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

Science.gov (United States)

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.

Newly Identified Wild Rice Accessions Conferring High Salt Tolerance Might Use a Tissue Tolerance Mechanism in Leaf

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Prusty, Manas R.; Kim, Sung-Ryul; Vinarao, Ricky; Entila, Frederickson; Egdane, James; Diaz, Maria G. Q.; Jena, Kshirod K.

2018-01-01

Cultivated rice (Oryza sativa L.) is very sensitive to salt stress. So far a few rice landraces have been identified as a source of salt tolerance and utilized in rice improvement. These tolerant lines primarily use Na+ exclusion mechanism in root which removes Na+ from the xylem stream by membrane Na+ and K+ transporters, and resulted in low Na+ accumulation in shoot. Identification of a new donor source conferring high salt tolerance is imperative. Wild relatives of rice having wide genetic diversity are regarded as a potential source for crop improvement. However, they have been less exploited against salt stress. Here, we simultaneously evaluated all 22 wild Oryza species along with the cultivated tolerant lines including Pokkali, Nona Bokra, and FL478, and sensitive check varieties under high salinity (240 mM NaCl). Based on the visual salt injury score, three species (O. alta, O. latifolia, and O. coarctata) and four species (O. rhizomatis, O. eichingeri, O. minuta, and O. grandiglumis) showed higher and similar level of tolerance compared to the tolerant checks, respectively. All three CCDD genome species exhibited salt tolerance, suggesting that the CCDD genome might possess the common genetic factors for salt tolerance. Physiological and biochemical experiments were conducted using the newly isolated tolerant species together with checks under 180 mM NaCl. Interestingly, all wild species showed high Na+ concentration in shoot and low concentration in root unlike the tolerant checks. In addition, the wild-tolerant accessions showed a tendency of a high tissue tolerance in leaf, low malondialdehyde level in shoot, and high retention of chlorophyll in the young leaves. These results suggest that the wild species employ tissue tolerance mechanism to manage salt stress. Gene expression analyses of the key salt tolerance-related genes suggested that high Na+ in leaf of wild species might be affected by OsHKT1;4-mediated Na+ exclusion in leaf and the following Na

Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex.

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Singh, Balwant; Singh, Nisha; Mishra, Shefali; Tripathi, Kabita; Singh, Bikram P; Rai, Vandna; Singh, Ashok K; Singh, Nagendra K

2018-01-01

Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India's huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon , and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated 'Pro-Indica,' 'Pro-Aus,' and 'Mid-Gangetic,' which showed poor correspondence with the morpho - taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the 'Pro-Indica' and 'Pro-Aus' sub-populations across agro-climatic zones, indicating a more

Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex

Science.gov (United States)

Singh, Balwant; Singh, Nisha; Mishra, Shefali; Tripathi, Kabita; Singh, Bikram P.; Rai, Vandna; Singh, Ashok K.; Singh, Nagendra K.

2018-01-01

Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India’s huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon, and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated ‘Pro-Indica,’ ‘Pro-Aus,’ and ‘Mid-Gangetic,’ which showed poor correspondence with the morpho-taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the ‘Pro-Indica’ and ‘Pro-Aus’ sub-populations across agro-climatic zones

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

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Cruz-Garcia Gisella S

2011-11-01

Full Text Available Abstract 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.

Phylogeny and biogeography of North-American wild rice (Zizania L.Poaceae)

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The wild-rice genus Zizania includes four species disjunctly distributed in eastern Asia and North America, with three species (Z. aquatica, Z. palustris, and Z. texana) in North America and one (Z. latifolia) in eastern Asia. The phylogeny and biogeography of Zizania were explored using sequences o...

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice

OpenAIRE

Wang, Hongru; Garrett Vieira, Filipe Jorge; Crawford, Jacob E.; Chu, Chengcai; Nielsen, Rasmus

2017-01-01

The domestication history of rice remains controversial, with multiple studies reaching different conclusions regarding its origin(s). These studies have generally assumed that populations of living wild rice, O. rufipogon, are descendants of the ancestral population that gave rise to domesticated rice, but relatively little attention has been paid to the origins and history of wild rice itself. Here, we investigate the genetic ancestry of wild rice by analyzing a diverse panel of rice genome...

?-Oryzanols of North American Wild Rice (Zizania palustris)

OpenAIRE

Aladedunye, Felix; Przybylski, Roman; Rudzinska, Magdalena; Klensporf-Pawlik, Dorota

2013-01-01

?-Oryzanol, a natural mixture of ferulic acid esters of triterpene alcohols and sterols, are an important bioactive components present in rice bran oil. In light of the recent increase in the popularity of wild rice among consumers, and the possibility of a direct relationship between ?-oryzanol composition and its bioactivity, the oryzanol profile of major wild rice (Zizania palustris) grown in North America was studied and compared to regular brown rice (Oryza sativa L.). A total of twenty-...

Morphoagronomic genetic diversity in american wild rice species

Directory of Open Access Journals (Sweden)

Elizabeth Ann Veasey

2008-02-01

Full Text Available To characterize the genetic variability among species and populations of South American wild rice, eleven populations of Oryza glumaepatula, seven of O. grandiglumis, four of O. latifolia and one of O. alta, from Brazil and Argentina, were evaluated. A greenhouse experiment was conducted in completely randomized blocks with 23 treatments. Twenty morphoagronomic traits were assessed. Univariate analyses were performed with 16 quantitative traits with the partitioning of populations within species. Significant differences (pVisando caracterizar a diversidade genética entre espécies e populações de arroz selvagem da América do Sul, foram avaliadas 11 populações de Oryza glumaepatula, sete de O. grandiglumis, quatro de O. latifolia e uma população de O. alta, originárias do Brasil e Argentina. Foi conduzido um experimento em casa-de-vegetação em blocos ao acaso com 23 tratamentos. Vinte caracteres agro-morfológicos foram avaliados. Análises univariadas foram realizadas para 16 caracteres quantitativos, desdobrando-se o efeito de populações dentro de espécies. Diferenças significativas (p<0,001 entre espécies foram observadas para todos os caracteres bem como entre populações dentro de espécies. A mais variável foi O. glumaepatula seguida de O. latifolia. Análises de agrupamento e discriminante canônica confirmaram a separação das populações de O. glumaepatula das espécies tetraplóides, e a grande variação genética entre populações de O. latifolia. Diferenças morfológicas entre as três espécies tetraplóides parecem suficientes para classificá-las como espécies pelo menos na condição statu nascendi.

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

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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.

Modeling the relationship between water level, wild rice abundance, and waterfowl abundance at a central North American wetland

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Aagaard, Kevin; Eash, Josh D.; Ford, Walt; Heglund, Patricia J.; McDowell, Michelle; Thogmartin, Wayne E.

2018-01-01

Recent evidence suggests wild rice (Zizania palustris), an important resource for migrating waterfowl, is declining in parts of central North America, providing motivation to rigorously quantify the relationship between waterfowl and wild rice. A hierarchical mixed-effects model was applied to data on waterfowl abundance for 16 species, wild rice stem density, and two measures of water depth (true water depth at vegetation sampling locations and water surface elevation). Results provide evidence for an effect of true water depth (TWD) on wild rice abundance (posterior mean estimate for TWD coefficient, β TWD = 0.92, 95% confidence interval = 0.11—1.74), but not for an effect of wild rice stem density or water surface elevation on local waterfowl abundance (posterior mean values for relevant parameters overlapped 0). Refined protocols for sampling design and more consistent sampling frequency to increase data quality should be pursued to overcome issues that may have obfuscated relationships evaluated here.

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

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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.

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

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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.

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

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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.

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

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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. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

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

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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.

Diseases of wild rice

Science.gov (United States)

Diseases are much more pronounced in cultivated wild rice than in natural stands, most likely due to the narrower genetic base of the populations, plant stress due to high planting density and floodwater removal prior to harvest, and high relative humidity in the plant canopy. Yield losses occur as ...

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

Science.gov (United States)

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...

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

Science.gov (United States)

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.

7 CFR 457.170 - Cultivated wild rice crop insurance provisions.

Science.gov (United States)

2010-01-01

... reinsured policies: Cultivated Wild Rice Crop Provisions. 1. Definitions Approved laboratory. A testing.... Cultivated Wild Rice. A member of the grass family Zizania Palustris L., adapted for growing in man-made... for the crop year. Planted acreage. In addition to the definition contained in the Basic Provisions...

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

OpenAIRE

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 b...

Os11Gsk gene from a wild rice, Oryza rufipogon improves yield in rice.

Science.gov (United States)

Thalapati, Sudhakar; Batchu, Anil K; Neelamraju, Sarla; Ramanan, Rajeshwari

2012-06-01

Chromosomal segments from wild rice species Oryza rufipogon, introgressed into an elite indica rice restorer line (KMR3) using molecular markers, resulted in significant increase in yield. Here we report the transcriptome analysis of flag leaves and fully emerged young panicles of one of the high yielding introgression lines IL50-7 in comparison to KMR3. A 66-fold upregulated gene Os11Gsk, which showed no transcript in KMR3 was highly expressed in O. rufipogon and IL50-7. A 5-kb genomic region including Os11Gsk and its flanking regions could be PCR amplified only from IL50-7, O. rufipogon, japonica varieties of rice-Nipponbare and Kitaake but not from the indica varieties, KMR3 and Taichung Native-1. Three sister lines of IL50-7 yielding higher than KMR3 showed presence of Os11Gsk, whereas the gene was absent in three other ILs from the same cross having lower yield than KMR3, indicating an association of the presence of Os11Gsk with high yield. Southern analysis showed additional bands in the genomic DNA of O. rufipogon and IL50-7 with Os11Gsk probe. Genomic sequence analysis of ten highly co-expressed differentially regulated genes revealed that two upregulated genes in IL50-7 were derived from O. rufipogon and most of the downregulated genes were either from KMR3 or common to KMR3, IL50-7, and O. rufipogon. Thus, we show that Os11Gsk is a wild rice-derived gene introduced in KMR3 background and increases yield either by regulating expression of functional genes sharing homology with it or by causing epigenetic modifications in the introgression line.

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

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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. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

Competitive and Allelopathic Effects of Wild Rice Accessions (Oryza longistaminata) at Different Growth Stages.

