could open at cooler temperatures. Under these conditions, spikelet sterility significantly increased in Koshihikari, but did not in the EMF line. The number of sterile spikelets increased as their flowering time was delayed in Koshihikari. Furthermore, the chamber experiments revealed that 60 % of the spikelets from both lines were sterile when exposed to 38 °C at anthesis, indicating that tolerance of high temperature was similar in both genotypes. Conclusions Reduced sterility in the EMF line subjected to rising temperatures at anthesis in the greenhouse was attributed to an earlier flowering time compared with Koshihikari. The EMF trait of wild rice is effective in mitigating anticipated yield loss due to global warming by escaping high-temperature stress at anthesis during the daytime. PMID:20566680

  8. Map-based Cloning and Characterization of the BPH18 Gene from Wild Rice Conferring Resistance to Brown Planthopper (BPH) Insect Pest

    PubMed Central

    Ji, Hyeonso; Kim, Sung-Ryul; Kim, Yul-Ho; Suh, Jung-Pil; Park, Hyang-Mi; Sreenivasulu, Nese; Misra, Gopal; Kim, Suk-Man; Hechanova, Sherry Lou; Kim, Hakbum; Lee, Gang-Seob; Yoon, Ung-Han; Kim, Tae-Ho; Lim, Hyemin; Suh, Suk-Chul; Yang, Jungil; An, Gynheung; Jena, Kshirod K.

    2016-01-01

    Brown planthopper (BPH) is a phloem sap-sucking insect pest of rice which causes severe yield loss. We cloned the BPH18 gene from the BPH-resistant introgression line derived from the wild rice species Oryza australiensis. Map-based cloning and complementation test revealed that the BPH18 encodes CC-NBS-NBS-LRR protein. BPH18 has two NBS domains, unlike the typical NBS-LRR proteins. The BPH18 promoter::GUS transgenic plants exhibited strong GUS expression in the vascular bundles of the leaf sheath, especially in phloem cells where the BPH attacks. The BPH18 proteins were widely localized to the endo-membranes in a cell, including the endoplasmic reticulum, Golgi apparatus, trans-Golgi network, and prevacuolar compartments, suggesting that BPH18 may recognize the BPH invasion at endo-membranes in phloem cells. Whole genome sequencing of the near-isogenic lines (NILs), NIL-BPH18 and NIL-BPH26, revealed that BPH18 located at the same locus of BPH26. However, these two genes have remarkable sequence differences and the independent NILs showed differential BPH resistance with different expression patterns of plant defense-related genes, indicating that BPH18 and BPH26 are functionally different alleles. These findings would facilitate elucidation of the molecular mechanism of BPH resistance and the identified novel alleles to fast track breeding BPH resistant rice cultivars. PMID:27682162

  9. Phylogenetic diversity of culturable endophytic fungi in Dongxiang wild rice (Oryza rufipogon Griff), detection of polyketide synthase gene and their antagonistic activity analysis.

    PubMed

    Wang, Ya; Gao, Bo Liang; Li, Xi Xi; Zhang, Zhi Bin; Yan, Ri Ming; Yang, Hui Lin; Zhu, Du

    2015-11-01

    The biodiversity of plant endophytic fungi is enormous, numerous competent endophytic fungi are capable of providing different forms of fitness benefits to host plants and also could produce a wide array of bioactive natural products, which make them a largely unexplored source of novel compounds with potential bioactivity. In this study, we provided a first insights into revealing the diversity of culturable endophytic fungi in Dongxiang wild rice (Oryza rufipogon Griff.) from China using rDNA-ITS phylogenetic analysis. Here, the potential of fungi in producing bioactive natural products was estimated based on the beta-ketosynthase detected in the polyketide synthase (PKS) gene cluster and on the bioassay of antagonistic activity against two rice phytopathogens Thanatephorus cucumeris and Xanthomonas oryzae. A total of 229 endophytic fungal strains were validated in 19 genera. Among the 24 representative strains, 13 strains displayedantagonistic activity against the phytopathogens. Furthermore, PKS genes were detected in 9 strains, indicating their potential for synthesising PKS compounds. Our study confirms the phylogenetic diversity of endophytic fungi in O. rufipogon G. and highlights that endophytic fungi are not only promising resources of biocontrol agents against phytopathogens of rice plants, but also of bioactive natural products and defensive secondary metabolites.

  10. Map-based Cloning and Characterization of the BPH18 Gene from Wild Rice Conferring Resistance to Brown Planthopper (BPH) Insect Pest.

    PubMed

    Ji, Hyeonso; Kim, Sung-Ryul; Kim, Yul-Ho; Suh, Jung-Pil; Park, Hyang-Mi; Sreenivasulu, Nese; Misra, Gopal; Kim, Suk-Man; Hechanova, Sherry Lou; Kim, Hakbum; Lee, Gang-Seob; Yoon, Ung-Han; Kim, Tae-Ho; Lim, Hyemin; Suh, Suk-Chul; Yang, Jungil; An, Gynheung; Jena, Kshirod K

    2016-09-29

    Brown planthopper (BPH) is a phloem sap-sucking insect pest of rice which causes severe yield loss. We cloned the BPH18 gene from the BPH-resistant introgression line derived from the wild rice species Oryza australiensis. Map-based cloning and complementation test revealed that the BPH18 encodes CC-NBS-NBS-LRR protein. BPH18 has two NBS domains, unlike the typical NBS-LRR proteins. The BPH18 promoter::GUS transgenic plants exhibited strong GUS expression in the vascular bundles of the leaf sheath, especially in phloem cells where the BPH attacks. The BPH18 proteins were widely localized to the endo-membranes in a cell, including the endoplasmic reticulum, Golgi apparatus, trans-Golgi network, and prevacuolar compartments, suggesting that BPH18 may recognize the BPH invasion at endo-membranes in phloem cells. Whole genome sequencing of the near-isogenic lines (NILs), NIL-BPH18 and NIL-BPH26, revealed that BPH18 located at the same locus of BPH26. However, these two genes have remarkable sequence differences and the independent NILs showed differential BPH resistance with different expression patterns of plant defense-related genes, indicating that BPH18 and BPH26 are functionally different alleles. These findings would facilitate elucidation of the molecular mechanism of BPH resistance and the identified novel alleles to fast track breeding BPH resistant rice cultivars.

  11. Pigeon paramyxovirus: association with common avian pathogens in chickens and serologic survey in wild birds.

    PubMed

    Toro, H; Hoerr, F J; Farmer, K; Dykstra, C C; Roberts, S R; Perdue, M

    2005-03-01

    Pigeon paramyxovirus-1 (PPMV-1) was isolated from pigeons from east-central Alabama and used in association with chicken anemia virus (CAV), infectious bursal disease virus (IBDV), or finch Mycoplasma gallisepticum (MG) in specific-pathogen-free chickens to assess dinical disease and pathology. PPMV-1 infection in all groups was conducted at day 10 of age via the ocular route. The low passage PPMV-1 isolate was inoculated into chickens in different groups at 10 days post-CAV infection, 6 days post-IBDV infection, and 6 days post-finch MG infection, respectively. Additionally, to obtain information on the status of paramyxovirus infection in the wild bird population of the region, we used a multispecies competitive enzyme-linked immunosorbent assay kit to assess serum samples from 180 wild birds representing 24 species obtained throughout 2001. Mild respiratory signs characterized by sneezing were observed in PPMV-1-infected chicks. In the brain, PPMV-1 caused disseminated vasculitis in the neuropile and meninges, sometimes with small foci of gliosis. Most brains had only mild lesions. In the upper respiratory tract, lesions were confined to the larynx and proximal trachea as hyperplasia of laryngeal mucosa-associated lymphoid tissue. In the lung, PPMV-1 caused minimal to moderate multifocal interstitial pneumonia. Lymphocytic expansion occurred in the interstitium of the Harderian gland. PPMV-1 in the spleen caused expansion of the white pulp as a result of hypertrophy of the macrophages in the periarteriolar sheaths accompanied by lymphocytic hyperplasia at the periphery. No severe aggravation of either signs or lesions could be attributed to any of the avian pathogens used in association with PPMV-1. The serologic survey in wild birds showed antibody levels that were considered negative or doubtful. Interestingly, significantly (P < 0.05) higher mean titers were observed during the months of October and November 2001, following closely multiple PPMV-1 episodes of

  12. Are habitat fragmentation, local adaptation and isolation-by-distance driving population divergence in wild rice Oryza rufipogon?

    PubMed

    Zhao, Yao; Vrieling, Klaas; Liao, Hui; Xiao, Manqiu; Zhu, Yongqing; Rong, Jun; Zhang, Wenju; Wang, Yuguo; Yang, Ji; Chen, Jiakuan; Song, Zhiping

    2013-11-01

    Habitat fragmentation weakens the connection between populations and is accompanied with isolation by distance (IBD) and local adaptation (isolation by adaptation, IBA), both leading to genetic divergence between populations. To understand the evolutionary potential of a population and to formulate proper conservation strategies, information on the roles of IBD and IBA in driving population divergence is critical. The putative ancestor of Asian cultivated rice (Oryza sativa) is endangered in China due to habitat loss and fragmentation. We investigated the genetic variation in 11 Chinese Oryza rufipogon populations using 79 microsatellite loci to infer the effects of habitat fragmentation, IBD and IBA on genetic structure. Historical and current gene flows were found to be rare (mh  = 0.0002-0.0013, mc  = 0.007-0.029), indicating IBD and resulting in a high level of population divergence (FST  = 0.343). High within-population genetic variation (HE  = 0.377-0.515), relatively large effective population sizes (Ne  = 96-158), absence of bottlenecks and limited gene flow were found, demonstrating little impact of recent habitat fragmentation on these populations. Eleven gene-linked microsatellite loci were identified as outliers, indicating local adaptation. Hierarchical AMOVA and partial Mantel tests indicated that population divergence of Chinese O. rufipogon was significantly correlated with environmental factors, especially habitat temperature. Common garden trials detected a significant adaptive population divergence associated with latitude. Collectively, these findings imply that IBD due to historical rather than recent fragmentation, followed by local adaptation, has driven population divergence in O. rufipogon. © 2013 John Wiley & Sons Ltd.

  13. Differences in meristem size and expression of branching genes are associated with variation in panicle phenotype in wild and domesticated African rice.

    PubMed

    Ta, K N; Adam, H; Staedler, Y M; Schönenberger, J; Harrop, T; Tregear, J; Do, N V; Gantet, P; Ghesquière, A; Jouannic, S

    2017-01-01

    The African rice Oryza glaberrima was domesticated from its wild relative Oryza barthii about 3000 years ago. During the domestication process, panicle complexity changed from a panicle with low complexity in O. barthii, to a highly branched panicle carrying more seeds in O. glaberrima. To understand the basis of this differential panicle development between the two species, we conducted morphological and molecular analyses of early panicle development. Using X-ray tomography, we analyzed the morphological basis of early developmental stages of panicle development. We uncovered evidence for a wider rachis meristem in O. glaberrima than in O. barthii. At the molecular level, spatial and temporal expression profiles of orthologs of O. sativa genes related to meristem activity and meristem fate control were obtained using in situ hybridization and qRT-PCR. Despite highly conserved spatial expression patterns between O. glaberrima and O. barthii, differences in the expression levels of these early acting genes were detected. The higher complexity of the O. glaberrima panicle compared to that of its wild relative O. barthii is associated with a wider rachis meristem and a modification of expression of branching-related genes. Our study indicates that the expression of genes in the miR156/miR529/SPL and TAW1 pathways, along with that of their target genes, is altered from the unbranched stage of development. This suggests that differences in panicle complexity between the two African rice species result from early alterations to gene expression during reproductive development.

  14. Expression of the nifH gene of a Herbaspirillum endophyte in wild rice species: daily rhythm during the light-dark cycle.

    PubMed

    You, Mu; Nishiguchi, Tomohiro; Saito, Asami; Isawa, Tsuyoshi; Mitsui, Hisayuki; Minamisawa, Kiwamu

    2005-12-01

    The expression of nitrogenase genes of Herbaspirillum sp. B501 associated in shoot (leaf and stem) of wild rice, Oryza officinalis, was studied by means of reverse transcription-PCR (RT-PCR) targeted at the nifH gene. RT-PCR analyses indicate that nifH transcript was detected exclusively from nitrogen-fixing cells of gfp-tagged strain B501gfp1 in both free-living and endophytic states by using a constitutive gfp gene transcript as a positive control. Transcription of nifH and nitrogen fixation in free-living cells were induced maximally at a 2% O2 concentration and repressed in free air (21% O2). nifH transcription was monitored in the endophytic cells by using total RNA extracted from B501gfp1-inoculated wild rice plants during daily light-dark cycles. The level of nifH transcription in planta varied dramatically, with a maximum during the light period. Moreover, the light radiation enhanced nifH expression even in free-living cells grown in culture. These results suggest that in planta nitrogen fixation by the endophyte shows a daily rhythm determined by the plant's light environment.

  15. Fipronil application on rice paddy fields reduces densities of common skimmer and scarlet skimmer.

    PubMed

    Kasai, Atsushi; Hayashi, Takehiko I; Ohnishi, Hitoshi; Suzuki, Kazutaka; Hayasaka, Daisuke; Goka, Koichi

    2016-03-16

    Several reports suggested that rice seedling nursery-box application of some systemic insecticides (neonicotinoids and fipronil) is the cause of the decline in dragonfly species noted since the 1990s in Japan. We conducted paddy mesocosm experiments to investigate the effect of the systemic insecticides clothianidin, fipronil and chlorantraniliprole on rice paddy field biological communities. Concentrations of all insecticides in the paddy water were reduced to the limit of detection within 3 months after application. However, residuals of these insecticides in the paddy soil were detected throughout the experimental period. Plankton species were affected by clothianidin and chlorantraniliprole right after the applications, but they recovered after the concentrations decreased. On the other hand, the effects of fipronil treatment, especially on Odonata, were larger than those of any other treatment. The number of adult dragonflies completing eclosion was severely decreased in the fipronil treatment. These results suggest that the accumulation of these insecticides in paddy soil reduces biodiversity by eliminating dragonfly nymphs, which occupy a high trophic level in paddy fields.

  16. Fipronil application on rice paddy fields reduces densities of common skimmer and scarlet skimmer

    PubMed Central

    Kasai, Atsushi; Hayashi, Takehiko I.; Ohnishi, Hitoshi; Suzuki, Kazutaka; Hayasaka, Daisuke; Goka, Koichi

    2016-01-01

    Several reports suggested that rice seedling nursery-box application of some systemic insecticides (neonicotinoids and fipronil) is the cause of the decline in dragonfly species noted since the 1990s in Japan. We conducted paddy mesocosm experiments to investigate the effect of the systemic insecticides clothianidin, fipronil and chlorantraniliprole on rice paddy field biological communities. Concentrations of all insecticides in the paddy water were reduced to the limit of detection within 3 months after application. However, residuals of these insecticides in the paddy soil were detected throughout the experimental period. Plankton species were affected by clothianidin and chlorantraniliprole right after the applications, but they recovered after the concentrations decreased. On the other hand, the effects of fipronil treatment, especially on Odonata, were larger than those of any other treatment. The number of adult dragonflies completing eclosion was severely decreased in the fipronil treatment. These results suggest that the accumulation of these insecticides in paddy soil reduces biodiversity by eliminating dragonfly nymphs, which occupy a high trophic level in paddy fields. PMID:26979488

  17. The common ecotoxicology laboratory strain of Hyalella azteca is genetically distinct from most wild strains sampled in eastern North America.

    PubMed

    Major, Kaley; Soucek, David J; Giordano, Rosanna; Wetzel, Mark J; Soto-Adames, Felipe

    2013-11-01

    The amphipod Hyalella azteca is commonly used as a model for determining safe concentrations of contaminants in freshwaters. The authors sequenced the mitochondrial cytochrome c oxidase subunit I (COI) gene for representatives of 38 populations of this species complex from US and Canadian toxicology research laboratories and eastern North American field sites to determine their genetic relationships. With 1 exception, all US and Canadian laboratory cultures sampled were identified as conspecific. In 22 wild populations spanning 5 US states and 1 Canadian province, the commonly occurring laboratory species was found only in northern Florida, USA. Therefore, the diversity of the H. azteca species complex detected in the wild is not accurately represented in North American laboratories, questioning the reliability of H. azteca cultures currently in use to accurately predict the responses of wild populations in ecotoxicological assays. The authors also examined the utility of different COI nucleotide fragments presently in use to determine phylogenetic relationships in this group and concluded that saturation in DNA sequences leads to inconsistent relationships between clades. Amino acid sequences for COI were not saturated and may allow a more accurate phylogeny estimate. Hyalella azteca is crucial for developing water-quality regulations; therefore, laboratories should know and standardize the strain(s) they use to confidently compare toxicity tests across laboratories and determine whether they are an appropriate surrogate for their regions. © 2013 SETAC.

  18. Onchocerca dewittei japonica n. subsp., a common parasite from wild boar in Kyushu Island, Japan.

    PubMed

    Uni, S; Bain, O; Takaoka, H; Miyashita, M; Suzuki, Y

    2001-09-01

    We describe Onchocerca dewittei japonica n. subsp. from the Japanese wild boar, Sus scrofa leucomystax, in Oita, Kyushu Island, where all seven animals examined were found to be infected. This study began with efforts to identify the causative species in a recent case of zoonotic onchocerciasis. Compared with Onchocerca dewittei dewittei from Sus scrofa jubatus in Malaysia, which was reexamined here, our new subspecies has much greater space between the ridges on the females. In addition, its microfilariae (from uteri) are shorter (192-210 microns compared with 228-247 microns), and only the posterior third of the microfilarial body is coiled, instead of the entire body. The Onchocerca species parasitic in suids (these two subspecies and O. ramachandrini from the warthog in the Ethiopian region) form a group sharing several characters. Among the most unusual characters are the body swellings (a specialized apparatus for mating, known in only a few other genera). In addition, longitudinal cuticular crests were found on males of both subspecies from wild boar and on females of O. ramachandrini.

  19. Successful introgression of abiotic stress tolerance from wild tepary bean to common bean

    USDA-ARS?s Scientific Manuscript database

    Common bean (Phaseolus vulgaris L.) production is severely limited due to abiotic stresses, including drought and sub-zero temperatures. Tepary bean (Phaseolus acutifolius Gray), a relative of common bean, has demonstrated tolerance to these stresses. Preliminary studies screening tepary accessions ...

  20. Behavioral strategies and hormonal profiles of dominant and subordinate common marmoset (Callithrix jacchus) females in wild monogamous groups.

    PubMed

    Sousa, Maria Bernardete Cordeiro; Albuquerque, Ana Claudia Sales da Rocha; Albuquerque, Fabiola da Silva; Araujo, Arrilton; Yamamoto, Maria Emilia; Arruda, Maria de Fatima

    2005-09-01

    New insights into the mating systems of common marmosets suggest that they are mainly monogamous, although polygyny and polyandry occasionally occur. Long-term monitoring of wild common marmosets has shown that some reports of polygynous groups (i.e., groups that contain more than one reproducing female) in fact indicate an unbalanced reproductive output associated with extragroup copulation. In this study we describe the behavioral and hormonal profiles of common marmoset (Callithrix jacchus) females living in three wild monogamous groups (Q, PBf, and T), varying from five to 11 individuals, at Nísia Floresta field station, RN, Brazil. The mating system of the groups was previously characterized in terms of affiliative, sexual, and mate-guarding behaviors. Behavioral data were collected once a week, and fecal samples were collected at least twice a week for 10-16 months, depending on the group. A preferential allogrooming relationship was recorded between dominant males and females. Under field conditions the reproductive inhibition of subordinate females appears to be more behavioral than hormonal, since subordinate females of the three groups ovulated and two conceived during the study. In these cases, the subordinate and dominant females reproduced 1 month apart, and infanticide (one case confirmed and one suspected) appeared to be part of the reproductive strategy of dominant females. Following the infanticide, ovarian inhibition (group T) or emigration and return to the natal group (group PBf) were observed. In the third group (Q) the subordinate female showed hormonal profiles compatible with pregnancy, but no infants were seen. These findings reflect the different alternatives that wild subordinate common marmoset females use to reproduce.

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

    USDA-ARS?s Scientific Manuscript database

    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,...

  2. Manoomin: place-based research with Native American students on wild rice lakes on the Fond du Lac Band of Lake Superior Chippewa Reservation, northern Minnesota

    NASA Astrophysics Data System (ADS)

    Ito, E.; Myrbo, A.; Dalbotten, D. M.; Pellerin, H.; Greensky, L.; Howes, T.; Wold, A.; McEathron, M. A.; Shanker, V.

    2010-12-01

    The manoomin project is a collaboration between Fond du Lac Tribal and Community College (Cloquet, MN), the Reservation’s Resource Management Division, and the University of Minnesota funded by the NSF GEO-OEDG Program. It builds on a successful seven-year history of collaboration between these parties, including regular science camps (gidaakiimanaanimigawig, Our Earth Lodge) for students of a wide range of ages. We are working as a team with Native students to study the history of wild rice (manoomin; Zizania palustris), a culturally important resource, growing on Reservation lakes. The joint project takes two main approaches: study of sediment core samples collected from Reservation lakes; and the collection of traditional knowledge about wild rice from the Elders. Science campers collect lake cores during winter with the assistance of the U of MN’s LacCore (National Lacustrine Core Facility) and Resource Management and visit LacCore to log, split and describe cores soon thereafter. Academic mentors with a range of specialties (phytoliths, pollen, plant macrofossils, sedimentology, geochemistry, magnetics) spend 1-2 weeks during the summer with small groups of college-age (>18, many nontraditional) student interns working on a particular paleoenvironmental proxy from the sediment cores. Younger students (middle and high school) also work in small teams in half day units with the same mentors. All campers become comfortable in an academic setting, gain experience working in research labs learning and practicing techniques, and jointly interpret collective results. The continuation of the project over five years (2009-2014) will allow these students to develop relationships with scientists and to receive mentoring beyond the laboratory as they make transitions into 2- and 4-year colleges and into graduate school. Their research provides historical and environmental information that is relevant to their own land that will be used by Resource Management which is

  3. Biodiversity effects in the wild are common and as strong as key drivers of productivity

    NASA Astrophysics Data System (ADS)

    Duffy, J. Emmett; Godwin, Casey M.; Cardinale, Bradley J.

    2017-09-01

    More than 500 controlled experiments have collectively suggested that biodiversity loss reduces ecosystem productivity and stability. Yet the importance of biodiversity in sustaining the world’s ecosystems remains controversial, largely because of the lack of validation in nature, where strong abiotic forcing and complex interactions are assumed to swamp biodiversity effects. Here we test this assumption by analysing 133 estimates reported in 67 field studies that statistically separated the effects of biodiversity on biomass production from those of abiotic forcing. Contrary to the prevailing opinion of the previous two decades that biodiversity would have rare or weak effects in nature, we show that biomass production increases with species richness in a wide range of wild taxa and ecosystems. In fact, after controlling for environmental covariates, increases in biomass with biodiversity are stronger in nature than has previously been documented in experiments and comparable to or stronger than the effects of other well-known drivers of productivity, including climate and nutrient availability. These results are consistent with the collective experimental evidence that species richness increases community biomass production, and suggest that the role of biodiversity in maintaining productive ecosystems should figure prominently in global change science and policy.

  4. Systemic Collyriclum faba (Trematoda: Collyriclidae) Infection in a Wild Common Raven ( Corvus corax ).

    PubMed

    Mete, Aslı; Rogers, Krysta; Houston, Robin

    2017-01-01

    A hatch-year Common Raven ( Corvus corax ) with subcutaneous and internal pseudocysts, filled with fluid, containing a pair of adult trematodes and numerous eggs consistent with Collyriclum faba, died near a riverbank in California, US. While C. faba is incidental in many Passeriformes, this case was a fatal systemic infection.

  5. Use of wild relatives and closely-related species to adapt common bean to climate change

    USDA-ARS?s Scientific Manuscript database

    Common bean (Phaseolus vulgaris L.) is an important legume crop worldwide. However, abiotic and biotic stress limits bean yields less than 600 kg/ha in low-income countries. Current low yields result in food insecurity, while demands for increased yields to match the rate of population growth combin...

  6. The semifossorial function of the forelimb in the common rice tenrec (Oryzorictes hova) and the streaked tenrec (Hemicentetes hemispinosus).

    PubMed

    Endo, H; Oishi, M; Yonezawa, T; Rakotondraparany, F; Hasegawa, M

    2007-12-01

    The forelimb muscles of the two semifossorial species of Tenrecidae (Oryzoryctinae: common rice tenrec; and Tenrecinae: streaked tenrec) were compared macroscopically with those of the unspecialized terrestrial-arboreal species, the Talazac long-tailed tenrec. The structure of the hand was also observed using three-dimensional reconstructed images from computed tomography data. The two semifossorial species had similar muscle weight ratios in the lateral and long heads of M. triceps brachii and M. teres major. A similar hand skeleton structure (in which the second, third and fourth metacarpals and phalanges act as a digging apparatus) was observed in both species. Our observations confirm that both these species have muscular-skeletal adaptations supporting fossorial locomotion. As each species belongs to a monophyletic subfamily within the Tenrecidae isolated in Madagascar, such semifossorial adaptations are assumed to have evolved convergently.

  7. Optimization of synthesis and characterization of nanosilica produced from rice husk (a common waste material)

    NASA Astrophysics Data System (ADS)

    Rafiee, Ezzat; Shahebrahimi, Shabnam; Feyzi, Mostafa; Shaterzadeh, Mahdi

    2012-10-01

    Rice husk (RH), an inexpensive waste material, was used to produce nanosilica. Acid treatment of RH followed by thermal combustion under controlled conditions gave 22.50% ash of which 90.469% was silica. Various chemical treatments in varied conditions for controlled combustion were investigated in order to produce highly purified nanosilica. The structural properties (such as X-ray diffraction, Brunauer-Emmett-Teller, Fourier transform infrared spectroscopy, and transmission electron microscopy) of the silica were studied. The method was optimized, and the chemical composition of the product was determined by X-ray fluorescence and carbon, hydrogen, and nitrogen analysis. Lime reactivity of the ashes was determined. At optimized conditions, a nanosized, highly purified silica (98.8 mass percentage) was produced with a high surface area, high reactivity, and 99.9% amorphous in form. Strength and number of acidic sites were measured by potentiometric titration. This nanosilica showed strong and a large number of acidic sites in comparison with commercial silica, making it as a good support for catalysts. This economic technology, as applied to waste material, also provides many benefits to the local agro-industry.

  8. Effects of dietary carbohydrate replaced with wild rice (Zizania latifolia (Griseb) Turcz) on insulin resistance in rats fed with a high-fat/cholesterol diet.

    PubMed

    Han, Shufen; Zhang, Hong; Qin, Liqiang; Zhai, Chengkai

    2013-02-15

    Wild rice (WR) is a very nutritious grain that has been used to treat diabetes in Chinese medicinal practice. City diet (CD) is based on the diet consumed by Asian area residents in modern society, which is rich in saturated fats, cholesterol and carbohydrates. The present study was aimed at evaluating the effects of replacing white rice and processed wheat starch of CD with WR as the chief source of dietary carbohydrates on insulin resistance in rats fed with a high-fat/cholesterol diet. Except the rats of the low-fat (LF) diet group, the rats of the other three groups, including to high-fat/cholesterol (HFC) diet, CD and WR diet, were fed with high-fat/cholesterol diets for eight weeks. The rats fed with CD exhibited higher weight gain and lower insulin sensitivity compared to the rats consuming a HFC diet. However, WR suppressed high-fat/cholesterol diet-induced insulin resistance. WR decreased liver homogenate triglyceride and free fatty acids levels, raised serum adiponectin concentration and reduced serum lipocalin-2 and visfatin concentrations. In addition, the WR diet potently augmented the relative expressions of adiponectin receptor 2, peroxisome proliferator-activated receptors, alpha and gamma, and abated relative expressions of leptin and lipocalin-2 in the tissues of interest. These findings indicate that WR is effective in ameliorating abnormal glucose metabolism and insulin resistance in rats, even when the diet consumed is high in fat and cholesterol.

  9. Association between the geographic distribution during the last glacial maximum of Asian wild rice, Oryza rufipogon (Poaceae), and its current genetic variation.

    PubMed

    Huang, Pu; Schaal, Barbara A

    2012-11-01

    The combination of traditional population genetic studies and species distribution modeling (SDM) provides many new insights in detecting phylogeographic signals. In Asian wild rice (Oryza rufipogon), the progenitor of cultivated Asian rice, geographical subdivision has been documented in many genetic studies although the root cause of this subdivision remains unknown. Surprisingly, environmental factors associated with the spatial and temporal distribution of O. rufipogon have rarely been examined. The aim of this study is to understand the historical distribution of O. rufipogon and its relationship to the current geographical pattern of genetic variation. We used SDM to examine the present, past, and future distribution of O. rufipogon. The estimated distribution during the Last Glacial Maximum was then compared with genetic data from our previous work. The predicted paleodistribution of O. rufipogon at the Last Glacial Maximum was separated into disconnected east and west ranges. This past distribution is consistent with the current geographic pattern of genetic variation, with two genetic groups that intergrade. Annual precipitation is the single factor that contributes most to SDM estimates. SDM predictions for 2080 indicate a general trend of increasing probability of presence and range expansion. (1) The historically disjunct distribution potentially contributes to the current genetic subdivision of O. rufipogon. (2) Water availability is an important factor that limits the distribution of O. rufipogon. (3) Global warming is a lesser threat than other human-mediated factors to the conservation of this endangered species.

  10. A new species of Harpophora (Magnaporthaceae) recovered from healthy wild rice (Oryza granulata) roots, representing a novel member of a beneficial dark septate endophyte.

    PubMed

    Yuan, Zhi-Lin; Lin, Fu-Cheng; Zhang, Chu-Long; Kubicek, Christian P

    2010-06-01

    A survey of the endophytic fungal community of wild rice (Oryza granulata) in China was conducted. Two isolates recovered from healthy roots are assumed to be dark septate endophytes (DSEs). They are morphologically similar to species from the genus Harpophora and are identified as a new species, Harpophora oryzae, based on the molecular phylogeny and morphological characteristics. A neighbor-joining tree constructed from ITS-5.8S rRNA gene regions reveals that H. oryzae forms a distinctive subclade within the genus Harpophora, and is not genetically close to other species of Harpophora. Harpophora oryzae exhibits a moderate growth rate, with a frequent production of rope-like strands. It sporulates readily on artificial medium. Phialides are usually flask or bottle shaped and occur singly along hyphae or laterally and terminally on branched, hyaline to brown conidiophores, and also form whorls on metulae. Conidiophores are mostly branched with a slightly thickened wall, varying in dimensions. Conidia are one-celled and hyaline, most of them being falcate and strongly curved. The morphological differences between Harpophora spp. and Harpophora-like anamorphs representing different orders are also discussed. An in vitro inoculation test showed that H. oryzae may contribute towards improving rice (Oryza sativa L.) growth. Microscopic inspection of roots and phylogenetic placement of isolates further confirmed that H. oryzae represents a novel member of DSEs.

  11. Increasing cadmium and zinc levels in wild common eiders breeding along Canada's remote northern coastline.

    PubMed

    Mallory, Mark L; Braune, Birgit M; Robertson, Gregory J; Gilchrist, H Grant; Mallory, Conor D; Forbes, Mark R; Wells, Regina

    2014-04-01

    The common eider (Somateria mollissima) is an abundant sea duck breeding around the circumpolar Arctic, and is an important component of subsistence and sport harvest in some regions. We determined hepatic cadmium (Cd) and zinc (Zn) concentrations in the livers of breeding females sampled during three time periods including 1992/3, 2001/2 and 2008 at three sites spanning 53.7°N-75.8°N in the eastern Canadian Arctic. At all sites, concentrations of both Cd and Zn increased ~300% over this time period. The reasons for this rapid increase in concentrations are unclear.

  12. Human-Mediated Emergence as a Weed and Invasive Radiation in the Wild of the CD Genome Allotetraploid Rice Species (Oryza, Poaceae) in the Neotropics

    PubMed Central

    Second, Gérard; Rouhan, Germinal

    2008-01-01

    Background The genus Oryza is being used as a model in plant genomic studies although there are several issues still to be resolved regarding the spatio-temporal evolution of this ancient genus. Particularly contentious is whether undated transoceanic natural dispersal or recent human interference has been the principal agent determining its present distribution and differentiation. In this context, we studied the origin and distribution history of the allotetraploid CD rice genome. It is endemic to the Neotropics but the genus is thought to have originated in the Paleotropics, and there is relatively little genetic divergence between some orthologous sequences of the C genome component and their Old World counterparts. Methodology/Principal Findings Because of its allotetraploidy, there are several potential pitfalls in trying to date the formation of the CD genome using molecular data and this could lead to erroneous estimates. Therefore, we rather chose to rely on historical evidence to determine whether or not the CD genome was present in the Neotropics before the arrival of Columbus. We searched early collections of herbarium specimens and studied the reports of explorers of the tropical Americas for references to rice. In spite of numerous collectors traveling inland and collecting Oryza, plants determined as CD genome species were not observed away from cultivated rice fields until 1869. Various arguments suggest that they only consisted of weedy forms until that time. Conclusions/Significance The spatio-temporal distribution of herbarium collections fits a simple biogeographical scenario for the emergence in cultivated rice fields followed by radiation in the wild of the CD genome in the Neotropics during the last four centuries. This probably occurred from species introduced to the Americas by humans and we found no evidence that the CD genome pre-existed in the Old World. We therefore propose a new evolutionary hypothesis for such a recent origin of the

  13. Mr. ATOD's wild ride: what do alcohol, tobacco, and other drugs have in common?

    PubMed

    Courtwright, David T

    2005-01-01

    All researchers agree that individuals can become intoxicated by and dependent on alcohol, tobacco, and other psychoactive drugs. But they have disagreed over whether, and to what extent, drug pathologies comprise a unitary medical problem. Most critically, does addiction have a biological common denominator? Consensus on this question has shifted back and forth. In the late nineteenth and early twentieth centuries, physicians often studied and treated various drug addictions together, working under the "inebriety" paradigm. By the mid-twentieth century the inebriety paradigm had collapsed. Tobacco and alcohol had split off, both in the medical research community and in western popular culture. This article argues that neuroscientific, genetic, epidemiological, and historical evidence helped to reunify the addiction field in the late twentieth century. A new unifying paradigm emerged, variously called chemical dependency, substance abuse, or simply ATOD -- alcohol, tobacco, and other drugs.

  14. Characterization and evolutionary analysis of ent-kaurene synthase like genes from the wild rice species Oryza rufipogon.

    PubMed

    Toyomasu, Tomonobu; Miyamoto, Koji; Shenton, Matthew R; Sakai, Arisa; Sugawara, Chizu; Horie, Kiyotaka; Kawaide, Hiroshi; Hasegawa, Morifumi; Chuba, Masaru; Mitsuhashi, Wataru; Yamane, Hisakazu; Kurata, Nori; Okada, Kazunori

    2016-11-18

    Cultivated rice (Oryza sativa) possesses various labdane-related diterpene synthase genes, homologs of ent-copalyl diphosphate synthase (CPS) and ent-kaurene synthase (KS) that are responsible for the biosynthesis of phytohormone gibberellins. The CPS homologs and KS like (KSL) homologs successively converted geranylgeranyl diphosphate to cyclic diterpene hydrocarbons via ent-copalyl diphosphate or syn-copalyl diphosphate in O. sativa. Consequently, a variety of labdane-related diterpenoids, including phytoalexin phytocassanes, momilactones and oryzalexins, have been identified from cultivated rice. Our previous report indicated that the biosynthesis of phytocassanes and momilactones is conserved in Oryza rufipogon, the progenitor of Asian cultivated rice. Moreover, their biosynthetic gene clusters, containing OsCPS2 and OsKSL7 for phytocassane biosynthesis and OsCPS4 and OsKSL4 for momilactone biosynthesis, are also present in the O. rufipogon genome. We herein characterized O. rufipogon homologs of OsKSL5, OsKSL6, OsKSL8 responsible for oryzalexin S biosynthesis, and OsKSL10 responsible for oryzalexins A-F biosynthesis, to obtain more evolutionary insight into diterpenoid biosynthesis in O. sativa. Our phytoalexin analyses showed that no accumulation of oryzalexins was detected in extracts from O. rufipogon leaf blades. In vitro functional analyses indicated that unlike OsKSL10, O. rufipogon KSL10 functions as an ent-miltiradiene synthase, which explains the lack of accumulation of oryzalexins A-F in O. rufipogon. The different functions of KSL5 and KSL8 in O. sativa japonica to those in indica are conserved in each type of O. rufipogon, while KSL6 functions (ent-isokaurene synthases) are well conserved. Our study suggests that O. sativa japonica has evolved distinct specialized diterpenoid metabolism, including the biosynthesis of oryzalexins. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. In search of the last common ancestor: new findings on wild chimpanzees.

    PubMed

    McGrew, W C

    2010-10-27

    Modelling the behaviour of extinct hominins is essential in order to devise useful hypotheses of our species' evolutionary origins for testing in the palaeontological and archaeological records. One approach is to model the last common ancestor (LCA) of living apes and humans, based on current ethological and ecological knowledge of our closest living relations. Such referential modelling is based on rigorous, ongoing field studies of the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). This paper reviews recent findings from nature, focusing on those with direct implications for hominin evolution, e.g. apes, using elementary technology to access basic resources such as food and water, or sheltering in caves or bathing as thermoregulatory adaptations. I give preference to studies that directly address key issues, such as whether stone artefacts are detectible before the Oldowan, based on the percussive technology of hammer and anvil use by living apes. Detailed comparative studies of chimpanzees living in varied habitats, from rainforest to savannah, reveal that some behavioural patterns are universal (e.g. shelter construction), while others show marked (e.g. extractive foraging) or nuanced (e.g. courtship) cross-populational variation. These findings allow us to distinguish between retained, primitive traits of the LCA versus derived ones in the human lineage.

  16. In search of the last common ancestor: new findings on wild chimpanzees

    PubMed Central

    McGrew, W. C.

    2010-01-01

    Modelling the behaviour of extinct hominins is essential in order to devise useful hypotheses of our species' evolutionary origins for testing in the palaeontological and archaeological records. One approach is to model the last common ancestor (LCA) of living apes and humans, based on current ethological and ecological knowledge of our closest living relations. Such referential modelling is based on rigorous, ongoing field studies of the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). This paper reviews recent findings from nature, focusing on those with direct implications for hominin evolution, e.g. apes, using elementary technology to access basic resources such as food and water, or sheltering in caves or bathing as thermoregulatory adaptations. I give preference to studies that directly address key issues, such as whether stone artefacts are detectible before the Oldowan, based on the percussive technology of hammer and anvil use by living apes. Detailed comparative studies of chimpanzees living in varied habitats, from rainforest to savannah, reveal that some behavioural patterns are universal (e.g. shelter construction), while others show marked (e.g. extractive foraging) or nuanced (e.g. courtship) cross-populational variation. These findings allow us to distinguish between retained, primitive traits of the LCA versus derived ones in the human lineage. PMID:20855301

  17. Is polyandry a common event among wild populations of the pest Ceratitis capitata?

    PubMed

    Bonizzoni, Mariangela; Gomulski, Ludvik M; Mossinson, Sigalit; Guglielmino, Carmela R; Malacrida, Anna R; Yuval, Boaz; Gasperi, Giuliano

    2006-08-01

    In many insect species, females can mate more than once and store sperm from more than one male. An assessment and understanding of polyandry in the field can be important for pest species with a high colonization potential, such as the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), which is also highly polyphagous and among the most destructive agricultural insects. The use of polymorphic microsatellite markers, combined with different statistical approaches, provides evidence that polyandry occurs in two C. capitata natural populations, one population from the Greek island of Chios and one population from Rehovot, in Israel. The observed different level of polyandry is discussed in relation to the genetic diversity, seasonality, and demography of the two populations. When polyandry is present, paternity analysis also indicates that one male, presumably the last, tends to sire most of the progeny. Polyandry and paternity skew may have important implications for the evolution of the species, in terms of maintenance of the genetic variability. Moreover, these aspects of the mating behavior, i.e., remating frequency and paternity skew, may locally affect the sterile insect technique, the most commonly applied control strategy against C. capitata.

  18. Milk protein-based infant formula containing rice starch and low lactose reduces common regurgitation in healthy term infants: a randomized, blinded, and prospective trial.