Science.gov (United States)

Shen, Shicai; Xu, Gaofeng; Clements, David Roy; Jin, Guimei; Zhang, Fudou; Tao, Dayun; Xu, Peng

2016-01-01

The competitive and allelopathic effects of wild rice (Oryza longistaminata) accessions on barnyard grass at different growth stages determined by days after sowing (0, 30, 60 and 90 days) were studied in greenhouse pot experiments. Wild rice accession RL159 exhibited the greatest height and tillering. The weed suppression rates of wild rice accessions OL and F1 on barnyard grass were significantly higher than for other rice accessions, with the lowest being O. sativa cultivar RD23. The highest suppression rates of OL and F1 were 80.23 and 73.96% at barnyard grass growth stages of 90 days and 60 days. At a 90 growth stage, wild rice accessions RL159 and RL169 caused 61.33 and 54.51% inhibition in barnyard grass growth, respectively. Under the same conditions, the competitive inhibition rates of OL, F1, RL159, RL169 and RL219 against barnyard grass were markedly lower than their weed suppressive effects, but were relatively similar for RD23. The allelopathic inhibition of OL and F1 on barnyard grass was significantly higher than other rice accessions. The highest allelopathic rates of OL and F1 were 60.61 and 56.87% at the 0 day growth stage. It is concluded that wild rice accessions OL and F1 exhibited the highest allelopathic activity along with moderate competitive ability against barnyard grass; wild rice accession RL159 had the highest competitive ability and moderate allelopathic activity on barnyard grass. Thus, the three wild rice accessions OL, F1 and RL159 could be used as ideal breeding materials for cultivated rice improvement.

Gene interaction at seed-awning loci in the genetic background of wild rice.

Science.gov (United States)

Ikemoto, Mai; Otsuka, Mitsuharu; Thanh, Pham Thien; Phan, Phuong Dang Thai; Ishikawa, Ryo; Ishii, Takashige

2017-09-12

Seed awning is one of the important traits for successful propagation in wild rice. During the domestication of rice by ancient humans, plants with awnless seeds may have been selected because long awns hindered collection and handling activities. To investigate domestication of awnless rice, QTL analysis for seed awning was first carried out using backcross recombinant inbred lines between Oryza sativa Nipponbare (recurrent parent) and O. rufipogon W630 (donor parent). Two strong QTLs were detected in the same regions as known major seed-awning loci, An-1 and RAE2. Subsequent causal mutation surveying and fine mapping confirmed that O. rufipogon W630 has functional alleles at both loci. The gene effects and interactions at these loci were examined using two backcross populations with reciprocal genetic backgrounds of O. sativa Nipponbare and O. rufipogon W630. As awn length in wild rice varied among seeds even in the same plant, awn length was measured based on spikelet position. In the genetic background of cultivated rice, the wild alleles at An-1 and RAE2 had awning effects, and plants having both wild homozygous alleles produced awns whose length was about 70% of those of the wild parent. On the other hand, in the genetic background of wild rice, the substitution of cultivated alleles at An-1 and RAE2 contributed little to awn length reduction. These results indicate that the domestication process of awnless seeds was complicated because many genes are involved in awn formation in wild rice.

Radial Oxygen Loss in the Rhizosphere of Wild Rice as a Control On Root Surface Mineral Precipitation

Science.gov (United States)

Murphy, K.; Trejo, B.; LaFond-Hudson, S.

2017-12-01

Wild rice (Zizania palustris) is an aquatic plant native to the Great Lakes region that is culturally and nutritionally significant for the Ojibwe people of Northern Minnesota. Concern for the future health of wild rice populations has increased amidst ongoing pressures from proposed mining projects that risk sulfate contamination to natural waters. Although sulfate itself is not toxic to wild rice, bacteria living in anoxic sediments use the sulfate as an electron acceptor, converting it to sulfide, which subsequently precipitates in the form of iron-sulfide on the root surface of wild rice. These precipitates are linked to lowered viability of wild rice. Most wetland plants are able to shield against the harmful accumulation of these precipitates through a process known as radial oxygen loss (ROL), in which oxygen leaches from roots into anoxic sediments to form protective iron-oxide plaques. This mechanism, however, had yet to be experimentally confirmed in wild rice. In this study, we eliminated the potential for ROL to occur in wild rice prior to the reproductive phase, and measured the rates of iron-sulfide accumulation on the roots and in associated sediments. We compared these data with the geochemical composition of roots and sediment from wild rice that accumulated iron-sulfide precipitate during the reproductive phase. In doing so, we demonstrate that ROL is indeed a mechanism by which wild rice protects itself against sulfide exposure, and examine the nuances of ROL as it relates to the life cycle of wild rice. The better we understand the vulnerability of wild rice across its life cycle and comparative rates of both toxic and protective precipitate accumulation, the better we can approach wild rice conservation.

Maple Sugar Harvesting/Wild Rice Harvesting.

Science.gov (United States)

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…

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

Science.gov (United States)

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

Mutant-inducing effect of γ-ray irradiation for hybrid rice F1 derived from cross of black glutinous rice x wild rice

International Nuclear Information System (INIS)

Mao Dezhi; Tang Yilan

1998-01-01

The hybrid rice F 1 plant derived from the back crossing of glutinous rice x wild rice was irradiated with γ-ray. The result of investigation to the induced mutant showed that through the selection and backcross, a black glutinous rice strain with the short stem, cold tolerance and high yield was developed. The analysis of the ability of heredity variance showed that the selection was effective for the husk colour, black glutinous and black Indica rice, but ineffective for the white Indica rice and seed setting

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

Science.gov (United States)

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.

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

Science.gov (United States)

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. © 2015 American Society of Plant Biologists. All rights reserved.

OryzaGenome: Genome Diversity Database of Wild Oryza Species

KAUST Repository

Ohyanagi, Hajime

2015-11-18

The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a textbased browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tabdelimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/ scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.

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

Science.gov (United States)

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

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

Scafaro, Andrew P; Yamori, Wataru; Carmo-Silva, A Elizabete; Salvucci, Michael E; von Caemmerer, Susanne; Atwell, Brian J

2012-09-01

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 undertaken to identify the impact of temperature on key events in photosynthesis. At an ambient CO(2) partial pressure of 38 Pa and irradiance of 1500 µmol quanta m(-2) s(-1), the temperature optimum of photosynthesis was 33.7 ± 0.8°C for O. meridionalis, significantly higher than the 30.6 ± 0.7°C temperature optimum of O. sativa. To understand the basis for this difference, we measured gas exchange and rubisco activation state between 20 and 42°C and modeled the response to determine the rate-limiting steps of photosynthesis. The temperature response of light respiration (R(light)) and the CO(2) compensation point in the absence of respiration (Γ(*)) were determined and found to be similar for the two species. C3 photosynthesis modeling showed that despite the difference in susceptibility to high temperature, both species had a similar temperature-dependent limitation to photosynthesis. Both rice species were limited by ribulose-1,5-bisphosphate (RuBP) regeneration at temperatures of 25 and 30°C but became RuBP carboxylation limited at 35 and 40°C. The activation state of rubisco in O. meridionalis was more stable at higher temperatures, explaining its greater heat tolerance compared with O. sativa. Copyright © Physiologia Plantarum 2012.

Protective potentials of wild rice (Zizania latifolia (Griseb) Turcz) against obesity and lipotoxicity induced by a high-fat/cholesterol diet in rats.

Science.gov (United States)

Han, Shu-Fen; Zhang, Hong; Zhai, Cheng-Kai

2012-07-01

The study evaluates the protective potentials of wild rice against obesity and lipotoxicity induced by a high-fat/cholesterol diet in rats. In addition to the rats of low-fat diet group, others animals were exposed to a high-fat/cholesterol diet condition for 8 weeks. The city diet (CD) is based on the diet consumed by urban residents in modern China, which is rich in fat/cholesterol and high in carbohydrates from white rice and processed wheat starch. The chief source of dietary carbohydrates of wild rice diet (WRD) is from Chinese wild rice and other compositions are the same with CD. Rats fed CD showed elevated body and liver organ weights, lipid profiles, free fatty acids (FFA) and leptin comparable with rats fed high-fat/cholesterol diet (HFD) known to induce obesity and hyperlipidaemia in this species. However, rats consuming WRD suppressed the increase of lipid droplets accumulation, FFA, and leptin, and the decrease of lipoprotein lipase and adipose triglyceride lipase. Meanwhile, WRD prevented high-fat/cholesterol diet-induced elevation in protein expression of sterol-regulatory element binding protein-1c, and gene expression of fatty acid synthase and acetyl-CoA carboxylase. These findings indicate that wild rice as a natural food has the potentials of preventing obesity and liver lipotoxicity induced by a high-fat/cholesterol diet in rats. Copyright © 2012 Elsevier Ltd. All rights reserved.

Rice as commodity and anti-commodity

NARCIS (Netherlands)

Richards, P.

2016-01-01

On the Upper West Africa coast rice belongs to two species — African rice (Oryza glaberrima Steud.) and Asian rice (Oryza sativa L.). African rice was domesticated in the region, perhaps three millennia ago, from a presumed wild ancestor, O. barthii. Asian rice was introduced via trans-Saharan

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

Science.gov (United States)

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.

Deciphering the role of a miRNA in rice domestication

Directory of Open Access Journals (Sweden)

Swetha Chenna

2017-10-01

Full Text Available MicroRNAs (miRNAs are a class of 21 nt non-coding small RNAs (sRNAs produced from endogenously expressed MIR genes. miRNAs are mostly involved in development and disease resistance. We are interested in identifying key miRNAs that are differentially expressed among wild and cultivated rice species. Analysis of sRNA datasets from two wild species (O. nivara and O. rufipogon and one cultivated species of rice (O. sativa var. indica Pusa Basmati-1, revealed a surprisingly higher abundance of small RNAs originating from Chromosome 2 in wild rice species. This locus codes for a novel 22 nt miRNA. This novel miRNA was found to be highly abundant in flag leaf of wild species, a tissue that usually provides 70% of energy required for grain filling. This miRNA targets a group of proteins (Os03g0273200, Os01g0827300, Os01g0850700, Os11g0708100 and Os01g0842500 which are involved in secondary metabolite production, although a functional significance of this interaction has not been understood. The expression of these targets also differs across the species. Typical of 22 nt miRNAs, the identified miRNA also triggers a secondary cascade silencing by producing small interfering RNAs (siRNAs from target mRNAs in O. nivara. These secondary siRNAs are observed only among wild rice species but not in cultivated rice. Currently we are using a range of genetic, biochemical and molecular techniques to understand role of this novel miRNA in domestication of rice.

Detection of quantitative trait loci controlling grain zinc concentration using Australian wild rice, Oryza meridionalis, a potential genetic resource for biofortification of rice.

Science.gov (United States)

Ishikawa, Ryo; Iwata, Masahide; Taniko, Kenta; Monden, Gotaro; Miyazaki, Naoya; Orn, Chhourn; Tsujimura, Yuki; Yoshida, Shusaku; Ma, Jian Feng; Ishii, Takashige

2017-01-01

Zinc (Zn) is one of the essential mineral elements for both plants and humans. Zn deficiency in human is one of the major causes of hidden hunger, a serious health problem observed in many developing countries. Therefore, increasing Zn concentration in edible part is an important issue for improving human Zn nutrition. Here, we found that an Australian wild rice O. meridionalis showed higher grain Zn concentrations compared with cultivated and other wild rice species. The quantitative trait loci (QTL) analysis was then performed to identify the genomic regions controlling grain Zn levels using backcross recombinant inbred lines derived from O. sativa 'Nipponbare' and O. meridionalis W1627. Four QTLs responsible for high grain Zn were detected on chromosomes 2, 9, and 10. The QTL on the chromosome 9 (named qGZn9), which showed the largest effect on grain Zn concentration was confirmed with the introgression line, which had a W1627 chromosomal segment covering the qGZn9 region in the genetic background of O. sativa 'Nipponbare'. Fine mapping of this QTL resulted in identification of two tightly linked loci, qGZn9a and qGZn9b. The candidate regions of qGZn9a and qGZn9b were estimated to be 190 and 950 kb, respectively. Furthermore, we also found that plants having a wild chromosomal segment covering qGZn9a, but not qGZn9b, is associated with fertility reduction. qGZn9b, therefore, provides a valuable allele for breeding rice with high Zn in the grains.

Detection of quantitative trait loci controlling grain zinc concentration using Australian wild rice, Oryza meridionalis, a potential genetic resource for biofortification of rice.

Directory of Open Access Journals (Sweden)

Ryo Ishikawa

Full Text Available Zinc (Zn is one of the essential mineral elements for both plants and humans. Zn deficiency in human is one of the major causes of hidden hunger, a serious health problem observed in many developing countries. Therefore, increasing Zn concentration in edible part is an important issue for improving human Zn nutrition. Here, we found that an Australian wild rice O. meridionalis showed higher grain Zn concentrations compared with cultivated and other wild rice species. The quantitative trait loci (QTL analysis was then performed to identify the genomic regions controlling grain Zn levels using backcross recombinant inbred lines derived from O. sativa 'Nipponbare' and O. meridionalis W1627. Four QTLs responsible for high grain Zn were detected on chromosomes 2, 9, and 10. The QTL on the chromosome 9 (named qGZn9, which showed the largest effect on grain Zn concentration was confirmed with the introgression line, which had a W1627 chromosomal segment covering the qGZn9 region in the genetic background of O. sativa 'Nipponbare'. Fine mapping of this QTL resulted in identification of two tightly linked loci, qGZn9a and qGZn9b. The candidate regions of qGZn9a and qGZn9b were estimated to be 190 and 950 kb, respectively. Furthermore, we also found that plants having a wild chromosomal segment covering qGZn9a, but not qGZn9b, is associated with fertility reduction. qGZn9b, therefore, provides a valuable allele for breeding rice with high Zn in the grains.

Anatomy and Histochemistry of Roots and Shoots in Wild Rice (Zizania latifolia Griseb.

Directory of Open Access Journals (Sweden)

Chaodong Yang

2014-01-01

Full Text Available Wild rice (Zizania latifolia Griseb. is a famous, perennial, emergent vegetable in China. The current work explores the anatomy and histochemistry of roots, stems, and leaves and the permeability of apoplastic barriers of wild rice. The adventitious roots in wild rice have suberized and lignified endodermis and adjacent, thick-walled cortical layers and suberized and lignified hypodermis, composed of a uniseriate sclerenchyma layer (SC underlying uniseriate exodermis; they also have lysigenous aerenchyma. Stems have a thickened epidermal cuticle, a narrow peripheral mechanical ring (PMR, an outer ring of vascular bundles, and an inner ring of vascular bundles embedded in a multiseriate sclerenchyma ring (SCR. There is evidence of suberin in stem SCR and PMR sclerenchyma cells. Sheathing leaves are characterized by thick cuticles and fibrous bundle sheath extensions. Air spaces in stems and leaves consist of mostly lysigenous aerenchyma and pith cavities in stems. Apoplastic barriers are found in roots and stems.

Fungicide sensitivity in the wild rice pathogen Bipolaris oryzae

Science.gov (United States)

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 ...

Sulfide Generated by Sulfate Reduction is a Primary Controller of the Occurrence of Wild Rice (Zizania palustris) in Shallow Aquatic Ecosystems

Science.gov (United States)

Myrbo, A.; Swain, E. B.; Engstrom, D. R.; Coleman Wasik, J.; Brenner, J.; Dykhuizen Shore, M.; Peters, E. B.; Blaha, G.

2017-11-01

Field observations suggest that surface water sulfate concentrations control the distribution of wild rice, an aquatic grass (Zizania palustris). However, hydroponic studies show that sulfate is not toxic to wild rice at even unrealistically high concentrations. To determine how sulfate might directly or indirectly affect wild rice, potential wild rice habitat was characterized for 64 chemical and physical variables in over 100 sites spanning a relatively steep climatic and geological gradient in Minnesota. Habitat suitability was assessed by comparing the occurrence of wild rice with the field variables, through binary logistic regression. This analysis demonstrated that sulfide in sediment pore water, generated by the microbial reduction of sulfate that diffuses or advects into the sediment, is the primary control of wild rice occurrence. Water temperature and water transparency independently control the suitability of habitat for wild rice. In addition to generating phytotoxic sulfide, sulfate reduction also supports anaerobic decomposition of organic matter, releasing nutrients that can compound the harm of direct sulfide toxicity. These results are important because they show that increases in sulfate loading to surface water can have multiple negative consequences for ecosystems, even though sulfate itself is relatively benign.

Inhibitory Effects of North American Wild Rice on Monocyte Adhesion and Inflammatory Modulators in Low-Density Lipoprotein Receptor-Knockout Mice.

Science.gov (United States)

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

2017-10-18

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 a cholesterol (0.06%, w/w)-supplemented diet with or without white or wild rice (60%, w/w) for 20 weeks. White rice significantly increased monocyte adhesion and 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 the control diet. Wild rice inhibited monocyte adhesion to the aorta, atherosclerosis, and 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.

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

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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.

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

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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.

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

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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.

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

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Itoh Takeshi

2010-02-01

Full Text Available Abstract 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

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

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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.

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

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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.

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

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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. Copyright © 2011. Published by Elsevier Ireland Ltd.

Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view.

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Huang, Pu; Molina, Jeanmaire; Flowers, Jonathan M; Rubinstein, Samara; Jackson, Scott A; Purugganan, Michael D; Schaal, Barbara A

2012-09-01

Asian wild rice (Oryza rufipogon) that ranges widely across the eastern and southern part of Asia is recognized as the direct ancestor of cultivated Asian rice (O. sativa). Studies of the geographic structure of O. rufipogon, based on chloroplast and low-copy nuclear markers, reveal a possible phylogeographic signal of subdivision in O. rufipogon. However, this signal of geographic differentiation is not consistently observed among different markers and studies, with often conflicting results. To more precisely characterize the phylogeography of O. rufipogon populations, a genome-wide survey of unlinked markers, intensively sampled from across the entire range of O. rufipogon is critical. In this study, we surveyed sequence variation at 42 genome-wide sequence tagged sites (STS) in 108 O. rufipogon accessions from throughout the native range of the species. Using Bayesian clustering, principal component analysis and amova, we conclude that there are two genetically distinct O. rufipogon groups, Ruf-I and Ruf-II. The two groups exhibit a clinal variation pattern generally from north-east to south-west. Different from many earlier studies, Ruf-I, which is found mainly in China and the Indochinese Peninsula, shows genetic similarity with one major cultivated rice variety, O. satvia indica, whereas Ruf-II, mainly from South Asia and the Indochinese Peninsula, is not found to be closely related to cultivated rice varieties. The other major cultivated rice variety, O. sativa japonica, is not found to be similar to either O. rufipogon groups. Our results support the hypothesis of a single origin of the domesticated O. sativa in China. The possible role of palaeoclimate, introgression and migration-drift balance in creating this clinal variation pattern is also discussed. © 2012 Blackwell Publishing Ltd.

Fine mapping and identification of a novel locus qGL12.2 control grain length in wild rice (Oryza rufipogon Griff.).

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Qi, Lan; Ding, Yingbin; Zheng, Xiaoming; Xu, Rui; Zhang, Lizhen; Wang, Yanyan; Wang, Xiaoning; Zhang, Lifang; Cheng, Yunlian; Qiao, Weihua; Yang, Qingwen

2018-04-19

A wild rice QTL qGL12.2 for grain length was fine mapped to an 82-kb interval in chromosome 12 containing six candidate genes and none was reported previously. Grain length is an important trait for yield and commercial value in rice. Wild rice seeds have a very slender shape and have many desirable genes that have been lost in cultivated rice during domestication. In this study, we identified a quantitative trait locus, qGL12.2, which controls grain length in wild rice. First, a wild rice chromosome segment substitution line, CSSL41, was selected that has longer glume and grains than does the Oryza sativa indica cultivar, 9311. Next, an F 2 population was constructed from a cross between CSSL41 and 9311. Using the next-generation sequencing combined with bulked-segregant analysis and F 3 recombinants analysis, qGL12.2 was finally fine mapped to an 82-kb interval in chromosome 12. Six candidate genes were found, and no reported grain length genes were found in this interval. Using scanning electron microscopy, we found that CSSL41 cells are significantly longer than those of 9311, but there is no difference in cell widths. These data suggest that qGL12.2 is a novel gene that controls grain cell length in wild rice. Our study provides a new genetic resource for rice breeding and a starting point for functional characterization of the wild rice GL gene.

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

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Seonghee Lee

Full Text Available 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.

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

Science.gov (United States)

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

Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression

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Li Xin

2012-07-01

Full Text Available Abstract Background DNA methylation plays important biological roles in plants and animals. To examine the rice genomic methylation landscape and assess its functional significance, we generated single-base resolution DNA methylome maps for Asian cultivated rice Oryza sativa ssp. japonica, indica and their wild relatives, Oryza rufipogon and Oryza nivara. Results The overall methylation level of rice genomes is four times higher than that of Arabidopsis. Consistent with the results reported for Arabidopsis, methylation in promoters represses gene expression while gene-body methylation generally appears to be positively associated with gene expression. Interestingly, we discovered that methylation in gene transcriptional termination regions (TTRs can significantly repress gene expression, and the effect is even stronger than that of promoter methylation. Through integrated analysis of genomic, DNA methylomic and transcriptomic differences between cultivated and wild rice, we found that primary DNA sequence divergence is the major determinant of methylational differences at the whole genome level, but DNA methylational difference alone can only account for limited gene expression variation between the cultivated and wild rice. Furthermore, we identified a number of genes with significant difference in methylation level between the wild and cultivated rice. Conclusions The single-base resolution methylomes of rice obtained in this study have not only broadened our understanding of the mechanism and function of DNA methylation in plant genomes, but also provided valuable data for future studies of rice epigenetics and the epigenetic differentiation between wild and cultivated rice.

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

DEFF Research Database (Denmark)

Xu, Xun; Liu, Xin; Ge, Song

2012-01-01

Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 x...... diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable...... raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower...

WRKY transcription factor genes in wild rice Oryza nivara.

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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.

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

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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.

Grain Unloading Of Arsenic Species In Rice

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Rice (Oryza sativa) is the staple food for over half the world's population yet may represent a significant dietary source of inorganic arsenic (As), a nonthreshold, class 1 human carcinogen. Rice grain As is dominated by the inorganic species, and the organic species dim...