    PubMed

    Lasekan, John B; Linke, Hawley K; Oliver, Jeffery S; Carver, Jane D; Blatter, Mark M; Kuchan, Matthew J; Cramer, Jenna M; Pollack, Paul F

    2014-01-01

    Spit-up (regurgitation) reduction with prethickened milk protein-based infant formulas containing rice starch has been clinically demonstrated in infants with heavy spit-ups but not in otherwise healthy normal infants with common spit-ups. The objective of this study was to evaluate growth, gastrointestinal tolerance, and efficacy to reduce common spit-up in normal, healthy term infants fed an investigational rice starch prethickened lactose-free milk protein-based infant formula. This double-blind, randomized, parallel study evaluated the investigational rice starch prethickened lactose-free (low lactose < 100 mg/L) milk protein-based infant formula compared to a standard, commercially available, iso-nutrient, lactose-containing (100% of carbohydrate) milk-based infant formula (control) for growth and gastrointestinal tolerance in healthy term infants (n = 132/group) fed from 14 ± 3 days to 112 days of age. Data were classified and analyzed as evaluable (EV; subjects completing study per protocol) or intent-to-treat data (ITT; all subjects with available data). Growth as indicated by weight gain (primary variable) and formula intake were not significantly different (p > 0.05) between feeding groups (EV or ITT). Though both formulas were well tolerated, spit-up frequency was significantly lower (p < 0.05) in the rice versus control group by 53% at 28 days of age, 54% at 56 days, 48% at 84 days, and 32% at 112 days (EV). Importantly, infants in the rice group were 1.6 to 1.8 times more likely to report zero spit-up than infants in the control group. The rice group also had higher percentages of soft and yellow stools. The rice starch prethickened lactose-free milk protein-based formula (rice) supported normal growth and safe use as the sole source of feeding for normal infants over the first 4 months of life. The rice formula was efficacious in providing a clinically relevant reduction of spit-up frequency in otherwise healthy term infants.

  19. Population genetic patterns suggest a behavioural change in wild common frogs (Rana temporaria) following disease outbreaks (Ranavirus).

    PubMed

    Teacher, Amber G F; Garner, Trenton W J; Nichols, Richard A

    2009-08-01

    We use 14 microsatellite loci to investigate the impact of a viral disease (Ranavirus) on the population genetic structure of wild common frogs (Rana temporaria). Populations with a history of Ranavirus mortalities (and 83% declines in the number of frogs) were compared with populations with no history of infection. Infected ponds showed significantly elevated F(IS) (homozygote excess), significantly reduced relatedness, and no detectable effect on allelic richness. We hypothesize that the elevated F(IS) and reduced relatedness are consequences of assortative mating, and that allelic richness is maintained by immigration from nearby populations. Simulations indicate that the elevated F(IS) cannot be explained by population size reductions, but can indeed be explained by assortative mating (even if a mate choice locus is unlinked to the genetic markers). While the majority of studies consider demographic outcomes following disease outbreaks, our results indicate that emerging infectious diseases could also result in behavioural changes.

  20. The Puzzle of Italian Rice Origin and Evolution: Determining Genetic Divergence and Affinity of Rice Germplasm from Italy and Asia

    PubMed Central

    Jiang, Zhuxi; Basso, Barbara; Sala, Francesco; Spada, Alberto; Grassi, Fabrizio; Lu, Bao-Rong

    2013-01-01

    The characterization of genetic divergence and relationships of a set of germplasm is essential for its efficient applications in crop breeding and understanding of the origin/evolution of crop varieties from a given geographical region. As the largest rice producing country in Europe, Italy holds rice germplasm with abundant genetic diversity. Although Italian rice varieties and the traditional ones in particular have played important roles in rice production and breeding, knowledge concerning the origin and evolution of Italian traditional varieties is still limited. To solve the puzzle of Italian rice origin, we characterized genetic divergence and relationships of 348 rice varieties from Italy and Asia based on the polymorphisms of microsatellite fingerprints. We also included common wild rice O. rufipogon as a reference in the characterization. Results indicated relatively rich genetic diversity (He = 0.63-0.65) in Italian rice varieties. Further analyses revealed a close genetic relationship of the Italian traditional varieties with those from northern China, which provides strong genetic evidence for tracing the possible origin of early established rice varieties in Italy. These findings have significant implications for the rice breeding programs, in which appropriate germplasm can be selected from a given region and utilized for transferring unique genetic traits based on its genetic diversity and evolutionary relationships. PMID:24265814

  1. 29 CFR 780.114 - Wild commodities.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... harvesting of wild commodities such as mosses, wild rice, burls and laurel plants, the trapping of wild animals, or the appropriation of minerals and other uncultivated products from the soil are not employed...

  2. 29 CFR 780.114 - Wild commodities.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... harvesting of wild commodities such as mosses, wild rice, burls and laurel plants, the trapping of wild animals, or the appropriation of minerals and other uncultivated products from the soil are not employed...

  3. Structural characterization of an alpha-amylase inhibitor from a wild common bean (Phaseolus vulgaris): insight into the common structural features of leguminous alpha-amylase inhibitors.

    PubMed

    Nakaguchi, T; Arakawa, T; Philo, J S; Wen, J; Ishimoto, M; Yamaguchi, H

    1997-02-01

    The primary structures of two subunits of an alpha-amylase inhibitor (alpha AI-2) from a wild common bean (Phaseolus vulgaris) were revealed by a comparison of the amino acid sequence previously deduced from the nucleotide sequence with the amino- and carboxyl-terminal amino acid sequences determined by conventional methods. The polypeptide molecular weight of alpha AI-2 obtained by the light-scattering technique, considered together with the sequence molecular weights revealed for the subunits, indicated that alpha AI-2 has the subunit stoichiometry of an alpha 2 beta 2 complex. These structural features were closely similar to those recently elucidated for a white kidney bean (P. vulgaris) alpha-amylase inhibitor, which is quite different in the inhibitory specificity from alpha AI-2. The post-translational processing of the precursor glycoproteins to form the tetrameric structure appeared to require an Arg residue close to the processing site. Further, the proper associations of the subunits into the tetrameric structures seemed to be strictly controlled by a few amino acids on the subunit interfaces.

  4. Validation of a sensitive DNA walking strategy to characterise unauthorised GMOs using model food matrices mimicking common rice products.

    PubMed

    Fraiture, Marie-Alice; Herman, Philippe; Taverniers, Isabel; De Loose, Marc; Van Nieuwerburgh, Filip; Deforce, Dieter; Roosens, Nancy H

    2015-04-15

    To identify unauthorised GMOs in food and feed matrices, an integrated approach has recently been developed targeting pCAMBIA family vectors, highly present in transgenic plants. Their presence is first assessed by qPCR screening and is subsequently confirmed by characterising the transgene flanking regions, using DNA walking. Here, the DNA walking performance has been thoroughly tested for the first time, regarding the targeted DNA quality and quantity. Several assays, on model food matrices mimicking common rice products, have allowed to determine the limit of detection as well as the potential effects of food mixture and processing. This detection system allows the identification of transgenic insertions as low as 10 HGEs and was not affected by the presence of untargeted DNA. Moreover, despite the clear impact of food processing on DNA quality, this method was able to cope with degraded DNA. Given its specificity, sensitivity, reliability, applicability and practicability, the proposed approach is a key detection tool, easily implementable in enforcement laboratories. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  5. Constitutive activity of G-protein-coupled receptors: cause of disease and common property of wild-type receptors.

    PubMed

    Seifert, Roland; Wenzel-Seifert, Katharina

    2002-11-01

    The aim of this review is to provide a systematic overview on constitutively active G-protein-coupled receptors (GPCRs), a rapidly evolving area in signal transduction research. We will discuss mechanisms, pharmacological tools and methodological approaches to analyze constitutive activity. The two-state model defines constitutive activity as the ability of a GPCR to undergo agonist-independent isomerization from an inactive (R) state to an active (R*) state. While the two-state model explains basic concepts of constitutive GPCR activity and inverse agonism, there is increasing evidence for multiple active GPCR conformations with distinct biological activities. As a result of constitutive GPCR activity, basal G-protein activity increases. Until now, constitutive activity has been observed for more than 60 wild-type GPCRs from the families 1-3 and from different species including humans and commonly used laboratory animal species. Additionally, several naturally occurring and disease-causing GPCR mutants with increased constitutive activity relative to wild-type GPCRs have been identified. Alternative splicing, RNA editing, polymorphisms within a given species, species variants and coupling to specific G-proteins all modulate the constitutive activity of GPCRs, providing multiple regulatory switches to fine-tune basal cellular activities. The most important pharmacological tools to analyze constitutive activity are inverse agonists and Na(+) that stabilize the R state, and pertussis toxin that uncouples GPCRs from G(i)/G(o)-proteins. Constitutive activity is observed at low and high GPCR expression levels, in native systems and in recombinant systems, and has been reported for GPCRs coupled to G(s)-, G(i)- and G(q)-proteins. Constitutive activity of neurotransmitter GPCRs may provide a tonic support for basal neuronal activity. For the majority of GPCRs known to be constitutively active, inverse agonists have already been identified. Inverse agonists may be useful

  6. Effects of water management practices on residue decomposition and degradation of Cry1Ac protein from crop-wild Bt rice hybrids and parental lines during winter fallow season.

    PubMed

    Xiao, Manqiu; Dong, Shanshan; Li, Zhaolei; Tang, Xu; Chen, Yi; Yang, Shengmao; Wu, Chunyan; Ouyang, Dongxin; Fang, Changming; Song, Zhiping

    2015-12-01

    Rice is the staple diet of over half of the world's population and Bacillus thuringiensis (Bt) rice expressing insecticidal Cry proteins is ready for deployment. An assessment of the potential impact of Bt rice on the soil ecosystem under varied field management practices is urgently required. We used litter bags to assess the residue (leaves, stems and roots) decomposition dynamics of two transgenic rice lines (Kefeng6 and Kefeng8) containing stacked genes from Bt and sck (a modified CpTI gene encoding a cowpea trypsin inhibitor) (Bt/CpTI), a non-transgenic rice near-isoline (Minghui86), wild rice (Oryza rufipogon) and crop-wild Bt rice hybrid under contrasting conditions (drainage or continuous flooding) in the field. No significant difference was detected in the remaining mass, total C and total N among cultivars under aerobic conditions, whereas significant differences in the remaining mass and total C were detected between Kefeng6 and Kefeng8 and Minghui86 under the flooded condition. A higher decomposition rate constant (km) was measured under the flooded condition compared with the aerobic condition for leaf residues, whereas the reverse was observed for root residues. The enzyme-linked immunosorbent assay (ELISA), which was used to monitor the changes in the Cry1Ac protein in Bt rice residues, indicated that (1) the degradation of the Cry1Ac protein under both conditions best fit first-order kinetics, and the predicted DT50 (50% degradation time) of the Cry1Ac protein ranged from 3.6 to 32.5 days; (2) the Cry1Ac protein in the residue degraded relatively faster under aerobic conditions; and (3) by the end of the study (~154 days), the protein was present at a low concentration in the remaining residues under both conditions. The degradation rate constant was negatively correlated with the initial carbon content and positively correlated with the initial Cry1Ac protein concentration, but it was only correlated with the mass decomposition rate constants under

  7. 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

  8. Analysis of random and specific sequences of nuclear and cytoplasmic DNA in diploid and tetraploid american wild rice species (Oryza spp.).

    PubMed

    Buso, G S; Rangel, P H; Ferreira, M E

    2001-06-01

    A sample of American wild rice and other accessions of the genus Oryza were studied at polymorphic regions of nuclear, mitochondrial, and chloroplastic genomes. First, flow cytometry, genome-specific RAPD markers, and chromosome counting were utilized to verify the original ploidy and classification of 230 accessions studied. Based on these methods, 8% of the accessions were considered to be misclassified either taxonomically or as a result of contamination. Second, a fine resolution analysis was conducted at genomic regions sampled at random by RAPD markers and at specific sites of the chloroplast and mitochondrial DNA by cleaved amplified polymorphic sequence (CAPS) analysis. Phylogenetic trees resulting from phenetic and cladistic analyses of RAPD, cpDNA, and mtDNA polymorphisms were obtained. The results indicated that the American diploid species O. glumaepatula should be considered an individual species, distinct from O. rufipogon, and confirmed that the American tetraploid species (O. alta, O. grandiglumis, and O. latifolia) belong to the O. officinalis complex. The data indicate that these species should still be treated as a group rather than as three distinct species and that their closest relative is a CC-genome species. It was estimated that the diploid and tetraploid American species diverged from O. sativa - O. nivara (AA genome) and CC- and BBCC-genome species, respectively, 20 million years ago.

  9. A Comparative Study of the Common Protozoan Parasites of Clarias gariepinus from the Wild and Cultured Environments in Benue State, Nigeria.

    PubMed

    Omeji, S; Solomon, S G; Idoga, E S

    2011-01-01

    A total of one hundred and twenty Clarias gariepinus comprising 30 dead and 30 live fishes were examined for protozoan parasites infestation, sixty each from the wild and a pond (cultured environment) over a period of six months. Ichthyophthirius multifiliis was the most common protozoan parasites found in C. gariepinus from the wild (River Benue) and cultured (pond) environments. These protozoan parasites constitute 37.08% of the total parasites encountered for fishes in the pond and 42.51% of fishes in the wild. Among the body parts of the sampled fishes from the pond, the gills had the highest parasite load (38.86%). Also, the gills had the highest parasite load (40.54%) among the body parts of the fishes sampled from the wild. Fishes not infested with any protozoan parasites from the pond constituted 36.70% of the total fish sampled. On the other hand, fishes not infested with any protozoan parasites from the wild constituted 31.65% of the total fish sampled. Female fishes had more protozoan parasites than the male fishes. Bigger fishes of total length (25-48 cm) had more parasite load than the smaller ones (19-24 cm). Also, fishes between 150-750 g had more parasite load than the smaller ones of less than 150 g. Protozoan parasite load of fish from the cultured environment (pond) did not differ significantly (P < 0.05) from those from River Benue (wild).

  10. Asymmetry of gene flow and differential geographical structure of molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica.

    PubMed

    Papa, R; Gepts, P

    2003-01-01

    Using amplified fragment length polymorphisms (AFLPs), we analyzed the genetic structure of wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica at different geographical levels to test the hypothesis of asymmetric gene flow and investigate the origin of weedy populations. We showed both by phenetic and admixture population analyses that gene flow is about three- to four-fold higher from domesticated to wild populations than in the reverse direction. This result, combined with other work, points to a displacement of genetic diversity in wild populations due to gene flow from the domesticated populations. The weedy populations appear to be genetically intermediate between domesticated and wild populations, suggesting that they originated by hybridization between wild and domesticated types rather than by escape from cultivation. In addition, the domesticated bean races were genetically similar confirming a single domestication event for the Mesoamerican gene pool. Finally, the genetic diversity of the domesticated bean population showed a lower level of geographic structure in comparison to that of the wild populations.

  11. Artificial Selection of Gn1a Plays an Important role in Improving Rice Yields Across Different Ecological Regions.

    PubMed

    Wang, Jie; Xu, Huaxue; Li, Nengwu; Fan, Fengfeng; Wang, Liuting; Zhu, Yingguo; Li, Shaoqing

    2015-12-01

    Rice is one of the most important crops, and it is essential to improve rice productivity to satisfy the future global food supply demands. Gn1a (OsCKX2), which encodes cytokinin oxidase/dehydrogenase, plays an important role in regulating rice grain yield. In this study, we analyzed the genetic variation of Gn1a, which influences grain yield through controlling the number of spikelets in rice. The allelic variations in the promoter, 5' untranslated region (UTR) and coding sequence (CDS) of Gn1a were investigated in 175 cultivars and 21 wild rice accessions. We found that Gn1a showed less sequence variation in the cultivars, but exhibited significant nucleotide diversity in wild rice. A total of 14 alleles, named AP1 to AP14, were identified in the cultivars based on the amino acid divergence of GN1A. Association analysis revealed that the number of spikelets and grain yield were significantly different between the different alleles. Phylogenetic analysis indicated that the three main alleles, AP3, AP8 and AP9, in the cultivars might originate from a common ancestor allele, AP1, in wild rice. Of these alleles in the cultivars, AP9 was suggested as the best allele in indica, as it has shown strong artificial selection in breeding high-yield rice in the past. It might be valuable to explore the high-yield-related alleles of Gn1a to develop high-yield rice cultivars in future breeding programs.

  12. Evaluation of various QuEChERS based methods for the analysis of herbicides and other commonly used pesticides in polished rice by LC-MS/MS.

    PubMed

    Pareja, Lucía; Cesio, Verónica; Heinzen, Horacio; Fernández-Alba, Amadeo R

    2011-02-15

    Four different extraction and clean-up protocols based on the QuEChERS method were compared for the development of an optimized sample preparation procedure for the multiresidue analysis of 16 commonly applied herbicides in rice crops using LC-QqQ/MS. Additionally the methods were evaluated for the analysis of 26 insecticides and fungicides currently used in rice crops. The methods comprise, in general, the hydratation of the sample with water followed by the extraction with acetonitrile, phase separation with the addition of different salts and finally a clean-up step with various sorbents. Matrix effects were evaluated for the 4 studied methods using LC-QqQ/MS. Additionally LC-TOF/MS was used to compare the co-extractants obtained with the four assayed methodologies. Thirty-six pesticides presented good performance with recoveries in the range 70-120% and relative standard deviations below 20% using 7.5 g of milled polished rice and the buffered acetate QuEChERS method without clean-up at both fortification levels: 10 and 300 μg kg(-1). The other six pesticides presented low recovery rates, nevertheless all these analytes could be analyzed with at least one of the other three studied procedures. Copyright © 2010. Published by Elsevier B.V.

  13. 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

  14. 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

  15. Molecular ecology and selection in the drought-related Asr gene polymorphisms in wild and cultivated common bean (Phaseolus vulgaris L.)

    PubMed Central

    2012-01-01

    Background The abscisic acid (ABA) pathway plays an important role in the plants’ reaction to drought stress and ABA-stress response (Asr) genes are important in controlling this process. In this sense, we accessed nucleotide diversity at two candidate genes for drought tolerance (Asr1 and Asr2), involved in an ABA signaling pathway, in the reference collection of cultivated common bean (Phaseolus vulgaris L.) and a core collection of wild common bean accessions. Results Our wild population samples covered a range of mesic (semi-arid) to very dry (desert) habitats, while our cultivated samples presented a wide spectrum of drought tolerance. Both genes showed very different patterns of nucleotide variation. Asr1 exhibited very low nucleotide diversity relative to the neutral reference loci that were previously surveyed in these populations. This suggests that strong purifying selection has been acting on this gene. In contrast, Asr2 exhibited higher levels of nucleotide diversity, which is indicative of adaptive selection. These patterns were more notable in wild beans than in cultivated common beans indicting that natural selection has played a role over long time periods compared to farmer selection since domestication. Conclusions Together these results suggested the importance of Asr1 in the context of drought tolerance, and constitute the first steps towards an association study between genetic polymorphism of this gene family and variation in drought tolerance traits. Furthermore, one of our major successes was to find that wild common bean is a reservoir of genetic variation and selection signatures at Asr genes, which may be useful for breeding drought tolerance in cultivated common bean. PMID:22799462

  16. Genome-wide identification of microRNAs and their targets in wild type and phyB mutant provides a key link between microRNAs and the phyB-mediated light signaling pathway in rice

    PubMed Central

    Sun, Wei; Xu, Xiao Hui; Wu, Xiu; Wang, Yong; Lu, Xingbo; Sun, Hongwei; Xie, Xianzhi

    2015-01-01

    Phytochrome B (phyB), a member of the phytochrome family in rice, plays important roles in regulating a range of developmental processes and stress responses. However, little information about the mechanisms involved in the phyB-mediated light signaling pathway has been reported in rice. MicroRNAs (miRNAs) also perform important roles in plant development and stress responses. Thus, it is intriguing to explore the role of miRNAs in the phyB-mediated light signaling pathway in rice. In this study, comparative high-throughput sequencing and degradome analysis were used to identify candidate miRNAs and their targets that participate in the phyB-mediated light signaling pathway. A total of 720 known miRNAs, 704 novel miRNAs and 1957 target genes were identified from the fourth leaves of wild-type (WT) and phyB mutant rice at the five-leaf stage. Among them, 135 miRNAs showed differential expression, suggesting that the expression of these miRNAs is directly or indirectly under the control of phyB. In addition, 32 out of the 135 differentially expressed miRNAs were found to slice 70 genes in the rice genome. Analysis of these target genes showed that members of various transcription factor families constituted the largest proportion, indicating miRNAs are probably involved in the phyB-mediated light signaling pathway mainly by regulating the expression of transcription factors. Our results provide new clues for functional characterization of miRNAs in the phyB-mediated light signaling pathway, which should be helpful in comprehensively uncovering the molecular mechanisms of phytochrome-mediated photomorphogenesis and stress responses in plants. PMID:26074936

  17. Effects of physical and biogeochemical processes on aquatic ecosystems at the groundwater-surface water interface: An evaluation of a sulfate-impacted wild rice stream in Minnesota (USA)

    NASA Astrophysics Data System (ADS)

    Ng, G. H. C.; Yourd, A. R.; Myrbo, A.; Johnson, N.

    2015-12-01

    Significant uncertainty and variability in physical and biogeochemical processes at the groundwater-surface water interface complicate how surface water chemistry affects aquatic ecosystems. Questions surrounding a unique 10 mg/L sulfate standard for wild rice (Zizania sp.) waters in Minnesota are driving research to clarify conditions controlling the geochemistry of shallow sediment porewater in stream- and lake-beds. This issue raises the need and opportunity to carry out in-depth, process-based analysis into how water fluxes and coupled C, S, and Fe redox cycles interact to impact aquatic plants. Our study builds on a recent state-wide field campaign that showed that accumulation of porewater sulfide from sulfate reduction impairs wild rice, an annual grass that grows in shallow lakes and streams in the Great Lakes region of North America. Negative porewater sulfide correlations with organic C and Fe quantities also indicated that lower redox rates and greater mineral precipitation attenuate sulfide. Here, we focus on a stream in northern Minnesota that receives high sulfate loading from iron mining activity yet maintains wild rice stands. In addition to organic C and Fe effects, we evaluate the degree to which streambed hydrology, and in particular groundwater contributions, accounts for the active biogeochemistry. We collect field measurements, spanning the surrounding groundwater system to the stream, to constrain a reactive-transport model. Observations from seepage meters, temperature probes, and monitoring wells delineate upward flow that may lessen surface water impacts below the stream. Geochemical analyses of groundwater, porewater, and surface water samples and of sediment extractions reveal distinctions among the different domains and stream banks, which appear to jointly control conditions in the streambed. A model based on field conditions can be used to evaluate the relative the importance and the spatiotemporal scales of diverse flux and

  18. Commonality.

    ERIC Educational Resources Information Center

    Beaton, Albert E., Jr.

    Commonality analysis is an attempt to understand the relative predictive power of the regressor variables, both individually and in combination. The squared multiple correlation is broken up into elements assigned to each individual regressor and to each possible combination of regressors. The elements have the property that the appropriate sums…

  19. Common cancer in a wild animal: the California sea lion (Zalophus californianus) as an emerging model for carcinogenesis.

    PubMed

    Browning, Helen M; Gulland, Frances M D; Hammond, John A; Colegrove, Kathleen M; Hall, Ailsa J

    2015-07-19

    Naturally occurring cancers in non-laboratory species have great potential in helping to decipher the often complex causes of neoplasia. Wild animal models could add substantially to our understanding of carcinogenesis, particularly of genetic and environmental interactions, but they are currently underutilized. Studying neoplasia in wild animals is difficult and especially challenging in marine mammals owing to their inaccessibility, lack of exposure history, and ethical, logistical and legal limits on experimentation. Despite this, California sea lions (Zalophus californianus) offer an opportunity to investigate risk factors for neoplasia development that have implications for terrestrial mammals and humans who share much of their environment and diet. A relatively accessible California sea lion population on the west coast of the USA has a high prevalence of urogenital carcinoma and is regularly sampled during veterinary care in wildlife rehabilitation centres. Collaborative studies have revealed that genotype, persistent organic pollutants and a herpesvirus are all associated with this cancer. This paper reviews research to date on the epidemiology and pathogenesis of urogenital carcinoma in this species, and presents the California sea lion as an important and currently underexploited wild animal model of carcinogenesis. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  20. Common cancer in a wild animal: the California sea lion (Zalophus californianus) as an emerging model for carcinogenesis

    PubMed Central

    Browning, Helen M.; Gulland, Frances M. D.; Hammond, John A.; Colegrove, Kathleen M.; Hall, Ailsa J.

    2015-01-01

    Naturally occurring cancers in non-laboratory species have great potential in helping to decipher the often complex causes of neoplasia. Wild animal models could add substantially to our understanding of carcinogenesis, particularly of genetic and environmental interactions, but they are currently underutilized. Studying neoplasia in wild animals is difficult and especially challenging in marine mammals owing to their inaccessibility, lack of exposure history, and ethical, logistical and legal limits on experimentation. Despite this, California sea lions (Zalophus californianus) offer an opportunity to investigate risk factors for neoplasia development that have implications for terrestrial mammals and humans who share much of their environment and diet. A relatively accessible California sea lion population on the west coast of the USA has a high prevalence of urogenital carcinoma and is regularly sampled during veterinary care in wildlife rehabilitation centres. Collaborative studies have revealed that genotype, persistent organic pollutants and a herpesvirus are all associated with this cancer. This paper reviews research to date on the epidemiology and pathogenesis of urogenital carcinoma in this species, and presents the California sea lion as an important and currently underexploited wild animal model of carcinogenesis. PMID:26056370

  1. An injury equivalency system for establishing a common economic threshold for three species of rice planthoppers (Hemiptera: Delphacidae) in Taiwan.

    PubMed

    Huang, Shou-Horng; Chen, Ching-Huan; Chen, Chiou-Nan; Wu, Wen-Jer

    2013-04-01

    The economic threshold (ET) for multiple pest species that share the same injury type on host plants (feeding guild) has been proposed for decision-making in integrated management framework of many defoliating insect pests. However, only a few consider agricultural pests with sucking mouthparts. This study presents the first injury equivalency system for the feeding guild made up of three rice (Oryza sativa L.) planthopper (Hemiptera: Delphacidae) species--Nilaparvata lugens (Stål), Sogatella furcifera (Harváth), and Laodelphax striatellus (Fallén)--by using relative amount of honeydew excretion of each species. The intraspecific injury equivalent coefficient was determined; this coefficient provides an exchange rate for different developmental stages in a species. N. lugens was chosen as the standard species to obtain interspecific injury equivalents for other individuals in the guild, allowing estimates of total guild injury feasible. For extension purposes, the injury equivalency was simplified by pooling all nymphs and adults in the guild to mitigate the potential confusion resulting from uncertainty of instars or wing form. A matrix of ETs established on previous studies and incorporating changes of management cost and rice price was used and served as a control decision guide for the guild samples. The validity of the proposed injury equivalency system was tested using several field data sets, and the results are generally promising and meaningfully elevate the accuracy of estimating combined injury and damage to rice, suggesting that the proposed system is a better integrated pest management decision-making system compared with conventional practices.

  2. Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns.

    PubMed

    Kawaura, Kanako; Mochida, Keiichi; Enju, Akiko; Totoki, Yasushi; Toyoda, Atsushi; Sakaki, Yoshiyuki; Kai, Chikatoshi; Kawai, Jun; Hayashizaki, Yoshihide; Seki, Motoaki; Shinozaki, Kazuo; Ogihara, Yasunari

    2009-06-18

    Wheat is an allopolyploid plant that harbors a huge, complex genome. Therefore, accumulation of expressed sequence tags (ESTs) for wheat is becoming particularly important for functional genomics and molecular breeding. We prepared a comprehensive collection of ESTs from the various tissues that develop during the wheat life cycle and from tissues subjected to stress. We also examined their expression profiles in silico. As full-length cDNAs are indispensable to certify the collected ESTs and annotate the genes in the wheat genome, we performed a systematic survey and sequencing of the full-length cDNA clones. This sequence information is a valuable genetic resource for functional genomics and will enable carrying out comparative genomics in cereals. As part of the functional genomics and development of genomic wheat resources, we have generated a collection of full-length cDNAs from common wheat. By grouping the ESTs of recombinant clones randomly selected from the full-length cDNA library, we were able to sequence 6,162 independent clones with high accuracy. About 10% of the clones were wheat-unique genes, without any counterparts within the DNA database. Wheat clones that showed high homology to those of rice were selected in order to investigate their expression patterns in various tissues throughout the wheat life cycle and in response to abiotic-stress treatments. To assess the variability of genes that have evolved differently in wheat and rice, we calculated the substitution rate (Ka/Ks) of the counterparts in wheat and rice. Genes that were preferentially expressed in certain tissues or treatments had higher Ka/Ks values than those in other tissues and treatments, which suggests that the genes with the higher variability expressed in these tissues is under adaptive selection. We have generated a high-quality full-length cDNA resource for common wheat, which is essential for continuation of the ongoing curation and annotation of the wheat genome. The data

  3. 29 CFR 780.114 - Wild commodities.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... harvesting of wild commodities such as mosses, wild rice, burls and laurel plants, the trapping of wild... in “the production, cultivation, growing, and harvesting of agricultural or horticultural commodities... ordinarily grows wild without being cultivated does not preclude them from being classed as “agricultural...

  4. 29 CFR 780.114 - Wild commodities.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... harvesting of wild commodities such as mosses, wild rice, burls and laurel plants, the trapping of wild... in “the production, cultivation, growing, and harvesting of agricultural or horticultural commodities... ordinarily grows wild without being cultivated does not preclude them from being classed as “agricultural...

  5. 29 CFR 780.114 - Wild commodities.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... harvesting of wild commodities such as mosses, wild rice, burls and laurel plants, the trapping of wild... in “the production, cultivation, growing, and harvesting of agricultural or horticultural commodities... ordinarily grows wild without being cultivated does not preclude them from being classed as “agricultural...

  6. The effect of salinity on chlorophyll, proline and mineral nutrients in common weeds of coastal rice fields in Malaysia.

    PubMed

    Hakim, M A; Juraimi, Abdul Shukor; Hanafi, M M; Ismail, Mohd Razi; Rafii, M Y; Aslani, Fazad; Selamat, A

    2014-09-01

    Six weed species (Leptochola chinensis, Echinochloa crus-galli, Echinochloa colona, Jussiaea linifolia, Oryza sativa (weedy rice) and Cyperus iria) were tested for their salt tolerant traits in terms of chlorophyll, proline and mineral nutrients accumulation against different salinity levels (0, 4, 8, 16, 24, 32, and 40 dS m(-1)). Chlorophyll a, b and total chlorophyll content, proline and mineral nutrients accumulation were determined. Salt stress showed prominent effect on all the parameters investigated and there were significant variations between the all weed species. Chlorophyll content, K+, Ca(2+) and Mg(2+) ions in both shoots and roots significantly decreased; while proline and Na+ accumulation significantly increased with increasing salinity up to 40 dS m(-1). In terms of overall performance, Cyperus iria and E. crus-galliwere relatively more tolerant; E. colona and J. linifolia were tolerant; L. chinensis and O. sativa L were salt sensitive, respectively.

  7. A Common Caatinga Cactus, Pilosocereus gounellei, is an Important Ecotope of Wild Triatoma brasiliensis Populations in the Jaguaribe Valley of Northeastern Brazil

    PubMed Central

    Valença-Barbosa, Carolina; Lima, Marli M.; Sarquis, Otília; Bezerra, Claudia M.; Abad-Franch, Fernando

    2014-01-01

    Triatoma brasiliensis is the most important vector of Chagas disease in the Caatinga eco-region of northeastern Brazil. Wild T. brasiliensis populations have been reported only from rocky outcrops. However, this species frequently infests/re-infests houses in rock-free sedimentary lowlands. We therefore hypothesized that it should also occupy other natural ecotopes. We show that a common Caatinga cactus, Pilosocereus gounellei, locally known as xiquexique, often harbors T. brasiliensis breeding colonies apparently associated with rodents (n = 44 cacti, infestation rate = 47.7%, 157 bugs captured). Our findings suggest that infested cacti might be involved in house re-infestation by T. brasiliensis in the Caatinga region. PMID:24710611

  8. Common variants of the BRCA1 wild-type allele modify the risk of breast cancer in BRCA1 mutation carriers.

    PubMed

    Cox, David G; Simard, Jacques; Sinnett, Daniel; Hamdi, Yosr; Soucy, Penny; Ouimet, Manon; Barjhoux, Laure; Verny-Pierre, Carole; McGuffog, Lesley; Healey, Sue; Szabo, Csilla; Greene, Mark H; Mai, Phuong L; Andrulis, Irene L; Thomassen, Mads; Gerdes, Anne-Marie; Caligo, Maria A; Friedman, Eitan; Laitman, Yael; Kaufman, Bella; Paluch, Shani S; Borg, Åke; Karlsson, Per; Askmalm, Marie Stenmark; Bustinza, Gisela Barbany; Nathanson, Katherine L; Domchek, Susan M; Rebbeck, Timothy R; Benítez, Javier; Hamann, Ute; Rookus, Matti A; van den Ouweland, Ans M W; Ausems, Margreet G E M; Aalfs, Cora M; van Asperen, Christi J; Devilee, Peter; Gille, Hans J J P; Peock, Susan; Frost, Debra; Evans, D Gareth; Eeles, Ros; Izatt, Louise; Adlard, Julian; Paterson, Joan; Eason, Jacqueline; Godwin, Andrew K; Remon, Marie-Alice; Moncoutier, Virginie; Gauthier-Villars, Marion; Lasset, Christine; Giraud, Sophie; Hardouin, Agnès; Berthet, Pascaline; Sobol, Hagay; Eisinger, François; Bressac de Paillerets, Brigitte; Caron, Olivier; Delnatte, Capucine; Goldgar, David; Miron, Alex; Ozcelik, Hilmi; Buys, Saundra; Southey, Melissa C; Terry, Mary Beth; Singer, Christian F; Dressler, Anne-Catharina; Tea, Muy-Kheng; Hansen, Thomas V O; Johannsson, Oskar; Piedmonte, Marion; Rodriguez, Gustavo C; Basil, Jack B; Blank, Stephanie; Toland, Amanda E; Montagna, Marco; Isaacs, Claudine; Blanco, Ignacio; Gayther, Simon A; Moysich, Kirsten B; Schmutzler, Rita K; Wappenschmidt, Barbara; Engel, Christoph; Meindl, Alfons; Ditsch, Nina; Arnold, Norbert; Niederacher, Dieter; Sutter, Christian; Gadzicki, Dorothea; Fiebig, Britta; Caldes, Trinidad; Laframboise, Rachel; Nevanlinna, Heli; Chen, Xiaoqing; Beesley, Jonathan; Spurdle, Amanda B; Neuhausen, Susan L; Ding, Yuan C; Couch, Fergus J; Wang, Xianshu; Peterlongo, Paolo; Manoukian, Siranoush; Bernard, Loris; Radice, Paolo; Easton, Douglas F; Chenevix-Trench, Georgia; Antoniou, Antonis C; Stoppa-Lyonnet, Dominique; Mazoyer, Sylvie; Sinilnikova, Olga M

    2011-12-01

    Mutations in the BRCA1 gene substantially increase a woman's lifetime risk of breast cancer. However, there is great variation in this increase in risk with several genetic and non-genetic modifiers identified. The BRCA1 protein plays a central role in DNA repair, a mechanism that is particularly instrumental in safeguarding cells against tumorigenesis. We hypothesized that polymorphisms that alter the expression and/or function of BRCA1 carried on the wild-type (non-mutated) copy of the BRCA1 gene would modify the risk of breast cancer in carriers of BRCA1 mutations. A total of 9874 BRCA1 mutation carriers were available in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) for haplotype analyses of BRCA1. Women carrying the rare allele of single nucleotide polymorphism rs16942 on the wild-type copy of BRCA1 were at decreased risk of breast cancer (hazard ratio 0.86, 95% confidence interval 0.77-0.95, P = 0.003). Promoter in vitro assays of the major BRCA1 haplotypes showed that common polymorphisms in the regulatory region alter its activity and that this effect may be attributed to the differential binding affinity of nuclear proteins. In conclusion, variants on the wild-type copy of BRCA1 modify risk of breast cancer among carriers of BRCA1 mutations, possibly by altering the efficiency of BRCA1 transcription.

  9. Common variants of the BRCA1 wild-type allele modify the risk of breast cancer in BRCA1 mutation carriers

    PubMed Central

    Cox, David G.; Simard, Jacques; Sinnett, Daniel; Hamdi, Yosr; Soucy, Penny; Ouimet, Manon; Barjhoux, Laure; Verny-Pierre, Carole; McGuffog, Lesley; Healey, Sue; Szabo, Csilla; Greene, Mark H.; Mai, Phuong L.; Andrulis, Irene L.; Thomassen, Mads; Gerdes, Anne-Marie; Caligo, Maria A.; Friedman, Eitan; Laitman, Yael; Kaufman, Bella; Paluch, Shani S.; Borg, Åke; Karlsson, Per; Stenmark Askmalm, Marie; Barbany Bustinza, Gisela; Nathanson, Katherine L.; Domchek, Susan M.; Rebbeck, Timothy R.; Benítez, Javier; Hamann, Ute; Rookus, Matti A.; van den Ouweland, Ans M.W.; Ausems, Margreet G.E.M.; Aalfs, Cora M.; van Asperen, Christi J.; Devilee, Peter; Gille, Hans J.J.P.; Peock, Susan; Frost, Debra; Evans, D. Gareth; Eeles, Ros; Izatt, Louise; Adlard, Julian; Paterson, Joan; Eason, Jacqueline; Godwin, Andrew K.; Remon, Marie-Alice; Moncoutier, Virginie; Gauthier-Villars, Marion; Lasset, Christine; Giraud, Sophie; Hardouin, Agnès; Berthet, Pascaline; Sobol, Hagay; Eisinger, François; Bressac de Paillerets, Brigitte; Caron, Olivier; Delnatte, Capucine; Goldgar, David; Miron, Alex; Ozcelik, Hilmi; Buys, Saundra; Southey, Melissa C.; Terry, Mary Beth; Singer, Christian F.; Dressler, Anne-Catharina; Tea, Muy-Kheng; Hansen, Thomas V.O.; Johannsson, Oskar; Piedmonte, Marion; Rodriguez, Gustavo C.; Basil, Jack B.; Blank, Stephanie; Toland, Amanda E.; Montagna, Marco; Isaacs, Claudine; Blanco, Ignacio; Gayther, Simon A.; Moysich, Kirsten B.; Schmutzler, Rita K.; Wappenschmidt, Barbara; Engel, Christoph; Meindl, Alfons; Ditsch, Nina; Arnold, Norbert; Niederacher, Dieter; Sutter, Christian; Gadzicki, Dorothea; Fiebig, Britta; Caldes, Trinidad; Laframboise, Rachel; Nevanlinna, Heli; Chen, Xiaoqing; Beesley, Jonathan; Spurdle, Amanda B.; Neuhausen, Susan L.; Ding, Yuan C.; Couch, Fergus J.; Wang, Xianshu; Peterlongo, Paolo; Manoukian, Siranoush; Bernard, Loris; Radice, Paolo; Easton, Douglas F.; Chenevix-Trench, Georgia; Antoniou, Antonis C.; Stoppa-Lyonnet, Dominique; Mazoyer, Sylvie; Sinilnikova, Olga M.

    2011-01-01

    Mutations in the BRCA1 gene substantially increase a woman's lifetime risk of breast cancer. However, there is great variation in this increase in risk with several genetic and non-genetic modifiers identified. The BRCA1 protein plays a central role in DNA repair, a mechanism that is particularly instrumental in safeguarding cells against tumorigenesis. We hypothesized that polymorphisms that alter the expression and/or function of BRCA1 carried on the wild-type (non-mutated) copy of the BRCA1 gene would modify the risk of breast cancer in carriers of BRCA1 mutations. A total of 9874 BRCA1 mutation carriers were available in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) for haplotype analyses of BRCA1. Women carrying the rare allele of single nucleotide polymorphism rs16942 on the wild-type copy of BRCA1 were at decreased risk of breast cancer (hazard ratio 0.86, 95% confidence interval 0.77–0.95, P = 0.003). Promoter in vitro assays of the major BRCA1 haplotypes showed that common polymorphisms in the regulatory region alter its activity and that this effect may be attributed to the differential binding affinity of nuclear proteins. In conclusion, variants on the wild-type copy of BRCA1 modify risk of breast cancer among carriers of BRCA1 mutations, possibly by altering the efficiency of BRCA1 transcription. PMID:21890493

  10. Genome assembly of the fungus Cochliobolus miyabeanus, and transcriptome analysis during early stages of infection on American wild rice (Zizania palustris L.)