Analysis of QTLs for yield-related traits in Yuanjiang common wild rice (Oryza rufipogon Griff.).

Science.gov (United States)

Fu, Qiang; Zhang, Peijiang; Tan, Lubin; Zhu, Zuofeng; Ma, Dan; Fu, Yongcai; Zhan, Xinchun; Cai, Hongwei; Sun, Chuanqing

2010-02-01

Using an accession of common wild rice (Oryza rufipogon Griff.) collected from Yuanjiang County, Yunnan Province, China, as the donor and an elite cultivar 93-11, widely used in two-line indica hybrid rice production in China, as the recurrent parent, an advanced backcross populations were developed. Through genotyping of 187 SSR markers and investigation of six yield-related traits of two generations (BC(4)F(2) and BC(4)F(4)), a total of 26 QTLs were detected by employing single point analysis and interval mapping in both generations. Of the 26 QTLs, the alleles of 10 (38.5%) QTLs originating from O. rufipogon had shown a beneficial effect for yield-related traits in the 93-11 genetic background. In addition, five QTLs controlling yield and its components were newly identified, indicating that there are potentially novel alleles in Yuanjiang common wild rice. Three regions underling significant QTLs for several yield-related traits were detected on chromosome 1, 7 and 12. The QTL clusters were founded and corresponding agronomic traits of those QTLs showed highly significant correlation, suggesting the pleiotropism or tight linkage. Fine-mapping and cloning of these yield-related QTLs from wild rice would be helpful to elucidating molecular mechanism of rice domestication and rice breeding in the future. Copyright 2010 Institute of Genetics and Developmental Biology and the Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

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

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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.

Development of Novel Cytoplasmic Male Sterile Source from Dongxiang Wild Rice (Oryza rufipogon

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Xian-hua SHEN

2013-09-01

Full Text Available This study was conducted to develop and characterize a novel cytoplasmic male sterile (CMS source which was identified from Dongxiang wild rice (Oryza rufipogon by crossing Dongxiang wild rice as female with Zhongzao 35, an indica inbred variety, as male and continuous backcrossing with Zhongzao 35. Observation under optical microscope manifested that this novel CMS belonged to typical abortion type with less pollen compared with wild abortive type cytoplasm (CMS-WA. Sequential planting showed that this novel CMS has complete and stable male sterility. Testcross experiment showed that all the 24 tested materials including maintainer and restorer lines of CMS-WA and Honglian type cytoplasm (CMS-HL and other indica inbred varieties are the maintainers with complete maintaining ability, suggesting that this novel CMS has fertility restoration totally different from CMS-WA and CMS-HL and belongs to a novel type of CMS. So far, we only discovered a unique fertility restoration source for this novel CMS. Inheritance analysis showed that the fertility restoration of this CMS was governed by three pairs of independent dominant genes. Prospect for application of this novel CMS system in hybrid rice breeding was also discussed.

Transcriptome analysis of phosphorus stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.).

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Deng, Qian-Wen; Luo, Xiang-Dong; Chen, Ya-Ling; Zhou, Yi; Zhang, Fan-Tao; Hu, Biao-Lin; Xie, Jian-Kun

2018-03-15

Low phosphorus availability is a major factor restricting rice growth. Dongxiang wild rice (Oryza rufipogon Griff.) has many useful genes lacking in cultivated rice, including stress resistance to phosphorus deficiency, cold, salt and drought, which is considered to be a precious germplasm resource for rice breeding. However, the molecular mechanism of regulation of phosphorus deficiency tolerance is not clear. In this study, cDNA libraries were constructed from the leaf and root tissues of phosphorus stressed and untreated Dongxiang wild rice seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in phosphorus stress response. The results indicated that 1184 transcripts were differentially expressed in the leaves (323 up-regulated and 861 down-regulated) and 986 transcripts were differentially expressed in the roots (756 up-regulated and 230 down-regulated). 43 genes were up-regulated both in leaves and roots, 38 genes were up-regulated in roots but down-regulated in leaves, and only 2 genes were down-regulated in roots but up-regulated in leaves. Among these differentially expressed genes, the detection of many transcription factors and functional genes demonstrated that multiple regulatory pathways were involved in phosphorus deficiency tolerance. Meanwhile, the differentially expressed genes were also annotated with gene ontology terms and key pathways via functional classification and Kyoto Encyclopedia of Gene and Genomes pathway mapping, respectively. A set of the most important candidate genes was then identified by combining the differentially expressed genes found in the present study with previously identified phosphorus deficiency tolerance quantitative trait loci. The present work provides abundant genomic information for functional dissection of the phosphorus deficiency resistance of Dongxiang wild rice, which will be help to understand the biological regulatory mechanisms of phosphorus

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

NARCIS (Netherlands)

Cruz Garcia, G.S.; Price, L.L.

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

Cell fusion as a tool for rice improvement

Energy Technology Data Exchange (ETDEWEB)

Hayashi, Y; Kyozuka, J; Terada, R; Nishibayashi, S; Shimamoto, K [Plantech Research Institute, Kamoshida, Midori-ku, Yokohama (Japan)

1990-01-01

Full text: Cell fusion offers a unique opportunity to hybridize sexually incompatible species and to mix cytoplasmic genomes in higher plants. Recent progress in plant regeneration from rice protoplasts facilitates an evaluation of the cell fusion method for rice improvement. By using electrofusion of protoplasts, we obtained hybrid/cybrid plants of the following combinations: Hybrids of rice x barnyard grass (E. oryzicola); Hybrids of rice x wild Oryza species; Cybrids of rice with transferred cms cytoplasm. For the latter, protoplasts irradiated with 70 krad x-rays were used. (author)

Identification of phasiRNAs in wild rice (Oryza rufipogon).

Science.gov (United States)

Liu, Yang; Wang, Yu; Zhu, Qian-Hao; Fan, Longjiang

2013-08-01

Plant miRNAs can trigger the production of phased, secondary siRNAs from either non-coding or protein-coding genes. In this study, at least 864 and 3,961 loci generating 21-nt and 24-nt phased siRNAs (phasiRNAs),respectively, were identified in three tissues from wild rice. Of these phasiRNA-producing loci, or PHAS genes, biogenesis of phasiRNAs in at least 160 of 21-nt and 254 of 24-nt loci could be triggered by interaction with miRNA(s). Developing seeds had more PHAS genes than leaves and roots. Genetic constrain on miRNA-triggered PHAS genes suggests that phasiRNAs might be one of the driving forces contributed to rice domestication.

Molecular evolution of the endosperm starch synthesis pathway genes in rice (Oryza sativa L.) and its wild ancestor, O. rufipogon L.

Science.gov (United States)

Yu, Guoqin; Olsen, Kenneth M; Schaal, Barbara A

2011-01-01

The evolution of metabolic pathways is a fundamental but poorly understood aspect of evolutionary change. One approach for understanding the complexity of pathway evolution is to examine the molecular evolution of genes that together comprise an integrated metabolic pathway. The rice endosperm starch biosynthetic pathway is one of the most thoroughly characterized metabolic pathways in plants, and starch is a trait that has evolved in response to strong selection during rice domestication. In this study, we have examined six key genes (AGPL2, AGPS2b, SSIIa, SBEIIb, GBSSI, ISA1) in the rice endosperm starch biosynthesis pathway to investigate the evolution of these genes before and after rice domestication. Genome-wide sequence tagged sites data were used as a neutral reference to overcome the problems of detecting selection in species with complex demographic histories such as rice. Five variety groups of Oryza sativa (aus, indica, tropical japonica, temperate japonica, aromatic) and its wild ancestor (O. rufipogon) were sampled. Our results showed evidence of purifying selection at AGPL2 in O. rufipogon and strong evidence of positive selection at GBSSI in temperate japonica and tropical japonica varieties and at GBSSI and SBEIIb in aromatic varieties. All the other genes showed a pattern consistent with neutral evolution in both cultivated rice and its wild ancestor. These results indicate the important role of positive selection in the evolution of starch genes during rice domestication. We discuss the role of SBEIIb and GBSSI in the evolution of starch quality during rice domestication and the power and limitation of detecting selection using genome-wide data as a neutral reference.

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.

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

2010-03-01

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.

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

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

2017-08-01

The sensitivity of wild rice (Zizania palustris) to sulfide is not well understood. Because sulfate in surface waters is reduced to sulfide by anaerobic bacteria in sediments and historical information indicated that 10 mg/L sulfate in Minnesota (USA) surface water reduced Z. palustris abundance, the Minnesota Pollution Control Agency established 10 mg/L sulfate as a water quality criterion in 1973. A 21-d daily-renewal hydroponic study was conducted to evaluate sulfide toxicity to wild rice and the potential mitigation of sulfide toxicity by iron (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 d after 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 d). The results indicate that exposure of developing wild rice to sulfide at ≥3.1 mg sulfide/L in the presence of 0.8 mg/L Fe reduced mesocotyl emergence. Sulfide toxicity was mitigated by the addition of Fe at 2.8 mg/L 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 taking into account factors that alter toxicity, including sediment Fe and organic carbon, are necessary. Environ Toxicol Chem 2017;36:2217-2226. © 2017 SETAC. © 2017 SETAC.

The Evolutionary Basis of Naturally Diverse Rice Leaves Anatomy.

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Jolly Chatterjee

Full Text Available 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.

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

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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.

Genome Sequences of Oryza Species

KAUST Repository

Kumagai, Masahiko

2018-02-14

This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

Genome Sequences of Oryza Species

KAUST Repository

Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

2018-01-01

This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

Wildly Growing Asparagus (Asparagus officinalis L.) Hosts Pathogenic Fusarium Species and Accumulates Their Mycotoxins.

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Stępień, Łukasz; Waśkiewicz, Agnieszka; Urbaniak, Monika

2016-05-01

Asparagus officinalis L. is an important crop in many European countries, likely infected by a number of Fusarium species. Most of them produce mycotoxins in plant tissues, thus affecting the physiology of the host plant. However, there is lack of information on Fusarium communities in wild asparagus, where they would definitely have considerable environmental significance. Therefore, the main scientific aim of this study was to identify the Fusarium species and quantify their typical mycotoxins present in wild asparagus plants collected at four time points of the season. Forty-four Fusarium strains of eight species--Fusarium acuminatum, Fusarium avenaceum, Fusarium culmorum, Fusarium equiseti, Fusarium oxysporum, Fusarium proliferatum, Fusarium sporotrichioides, and Fusarium tricinctum--were isolated from nine wild asparagus plants in 2013 season. It is the first report of F. sporotrichioides isolated from this particular host. Fumonisin B1 was the most abundant mycotoxin, and the highest concentrations of fumonisins B1-B3 and beauvericin were found in the spears collected in May. Moniliformin and enniatins were quantified at lower concentrations. Mycotoxins synthesized by individual strains obtained from infected asparagus tissues were assessed using in vitro cultures on sterile rice grain. Most of the F. sporotrichioides strains synthesized HT-2 toxin and F. equiseti strains were found to be effective zearalenone producers.

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

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Ethel Sánchez

2005-06-01

Full Text Available Oryza glumaepatula is a perennial wild rice species,endemic to tropical America, previously known as the Latin American race of Oryza 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.sativa 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 mu m in length and small hirsute trichomes of ca. 32 mu m in length.The central vein is covered with large,globular papillae of ca. 146 mu m 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 mu m in length.Auricles have attenuated trichomes of ca .5.5 mm in length on the edges and small bicellular trichomes of 120 mu m in length on the surface.The ligule has a large number of short attenuated trichomes on its surface of 100 mu m 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.glumaepatula from

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.

Science.gov (United States)

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.

Mycoflora and aflatoxigenic species in derivatives of milled rice

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LIMA Carlos A. P.

2000-01-01

Full Text Available Thirty samples of rough rice stored for 6, 12 and 24 months in government authorized warehouses of the state of Rio Grande do Sul, Brazil, were simultaneously collected. After milling of the product, 90 samples (30 of polished rice, 30 of rice bran and 30 of rice hull were evaluated for their mycoflora, aflatoxigenic species and aflatoxin contamination. The following fungi, listed in decreasing order of frequency, were isolated on Potato-Dextrose Agar: Aspergillus spp., Nigrospora spp., Penicillium spp.; Fusarium spp.; Mucor spp.; Cladosporium spp.; Trichosporon spp. and non-sporulated fungi. The degree of fungal contamination (colony forming units per gram of product was lowest in polished rice, increasing progressively in samples of rice bran and rice hull. Among the Aspergillus species, A. flavus and A. candidus were isolated most frequently. Of the A. flavus isolates, 52.6% strains were found to be toxigenic and produced only Group B aflatoxins. Analysis of the 90 samples did not reveal the presence of aflatoxins in the rice derivatives.

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

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Olsen Kenneth M

2010-06-01

Full Text Available Abstract 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.

Multiple cold resistance loci confer the high cold tolerance adaptation of Dongxiang wild rice (Oryza rufipogon) to its high-latitude habitat.

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Mao, Donghai; Yu, Li; Chen, Dazhou; Li, Lanying; Zhu, Yuxing; Xiao, Yeqing; Zhang, Dechun; Chen, Caiyan

2015-07-01

Dongxiang wild rice is phylogenetically close to temperate japonica and contains multiple cold resistance loci conferring its adaptation to high-latitude habitat. Understanding the nature of adaptation in wild populations will benefit crop breeding in the development of climate-resilient crop varieties. Dongxiang wild rice (DXWR), the northernmost common wild rice known, possesses a high degree of cold tolerance and can survive overwintering in its native habitat. However, to date, it is still unclear how DXWR evolved to cope with low-temperature environment, resulting in limited application of DXWR in rice breeding programs. In this study, we carried out both QTL mapping and phylogenetic analysis to discern the genetic mechanism underlying the strong cold resistance. Through a combination of interval mapping and single locus analysis in two genetic populations, at least 13 QTLs for seedling cold tolerance were identified in DXWR. A phylogenetic study using both genome-wide InDel markers and markers associated with cold tolerance loci reveals that DXWR belongs to the Or-III group, which is most closely related to cold-tolerant Japonica rice rather than to the Indica cultivars that are predominant in the habitat where DXWR grows. Our study paves the way toward an understanding of the nature of adaptation to a northern habitat in O. rufipogon. The QTLs identified in DXWR in this study will be useful for molecular breeding of cold-tolerant rice.

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

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

2015-01-01

The resistance (R) genes and defense response (DR) genes have become very important resources for the development of disease resistant cultivars. In the present investigation, genome-wide identification, expression, phylogenetic and synteny analysis was done for R and DR-genes across three species of rice viz: Oryza sativa ssp indica cv 93-11, Oryza sativa ssp japonica and wild rice species, Oryza brachyantha. We used the in silico approach to identify and map 786 R -genes and 167 DR-genes, 672 R-genes and 142 DR-genes, 251 R-genes and 86 DR-genes in the japonica, indica and O. brachyanth a genomes, respectively. Our analysis showed that 60.5% and 55.6% of the R-genes are tandemly repeated within clusters and distributed over all the rice chromosomes in indica and japonica genomes, respectively. The phylogenetic analysis along with motif distribution shows high degree of conservation of R- and DR-genes in clusters. In silico expression analysis of R-genes and DR-genes showed more than 85% were expressed genes showing corresponding EST matches in the databases. This study gave special emphasis on mechanisms of gene evolution and duplication for R and DR genes across species. Analysis of paralogs across rice species indicated 17% and 4.38% R-genes, 29% and 11.63% DR-genes duplication in indica and Oryza brachyantha, as compared to 20% and 26% duplication of R-genes and DR-genes in japonica respectively. We found that during the course of duplication only 9.5% of R- and DR-genes changed their function and rest of the genes have maintained their identity. Syntenic relationship across three genomes inferred that more orthology is shared between indica and japonica genomes as compared to brachyantha genome. Genome wide identification of R-genes and DR-genes in the rice genome will help in allele mining and functional validation of these genes, and to understand molecular mechanism of disease resistance and their evolution in rice and related species. PMID:25902056

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

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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

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

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Mahbod Sahebi

2017-01-01

Full Text Available 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.

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

Science.gov (United States)

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.

Hybridization study of wild rice Oryza glumaepatula with varieties of cultivated rice (O. sativa) and wild (O. grandiglumis)

International Nuclear Information System (INIS)

Villalobos Cascante, Eddier

2015-01-01

The process of interspecific hybridization of the wild species O. glumaepatula is studied with commercial varieties of the species O. sativa and O. grandiglumis, by morphological evaluation and hybrid flow cytometry. Hybrid plants were evaluated of cross between O. glumaepatula, located in the wetlands of Rio Medio Queso and two varieties of O. sativa, Puita Inta and CFX 18 resistant to a herbicide. The technique of Polymerase Chain Reaction Allele Specifies Oligonucleotide (PCR-ASO) was used to detect allelic mutations in the ALS gene conferring herbicide resistance, and it is confirmed the hybrid nature of the plants obtained at crossings. 68 hybrids were obtained: O. glumaepatula x P. Inta, 21 hybrids P. Inta x O. glumaepatula, 4 hybrids O. glumaepatula x CFX-18 and 15 hybrids CFX-18 x O. glumaepatula. 10 morphological descriptors of the genus Oryza were evaluated and determined that are indifferent to the direction and type of crossing, the hybrids resemble to the wild species O. glumaepatula for characters: height, panicle length and ligule length. All hybrids have showed similarity to commercial varieties in flag leaf length. Other characters evaluated in the hybrids have presented maternal effect, heterosis and intermediate values. The protocol of flow cytometry (FCM) is standardized species for Oryza genus analyzing nuclear DNA content of 106 samples of leaf tissue of wild species O. glumaepatula, O. grandiglumis; whose average has been of 0.73 picograms, and natural hybrids product of the cross of these species. The result has been intermediate compared with O. grandiglumis and O. glumaepatula that have made available to 1.0 picograms and 0.50 of DNA respectively. The molecular nature of the hybrids was confirmed in this way. (author) [es

Grain Unloading of Arsenic Species in Rice

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Carey, Anne-Marie; Scheckel, Kirk G.; Lombi, Enzo; Newville, Matt; Choi, Yongseong; Norton, Gareth J.; Charnock, John M.; Feldmann, Joerg; Price, Adam H.; Meharg, Andrew A. (EPA); (U. South Australia); (Manchester); (Aberdeen); (UC)

2010-01-11

Rice (Oryza sativa) is the staple food for over half the world's population yet may represent a significant dietary source of inorganic arsenic (As), a nonthreshold, class 1 human carcinogen. Rice grain As is dominated by the inorganic species, and the organic species dimethylarsinic acid (DMA). To investigate how As species are unloaded into grain rice, panicles were excised during grain filling and hydroponically pulsed with arsenite, arsenate, glutathione-complexed As, or DMA. Total As concentrations in flag leaf, grain, and husk, were quantified by inductively coupled plasma mass spectroscopy and As speciation in the fresh grain was determined by x-ray absorption near-edge spectroscopy. The roles of phloem and xylem transport were investigated by applying a {+-} stem-girdling treatment to a second set of panicles, limiting phloem transport to the grain in panicles pulsed with arsenite or DMA. The results demonstrate that DMA is translocated to the rice grain with over an order magnitude greater efficiency than inorganic species and is more mobile than arsenite in both the phloem and the xylem. Phloem transport accounted for 90% of arsenite, and 55% of DMA, transport to the grain. Synchrotron x-ray fluorescence mapping and fluorescence microtomography revealed marked differences in the pattern of As unloading into the grain between DMA and arsenite-challenged grain. Arsenite was retained in the ovular vascular trace and DMA dispersed throughout the external grain parts and into the endosperm. This study also demonstrates that DMA speciation is altered in planta, potentially through complexation with thiols.

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

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Gao, Li-Zhi; Gao, Cheng-Wen

2016-01-01

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. 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 homozygotes and thus high inbreeding depression in

Selection of Wild Plant Species from Organic Rice Field in Sumberngepoh Village in Malang as Attractant of Trichogramma spp. (Hymenoptera, Trichogrammatidae

Directory of Open Access Journals (Sweden)

Wahyu Kusumayanti Putri

2014-09-01

Full Text Available One of the actions in biological control is the use of parasitoid. Some wild plant species can attract those parasitoid. By the fact, the objective of this research are to select some of wild plant species attracting Trichogramma spp. These wild plant were belong to Asteraceae (Eupatorium odoratum, Bidens pilosa, Crassocephalum crepidioides and Mimosaceae (Parkia speciosa, Leucaena glauca, Mimosa pudica. Mass rearing of trichogramma spp. was prepared for those purpose. The selection were conducted by using four armed olfactometer. The percentage of the tested Trichogramma spp. attracted to the wild plant species was noted as well as their orientation duration to select the plant species. The difference of the mean of their orientation duration was analyzed statistically by T-Test. Both of plant familia can attract the parasitoid. This were the plant species that attracted Trichogramma spp. From the most attractive to the lowest one : B. pilosa 22 %, E. odoratum 18.6 %, M. pudica 18.2 %, C. crepidioides 13.8 %, P. speciosa 13.6 %, and L. glauca 13.6 %. For the orientation duration, this are the plant species that can attract the parasitoid from the fastest one to the slowest one : P. speciosa 45.5 seconds, C. crepidioides 46.2 seconds, L. glauca 49 seconds, E. odoratum 50.6 seconds , B. pilosa 53.4 seconds, and M. pudica 55.2 seconds. Keywords : Asteraceae, Mimosaceae, Trichogramma spp.

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

OpenAIRE

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

2016-01-01

Summary 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 infere...