    USDA-ARS?s Scientific Manuscript database

    Cochliobolus miyabeanus causes a severe, yield-reducing leaf spot disease on rice (Oryza sativa) and two North American specialty crops, American wildrice (Zizania palustris) and switchgrass (Panicum virgatum). Despite the importance of the pathogen in wildrice, little is known about mechanisms of p...

  11. Gene flow and population structure of a common agricultural wild species (Microtus agrestis) under different land management regimes

    PubMed Central

    Marchi, C; Andersen, L W; Damgaard, C; Olsen, K; Jensen, T S; Loeschcke, V

    2013-01-01

    The impact of landscape structure and land management on dispersal of populations of wild species inhabiting the agricultural landscape was investigated focusing on the field vole (Microtus agrestis) in three different areas in Denmark using molecular genetic markers. The main hypotheses were the following: (i) organic farms act as genetic sources and diversity reservoirs for species living in agricultural areas and (ii) gene flow and genetic structure in the agricultural landscape are influenced by the degree of landscape complexity and connectivity. A total of 443 individual voles were sampled within 2 consecutive years from two agricultural areas and one relatively undisturbed grassland area. As genetic markers, 15 polymorphic microsatellite loci (nuclear markers) and the central part of the cytochrome-b (mitochondrial sequence) were analysed for all samples. The results indicate that management (that is, organic or conventional management) was important for genetic population structure across the landscape, but that landscape structure was the main factor shaping gene flow and genetic diversity. More importantly, the presence of organically managed areas did not act as a genetic reservoir for conventional areas, instead the most important predictor of effective population size was the amount of unmanaged available habitat (core area). The relatively undisturbed natural area showed a lower level of genetic structuring and genetic diversity compared with the two agricultural areas. These findings altogether suggest that political decisions for supporting wildlife friendly land management should take into account both management and landscape structure factors. PMID:23900396

  12. Genetic and comparative genomics mapping reveals that a powdery mildew resistance gene Ml3D232 originating from wild emmer co-segregates with an NBS-LRR analog in common wheat (Triticum aestivum L.).

    PubMed

    Zhang, Hongtao; Guan, Haiying; Li, Jingting; Zhu, Jie; Xie, Chaojie; Zhou, Yilin; Duan, Xiayu; Yang, Tsomin; Sun, Qixin; Liu, Zhiyong

    2010-11-01

    Powdery mildew caused by Blumeria graminis f. sp. tritici is one of the most important wheat diseases worldwide and breeding for resistance using diversified disease resistance genes is the most promising approach to prevent outbreaks of powdery mildew. A powdery mildew resistance gene, originating from wild emmer wheat (Triticum turgidum var. dicoccoides) accessions collected from Israel, has been transferred into the hexaploid wheat line 3D232 through crossing and backcrossing. Inoculation results with 21 B. graminis f. sp. tritici races indicated that 3D232 is resistant to all of the powdery mildew isolates tested. Genetic analyses of 3D232 using an F(2) segregating population and F(3) families indicated that a single dominant gene, Ml3D232, confers resistance in the host seedling stage. By applying molecular markers and bulked segregant analysis (BSA), we have identified polymorphic simple sequence repeats (SSR), expressed sequence tags (EST) and derived sequence tagged site (STS) markers to determine that the Ml3D232 is located on chromosome 5BL bin 0.59-0.76. Comparative genetic analyses using mapped EST markers and genome sequences of rice and Brachypodium established co-linearity of the Ml3D232 genomic region with a 1.4 Mb genomic region on Brachypodium distachyon chromosome 4, and a 1.2 Mb contig located on the Oryza sativa chromosome 9. Our comparative approach enabled us to develop new EST-STS markers and to delimit the genomic region carrying Ml3D232 to a 0.8 cM segment that is collinear with a 558 kb region on B. distachyon. Eight EST markers, including an NBS-LRR analog, co-segregated with Ml3D232 to provide a target site for fine genetic mapping, chromosome landing and map-based cloning of the powdery mildew resistance gene. This newly developed common wheat germplasm provides broad-spectrum resistance to powdery mildew and a valuable resource for wheat breeding programs.

  13. Common Genetic Pathways Regulate Organ-Specific Infection-Related Development in the Rice Blast Fungus[W

    PubMed Central

    Tucker, Sara L.; Besi, Maria I.; Galhano, Rita; Franceschetti, Marina; Goetz, Stephan; Lenhert, Steven; Osbourn, Anne; Sesma, Ane

    2010-01-01

    Magnaporthe oryzae is the most important fungal pathogen of rice (Oryza sativa). Under laboratory conditions, it is able to colonize both aerial and underground plant organs using different mechanisms. Here, we characterize an infection-related development in M. oryzae produced on hydrophilic polystyrene (PHIL-PS) and on roots. We show that fungal spores develop preinvasive hyphae (pre-IH) from hyphopodia (root penetration structures) or germ tubes and that pre-IH also enter root cells. Changes in fungal cell wall structure accompanying pre-IH are seen on both artificial and root surfaces. Using characterized mutants, we show that the PMK1 (for pathogenicity mitogen-activated protein kinase 1) pathway is required for pre-IH development. Twenty mutants with altered pre-IH differentiation on PHIL-PS identified from an insertional library of 2885 M. oryzae T-DNA transformants were found to be defective in pathogenicity. The phenotypic analysis of these mutants revealed that appressorium, hyphopodium, and pre-IH formation are genetically linked fungal developmental processes. We further characterized one of these mutants, M1373, which lacked the M. oryzae ortholog of exportin-5/Msn5p (EXP5). Mutants lacking EXP5 were much less virulent on roots, suggesting an important involvement of proteins and/or RNAs transported by EXP5 during M. oryzae root infection. PMID:20348434

  14. Identification of common inhibitors of wild-type and T315I mutant of BCR-ABL through the parallel structure-based virtual screening

    NASA Astrophysics Data System (ADS)

    Park, Hwangseo; Hong, Seunghee; Hong, Sungwoo

    2012-08-01

    Although the constitutively activated break-point cluster region-Abelson (BCR-ABL) tyrosine kinase was well known to be responsible for chronic myelogenous leukemia (CML), the existence of drug-resistant mutants of BCR-ABL has made it difficult to develop effective anti-CML drugs. Here, we report the first example for a successful application of the structure-based virtual screening to identify two common inhibitors equipotent for the wild type and the most drug-resistant T315I mutant of BCR-ABL. Because both inhibitors were screened for having desirable physicochemical properties as a drug candidate and revealed micromolar inhibitory activities, they deserve consideration for further development by structure-activity relationship (SAR) studies to optimize the anti-CML activity. We also address the structural features relevant to the stabilizations of the identified inhibitors in the ATP-binding sites. The results indicate that the inhibitors should be less stabilized by the hydrogen-bond interactions with the change of the receptor from the wild type to T315I mutant due to the replacement of the hydroxy group with the ethyl moiety in the ATP-binding site. Nonetheless, the inhibitors are found to be capable of maintaining the potency for the mutant through the strengthening of hydrophobic interactions to the extent sufficient to compensate for the loss of some hydrogen bonds. This differential binding mode may serve as key information for designing new common inhibitors of the wild type and T315I mutant of BCR-ABL.

  15. Evidence for Directional Selection at a Novel Major Histocompatibility Class I Marker in Wild Common Frogs (Rana temporaria) Exposed to a Viral Pathogen (Ranavirus)

    PubMed Central

    Teacher, Amber G. F.; Garner, Trenton W. J.; Nichols, Richard A.

    2009-01-01

    Whilst the Major Histocompatibility Complex (MHC) is well characterized in the anuran Xenopus, this region has not previously been studied in another popular model species, the common frog (Rana temporaria). Nor, to date, have there been any studies of MHC in wild amphibian host-pathogen systems. We characterise an MHC class I locus in the common frog, and present primers to amplify both the whole region, and specifically the antigen binding region. As no more than two expressed haplotypes were found in over 400 clones from 66 individuals, it is likely that there is a single class I locus in this species. This finding is consistent with the single class I locus in Xenopus, but contrasts with the multiple loci identified in axolotls, providing evidence that the diversification of MHC class I into multiple loci likely occurred after the Caudata/Anura divergence (approximately 350 million years ago) but before the Ranidae/Pipidae divergence (approximately 230 mya). We use this locus to compare wild populations of common frogs that have been infected with a viral pathogen (Ranavirus) with those that have no history of infection. We demonstrate that certain MHC supertypes are associated with infection status (even after accounting for shared ancestry), and that the diseased populations have more similar supertype frequencies (lower FST) than the uninfected. These patterns were not seen in a suite of putatively neutral microsatellite loci. We interpret this pattern at the MHC locus to indicate that the disease has imposed selection for particular haplotypes, and hence that common frogs may be adapting to the presence of Ranavirus, which currently kills tens of thousands of amphibians in the UK each year. PMID:19240796

  16. Wild Marshmallows.

    ERIC Educational Resources Information Center

    Kallas, John N.

    1984-01-01

    Provides information for teaching a unit on wild plants, including resources to use, plants to learn, safety considerations, list of plants (with scientific name, edible parts, and uses), list of plants that might cause allergic reactions when eaten. Also describes the chickweed, bull thistle, and common mallow. (BC)

  17. Wild Marshmallows.

    ERIC Educational Resources Information Center

    Kallas, John N.

    1984-01-01

    Provides information for teaching a unit on wild plants, including resources to use, plants to learn, safety considerations, list of plants (with scientific name, edible parts, and uses), list of plants that might cause allergic reactions when eaten. Also describes the chickweed, bull thistle, and common mallow. (BC)

  18. Selenium concentrations and enzyme activities of glutathione metabolism in wild long-tailed ducks and common eiders.

    PubMed

    Franson, J Christian; Hoffman, David J; Flint, Paul L

    2011-06-01

    The relationships of selenium (Se) concentrations in whole blood with plasma activities of total glutathione peroxidase, Se-dependent glutathione peroxidase, and glutathione reductase were studied in long-tailed ducks (Clangula hyemalis) and common eiders (Somateria mollissima) sampled along the Beaufort Sea coast of Alaska, USA. Blood Se concentrations were >8 µg/g wet weight in both species. Linear regression revealed that the activities of total and Se-dependent glutathione peroxidase were significantly related to Se concentrations only in long-tailed ducks, raising the possibility that these birds were experiencing early oxidative stress.

  19. Selenium concentrations and enzyme activities of glutathione metabolism in wild long-tailed ducks and common eiders

    USGS Publications Warehouse

    Franson, J. Christian; Hoffman, David J.; Flint, Paul L.

    2011-01-01

    The relationships of selenium (Se) concentrations in whole blood with plasma activities of total glutathione peroxidase, Se-dependent glutathione peroxidase, and glutathione reductase were studied in long-tailed ducks (Clangula hyemalis) and common eiders (Somateria mollissima) sampled along the Beaufort Sea coast of Alaska, USA. Blood Se concentrations were >8 μg/g wet weight in both species. Linear regression revealed that the activities of total and Se-dependent glutathione peroxidase were significantly related to Se concentrations only in long-tailed ducks, raising the possibility that these birds were experiencing early oxidative stress.

  20. 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.

  1. Cross-species bacterial artificial chromosome (BAC) library screening via overgo-based hybridization and BAC-contig mapping of a yield enhancement quantitative trait locus (QTL) yld1.1 in the Malaysian wild rice Oryza rufipogon.

    PubMed

    Song, Beng-Kah; Nadarajah, Kalaivani; Romanov, Michael N; Ratnam, Wickneswari

    2005-01-01

    The construction of BAC-contig physical maps is an important step towards a partial or ultimate genome sequence analysis. Here, we describe our initial efforts to apply an overgo approach to screen a BAC library of the Malaysian wild rice species, Oryza rufipogon. Overgo design is based on repetitive element masking and sequence uniqueness, and uses short probes (approximately 40 bp), making this method highly efficient and specific. Pairs of 24-bp oligos that contain an 8-bp overlap were developed from the publicly available genomic sequences of the cultivated rice, O. sativa, to generate 20 overgo probes for a 1-Mb region that encompasses a yield enhancement QTL yld1.1 in O. rufipogon. The advantages of a high similarity in melting temperature, hybridization kinetics and specific activities of overgos further enabled a pooling strategy for library screening by filter hybridization. Two pools of ten overgos each were hybridized to high-density filters representing the O. rufipogon genomic BAC library. These screening tests succeeded in providing 69 PCR-verified positive hits from a total of 23,040 BAC clones of the entire O. rufipogon library. A minimal tilling path of clones was generated to contribute to a fully covered BAC-contig map of the targeted 1-Mb region. The developed protocol for overgo design based on O. sativa sequences as a comparative genomic framework, and the pooled overgo hybridization screening technique are suitable means for high-resolution physical mapping and the identification of BAC candidates for sequencing.

  2. Seeing Red: The Origin of Grain Pigmentation in US Weedy Rice

    PubMed Central

    Gross, Briana L.; Reagon, Michael; Hsu, Shih-Chung; Caicedo, Ana L.; Jia, Yulin; Olsen, Kenneth M.

    2010-01-01

    Weedy forms of crop species infest agricultural fields worldwide and are a leading cause of crop losses, yet little is known about how these weeds evolve. Red rice (Oryza sativa), a major weed of cultivated rice fields in the US, is recognized by the dark-pigmented grain that gives it its common name. Studies using neutral molecular markers have indicated a close relationship between US red rice and domesticated rice, suggesting that the weed may have originated through reversion of domesticated rice to a feral form. We have tested this reversion hypothesis by examining molecular variation at Rc, the regulatory gene responsible for grain pigmentation differences between domesticated and wild rice. Loss-of-function mutations at Rc account for the absence of proanthocyanidin pigments in cultivated rice grains, and the major rc domestication allele has been shown to be capable of spontaneous reversion to a functional form through additional mutations at the Rc locus. Using a diverse sample of 156 weedy, domesticated, and wild Oryzas, we analyzed DNA sequence variation at Rc and its surrounding 4 Mb genomic region. We find that reversion of domestication alleles does not account for the pigmented grains of weed accessions; moreover, we find that haplotypes characterizing the weed are either absent or very rare in cultivated rice. Sequences from genomic regions flanking Rc are consistent with a genomic footprint of the rc selective sweep in cultivated rice, and are compatible with a close relationship of red rice to Asian Oryzas that have never been cultivated in the US. PMID:20584133

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

    USDA-ARS?s Scientific Manuscript database

    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 (...

  4. Wild-type and mutant SOD1 share an aberrant conformation and a common pathogenic pathway in ALS

    PubMed Central

    Bosco, Daryl A.; Morfini, Gerardo; Karabacak, N. Murat; Song, Yuyu; Gros-Louis, Francois; Pasinelli, Piera; Goolsby, Holly; Fontaine, Benjamin A.; Lemay, Nathan; McKenna-Yasek, Diane; Frosch, Matthew P.; Agar, Jeffery N.; Julien, Jean-Pierre; Brady, Scott T.; Brown, Robert H.

    2010-01-01

    Many mutations confer upon copper/zinc superoxide dismutase-1 (SOD1) one or more toxic function(s) that impair motor neuron viability and cause familial amyotrophic lateral sclerosis (FALS). Using a conformation-specific antibody that detects misfolded SOD1 (C4F6), we demonstrate that oxidized WT-SOD1 and mutant-SOD1 share a conformational epitope that is not present in normal WT-SOD1. In a subset of human sporadic ALS (SALS) cases, motor neurons in the lumbosacral spinal cord displayed striking C4F6 immunoreactivity, denoting the presence of aberrant WT-SOD1 species. Recombinant, oxidized WT-SOD1 and WT-SOD1 immunopurified from SALS tissues inhibited kinesin-based fast axonal transport in a manner similar to FALS-linked mutant SOD1. Studies here suggest that WT-SOD1 can be pathogenic in SALS and identifies an SOD1-dependent pathogenic mechanism common to FALS and SALS. PMID:20953194

  5. A common Caatinga cactus, Pilosocereus gounellei, is an important ecotope of wild Triatoma brasiliensis populations in the Jaguaribe valley of northeastern Brazil.

    PubMed

    Valença-Barbosa, Carolina; Lima, Marli M; Sarquis, Otília; Bezerra, Claudia M; Abad-Franch, Fernando

    2014-06-01

    Triatoma brasiliensis is the most important vector of Chagas disease in the Caatinga eco-region of northeastern Brazil. Wild T. brasiliensis populations have been reported only from rocky outcrops. However, this species frequently infests/re-infests houses in rock-free sedimentary lowlands. We therefore hypothesized that it should also occupy other natural ecotopes. We show that a common Caatinga cactus, Pilosocereus gounellei, locally known as xiquexique, often harbors T. brasiliensis breeding colonies apparently associated with rodents (n = 44 cacti, infestation rate = 47.7%, 157 bugs captured). Our findings suggest that infested cacti might be involved in house re-infestation by T. brasiliensis in the Caatinga region. © The American Society of Tropical Medicine and Hygiene.

  6. Characterization of functional trait diversity among Indian cultivated and weedy rice populations

    PubMed Central

    Rathore, M.; Singh, Raghwendra; Kumar, B.; Chauhan, B. S.

    2016-01-01

    Weedy rice, a menace in rice growing areas globally, is biosimilar having attributes similar to cultivated and wild rice, and therefore is difficult to manage. A study was initiated to characterize the functional traits of 76 weedy rice populations and commonly grown rice cultivars from different agro-climatic zones for nine morphological, five physiological, and three phenological parameters in a field experiment under an augmented block design. Comparison between weedy and cultivated rice revealed a difference in duration (days) from panicle emergence to heading as the most variable trait and awn length as the least variable one, as evidenced from their coefficients of variation. The results of principal component analysis revealed the first three principal components to represent 47.3% of the total variation, which indicates an important role of transpiration, conductance, leaf-air temperature difference, days to panicle emergence, days to heading, flag leaf length, SPAD (soil-plant analysis development), grain weight, plant height, and panicle length to the diversity in weedy rice populations. The variations existing in weedy rice population are a major reason for its wider adaptability to varied environmental conditions and also a problem while trying to manage it. PMID:27072282

  7. Polyandry Is a Common Event in Wild Populations of the Tsetse Fly Glossina fuscipes fuscipes and May Impact Population Reduction Measures

    PubMed Central

    Bonomi, Angelica; Bassetti, Federico; Gabrieli, Paolo; Beadell, Jon; Falchetto, Marco; Scolari, Francesca; Gomulski, Ludvik M.; Regazzini, Eugenio; Ouma, Johnson O.; Caccone, Adalgisa; Okedi, Loyce M.; Attardo, Geoffrey M.; Guglielmino, Carmela R.; Aksoy, Serap; Malacrida, Anna R.

    2011-01-01

    Background Glossina fuscipes fuscipes is the main vector of human and animal trypanosomiasis in Africa, particularly in Uganda. Attempts to control/eradicate this species using biological methods require knowledge of its reproductive biology. An important aspect is the number of times a female mates in the wild as this influences the effective population size and may constitute a critical factor in determining the success of control methods. To date, polyandry in G.f. fuscipes has not been investigated in the laboratory or in the wild. Interest in assessing the presence of remating in Ugandan populations is driven by the fact that eradication of this species is at the planning stage in this country. Methodology/Principal Findings Two well established populations, Kabukanga in the West and Buvuma Island in Lake Victoria, were sampled to assess the presence and frequency of female remating. Six informative microsatellite loci were used to estimate the number of matings per female by genotyping sperm preserved in the female spermathecae. The direct count of the minimum number of males that transferred sperm to the spermathecae was compared to Maximum Likelihood and Bayesian probability estimates. The three estimates provided evidence that remating is common in the populations but the frequency is substantially different: 57% in Kabukanga and 33% in Buvuma. Conclusions/Significance The presence of remating, with females maintaining sperm from different mates, may constitute a critical factor in cases of re-infestation of cleared areas and/or of residual populations. Remating may enhance the reproductive potential of re-invading propagules in terms of their effective population size. We suggest that population age structure may influence remating frequency. Considering the seasonal demographic changes that this fly undergoes during the dry and wet seasons, control programmes based on SIT should release large numbers of sterile males, even in residual surviving target

  8. Polyandry is a common event in wild populations of the Tsetse fly Glossina fuscipes fuscipes and may impact population reduction measures.

    PubMed

    Bonomi, Angelica; Bassetti, Federico; Gabrieli, Paolo; Beadell, Jon; Falchetto, Marco; Scolari, Francesca; Gomulski, Ludvik M; Regazzini, Eugenio; Ouma, Johnson O; Caccone, Adalgisa; Okedi, Loyce M; Attardo, Geoffrey M; Guglielmino, Carmela R; Aksoy, Serap; Malacrida, Anna R

    2011-06-01

    Glossina fuscipes fuscipes is the main vector of human and animal trypanosomiasis in Africa, particularly in Uganda. Attempts to control/eradicate this species using biological methods require knowledge of its reproductive biology. An important aspect is the number of times a female mates in the wild as this influences the effective population size and may constitute a critical factor in determining the success of control methods. To date, polyandry in G.f. fuscipes has not been investigated in the laboratory or in the wild. Interest in assessing the presence of remating in Ugandan populations is driven by the fact that eradication of this species is at the planning stage in this country. Two well established populations, Kabukanga in the West and Buvuma Island in Lake Victoria, were sampled to assess the presence and frequency of female remating. Six informative microsatellite loci were used to estimate the number of matings per female by genotyping sperm preserved in the female spermathecae. The direct count of the minimum number of males that transferred sperm to the spermathecae was compared to Maximum Likelihood and Bayesian probability estimates. The three estimates provided evidence that remating is common in the populations but the frequency is substantially different: 57% in Kabukanga and 33% in Buvuma. The presence of remating, with females maintaining sperm from different mates, may constitute a critical factor in cases of re-infestation of cleared areas and/or of residual populations. Remating may enhance the reproductive potential of re-invading propagules in terms of their effective population size. We suggest that population age structure may influence remating frequency. Considering the seasonal demographic changes that this fly undergoes during the dry and wet seasons, control programmes based on SIT should release large numbers of sterile males, even in residual surviving target populations, in the dry season.

  9. PDH45 overexpressing transgenic tobacco and rice plants provide salinity stress tolerance via less sodium accumulation.

    PubMed

    Nath, Manoj; Garg, Bharti; Sahoo, Ranjan Kumar; Tuteja, Narendra

    2015-01-01

    Salinity stress negatively affects the crop productivity worldwide, including that of rice. Coping with these losses is a major concern for all countries. The pea DNA helicase, PDH45 is a unique member of helicase family involved in the salinity stress tolerance. However, the exact mechanism of the PDH45 in salinity stress tolerance is yet to be established. Therefore, the present study was conducted to investigate the mechanism of PDH45-mediated salinity stress tolerance in transgenic tobacco and rice lines along with wild type (WT) plants using CoroNa Green dye based sodium localization in root and shoot sections. The results showed that under salinity stress root and shoot of PDH45 overexpressing transgenic tobacco and rice accumulated less sodium (Na(+)) as compared to their respective WT. The present study also reports salinity tolerant (FL478) and salinity susceptible (Pusa-44) varieties of rice accumulated lowest and highest Na(+) level, respectively. All the varieties and transgenic lines of rice accumulate differential Na(+) ions in root and shoot. However, roots accumulate high Na(+) as compared to the shoots in both tobacco and rice transgenic lines suggesting that the Na(+) transport in shoot is somehow inhibited. It is proposed that the PDH45 is probably involved in the deposition of apoplastic hydrophobic barriers and consequently inhibit Na(+) transport to shoot and therefore confers salinity stress tolerance to PDH45 overexpressing transgenic lines. This study concludes that tobacco (dicot) and rice (monocot) transgenic plants probably share common salinity tolerance mechanism mediated by PDH45 gene.

  10. Does density influence relative growth performance of farm, wild and F1 hybrid Atlantic salmon in semi-natural and hatchery common garden conditions?

    PubMed

    Harvey, Alison C; Juleff, Gareth; Carvalho, Gary R; Taylor, Martin I; Solberg, Monica F; Creer, Simon; Dyrhovden, Lise; Matre, Ivar-Helge; Glover, Kevin A

    2016-07-01

    The conditions encountered by Atlantic salmon, Salmo salar L., in aquaculture are markedly different from the natural environment. Typically, farmed salmon experience much higher densities than wild individuals, and may therefore have adapted to living in high densities. Previous studies have demonstrated that farmed salmon typically outgrow wild salmon by large ratios in the hatchery, but these differences are much less pronounced in the wild. Such divergence in growth may be explained partly by the offspring of wild salmon experiencing higher stress and thus lower growth when compared under high-density farming conditions. Here, growth of farmed, wild and F1 hybrid salmon was studied at contrasting densities within a hatchery and semi-natural environment. Farmed salmon significantly outgrew hybrid and wild salmon in all treatments. Importantly, however, the reaction norms were similar across treatments for all groups. Thus, this study was unable to find evidence that the offspring of farmed salmon have adapted more readily to higher fish densities than wild salmon as a result of domestication. It is suggested that the substantially higher growth rate of farmed salmon observed in the hatchery compared with wild individuals may not solely be caused by differences in their ability to grow in high-density hatchery scenarios.

  11. Does density influence relative growth performance of farm, wild and F1 hybrid Atlantic salmon in semi-natural and hatchery common garden conditions?

    PubMed Central

    Juleff, Gareth; Carvalho, Gary R.; Taylor, Martin I.; Creer, Simon; Dyrhovden, Lise; Matre, Ivar-Helge; Glover, Kevin A.

    2016-01-01

    The conditions encountered by Atlantic salmon, Salmo salar L., in aquaculture are markedly different from the natural environment. Typically, farmed salmon experience much higher densities than wild individuals, and may therefore have adapted to living in high densities. Previous studies have demonstrated that farmed salmon typically outgrow wild salmon by large ratios in the hatchery, but these differences are much less pronounced in the wild. Such divergence in growth may be explained partly by the offspring of wild salmon experiencing higher stress and thus lower growth when compared under high-density farming conditions. Here, growth of farmed, wild and F1 hybrid salmon was studied at contrasting densities within a hatchery and semi-natural environment. Farmed salmon significantly outgrew hybrid and wild salmon in all treatments. Importantly, however, the reaction norms were similar across treatments for all groups. Thus, this study was unable to find evidence that the offspring of farmed salmon have adapted more readily to higher fish densities than wild salmon as a result of domestication. It is suggested that the substantially higher growth rate of farmed salmon observed in the hatchery compared with wild individuals may not solely be caused by differences in their ability to grow in high-density hatchery scenarios. PMID:27493772

  12. A knowledge-based molecular screen uncovers a broad-spectrum OsSWEET14 resistance allele to bacterial blight from wild rice.

    PubMed

    Hutin, Mathilde; Sabot, François; Ghesquière, Alain; Koebnik, Ralf; Szurek, Boris

    2015-11-01

    Transcription activator-like (TAL) effectors are type III-delivered transcription factors that enhance the virulence of plant pathogenic Xanthomonas species through the activation of host susceptibility (S) genes. TAL effectors recognize their DNA target(s) via a partially degenerate code, whereby modular repeats in the TAL effector bind to nucleotide sequences in the host promoter. Although this knowledge has greatly facilitated our power to identify new S genes, it can also be easily used to screen plant genomes for variations in TAL effector target sequences and to predict for loss-of-function gene candidates in silico. In a proof-of-principle experiment, we screened a germplasm of 169 rice accessions for polymorphism in the promoter of the major bacterial blight susceptibility S gene OsSWEET14, which encodes a sugar transporter targeted by numerous strains of Xanthomonas oryzae pv. oryzae. We identified a single allele with a deletion of 18 bp overlapping with the binding sites targeted by several TAL effectors known to activate the gene. We show that this allele, which we call xa41(t), confers resistance against half of the tested Xoo strains, representative of various geographic origins and genetic lineages, highlighting the selective pressure on the pathogen to accommodate OsSWEET14 polymorphism, and reciprocally the apparent limited possibilities for the host to create variability at this particular S gene. Analysis of xa41(t) conservation across the Oryza genus enabled us to hypothesize scenarios as to its evolutionary history, prior to and during domestication. Our findings demonstrate that resistance through TAL effector-dependent loss of S-gene expression can be greatly fostered upon knowledge-based molecular screening of a large collection of host plants.

  13. Transport characteristics and morphology of the colon and coprodeum in two wild birds of different habitats, the rock ptarmigan (Lagopus mutus) and the common murre (Uria aalge).

    PubMed

    Árnason, Sighvatur S; Elbrønd, Vibeke S; Laverty, Gary

    2015-09-01

    Dietary salt intake in domestic fowl affects epithelial transport and morphology of the lower intestine (colon and coprodeum). This study investigated lower intestinal morphology and transport activity in two wild bird species with natural diets containing either low or high salt. Tissues from rock ptarmigan (Lagopus mutus) and common murres (Uria aalge) were sampled for histology and electrophysiological analyses. The ptarmigan exists on a low salt diet, while the murre lives on a high protein and high salt diet. The ptarmigan colon and coprodeum had villi/folds and crypts and the epithelium contained absorptive epithelial cells, mitochondria-rich cells and goblet cells. The colon had significant amiloride-inhibitable Isc, 5-15 μA/cm(2), with no glucose-stimulated Isc, and no significant phloridzin inhibition. The coprodeum also had high amiloride-inhibitable Isc. This transport pattern corresponded to that of chickens on low-salt diets. However, the ptarmigan colon also had a significant lysine/leucine-stimulated Isc of 3±1.0 μA/cm(2). The short U. aalge colon was similar to that of ptarmigans, but with no villi. It demonstrated a significant lysine/leucine-stimulated Isc (11±3.5 μA/cm(2)) with no amiloride-inhibitable Isc, similar to the high-salt chicken colon, but with no Na(+)-glucose cotransport. The murre coprodeum was inert to all substances and showed high resistance (1000 Ω·cm(2)), with a multilayered squamous epithelium. Despite some variations possibly associated with dietary protein intake, we conclude that natural high and low salt diets in different avian species are associated with different lower intestinal transport patterns, providing for post-renal adjustments in ion and water excretion. Copyright © 2015 Elsevier Inc. All rights reserved.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  15. Suppressor of rid1 (SID1) shares common targets with RID1 on florigen genes to initiate floral transition in rice

    PubMed Central

    Shen, Jianqiang; Xiao, Jinghua; Wu, Changyin

    2017-01-01

    The transition from vegetative to reproductive growth is a critical process in the life cycle of higher plants. Previously, we cloned Rice Indeterminate 1 (RID1), which acts as the master switch for the transition from the vegetative to reproductive phase in rice. Although the photoperiod pathway of RID1 inducing expression of the florigen genes Hd3a and RFT1 via Ehd1 has been established, the alternative pathways for the essential flowering transition need to be further examined. Here, we identified a Suppressor of rid1 (SID1), which rescues the never-flowering phenotype of rid1. SID1 encodes an INDETERMINATE DOMAIN (IDD) transcription factor. Mutation in SID1 showed the delayed flowering phenotype. Gain-of-function of SID1, OsIDD1, or OsIDD6 could restore the rid1 to flowering. Further analyses showed SID1 and RID1 directly target the promoter regions of Hd3a and RFT1, two florigen genes in rice. Taken together, our results reveal an autonomous flowering pathway might be mediated by RID1, thereby controlling the phase transition from vegetative to reproductive development in rice. PMID:28234896

  16. Oryzabase. An integrated biological and genome information database for rice.

    PubMed

    Kurata, Nori; Yamazaki, Yukiko

    2006-01-01

    The aim of Oryzabase is to create a comprehensive view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information (http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp). The database contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. The anatomical description of rice development is unique and is the first known representation for rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. The systematic presentation of a large number of rice mutant and mutant trait genes is indispensable, as is description of research in wild strains, core collections, and their detailed characterization. Several genetic, physical, and expression maps with full genome and cDNA sequences are also combined with biological data in Oryzabase. These datasets, when pooled together, could provide a useful tool for gaining greater knowledge about the life cycle of rice, the relationship between phenotype and gene function, and rice genetic diversity. For exchanging community information, Oryzabase publishes the Rice Genetics Newsletter organized by the Rice Genetics Cooperative and provides a mailing service, rice-e-net/rice-net.

  17. Golden Rice is an effective source for vitamin A

    USDA-ARS?s Scientific Manuscript database

    Genetically engineered "Golden Rice" contains up to 35 ug Beta-carotene per gram of rice. It is important to determine the vitamin A equivalency of Golden Rice Beta-carotene to project the potential effect of this biofortified grain in rice-consuming populations that commonly exhibit low vitamin A s...

  18. Changes in rice allelopathy and rhizosphere microflora by inhibiting rice phenylalanine ammonia-lyase gene expression.

    PubMed

    Fang, Changxun; Zhuang, Yuee; Xu, Tiecheng; Li, Yingzhe; Li, Yue; Lin, Wenxiong

    2013-02-01

    Gene expression of phenylalanine ammonia-lyase (PAL) in allelopathic rice PI312777 was inhibited by RNA interference (RNAi). Transgenic rice showed lower levels of PAL gene expression and PAL activity than wild type rice (WT). The concentrations of phenolic compounds were lower in the root tissues and root exudates of transgenic rice than in those of wild type plants. When barndyardgrass (BYG) was used as the receiver plant, the allelopathic potential of transgenic rice was reduced. The sizes of the bacterial and fungal populations in rice rhizospheric soil at the 3-, 5-, and 7-leaf stages were estimated by using quantitative PCR (qPCR), which showed a decrease in both populations at all stages of leaf development analyzed. However, PI312777 had a larger microbial population than transgenic rice. In addition, in T-RFLP studies, 14 different groups of bacteria were detected in WT and only 6 were detected in transgenic rice. This indicates that there was less rhizospheric bacterial diversity associated with transgenic rice than with WT. These findings collectively suggest that PAL functions as a positive regulator of rice allelopathic potential.

  19. 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.

  20. Relative competitive ability of rice with strawhull and blackhull red rice biotypes

    USDA-ARS?s Scientific Manuscript database

    Weed interference depends largely upon the species composition of the weed community and an ability to compete with the cultured crop. Weedy red rice is a major weed pest of rice in the southern U.S. The focus of this study was to evaluate the competitive ability of rice against common, genetically ...

  1. Timing is everything: early degradation of abscission layer is associated with increased seed shattering in U.S. weedy rice

    PubMed Central

    2011-01-01

    Background Seed shattering, or shedding, is an important fitness trait for wild and weedy grasses. U.S. weedy rice (Oryza sativa) is a highly shattering weed, thought to have evolved from non-shattering cultivated ancestors. All U.S. weedy rice individuals examined to date contain a mutation in the sh4 locus associated with loss of shattering during rice domestication. Weedy individuals also share the shattering trait with wild rice, but not the ancestral shattering mutation at sh4; thus, how weedy rice reacquired the shattering phenotype is unknown. To establish the morphological basis of the parallel evolution of seed shattering in weedy rice and wild, we examined the abscission layer at the flower-pedicel junction in weedy individuals in comparison with wild and cultivated relatives. Results Consistent with previous work, shattering wild rice individuals possess clear, defined abscission layers at flowering, whereas non-shattering cultivated rice individuals do not. Shattering weedy rice from two separately evolved populations in the U.S. (SH and BHA) show patterns of abscission layer formation and degradation distinct from wild rice. Prior to flowering, the abscission layer has formed in all weedy individuals and by flowering it is already degrading. In contrast, wild O. rufipogon abscission layers have been shown not to degrade until after flowering has occurred. Conclusions Seed shattering in weedy rice involves the formation and degradation of an abscission layer in the flower-pedicel junction, as in wild Oryza, but is a developmentally different process from shattering in wild rice. Weedy rice abscission layers appear to break down earlier than wild abscission layers. The timing of weedy abscission layer degradation suggests that unidentified regulatory genes may play a critical role in the reacquisition of shattering in weedy rice, and sheds light on the morphological basis of parallel evolution for shattering in weedy and wild rice. PMID:21235796

  2. Little white lies: pericarp color provides insights into the origins and evolution of Southeast Asian weedy rice

    USDA-ARS?s Scientific Manuscript database

    Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy ...

  3. 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.

  4. Twin Valley, Wild Rice River, Minnesota. Addendum.

    DTIC Science & Technology

    1976-05-01

    David Rockwell, TSB, EPA Billy Fairless, CRL. EPA Gary Schenzel, Water Div, EPA Charlie Delos, Planning. EPA Michael Sullivan, Planning, EPA Harlan Hirt...Twin Valley-Norman 868 " WRR Hahnomen-Mahn 1,312 " WRR Felton-Clay 232 " Felton D. WRR Borup-Norman 128 " Ditch SBWRR Begon -Mahnomen 157 None Marsh WRR

  5. Polymorphism of a complex resistance gene candidate family in wild populations of common bean (Phaseolus vulgaris) in Argentina: comparison with phenotypic resistance polymorphism.

    PubMed

    De Meaux, J; Cattan-Toupance, I; Lavigne, C; Langin, T; Neema, C

    2003-01-01

    Fifteen populations of wild bean (Phaseolus vulgaris), located in three provinces in Argentina, were analysed for their polymorphism for a complex resistance gene candidate (RGC) family clustered on the genome and for resistance phenotypes to strains of Colletotrichum lindemuthianum. Results indicate that RGC polymorphism is high. Population structure obtained for markers related to resistance was compared to population structure obtained for RAPD markers in order to infer the evolutionary forces driving polymorphism for resistance in wild populations at both molecular and phenotypic levels. Hierarchical analysis of differentiation showed that, within provinces, populations were differentiated for RAPD as well as for molecular and phenotypic markers of resistance. In contrast, provinces were differentiated only for RAPD and RGC markers and not for resistance phenotypes. The discrepancies found between diversity structures for molecular markers (RAPD and RGCs) and for resistance phenotypes suggest an effect of selection and indicate that diversity for resistance may not be driven by the same selective forces at the molecular and phenotypic levels. We further discuss whether specific selective forces are exerted on RGC markers and underline the importance of spatial scale of analysis for demonstrating an impact of selection.

  6. The tomato wilt fungus Fusarium oxysporum f. sp. lycopersici shares common ancestors with nonpathogenic F. oxysporum isolated from wild tomatoes in the Peruvian Andes.

    PubMed

    Inami, Keigo; Kashiwa, Takeshi; Kawabe, Masato; Onokubo-Okabe, Akiko; Ishikawa, Nobuko; Pérez, Enrique Rodríguez; Hozumi, Takuo; Caballero, Liliana Aragón; de Baldarrago, Fatima Cáceres; Roco, Mauricio Jiménez; Madadi, Khalid A; Peever, Tobin L; Teraoka, Tohru; Kodama, Motoichiro; Arie, Tsutomu

    2014-01-01

    Fusarium oxysporum is an ascomycetous fungus that is well-known as a soilborne plant pathogen. In addition, a large population of nonpathogenic F. oxysporum (NPF) inhabits various environmental niches, including the phytosphere. To obtain an insight into the origin of plant pathogenic F. oxysporum, we focused on the tomato (Solanum lycopersicum) and its pathogenic F. oxysporum f. sp. lycopersici (FOL). We collected F. oxysporum from wild and transition Solanum spp. and modern cultivars of tomato in Chile, Ecuador, Peru, Mexico, Afghanistan, Italy, and Japan, evaluated the fungal isolates for pathogenicity, VCG, mating type, and distribution of SIX genes related to the pathogenicity of FOL, and constructed phylogenies based on ribosomal DNA intergenic spacer sequences. All F. oxysporum isolates sampled were genetically more diverse than FOL. They were not pathogenic to the tomato and did not carry SIX genes. Certain NPF isolates including those from wild Solanum spp. in Peru were grouped in FOL clades, whereas most of the NPF isolates were not. Our results suggested that the population of NPF isolates in FOL clades gave rise to FOL by gaining pathogenicity.

  7. The Tomato Wilt Fungus Fusarium oxysporum f. sp. lycopersici shares Common Ancestors with Nonpathogenic F. oxysporum isolated from Wild Tomatoes in the Peruvian Andes

    PubMed Central

    Inami, Keigo; Kashiwa, Takeshi; Kawabe, Masato; Onokubo-Okabe, Akiko; Ishikawa, Nobuko; Pérez, Enrique Rodríguez; Hozumi, Takuo; Caballero, Liliana Aragón; de Baldarrago, Fatima Cáceres; Roco, Mauricio Jiménez; Madadi, Khalid A.; Peever, Tobin L.; Teraoka, Tohru; Kodama, Motoichiro; Arie, Tsutomu

    2014-01-01

    Fusarium oxysporum is an ascomycetous fungus that is well-known as a soilborne plant pathogen. In addition, a large population of nonpathogenic F. oxysporum (NPF) inhabits various environmental niches, including the phytosphere. To obtain an insight into the origin of plant pathogenic F. oxysporum, we focused on the tomato (Solanum lycopersicum) and its pathogenic F. oxysporum f. sp. lycopersici (FOL). We collected F. oxysporum from wild and transition Solanum spp. and modern cultivars of tomato in Chile, Ecuador, Peru, Mexico, Afghanistan, Italy, and Japan, evaluated the fungal isolates for pathogenicity, VCG, mating type, and distribution of SIX genes related to the pathogenicity of FOL, and constructed phylogenies based on ribosomal DNA intergenic spacer sequences. All F. oxysporum isolates sampled were genetically more diverse than FOL. They were not pathogenic to the tomato and did not carry SIX genes. Certain NPF isolates including those from wild Solanum spp. in Peru were grouped in FOL clades, whereas most of the NPF isolates were not. Our results suggested that the population of NPF isolates in FOL clades gave rise to FOL by gaining pathogenicity. PMID:24909710

  8. 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.

  9. 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

  10. Genetic and physiological analysis of a novel type of interspecific hybrid weakness in rice.

    PubMed

    Chen, Chen; Chen, Hao; Shan, Jun-Xiang; Zhu, Mei-Zhen; Shi, Min; Gao, Ji-Ping; Lin, Hong-Xuan

    2013-05-01

    Hybrid weakness is an important reproductive barrier that hinders genetic exchange between different species at the post-zygotic stage. However, our understanding of the molecular mechanisms underlying hybrid weakness is limited. In this study, we report discovery of a novel interspecific hybrid weakness in a rice chromosome segment substitution line (CSSL) library derived from a cross between the indica variety Teqing (Oryza sativa) and common wild rice (O. rufipogon). The dominant Hybrid weakness i1 (Hwi1) gene from wild rice is genetically incompatible with Teqing and induced a set of weakness symptoms, including growth suppression, yield decrease, impaired nutrient absorption, and the retardation of crown root initiation. Phytohormone treatment showed that salicylic acid (SA) could restore the height of plants expressing hybrid weakness, while other phytohormones appear to have little effect. Fine mapping indicated that Hwi1 is located in a tandem leucine-rich repeat receptor-like kinase (LRR-RLK) gene cluster. Within the 13.2-kb candidate region on the short arm of chromosome 11, there are two annotated LRR-RLK genes, LOC_Os11g07230 and LOC_Os11g07240. The Teqing allele of LOC_Os11g07230 and the wild rice allele of LOC_Os11g07240 encode predicted functional proteins. Based on the genetic inheritance of hybrid weakness, LOC_Os11g07240 is implicated as the candidate gene for Hwi1. Functional analysis of Hwi1 will expand our knowledge of the regulation of hybrid weakness in rice.

  11. 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.

  12. 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

  13. 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.

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    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.

  16. Nucleotide diversity of a genomic sequence similar to SHATTERPROOF (PvSHP1) in domesticated and wild common bean (Phaseolus vulgaris L.).

    PubMed

    Nanni, L; Bitocchi, E; Bellucci, E; Rossi, M; Rau, D; Attene, G; Gepts, P; Papa, R

    2011-12-01

    Evolutionary studies in plant and animal breeding are aimed at understanding the structure and organization of genetic variations of species. We have identified and characterized a genomic sequence in Phaseolus vulgaris of 1,200 bp (PvSHP1) that is homologous to SHATTERPROOF-1 (SHP1), a gene involved in control of fruit shattering in Arabidopsis thaliana. The PvSHP1 fragment was mapped to chromosome Pv06 in P. vulgaris and is linked to the flower and seed color gene V. Amplification of the PvSHP1 sequence from the most agronomically important legume species showed a high degree of interspecies diversity in the introns within the Phaseoleae, while the coding region was conserved across distant taxa. Sequencing of the PvSHP1 sequence in a sample of 91 wild and domesticated genotypes that span the geographic distribution of this species in the centers of origin showed that PvSHP1 is highly polymorphic and, therefore, particularly useful to further investigate the origin and domestication history of P. vulgaris. Our data confirm the gene pool structure seen in P. vulgaris along with independent domestication processes in the Andes and Mesoamerica; they provide additional evidence for a single domestication event in Mesoamerica. Moreover, our results support the Mesoamerican origin of this species. Finally, we have developed three indel-spanning markers that will be very useful for bean germplasm characterization, and particularly to trace the distribution of the domesticated Andean and Mesoamerican gene pools.

  17. Identification of rice sheath blight QTLs in a Bengal/O. nivara advanced backcross population

    USDA-ARS?s Scientific Manuscript database

    Rice wild relatives contain novel genes for important biotic and abiotic stresses. Rice sheath blight disease, caused by Rhizoctonia solani, is a very important disease of rice worldwide. We screened 67 accessions from 15 Oryza species, and identified seven moderately resistant accessions. Using the...

  18. 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

  19. 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.

  20. Rice Shaker Potassium Channel OsKAT1 Confers Tolerance to Salinity Stress on Yeast and Rice Cells1[OA

    PubMed Central

    Obata, Toshihiro; Kitamoto, Hiroko K.; Nakamura, Atsuko; Fukuda, Atsunori; Tanaka, Yoshiyuki

    2007-01-01

    We screened a rice (Oryza sativa L. ‘Nipponbare’) full-length cDNA expression library through functional complementation in yeast (Saccharomyces cerevisiae) to find novel cation transporters involved in salt tolerance. We found that expression of a cDNA clone, encoding the rice homolog of Shaker family K+ channel KAT1 (OsKAT1), suppressed the salt-sensitive phenotype of yeast strain G19 (Δena1–4), which lacks a major component of Na+ efflux. It also suppressed a K+-transport-defective phenotype of yeast strain CY162 (Δtrk1Δtrk2), suggesting the enhancement of K+ uptake by OsKAT1. By the expression of OsKAT1, the K+ contents of salt-stressed G19 cells increased during the exponential growth phase. At the linear phase, however, OsKAT1-expressing G19 cells accumulated less Na+ than nonexpressing cells, but almost the same K+. The cellular Na+ to K+ ratio of OsKAT1-expressing G19 cells remained lower than nonexpressing cells under saline conditions. Rice cells overexpressing OsKAT1 also showed enhanced salt tolerance and increased cellular K+ content. These functions of OsKAT1 are likely to be common among Shaker K+ channels because OsAKT1 and Arabidopsis (Arabidopsis thaliana) KAT1 were able to complement the salt-sensitive phenotype of G19 as well as OsKAT1. The expression of OsKAT1 was restricted to internodes and rachides of wild-type rice, whereas other Shaker family genes were expressed in various organs. These results suggest that OsKAT1 is involved in salt tolerance of rice in cooperation with other K+ channels by participating in maintenance of cytosolic cation homeostasis during salt stress and thus protects cells from Na+. PMID:17586689

  1. Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China.

    PubMed

    Sun, Jian; Qian, Qian; Ma, Dian-Rong; Xu, Zheng-Jin; Liu, Dan; Du, Hong-Bo; Chen, Wen-Fu

    2013-01-01

    As a weed of rice paddy fields, weedy rice has spread worldwide. In northern China, the expansion of weedy rice has been rapid over the past two decades. Its evolutionary history and adaptive mechanisms are poorly understood. Evolutionary relationships between northern weedy rice and rice cultivars were analyzed using presumed neutral markers sampled across the rice genome. Genes involved in rice domestication were evaluated for their potential roles in weedy rice adaptation. Seed longevity, a critical trait of weedy rice, was examined in an F(2) population derived from a cross between weedy rice and a rice cultivar to evaluate weedy rice adaptation and the potential effect of candidate genes. Weedy rice in northern China was not derived directly from closely related wild Oryza species or from the introgression of indica subspecies. Introgression with local cultivars, coupled with selection that maintained weedy identity, shaped the evolution of weedy rice in northern China. Weedy rice is a unique system with which to investigate how weedy plants adapt to an agricultural environment. Our finding that extensive introgression from local cultivars, combined with the continuing ability to maintain weedy genes, is characteristic of weedy rice in northern China provides a clue for the field control of weedy rice. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

  2. 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.

  3. The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice

    PubMed Central

    Choi, Jae Young; Platts, Adrian E.; Fuller, Dorian Q.; Hsing (邢禹依), Yue-Ie; Wing, Rod A.

    2017-01-01

    Abstract The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1–24.1 ka, which is an order of magnitude older then the earliest archeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 ka and archeological evidence for early wild rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated indica and aus rice. PMID:28087768

  4. Evidence for common ancestry among viruses isolated from wild birds in Beringia and highly pathogenic intercontinental reassortant H5N1 and H5N2 influenza A viruses

    USGS Publications Warehouse

    Ramey, Andy M.; Reeves, Andrew; Teslaa, Joshua L.; Nashold, Sean W.; Donnelly, Tyrone F.; Bahl, Justin; Hall, Jeffrey S.

    2016-01-01

    Highly pathogenic clade 2.3.4.4 H5N8, H5N2, and H5N1 influenza A viruses were first detected in wild, captive, and domestic birds in North America in November–December 2014. In this study, we used wild waterbird samples collected in Alaska prior to the initial detection of clade 2.3.4.4 H5 influenza A viruses in North America to assess the evidence for: (1) dispersal of highly pathogenic influenza A viruses from East Asia to North America by migratory birds via Alaska and (2) ancestral origins of clade 2.3.4.4 H5 reassortant viruses in Beringia. Although we did not detect highly pathogenic influenza A viruses in our sample collection from western Alaska, we did identify viruses that contained gene segments sharing recent common ancestry with intercontinental reassortant H5N2 and H5N1 viruses. Results of phylogenetic analyses and estimates for times of most recent common ancestry support migratory birds sampled in Beringia as maintaining viral diversity closely related to novel highly pathogenic influenza A virus genotypes detected in North America. Although our results do not elucidate the route by which highly pathogenic influenza A viruses were introduced into North America, genetic evidence is consistent with the hypothesized trans-Beringian route of introduction via migratory birds.

  5. Evidence for common ancestry among viruses isolated from wild birds in Beringia and highly pathogenic intercontinental reassortant H5N1 and H5N2 influenza A viruses.

    PubMed

    Ramey, Andrew M; Reeves, Andrew B; TeSlaa, Joshua L; Nashold, Sean; Donnelly, Tyrone; Bahl, Justin; Hall, Jeffrey S

    2016-06-01

    Highly pathogenic clade 2.3.4.4 H5N8, H5N2, and H5N1 influenza A viruses were first detected in wild, captive, and domestic birds in North America in November-December 2014. In this study, we used wild waterbird samples collected in Alaska prior to the initial detection of clade 2.3.4.4 H5 influenza A viruses in North America to assess the evidence for: (1) dispersal of highly pathogenic influenza A viruses from East Asia to North America by migratory birds via Alaska and (2) ancestral origins of clade 2.3.4.4 H5 reassortant viruses in Beringia. Although we did not detect highly pathogenic influenza A viruses in our sample collection from western Alaska, we did identify viruses that contained gene segments sharing recent common ancestry with intercontinental reassortant H5N2 and H5N1 viruses. Results of phylogenetic analyses and estimates for times of most recent common ancestry support migratory birds sampled in Beringia as maintaining viral diversity closely related to novel highly pathogenic influenza A virus genotypes detected in North America. Although our results do not elucidate the route by which highly pathogenic influenza A viruses were introduced into North America, genetic evidence is consistent with the hypothesized trans-Beringian route of introduction via migratory birds. Published by Elsevier B.V.

  6. Molecular evolution of the rice blast resistance gene Pi-ta in invasive weedy rice in the USA.

    PubMed

    Lee, Seonghee; Jia, Yulin; Jia, Melissa; Gealy, David R; Olsen, Kenneth M; Caicedo, Ana L

    2011-01-01

    The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus), which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta) found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH), suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s) required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta), not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing.

  7. Molecular Evolution of the Rice Blast Resistance Gene Pi-ta in Invasive Weedy Rice in the USA

    PubMed Central

    Lee, Seonghee; Jia, Yulin; Jia, Melissa; Gealy, David R.; Olsen, Kenneth M.; Caicedo, Ana L.

    2011-01-01

    The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus), which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta) found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH), suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s) required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta), not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing. PMID:22043312

  8. Glycaemic index of some commercially available rice and rice products in Great Britain.

    PubMed

    Ranawana, D V; Henry, C J K; Lightowler, H J; Wang, D

    2009-01-01

    The glycaemic response to nine types of rice (white basmati, brown basmati, white and brown basmati, easy-cook basmati, basmati and wild rice, long-grain rice, easy-cook long-grain rice, Thai red rice, Thai glutinous rice) and two types of rice vermicelli (Guilin rice vermicelli, Jiangxi rice vermicelli) commercially available in the United Kingdom were compared against a glucose standard in a non-blind, randomized, repeated-measure, crossover design trial. Fourteen healthy subjects (six males, eight females), mean age 38 (standard deviation 16) years and mean body mass index 21.3 (standard deviation 2.3) kg/m(2), were recruited for the study. Subjects were served portions of the test foods and a standard food (glucose), on separate occasions, each containing 50 g available carbohydrates. Capillary blood glucose was measured from finger-prick samples in fasted subjects (-5 and 0 min) and at 15, 30, 45, 60, 90 and 120 min after the consumption of each test food. For each type of food, its glycaemic index (GI) was calculated geometrically by expressing the incremental area under the blood glucose curve as a percentage of each subject's average incremental area under the blood glucose curve for the standard food. The 10 foods exhibited a range of GI values from 37 to 92. The study indicated that rice noodles, long-grain rice, easy-cook long-grain rice and white basmati rice were low-GI foods, whilst all of the other foods were medium-GI and high-GI foods. The information presented in this paper may be useful in helping people select low-GI foods from the customary foods consumed by the British and Asian populations.

  9. Wild Animals.

    ERIC Educational Resources Information Center

    Web Feet K-8, 2000

    2000-01-01

    This annotated subject guide to Web sites and other resources focuses on wild animals. Includes Web sites, CD-ROMs and software, videos, books, audios, magazines, and professional resources, as well as a class activity. (LRW)

  10. The genetics of domestication of rice bean, Vigna umbellata

    PubMed Central

    Isemura, Takehisa; Kaga, Akito; Tomooka, Norihiko; Shimizu, Takehiko; Vaughan, Duncan Alexander

    2010-01-01

    Background and Aims The Asian genus Vigna, to which four cultivated species (rice bean, azuki bean, mung bean and black gram) belong, is suitable for comparative genomics. The aims were to construct a genetic linkage map of rice bean, to identify the genomic regions associated with domestication in rice bean, and to compare these regions with those in azuki bean. Methods A genetic linkage map was constructed by using simple sequence repeat and amplified fragment length polymorphism markers in the BC1F1 population derived from a cross between cultivated and wild rice bean. Using this map, 31 domestication-related traits were dissected into quantitative trait loci (QTLs). The genetic linkage map and QTLs of rice bean were compared with those of azuki bean. Key Results A total of 326 markers converged into 11 linkage groups (LGs), corresponding to the haploid number of rice bean chromosomes. The domestication-related traits in rice bean associated with a few major QTLs distributed as clusters on LGs 2, 4 and 7. A high level of co-linearity in marker order between the rice bean and azuki bean linkage maps was observed. Major QTLs in rice bean were found on LG4, whereas major QTLs in azuki bean were found on LG9. Conclusions This is the first report of a genetic linkage map and QTLs for domestication-related traits in rice bean. The inheritance of domestication-related traits was so simple that a few major QTLs explained the phenotypic variation between cultivated and wild rice bean. The high level of genomic synteny between rice bean and azuki bean facilitates QTL comparison between species. These results provide a genetic foundation for improvement of rice bean; interchange of major QTLs between rice bean and azuki bean might be useful for broadening the genetic variation of both species. PMID:20880934

  11. 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.

  12. Association of Commercial Rice Varieties with Weedy Rice Accessions (Oryza sativa complex) in Pulau Pinang’s Rice Granary Area

    PubMed Central

    Hussain, Zainudin; Man, Azmi; Othman, Ahmad Sofiman

    2011-01-01

    Weedy rice (WR) is the most significant weed in direct-seeded fields. It has morphological characteristics similar to those of cultivated rice varieties. WR is more difficult to control than other weeds. We collected WR accessions from four sites within the Pulau Pinang rice growing areas. Thirty six different accessions were collected from each site: B, the northern site; P, the central site; A, the southern site; and N, the southwestern site. Wild rice (Oryza rufipogon), which grows in the sampled areas, was also collected together with four varieties (MR84, MR185, MR211 and MR219) that have been widely planted in these areas for a long period of time. The objective of this study was to compare the morphological characteristics of the WR accessions and cultivated rice. Twenty characteristics were observed for the comparison of WR accessions and rice cultivars. Morpho-matrix analyses allowed the specimens to be grouped to two main groups (A and B), based on a 95% dissimilarity matrix. Group A was subdivided into 7 subgroups consisting of a few WR accessions, wild rice and MR211 (control), and group B was subdivided to 10 subgroups consisting of other WR accessions and the 3 other control varieties. Dendrogram analysis indicated that the morphological traits used in this study were able to differentiate among the WR accessions and the cultivars, except for rice cultivar MR211 and WRA8, which grouped together in subgroup A2. STRUCTURE program analysis indicated that all individuals were distinguishable and were divided into 18 clusters. These results suggest that some genes of the WR accessions have been influenced by commercial varieties. The information gained from this study will be useful to develop rice weed management protocols and good agricultural practices to control WR in the future. PMID:24575213

  13. Wild birds as biological indicators of environmental pollution: antimicrobial resistance patterns of Escherichia coli and enterococci isolated from common buzzards (Buteo buteo).

    PubMed

    Radhouani, Hajer; Poeta, Patrícia; Gonçalves, Alexandre; Pacheco, Rui; Sargo, Roberto; Igrejas, Gilberto

    2012-06-01

    A total of 36 Escherichia coli and 31 enterococci isolates were recovered from 42 common buzzard faecal samples. The E. coli isolates showed high levels of resistance to streptomycin and tetracycline. The following resistance genes were detected: bla(TEM) (20 of 22 ampicillin-resistant isolates), tet(A) and/or tet(B) (16 of 27 tetracycline-resistant isolates), aadA1 (eight of 27 streptomycin-resistant isolates), cmlA (three of 15 chloramphenicol-resistant isolates), aac(3)-II with/without aac(3)-IV (all seven gentamicin-resistant isolates) and sul1 and/or sul2 and/or sul3 [all eight sulfamethoxazole/trimethoprim-resistant (SXT) isolates]. intI1 and intI2 genes were detected in four SXT-resistant isolates. The virulence-associated genes fimA (type 1 fimbriae), papC (P fimbriae) and aer (aerobactin) were detected in 61.1, 13.8 and 11.1% of the isolates, respectively. The isolates belonged to phylogroups A (47.2%), B1 (8.3%), B2 (13.9%) and D (30.5%). For the enterococci isolates, Enterococcus faecium was the most prevalent species (48.4%). High levels of tetracycline and erythromycin resistance were found among our isolates (87 and 81%, respectively). Most of the tetracycline-resistant strains carried the tet(M) and/or tet(L) genes. The erm(B) gene was detected in 80% of erythromycin-resistant isolates. The vat(D) and/or vat(E) genes were found in nine of the 17 quinupristin-dalfopristin-resistant isolates. The enterococcal isolates showing high-level resistance for kanamycin, gentamicin and streptomycin contained the aph(3')-IIIa, aac(6')-aph(2″) and ant(6)-Ia genes, respectively. This report reveals that common buzzards seem to represent an important reservoir, or at least a source, of multi-resistant E. coli and enterococci isolates, and consequently may represent a considerable hazard to human and animal health by transmission of these isolates to waterways and other environmental sources via their faecal deposits.

  14. Indica rice (Oryza sativa, BR29 and IR64).

    PubMed

    Datta, Karabi; Datta, Swapan Kumar

    2006-01-01

    Rice is the world's most important food crop. Indica-type rice provides the staple food for more than half of the world population. To satisfy the growing demand of the ever-increasing population, more sustained production of indica-type rice is needed. In addition, because of the high per capita consumption of indica rice, improvement of any traits including its nutritive value may have a significant positive health outcome for the rice-consuming population. Rice yield productivity is greatly affected by different biotic stresses, like diseases and insect pests, and abiotic stresses like drought, cold, and salinity. Attempts to improve resistance in rice to these stresses by conventional breeding through introgression of traits have limited success owing to a lack of resistance germplasm in the wild relatives. Gene transfer technology with genes from other sources can be used to make rice plants resistant or tolerant to insect pests, diseases, and different environmental stresses. For improving the nutritional value of the edible endosperm part of the rice, genes for increasing iron, beta-carotene, or better quality protein can be introduced in rice plants by genetic engineering. Different crops have been transformed using various gene transfer methods, such as protoplast transformation, biolistic, and Agrobacterium-mediated transformation. This chapter describes the Agrobacterium-mediated transformation protocol for indica-type rice. The selectable marker genes used are hygromycin phosphotransferase (hpt), neomycin phosphotransferase (nptII), or phosphomannose isomerase (pmi), and, accordingly, the selection agents are hygromycin, kanamycin (G418), or mannose, respectively.

  15. A rhamnose-deficient lipopolysaccharide mutant of Rhizobium sp. IRBG74 is defective in root colonization and beneficial interactions with its flooding-tolerant hosts Sesbania cannabina and wetland rice.

    PubMed

    Mitra, Shubhajit; Mukherjee, Arijit; Wiley-Kalil, Audrey; Das, Seema; Owen, Heather; Reddy, Pallavolu M; Ané, Jean-Michel; James, Euan K; Gyaneshwar, Prasad

    2016-10-01

    Rhizobium sp. IRBG74 develops a classical nitrogen-fixing symbiosis with the aquatic legume Sesbania cannabina (Retz.). It also promotes the growth of wetland rice (Oryza sativa L.), but little is known about the rhizobial determinants important for these interactions. In this study, we analyzed the colonization of S. cannabina and rice using a strain of Rhizobium sp. IRBG74 dually marked with β-glucuronidase and the green fluorescent protein. This bacterium colonized S. cannabina by crack entry and through root hair infection under flooded and non-flooded conditions, respectively. Rhizobium sp. IRBG74 colonized the surfaces of wetland rice roots, but also entered them at the base of lateral roots. It became endophytically established within intercellular spaces in the rice cortex, and intracellularly within epidermal and hypodermal cells. A mutant of Rhizobium sp. IRBG74 altered in the synthesis of the rhamnose-containing O-antigen exhibited significant defects, not only in nodulation and symbiotic nitrogen fixation with S. cannabina, but also in rice colonization and plant growth promotion. Supplementation with purified lipopolysaccharides from the wild-type strain, but not from the mutant, restored the beneficial colonization of rice roots, but not fully effective nodulation of S. cannabina Commonalities and differences in the rhizobial colonization of the roots of wetland legume and rice hosts are discussed.

  16. Wild turkey

    Treesearch

    William F. Moore; John C. Kilgo; William D. Carlisle; Michael B. Caudell

    2005-01-01

    Wild turkeys (Meleagris gallopavo) were once abundant throughout the southeast, but unregulated hunting and habitat destruction greatly reduced populations to a few thousand birds by 1930 (Hust and Dickson 1992). Though intensive restocking efforts beginning in the 1950s, protection from hunting, and reforestation, southeastern turkey populations...

  17. Correlation analysis of simulated MODIS vegetation indices and the red edge and rice agricultural parameter

    NASA Astrophysics Data System (ADS)

    Cheng, Qian; Wu, Xiuju

    2007-10-01

    In this study, Hyperspectral data of two variety of rice (common rice and hybrid rice) in whole growing stage during 2002 and 2003 was measured using the ASD FieldSpec UV/VNIR Spectroradiometer with resolution of 3 nm, and the LAI and leaf chlorophyll content of rice agricultural parameter were obtained. Analyses of the correlation between rice agricultural parameter, and hyperspectal data, normalized difference vegetation index (NDVI), enhanced vegetation index (EVI) and the red-edge position (REP) were studied. Results showed that a strong non-linear correlation was found between the rice LAI of two varieties and REP. The REP, EVI and NDVI were well related with LAI for the common rice, but the REP and EVI were more sensitive than the NDVI to rice LAI for the hybrid rice because of different body for two variety rice.

  18. Reciprocating Internal Combustion Engines (RICE) | New ...

    EPA Pesticide Factsheets

    2017-05-25

    RICE use pistons that alternatively move back and forth to convert pressure into rotating motion. They're commonly used at power and manufacturing plants to generate electricity and to power pumps and compressors.

  19. Direct and reverse pollen-mediated gene flow between GM rice and red rice weed

    PubMed Central

    Serrat, X.; Esteban, R.; Peñas, G.; Català, M. M.; Melé, E.; Messeguer, J.

    2013-01-01

    Potential risks of genetically modified (GM) crops must be identified before their commercialization, as happens with all new technologies. One of the major concerns is the proper risk assessment of adventitious presence of transgenic material in rice fields due to cross-pollination. Several studies have been conducted in order to quantify pollen-mediated gene flow from transgenic rice (Oryza sativa) to both conventional rice and red rice weed (O. sativa f. spontanea) under field conditions. Some of these studies reported GM pollen-donor rice transferring GM traits to red rice. However, gene flow also occurs in the opposite direction, in a phenomenon that we have called reverse gene flow, resulting in transgenic seeds that have incorporated the traits of wild red rice. We quantified reverse gene flow using material from two field trials. A molecular analysis based on amplified fragment length polymorphisms was carried out, being complemented with a phenotypic identification of red rice traits. In both field trials, the reverse gene flow detected was greater than the direct gene flow. The rate of direct gene flow varied according to the relative proportions of the donor (GM rice) and receptor (red rice) plants and was influenced by wind direction. The ecological impact of reverse gene flow is limited in comparison with that of direct gene flow because non-shattered and non-dormant seeds would be obtained in the first generation. Hybrid seed would remain in the spike and therefore most of it would be removed during harvesting. Nevertheless, this phenomenon must be considered in fields used for elite seed production and in developing countries where farmers often keep some seed for planting the following year. In these cases, there is a higher risk of GM red rice weed infestation increasing from year to year and therefore a proper monitoring plan needs to be established.

  20. Natural rice rhizospheric microbes suppress rice blast infections

    PubMed Central

    2014-01-01

    Background The natural interactions between plant roots and their rhizospheric microbiome are vital to plant fitness, modulating both growth promotion and disease suppression. In rice (Oryza sativa), a globally important food crop, as much as 30% of yields are lost due to blast disease caused by fungal pathogen Magnaporthe oryzae. Capitalizing on the abilities of naturally occurring rice soil bacteria to reduce M. oryzae infections could provide a sustainable solution to reduce the amount of crops lost to blast disease. Results Naturally occurring root-associated rhizospheric bacteria were isolated from California field grown rice plants (M-104), eleven of which were taxonomically identified by16S rRNA gene sequencing and fatty acid methyl ester (FAME) analysis. Bacterial isolates were tested for biocontrol activity against the devastating foliar rice fungal pathogen, M. oryzae pathovar 70–15. In vitro, a Pseudomonas isolate, EA105, displayed antibiosis through reducing appressoria formation by nearly 90% as well as directly inhibiting fungal growth by 76%. Although hydrogen cyanide (HCN) is a volatile commonly produced by biocontrol pseudomonads, the activity of EA105 seems to be independent of its HCN production. During in planta experiments, EA105 reduced the number of blast lesions formed by 33% and Pantoea agglomerans isolate, EA106 by 46%. Our data also show both EA105 and EA106 trigger jasmonic acid (JA) and ethylene (ET) dependent induced systemic resistance (ISR) response in rice. Conclusions Out of 11 bacteria isolated from rice soil, pseudomonad EA105 most effectively inhibited the growth and appressoria formation of M. oryzae through a mechanism that is independent of cyanide production. In addition to direct antagonism, EA105 also appears to trigger ISR in rice plants through a mechanism that is dependent on JA and ET signaling, ultimately resulting in fewer blast lesions. The application of native bacteria as biocontrol agents in combination with

  1. Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations found in North-eastern China revealed by simple sequence repeat (SSR) markers.

    PubMed

    Cao, Qianjin; Lu, Bao-Rong; Xia, Hui; Rong, Jun; Sala, Francesco; Spada, Alberto; Grassi, Fabrizio

    2006-12-01

    Weedy rice (Oryza sativa f. spontanea) is one of the most notorious weeds occurring in rice-planting areas worldwide. The objectives of this study are to determine the genetic diversity and differentiation of weedy rice populations from Liaoning Province in North-eastern China and to explore the possible origin of these weedy populations by comparing their genetic relationships with rice varieties (O. sativa) and wild rice (O. rufipogon) from different sources. Simple sequence repeat (SSR) markers were used to estimate the genetic diversity of 30 weedy rice populations from Liaoning, each containing about 30 individuals, selected rice varieties and wild O. rufipogon. Genetic differentiation and the relationships of weedy rice populations were analysed using cluster analysis (UPGMA) and principle component analysis (PCA). The overall genetic diversity of weedy rice populations from Liaoning was relatively high (H(e) = 0.313, I = 0.572), with about 35 % of the genetic variation found among regions. The Liaoning weedy rice populations were closely related to rice varieties from Liaoning and japonica varieties from other regions but distantly related to indica rice varieties and wild O. rufipogon. Weedy rice populations from Liaoning are considerably variable genetically and most probably originated from Liaoning rice varieties by mutation and intervarietal hybrids. Recent changes in farming practices and cultivation methods along with less weed management may have promoted the re-emergence and divergence of weedy rice in North-eastern China.

  2. Assessment of cultivated and wild, weedy rice lines to concurrent changes in CO2 concentration and air temperature: Determining traits for enhanced seed yield with increasing atmospheric CO2

    USDA-ARS?s Scientific Manuscript database

    Although a number of studies have examined intra-specific variability in growth and yield to projected atmospheric CO2 concentration, [CO2], none have compared the relative responses of cultivated and wild, weedy crop lines. We quantified the growth and seed yield response for three cultivated ("44...

  3. Elemental composition of Malawian rice.

    PubMed

    Joy, Edward J M; Louise Ander, E; Broadley, Martin R; Young, Scott D; Chilimba, Allan D C; Hamilton, Elliott M; Watts, Michael J

    2017-08-01

    Widespread potential dietary deficiencies of calcium (Ca), iron (Fe), iodine (I), selenium (Se) and zinc (Zn) have been identified in Malawi. Several deficiencies are likely to be compounded by high phytic acid (PA) consumption. Rice (Oryza sativa) is commonly consumed in some Malawian populations, and its mineral micronutrient content is important for food security. The considerable irrigation requirements and flooded conditions of paddy soils can also introduce or mobilise potentially toxic elements including arsenic (As), cadmium (Cd) and lead (Pb). The aim of this study was to determine the mineral composition of rice sampled from farmers' fields and markets in Malawi. Rice was sampled from 18 extension planning areas across Malawi with 21 white (i.e. polished) and 33 brown samples collected. Elemental composition was determined by inductively coupled plasma-mass spectrometry (ICP-MS). Arsenic speciation was performed using high-performance liquid chromatography (HPLC)-ICP-MS. Concentration of PA was determined using a PA-total phosphorus assay. Median total concentrations (mg kg(-1), dry weight) of elements important for human nutrition in brown and white rice, respectively, were: Ca = 66.5 and 37.8; Cu = 3.65 and 2.49; Fe = 22.1 and 7.2; I = 0.006 and <0.005; Mg = 1130 and 265; Mn = 18.2 and 9.6; Se = 0.025 and 0.028; and Zn = 17.0 and 14.4. In brown and white rice samples, respectively, median PA concentrations were 5438 and 1906 mg kg(-1), and median PA:Zn molar ratios were 29 and 13. Concentrations of potentially toxic elements (mg kg(-1), dry weight) in brown and white rice samples, respectively, were: As = 0.030 and 0.006; Cd  ≤ 0.002 and 0.006; Pb = 0.008 and 0.008. Approximately 95 % of As was found to be inorganic As, where this could be quantified. Malawian rice, like the more widely consumed staple grain maize, contains inadequate Ca, I, Se or Zn to meet dietary requirements. Biofortification strategies could

  4. Association of Rice and Rice-Product Consumption With Arsenic Exposure Early in Life.

    PubMed

    Karagas, Margaret R; Punshon, Tracy; Sayarath, Vicki; Jackson, Brian P; Folt, Carol L; Cottingham, Kathryn L

    2016-06-01

    Rice-a typical first food and major ingredient in various infant foods-contains inorganic arsenic (As), but the extent of As exposure from these foods has not been well characterized in early childhood. To determine the types and frequency of rice and rice-containing products consumed by infants in the first year of life and the association with As biomarker concentrations. Included were infants from singleton births of pregnant women enrolled in the New Hampshire Birth Cohort Study from 2011 to 2014 whose parents were interviewed during their first year of life. Enrolled women from selected clinics were aged 18 to 45 years, living in the same residence since their last menstrual period, in households served by a private water system, and had no plans to move during pregnancy. Data on infants' intake of rice and rice products were collected from interviews with their parents at 4, 8, and 12 months' follow-up and from a 3-day food diary at 12 months from March 2013 to August 2014. Infants' intake of rice and rice products. Total urinary As and the sum of As species measured using inductively coupled mass spectrometry and high-performance liquid chromatography with inductively coupled mass spectrometry. Commonly reported infant rice snacks were tested for As. We obtained dietary data on 759 of 951 infants (79.8% participation rate). Of these, 391 infants (51.7%) were male, and the mean (SD) gestational age was 39.4 (1.7) weeks. An estimated 80% were introduced to rice cereal during their first year. At 12 months, 32.6% of infants (42 of 129) were fed rice snacks. Among infants aged 12 months who did not eat fish or seafood, the geometric mean total urinary As concentrations were higher among those who ate infant rice cereal (9.53 µg/L) or rice snacks (4.97 µg/L) compared with those who did not eat rice or rice products (2.85 µg/L; all P < .01). Infant rice snacks contained between 36 and 568 ng/g of As and 5 to 201 ng/g of inorganic As. Our findings indicate

  5. Genetic shift in local rice populations during rice breeding programs in the northern limit of rice cultivation in the world.

    PubMed

    Fujino, Kenji; Obara, Mari; Ikegaya, Tomohito; Tamura, Kenichi

    2015-09-01

    The rapid accumulation of pre-existing mutations may play major roles in the establishment and shaping of adaptability for local regions in current rice breeding programs. The cultivated rice, Oryza sativa L., which originated from tropical regions, is now grown worldwide due to the concerted efforts of breeding programs. However, the process of establishing local populations and their origins remain unclear. In the present study, we characterized DNA polymorphisms in the rice variety KITAAKE from Hokkaido, one of the northern limits of rice cultivation in the world. Indel polymorphisms were attributed to transposable element-like insertions, tandem duplications, and non-TE deletions as the original mutation events in the NIPPONBARE and KITAAKE genomes. The allele frequencies of the KITAAKE alleles markedly shifted to the current variety types among the local population from Hokkaido in the last two decades. The KITAAKE alleles widely distributed throughout wild rice and cultivated rice over the world. These have accumulated in the local population from Hokkaido via Japanese landraces as the ancestral population of Hokkaido. These results strongly suggested that combinations of pre-existing mutations played a role in the establishment of adaptability. This approach using the re-sequencing of local varieties in unique environmental conditions will be useful as a genetic resource in plant breeding programs in local regions.

  6. Rice ( Oryza) hemoglobins

    PubMed Central

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

    2014-01-01

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

  7. Rice ( Oryza) hemoglobins.

    PubMed

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

    2014-01-01

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

  8. Relationship between disease resistance and rice oxalate oxidases in transgenic rice.

    PubMed

    Zhang, Xian Yong; Nie, Zhuan Hua; Wang, Wen Juan; Leung, David W M; Xu, Da Gao; Chen, Bai Ling; Chen, Zhe; Zeng, Lie Xian; Liu, E E

    2013-01-01

    Differential expression of rice oxalate oxidase genes (OsOxO1-4) in rice leaves (Oryza sativa L.) in response to biotic stress was assayed using RT-PCR. OsOxO4 was induced transiently at 12 h in plants inoculated with the pathogens of bacterial blight and that of the wounding control. Inoculation with the rice blast pathogen induced OsOxO2 expression compared to the mock spray control. Overexpressing OsOxO1 or OsOxO4 in rice resulted in elevated transcript levels of the respective transgene as well as OsOxO3 in leaves compared to that in untransformed wild type (WT). In a line of RNA-i transgenic rice plants (i-12), expression of all four OsOxO genes except that of OsOxO2 was severely inhibited. Oxalate oxidase (OxO, EC 1.2.3.4) activity in plants overexpressing OsOxO1 or OsOxO4 was substantially higher than that in WT and the RNA-i lines. It was found that transgenic rice plants with substantially higher OxO activity were not more resistant to rice blast and bacterial blight than WT. In contrast, some RNA-i lines with less OxO activity seemed to be more resistant to rice blast while some overexpressing lines were more susceptible to rice blast than WT. Therefore, OxO might not be a disease resistance factor in rice.

  9. [Safety of rice grains and mycotoxins - a historical review of yellow rice mycotoxicoses].

    PubMed

    Udagawa, Shun-ichi; Tatsuno, Takashi

    2004-01-01

    Aflatoxins, the most powerful mycotoxins, were brought to the attention fo the people in the early 1960s with the outbreak of the turkey "X" disease in England. However, the history of mycotoxin research in Japan began 100 years ago. In 1891, Sakaki demonstrated that moldy, unpolished rice was fatal to experimental animals, with symptoms indicating paralysis of the central nervous system (Shoshin-kakke). In 1920, Prof. I. Miyake and Dr. Takada first reported that Penicillium commune, which was known as a causal agent of "Mossy diseased rice" was found to be toxic to experimental animals by feeding the moldy rice to rabbits and rats.With such a historical background, taking the idea of "rice, fungus and toxin" as a working hypothesis, Miyake and his co-workers discovered the first sample of yellow rice grains from Taiwanese and domestic rice, from which was isolated a species of Penicillium and later identified it with P. citreonigrum (=P. toxicarium). The fungus produced a highly toxic metabolite, citreoviridin. Unfortunately because this study was published during wartime, it failed to alert the world to the potential or actual dangers of the toxicity of common molds. After World War II, Japanese people suffered for some years from a shortage in domestic rice production and depended on foreign countries to supply rice, which led to the toxicological screening on fungal isolates from polluted rice grains by Dr. Tsunoda and his co-workers. AMong the isolates from imported rice, there were two species of Penicillium which were particularly associated with high toxicity; P. islandicum responsible for brownish discolored rice, and P. citrinum responsible for yellowish rice. P. islandicum produces two hepatotoxic metabolites: luteoskyrin and cyclochlorotine, while a nephrotoxic of P. citrinum is citrinin. These toxicological characters, including the induction of cancer and chemical structures, were studied by Profs. uraguchi, Saito, Shibata, Tatsuno and their co

  10. Association of Rice and Rice-Product Consumption With Arsenic Exposure Early in Life

    PubMed Central

    Karagas, Margaret R.; Punshon, Tracy; Sayarath, Vicki; Jackson, Brian P.; Folt, Carol L.; Cottingham, Kathryn L.