Recent and projected increases in atmospheric CO2 concentration can enhance gene flow between wild and genetically altered rice (Oryza sativa.

Directory of Open Access Journals (Sweden)

Lewis H Ziska

Full Text Available 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 CO(2 between genetically modified crops and wild, weedy relatives increase the spread of novel genes, potentially altering evolutionary fitness? Here we show that increasing CO(2 from an early 20(th century concentration (300 µmol mol(-1 to current (400 µmol mol(-1 and projected, mid-21(st 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 CO(2 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 CO(2 could result in enhanced flow of novel genes and greater success of feral plant species in agroecosystems.

Recent and projected increases in atmospheric CO2 concentration can enhance gene flow between wild and genetically altered rice (Oryza sativa).

Science.gov (United States)

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 CO(2) between genetically modified crops and wild, weedy relatives increase the spread of novel genes, potentially altering evolutionary fitness? Here we show that increasing CO(2) from an early 20(th) century concentration (300 µmol mol(-1)) to current (400 µmol mol(-1)) and projected, mid-21(st) 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 CO(2) 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 CO(2) could result in enhanced flow of novel genes and greater success of feral plant species in agroecosystems.

Wild harvest

NARCIS (Netherlands)

Cruz-Garcia, G.S.; Struik, P.C.; Johnson, D.E.

2016-01-01

Rice fields provide not only a staple food but are also bio-diverse and multi-functional ecosystems. Wild food plants are important elements of biodiversity in rice fields and are critical components to the subsistence of poor farmers. The spatial and seasonal distribution of wild food plants

Symbiont-mediated adaptation by planthoppers and leafhoppers to resistant rice varieties

NARCIS (Netherlands)

Ferrater, J.B.; Jong, de P.W.; Dicke, M.; Chen, Y.H.; Horgan, F.G.

2013-01-01

For over 50 years, host plant resistance has been the principal focus of public research to reduce planthopper and leafhopper damage to rice in Asia. Several resistance genes have been identified from native varieties and wild rice species, and some of these have been incorporated into high-yielding

Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression

DEFF Research Database (Denmark)

Li, Xin; Zhu, Jingde; Hu, Fengyi

2012-01-01

DNA methylation plays important biological roles in plants and animals. To examine the rice genomic methylation landscape and assess its functional significance, we generated single-base resolution DNA methylome maps for Asian cultivated rice Oryza sativa ssp. japonica, indica and their wild rela...

Speciation of Six-Arsenic Species of Rice in Korea by HPLC/ICPMS

Directory of Open Access Journals (Sweden)

Kim J.Y.

2013-04-01

Full Text Available Determination of arsenic (As speciation in rice is necessary because inorganic As species are more toxic than organic As. Arsenic levels of rice in Korea were determined by microwave extraction and High Performance Liquid Chromatography coupled with Inductively Coupled Plasma-Mass Spectrometry. The extraction method showed a high recovery and low Limit of Detection (LOD and Limit of Quantitation (LOQ. Most of the As species in rice were noticed to be inorganic [Arsenite (AsIII, Dimethylarsinic acid (DMA]. The percentage of inorganic As/total As is 69.01 % (36.40-87.86 %. Arsenite and DMA were the major compounds in rice in Korea when compare to U.S. rice. The order and percentage of As species showed were AsIII (56-70 %>DMA (23-38 %>AsV (5 %>MMA(1 %.

Geographic distribution of wild potato species

NARCIS (Netherlands)

Hijmans, R.J.; Spooner, D.M.

2001-01-01

The geographic distribution of wild potatoes (Solanaceae sect. Petota) was analyzed using a database of 6073 georeferenced observations. Wild potatoes occur in 16 countries, but 88% of the observations are from Argentina, Bolivia, Mexico, and Peru. Most species are rare and narrowly endemic: for 77

Arsenic species in raw and cooked rice: Implications for human health in rural Bengal

Energy Technology Data Exchange (ETDEWEB)

Halder, Dipti, E-mail: dipti@kth.se [KTH-International Groundwater Arsenic Research Group, Division of Land and Water Resources Engineering, Department of Sustainable Development, Environmental Sciences and Engineering, KTH Royal Institute of Technology, Teknikringen 76, SE-100 44 Stockholm (Sweden); Department of Chemistry, University of Kalyani, Kalyani, 741 235, West Bengal (India); Biswas, Ashis [KTH-International Groundwater Arsenic Research Group, Division of Land and Water Resources Engineering, Department of Sustainable Development, Environmental Sciences and Engineering, KTH Royal Institute of Technology, Teknikringen 76, SE-100 44 Stockholm (Sweden); Department of Chemistry, University of Kalyani, Kalyani, 741 235, West Bengal (India); Šlejkovec, Zdenka [Environmental Sciences Department, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana (Slovenia); Chatterjee, Debashis [Department of Chemistry, University of Kalyani, Kalyani, 741 235, West Bengal (India); Nriagu, Jerome [Department of Environmental Health Sciences, School of Public Health, University of Michigan, 109 Observatory Street, Ann Arbor, MI 48109-2029 (United States); Jacks, Gunnar; Bhattacharya, Prosun [KTH-International Groundwater Arsenic Research Group, Division of Land and Water Resources Engineering, Department of Sustainable Development, Environmental Sciences and Engineering, KTH Royal Institute of Technology, Teknikringen 76, SE-100 44 Stockholm (Sweden)

2014-11-01

This study compares the concentrations of total and different species of arsenic (As) in 29 pairs of raw and cooked rice samples collected from households in an area of West Bengal affected by endemic arsenicism. The aim is to investigate the effects of indigenous cooking practice of the rural villagers on As accumulation and speciation in cooked rice. It is found that inorganic As is the predominant species in both raw (93.8%) and cooked rice (88.1%). Cooking of rice with water low in As (< 10 μg L{sup −1}) significantly decreases the total and inorganic As content in cooked rice compared to raw rice. Arsenic concentration is mainly decreased during boiling of rice grains with excess water. Washing of rice grains with low As water has negligible effect on grain As concentration. The study suggests that rice cooking with low As water by the villagers is a beneficial risk reduction strategy. Despite reductions in As content in cooked rice because of cooking with low As water, the consumption of cooked rice represents a significant health threat (in terms of chronic As toxicity) to the study population. - Highlights: • Pairs of raw and cooked rice samples are collected from households. • Total and different species of As in raw and cooked rice samples are compared. • Cooking with As safe water reduces total and inorganic As contents in cooked rice. • Inorganic As is the predominant species in both raw (93.8%) and cooked rice (88.1%). • Risks of As exposure from cooked rice consumption exceed the safety standards.

Arsenic species in raw and cooked rice: Implications for human health in rural Bengal

International Nuclear Information System (INIS)

Halder, Dipti; Biswas, Ashis; Šlejkovec, Zdenka; Chatterjee, Debashis; Nriagu, Jerome; Jacks, Gunnar; Bhattacharya, Prosun

2014-01-01

This study compares the concentrations of total and different species of arsenic (As) in 29 pairs of raw and cooked rice samples collected from households in an area of West Bengal affected by endemic arsenicism. The aim is to investigate the effects of indigenous cooking practice of the rural villagers on As accumulation and speciation in cooked rice. It is found that inorganic As is the predominant species in both raw (93.8%) and cooked rice (88.1%). Cooking of rice with water low in As (< 10 μg L −1 ) significantly decreases the total and inorganic As content in cooked rice compared to raw rice. Arsenic concentration is mainly decreased during boiling of rice grains with excess water. Washing of rice grains with low As water has negligible effect on grain As concentration. The study suggests that rice cooking with low As water by the villagers is a beneficial risk reduction strategy. Despite reductions in As content in cooked rice because of cooking with low As water, the consumption of cooked rice represents a significant health threat (in terms of chronic As toxicity) to the study population. - Highlights: • Pairs of raw and cooked rice samples are collected from households. • Total and different species of As in raw and cooked rice samples are compared. • Cooking with As safe water reduces total and inorganic As contents in cooked rice. • Inorganic As is the predominant species in both raw (93.8%) and cooked rice (88.1%). • Risks of As exposure from cooked rice consumption exceed the safety standards

Focal species candidates for pesticide risk assessment in European rice fields: A review.

Science.gov (United States)

Vallon, Martin; Dietzen, Christian; Laucht, Silke; Ludwigs, Jan-Dieter

2018-04-25

An assessment of potential risks of pesticides on wildlife is required during the process of product registration within Europe because of the importance of agricultural landscapes as wildlife habitats. Despite their peculiarity and their specific role as artificial wetlands, rice paddies are to date pooled with cereals in guidance documents on how to conduct risk assessments for birds and mammals in Europe. Hence, the focal species currently considered in risk assessments for rice paddies are those known from cereal fields and can therefore be expected to differ significantly from the species actually occurring in the wet environments of rice paddies. We present results of a comprehensive review on bird and mammal species regularly occurring in rice paddies during a time of potential pesticide exposure to identify appropriate focal species candidates for ecotoxicological pesticide risk assessment according to the European Food Safety Authority (EFSA). In addition, we present data on rice cultivation areas and agricultural practices in Europe to give background information supporting the species selection process. Our literature search identified a general scarcity of relevant data, particularly for mammals, which highlights the need for crop-specific focal species studies. However, our results clearly indicate that the relevant bird and mammal species in rice fields indeed differ strongly from the focal species used for the cereal risk assessment. They can thus be used as a baseline for more realistic wildlife risk assessments specific to rice and the development of a revised guidance document to bridge the gap for regulatory decision makers. Integr Environ Assess Manag 2018;00:000-000. © 2018 SETAC. © 2018 SETAC.

Rice flakes produced from commercial wild rice: Chemical compositions, vitamin B compounds, mineral and trace element contents and their dietary intake evaluation.

Science.gov (United States)

Sumczynski, Daniela; Koubová, Eva; Šenkárová, Lenka; Orsavová, Jana

2018-10-30

Non-traditional wild rice flakes were analysed for chemical composition, vitamin B compounds, α-tocopherol, mineral and trace elements. Dietary intakes of vitamins, minerals and trace elements were evaluated using FAO/WHO and Institute of Medicine regulations. Wild rice flakes proved to be significant contributors of pyridoxine, pantothenic and folic acids, niacin, thiamine, chromium, magnesium, manganese, phosphorus, zinc, copper, molybdenum and iron to essential dietary intakes values. Toxic dietary intake values for aluminium, cadmium, tin and mercury were less than 33%, which complies the limits for adults set by FAO/WHO for toxic elements intake related to the body weight of 65 kg for females and 80 kg for males taking 100 g of flakes as a portion. However, concentrations of Hg reaching between 3.67 and 12.20 µg/100 g in flakes exceeded the average Hg value of 0.27-1.90 μg/100 g in cereals consumed in the EU. It has to be respected in the future. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

Science.gov (United States)

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 ...

Chloroplast DNA polymorphism and evolutional relationships between Asian cultivated rice (Oryza sativa) and its wild relatives (O. rufipogon).