    2016-01-01

    IMPORTANCE Rice—a typical first food and major ingredient in various infant foods—contains inorganic arsenic (As), but the extent of As exposure from these foods has not been well characterized in early childhood. OBJECTIVE To determine the types and frequency of rice and rice-containing products consumed by infants in the first year of life and the association with As biomarker concentrations. DESIGN, SETTING, AND PARTICIPANTS Included were infants from singleton births of pregnant women enrolled in the New Hampshire Birth Cohort Study from 2011 to 2014 whose parents were interviewed during their first year of life. Enrolled women from selected clinics were aged 18 to 45 years, living in the same residence since their last menstrual period, in households served by a private water system, and had no plans to move during pregnancy. Data on infants’ intake of rice and rice products were collected from interviews with their parents at 4, 8, and 12 months’ follow-up and from a 3-day food diary at 12 months from March 2013 to August 2014. EXPOSURES Infants’ intake of rice and rice products. MAIN OUTCOMES AND MEASURES Total urinary As and the sum of As species measured using inductively coupled mass spectrometry and high-performance liquid chromatography with inductively coupled mass spectrometry. Commonly reported infant rice snacks were tested for As. RESULTS We obtained dietary data on 759 of 951 infants (79.8% participation rate). Of these, 391 infants (51.7%) were male, and the mean (SD) gestational age was 39.4 (1.7) weeks. An estimated 80% were introduced to rice cereal during their first year. At 12 months, 32.6% of infants (42 of 129) were fed rice snacks. Among infants aged 12 months who did not eat fish or seafood, the geometric mean total urinary As concentrations were higher among those who ate infant rice cereal (9.53 μg/L) or rice snacks (4.97 μg/L) compared with those who did not eat rice or rice products (2.85 μg/L; all P < .01). Infant rice

  11. Lead in rice: analysis of baseline lead levels in market and field collected rice grains.

    PubMed

    Norton, Gareth J; Williams, Paul N; Adomako, Eureka E; Price, Adam H; Zhu, Yongguan; Zhao, Fang-Jie; McGrath, Steve; Deacon, Claire M; Villada, Antia; Sommella, Alessia; Lu, Ying; Ming, Lei; De Silva, P Mangala C S; Brammer, Hugh; Dasgupta, Tapash; Islam, M Rafiqul; Meharg, Andrew A

    2014-07-01

    In a large scale survey of rice grains from markets (13 countries) and fields (6 countries), a total of 1578 rice grain samples were analysed for lead. From the market collected samples, only 0.6% of the samples exceeded the Chinese and EU limit of 0.2 μg g(-1) lead in rice (when excluding samples collected from known contaminated/mine impacted regions). When evaluating the rice grain samples against the Food and Drug Administration's (FDA) provisional total tolerable intake (PTTI) values for children and pregnant women, it was found that only people consuming large quantities of rice were at risk of exceeding the PTTI from rice alone. Furthermore, 6 field experiments were conducted to evaluate the proportion of the variation in lead concentration in rice grains due to genetics. A total of 4 of the 6 field experiments had significant differences between genotypes, but when the genotypes common across all six field sites were assessed, only 4% of the variation was explained by genotype, with 9.5% and 11% of the variation explained by the environment and genotype by environment interaction respectively. Further work is needed to identify the sources of lead contamination in rice, with detailed information obtained on the locations and environments where the rice is sampled, so that specific risk assessments can be performed.

  12. Improving folate (vitamin B9) stability in biofortified rice through metabolic engineering.

    PubMed

    Blancquaert, Dieter; Van Daele, Jeroen; Strobbe, Simon; Kiekens, Filip; Storozhenko, Sergei; De Steur, Hans; Gellynck, Xavier; Lambert, Willy; Stove, Christophe; Van Der Straeten, Dominique

    2015-10-01

    Biofortification of staple crops could help to alleviate micronutrient deficiencies in humans. We show that folates in stored rice grains are unstable, which reduces the potential benefits of folate biofortification. We obtain folate concentrations that are up to 150 fold higher than those of wild-type rice by complexing folate to folate-binding proteins to improve folate stability, thereby enabling long-term storage of biofortified high-folate rice grains.

  13. Comparison on cellular mechanisms of iron and cadmium accumulation in rice: prospects for cultivating Fe-rich but Cd-free rice.

    PubMed

    Gao, Lei; Chang, Jiadong; Chen, Ruijie; Li, Hubo; Lu, Hongfei; Tao, Longxing; Xiong, Jie

    2016-12-01

    Iron (Fe) is essential for rice growth and humans consuming as their staple food but is often deficient because of insoluble Fe(III) in soil for rice growth and limited assimilation for human bodies, while cadmium (Cd) is non-essential and toxic for rice growth and humans if accumulating at high levels. Over-accumulated Cd can cause damage to human bodies. Selecting and breeding Fe-rich but Cd-free rice cultivars are ambitious, challenging and meaningful tasks for researchers. Although evidences show that the mechanisms of Fe/Cd uptake and accumulation in rice are common to some extent as a result of similar entry routes within rice, an increasing number of researchers have discovered distinct mechanisms between Fe/Cd uptake and accumulation in rice. This comprehensive review systematically elaborates and compares cellular mechanisms of Fe/Cd uptake and accumulation in rice, respectively. Mechanisms for maintaining Fe homeostasis and Cd detoxicification are also elucidated. Then, effects of different fertilizer management on Fe/Cd accumulation in rice are discussed. Finally, this review enumerates various approaches for reducing grain Cd accumulation and enhancing Fe content in rice. In summary, understanding of discrepant cellular mechanisms of Fe/Cd accumulation in rice provides guidance for cultivating Fe-fortified rice and has paved the way to develop rice that are tolerant to Cd stress, aiming at breeding Fe-rich but Cd-free rice.

  14. Nutritionally enhanced rice to combat malnutrition disorders of the poor.

    PubMed

    Potrykus, Ingo

    2003-06-01

    Major deficiency disorders, including vitamin A deficiency, are especially common in countries in which rice is the staple food. In response to the devastating effects of vitamin A deficiency, which may include blindness and, even death, "Golden Rice" has been developed to deliver this nutrient to those populations who need it most. The case of Golden Rice is used to demonstrate the challenges of radical GMO opposition, consumer acceptance, and regulation of biotechnology-derived foods.

  15. Golden Rice is an effective source of vitamin A.

    PubMed

    Tang, Guangwen; Qin, Jian; Dolnikowski, Gregory G; Russell, Robert M; Grusak, Michael A

    2009-06-01

    Genetically engineered "Golden Rice" contains up to 35 microg beta-carotene per gram of rice. It is important to determine the vitamin A equivalency of Golden Rice beta-carotene to project the potential effect of this biofortified grain in rice-consuming populations that commonly exhibit low vitamin A status. The objective was to determine the vitamin A value of intrinsically labeled dietary Golden Rice in humans. Golden Rice plants were grown hydroponically with heavy water (deuterium oxide) to generate deuterium-labeled [2H]beta-carotene in the rice grains. Golden Rice servings of 65-98 g (130-200 g cooked rice) containing 0.99-1.53 mg beta-carotene were fed to 5 healthy adult volunteers (3 women and 2 men) with 10 g butter. A reference dose of [13C10]retinyl acetate (0.4-1.0 mg) in oil was given to each volunteer 1 wk before ingestion of the Golden Rice dose. Blood samples were collected over 36 d. Our results showed that the mean (+/-SD) area under the curve for the total serum response to [2H]retinol was 39.9 +/- 20.7 microg x d after the Golden Rice dose. Compared with that of the [13C10]retinyl acetate reference dose (84.7 +/- 34.6 microg x d), Golden Rice beta-carotene provided 0.24-0.94 mg retinol. Thus, the conversion factor of Golden Rice beta-carotene to retinol is 3.8 +/- 1.7 to 1 with a range of 1.9-6.4 to 1 by weight, or 2.0 +/- 0.9 to 1 with a range of 1.0-3.4 to 1 by moles. Beta-carotene derived from Golden Rice is effectively converted to vitamin A in humans. This trial was registered at clinicaltrials.gov as NCT00680355.

  16. Conserving waste rice for wintering waterfowl in the Mississippi Alluvial Valley

    USGS Publications Warehouse

    Kross, J.P.; Kaminski, R.M.; Reinecke, K.J.; Pearse, A.T.

    2008-01-01

    Rice lost before or during harvest operations (hereafter waste rice) provides important food for waterfowl in the Mississippi Alluvial Valley, USA, but >70% of waste rice is lost during autumn. We conducted experiments in 19 production rice fields in Arkansas and Mississippi during autumns 2003 and 2004 to evaluate the ability of common postharvest practices (i.e., burn, mow, roll, disk, or standing stubble) to conserve waste rice. We detected a postharvest treatment effect and a positive effect of initial abundance of waste rice on late-autumn abundance of waste rice (P < 0.022). Standing stubble contained the greatest abundance of waste rice followed by burned, mowed, rolled, and disked stubble. We recommend standing stubble or burning to maximize waste rice abundance for wintering waterfowl.

  17. Conserving waste rice for wintering waterfowl in the Mississippi Alluvial Valley

    USGS Publications Warehouse

    Kross, J.P.; Kaminski, R.M.; Reinecke, K.J.; Pearse, A.T.

    2008-01-01

    Rice lost before or during harvest operations (hereafter waste rice) provides important food for waterfowl in the Mississippi Alluvial Valley, USA, but >70% of waste rice is lost during autumn. We conducted experiments in 19 production rice fields in Arkansas and Mississippi during autumns 2003 and 2004 to evaluate the ability of common postharvest practices (i.e., burn, mow, roll, disk, or standing stubble) to conserve waste rice. We detected a postharvest treatment effect and a positive effect of initial abundance of waste rice on late-autumn abundance of waste rice (P ??? 0.022). Standing stubble contained the greatest abundance of waste rice followed by burned, mowed, rolled, and disked stubble. We recommend standing stubble or burning to maximize waste rice abundance for wintering waterfowl.

  18. Rice Production and Marketing.

    ERIC Educational Resources Information Center

    Briers, Gary; Lee, Jasper S.

    This guide contains lesson plans for use in secondary programs of agricultural education in geographical areas in which rice is produced. Six units and 13 problem areas are organized into teaching plans that cover the broad nature of rice production. The six units are: (1) determining the importance and history of rice production; (2) determining…

  19. Enhanced disease resistance and drought tolerance in transgenic rice plants overexpressing protein elicitors from Magnaporthe oryzae.

    PubMed

    Wang, Zhenzhen; Han, Qiang; Zi, Qian; Lv, Shun; Qiu, Dewen; Zeng, Hongmei

    2017-01-01

    Exogenous application of the protein elicitors MoHrip1 and MoHrip2, which were isolated from the pathogenic fungus Magnaporthe oryzae (M. oryzae), was previously shown to induce a hypersensitive response in tobacco and to enhance resistance to rice blast. In this work, we successfully transformed rice with the mohrip1 and mohrip2 genes separately. The MoHrip1 and MoHrip2 transgenic rice plants displayed higher resistance to rice blast and stronger tolerance to drought stress than wild-type (WT) rice and the vector-control pCXUN rice. The expression of salicylic acid (SA)- and abscisic acid (ABA)-related genes was also increased, suggesting that these two elicitors may trigger SA signaling to protect the rice from damage during pathogen infection and regulate the ABA content to increase drought tolerance in transgenic rice. Trypan blue staining indicated that expressing MoHrip1 and MoHrip2 in rice plants inhibited hyphal growth of the rice blast fungus. Relative water content (RWC), water usage efficiency (WUE) and water loss rate (WLR) were measured to confirm the high capacity for water retention in transgenic rice. The MoHrip1 and MoHrip2 transgenic rice also exhibited enhanced agronomic traits such as increased plant height and tiller number.

  20. Ecotoxicology of Wild Mammals

    USGS Publications Warehouse

    2001-01-01

    An international group of 32 scientists has critically reviewed the scientific literature on exposure and effects of environmental contaminants in wild mammals. The underlying theme of this text is encompassed by the following four questions: What exactly do we know about environmental contaminants in mammals? What are the commonalities and differences between mammal orders/species in the effects that contaminants have? How and to what degree of accuracy can we predict the adverse effects of environmental contaminants on mammalian wildlife? How significant are contaminant insults compared with other density-independent and -dependent factors such as habitat loss, climatic factors and disease? The book is organized three topical sections including introductory chapters that provide a background on environmental contaminants and the mammalian orders, eight taxonomic chapters discussing all aspects of the exposure to and effects of contaminants in mammalian orders, and four thematic chapters that review and discuss generic issues including biomarkers, prediction and extrapolation of exposure and effects, hazard and risk assessment, and the relative significance of contaminants on mammals compared with other commonly encountered stressors. A final a summary chapter identifies phylogenetic trends, critical data gaps, and overarching research needs. Although the absolute number of toxicological studies in domesticated and wild mammals eclipses that wildlife species, a detailed examination of our knowledge base reveals that information for 'wild' birds is actually greater than that for 'wild' mammals. Of the various mammalian taxa, ecotoxicological data is most noticeably lacking for marsupials and monotremes. In contrast, rodents (comprising 43% of all mammal species) have been studied extensively, despite evidence of their tolerance to some organochlorine compounds, rodenticides, and even radionuclides. Mammalian species at greatest risk of exposure include those that

  1. 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.

  2. Comparative proteomics reveals differential induction of both biotic and abiotic stress response associated proteins in rice during Xanthomonas oryzae pv. oryzae infection.

    PubMed

    Kumar, Anirudh; Bimolata, Waikhom; Kannan, Monica; Kirti, P B; Qureshi, Insaf Ahmed; Ghazi, Irfan Ahmad

    2015-07-01

    Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight disease in rice and brutally affects the yield up to 50 % of total production. Here, we report a comparative proteomics analysis of total foliar protein isolated from infected rice leaves of susceptible Pusa Basmati 1 (PB1) and resistant Oryza longistaminata genotypes. Two-dimensional gel electrophoresis (2-DE) coupled with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) approaches identified 29 protein spots encoding unique proteins from both the genotypes. Identified proteins belonged to a large number of biological and molecular functions related to biotic and abiotic stress proteins which are potentially involved during Xoo infection. Biotic and abiotic stress-related proteins were induced during Xoo infection, indicating the activation of common stress pathway during bacterial blight infection. Candidate genes conferring tolerance against bacterial blight, which include germin-like protein, putative r40c1, cyclin-dependent kinase C, Ent-isokaur-15-ene synthase and glutathione-dependent dehydroascorbate reductase 1 (GSH-DHAR1), were also induced, with germin-like proteins induced only in the resistant rice genotype O. longistaminata. Energy, metabolism and hypothetical proteins were common among both the genotypes. Further, host defence/stress-related proteins were mostly expressed in resistant genotype O. longistaminata, indicating possible co-evolution of the pathogen and the wild rice, O. longistaminata.

  3. Avian influenza, domestic ducks and rice agriculture in Thailand

    PubMed Central

    Gilbert, Marius; Xiao, Xiangming; Chaitaweesub, Prasit; Kalpravidh, Wantanee; Premashthira, Sith; Boles, Stephen; Slingenbergh, Jan

    2008-01-01

    Highly pathogenic avian influenza (HPAI) caused by H5N1 viruses has become a global scale problem which first emerged in southern China and from there spread to other countries in Southeast and East Asia, where it was first confirmed in end 2003. In previous work, geospatial analyses demonstrated that free grazing ducks played critical role in the epidemiology of the disease in Thailand in the winter 2004/2005, both in terms of HPAI emergence and spread. This study explored the geographic association between free grazing duck census counts and current statistics on the spatial distribution of rice crops in Thailand, in particular the crop calendar of rice production. The analysis was carried out using both district level rice statistics and rice distribution data predicted with the aid of remote sensing, using a rice-detection algorithm. The results indicated a strong association between the number of free grazing ducks and the number of months during which second-crop rice harvest takes place, as well as with the rice crop intensity as predicted by remote sensing. These results confirmed that free grazing duck husbandry was strongly driven by agricultural land use and rice crop intensity, and that this later variable can be readily predicted using remote sensing. Analysis of rice cropping patterns may provide an indication of the location of populations of free grazing ducks in other countries with similar mixed duck and rice production systems and less detailed duck census data. Apart from free ranging ducks and rice cropping, the role of hydrology and seasonality of wetlands and water bodies in the HPAI risk analysis is also discussed in relation to the presumed dry season aggregation of wild waterfowl and aquatic poultry offering much scope for virus transmission. PMID:18418464

  4. Avian influenza, domestic ducks and rice agriculture in Thailand.

    PubMed

    Gilbert, Marius; Xiao, Xiangming; Chaitaweesub, Prasit; Kalpravidh, Wantanee; Premashthira, Sith; Boles, Stephen; Slingenbergh, Jan

    2007-01-01

    Highly pathogenic avian influenza (HPAI) caused by H5N1 viruses has become a global scale problem which first emerged in southern China and from there spread to other countries in Southeast and East Asia, where it was first confirmed in end 2003. In previous work, geospatial analyses demonstrated that free grazing ducks played critical role in the epidemiology of the disease in Thailand in the winter 2004/2005, both in terms of HPAI emergence and spread. This study explored the geographic association between free grazing duck census counts and current statistics on the spatial distribution of rice crops in Thailand, in particular the crop calendar of rice production. The analysis was carried out using both district level rice statistics and rice distribution data predicted with the aid of remote sensing, using a rice-detection algorithm. The results indicated a strong association between the number of free grazing ducks and the number of months during which second-crop rice harvest takes place, as well as with the rice crop intensity as predicted by remote sensing. These results confirmed that free grazing duck husbandry was strongly driven by agricultural land use and rice crop intensity, and that this later variable can be readily predicted using remote sensing. Analysis of rice cropping patterns may provide an indication of the location of populations of free grazing ducks in other countries with similar mixed duck and rice production systems and less detailed duck census data. Apart from free ranging ducks and rice cropping, the role of hydrology and seasonality of wetlands and water bodies in the HPAI risk analysis is also discussed in relation to the presumed dry season aggregation of wild waterfowl and aquatic poultry offering much scope for virus transmission.

  5. Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis

    PubMed Central

    2010-01-01

    Background Rice is one of the most important food crops in the world. With increasing world demand for food crops, there is an urgent need to develop new cultivars that have enhanced performance with regard to yield, disease resistance, and so on. Wild rice is expected to provide useful genetic resources that could improve the present cultivated species. However, the quantity and quality of these unexplored resources remain unclear. Recent accumulation of the genomic information of both cultivated and wild rice species allows for their comparison at the molecular level. Here, we compared the genome sequence of Oryza sativa ssp. japonica with sets of bacterial artificial chromosome end sequences (BESs) from two wild rice species, O. rufipogon and O. nivara, and an African rice species, O. glaberrima. Results We found that about four to five percent of the BESs of the two wild rice species and about seven percent of the African rice could not be mapped to the japonica genome, suggesting that a substantial number of genes have been lost in the japonica rice lineage; however, their close relatives still possess their counterpart genes. We estimated that during evolution, O. sativa has lost at least one thousand genes that are still preserved in the genomes of the other species. In addition, our BLASTX searches against the non-redundant protein sequence database showed that disease resistance-related proteins were significantly overrepresented in the close relative-specific genomic portions. In total, 235 unmapped BESs of the three relatives matched 83 non-redundant proteins that contained a disease resistance protein domain, most of which corresponded to an NBS-LRR domain. Conclusion We found that the O. sativa lineage appears to have recently experienced massive gene losses following divergence from its wild ancestor. Our results imply that the domestication process accelerated large-scale genomic deletions in the lineage of Asian cultivated rice and that the close

  6. 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

  7. Volatile profiles of aromatic and non-aromatic rice

    USDA-ARS?s Scientific Manuscript database

    Rice is enjoyed by many people as a staple food because of its flavor and texture. Some scented varieties command a premium in the marketplace because of their distinctive aroma and flavor. The compound most commonly associated with the popcorn or nutty scent of aromatic rice is 2-acetyl-1-pyrroline...

  8. Research in rice fields

    USGS Publications Warehouse

    ,

    2000-01-01

    Between 1987 and 1999, 2.4-3 million acres of rice were planted annually nationwide. Rice fields are a major component of the contemporary landscapes in the Gulf Coastal Plain, the Mississippi Alluvial Valley, and Central Valley of California. In 1998, approximately 600,000 acres of rice were planted in Louisiana. In the Louisiana plant commodities report for 1998, total value for rice was over $350 million; sugarcane was the only plant commodity that exceeded this value. Louisiana has over 2,000 rice farmers supporting over 12,000 jobs in the state. Rice fields in the United States receive high use by wildlife, especially shorebirds, wading birds, and waterfowl. Waterbirds use rice fields for food, shelter, and breeding habitat.

  9. Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice

    PubMed Central

    2010-01-01

    Background Weedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP) variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution. Results We find greater population structure than has been previously reported for U.S. weedy rice, and that the multiple, genetically divergent populations have separate origins. The two main U.S. weedy rice populations share genetic backgrounds with cultivated O. sativa varietal groups not grown commercially in the U.S., suggesting weed origins from domesticated ancestors. Hybridization between weedy groups and between weedy rice and local crops has also led to the evolution of distinct U.S. weedy rice populations. Demographic simulations indicate differences among the main weedy groups in the impact of bottlenecks on their establishment in the U.S., and in the timing of divergence from their cultivated relatives. Conclusions Unlike prior research, we did not find unambiguous evidence for U.S. weedy rice originating via hybridization between cultivated and wild Oryza species. Our results demonstrate the potential for weedy life-histories to evolve directly from within domesticated lineages. The diverse origins of U.S. weedy rice populations demonstrate the multiplicity of evolutionary forces that can influence the emergence of weeds from a single species complex. PMID:20550656

  10. Rice_Phospho 1.0: a new rice-specific SVM predictor for protein phosphorylation sites

    PubMed Central

    Lin, Shoukai; Song, Qi; Tao, Huan; Wang, Wei; Wan, Weifeng; Huang, Jian; Xu, Chaoqun; Chebii, Vivien; Kitony, Justine; Que, Shufu; Harrison, Andrew; He, Huaqin

    2015-01-01

    Experimentally-determined or computationally-predicted protein phosphorylation sites for distinctive species are becoming increasingly common. In this paper, we compare the predictive performance of a novel classification algorithm with different encoding schemes to develop a rice-specific protein phosphorylation site predictor. Our results imply that the combination of Amino acid occurrence Frequency with Composition of K-Spaced Amino Acid Pairs (AF-CKSAAP) provides the best description of relevant sequence features that surround a phosphorylation site. A support vector machine (SVM) using AF-CKSAAP achieves the best performance in classifying rice protein phophorylation sites when compared to the other algorithms. We have used SVM with AF-CKSAAP to construct a rice-specific protein phosphorylation sites predictor, Rice_Phospho 1.0 (http://bioinformatics.fafu.edu.cn/rice_phospho1.0). We measure the Accuracy (ACC) and Matthews Correlation Coefficient (MCC) of Rice_Phospho 1.0 to be 82.0% and 0.64, significantly higher than those measures for other predictors such as Scansite, Musite, PlantPhos and PhosphoRice. Rice_Phospho 1.0 also successfully predicted the experimentally identified phosphorylation sites in LOC_Os03g51600.1, a protein sequence which did not appear in the training dataset. In summary, Rice_phospho 1.0 outputs reliable predictions of protein phosphorylation sites in rice, and will serve as a useful tool to the community. PMID:26149854

  11. Evidence for mid-Holocene rice domestication in the Americas.

    PubMed

    Hilbert, Lautaro; Neves, Eduardo Góes; Pugliese, Francisco; Whitney, Bronwen S; Shock, Myrtle; Veasey, Elizabeth; Zimpel, Carlos Augusto; Iriarte, José

    2017-10-09

    The development of agriculture is one of humankind's most pivotal achievements. Questions about plant domestication and the origins of agriculture have engaged scholars for well over a century, with implications for understanding its legacy on global subsistence strategies, plant distribution, population health and the global methane budget. Rice is one of the most important crops to be domesticated globally, with both Asia (Oryza sativa L.) and Africa (Oryza glaberrima Steud.) discussed as primary centres of domestication. However, until now the pre-Columbian domestication of rice in the Americas has not been documented. Here we document the domestication of Oryza sp. wild rice by the mid-Holocene residents of the Monte Castelo shell mound starting at approximately 4,000 cal. yr BP, evidenced by increasingly larger rice husk phytoliths. Our data provide evidence for the domestication of wild rice in a region of the Amazon that was also probably the cradle of domestication of other major crops such as cassava (Manihot esculenta), peanut (Arachis hypogaea) and chilli pepper (Capsicum sp.). These results underline the role of wetlands as prime habitats for plant domestication worldwide.4,000-year-old phytoliths (plant microfossils) from the Monte Castelo shell mound (southwestern Amazonia) provide evidence for an independent rice domestication event in the Americas.

  12. Selection on grain shattering genes and rates of rice domestication.

    PubMed

    Zhang, Lin-Bin; Zhu, Qihui; Wu, Zhi-Qiang; Ross-Ibarra, Jeffrey; Gaut, Brandon S; Ge, Song; Sang, Tao

    2009-11-01

    Molecular cloning of major quantitative trait loci (QTLs) responsible for the reduction of rice grain shattering, a hallmark of cereal domestication, provided opportunities for in-depth investigation of domestication processes. Here, we studied nucleotide variation at the shattering loci, sh4 and qSH1, for cultivated rice, Oryza sativa ssp. indica and Oryza sativa ssp. japonica, and the wild progenitors, Oryza nivara andOryza rufipogon. The nonshattering sh4 allele was fixed in all rice cultivars, with levels of sequence polymorphism significantly reduced in both indica and japonica cultivars relative to the wild progenitors. The sh4 phylogeny together with the neutrality tests and coalescent simulations suggested that sh4 had a single origin and was fixed by artificial selection during the domestication of rice. Selection on qSH1 was not detected in indica and remained unclear in japonica. Selection on sh4 could be strong enough to have driven its fixation in a population of cultivated rice within a period of c. 100 yr. The slow fixation of the nonshattering phenotype observed at the archeological sites might be a result of relatively weak selection on mutations other than sh4 in early rice cultivation. The fixation of sh4 could have been achieved later through strong selection for the optimal phenotype.

  13. 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.

  14. 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.

  15. A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement

    PubMed Central

    2014-01-01

    Background The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant. Results We used an integrated approach to compare the transcriptome, proteome and metabolome of the rhizome to other tissues of red rice. 116 Gb of transcriptome sequence was obtained from various tissues and used to identify rhizome-specific and preferentially expressed genes, including transcription factors and hormone metabolism and stress response-related genes. Proteomics and metabolomics approaches identified 41 proteins and more than 100 primary metabolites and plant hormones with rhizome preferential accumulation. Of particular interest was the identification of a large number of gene transcripts from Magnaportha oryzae, the fungus that causes rice blast disease in cultivated rice, even though the red rice plants showed no sign of disease. Conclusions A significant set of genes, proteins and metabolites appear to be specifically or preferentially expressed in the rhizome of O. longistaminata. The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease. PMID:24521476

  16. Teosinte Branched 1 modulates tillering in rice plants.

    PubMed

    Choi, Min-Seon; Woo, Mi-Ok; Koh, Eun-Byeol; Lee, Joohyun; Ham, Tae-Ho; Seo, Hak Soo; Koh, Hee-Jong

    2012-01-01

    Tillering is an important trait of cereal crops that optimizes plant architecture for maximum yield. Teosinte Branched 1 (TB1) is a negative regulator of lateral branching and an inducer of female inflorescence formation in Zea mays (maize). Recent studies indicate that TB1 homologs in Oryza sativa (rice), Sorghum bicolor and Arabidopsis thaliana act downstream of the auxin and MORE AUXILIARY GROWTH (MAX) pathways. However, the molecular mechanism by which rice produces tillers remains unknown. In this study, transgenic rice plants were produced that overexpress the maize TB1 (mTB1) or rice TB1 (OsTB1) genes and silence the OsTB1 gene through RNAi-mediated knockdown. Because lateral branching in rice is affected by the environmental conditions, the phenotypes of transgenic plants were observed in both the greenhouse and the paddy field. Compared to wild-type plants, the number of tillers and panicles was reduced and increased in overexpressed and RNAi-mediated knockdown OsTB1 rice plants, respectively, under both environmental conditions. However, the effect was small for plants grown in paddy fields. These results demonstrate that both mTB1 and OsTB1 moderately regulate the tiller development in rice.

  17. Mapping QTLs for Fertility Restoration of Different Cytoplasmic Male Sterility Types in Rice Using Two Oryza sativa ×O. rufipogon Backcross Inbred Line Populations.

    PubMed

    Hu, Biao-Lin; Xie, Jian-Kun; Wan, Yong; Zhang, Jin-Wei; Zhang, Fan-Tao; Li, Xia

    2016-01-01

    Hybrid rice breeding using cytoplasmic male sterility/fertility restoration (CMS/Rf) systems plays an important role in ensuring global food security. Two backcross inbred line (BIL) populations derived from either Xieqingzao B (XB)//XB/Dongxiang wild rice (DWR) (XXD) or XB//DWR/XB (XDX) were used to detect quantitative trait loci (QTLs) for fertility restoration of Dwarf wild abortive- (DA-), Indonesia Paddy- (ID-), and DWR-type CMS in rice. Lines with ID- and DA-type CMS were testcrossed with both the XXD- and XDX-BILs, while the line with DWR-type CMS was testcrossed with the XDX-BILs only. A total of 16 QTLs for fertility restoration of CMS systems were identified, including three for DWR-type CMS, six for DA-type CMS, and seven for ID-type CMS. All of the additive alleles in the QTLs were derived from Oryza rufipogon. Eleven QTLs were clustered in five chromosomal regions, indicating that common Rf loci restored different CMS systems, and the favorable O. rufipogon alleles could be used to develop restorer lines for various CMS types by marker-assisted selection.

  18. Mapping QTLs for Fertility Restoration of Different Cytoplasmic Male Sterility Types in Rice Using Two Oryza sativa ×O. rufipogon Backcross Inbred Line Populations

    PubMed Central

    Hu, Biao-lin; Wan, Yong; Zhang, Jin-wei; Zhang, Fan-tao; Li, Xia

    2016-01-01

    Hybrid rice breeding using cytoplasmic male sterility/fertility restoration (CMS/Rf) systems plays an important role in ensuring global food security. Two backcross inbred line (BIL) populations derived from either Xieqingzao B (XB)//XB/Dongxiang wild rice (DWR) (XXD) or XB//DWR/XB (XDX) were used to detect quantitative trait loci (QTLs) for fertility restoration of Dwarf wild abortive- (DA-), Indonesia Paddy- (ID-), and DWR-type CMS in rice. Lines with ID- and DA-type CMS were testcrossed with both the XXD- and XDX-BILs, while the line with DWR-type CMS was testcrossed with the XDX-BILs only. A total of 16 QTLs for fertility restoration of CMS systems were identified, including three for DWR-type CMS, six for DA-type CMS, and seven for ID-type CMS. All of the additive alleles in the QTLs were derived from Oryza rufipogon. Eleven QTLs were clustered in five chromosomal regions, indicating that common Rf loci restored different CMS systems, and the favorable O. rufipogon alleles could be used to develop restorer lines for various CMS types by marker-assisted selection. PMID:27872859

  19. Unravelling the proteomic profile of rice meiocytes during early meiosis

    PubMed Central

    Collado-Romero, Melania; Alós, Enriqueta; Prieto, Pilar

    2014-01-01

    Transfer of genetic traits from wild or related species into cultivated rice is nowadays an important aim in rice breeding. Breeders use genetic crosses to introduce desirable genes from exotic germplasms into cultivated rice varieties. However, in many hybrids there is only a low level of pairing (if existing) and recombination at early meiosis between cultivated rice and wild relative chromosomes. With the objective of getting deeper into the knowledge of the proteins involved in early meiosis, when chromosomes associate correctly in pairs and recombine, the proteome of isolated rice meiocytes has been characterized by nLC-MS/MS at every stage of early meiosis (prophase I). Up to 1316 different proteins have been identified in rice isolated meiocytes in early meiosis, being 422 exclusively identified in early prophase I (leptotene, zygotene, or pachytene). The classification of proteins in functional groups showed that 167 were related to chromatin structure and remodeling, nucleic acid binding, cell-cycle regulation, and cytoskeleton. Moreover, the putative roles of 16 proteins which have not been previously associated to meiosis or were not identified in rice before, are also discussed namely: seven proteins involved in chromosome structure and remodeling, five regulatory proteins [such as SKP1 (OSK), a putative CDK2 like effector], a protein with RNA recognition motifs, a neddylation-related protein, and two microtubule-related proteins. Revealing the proteins involved in early meiotic processes could provide a valuable tool kit to manipulate chromosome associations during meiosis in rice breeding programs. The data have been deposited to the ProteomeXchange with the PXD001058 identifier. PMID:25104955

  20. Convergent Loss of Awn in Two Cultivated Rice Species Oryza sativa and Oryza glaberrima Is Caused by Mutations in Different Loci.

    PubMed

    Furuta, Tomoyuki; Komeda, Norio; Asano, Kenji; Uehara, Kanako; Gamuyao, Rico; Angeles-Shim, Rosalyn B; Nagai, Keisuke; Doi, Kazuyuki; Wang, Diane R; Yasui, Hideshi; Yoshimura, Atsushi; Wu, Jianzhong; McCouch, Susan R; Ashikari, Motoyuki

    2015-09-02

    A long awn is one of the distinct morphological features of wild rice species. This organ is thought to aid in seed dispersal and prevent predation by animals. Most cultivated varieties of Oryza sativa and Oryza glaberrima, however, have lost the ability to form long awns. The causal genetic factors responsible for the loss of awn in these two rice species remain largely unknown. Here, we evaluated three sets of chromosome segment substitution lines (CSSLs) in a common O. sativa genetic background (cv. Koshihikari) that harbor genomic fragments from Oryza nivara, Oryza rufipogon, and Oryza glaberrima donors. Phenotypic analyses of these libraries revealed the existence of three genes, Regulator of Awn Elongation 1 (RAE1), RAE2, and RAE3, involved in the loss of long awns in cultivated rice. Donor segments at two of these genes, RAE1 and RAE2, induced long awn formation in the CSSLs whereas an O. sativa segment at RAE3 induced long awn formation in O. glaberrima. These results suggest that the two cultivated rice species, O. sativa and O. glaberrima, have taken independent paths to become awnless. Copyright © 2015 Furuta et al.

  1. Prevalence of intestinal and blood parasites among wild rats in Kuala Lumpur, Malaysia.

    PubMed

    Siti Shafiyyah, C O; Jamaiah, I; Rohela, M; Lau, Y L; Siti Aminah, F

    2012-12-01

    A survey was undertaken to investigate the prevalence of intestinal and blood parasites among wild rats in urban area of Kuala Lumpur, Malaysia. A total of 137 stool and blood samples were collected from wild rats from Sentul and Chow Kit areas. Five species of rats were captured and supplied by Kuala Lumpur City Hall. The most common was Rattus rattus diardii (Malayan Black rat), 67%, followed by Rattus norvegicus (Norway rat), 10%, Rattus argentiventer (rice-field rat), 10%, Rattus tiomanicus (Malaysian field rat), 9% and Rattus exulans (Polynesian rat), 4%. Rattus rattus diardii is commonly known to live in human environment and they are normally identified as pests to human community. More male rats were captured (61%) compared to female (39%). Out of 137 samples, 81.8% samples were positive with intestinal parasites, with 86.2% from Sentul area and 78.5% from Chow Kit area. Six different parasites were detected. The most common intestinal helminth parasite detected was Nippostrongylus brasiliensis (80.3%), followed by Hymenolepis nana (23.4%), Capillaria hepatica (13.9%) and Hymenolepis diminuta (2.9%). Intestinal protozoan detected was Entamoeba histolytica/E. dispar (8.8%). Trypanosoma lewisi (1.5%) was the only blood parasite detected.

  2. Post-harvest field manipulations to conserve waste rice for waterfowl

    USGS Publications Warehouse

    Stafford, J.D.; Kaminski, R.M.; Reinecke, K.J.; Kurtz, M.E.; Manley, S.W.

    2005-01-01

    Rice seeds escaping collection by combines during harvest (hereafter, waste rice) provide quality forage for migrating and wintering waterfowl in the Lower Mississippi Alluvial Valley (MAV) and other rice growing regions in the United States. Recent sample surveys across the MAV have revealed abundance of waste rice in fields declined an average of 71% between harvest and late autumn. Thus, we evaluated the ability of common post-harvest, field-management practices to conserve waste rice for waterfowl until early winter via controlled experiments in Mississippi rice test plots in 2001 and 2003 and analyses of data from MAV-wide surveys of waste rice in rice production fields in 2000-2002. Our experiments indicated test plots with burned rice stubble that were not flooded during autumn contained more waste rice than other treatments in 2001 (P?0.10). Waste-rice abundance in test plots did not differ among postharvest treatments in 2003 (P = 0.97). Our analyses of data from the MAV sample surveys did not detect differences in abundance of waste rice among fields burned, rolled, disked, or left in standing stubble post-harvest (P?0.04; Bonferroni corrected critical ( a= 0.017). Because results from test-plot experiments were inconclusive, we based our primary inference regarding best post-harvest treatments on patterns of rice abundance identified from the MAV surveys and previously documented environmental and agronomic benefits of managing harvested rice fields for wintering waterfowl. Therefore, we recommend leaving standing stubble in rice fields after harvest as a preliminary beneficial management practice. We suggest future research evaluate potential of postharvest practices to conserve waste rice for waterfowl and reduce straw in production rice fields managed for wintering waterfowl throughout the MAV.

  3. Determinants for grading Malaysian rice

    NASA Astrophysics Data System (ADS)

    ChePa, Noraziah; Yusoff, Nooraini; Ahmad, Norhayati

    2016-08-01

    Due to un-uniformity of rice grading practices in Malaysia, zones which actively producing rice in Malaysia are using their own way of grading rice. Rice grading is important in determining rice quality and its subsequent price in the market. It is an important process applied in the rice production industry with the purpose of ensuring that the rice produced for the market meets the quality requirements of consumer. Two important aspects that need to be considered in determining rice grades are grading technique and determinants to be used for grading (usually referred as rice attributes). This article proposes the list of determinants to be used in grading Malaysian rice. Determinants were explored through combination of extensive literature review and series of interview with the domain experts and practitioners. The proposed determinants are believed to be beneficial to BERNAS in improving the current Malaysian rice grading process.

  4. Wild Plants Used by the Native Americans.

    ERIC Educational Resources Information Center

    Nature Study, 1984

    1984-01-01

    Describes 10 wild plants used by Native Americans. They include: rose hips; the common milkweed; cattails; elderberries; cactus fruits; lamb's quarters pigweeds (Chenopodium sp.); persimmons; mints (Monardo sp.); the yucca; and the hawthorn. Illustrations of each plant are included. (JN)

  5. Wild Plants Used by the Native Americans.

    ERIC Educational Resources Information Center

    Nature Study, 1984

    1984-01-01

    Describes 10 wild plants used by Native Americans. They include: rose hips; the common milkweed; cattails; elderberries; cactus fruits; lamb's quarters pigweeds (Chenopodium sp.); persimmons; mints (Monardo sp.); the yucca; and the hawthorn. Illustrations of each plant are included. (JN)

  6. The archaeobotany of Asian rice expansion and the development of wet-field cultivation

    NASA Astrophysics Data System (ADS)

    Fuller, D.

    2008-12-01

    Archaeobotanical evidence provides direct data on past human diet and agriculture, including a geographical and chronological framework for studying the expansion of rice agriculture. The growth of systematic archaeobotanical sampling in recent years has allowed for the past presence of rice to be seen in relation to cultivation of other crops and associated weeds. The weed flora provides a basis for inferring the nature of cultivation systems, whether rain-fed dry rice or wetland "paddy" rice, a key distinction for considerations of past methane production. Nevertheless, current data is very unevenly distributed. This poster will summarize available evidence for the origins and spread of rice in South Asia (India and Pakistan), and mainland and Island Southeast Asia deriving from an earlier Chinese domestication. Where possible, such as in India or China, the potential of the weed flora remains for distinguishing wetland rice crops will be summarized. In broad terms, although the origins of rice use and cultivation begins by or during the Middle Holocene (6000- 3000 BC), rice cultivation spread outside the regions of the wild progenitor after this time. Two phases of rice expansion can be distinguished. Phase 1, between 3000 and 1500 BC, introduced rice to Southeast Asia, probably under wetland cultivation, and the spread of dry rice over northern India and Pakistan. Phase 2, taking place between 1000 and 0 BC, sees the spread of rice throughout the Southern Indian Peninsula, with weed evidence suggesting irrigated wetland rice. Similarly, this period sees the spread of intensive paddy agriculture through Korea and Japan, but in Southeast Asia is probably related to a spread of rice in upland, dry field systems.

  7. Relating raw rice color and composition to cooked rice color.

    USDA-ARS?s Scientific Manuscript database

    Traditionally, the color of milled rice is economically important. The whiter the rice the more it is preferred by consumers and the more value it has in the market place. Little attention has been given to relating raw rice color to cooked milled rice color and, specifically, to determining the i...

  8. 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

  9. Evaluation of the cancer chemopreventive efficacy of rice bran in genetic mouse models of breast, prostate and intestinal carcinogenesis

    PubMed Central

    Verschoyle, R D; Greaves, P; Cai, H; Edwards, R E; Steward, W P; Gescher, A J

    2007-01-01

    Brown rice is a staple dietary constituent in Asia, whereas rice consumed in the Western world is generally white, obtained from brown rice by removal of the bran. We tested the hypothesis that rice bran interferes with development of tumours in TAg, TRansgenic Adenocarcinoma of the Mouse Prostate (TRAMP) or ApcMin mice, genetic models of mammary, prostate and intestinal carcinogenesis, respectively. Mice received rice bran (30%) in AIN-93G diet throughout their post-weaning lifespan. In TAg and TRAMP mice, rice bran did not affect carcinoma development. In TRAMP or wild-type C57Bl6/J mice, dietary rice bran increased kidney weight by 18 and 20%, respectively. Consumption of rice bran reduced numbers of intestinal adenomas in ApcMin mice by 51% (P<0.01), compared to mice on control diet. In parallel, dietary rice bran decreased intestinal haemorrhage in these mice, as reflected by increased haematocrit. At 10% in the diet, rice bran did not significantly retard ApcMin adenoma development. Likewise, low-fibre rice bran (30% in the diet) did not affect intestinal carcinogenesis, suggesting that the fibrous constituents of the bran mediate chemopreventive efficacy. The results suggest that rice bran might be beneficially evaluated as a putative chemopreventive intervention in humans with intestinal polyps. PMID:17211473

  10. Rice (Oryza) hemoglobins

    USDA-ARS?s Scientific Manuscript database

    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 sin...

  11. Making rice even healthier!

    USDA-ARS?s Scientific Manuscript database

    Rice is a naturally healthy food, but what if it could be made even healthier? Would Americans eat more rice if it could be advertised to be a 'New and Improved' source of calcium to promote bone growth, or iron to prevent anemia? Grocery stores are full of foods that are vitamin enhanced to attract...

  12. Why is golden rice golden (yellow) instead of red?

    PubMed

    Schaub, Patrick; Al-Babili, Salim; Drake, Rachel; Beyer, Peter

    2005-05-01

    The endosperm of Golden Rice (Oryza sativa) is yellow due to the accumulation of beta-carotene (provitamin A) and xanthophylls. The product of the two carotenoid biosynthesis transgenes used in Golden Rice, phytoene synthase (PSY) and the bacterial carotene desaturase (CRTI), is lycopene, which has a red color. The absence of lycopene in Golden Rice shows that the pathway proceeds beyond the transgenic end point and thus that the endogenous pathway must also be acting. By using TaqMan real-time PCR, we show in wild-type rice endosperm the mRNA expression of the relevant carotenoid biosynthetic enzymes encoding phytoene desaturase, zeta-carotene desaturase, carotene cis-trans-isomerase, beta-lycopene cyclase, and beta-carotene hydroxylase; only PSY mRNA was virtually absent. We show that the transgenic phenotype is not due to up-regulation of expression of the endogenous rice pathway in response to the transgenes, as was suggested to be the case in tomato (Lycopersicon esculentum) fruit, where CRTI expression resulted in a similar carotenoid phenomenon. This means that beta-carotene and xanthophyll formation in Golden Rice relies on the activity of constitutively expressed intrinsic rice genes (carotene cis-trans-isomerase, alpha/beta-lycopene cyclase, beta-carotene hydroxylase). PSY needs to be supplemented and the need for the CrtI transgene in Golden Rice is presumably due to insufficient activity of the phytoene desaturase and/or zeta-carotene desaturase enzyme in endosperm. The effect of CRTI expression was also investigated in leaves of transgenic rice and Arabidopsis (Arabidopsis thaliana). Here, again, the mRNA levels of intrinsic carotenogenic enzymes remained unaffected; nevertheless, the carotenoid pattern changed, showing a decrease in lutein, while the beta-carotene-derived xanthophylls increased. This shift correlated with CRTI-expression and is most likely governed at the enzyme level by lycopene-cis-trans-isomerism. Possible implications are

  13. Rice bran: a novel functional ingredient.

    PubMed

    Sharif, Mian Kamran; Butt, Masood Sadiq; Anjum, Faqir Muhammad; Khan, Saima Hafiz

    2014-01-01

    Rice (Oryza sativa) is the most important staple food for a large part of the world's human population, especially in East and South Asia, the Middle East, Latin America, and the West Indies. It provides more than one fifth of the calories consumed worldwide by the human. It is the second leading cereal crop and staple food of half of the world's population. It is grown in at least 114 countries with global production of 645 million tons; share of Asian farmers is about 90% of the total produce. Rice bran, brown outer layer of rice kernel, is mainly composed of pericarp, aleurone, subaleurone layer, and germ. It contains appreciable quantities of nutrients like protein, fat, and dietary fiber. Furthermore, it contains substantial amount of minerals like K, Ca, Mg, and Fe. Presence of antioxidants like tocopherols, tocotrienols, and γ-oryzanol also brighten prospects of rice bran utilization for humans as functional ingredient to mitigate the life-threatening disorders. Moreover, in the developing countries, budding dilemma of food crisis, arising due to lower crop yields and escalating population, needs to utilize each pent of available resources. To provide enough food to all people, there is the holistic approach of using the by-products generated during food processing and preparations. Rice is being processed in well-established industry, but the major apprehension is the utilization of its by-products; rice bran (5-8%) and polishing (2-3%) that are going as waste. Rice processing or milling produces several streams of materials including milled rice, bran, and husk. In developing countries, rice bran is considered as a by-product of the milling process and commonly used in animal feed or discarded as a waste. The potential of producing rice bran at the global level is 29.3 million tons annually, whereas the share of Pakistan is worked out to be 0.5 million tons. In present paper, attempt has been made to highlight the significance of these valuable but

  14. Crop water use predictions available on-line for sprinkler irrigated rice in the United States and South Africa

    USDA-ARS?s Scientific Manuscript database

    Rice is an important food source for people in most of the world. Traditional rice culture requires flood irrigation which commonly uses 60 to 150 cm of water per growing season. Rice production is limited to fields with enough clay in the soils to retain 5 to 10 cm floodwater on the surface and p...

  15. Crop management strategies and disease resistance control the severity of false smut and kernel smut of rice

    USDA-ARS?s Scientific Manuscript database

    False smut and kernel smut are common diseases of rice capable of severe epidemics with dramatic yield losses. The importance of rice smuts is often overlooked in the US, and highly susceptible varieties are now being grown on the majority of production acres in the southern rice producing states. O...

  16. Global Identification of Genes Specific for Rice Meiosis.

    PubMed

    Zhang, Bingwei; Xu, Meng; Bian, Shiquan; Hou, Lili; Tang, Ding; Li, Yafei; Gu, Minghong; Cheng, Zhukuan; Yu, Hengxiu

    2015-01-01

    The leptotene-zygotene transition is a major step in meiotic progression during which pairing between homologous chromosomes is initiated and double strand breaks occur. OsAM1, a homologue of maize AM1 and Arabidopsis SWI1, encodes a protein with a coiled-coil domain in its central region that is required for the leptotene-zygotene transition during rice meiosis. To gain more insight into the role of OsAM1 in rice meiosis and identify additional meiosis-specific genes, we characterized the transcriptomes of young panicles of Osam1 mutant and wild-type rice plants using RNA-Seq combined with bioinformatic and statistical analyses. As a result, a total of 25,750 and 28,455 genes were expressed in young panicles of wild-type and Osam1 mutant plants, respectively, and 4,400 differentially expressed genes (DEGs; log2 Ratio ≥ 1, FDR ≤ 0.05) were identified. Of these DEGs, four known rice meiosis-specific genes were detected, and 22 new putative meiosis-related genes were found by mapping these DEGs to reference biological pathways in the KEGG database. We identified eight additional well-conserved OsAM1-responsive rice meiotic genes by comparing our RNA-Seq data with known meiotic genes in Arabidopsis and fission yeast.

  17. Global Identification of Genes Specific for Rice Meiosis

    PubMed Central

    Zhang, Bingwei; Xu, Meng; Bian, Shiquan; Hou, Lili; Tang, Ding; Li, Yafei; Gu, Minghong; Cheng, Zhukuan; Yu, Hengxiu

    2015-01-01

    The leptotene-zygotene transition is a major step in meiotic progression during which pairing between homologous chromosomes is initiated and double strand breaks occur. OsAM1, a homologue of maize AM1 and Arabidopsis SWI1, encodes a protein with a coiled-coil domain in its central region that is required for the leptotene-zygotene transition during rice meiosis. To gain more insight into the role of OsAM1 in rice meiosis and identify additional meiosis-specific genes, we characterized the transcriptomes of young panicles of Osam1 mutant and wild-type rice plants using RNA-Seq combined with bioinformatic and statistical analyses. As a result, a total of 25,750 and 28,455 genes were expressed in young panicles of wild-type and Osam1 mutant plants, respectively, and 4,400 differentially expressed genes (DEGs; log2 Ratio ≥ 1, FDR ≤ 0.05) were identified. Of these DEGs, four known rice meiosis-specific genes were detected, and 22 new putative meiosis-related genes were found by mapping these DEGs to reference biological pathways in the KEGG database. We identified eight additional well-conserved OsAM1-responsive rice meiotic genes by comparing our RNA-Seq data with known meiotic genes in Arabidopsis and fission yeast. PMID:26394329

  18. The Evolutionary Basis of Naturally Diverse Rice Leaves Anatomy

    PubMed Central

    Chatterjee, Jolly; Dionora, Jacqueline; Elmido-Mabilangan, Abigail; Wanchana, Samart; Thakur, Vivek; Bandyopadhyay, Anindya; Brar, Darshan S.; Quick, William Paul

    2016-01-01

    Rice contains genetically and ecologically diverse wild and cultivated species that show a wide variation in plant and leaf architecture. A systematic characterization of leaf anatomy is essential in understanding the dynamics behind such diversity. Therefore, leaf anatomies of 24 Oryza species spanning 11 genetically diverse rice genomes were studied in both lateral and longitudinal directions and possible evolutionary trends were examined. A significant inter-species variation in mesophyll cells, bundle sheath cells, and vein structure was observed, suggesting precise genetic control over these major rice leaf anatomical traits. Cellular dimensions, measured along three growth axes, were further combined proportionately to construct three-dimensional (3D) leaf anatomy models to compare the relative size and orientation of the major cell types present in a fully expanded leaf. A reconstruction of the ancestral leaf state revealed that the following are the major characteristics of recently evolved rice species: fewer veins, larger and laterally elongated mesophyll cells, with an increase in total mesophyll area and in bundle sheath cell number. A huge diversity in leaf anatomy within wild and domesticated rice species has been portrayed in this study, on an evolutionary context, predicting a two-pronged evolutionary pathway leading to the ‘sativa leaf type’ that we see today in domesticated species. PMID:27792743

  19. Agronomic performance of F1, F2 and F3 hybrids between weedy rice and transgenic glufosinate-resistant rice.

    PubMed

    Song, Xiaoling; Wang, Zhou; Qiang, Sheng

    2011-08-01

    Studies of hybrid fitness, of which agronomic performance may be an indicator, can help in evaluating the potential for introgression of a transgene from a transgenic crop to wild relatives. The objective of this study was to assess the agronomic performance of reciprocal hybrids between two transgenic glufosinate-resistant rice lines, Y0003 and 99-t, and two weedy rice accessions, WR1 and WR2, in the greenhouse. F1 hybrids displayed heterosis in height, flag leaf area and number of spikelets per panicle. The agronomic performance of F1 between WR1 and Y0003 was not affected by crossing direction. The tiller and panicle numbers of F1 individuals were higher than their F2 counterparts. However, these traits did not change significantly from the F2 to the F3 generation or in hybrids with weedy rice as maternal or paternal plants. For all hybrids, the in vitro germination rates of fresh pollen were similar and significantly lower than those of their parents, seed sets were similar to or of lower value than those of weedy rice parents and seed shattering characteristics were partially suppressed, but the survival of hybrids over winter in the field was similar to that of weedy rice parents. All F1, F2 and F3 hybrids had similar composite agronomic performance to weedy rice parents. There was no significant decrease in the composite agronomic performance of any of the hybrids compared with weedy rice. This implies that gene flow from transgenic cultivated rice to weedy rice could occur under natural conditions. Copyright © 2011 Society of Chemical Industry.

  20. Little White Lies: Pericarp Color Provides Insights into the Origins and Evolution of Southeast Asian Weedy Rice

    PubMed Central

    Cui, Yongxia; Song, Beng Kah; Li, Lin-Feng; Li, Ya-Ling; Huang, Zhongyun; Caicedo, Ana L.; Jia, Yulin; Olsen, Kenneth M.

    2016-01-01

    Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here, we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation. Functional alleles of the Rc gene confer proanthocyanidin pigmentation of the pericarp, a trait found in most wild and weedy Oryzas and associated with seed dormancy; nonfunctional rc alleles were strongly favored during rice domestication, and most cultivated varieties have nonpigmented pericarps. Phenotypic characterizations of 52 Malaysian weeds revealed that most strains are characterized by the pigmented pericarp; however, some weeds have white pericarps, suggesting close relationships to cultivated rice. Phylogenetic analyses indicate that the Rc haplotypes present in Malaysian weeds likely have at least three distinct origins: wild O. rufipogon, white-pericarp cultivated rice, and red-pericarp cultivated rice. These diverse origins contribute to high Rc nucleotide diversity in the Malaysian weeds. Comparison of Rc allelic distributions with other rice domestication genes suggests that functional Rc alleles may confer particular fitness benefits in weedy rice populations, for example, by conferring seed dormancy. This may promote functional Rc introgression from local wild Oryza populations. PMID:27729434

  1. Little White Lies: Pericarp Color Provides Insights into the Origins and Evolution of Southeast Asian Weedy Rice.

    PubMed

    Cui, Yongxia; Song, Beng Kah; Li, Lin-Feng; Li, Ya-Ling; Huang, Zhongyun; Caicedo, Ana L; Jia, Yulin; Olsen, Kenneth M

    2016-12-07

    Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here, we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation. Functional alleles of the Rc gene confer proanthocyanidin pigmentation of the pericarp, a trait found in most wild and weedy Oryzas and associated with seed dormancy; nonfunctional rc alleles were strongly favored during rice domestication, and most cultivated varieties have nonpigmented pericarps. Phenotypic characterizations of 52 Malaysian weeds revealed that most strains are characterized by the pigmented pericarp; however, some weeds have white pericarps, suggesting close relationships to cultivated rice. Phylogenetic analyses indicate that the Rc haplotypes present in Malaysian weeds likely have at least three distinct origins: wild O. rufipogon, white-pericarp cultivated rice, and red-pericarp cultivated rice. These diverse origins contribute to high Rc nucleotide diversity in the Malaysian weeds. Comparison of Rc allelic distributions with other rice domestication genes suggests that functional Rc alleles may confer particular fitness benefits in weedy rice populations, for example, by conferring seed dormancy. This may promote functional Rc introgression from local wild Oryza populations.

  2. Genetic control of a transition from black to straw-white seed hull in rice domestication.

    PubMed

    Zhu, Bo-Feng; Si, Lizhen; Wang, Zixuan; Zhou, Yan; Zhu, Jinjie; Shangguan, Yingying; Lu, Danfeng; Fan, Danlin; Li, Canyang; Lin, Hongxuan; Qian, Qian; Sang, Tao; Zhou, Bo; Minobe, Yuzo; Han, Bin

    2011-03-01

    The genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (Oryza rufipogon and Oryza nivara) to the straw-white seed hull of cultivated rice (Oryza sativa) during grain ripening remains unknown. We report that the black hull of O. rufipogon was controlled by the Black hull4 (Bh4) gene, which was fine-mapped to an 8.8-kb region on rice chromosome 4 using a cross between O. rufipogon W1943 (black hull) and O. sativa indica cv Guangluai 4 (straw-white hull). Bh4 encodes an amino acid transporter. A 22-bp deletion within exon 3 of the bh4 variant disrupted the Bh4 function, leading to the straw-white hull in cultivated rice. Transgenic study indicated that Bh4 could restore the black pigment on hulls in cv Guangluai 4 and Kasalath. Bh4 sequence alignment of all taxa with the outgroup Oryza barthii showed that the wild rice maintained comparable levels of nucleotide diversity that were about 70 times higher than those in the cultivated rice. The results from the maximum likelihood Hudson-Kreitman-Aguade test suggested that the significant reduction in nucleotide diversity in rice cultivars could be caused by artificial selection. We propose that the straw-white hull was selected as an important visual phenotype of nonshattered grains during rice domestication.

  3. A rice chloroplast transit peptide sequence does not alter the cytoplasmic localization of sheep serotonin N-acetyltransferase expressed in transgenic rice plants.

    PubMed

    Byeon, Yeong; Lee, Hyoung Yool; Lee, Kyungjin; Back, Kyoungwhan

    2014-09-01

    Ectopic overexpression of melatonin biosynthetic genes of animal origin has been used to generate melatonin-rich transgenic plants to examine the functional roles of melatonin in plants. However, the subcellular localization of these proteins expressed in the transgenic plants remains unknown. We studied the localization of sheep (Ovis aries) serotonin N-acetyltransferase (OaSNAT) and a translational fusion of a rice SNAT transit peptide to OaSNAT (TS:OaSNAT) in plants. Laser confocal microscopy analysis revealed that both OaSNAT and TS:OaSNAT proteins were localized to the cytoplasm even with the addition of the transit sequence to OaSNAT. Transgenic rice plants overexpressing the TS:OaSNAT fusion transgene exhibited high SNAT enzyme activity relative to untransformed wild-type plants, but lower activity than transgenic rice plants expressing the wild-type OaSNAT gene. Melatonin levels in both types of transgenic rice plant corresponded well with SNAT enzyme activity levels. The TS:OaSNAT transgenic lines exhibited increased seminal root growth relative to wild-type plants, but less than in the OaSNAT transgenic lines, confirming that melatonin promotes root growth. Seed-specific OaSNAT expression under the control of a rice prolamin promoter did not confer high levels of melatonin production in transgenic rice seeds compared with seeds from transgenic plants expressing OaSNAT under the control of the constitutive maize ubiquitin promoter.

  4. Physical and thermochemical properties of rice husk

    SciTech Connect

    Mansaray, K.G.; Ghaly, A.E.

    1997-11-01

    Rice husk a major by-product of the rice milling industry, is one of the most commonly available lignocellulosic materials that can be converted to different types of fuels and chemical feedstocks through a variety of thermochemical conversion processes. Proper understanding of the physical and thermochemical properties of rice husk is necessary for the design of thermochemical conversion systems. This study provides information on moisture content, bulk density, particle size, heating values, proximate analysis, ultimate analysis, ash composition, and ash fusibility characteristics for six rice husk varieties. The moisture content ranged from 8.68 to 10.44%, and the bulk density ranged from 86 to 114 kg/m{sup 3}. The results showed excessive volatile release of over 60%, high ash content ranging from 15.30 to 24.60% (dry weight basis), and high silica content of the ash ranging from 90 to 97%. The lower heating values ranged from 13.24 to 16.20 MJ/kg (dry weight basis). The ash fusion temperatures of all the varieties were found to be over 1,600 C. The differences in varietal characteristics have significant effects on the chemical properties of rice husk.

  5. Red River of the North, Reconnaissance Report: Wild Rice River.

    DTIC Science & Technology

    1980-12-01

    report for the whole of the Red River Basin. The reconnaissance report is itself part of the over- all Red Rivet oT the North study , which was initiated...by Congress in 1957 in order to develop solutions for flooding problems within the basin. The purpose of a reconnaissance study is to provide an...Dakota are included in the study area. The subbasin is bordered on the north by the Sheyenne River Subbasin and to the east and south by the Main Stem

  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. Iron absorption from brown rice/brown rice-based meal and milled rice/milled rice-based meal.

    PubMed

    Trinidad, Trinidad P; Mallillin, Aida C; Sagum, Rosario S; Briones, Dave P; Encabo, Rosario R; Juliano, Bienvenido O

    2009-12-01

    Milled rice is the staple food among Filipinos and is mostly consumed three times a day. Rice as a source of iron could therefore have an important role in the existing 37% prevalence of iron-deficiency anemia in the country. Previous iron absorption studies in Filipinos from rice and rice-based meals were carried out on milled rice but no research was done on brown rice of the same variety. This leads to the hypothesis that brown rice may be better than milled rice in terms of iron content. To determine iron absorption from brown rice and brown rice-based meal, and from milled rice and milled rice-based meal of the same variety. The rice variety used in the study was F(2) seeds of PSB Rc72H. Iron absorption from brown/milled rice and brown/milled rice-based meals was determined in 12 healthy human subjects from the incorporation of radioisotopes of iron into erythrocytes 14 days after administration of the labeled rice/rice-based meals. The above samples were also analyzed for nutrient content, including dietary fiber, and iron. The iron content of brown rice was significantly higher (1.1 +/- 0.1 mg/100 g) than that of milled rice (0.6 +/- 0.1 mg/100 g). Brown rice has significantly greater amounts of total dietary fiber (5.4 +/- 0.4%) than milled rice (1.7 +/- 0.2%; P < 0.05). Both tannic acid and phytic acid contents in brown rice (56.9 +/- 3.2 mg/100 g and 290.1 +/- 18.0 mg/100 g, respectively) were significantly higher than those of milled rice (21.3 +/- 2.3 mg/100 g and 84.0 +/- 12.4 mg/100 g, respectively; P<0.05). The amount of iron absorbed from brown rice (0.13 +/- 0.02 mg) did not differ significantly from that from milled rice (0.14 +/- 0.02 mg). However, the amount from brown rice-based meal (0.36 +/- 0.04 mg) differed significantly from that from brown rice (P<0.05) as well as that from milled rice-based meal (0.35 +/- 0.03 mg) from that from milled rice (P<0.05). Moreover, brown rice-based meal did not differ significantly from milled rice-based meal

  8. Calcium apatite crystals in synovial fluid rice bodies.

    PubMed

    Li-Yu, J; Clayburne, G M; Sieck, M S; Walker, S E; Athreya, B H; DeHoratius, R J; Schumacher, H R

    2002-05-01

    Rice bodies can occur in the joints in many rheumatic conditions, but they are most common in rheumatoid arthritis. They are generally believed to occur rarely in patients with osteoarthritis, but one study reported rice bodies with apatite crystals. To report on a series of joint fluids with rice bodies containing apatite clumps and examine their clinical pictures. All synovial fluid analysis reports for 10 years were reviewed for rice bodies and eight patients were reported on. A series of patients with a variety of diseases with synovial fluid rice bodies found to contain calcific material is described. All were examined by compensated polarised light and alizarin red stain, and four were examined by electron microscopy. The eight patients all had alizarin red S chunks embedded throughout the rice body. Transmission electron microscopy disclosed the presence of a matrix of collagen, fibrin, and amorphous materials containing typical apatite crystals. Clinical diagnoses, radiographic findings, and leucocyte counts varied, but six of the eight patients had had previous repeated corticosteroid injections into the joints. Aggregates of apatites may be more common than previously recognised in rice bodies as they are not routinely sought. Whether they are a result of joint damage or depot steroid injections and whether that might contribute to further joint injury now needs to be investigated.

  9. Calcium apatite crystals in synovial fluid rice bodies

    PubMed Central

    Li-Yu, J; Clayburne, G; Sieck, M; Walker, S; Athreya, B; DeHoratius, R; Schumacher, H

    2002-01-01

    Background: Rice bodies can occur in the joints in many rheumatic conditions, but they are most common in rheumatoid arthritis. They are generally believed to occur rarely in patients with osteoarthritis, but one study reported rice bodies with apatite crystals. Objective: To report on a series of joint fluids with rice bodies containing apatite clumps and examine their clinical pictures. Methods: All synovial fluid analysis reports for 10 years were reviewed for rice bodies and eight patients were reported on. A series of patients with a variety of diseases with synovial fluid rice bodies found to contain calcific material is described. All were examined by compensated polarised light and alizarin red stain, and four were examined by electron microscopy. Results: The eight patients all had alizarin red S chunks embedded throughout the rice body. Transmission electron microscopy disclosed the presence of a matrix of collagen, fibrin, and amorphous materials containing typical apatite crystals. Clinical diagnoses, radiographic findings, and leucocyte counts varied, but six of the eight patients had had previous repeated corticosteroid injections into the joints. Conclusion: Aggregates of apatites may be more common than previously recognised in rice bodies as they are not routinely sought. Whether they are a result of joint damage or depot steroid injections and whether that might contribute to further joint injury now needs to be investigated. PMID:11959760

  10. Scorpion peptide LqhIT2 activates phenylpropanoid pathways via jasmonate to increase rice resistance to rice leafrollers.

    PubMed

    Tianpei, Xiuzi; Li, Dong; Qiu, Ping; Luo, Jie; Zhu, Yingguo; Li, Shaoqing

    2015-01-01

    LqhIT2 is an insect-specific toxin peptide identified in Leiurus quinquestriatus hebraeus that can be toxic to lepidoptera pests. However, whether LqhIT2 induces insect resistance in rice, and how the LqhIT2 influences the biochemical metabolism of rice plants remains unknown. Here, purified LqhIT2-GST fusion protein had toxicity to rice leafrollers. Meanwhile, in vitro and field trials showed that LqhIT2 transgenic rice plants were less damaged by rice leafrollers compared to the wild type plants. Introducing LqhIT2 primed the elevated expression of lipoxygenase, a key component of the jasmonic acid biosynthetic pathway, together with enhanced linolenic acid, cis-(+)-12-oxophytodienoic acid, jasmonic acid, and jasmonic acid-isoleucine levels. In addition, phenylalanine ammonia-lyase, a key gene of the phenylpropanoid pathway, was up-regulated. Correspondingly, the contents of downstream products of the phenylpropanoid pathway such as flavonoids and lignins, were also increased in LqhIT2 transgenic plants. These changes were paralleled by decreased starch, glucose, and glucose-6-phosphate accumulation, the key metabolites of glycolysis pathway that supplies the raw material and intermediate carbon products for phenylpropanoids biosyntheses. These findings suggest that, in addition to its own toxicity against pests, LqhIT2 activate the phenylpropanoid pathway via jasmonate-mediated priming, which subsequently increases flavonoid and lignin content and improves insect resistance in rice.

  11. Succession of methanogenic archaea in rice straw incorporated into a Japanese rice field: estimation by PCR-DGGE and sequence analyses

    PubMed Central

    Sugano, Atsuo; Tsuchimoto, Hidetaka; Cho, Tun Cho; Kimura, Makoto; Asakawa, Susumu

    2005-01-01

    The succession and phylogenetic profiles of methanogenic archaeal communities associated with rice straw decomposition in rice-field soil were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by 16S rDNA sequencing. Nylon bags containing either leaf sheaths or blades were buried in the plowed layer of a Japanese rice field under drained conditions during the off-crop season and under flooded conditions after transplanting. In addition, rice straw samples that had been buried in the rice field under drained conditions during the off-crop season were temporarily removed during spring plowing and then re-buried in the same rice field under flooded conditions at transplanting. Populations of methanogenic archaea were examined by amplification of the 16S rRNA genes in the DNA extracted from the rice straw samples. No PCR product was produced for samples of leaf sheath or blade prior to burial or after burial under drained conditions, indicating that the methanogen population was very small during decomposition of rice straw under oxic conditions. Many common bands were observed in rice straw samples of leaf sheath and blade during decomposition of rice straw under flooded conditions. Cluster analysis based on DGGE patterns divided methanogenic archaeal communities into two groups before and after the mid-season drainage. Sequence analysis of DGGE bands that were commonly present were closely related to Methanomicrobiales and Rice cluster I. Methanomicrobiales, Rice cluster I and Methanosarcinales were major members before the mid-season drainage, whereas the DGGE bands that characterized methanogenic archaeal communities after the mid-season drainage were closely related to Methanomicrobiales. These results indicate that mid-season drainage affected the methanogenic archaeal communities irrespective of their location on rice straw (sheath and blade) and the previous history of decomposition during the off

  12. Oscar Wilde and the brain cell.

    PubMed

    Cohn, Elisha

    2013-01-01

    This chapter considers Oscar Wilde's interest in the brain cell as an aesthetic object. Offering an account of Wilde's career that analyzes his early interest in physiology and philosophy, this chapter argues that Wilde's uniquely aesthetic take on the brain suggests that he rejects an account of the self as autonomous or self-determining. For many late Victorians brain science threatened both the freedom of human action and the legitimacy of beauty because it had the potential to invalidate conscious experience. But writers whose work Wilde knew, like John Ruskin, W. K. Clifford, and John Tyndall, avoided the despair of materialism by using aesthetic terms in their own discussions of life's invisible materials. Wilde's art collaborates with the contemporary sciences. His depictions of the cell direct the senses to a new field of being that emphasizes the molecular life all humans have in common, in which individual responsibility and activity matter less than the necessity of beauty.

  13. Innate immunity in rice

    PubMed Central

    Chen, Xuewei; Ronald, Pamela C.

    2011-01-01

    Advances in studies of rice innate immunity have led to the identification and characterization of host sensors encoding receptor kinases that perceive conserved microbial signatures. The non-RD domain, a newly recognized hallmark of these receptor kinases is highly expanded in rice (Oryza sativa) compared with Arabidopsis (Arabidopsis thaliana). Researchers have also identified a diverse array of microbial effectors from bacterial and fungal pathogens that triggers immune responses upon perception. These include both, effectors that indirectly target host Nucleotide binding site/Leucine rice repeat (NBS-LRR) proteins and transcription activator-like (TAL) effectors that directly bind promoters of host genes. Here we review the recognition and signaling events that govern rice innate immunity. PMID:21602092

  14. GAD1 Encodes a Secreted Peptide That Regulates Grain Number, Grain Length, and Awn Development in Rice Domestication[OPEN

    PubMed Central

    Hua, Lei; Zhao, Xinhui; Zhang, Weifeng; Liu, Fengxia; Fu, Yongcai; Cai, Hongwei; Sun, Xianyou; Gu, Ping; Xie, Daoxin

    2016-01-01

    Cultivated rice (Oryza sativa) was domesticated from wild rice (Oryza rufipogon), which typically displays fewer grains per panicle and longer grains than cultivated rice. In addition, wild rice has long awns, whereas cultivated rice has short awns or lacks them altogether. These changes represent critical events in rice domestication. Here, we identified a major gene, GRAIN NUMBER, GRAIN LENGTH AND AWN DEVELOPMENT1 (GAD1), that regulates those critical changes during rice domestication. GAD1 is located on chromosome 8 and is predicted to encode a small secretary signal peptide belonging to the EPIDERMAL PATTERNING FACTOR-LIKE family. A frame-shift insertion in gad1 destroyed the conserved cysteine residues of the peptide, resulting in a loss of function, and causing the increased number of grains per panicle, shorter grains, and awnless phenotype characteristic of cultivated rice. Our findings provide a useful paradigm for revealing functions of peptide signal molecules in plant development and helps elucidate the molecular basis of rice domestication. PMID:27634315

  15. Comparative Mapping of Seed Dormancy Loci Between Tropical and Temperate Ecotypes of Weedy Rice (Oryza sativa L.).

    PubMed

    Zhang, Lihua; Lou, Jieqiong; Foley, Michael E; Gu, Xing-You

    2017-08-07

    Genotypic variation at multiple loci for seed dormancy (SD) contributes to plant adaptation to diverse ecosystems. Weedy rice (Oryza sativa) was used as a model to address the similarity of SD genes between distinct ecotypes. A total of 12 quantitative trait loci (QTL) for SD were identified in one primary and two advanced backcross (BC) populations derived from a temperate ecotype of weedy rice (34.3°N Lat.). Nine (75%) of the 12 loci were mapped to the same positions as those identified from a tropical ecotype of weedy rice (7.1°N Lat.). The high similarity suggested that the majority of SD genes were conserved during the ecotype differentiation. These common loci are largely those collocated/linked with the awn, hull color, pericarp color, or plant height loci. Phenotypic correlations observed in the populations support the notion that indirect selections for the wild-type morphological characteristics, together with direct selections for germination time, were major factors influencing allelic distributions of SD genes across ecotypes. Indirect selections for crop-mimic traits (e.g., plant height and flowering time) could also alter allelic frequencies for some SD genes in agroecosystems. In addition, 3 of the 12 loci were collocated with segregation distortion loci, indicating that some gametophyte development genes could also influence the genetic equilibria of SD loci in hybrid populations. The SD genes with a major effect on germination across ecotypes could be used as silencing targets to develop transgene mitigation (TM) strategies to reduce the risk of gene flow from genetically modified crops into weed/wild relatives. Copyright © 2017 Zhang et al.

  16. Overexpression of rice serotonin N-acetyltransferase 1 in transgenic rice plants confers resistance to cadmium and senescence and increases grain yield.

    PubMed

    Lee, Kyungjin; Back, Kyoungwhan

    2017-04-01

    While ectopic overexpression of serotonin N-acetyltransferase (SNAT) in plants has been accomplished using animal SNAT genes, ectopic overexpression of plant SNAT genes in plants has not been investigated. Because the plant SNAT protein differs from that of animals in its subcellular localization and enzyme kinetics, its ectopic overexpression in plants would be expected to give outcomes distinct from those observed from overexpression of animal SNAT genes in transgenic plants. Consistent with our expectations, we found that transgenic rice plants overexpressing rice (Oryza sativa) SNAT1 (OsSNAT1) did not show enhanced seedling growth like that observed in ovine SNAT-overexpressing transgenic rice plants, although both types of plants exhibited increased melatonin levels. OsSNAT1-overexpressing rice plants did show significant resistance to cadmium and senescence stresses relative to wild-type controls. In contrast to tomato, melatonin synthesis in rice seedlings was not induced by selenium and OsSNAT1 transgenic rice plants did not show tolerance to selenium. T2 homozygous OsSNAT1 transgenic rice plants exhibited increased grain yield due to increased panicle number per plant under paddy field conditions. These benefits conferred by ectopic overexpression of OsSNAT1 had not been observed in transgenic rice plants overexpressing ovine SNAT, suggesting that plant SNAT functions differently from animal SNAT in plants. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  17. 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.

  18. Variation in arsenic bioavailability in rice genotypes using swine model: An animal study.

    PubMed

    Islam, Shofiqul; Rahman, Mohammad Mahmudur; Duan, Luchun; Islam, M R; Kuchel, Tim; Naidu, Ravi

    2017-12-01

    An in vivo assay using swine was used to measure the absolute bioavailability (AB) of As from cooked rice of twelve genotypes commonly grown in Bangladesh. An assessment of both total As in rice and its bioavailability is crucial for estimating human exposure following dietary intake by the local community. Average As concentrations in each rice genotype ranged from 108±4μg/kg to 580±6μg/kg. Arsenic speciation shows that most of the rice genotype contains 73 to 100% inorganic As. Swine were administered with As orally and via intravenous method, i.e. injection and fed certain common Bangladeshi rice genotypes (cooked). Swine blood As levels were measured to calculate As bioavailability from rice. Pilot studies shows that for As(III) and As(V), 90.8±12.4% and 85.0±19.2% of the administered oral dose was absorbed from the gastrointestinal tract whereas organic As was poorly absorbed resulting in low bioavailability values 20.2±2.6% (MMA) to 31.2±3.4% (DMA), respectively. These studies demonstrates that rice genotypic characters influenced As bioavailability in rice grown in As-contaminated areas and the bioavailability varied between 25% and 94%. Arsenic in salt tolerant rice genotypes Binadhan-10 and BRRI dhan47 as well as brown rice genotypes Kheali Boro and Local Boro has lower bioavailability (<50%) compared to other rice genotypes. The most commonly cultivated and consumed variety (BRRI dhan28) has As bioavailability of 70%, which poses a significant risk to consumers. Calculation of maximum tolerable daily intake (MTDI) for humans due to consumption of rice based on bioavailability data was higher than those calculated based on inorganic and organic As concentration in rice genotypes. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. 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.

  20. Evaluation of caspofungin susceptibility testing by the new Vitek 2 AST-YS06 yeast card using a unique collection of FKS wild-type and hot spot mutant isolates, including the five most common candida species.

    PubMed

    Astvad, Karen M; Perlin, David S; Johansen, Helle K; Jensen, Rasmus H; Arendrup, Maiken C

    2013-01-01

    FKS mutant isolates associated with breakthrough or failure cases are emerging in clinical settings. Discrimination of these from wild-type (wt) isolates in a routine laboratory setting is complicated. We evaluated the ability of caspofungin MIC determination using the new Vitek 2 AST-Y06 yeast susceptibility card to correctly identify the fks mutants from wt isolates and compared the performance to those of the CLSI and EUCAST reference methods. A collection of 98 Candida isolates, including 31 fks hot spot mutants, were included. Performance was evaluated using the FKS genotype as the "gold standard" and compared to those of the CLSI and EUCAST methodologies. The categorical agreement for Vitek 2 was 93.9%, compared to 88.4% for the CLSI method and 98.7% for the EUCAST method. Vitek 2 misclassified 19.4% (6/31) of the fks mutant isolates as susceptible, in contrast to <4% for each of the reference methods. The overall essential agreement between the CLSI method and Vitek 2 MICs was 92.6% (88/95) but was substantially lower for fks mutant isolates (78.6% [22/28]). Correct discrimination between susceptible and intermediate Candida glabrata isolates was not possible, as the revised species-specific susceptibility breakpoint was not included in the Vitek 2 detection range (MIC of ≤0.250 to ≥4 mg/liter). In conclusion, the Vitek 2 allowed correct categorization of all wt isolates as susceptible. However, despite an acceptable categorical agreement, it failed to reliably classify isolates harboring fks hot spot mutations as intermediate or resistant, which was in part due to the fact that the detection range did not span the susceptibility breakpoint for C. glabrata.

  1. Early flowering and rapid grain filling determine early maturity and escape from harvesting in weedy rice.

    PubMed

    Zhao, Can; Xu, Wenrong; Xiaoling, Song; Dai, Weimin; Dai, Lei; Zhang, Zheng; Sheng, Qiang

    2017-09-13

    Early maturity is an important trait that is essential to the survival of weedy rice. To explore the mechanism of early maturity in weedy rice, the reproductive development of a large sample of weedy rice accessions and cultivars was compared in a common garden study. A selected sample of both weedy and cultivated rices was sown at different dates in two years to study in more detail their flowering and grain filling patterns. The weedy rice from three major cropping regions matured 7-8 d earlier than their associated cultivars. Representative weedy rice accessions planted on conventional sowing dates flowered 3-26 d earlier than cultivars; delayed sowing caused divergence in the flowering regimes in weedy rice. However, regardless of the sowing date, weedy rice filled its grain 7-21 d faster than cultivars in both study years. Vegetative and reproductive traits of weedy and cultivated rice have different variation patterns with delayed planting. Early maturity is an essential factor determining the persistence of weedy rice by contributing to its seed escaping of being harvested with the rice crop. Both early flowering and shorter grain filling stages determine early maturity, and the flowering is more plastic than the grain filling. This article is protected by copyright. All rights reserved.

  2. A Phylogenetically Informed Comparison of GH1 Hydrolases between Arabidopsis and Rice Response to Stressors

    PubMed Central

    Cao, Yun-Ying; Yang, Jing-Fang; Liu, Tie-Yuan; Su, Zhen-Feng; Zhu, Fu-Yuan; Chen, Mo-Xian; Fan, Tao; Ye, Neng-Hui; Feng, Zhen; Wang, Ling-Juan; Hao, Ge-Fei; Zhang, Jianhua; Liu, Ying-Gao

    2017-01-01

    Glycoside hydrolases Family 1 (GH1) comprises enzymes that can hydrolyze β-O-glycosidic bond from a carbohydrate moiety. The plant GH1 hydrolases participate in a number of developmental processes and stress responses, including cell wall modification, plant hormone activation or deactivation and herbivore resistance. A large number of members has been observed in this family, suggesting their potential redundant functions in various biological processes. In this study, we have used 304 sequences of plant GH1 hydrolases to study the evolution of this gene family in plant lineage. Gene duplication was found to be a common phenomenon in this gene family. Although many members of GH1 hydrolases showed a high degree of similarity in Arabidopsis and rice, they showed substantial tissue specificity and differential responses to various stress treatments. This differential regulation implies each enzyme may play a distinct role in plants. Furthermore, some of salt-responsive Arabidopsis GH1 hydrolases were selected to test their genetic involvement in salt responses. The knockout mutants of AtBGLU1 and AtBGLU19 were observed to be less-sensitive during NaCl treatment in comparison to the wild type seedlings, indicating their participation in salt stress response. In summary, Arabidopsis and rice GH1 glycoside hydrolases showed distinct features in their evolutionary path, transcriptional regulation and genetic functions. PMID:28392792

  3. Overexpression of acetylcholinesterase gene in rice results in enhancement of shoot gravitropism.

    PubMed

    Yamamoto, Kosuke; Shida, Satoshi; Honda, Yoshihiro; Shono, Mariko; Miyake, Hiroshi; Oguri, Suguru; Sakamoto, Hikaru; Momonoki, Yoshie S

    2015-09-25

    Acetylcholine (ACh), a known neurotransmitter in animals and acetylcholinesterase (AChE) exists widely in plants, although its role in plant signal transduction is unclear. We previously reported AChE in Zea mays L. might be related to gravitropism based on pharmacological study using an AChE inhibitor. Here we clearly demonstrate plant AChE play an important role as a positive regulator in the gravity response of plants based on a genetic study. First, the gene encoding a second component of the ACh-mediated signal transduction system, AChE was cloned from rice, Oryza sativa L. ssp. Japonica cv. Nipponbare. The rice AChE shared high homology with maize, siratro and Salicornia AChEs. Similar to animal and other plant AChEs, the rice AChE hydrolyzed acetylthiocholine and propionylthiocholine, but not butyrylthiocholine. Thus, the rice AChE might be characterized as an AChE (E.C.3.1.1.7). Similar to maize and siratro AChEs, the rice AChE exhibited low sensitivity to the AChE inhibitor, neostigmine bromide, compared with the electric eel AChE. Next, the functionality of rice AChE was proved by overexpression in rice plants. The rice AChE was localized in extracellular spaces of rice plants. Further, the rice AChE mRNA and its activity were mainly detected during early developmental stages (2 d-10 d after sowing). Finally, by comparing AChE up-regulated plants with wild-type, we found that AChE overexpression causes an enhanced gravitropic response. This result clearly suggests that the function of the rice AChE relate to positive regulation of gravitropic response in rice seedlings.