Science.gov (United States)

Li, W J; Zhang, B; Huang, G W; Kang, G P; Liang, M Z; Chen, L B

2012-12-17

We analyzed chloroplast DNA (cpDNA) polymorphism and phylogenic relationships between 6 typical indica rice, 4 japonica rice, 8 javanica rice, and 12 Asian common wild rice (Oryza rufipogon) strains collected from different latitudes in China by comparing polymorphism at 9 highly variable regions. One hundred and forty-four polymorphic bases were detected. The O. rufipogon samples had 117 polymorphic bases, showing rich genetic diversity. One hundred and thirty-one bases at 13 sites were identified with indica/japonica characteristics; they showed differences between the indica and japonica subspecies at these sites. The javanica strains and japonica shared similar bases at these 131 polymorphic sites, suggesting that javanica is closely related to japonica. On the basis of length analyses of the open reading frame (ORF)100 and (ORF)29-tRNA-Cys(GCA) (TrnC(GCA)) fragments, the O. rufipogon strains were classified into indica/japonica subgroups, which was consistent with the results of the phylogenic tree assay based on concatenated datasets. These results indicated that differences in indica and japonica also exist in the cpDNA genome of the O. rufipogon strains. However, these differences demonstrated a certain degree of primitiveness and incompleteness, as an O. rufipogon line may show different indica/ japonica attributes at different sites. Consequently, O. rufipogon cannot be simply classified into the indica/japonica types as O. sativa. Our data support the hypothesis that Asian cultivated rice, O. indica and O. japonica, separately evolved from Asian common wild rice (O. rufipogon) strains, which have different indica-japonica differentiation trends.

Genome-wide patterns of nucleotide polymorphism in domesticated rice

DEFF Research Database (Denmark)

Caicedo, Ana L; Williamson, Scott H; Hernandez, Ryan D

2007-01-01

Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments......, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models...... to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been...

The whole chloroplast genome of wild rice (Oryza australiensis).

Science.gov (United States)

Wu, Zhiqiang; Ge, Song

2016-01-01

The whole chloroplast genome of wild rice (Oryza australiensis) is characterized in this study. The genome size is 135,224  bp, exhibiting a typical circular structure including a pair of 25,776  bp inverted repeats (IRa,b) separated by a large single-copy region (LSC) of 82,212  bp and a small single-copy region (SSC) of 12,470  bp. The overall GC content of the genome is 38.95%. 110 unique genes were annotated, including 76 protein-coding genes, 4 ribosomal RNA genes, and 30t RNA genes. Among these, 18 are duplicated in the inverted repeat regions, 13 genes contain one intron, and 2 genes (rps12 and ycf3) have two introns.

Speciation of arsenic in rice and estimation of daily intake of different arsenic species by Brazilians through rice consumption.

Science.gov (United States)

Batista, Bruno L; Souza, Juliana M O; De Souza, Samuel S; Barbosa, Fernando

2011-07-15

Rice is an important source of essential elements. However, rice may also contain toxic elements such as arsenic. Therefore, in the present study, the concentration of total arsenic and five main chemical species of arsenic (As(3+), As(5+), DMA, MMA and AsB) were evaluated in 44 different rice samples (white, parboiled white, brown, parboiled brown, parboiled organic and organic white) from different Brazilian regions using high-performance liquid chromatography hyphenated to inductively coupled plasma mass spectrometry (HPLC-ICP-MS). The mean level of total arsenic was 222.8 ng g(-1) and the daily intake of inorganic arsenic (the most toxic form) from rice consumption was estimated as 10% of the Provisional Tolerable Daily Intake (PTDI) with a daily ingestion of 88 g of rice. Inorganic arsenic (As(3+), As(5+)) and dimethylarsinic acid (DMA) are the predominant forms in all samples. The percentages of species were 38.7; 39.7; 3.7 and 17.8% for DMA, As(3+), MMA and As(5+), respectively. Moreover, rice samples harvested in the state of Rio Grande do Sul presented more fractions of inorganic arsenic than rice in Minas Gerais or Goiás, which could lead to different risks of arsenic exposure. Copyright © 2011 Elsevier B.V. All rights reserved.

LHD1, an allele of DTH8/Ghd8, controls late heading date in common wild rice (Oryza rufipogon).

Science.gov (United States)

Dai, Xiaodong; Ding, Younian; Tan, Lubin; Fu, Yongcai; Liu, Fengxia; Zhu, Zuofeng; Sun, Xianyou; Sun, Xuewen; Gu, Ping; Cai, Hongwei; Sun, Chuanqing

2012-10-01

Flowering at suitable time is very important for plants to adapt to complicated environments and produce their seeds successfully for reproduction. In rice (Oryza rufipogon Griff.) photoperiod regulation is one of the important factors for controlling heading date. Common wild rice, the ancestor of cultivated rice, exhibits a late heading date and a more sensitive photoperiodic response than cultivated rice. Here, through map-based cloning, we identified a major quantitative trait loci (QTL) LHD1 (Late Heading Date 1), an allele of DTH8/Ghd8, which controls the late heading date of wild rice and encodes a putative HAP3/NF-YB/CBF-A subunit of the CCAAT-box-binding transcription factor. Sequence analysis revealed that several variants in the coding region of LHD1 were correlated with a late heading date, and a further complementary study successfully rescued the phenotype. These results suggest that a functional site for LHD1 could be among those variants present in the coding region. We also found that LHD1 could down-regulate the expression of several floral transition activators such as Ehd1, Hd3a and RFT1 under long-day conditions, but not under short-day conditions. This indicates that LHD1 may delay flowering by repressing the expression of Ehd1, Hd3a and RFT1 under long-day conditions. © 2012 Institute of Botany, Chinese Academy of Sciences.

Analytical method for the determination of various arsenic species in rice, rice food products, apple juice, and other juices by ion chromatography-inductively coupled plasma/mass spectrometry.

Science.gov (United States)

Ellingson, David; Zywicki, Richard; Sullivan, Darryl

2014-01-01

Recent studies have shown that there are detectable levels of arsenic (As) in rice, rice food products, and apple juice. This has created significant concern to the public, the food industry, and various regulatory bodies. Classic test methods typically measure total As and are unable to differentiate the various As species. Since different As species have greatly different toxicities, an analytical method was needed to separate and quantify the different inorganic and organic species of As. The inorganic species arsenite [As(+3)] and arsenate [As(+5)] are highly toxic. With this in mind, an ion chromatography-inductively coupled plasma (IC-ICP/MS) method was developed and validated for rice and rice food products that can separate and individually measure multiple inorganic and organic species of As. This allows for the evaluation of the safety or risk associated with any product analyzed. The IC-ICP/MS method was validated on rice and rice food products, and it has been used successfully on apple juice. This paper provides details of the validated method as well as some lessons learned during its development. Precision and accuracy data are presented for rice, rice food products, and apple juice.

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.

Science.gov (United States)

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.

Higher taxa as surrogates of species richness of spiders in insect-resistant transgenic rice

Institute of Scientific and Technical Information of China (English)

Sheng Lin; Min-Sheng You; Liette Vasseur; Guang Yang; Feng-Jing Liu; Feng Guo

2012-01-01

Biodiversity assessments can often be time- and resource-consuming.Several alternative approaches have been proposed to reduce sampling efforts,including indicator taxa and surrogates.In this study,we examine the reliability of higher taxon surrogates to predict species richness in two experimental rice fields of Fujian Province,southeastern China during 2005 and 2009.Spider samples in transgenic and nontransgenic plots were collected using a suction sampler.Both the genus and family surrogates had significant and positive linear relationships with species richness in the transgenic and nontransgenic rice fields.The rice varieties did not significantly influence the linear relationships.Our findings suggest that higher-taxon surrogacy could be a useful alternative to complete species inventory for risk assessments of transgenic rice.

Rice agroecosystem and the maintenance of biodiversity

International Nuclear Information System (INIS)

Ahyaudin Ali

2002-01-01

Rice fields are a special type of wetland. They are shallow, constantly disturbed and experience extremes in temperature and dissolved oxygen content. They receive nutrients in the form of fertilizers during rice cultivation. Rice fields; support a variety of flora and fauna that have adapted and adjusted themselves to the extreme conditions. Since rice fields also support populations of wild fish, rice?fish integration should be done in order to optimize land use and provide supplementary income to farmers. Rice?fish farming encourages farmers to judiciously apply pesticides and herbicides in their fields thus helping to control excessive and unwarranted use of these chemicals. Rice fields also support many migratory and nonmigratory bird species and provides habitat for small mammals. Thus the rice agroecosystem helps to maintain aquatic biodiversity. The Muda rice agroecosystem consists of a troika of interconnected ecosystems. The troika consisting of reservoirs, the connecting network of canals and the rice fields; should be investigated further. This data is needed for informed decision-making concerning development and management of the system so that productivity and biodiversity can be maintained and sustained. (Author)

Genetic diversity and population structure of Iranian wild Pleurotus eryngii species-complex strains revealed by URP-PCR markers

NARCIS (Netherlands)

Behnamian, Mahdi; Mohammadi, Seyed A.; Sonnenberg, A.S.M.; Goltapeh, Ebrahim M.; Hendrickx, P.M.

2010-01-01

In the present study, a set of 68 P. eryngii wild strains collected from nine locations in northwest and west of Iran along with six commercial strains were studied using universal rice primers (URP). The wild strains were isolated from Ferula ovina, F. haussknechtii, Cachrys ferulacea, Kellusia

The eco-evolutionary impacts of domestication and agricultural practices on wild species.

Science.gov (United States)

Turcotte, Martin M; Araki, Hitoshi; Karp, Daniel S; Poveda, Katja; Whitehead, Susan R

2017-01-19

Agriculture is a dominant evolutionary force that drives the evolution of both domesticated and wild species. However, the various mechanisms of agriculture-induced evolution and their socio-ecological consequences are not often synthetically discussed. Here, we explore how agricultural practices and evolutionary changes in domesticated species cause evolution in wild species. We do so by examining three processes by which agriculture drives evolution. First, differences in the traits of domesticated species, compared with their wild ancestors, alter the selective environment and create opportunities for wild species to specialize. Second, selection caused by agricultural practices, including both those meant to maximize productivity and those meant to control pest species, can lead to pest adaptation. Third, agriculture can cause non-selective changes in patterns of gene flow in wild species. We review evidence for these processes and then discuss their ecological and sociological impacts. We finish by identifying important knowledge gaps and future directions related to the eco-evolutionary impacts of agriculture including their extent, how to prevent the detrimental evolution of wild species, and finally, how to use evolution to minimize the ecological impacts of agriculture.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Author(s).

Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.

Directory of Open Access Journals (Sweden)

Xianfa Xie

Full Text Available Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa--indica and tropical japonica--as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups.