  4. Resistance of Rice Varieties to the Stored-Product Insect, Sitophilus zeamais (Coleoptera: Curculionidae).

    PubMed

    Antunes, Catarina; Mendes, Raquel; Lima, Arlindo; Barros, Graça; Fields, Paul; Da Costa, Luísa Beirão; Rodrigues, José Carlos; Silva, Maria José; Correia, Augusto Manuel; Carvalho, Maria Otilia

    2016-02-01

    Four common Portuguese rice varieties--Thaibonnet, Gladio, Albatros, and Eurosis--were tested for their relative susceptibility to Sitophilus zeamais Motschulsky, a common pest of stored rice in Portugal and in tropical countries. Physical (moisture content, hardness, length, and width) and chemical (by attenuated total reflection-Fourier transform infrared spectroscopy) properties of rice kernels were measured. Insect bioassays measured median developmental time, Dobie's index of susceptibility, percentage of damaged grains and weight loss, and progeny developed. This was done for paddy, brown rice, and polished rice for each variety. There were small, but significant, differences in insect resistance among the varieties. However, it was different for paddy and polished rice. In paddy, these differences were correlated with hull damage, and Eurosis was the most susceptible variety. In polished rice, resistance was correlated with hardness, and Thaibonnet was the most susceptible variety. In general, paddy rice was more resistant to insect attack, followed by polished rice and then brown rice. Paddy kernels selected with undamaged hull were completely resistant to attack. Implications for IPM and breeding for resistant varieties are discussed.

  5. Unavailability of wild relatives

    USDA-ARS?s Scientific Manuscript database

    The unavailability of crop wild relatives may come in many forms, including limited possibilities of gene flow with related species due to clonality, differing ploidy levels, or other crossing barriers between species. Alternatively, it may simply mean that we lack information about the wild relativ...

  6. Identification of rice sheath blight and blast quantitative trait loci in two different O. satival/O. nivara advanced backcross populations

    USDA-ARS?s Scientific Manuscript database

    Two accessions of the rice (Oryza sativa) wild ancestral species, O. nivara identified as being moderately resistant to sheath blight and leaf blast diseases, were used as donor parents to develop two advanced backcross populations with the U.S. rice cultivar, Bengal, as the recurrent parent. The O...

  7. Red Yeast Rice: An Introduction

    MedlinePlus

    ... help lower blood levels of cholesterol and related lipids. Red yeast rice products may not be safe; ... to lower blood levels of cholesterol and related lipids. Some red yeast rice products contain substances called ...

  8. Shaping a better rice plant.

    PubMed

    Springer, Nathan

    2010-06-01

    Two studies describe how regulatory variation at the rice gene OsSPL14 can lead to altered plant morphology and improve grain yield. These studies support the possibility of improving rice yield through changing plant architecture.

  9. Wild Mammalian Biomonitors for Assessing Impacts of Environmental Contamination on Population and Community Ecology

    DTIC Science & Technology

    1993-06-01

    rice seed germination, and Ceriodaphnia assays. At the ecosystem level, in situ small mammal total biomass, sex ratios, reproduction , recruit- ment...toxic study sites, which was reflected in common laboratory bioassay results using fathead minnow, microtox, rice seed germination, and Ceriodaphnia ...assays. At the ecosystem level, in situ small mammal total biomass, sex ratios, reproduction , recruitment, survival, and density were measured as

  10. 7 CFR 868.310 - Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice...

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice. (See also Â... Milled Rice Principles Governing Application of Standards § 868.310 Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice...

  11. 7 CFR 868.310 - Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice...

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice. (See also Â... Milled Rice Principles Governing Application of Standards § 868.310 Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice...

  12. 7 CFR 868.310 - Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice. (See also Â... Milled Rice Principles Governing Application of Standards § 868.310 Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice...

  13. Rheological properties of rice-blackgram batter while replacing white rice with brown rice.

    PubMed

    Manickavasagan, Annamalai; Al-Marhubi, Insaaf Mohd; Dev, Satyanarayan

    2014-06-01

    Rice-blackgram batter is a raw material for many traditional convenience foods in Asia. Reformulation of traditional convenience food by replacing white rice with whole rice (brown rice) is a novel method to reduce the consumption of refined grain and increase the intake of whole grain in our diet. In this study, rheological properties of rice-blackgram batter was investigated while replacing white rice with brown rice at five levels (T1--0% replacement (control), T2--25% replacement, T3--50% replacement, T4--75% replacement, and T5--100% replacement). The shear stress versus shear rate plot indicates that the rice-blackgram batter exhibited non-Newtonian fluid behavior (shear thinning property) even after 100% replacement of white rice with brown rice. The rheological characteristics of rice-blackgram batters fitted reasonably well in Cassan (r2 = 0.8521-0.9856) and power law (r2 = 0.8042-0.9823) models. Brown rice replacement at all levels did not affect the flow behavior index, yield stress, consistency coefficient, and apparent viscosity of batter at 25 degrees C. However, at higher temperature, the viscosity was greater for T4 and T5 (no difference between them) than T1, T2, and T3 (no difference between them) batters. Further research is required to determine the sensory attributes and acceptability of the cooked products with brown rice-blended batter.

  14. Sugarcane rice residue biochars and their applications

    NASA Astrophysics Data System (ADS)

    Wang, J. J.

    2014-12-01

    Sugarcane production in U.S. involves either pre-harvest burning or after-harvest burning of the residue. Approximately 70-90% of the dry matter of harvested sugarcane trash is lost through open field burning. This practice has caused considerable concerns over air quality and soil sustainability. We propose an alternative conservation approach to convert the sugarcane residue to biochar and used as soil amendment to conserve carbon and potentially improve soil fertility. In this study, fundamental properties of biochars made from sugarcane residue along with rice residues were tested for agronomic and environmental benefits. Sugarcane and rice harvest residues and milling processing byproducts bagasse and rice husk were converted to biochars at different pyrolysis temperatures and characterized. In general, sugarcane leave biochar contained more P, K, Ca and Mg than sugarcane bagasse biochar. Rice straw biochar had more S, K Ca but less P than rice husk biochar. Both biochars had higher available fraction of total P than that of total K. Sugarcane leave biochar converted at 450oC was dominated with various lignin derived phenols as well as non-specific aromatic compounds whereas bagasse biochar was with both lignin derived phenol and poly aromatic hydrocarbon (PAH). Rice straw char was dominated with non-specific aromatic compounds. At 750oC, charred material was dominated with aromatic ethers while losing the aromatic C=C structures. These molecular and surface property differences likely contributed to the difference in water holding capacities observed with these biochars. On the other hand, rice straw biochars produced at different pyrolysis temperatures had no significant effect on rice germination. Soils treated with sugarcane leave/trash biochar significantly enhanced sugarcane growth especially the root length. Treating soil with either sugarcane leave or bagasse char also enhanced soil adsorption capacity of atrazine; a common herbicide used in sugarcane

  15. Rayada specialty: the forgotten resource of elite features of rice

    PubMed Central

    2013-01-01

    Crop domestication and thereafter gradual selection or directional breeding have narrowed the genetic diversity of elite varieties and even promoted gathering of deleterious mutations in their stress response mechanisms, whereas local ecotypes, landraces and wild relatives still growing on native environment and preferences keep the genetic diversities for features like stress tolerance. Rayada is such an exceptional ecotype, variant of typical deepwater rice, completely endemic to certain areas of Madhumati river tracts of Bangladesh and still shares some features of wild rices. Multiple physiological features of Rayadas are distinctly different from typical deepwater rice. Tolerance to prolonged flood, submergence and cold are special features along with strong photoperiod sensitivity and lack of dormancy. Moreover, longer root system and prompt recovery capacity make it as an elite resource of stress tolerance. However, it has long been neglected because of mainly its long life cycle and poor yield. This review examines the specialty of Rayada rice and the potential use of its unique traits. PMID:24359642

  16. Golden Rice is an effective source of vitamin A1234

    PubMed Central

    Qin, Jian; Dolnikowski, Gregory G; Russell, Robert M; Grusak, Michael A

    2009-01-01

    Background: Genetically engineered “Golden Rice” contains up to 35 μg β-carotene per gram of rice. It is important to determine the vitamin A equivalency of Golden Rice β-carotene to project the potential effect of this biofortified grain in rice-consuming populations that commonly exhibit low vitamin A status. Objective: The objective was to determine the vitamin A value of intrinsically labeled dietary Golden Rice in humans. Design: Golden Rice plants were grown hydroponically with heavy water (deuterium oxide) to generate deuterium-labeled [2H]β-carotene in the rice grains. Golden Rice servings of 65–98 g (130–200 g cooked rice) containing 0.99–1.53 mg β-carotene were fed to 5 healthy adult volunteers (3 women and 2 men) with 10 g butter. A reference dose of [13C10]retinyl acetate (0.4–1.0 mg) in oil was given to each volunteer 1 wk before ingestion of the Golden Rice dose. Blood samples were collected over 36 d. Results: Our results showed that the mean (±SD) area under the curve for the total serum response to [2H]retinol was 39.9 ± 20.7 μg·d after the Golden Rice dose. Compared with that of the [13C10]retinyl acetate reference dose (84.7 ± 34.6 μg·d), Golden Rice β-carotene provided 0.24–0.94 mg retinol. Thus, the conversion factor of Golden Rice β-carotene to retinol is 3.8 ± 1.7 to 1 with a range of 1.9–6.4 to 1 by weight, or 2.0 ± 0.9 to 1 with a range of 1.0–3.4 to 1 by moles. Conclusion: β-Carotene derived from Golden Rice is effectively converted to vitamin A in humans. This trial was registered at clinicaltrials.gov as NCT00680355. PMID:19369372

  17. Rice bran oil and human health.

    PubMed

    Sugano, M; Tsuji, E

    1996-09-01

    The available data in humans suggest that rice bran oil (RBO) is an edible oil of preference for improving plasma lipid and lipoprotein profiles similar to more commonly used vegetable oils. The observation that blending RBO with safflower oil at a specific proportion magnifies the hypocholesterolemic efficacy is of particular interest with regard to utilization of this oil. The occurrence of peculiar components such as gamma-oryzanol and tocotrienols in RBO might be responsible for its hypocholesterolemic effect.

  18. Dark septate endophyte decreases stress on rice plants.

    PubMed

    Santos, Silvana Gomes Dos; Silva, Paula Renata Alves da; Garcia, Andres Calderin; Zilli, Jerri Édson; Berbara, Ricardo Luis Louro

    Abiotic stress is one of the major limiting factors for plant development and productivity, which makes it important to identify microorganisms capable of increasing plant tolerance to stress. Dark septate endophytes can be symbionts of plants. In the present study, we evaluated the ability of dark septate endophytes isolates to reduce the effects of water stress in the rice varieties Nipponbare and Piauí. The experiments were performed under gnotobiotic conditions, and the water stress was induced with PEG. Four dark septate endophytes were isolated from the roots of wild rice (Oryza glumaepatula) collected from the Brazilian Amazon. Plant height as well as shoot and root fresh and dry matter were measured. Leaf protein concentrations and antioxidant enzyme activity were also estimated. The dark septate endophytes were grown in vitro in Petri dishes containing culture medium; they exhibited different levels of tolerance to salinity and water stress. The two rice varieties tested responded differently to inoculation with dark septate endophytes. Endophytes promoted rice plant growth both in the presence and in the absence of a water deficit. Decreased oxidative stress in plants in response to inoculation was observed in nearly all inoculated treatments, as indicated by the decrease in antioxidant enzyme activity. Dark septate endophytes fungi were shown to increase the tolerance of rice plants to stress caused by water deficiency.

  19. Molecular analysis of rice plant mutated after space flight

    NASA Astrophysics Data System (ADS)

    Cheng, Z.; Li, C.; Wei, L.; Xu, D.; Gu, D.; Guan, S.; Zhao, H.; Xin, P.; Sun, Y.

    We have obtained several rice mutants planted from seeds flown on recoverable satellites. Some new traits, such as good yields, diseases resistances and higher nutrient values, have been identified, putatively as consequences of the space environment. Radiation inside the Chinese recoverable satellite was composed of low flux of high energy particles (>40 Mev/u). To study the mechanisms of plant mutations induced by the space environment, we used dry rice seeds as a model to identify the phenotype of mutations, and used the wealth of the rice genome to identify the mutated genes in the mutants. The research included collecting rice plant mutants in the seeds flown on the satellites, identifying the nature of genomic and proteomic alterations, modifications and identifying the functional changes of the specific genes. The study showed that the rice seeds are a good model for exploring biological effect of space environment since 1) it is easy fly the seeds without specific hardware and crew work, 2) it is easy to obtain pure mutant breed lines for cloning DNA sequence in order to compare with the sequence in the wild type, and 3) it is easy to quantitatively analyze genetics using advanced molecular techniques.

  20. [Anopheles funestus and rice agriculture in the Madagascar highlands].

    PubMed

    Marrama, L; Rajaonarivelo, E; Laventure, S; Rabarison, P

    1995-01-01

    An exhaustive study of the potential habitats of Anopheles funestus was led during 1992 in Ankazobe on the Plateau of Madagascar, 95 km northwest of the capital Tananarive. The rice fields provide more than 90% of the positive habitats versus less than 10% for the nonhuman biotopes. Larva are especially abundant on the surfaces of the rice during grain head formation and maturation. The dense vegetation coverage provides them with shade and protection against predators. After harvesting, the follows can be filled with water and wild vegetation, and then also provide an important share of the habitats. The rice fields are omnipresent on the Plateau where they supply the basis of local alimentation. A. funestus then constitutes a serious risk for all of the villages. The role of the rice fields as habitats for A. funestus has already been noted in Kenya but in West Africa the rice fields do not host this species, even if this species is very abundant in the other types of habitats.

  1. Genetic structure and isolation by distance in a landrace of Thai rice

    PubMed Central

    Pusadee, Tonapha; Jamjod, Sansanee; Chiang, Yu-Chung; Rerkasem, Benjavan; Schaal, Barbara A.

    2009-01-01

    Rice is among the 3 most important crops worldwide. While much of the world's rice harvest is based on modern high-yield varieties, traditional varieties of rice grown by indigenous groups have great importance as a resource for future crop improvement. These local landraces represent an intermediate stage of domestication between a wild ancestor and modern varieties and they serve as reservoirs of genetic variation. Such genetic variation is influenced both by natural processes such as selection and drift, and by the agriculture practices of local farmers. How these processes interact to shape and change the population genetics of landrace rice is unknown. Here, we determine the population genetic structure of a single variety of landrace rice, Bue Chomee, cultivated by Karen people of Thailand. Microsatellite markers reveal high level of genetic variation despite predominant inbreeding in the crop. Bue Chomee rice shows slight but significant genetic differentiation among Karen villages. Moreover, genetically determined traits such as flowering time can vary significantly among villages. An unanticipated result was the overall pattern of genetic differentiation across villages which conforms to an isolation by distance model of differentiation. Isolation by distance is observed in natural plant species where the likelihood of gene flow is inversely related to distance. In Karen rice, gene flow is the result of farmers' seed sharing networks. Taken together, these data suggest that landrace rice is a dynamic genetic system that responds to evolutionary forces, both natural and those imposed by humans. PMID:19651617

  2. Development and field performance of nitrogen use efficient rice lines for Africa.

    PubMed

    Selvaraj, Michael Gomez; Valencia, Milton Orlando; Ogawa, Satoshi; Lu, Yingzhi; Wu, Liying; Downs, Christopher; Skinner, Wayne; Lu, Zhongjin; Kridl, Jean C; Ishitani, Manabu; van Boxtel, Jos

    2016-11-27

    Nitrogen (N) fertilizers are a major input cost in rice production, and its excess application leads to major environmental pollution. Development of rice varieties with improved nitrogen use efficiency (NUE) is essential for sustainable agriculture. Here, we report the results of field evaluations of marker-free transgenic NERICA4 (New Rice for Africa 4) rice lines overexpressing barley alanine amino transferase (HvAlaAT) under the control of a rice stress-inducible promoter (pOsAnt1). Field evaluations over three growing seasons and two rice growing ecologies (lowland and upland) revealed that grain yield of pOsAnt1:HvAlaAT transgenic events was significantly higher than sibling nulls and wild-type controls under different N application rates. Our field results clearly demonstrated that this genetic modification can significantly increase the dry biomass and grain yield compared to controls under limited N supply. Increased yield in transgenic events was correlated with increased tiller and panicle number in the field, and evidence of early establishment of a vigorous root system in hydroponic growth. Our results suggest that expression of the HvAlaAT gene can improve NUE in rice without causing undesirable growth phenotypes. The NUE technology described in this article has the potential to significantly reduce the need for N fertilizer and simultaneously improve food security, augment farm economics and mitigate greenhouse gas emissions from the rice ecosystem.

  3. Rice Body Formation Within a Peri-Articular Shoulder Mass.

    PubMed

    Edison, Michele N; Caram, Anthony; Flores, Miguel; Scherer, Kurt

    2016-08-01

    Most commonly associated with chronic inflammatory conditions, rice bodies represent an uncommon, nonspecific, often intra-articular inflammatory process. Presumably, rice bodies represent the sequelae of microvascular infarcts of the joint synovium. However, rice bodies have been seen in pleural fluid, in the setting of bursitis, and within the tendon sheath. The etiology and prognostic significance of rice bodies are not clear. MRI is the diagnostic imaging modality of choice for the evaluation of rice body formation. Here we present a case of a 28-year-old female with a history of rheumatoid arthritis (RA) who presented to her primary care physician with a palpable mass around her right shoulder which was presumed to be a lipoma. An initial ultrasound showed a fluid filled structure with internal debris. Subsequent MRI evaluation was confirmatory for subacromial-subdeltoid bursitis with rice body formation. The salient point of this report is to highlight the importance of patient-specific differential diagnosis. While lipomas are a very common benign soft tissue tumor, patients with RA often have disease-specific sequelae that should be included in the diagnostic deliberation. Thus, when ordering diagnostic testing for patients with a palpable mass and rheumatoid arthritis, MRI--possibly preceded by conventional radiography--is the most appropriate diagnostic algorithm.

  4. Effect of rice variety and nutrient management on rice productivity in organic rice system

    USDA-ARS?s Scientific Manuscript database

    Demand for organic rice has been increasing for decades. However, the information on sustainable organic rice production systems is still lacking. The objective of this study was to investigate the effects of soil amendment products, nitrogen rate, and variety on rice grain yield, yield components, ...

  5. Methane potential and biodegradability of rice straw, rice husk and rice residues from the drying process.

    PubMed

    Contreras, L M; Schelle, H; Sebrango, C R; Pereda, I

    2012-01-01

    Agricultural solid residues are a potential renewable energy source. Rice harvesting and production in Sancti Spíritus province, Cuba, currently generates residues without an environmentally sustainable disposal route. Rice residues (rice straw, rice husk and rice residues from the drying process) are potentially an important carbon source for anaerobic digestion. For this paper, rice residues were placed for 36 days retention time in anaerobic batch reactor environments at both mesophilic (37 °C) and thermophilic (55 °C) conditions. Biogas and methane yield were determined as well as biogas composition. The results showed that rice straw as well as rice residues from the drying process had the highest biogas and methane yield. Temperature played an important role in determining both biogas yield and kinetics. In all cases, rice straw produced the highest yields; under mesophilic conditions the biogas yield was 0.43 m(3) kg(VS)(-1), under thermophilic conditions biogas yield reached 0.52 m(3) kg(VS)(-1). In the case of the rice husk, the biodegradability was very low. Methane content in all batches was kept above 55% vol. All digested material had a high carbon:nitrogen (C:N) ratio, even though significant biodegradation was recorded with the exception of rice husk. A first-order model can be used to describe the rice crop residues fermentation effectively.

  6. Common Cold

    MedlinePlus

    ... nose, coughing - everyone knows the symptoms of the common cold. It is probably the most common illness. In ... avoid colds. There is no cure for the common cold. For relief, try Getting plenty of rest Drinking ...

  7. Wheel running in the wild.

    PubMed

    Meijer, Johanna H; Robbers, Yuri

    2014-07-07

    The importance of exercise for health and neurogenesis is becoming increasingly clear. Wheel running is often used in the laboratory for triggering enhanced activity levels, despite the common objection that this behaviour is an artefact of captivity and merely signifies neurosis or stereotypy. If wheel running is indeed caused by captive housing, wild mice are not expected to use a running wheel in nature. This however, to our knowledge, has never been tested. Here, we show that when running wheels are placed in nature, they are frequently used by wild mice, also when no extrinsic reward is provided. Bout lengths of running wheel behaviour in the wild match those for captive mice. This finding falsifies one criterion for stereotypic behaviour, and suggests that running wheel activity is an elective behaviour. In a time when lifestyle in general and lack of exercise in particular are a major cause of disease in the modern world, research into physical activity is of utmost importance. Our findings may help alleviate the main concern regarding the use of running wheels in research on exercise.

  8. Characterization of resistance to three bruchid species (Callosobruchus spp., Coleoptera, Bruchidae) in cultivated rice bean (Vigna umbellata).

    PubMed

    Kashiwaba, K; Tomooka, N; Kaga, A; Han, O K; Vaughan, D A

    2003-02-01

    Resistance of wild and cultivated rice bean (Vigna umbellata [Thunberg] Ohwi and Ohashi) to three bruchid species, Callosobruchus chinensis L., Callosobruchus maculatus F., and Callosobruchus analis F., was evaluated. All but three accessions of cultivated, and all wild rice bean accessions tested, exhibited complete resistance to all three bruchid species. Rice bean seeds with seed coat removed also showed complete resistance to the three bruchid species. Results indicate that physical attributes and/or chemical(s) present in the seed coat of rice bean are not the main factors responsible for resistance. Feeding tests were performed by using artificial beans prepared with varying proportions of rice bean (resistant) and azuki bean (susceptible) flour. Number of bruchid adults that emerged decreased, and larval developmental period (days) was extended, when artificial beans with an increasing proportion of rice bean flour were used. These tests revealed that a chemical compound(s) contained in the cotyledon of rice bean has an inhibitory effect on the growth of these bruchid species. The results also indicate that the chemical(s) in rice bean cotyledon is most effective against C. maculatus.

  9. A double built-in containment strategy for production of recombinant proteins in transgenic rice.

    PubMed

    Zhang, Xianwen; Wang, Dongfang; Zhao, Sinan; Shen, Zhicheng

    2014-01-01

    Using transgenic rice as a bioreactor for mass production of pharmaceutical proteins could potentially reduce the cost of production significantly. However, a major concern over the bioreactor transgenic rice is the risk of its unintended spreading into environment and into food or feed supplies. Here we report a mitigating method to prevent unwanted transgenic rice spreading by a double built-in containment strategy, which sets a selectively termination method and a visual tag technology in the T-DNA for transformation. We created transgenic rice with an inserted T-DNA that harbors a human proinsulin gene fused with the far-red fluorescent protein gene mKate_S158A, an RNAi cassette suppressing the expression of the rice bentazon detoxification enzyme CYP81A6, and an EPSPS gene as the selection marker for transformation. Herbicide spray tests indicated that such transgenic rice plants can be killed selectively by a spray of bentazon at regular field application dosage for rice weed control. Moreover, the transgenic rice seeds were bright red in color due to the fused far-red fluorescent protein, and could be easily visualized under daylight by naked eyes. Thus, the transgenic rice plants reported in this study could be selectively killed by a commonly used herbicide during their growth stage, and their seeds may be detected visually during processing and consumption after harvest. This double built-in containment strategy may greatly enhance the confinement of the transgenic rice.

  10. White rice sold in Hawaii, Guam, and Saipan often lacks nutrient enrichment

    PubMed Central

    Gebhardt, Susan E.; Holden, Joanne; Kretsch, Mary J.; Todd, Karen; Novotny, Rachel; Murphy, Suzanne P.

    2009-01-01

    Rice is a commonly consumed food staple for many Asian and Pacific cultures; thus nutrient enrichment of rice has the potential to increase nutrient intakes for these populations. The objective of this study was to determine the levels of enrichment nutrients (thiamin, niacin, iron, and folic acid) in white rice found in Guam, Saipan (CNMI), and Oahu (Hawaii). The proportion of white rice that was labeled enriched varied by type, bag size, and location. Most long-grain rice was labeled enriched, while most medium-grain rice was not. Bags of either type weighing over 10 pounds were seldom labeled enriched in Hawaii or Saipan. Samples of various types of rice were collected on these three islands (n=19, 12 of which were labeled enriched) and analyzed for their content of the enrichment nutrients. Rice that was labeled enriched in Hawaii and Guam seldom met the minimum enrichment standards for the US. For comparison, three samples of enriched rice from California were also analyzed, and all met the enrichment standards. Nutritionists who are planning or evaluating the diets of these Pacific island populations cannot assume that rice is enriched. PMID:19782173

  11. A Double Built-In Containment Strategy for Production of Recombinant Proteins in Transgenic Rice

    PubMed Central

    Zhao, Sinan; Shen, Zhicheng

    2014-01-01

    Using transgenic rice as a bioreactor for mass production of pharmaceutical proteins could potentially reduce the cost of production significantly. However, a major concern over the bioreactor transgenic rice is the risk of its unintended spreading into environment and into food or feed supplies. Here we report a mitigating method to prevent unwanted transgenic rice spreading by a double built-in containment strategy, which sets a selectively termination method and a visual tag technology in the T-DNA for transformation. We created transgenic rice with an inserted T-DNA that harbors a human proinsulin gene fused with the far-red fluorescent protein gene mKate_S158A, an RNAi cassette suppressing the expression of the rice bentazon detoxification enzyme CYP81A6, and an EPSPS gene as the selection marker for transformation. Herbicide spray tests indicated that such transgenic rice plants can be killed selectively by a spray of bentazon at regular field application dosage for rice weed control. Moreover, the transgenic rice seeds were bright red in color due to the fused far-red fluorescent protein, and could be easily visualized under daylight by naked eyes. Thus, the transgenic rice plants reported in this study could be selectively killed by a commonly used herbicide during their growth stage, and their seeds may be detected visually during processing and consumption after harvest. This double built-in containment strategy may greatly enhance the confinement of the transgenic rice. PMID:25531447

  12. Synergism between southern rice black-streaked dwarf virus and rice ragged stunt virus enhances their insect vector acquisition.

    PubMed

    Li, Shu; Wang, Han; Zhou, Guohui

    2014-07-01

    Southern rice black-streaked dwarf virus (SRBSDV), a tentative species in the genus Fijivirus, family Reoviridae, is a novel rice virus transmitted by the white-backed planthopper (Sogatella furcifera). Since its discovery in 2001, SRBSDV has spread rapidly throughout eastern and southeastern Asia and caused large rice losses in China and Vietnam. Rice ragged stunt virus (RRSV) (genus Oryzavirus, family Reoviridae) is a common rice virus vectored by the brown planthopper (Nilaparvata lugens). RRSV is also widely distributed in eastern and southeastern Asia but has not previously caused serious problems in China owing to its low incidence. With SRBSDV's spread, however, RRSV has become increasingly common in China, and is frequently found in co-infection with SRBSDV. In this study, we show that SRBSDV and RRSV interact synergistically, the first example of synergism between plant viruses in the family Reoviridae. Rice plants co-infected with both viruses displayed enhanced stunting, earlier symptoms, and higher virus titers compared with singly infected plants. Furthermore, white-backed and brown planthoppers acquired SRBSDV and RRSV, respectively, from co-infected plants at higher rates. We propose that increased RRSV incidence in Chinese fields is partly due to synergism between SRBSDV and RRSV.

  13. The Wild Bunch.

    ERIC Educational Resources Information Center

    Booth, Bibi; Brook, Richard; Tisdale, Mary; Wooster, Elizabeth

    2001-01-01

    Summarizes the history of wild horses in North America and explains the social structure of horses. Discusses issues related to wildlife management. Presents activities for classroom use and includes a list of references and resources. (YDS)

  14. The Wild Bunch.

    ERIC Educational Resources Information Center

    Booth, Bibi; Brook, Richard; Tisdale, Mary; Wooster, Elizabeth

    2001-01-01

    Summarizes the history of wild horses in North America and explains the social structure of horses. Discusses issues related to wildlife management. Presents activities for classroom use and includes a list of references and resources. (YDS)

  15. Organic rice disease management using genetic resistance, cover crop and organic fertilizer

    USDA-ARS?s Scientific Manuscript database

    The strong market demand for organic rice has driven the continued increase of organic rice production in the US. However, growers still lack effective tools to manage narrow brown leaf spot (NBLS) caused by Cercospora janseana and brown spot caused by Cochliobolus miyabeanus, two common diseases af...

  16. Biocontrol-based sheath blight management to reduce fungicide use on rice

    USDA-ARS?s Scientific Manuscript database

    Sheath blight (ShB) caused by Rhizoctonia solani is one of the most important rice diseases in Texas, Arkansas, Mississippi, and other southern states. The lack of complete ShB resistance in the most commonly planted varieties and the severity of this disease results in southern U.S. rice farmers ap...

  17. Reduced Dependence of Crested Ibis on Winter-Flooded Rice Fields: Implications for Their Conservation

    PubMed Central

    Sun, Yiwen; Skidmore, Andrew K.; Wang, Tiejun; van Gils, Hein A. M. J.; Wang, Qi; Qing, Baoping; Ding, Changqing

    2014-01-01

    The Crested Ibis Nipponia nippon was once thought to be extinct in the wild until seven birds were discovered in a remote mountain village in China in 1981. Studies suggested that winter-flooded rice fields play an essential role in nest site selection by the Crested Ibis and hence in their survival. Considerable efforts were therefore made to conserve the winter-flooded rice fields, but these have caused conflicts between the agricultural and conservation communities. The population and geographical range of the wild Crested Ibis has expanded greatly since 1981, but there is no spatial information on the winter-flooded rice fields, nor on the current association of nest sites and winter-flooded rice fields. We mapped winter-flooded rice fields across the entire current range of Crested Ibis using innovative remote sensing and geographical information systems (GIS) techniques. The spatial relationships between the nest site clusters and winter-flooded rice fields were quantified using Ward's hierarchical clustering method and Ripley's K-function. We show that both have significantly clumped distribution patterns and that they are positively associated. However, the dependence of Crested Ibis on the winter-flooded rice fields varied significantly among the nest site clusters and has decreased over the years, indicating the absence of winter-flooded rice fields is not constraining their recovery and population expansion. We therefore recommend that efforts should be made to protect the existing winter-flooded rice fields and to restore the functionality of natural and semi-natural wetlands, to encourage both in-situ conservation and the re-introduction of the Crested Ibis. In addition, we recommend that caution should be exercised when interpreting the habitat requirements of species with a narrow distribution, particularly when that interpretation is based only on their current habitat. PMID:24874870

  18. Reduced dependence of Crested Ibis on winter-flooded rice fields: implications for their conservation.

    PubMed

    Sun, Yiwen; Skidmore, Andrew K; Wang, Tiejun; van Gils, Hein A M J; Wang, Qi; Qing, Baoping; Ding, Changqing

    2014-01-01

    The Crested Ibis Nipponia nippon was once thought to be extinct in the wild until seven birds were discovered in a remote mountain village in China in 1981. Studies suggested that winter-flooded rice fields play an essential role in nest site selection by the Crested Ibis and hence in their survival. Considerable efforts were therefore made to conserve the winter-flooded rice fields, but these have caused conflicts between the agricultural and conservation communities. The population and geographical range of the wild Crested Ibis has expanded greatly since 1981, but there is no spatial information on the winter-flooded rice fields, nor on the current association of nest sites and winter-flooded rice fields. We mapped winter-flooded rice fields across the entire current range of Crested Ibis using innovative remote sensing and geographical information systems (GIS) techniques. The spatial relationships between the nest site clusters and winter-flooded rice fields were quantified using Ward's hierarchical clustering method and Ripley's K-function. We show that both have significantly clumped distribution patterns and that they are positively associated. However, the dependence of Crested Ibis on the winter-flooded rice fields varied significantly among the nest site clusters and has decreased over the years, indicating the absence of winter-flooded rice fields is not constraining their recovery and population expansion. We therefore recommend that efforts should be made to protect the existing winter-flooded rice fields and to restore the functionality of natural and semi-natural wetlands, to encourage both in-situ conservation and the re-introduction of the Crested Ibis. In addition, we recommend that caution should be exercised when interpreting the habitat requirements of species with a narrow distribution, particularly when that interpretation is based only on their current habitat.

  19. The Overproduction of Indole-3-Acetic Acid (IAA) in Endophytes Upregulates Nitrogen Fixation in Both Bacterial Cultures and Inoculated Rice Plants.

    PubMed

    Defez, Roberto; Andreozzi, Anna; Bianco, Carmen

    2017-08-01

    Endophytic bacteria from roots and leaves of rice plants were isolated and identified in order to select the diazotrophs and improve their nitrogen-fixing abilities. The nitrogen-fixing endophytes were identified by PCR amplification of the nifH gene fragment. For this purpose, two isolates, Enterobacter cloacae RCA25 and Klebsiella variicola RCA26, and two model bacteria (Herbaspirillum seropedicae z67 and Sinorhizobium fredii NGR234) were transformed to increase the biosynthesis of the main plant auxin indole-3-acetic acid (IAA). A significant increase in the production of IAA was observed for all strains. When the expression of nifH gene and the activity of the nitrogenase enzyme were analyzed in liquid cultures, we found that they were positively affected in the IAA-overproducing endophytes as compared to the wild-type ones. Rice plants inoculated with these modified strains showed a significant upregulation of the nitrogenase activity when plants infected with the wild-type strains were used as reference. Similar results were obtained too with common bean plants infected with the S. fredii NGR234 strain. These findings suggest that IAA overproduction improves nitrogen-fixing apparatus of endophytic bacteria both in liquid cultures and in inoculated host plants. The present study highlights new perspectives to enhance nitrogen-fixing ability in non-legume crops. These strains could be used as bioinoculants to improve the growth and the yield of agricultural crops, offering an alternative to the use of chemical nitrogen fertilizers.

  20. Epigenetic inheritance in rice plants.

    PubMed

    Akimoto, Keiko; Katakami, Hatsue; Kim, Hyun-Jung; Ogawa, Emiko; Sano, Cecile M; Wada, Yuko; Sano, Hiroshi

    2007-08-01

    Epigenetics is defined as mechanisms that regulate gene expression without base sequence alteration. One molecular basis is considered to be DNA cytosine methylation, which reversibly modifies DNA or chromatin structures. Although its correlation with epigenetic inheritance over generations has been circumstantially shown, evidence at the gene level has been limited. The present study aims to find genes whose methylation status directly correlates with inheritance of phenotypic changes. DNA methylation in vivo was artificially reduced by treating rice (Oryza sativa ssp. japonica) seeds with 5-azadeoxycytidine, and the progeny were cultivated in the field for > 10 years. Genomic regions with changed methylation status were screened by the methylation-sensitive amplified polymorphysm (MSAP) method, and cytosine methylation was directly scanned by the bisulfite mapping method. Pathogen infection with Xanthomonas oryzae pv. oryzae, race PR2 was performed by the scissors-dip method on mature leaf blades. The majority of seedlings were lethal, but some survived to maturity. One line designated as Line-2 showed a clear marker phenotype of dwarfism, which was stably inherited by the progeny over nine generations. MSAP screening identified six fragments, among which two were further characterized by DNA blot hybridization and direct methylation mapping. One clone encoding a retrotransposon gag-pol polyprotein showed a complete erasure of 5-methylcytosines in Line-2, but neither translocation nor expression of this region was detectable. The other clone encoded an Xa21-like protein, Xa21G. In wild-type plants, all cytosines were methylated within the promoter region, whereas in Line-2, corresponding methylation was completely erased throughout generations. Expression of Xa21G was not detectable in wild type but was constitutive in Line-2. When infected with X. oryzae pv. oryzae, against which Xa21 confers resistance in a gene-for-gene manner, the progeny of Line-2 were

  1. Why phenolic acids are unlikely primary allelochemicals in rice.

    PubMed

    Olofsdotter, Maria; Rebulanan, Malou; Madrid, Artemio; Dali, Wang; Navarez, Domingo; Olk, Daniel C

    2002-01-01

    Allelopathy in rice (Oryza sativa, L.) effective against weeds has been found in about 3.5% of tested rice germplasm in both laboratory and field experimentation. However, the allelochemicals responsible for growth inhibition of rice-associated weeds have not yet been identified. In the literature, phenolic acids are often mentioned as putative allelochemicals. If phenolic acids commonly reach growth inhibitory concentrations in rice ecosystems, it must be expected that the degree of tolerance to phenolic acids will vary among traditional rice cultivars or plant species adapted to rice environments having inherently different phenolic acid concentrations. Phenolic acids concentrations are normally greater in submerged than in aerobic soils. A dose-response study, however, showed that seedlings of rice cultivars adapted to submerged anaerobic soils did not have higher level of tolerance against p-hydroxybenzoic acid than did seedlings of varieties adapted to aerobic upland soils. Moreover, traditional rice cultivars had no greater tolerance than did improved cultivars that were recently bred for traits other than tolerance of phenolic acids. Similarly, there were no differences in tolerance of p-hydroxybenzoic acid between two Echinochloa weed species adapted to either anaerobic or aerobic growth conditions. Thus, neither the rice cultivars nor weed species had evolved different tolerance levels against the phenolic acid. However, all rice cultivars had significantly greater tolerance of p-hydroxybenzoic acid than did either weed species. In a second experiment, the rates at which rice plants released phenolic acids into solution cultures were measured for at least one month, the time period of greatest allelopathic activity following planting under field conditions. The maximum release rate of phenolic acids during the first month of growth was approximately 10 microg/plant/day. At a conventional plant density, the release rate of phenolic acids would be

  2. Rice disease management under organic production

    USDA-ARS?s Scientific Manuscript database

    Interest in organic rice production has increased because of the increased market demand for organic rice. Texas organic rice acreage has constantly increased over the last decade, reaching 32,000 acres in 2012. Texas is now the leading state in organic rice production in the U.S. Organic rice is p...

  3. Organic Rice Production: Challenges and Opportunities

    USDA-ARS?s Scientific Manuscript database

    The market demand for organically produced rice has grown steadily with the majority of the acreage now being located in Texas and California. A wide range of organic products are marketed including conventional long and medium grain rice, aromatic or scented rice, rice with colored bran, and rice f...

  4. Does the presence of microplastics influence the acute toxicity of chromium(VI) to early juveniles of the common goby (Pomatoschistus microps)? A study with juveniles from two wild estuarine populations.

    PubMed

    Luís, Luís G; Ferreira, Pedro; Fonte, Elsa; Oliveira, Miguel; Guilhermino, Lúcia

    2015-07-01

    presence of MP, the negative effect caused by high concentrations of Cr(VI) on the predatory performance was significantly reduced in L-est fish but not in M-est fish, and Cr(VI) concentrations higher than 3.9mg/l caused oxidative damage in L-est fish but not in M-est fish. The acclimatization and test conditions were similar for fish from the two estuaries and these ecosystems have environmental differences. Thus, long-term exposure to distinct environmental conditions in the natural habitat during previous developmental phases influenced the sensitivity and responses of juveniles to Cr(VI), therefore, we rejected hypothesis 3. Overall, the results of this study indicate toxicological interactions between MP and Cr(VI) highlighting the importance of further investigating the combined effects of MP and other common contaminants.

  5. An adjuvant free mouse model of oral allergenic sensitization to rice seeds protein.

    PubMed

    Chen, Xiao-Wei; Lau, Ken Wan-Keung; Yang, Fan; Sun, Samuel Sai-Ming; Fung, Ming-Chiu

    2011-05-23

    Rice is commonly known as a staple crop consumed worldwide, though with several rice proteins being reported for allergic properties in clinical studies. Thus, there is a growing need for the development of an animal model to better understand the allergenicity of rice proteins and the immunological and pathophysiological mechanisms underlying the development of food allergy. Groups of BALB/c mice were sensitized daily with freshly homogenized rice flour (30 mg or 80 mg) without adjuvant by intragastric gavage. In addition, the mice were challenged with extracted rice flour proteins at several time points intragastrically. Hypersensitivity symptoms in mice were evaluated according to a scoring system. Vascular leakage, ELISA of rice protein-specific IgE, histopathology of small intestine, and passive cutaneous anaphylaxis were conducted on challenged mice. An adjuvant free mouse model of rice allergy was established with sensitized mice showing increased scratching behaviors and increased vascular permeability. Rice protein-specific IgE was detected after eighteen days of sensitization and from the fifth challenge onwards. Inflammatory damage to the epithelium in the small intestine of mice was observed beyond one month of sensitization. Passive cutaneous anaphylaxis results confirmed the positive rice allergy in the mouse model. We introduced a BALB/c mouse model of rice allergy with simple oral sensitization without the use of adjuvant. This model would serve as a useful tool for further analysis on the immunopathogenic mechanisms of the various rice allergens, for the evaluation of the hypersensitivity of rice or other cereal grains, and to serve as a platform for the development of immunotherapies against rice allergens.

  6. Microarray Analysis of Rice d1 (RGA1) Mutant Reveals the Potential Role of G-Protein Alpha Subunit in Regulating Multiple Abiotic Stresses Such as Drought, Salinity, Heat, and Cold.

    PubMed

    Jangam, Annie P; Pathak, Ravi R; Raghuram, Nandula

    2016-01-01

    The genome-wide role of heterotrimeric G-proteins in abiotic stress response in rice has not been examined from a functional genomics perspective, despite the availability of mutants and evidences involving individual genes/processes/stresses. Our rice whole transcriptome microarray analysis (GSE 20925 at NCBI GEO) using the G-alpha subunit (RGA1) null mutant (Daikoku 1 or d1) and its corresponding wild type (Oryza sativa Japonica Nipponbare) identified 2270 unique differentially expressed genes (DEGs). Out of them, we mined for all the potentially abiotic stress-responsive genes using Gene Ontology terms, STIFDB2.0 and Rice DB. The first two approaches produced smaller subsets of the 1886 genes found at Rice DB. The GO approach revealed similar regulation of several families of stress-responsive genes in RGA1 mutant. The Genevestigator analysis of the stress-responsive subset of the RGA1-regulated genes from STIFDB revealed cold and drought-responsive clusters. Meta data analysis at Rice DB revealed large stress-response categories such as cold (878 up/810 down), drought (882 up/837 down), heat (913 up/777 down), and salt stress (889 up/841 down). One thousand four hundred ninety-eight of them are common to all the four abiotic stresses, followed by fewer genes common to smaller groups of stresses. The RGA1-regulated genes that uniquely respond to individual stresses include 111 in heat stress, eight each in cold only and drought only stresses, and two genes in salt stress only. The common DEGs (1498) belong to pathways such as the synthesis of polyamine, glycine-betaine, proline, and trehalose. Some of the common DEGs belong to abiotic stress signaling pathways such as calcium-dependent pathway, ABA independent and dependent pathway, and MAP kinase pathway in the RGA1 mutant. Gene ontology of the common stress responsive DEGs revealed 62 unique molecular functions such as transporters, enzyme regulators, transferases, hydrolases, carbon and protein metabolism

  7. Genetic structure and diversity of indigenous rice (Oryza sativa) varieties in the Eastern Himalayan region of Northeast India.

    PubMed

    Choudhury, Baharul; Khan, Mohamed Latif; Dayanandan, Selvadurai

    2013-12-01

    The Eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which may serve as a valuable genetic resource for future crop improvement to meet the ever-increasing demand for food production. However, these varieties are rapidly being lost due to changes in land-use and agricultural practices, which favor agronomically improved varieties. A detailed understanding of the genetic structure and diversity of indigenous rice varieties is crucial for efficient utilization of rice genetic resources and for developing suitable conservation strategies. To explore the genetic structure and diversity of rice varieties in NE India, we genotyped 300 individuals of 24 indigenous rice varieties representing sali, boro, jum and glutinous types, 5 agronomically improved varieties, and one wild rice species (O. rufipogon) using seven SSR markers. A total of 85 alleles and a very high level of gene diversity (0.776) were detected among the indigenous rice varieties of the region. Considerable level of genetic variation was found within indigenous varieties whereas improved varieties were monoporphic across all loci. The comparison of genetic diversity among different types of rice revealed that sali type possessed the highest gene diversity (0.747) followed by jum (0.627), glutinous (0.602) and boro (0.596) types of indigenous rice varieties, while the lowest diversity was detected in agronomically improved varieties (0.459). The AMOVA results showed that 66% of the variation was distributed among varieties indicating a very high level of genetic differentiation in rice varieties in the region. Two major genetically defined clusters corresponding to indica and japonica groups were detected in rice varieties of the region. Overall, traditionally cultivated indigenous rice varieties in NE India showed high levels of genetic diversity comparable to levels of genetic diversity reported from wild rice populations in various parts of the

  8. A single amino acid mutation of OsSBEIIb contributes to resistant starch accumulation in rice.

    PubMed

    Yang, Ruifang; Bai, Jianjiang; Fang, Jun; Wang, Ying; Lee, Gangseob; Piao, Zhongze

    2016-09-01

    Foods rich in resistant starch can help prevent various diseases, including diabetes, colon cancers, diarrhea, and chronic renal and hepatic diseases. Variations in starch biosynthesis enzymes could contribute to the high content of resistant starch in some cultivars of rice (Oryza sativa L.). Our previously published work indicated that the sbe3-rs gene in the rice mutant line, 'Jiangtangdao1' was a putative allele of the rice starch branching enzyme gene SBEIIb (previously known as SBE3); sbe3-rs might control the biosynthesis of the high resistant starch content in the rice line. Biomolecular analysis showed that the activity of SBEs was significantly lower in soluble extracts of immature seeds harvested from 'Jiangtangdao1' 15 days after flowering than in the extracts of the wild-type rice line 'Huaqingdao'. We performed gene complementation assays by introducing the wild-type OsSBEIIb into the sbe3-rs mutant 'Jiangtangdao1'. The genetically complemented lines demonstrated restored seed-related traits. The structures of endosperm amylopectin and the morphological and physicochemical properties of the starch granules in the transformants recovered to wild-type levels. This study provides evidence that sbe3-rs is a novel allele of OsSBEIIb, responsible for biosynthesis of high resistant starch in 'Jiangtangdao1'.

  9. A single amino acid mutation of OsSBEIIb contributes to resistant starch accumulation in rice

    PubMed Central

    Yang, Ruifang; Bai, Jianjiang; Fang, Jun; Wang, Ying; Lee, Gangseob; Piao, Zhongze

    2016-01-01

    Foods rich in resistant starch can help prevent various diseases, including diabetes, colon cancers, diarrhea, and chronic renal and hepatic diseases. Variations in starch biosynthesis enzymes could contribute to the high content of resistant starch in some cultivars of rice (Oryza sativa L.). Our previously published work indicated that the sbe3-rs gene in the rice mutant line, ‘Jiangtangdao1’ was a putative allele of the rice starch branching enzyme gene SBEIIb (previously known as SBE3); sbe3-rs might control the biosynthesis of the high resistant starch content in the rice line. Biomolecular analysis showed that the activity of SBEs was significantly lower in soluble extracts of immature seeds harvested from ‘Jiangtangdao1’ 15 days after flowering than in the extracts of the wild-type rice line ‘Huaqingdao’. We performed gene complementation assays by introducing the wild-type OsSBEIIb into the sbe3-rs mutant ‘Jiangtangdao1’. The genetically complemented lines demonstrated restored seed-related traits. The structures of endosperm amylopectin and the morphological and physicochemical properties of the starch granules in the transformants recovered to wild-type levels. This study provides evidence that sbe3-rs is a novel allele of OsSBEIIb, responsible for biosynthesis of high resistant starch in ‘Jiangtangdao1’. PMID:27795673

  10. Branching in rice.

    PubMed

    Wang, Yonghong; Li, Jiayang

    2011-02-01

    Rice branching, including the formation of tillers and panicle branches, has been well investigated over the past several years because of its agronomic importance. A major breakthrough in elucidating rice tillering in the recent years was the discovery of strigolactones, a specific group of terpenoid lactones that can inhibit axillary bud outgrowth. Since that discovery, new tillering mutants, that is, dwarf 27 (d27) or dwarf14 (d14, also reported as d88 or htd2), have been identified with reduced strigolactone levels or strigolactone response. DWARF27 (D27) and DWARF14 (D14) probably act on strigolactone biosynthesis and signal transduction, respectively. Additionally, several genes controlling panicle branches have been identified recently. DEP1 and IPA1/WFP are essential dominant/semidominant regulators that determine rice panicle branches and thus affect the grain yields. More importantly, dep1 and ipa1 alleles have been shown to be applicable for the improvement of rice grain yields in molecular breeding. Copyright © 2010 Elsevier Ltd. All rights reserved.

  11. Rice: chemistry and technology.

    USDA-ARS?s Scientific Manuscript database

    Rice has taken center stage this last decade, not only as an important provider of nourishment for the world’s population, but as a grain now recognized as having many unique nutritional and functional attributes with potential to be captured in a multitude of value-added food and non-food applicati...

  12. Exploring Japan through Rice.

    ERIC Educational Resources Information Center

    Wojtan, Linda S.

    1998-01-01

    Explores the role of rice in Japanese culture by presenting historical background and teaching activities in a variety of categories, such as language, sociology, history, and contemporary politics. Suggests teachers create cross-cultural comparisons; for example, the role of corn in the United States. Provides a list of teacher resources. (CMK)

  13. Rice bran phytonutrients

    USDA-ARS?s Scientific Manuscript database

    The bran layer of the whole grain rice contains potential health-beneficial compounds. These include vitamin E homologs (tocopherols, tocotrienols), oryzanol fractions, simple phenolics and poly-phenolics. These are antioxidants that are believed to provide protection against diseases such as cancer...

  14. D-Psicose induces upregulation of defense-related genes and resistance in rice against bacterial blight.

    PubMed

    Kano, Akihito; Hosotani, Kouji; Gomi, Kenji; Yamasaki-Kokudo, Yumiko; Shirakawa, Chikage; Fukumoto, Takeshi; Ohtani, Kouhei; Tajima, Shigeyuki; Izumori, Ken; Tanaka, Keiji; Ishida, Yutaka; Nishizawa, Yoko; Ichimura, Kazuya; Tada, Yasuomi; Akimitsu, Kazuya

    2011-10-15

    We examined rice responses to a rare sugar, d-psicose. Rice growth was inhibited by d-psicose but not by common sugars. Microarray analysis revealed that d-psicose treatment caused an upregulation of many defense-related genes in rice, and dose-dependent upregulation of these genes was confirmed by quantitative reverse-transcription polymerase chain reaction. The level of upregulation of defense-related genes by d-psicose was low compared with that by d-allose, which is another rare sugar known to confer induction of resistance to rice bacterial blight in rice. Treatment with d-psicose conferred resistance to bacterial blight in rice in a dose-dependent manner, and the results indicate that d-psicose might be a candidate plant activator for reducing disease development in rice.

  15. 7 CFR 868.310 - Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice. (See also Â... classes Long Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice..., but any device or method which gives equivalent results may be used. 4 These limits do not apply to...

  16. 7 CFR 868.310 - Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice. (See also Â... classes Long Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice..., but any device or method which gives equivalent results may be used. 4 These limits do not apply to...

  17. Rice Glycosyltransferase (GT) Phylogenomic Database

    DOE Data Explorer

    Ronald, Pamela

    The Ronald Laboratory staff at the University of California-Davis has a primary research focus on the genes of the rice plant. They study the role that genetics plays in the way rice plants respond to their environment. They created the Rice GT Database in order to integrate functional genomic information for putative rice Glycosyltransferases (GTs). This database contains information on nearly 800 putative rice GTs (gene models) identified by sequence similarity searches based on the Carbohydrate Active enZymes (CAZy) database. The Rice GT Database provides a platform to display user-selected functional genomic data on a phylogenetic tree. This includes sequence information, mutant line information, expression data, etc. An interactive chromosomal map shows the position of all rice GTs, and links to rice annotation databases are included. The format is intended to "facilitate the comparison of closely related GTs within different families, as well as perform global comparisons between sets of related families." [From http://ricephylogenomics.ucdavis.edu/cellwalls/gt/genInfo.shtml] See also the primary paper discussing this work: Peijian Cao, Laura E. Bartley, Ki-Hong Jung and Pamela C. Ronalda. Construction of a Rice Glycosyltransferase Phylogenomic Database and Identification of Rice-Diverged Glycosyltransferases. Molecular Plant, 2008, 1(5): 858-877.

  18. Elevated production of melatonin in transgenic rice seeds expressing rice tryptophan decarboxylase.

    PubMed

    Byeon, Yeong; Park, Sangkyu; Lee, Hyoung Yool; Kim, Young-Soon; Back, Kyoungwhan

    2014-04-01

    A major goal of plant biotechnology is to improve the nutritional qualities of crop plants through metabolic engineering. Melatonin is a well-known bioactive molecule with an array of health-promoting properties, including potent antioxidant capability. To generate melatonin-rich rice plants, we first independently overexpressed three tryptophan decarboxylase isogenes in the rice genome. Melatonin levels were altered in the transgenic lines through overexpression of TDC1, TDC2, and TDC3; TDC3 transgenic seed (TDC3-1) had melatonin concentrations 31-fold higher than those of wild-type seeds. In TDC3 transgenic seedlings, however, only a doubling of melatonin content occurred over wild-type levels. Thus, a seed-specific accumulation of melatonin appears to occur in TDC3 transgenic lines. In addition to increased melatonin content, TDC3 transgenic lines also had enhanced levels of melatonin intermediates including 5-hydroxytryptophan, tryptamine, serotonin, and N-acetylserotonin. In contrast, expression levels of melatonin biosynthetic mRNA did not increase in TDC3 transgenic lines, indicating that increases in melatonin and its intermediates in these lines are attributable exclusively to overexpression of the TDC3 gene.

  19. Rice Sheath Rot: An Emerging Ubiquitous Destructive Disease Complex

    PubMed Central

    Bigirimana, Vincent de P.; Hua, Gia K. H.; Nyamangyoku, Obedi I.; Höfte, Monica

    2015-01-01

    Around one century ago, a rice disease characterized mainly by rotting of sheaths was reported in Taiwan. The causal agent was identified as Acrocylindrium oryzae, later known as Sarocladium oryzae. Since then it has become clear that various other organisms can cause similar disease symptoms, including Fusarium sp. and fluorescent pseudomonads. These organisms have in common that they produce a range of phytotoxins that induce necrosis in plants. The same agents also cause grain discoloration, chaffiness, and sterility and are all seed-transmitted. Rice sheath rot disease symptoms are found in all rice-growing areas of the world. The disease is now getting momentum and is considered as an important emerging rice production threat. The disease can lead to variable yield losses, which can be as high as 85%. This review aims at improving our understanding of the disease etiology of rice sheath rot and mainly deals with the three most reported rice sheath rot pathogens: S. oryzae, the Fusarium fujikuroi complex, and Pseudomonas fuscovaginae. Causal agents, pathogenicity determinants, interactions among the various pathogens, epidemiology, geographical distribution, and control options will be discussed. PMID:26697031

  20. Rice Sheath Rot: An Emerging Ubiquitous Destructive Disease Complex.

    PubMed

    Bigirimana, Vincent de P; Hua, Gia K H; Nyamangyoku, Obedi I; Höfte, Monica

    2015-01-01

    Around one century ago, a rice disease characterized mainly by rotting of sheaths was reported in Taiwan. The causal agent was identified as Acrocylindrium oryzae, later known as Sarocladium oryzae. Since then it has become clear that various other organisms can cause similar disease symptoms, including Fusarium sp. and fluorescent pseudomonads. These organisms have in common that they produce a range of phytotoxins that induce necrosis in plants. The same agents also cause grain discoloration, chaffiness, and sterility and are all seed-transmitted. Rice sheath rot disease symptoms are found in all rice-growing areas of the world. The disease is now getting momentum and is considered as an important emerging rice production threat. The disease can lead to variable yield losses, which can be as high as 85%. This review aims at improving our understanding of the disease etiology of rice sheath rot and mainly deals with the three most reported rice sheath rot pathogens: S. oryzae, the Fusarium fujikuroi complex, and Pseudomonas fuscovaginae. Causal agents, pathogenicity determinants, interactions among the various pathogens, epidemiology, geographical distribution, and control options will be discussed.

  1. Occupational noise in rice mills.

    PubMed

    Prasanna Kumar, G V; Dewangan, K N; Sarkar, Amaresh; Kumari, Amrita; Kar, Banani

    2008-01-01

    A major occupational hazard for the workers in rice mills is the noise during the operation of various machines. A noise survey was conducted in the workrooms of eight renowned rice mills of the north-eastern region of India established during the period between 1980 and 1985. The rice mills were selected on the basis of the outcome of a walk-through noise survey involving several rice mills of the region. A noise survey map of each rice mill was drawn to identify the predominant noise sources and the causes of high noise in the workrooms of the rice mill. The sound-pressure level (SPL) in the workrooms of the rice mill varied from 78 to 92 dBA. The paddy cleaner, rubber roll sheller, compartment separator, rice cleaner, auxiliary sieve shaker and an electric motor without enclosure were found to be the predominant noise sources in the workrooms of the mill. The causes of high noise in the rice mills may be attributed to the use of a long flat belt drive, crank-and-pitman mechanism, absence of an electric motor enclosure, poor machine maintenance and inadequate acoustic design of the workroom of the rice mill. About 26% of the total labourers were found to be exposed to higher levels of noise than 85 dBA. Subjective response indicated that about 26% of the total labourers felt noise interferes in their work and about 49% labourers were of opinion that noise interferes with their conversation. Noise from machines in the rice mills was found to be the major occupational hazard for the rice mill workers. The predominant noise sources need to be identified and the causes of high noise need to be studied to undertake the appropriate measures to reduce the noise level. To identify the predominant noise sources and their distributions in rice mills, to study the causes of high levels of noise in rice mills and to examine the response of the workers towards noise. A noise survey was conducted in eight renowned rice mills of the north-eastern region of India. The mills were

  2. Common cold

    MedlinePlus

    ... this page: //medlineplus.gov/ency/article/000678.htm Common cold To use the sharing features on this page, please enable JavaScript. The common cold most often causes a runny nose, nasal congestion, ...

  3. Pygmy Rice Rat as Potential Host of Castelo dos Sonhos Hantavirus

    PubMed Central

    Travassos da Rosa, Elizabeth S.; Medeiros, Daniele B. A.; Nunes, Márcio R.T.; Simith, Darlene B.; Pereira, Armando de Souza; Elkhoury, Mauro R.; Lavocat, Marília; Marques, Aparecido A.R.; Via, Alba Valéria; D’Andrea, Paulo; Bonvicino, Cibele R.; Lemos, Elba Regina S.

    2011-01-01

    To study the dynamics of wild rodent populations and identify potential hosts for hantavirus, we conducted an eco-epidemiologic study in Campo Novo do Parecis, Mato Grosso State, Brazil. We detected and genetically characterized Castelo dos Sonhos virus found in a species of pygmy rice rat (Oligoryzomys utiaritensis). PMID:21801642

  4. 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

  5. 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.

  6. Analysis of 142 genes resolves the rapid diversification of the rice genus

    PubMed Central

    Zou, Xin-Hui; Zhang, Fu-Min; Zhang, Jian-Guo; Zang, Li-Li; Tang, Liang; Wang, Jun; Sang, Tao; Ge, Song

    2008-01-01

    Background The completion of rice genome sequencing has made rice and its wild relatives an attractive system for biological studies. Despite great efforts, phylogenetic relationships among genome types and species in the rice genus have not been fully resolved. To take full advantage of rice genome resources for biological research and rice breeding, we will benefit from the availability of a robust phylogeny of the rice genus. Results Through screening rice genome sequences, we sampled and sequenced 142 single-copy genes to clarify the relationships among all diploid genome types of the rice genus. The analysis identified two short internal branches around which most previous phylogenetic inconsistency emerged. These represent two episodes of rapid speciation that occurred approximately 5 and 10 million years ago (Mya) and gave rise to almost the entire diversity of the genus. The known chromosomal distribution of the sampled genes allowed the documentation of whole-genome sorting of ancestral alleles during the rapid speciation, which was responsible primarily for extensive incongruence between gene phylogenies and persisting phylogenetic ambiguity in the genus. Random sample analysis showed that 120 genes with an average length of 874 bp were needed to resolve both short branches with 95% confidence. Conclusion Our phylogenomic analysis successfully resolved the phylogeny of rice genome types, which lays a solid foundation for comparative and functional genomic studies of rice and its relatives. This study also highlights that organismal genomes might be mosaics of conflicting genealogies because of rapid speciation and demonstrates the power of phylogenomics in the reconstruction of rapid diversification. PMID:18315873

  7. Ecotoxicology of wild mammals

    USGS Publications Warehouse

    Rattner, B.A.; Shore, R.F.

    2000-01-01

    An international group of 32 scientists has critically reviewed the scientific literature on exposure and effects of environmental contaminants in wild mammals. Although the absolute number of toxicological studies in domesticated and wild mammals eclipses that for birds, a detailed examination of scientific publications and databases reveal that information for 'wild' birds is actually greater than that for 'wild' mammals. Of the various taxa of mammals, ecotoxicological data is most noticeably lacking for marsupials and monotremes. In contrast, rodents (comprising 43% of all mammal species) have been studied extensively, despite evidence of their tolerance to some organochlorine compounds, rodenticides, and even radionuclides. Mammalian species at greatest risk of exposure include those that consume a high percentage of their body weight on a daily basis (e.g., shrews, moles and bats). Aquatic mammals tend to bioaccumulate tremendous burdens of lipophilic contaminants, although storage in their fat depots may actually limit toxicity. Carnivores appear to be more sensitive to adverse effects of environmental contaminants than herbivores. Remarkably few of the thousands of compounds manufactured worldwide have been toxicologically evaluated in wild mammals, and concentrations of even fewer have been monitored in tissues. Overarching research needs include: development of new exposure/effects models and better methods for estimation of species sensitivities; generation of comparative data on contaminant bioavailability, sublethal responses and detoxication mechanisms; enhanced understanding of pesticide, industrial contaminant and metal interactions; identification of endocrine disruptive contaminants and their overall ecological significance; and finally, estimating the relative contribution of environmental contamination as a factor affecting wild mammal populations.

  8. Accelerated Solvent Extraction of Insecticides from Rice Hulls, Rice Bran, and Polished Rice Grains.

    PubMed

    Teló, Gustavo Mack; Senseman, Scott Allen; Marchesan, Enio; Camargo, Edinalvo Rabaioli; Carson, Katherine

    2017-03-01

    Analysis of pesticide residues in irrigated rice grains is important for food security. In this study, we analyzed accelerated solvent extraction (ASE) conditions for the extraction of thiamethoxam and chlorantraniliprole insecticides from rice hulls, rice bran, and polished rice grains. Several variables, including extraction solvent, extraction temperature, extraction pressure, cell size, static extraction time, and sample concentration, were investigated. The average recoveries of the three matrixes were between 89.7 and 109.7% at the fortification level of 0.75 mg/kg. The optimum ASE operating conditions were acetonitrile (100%) as extraction solvent, extraction temperature of 75°C for rice hulls and 100°C for rice bran and polished rice grains, extraction cell pressure of 10.3 MPa, 22 mL cell size, and two extraction cycles. The total extraction time was approximately 25 min. The extracted volume was evaporated to dryness and the residues were redissolved in 2 mL acetonitrile after 1 min of vortex-shaking. Thiamethoxam and chlorantraniliprole were analyzed by ultra-HPLC with tandem MS. In conclusion, ASE in rice hulls, rice bran, and polished rice grains offers the possibility of a fast and simple method for obtaining a quantitative extraction of the studied pesticides.

  9. 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.

  10. The Rice Aquaporin Lsi1 Mediates Uptake of Methylated Arsenic Species1[W

    PubMed Central

    Li, Ren-Ying; Ago, Yukiko; Liu, Wen-Ju; Mitani, Namiki; Feldmann, Jörg; McGrath, Steve P.; Ma, Jian Feng; Zhao, Fang-Jie

    2009-01-01

    Pentavalent methylated arsenic (As) species such as monomethylarsonic acid [MMA(V)] and dimethylarsinic acid [DMA(V)] are used as herbicides or pesticides, and can also be synthesized by soil microorganisms or algae through As methylation. The mechanism of MMA(V) and DMA(V) uptake remains unknown. Recent studies have shown that arsenite is taken up by rice (Oryza sativa) roots through two silicon transporters, Lsi1 (the aquaporin NIP2;1) and Lsi2 (an efflux carrier). Here we investigated whether these two transporters also mediate the uptake of MMA(V) and DMA(V). MMA(V) was partly reduced to trivalent MMA(III) in rice roots, but only MMA(V) was translocated to shoots. DMA(V) was stable in plants. The rice lsi1 mutant lost about 80% and 50% of the uptake capacity for MMA(V) and DMA(V), respectively, compared with the wild-type rice, whereas Lsi2 mutation had little effect. The short-term uptake kinetics of MMA(V) can be described by a Michaelis-Menten plus linear model, with the wild type having 3.5-fold higher Vmax than the lsi1 mutant. The uptake kinetics of DMA(V) were linear with the slope being 2.8-fold higher in the wild type than the lsi1 mutant. Heterologous expression of Lsi1 in Xenopus laevis oocytes significantly increased the uptake of MMA(V) but not DMA(V), possibly because of a very limited uptake of the latter. Uptake of MMA(V) and DMA(V) by wild-type rice was increased as the pH of the medium decreased, consistent with an increasing proportion of the undissociated species. The results demonstrate that Lsi1 mediates the uptake of undissociated methylated As in rice roots. PMID:19542298

  11. Biofortification of rice with the essential amino acid lysine: molecular characterization, nutritional evaluation, and field performance.

    PubMed

    Yang, Qing-Qing; Zhang, Chang-Quan; Chan, Man-Ling; Zhao, Dong-Sheng; Chen, Jin-Zhu; Wang, Qing; Li, Qian-Feng; Yu, Heng-Xiu; Gu, Ming-Hong; Sun, Samuel Sai-Ming; Liu, Qiao-Quan

    2016-07-01

    Rice (Oryza sativa L.), a major staple crop worldwide, has limited levels of the essential amino acid lysine. We previously produced engineered rice with increased lysine content by expressing bacterial aspartate kinase and dihydrodipicolinate synthase and inhibiting rice lysine ketoglutarate reductase/saccharopine dehydrogenase activity. However, the grain quality, field performance, and integration patterns of the transgenes in these lysine-enriched lines remain unclear. In the present study, we selected several elite transgenic lines with endosperm-specific or constitutive regulation of the above key enzymes but lacking the selectable marker gene. All target transgenes were integrated into the intragenic region in the rice genome. Two pyramid transgenic lines (High Free Lysine; HFL1 and HFL2) with free lysine levels in seeds up to 25-fold that of wild type were obtained via a combination of the above two transgenic events. We observed a dramatic increase in total free amino acids and a slight increase in total protein content in both pyramid lines. Moreover, the general physicochemical properties were improved in pyramid transgenic rice, but the starch composition was not affected. Field trials indicated that the growth of HFL transgenic rice was normal, except for a slight difference in plant height and grain colour. Taken together, these findings will be useful for the potential commercialization of high-lysine transgenic rice.

  12. Biofortification of rice with the essential amino acid lysine: molecular characterization, nutritional evaluation, and field performance

    PubMed Central

    Yang, Qing-qing; Zhang, Chang-quan; Chan, Man-ling; Zhao, Dong-sheng; Chen, Jin-zhu; Wang, Qing; Li, Qian-feng; Yu, Heng-xiu; Gu, Ming-hong; Sun, Samuel Sai-ming; Liu, Qiao-quan

    2016-01-01

    Rice (Oryza sativa L.), a major staple crop worldwide, has limited levels of the essential amino acid lysine. We previously produced engineered rice with increased lysine content by expressing bacterial aspartate kinase and dihydrodipicolinate synthase and inhibiting rice lysine ketoglutarate reductase/saccharopine dehydrogenase activity. However, the grain quality, field performance, and integration patterns of the transgenes in these lysine-enriched lines remain unclear. In the present study, we selected several elite transgenic lines with endosperm-specific or constitutive regulation of the above key enzymes but lacking the selectable marker gene. All target transgenes were integrated into the intragenic region in the rice genome. Two pyramid transgenic lines (High Free Lysine; HFL1 and HFL2) with free lysine levels in seeds up to 25-fold that of wild type were obtained via a combination of the above two transgenic events. We observed a dramatic increase in total free amino acids and a slight increase in total protein content in both pyramid lines. Moreover, the general physicochemical properties were improved in pyramid transgenic rice, but the starch composition was not affected. Field trials indicated that the growth of HFL transgenic rice was normal, except for a slight difference in plant height and grain colour. Taken together, these findings will be useful for the potential commercialization of high-lysine transgenic rice. PMID:27252467

  13. Plant defence suppression is mediated by a fungal sirtuin during rice infection by Magnaporthe oryzae.

    PubMed

    Fernandez, Jessie; Marroquin-Guzman, Margarita; Nandakumar, Renu; Shijo, Sara; Cornwell, Kathryn M; Li, Gang; Wilson, Richard A

    2014-10-01

    Crop destruction by the hemibiotrophic rice pathogen Magnaporthe oryzae requires plant defence suppression to facilitate extensive biotrophic growth in host cells before the onset of necrosis. How this is achieved at the genetic level is not well understood. Here, we report that a M. oryzae sirtuin, MoSir2, plays an essential role in rice defence suppression and colonization by controlling superoxide dismutase (SOD) gene expression. Loss of MoSir2 function in Δsir2 strains did not affect appressorial function, but biotrophic growth in rice cells was attenuated. Compared to wild type, Δsir2 strains failed to neutralize plant-derived reactive oxygen species (ROS) and elicited robust defence responses in rice epidermal cells that included elevated pathogenesis-related gene expression and granular depositions. Deletion of a SOD-encoding gene under MoSir2 control generated Δsod1 deletion strains that mimicked Δsir2 for impaired rice defence suppression, confirming SOD activity as a downstream output of MoSir2. In addition, comparative protein acetylation studies and forward genetic analyses identified a JmjC domain-containing protein as a likely target of MoSir2, and a Δsir2 Δjmjc double mutant was restored for MoSOD1 expression and defence suppression in rice epidermal cells. Together, this work reveals MoSir2 and MoJmjC as novel regulators of early rice cell infection.

  14. Transgenic rice as a novel production system for Melanocarpus and Pycnoporus laccases.

    PubMed

    de Wilde, Chris; Uzan, Eva; Zhou, Zhongyi; Kruus, Kristiina; Andberg, Martina; Buchert, Johanna; Record, Eric; Asther, Marcel; Lomascolo, Anne

    2008-08-01

    Laccases have numerous biotechnological applications, among them food processing. The widespread use of laccases has increased the demand for an inexpensive and safe source of recombinant enzyme. We explored the use of a rice-based system for the production of two fungal laccases derived from the ascomycete Melanocarpus albomyces and the basidiomycete Pycnoporus cinnabarinus. High-expression levels of active recombinant laccases were achieved by targeting expression to the endosperm of rice seeds. The laccase cDNAs were fused to a plant-derived signal sequence for targeting to the secretory pathway, and placed under the control of a constitutive seed-specific promoter fused to an intron for enhanced expression. This construct enabled the recovery of on average 0.1-1% of soluble laccase in total soluble proteins (TSP). The highest yields of recombinant laccases obtained in rice seeds were 13 and 39 ppm for riceMaL and ricePycL, respectively. The rice-produced laccases were purified and characterized. The wild-type and the recombinant proteins showed similar biochemical features in terms of molecular mass, pI, temperature and optimal pH and the N-terminus was correctly processed. Although presenting lower kinetic parameters, the rice-produced laccases were also suitable for the oxidative cross-linking of a food model substrate [maize-bran feruloylated arabinoxylans (AX)].

  15. Genomic variation associated with local adaptation of weedy rice during de-domestication

    PubMed Central

    Qiu, Jie; Zhou, Yongjun; Mao, Lingfeng; Ye, Chuyu; Wang, Weidi; Zhang, Jianping; Yu, Yongyi; Fu, Fei; Wang, Yunfei; Qian, Feijian; Qi, Ting; Wu, Sanling; Sultana, Most Humaira; Cao, Ya-Nan; Wang, Yu; Timko, Michael P.; Ge, Song; Fan, Longjiang; Lu, Yongliang

    2017-01-01

    De-domestication is a unique evolutionary process by which domesticated crops are converted into ‘wild predecessor like' forms. Weedy rice (Oryza sativa f. spontanea) is an excellent model to dissect the molecular processes underlying de-domestication. Here, we analyse the genomes of 155 weedy and 76 locally cultivated rice accessions from four representative regions in China that were sequenced to an average 18.2 × coverage. Phylogenetic and demographic analyses indicate that Chinese weedy rice was de-domesticated independently from cultivated rice and experienced a strong genetic bottleneck. Although evolving from multiple origins, critical genes underlying convergent evolution of different weedy types can be found. Allele frequency analyses suggest that standing variations and new mutations contribute differently to japonica and indica weedy rice. We identify a Mb-scale genomic region present in weedy rice but not cultivated rice genomes that shows evidence of balancing selection, thereby suggesting that there might be more complexity inherent to the process of de-domestication. PMID:28537247

  16. A Novel Reference Plasmid for the Qualitative Detection of Genetically Modified Rice in Food and Feed

    PubMed Central

    Dong, Mei; An, Na; Liang, Lixia; Wan, Yusong

    2015-01-01

    Rice is one of the most important food crops in the world. Genetically modified (GM) technology has been used in rice to confer herbicide tolerance and pathogen or insect resistance. China invests heavily in research on GM rice. By the end of 2014, at least 250 transgenic rice lines had been developed in China. To monitor the presence of GM rice in food and feed, we collected information on foreign elements from 250 transgenic rice lines and found 5 elements, including the Agrobacterium tumefaciens nopaline synthase terminator (T-NOS), the cauliflower mosaic virus 35S promoter (CaMV35S), the ubiquitin gene (Ubi), the bar gene, and the hygromycin phosphotransferase gene (Hpt), that are commonly present in GM rice. Therefore, we constructed a novel plasmid (pBJGMM001) that contains fragments of these elements and two endogenous reference genes (the sucrose phosphate synthase gene, SPS, and the phosphoenolpyruvate carboxylase gene, PEPC). pBJGMM001 can serve as a standard for detecting 96% of GM rice lines in China. The primers, amplicons, reaction mixture, and PCR program were developed based on Chinese National Standards. The protocol was validated and determined to be suitable for practical use in monitoring and identifying GM rice. PMID:26495318

  17. A novel reference plasmid for the qualitative detection of genetically modified rice in food and feed.

    PubMed

    Li, Liang; Dong, Mei; An, Na; Liang, Lixia; Wan, Yusong; Jin, Wujun

    2015-01-01

    Rice is one of the most important food crops in the world. Genetically modified (GM) technology has been used in rice to confer herbicide tolerance and pathogen or insect resistance. China invests heavily in research on GM rice. By the end of 2014, at least 250 transgenic rice lines had been developed in China. To monitor the presence of GM rice in food and feed, we collected information on foreign elements from 250 transgenic rice lines and found 5 elements, including the Agrobacterium tumefaciens nopaline synthase terminator (T-NOS), the cauliflower mosaic virus 35S promoter (CaMV35S), the ubiquitin gene (Ubi), the bar gene, and the hygromycin phosphotransferase gene (Hpt), that are commonly present in GM rice. Therefore, we constructed a novel plasmid (pBJGMM001) that contains fragments of these elements and two endogenous reference genes (the sucrose phosphate synthase gene, SPS, and the phosphoenolpyruvate carboxylase gene, PEPC). pBJGMM001 can serve as a standard for detecting 96% of GM rice lines in China. The primers, amplicons, reaction mixture, and PCR program were developed based on Chinese National Standards. The protocol was validated and determined to be suitable for practical use in monitoring and identifying GM rice.

  18. Mechanisms controlling arsenic uptake in rice grown in mining impacted regions in South China.

    PubMed

    Li, Junhui; Dong, Fei; Lu, Ying; Yan, Qiuyan; Shim, Hojae

    2014-01-01

    Foods produced on soils impacted by Pb-Zn mining activities are a potential health risk due to plant uptake of the arsenic (As) associated with such mining. A field survey was undertaken in two Pb-Zn mining-impacted paddy fields in Guangdong Province, China to assess As accumulation and translocation, as well as other factors influencing As in twelve commonly grown rice cultivars. The results showed that grain As concentrations in all the surveyed rice failed national food standards, irrespective of As speciation. Among the 12 rice cultivars, "SY-89" and "DY-162" had the least As in rice grain. No significant difference for As concentration in grain was observed between the rice grown in the two areas that differed significantly for soil As levels, suggesting that the amount of As contamination in the soil is not necessarily the overriding factor controlling the As content in the rice grain. The iron and manganese plaque on the root surface curtailed As accumulation in rice roots. Based on our results, the accumulation of As within rice plants was strongly associated with such soil properties such as silicon, phosphorus, organic matter, pH, and clay content. Understanding the factors and mechanisms controlling As uptake is important to develop mitigation measures that can reduce the amount of As accumulated in rice grains produced on contaminated soils.

  19. Mechanisms Controlling Arsenic Uptake in Rice Grown in Mining Impacted Regions in South China

    PubMed Central

    Lu, Ying; Yan, Qiuyan; Shim, Hojae

    2014-01-01

    Foods produced on soils impacted by Pb-Zn mining activities are a potential health risk due to plant uptake of the arsenic (As) associated with such mining. A field survey was undertaken in two Pb-Zn mining-impacted paddy fields in Guangdong Province, China to assess As accumulation and translocation, as well as other factors influencing As in twelve commonly grown rice cultivars. The results showed that grain As concentrations in all the surveyed rice failed national food standards, irrespective of As speciation. Among the 12 rice cultivars, “SY-89” and “DY-162” had the least As in rice grain. No significant difference for As concentration in grain was observed between the rice grown in the two areas that differed significantly for soil As levels, suggesting that the amount of As contamination in the soil is not necessarily the overriding factor controlling the As content in the rice grain. The iron and manganese plaque on the root surface curtailed As accumulation in rice roots. Based on our results, the accumulation of As within rice plants was strongly associated with such soil properties such as silicon, phosphorus, organic matter, pH, and clay content. Understanding the factors and mechanisms controlling As uptake is important to develop mitigation measures that can reduce the amount of As accumulated in rice grains produced on contaminated soils. PMID:25251438

  20. The integration of ground investigations and radar images on rice yield prediction

    NASA Astrophysics Data System (ADS)

    Syu, Chien-Hui; Lo, Wei-Shen; Guo, Horng-Yuh

    2016-04-01

    Rice is the staple food and the largest crop in terms of area in Taiwan. Developing the real-time and accurate methods to predict rice yield of large area is important for food security. However, due to the size of rice fields is small and fragmented, and the disturbed weather in Taiwan. It difficult to acquire the information of cropping area and rice yield by optical satellite data, such as SPOT and FORMOSAT-2, because of the cloud cover commonly observed in the region. In contrast, the RADARSAT image data can overcome such problems due to which can penetrate through cloud. The aim of this study is to integrate the data of ground investigations and radar images to predict the rice yield of large area. We used the data of rice yield (ground investigation) and radar images to do regression analysis, and then predict the rice yield of large area. The results of ground investigation indicated that there were high correlation between sample sites yield and real harvest yield (R2 = 0.99), it reveals the investigating method has a high representativeness. The results of the pr