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

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Ethel Sánchez

2003-06-01

Full Text Available 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 through-out 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 µm, while Carara exhibits even sized prickle trichomes of ca. 93 µm. 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.La especie silvestre Oryza latifolia es endémica de América, tetraploide y de genoma CCDD. Pertenece a las especies del género Oryza del grupo officinalis. Presenta una amplia distribución en las tierras bajas de Costa Rica y se le encuentra en varias zonas de vida, mostrando una gran diversidad

Determination of sixteen elements and arsenic species in brown, polished and milled rice.

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Narukawa, Tomohiro; Matsumoto, Eri; Nishimura, Tsutomu; Hioki, Akiharu

2014-01-01

The concentrations of 16 elements in 10 rice flour samples and the distribution of the elements in the rice grains from which the flour were made were determined by ICP-MS and ICP-OES after microwave-assisted digestion of the samples. Arsenic speciation analysis was carried out by HPLC-ICP-MS following heat-assisted extraction of the sample. The concentrations of inorganic As (As(III) and As(V)), monomethylarsonic acid (MMAA) and dimethylarsinic acid (DMAA) and their distribution in the rice grains were determined. Portions of the brown rice were polished/milled to different degrees to yield milled off samples and polished rice samples. All samples were powdered and analyzed for 16 elements and for As species. The recoveries and mass balances for all elements in all samples showed good agreements with the starting materials. As(III), As(V), MMAA and DMAA were detected, and the sums of the concentrations of all species in the extract were 86-105% of the total As concentration in each case.

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

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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.

Identification and functional analysis of flowering related microRNAs in common wild rice (Oryza rufipogon Griff.).

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Chen, Zongxiang; Li, Fuli; Yang, Songnan; Dong, Yibo; Yuan, Qianhua; Wang, Feng; Li, Weimin; Jiang, Ying; Jia, Shirong; Pei, Xinwu

2013-01-01

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. 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. 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 for further study of phase change

Identification and functional analysis of flowering related microRNAs in common wild rice (Oryza rufipogon Griff..

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Zongxiang Chen

Full Text Available 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

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

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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

Prevalence of Campylobacter species in wild birds of South Korea.

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Kwon, Yong-Kuk; Oh, Jae-Young; Jeong, Ok-Mi; Moon, Oun-Kyoung; Kang, Min-Su; Jung, Byeong-Yeal; An, Byung-Ki; Youn, So-Youn; Kim, Hye-Ryoung; Jang, Il; Lee, Hee-Soo

2017-10-01

Campylobacter species cause human gastrointestinal infections worldwide. They commonly inhabit intestines of avian species including wild birds. They might play a role in the spread of infections to humans and other bird species. The prevalence of Campylobacter species in 2164 faecal samples of wild birds (representing 71 species and 28 families) captured across the Korean peninsula was evaluated in this study. The overall prevalence was 15.3% (332/2164). Bird species belonging to the family Charadriidae had the highest isolation rate (30.0%), followed by those belonging to the families Ardeidae (26.4%), Turdidae (21.9%), and Anatidae (15.3%). The prevalence of Campylobacter spp. differed significantly according to migratory habit. Stopover birds were the most commonly infected (19.0%), followed by winter migratory (16.7%) and summer migratory birds (12.3%). However, indigenous birds showed very low prevalence (2.7%). Antimicrobial susceptibility tests were performed for 213 isolates. Results showed that Campylobacter jejuni isolates (n = 169) exhibited resistance to nalidixic acid (5.3%), ciprofloxacin (3.0%), and tetracycline (1.8%), while Campylobacter lari (n = 1) displayed resistance to nalidixic acid and ciprofloxacin. However, all Campylobacter coli isolates (n = 20) were susceptible to all antimicrobials tested. This is the first report on the prevalence of Campylobacter species in wild birds that seasonally or indigenously inhabit the Korean peninsula. Our results indicate that the overall prevalence of Campylobacter in wild birds is moderate. Therefore, birds might serve as significant reservoirs for Campylobacter pathogens.

Identification of molecular markers linked to rice bacterial blight resistance genes from Oryza meyeriana

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Jing WANG,Chen CHENG,Yanru ZHOU,Yong YANG,Qiong MEI,Junmin LI,Ye CHENG,Chengqi YAN,Jianping CHEN

2015-09-01

Full Text Available Y73 is a progeny of asymmetric somatic hybridization between Oryza sativa cv. Dalixiang and the wild rice species Oryza meyeriana. Inoculation with a range of strains of Xanthomonas oryzae pv. oryzae showed that Y73 had inherited a high level of resistance to rice bacterial blight (BB from its wild parent. An F2 population of 7125 individuals was constructed from the cross between Y73 and a BB-susceptible cultivar IR24. After testing 615 SSR and STS markers covering the 12 rice chromosomes, 186 markers were selected that showed polymorphism between Y73 and IR24. Molecular markers linked to the BB resistance genes in Y73 were scanned using the F2 population and the polymorphic markers. The SSR marker RM128 on chromosome 1, the STS marker R03D159 on chromosome 3 and the STS marker R05D104 on chromosome 5 were found to be linked to the rice BB resistance genes in Y73.

Inter Simple Sequence Repeat (ISSR) analysis of wild and cultivated ...

African Journals Online (AJOL)

ONOS

2010-08-09

Aug 9, 2010 ... for 2 h at constant voltage of 100 V. The gel picture was taken after staining with ethidium ..... systems will provide a useful tool in the future design of collection strategies for ... The drop in diversity is substantially greater for genes involved in .... confirm the occurrence and distribution of wild rice species.

Evaluating the non-rice host plant species of Sesamia inferens (Lepidoptera: Noctuidae) as natural refuges: resistance management of Bt rice.

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Liu, Zhuorong; Gao, Yulin; Luo, Ju; Lai, Fengxiang; Li, Yunhe; Fu, Qiang; Peng, Yufa

2011-06-01

Although rice (Oryza sativa L.) lines that express Bacillus thuringiensis (Bt) toxins have shown great potential for managing the major Lepidoptera pests of rice in southern China, including Sesamia inferens, their long-term use is dependent on managing resistance development to Bt toxins in pest populations. The maintenance of "natural" refuges, non-Bt expressing plants that are hosts for a target pest, has been proposed as a means to minimize the evolution of resistance to Bt toxins in transgenic plants. In the current study, field surveys and greenhouse experiments were conducted to identify host plants of S. inferens that could serve as "natural" refuges in rice growing areas of southern China. A field survey showed that 34 plant species in four families can be alternative host plants of S. inferens. Based on injury level under field conditions, rice (Oryza sativa L.); water oat (Zizania latifolia Griseb.); corn (Zea mays L.); tidalmarsh flatsedge (Cyperus serotinus Rottb.); and narrow-leaved cat-tail (Typha angustifolia Linn.) were identified as the primary host plant species of S. inferens. Greenhouse experiments further demonstrated that water oat, corn, and narrow-leaved cat-tail could support the survival and development of S. inferens. Interestingly, greenhouse experiments showed that S. inferens preferred to lay eggs on tidalmarsh flatsedge compared with the other three nonrice host species, although no pupae were found in the plants examined in field surveys. Few larvae were found to survive on tidalmarsh flatsedge in greenhouse bioassays, suggesting that tidalmarsh flatsedge could serve as a "dead-end" trap crop for S. inferens, but is not a candidate to serve as natural refuge to maintain susceptible S. inferens. Overall, these results suggest that water-oat, corn, and narrow-leaved cat-tail might serve as "natural refuge" for S. inferens in rice planting area of southern China when Bt rice varieties are planted.

Genetic variability of concentration of microelements in wild sunflower species and hybrids

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Kastori Rudolf R.

2010-01-01

Full Text Available The aim of this work was to investigate genetic specificity of sunflower nutrition with microelements. Therefore, concentrations of essential (Zn, B, Mn, Cu, Fe and Ni and non-essential (Cr, Al, Cd, As, Pb and Ba micronutrients were analyzed. Five sunflower hybrids the most grown in Serbia and different populations of wild sunflower species originating from North America: Helianthus neglectus Heiser (3, Helianthus agrophyllus T&G (3, Helianthus petiolaris Nutt. (2, Helianthus annuus L. (4 were included in the experiment. Populations of wild sunflower species and hybrids differed significantly with respect to the concentration of analyzed elements. Manganese concentration was significantly higher in hybrids than in wild species. In all genotypes Fe, B and Mn had the highest concentration. Coefficient of variation of microelement concentration depended on genotype and particular element. In wild populations, for essential microelements, it was between 3.7 and 59.5, whereas in hybrids it varied from 10.0 to 48.8. Coefficient of variation of concentration of non-essential microelements in wild populations varied from 7.7 to 73.8, and in hybrids from 15.1 to 48.8. Average coefficient of variation in both wild species and hybrids was the lowest for Mn and Pb. It was the highest for Cr, Ni, and Zn in hybrids and for Cd, Ni, and Cr in wild species. The results suggest that genetic specificity with respect to uptake of microelements in wild species and hybrids is highly expressed. Broad genetic variability of concentrations of microelements in wild species and hybrids indicate that their reactions to deficiency and/or excess of those elements probably are not the same either. This finding may be used in breeding process aimed specifically at improvement of tolerance and capacity to accumulate microelements in sunflower. Phytoremediation technology designed to reduce the amount of microelements in the soil could thus be advanced by utilization of such

Saponin Profile of Wild Asparagus Species.

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Jaramillo-Carmona, Sara; Rodriguez-Arcos, Rocío; Jiménez-Araujo, Ana; López, Sergio; Gil, Juan; Moreno, Roberto; Guillén-Bejarano, Rafael

2017-03-01

The aim of this work was to study the saponin profiles from spears of different wild asparagus species in the context of its genetic diversity aside from geographical seed origin. They included Asparagus pseudoscaber Grecescu, Asparagus maritimus (L.) Mill., Asparagus brachiphyllus Turcz., Asparagus prostrates Dumort., and Asparagus officinalis L. The saponin analysis by LC-MS has shown that saponin profile from wild asparagus is similar to that previously described for triguero asparagus from Huétor-Tájar landrace (triguero HT), which had not ever been reported in the edible part of asparagus. All the samples, except A. officinalis, were characterized for having saponins distinct to protodioscin and the total saponin contents were 10-fold higher than those described for commercial hybrids of green asparagus. In particular, A. maritimus from different origins were rich in saponins previously found in triguero HT. These findings supported previous suggestion, based on genetic analysis, about A. maritimus being the origin of triguero HT. Multivariate statistics including principal component analysis and hierarchical clustering analysis were used to define both similarities and differences among samples. The results showed that the greatest variance of the tested wild asparagus could be attributed to differences in the concentration of particular saponins and this knowledge could be a tool for identifying similar species. © 2017 Institute of Food Technologists®.

Gene flow among wild and domesticated almond species: insights from chloroplast and nuclear markers

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Delplancke, Malou; Alvarez, Nadir; Espíndola, Anahí; Joly, Hélène; Benoit, Laure; Brouck, Elise; Arrigo, Nils

2012-01-01

Hybridization has played a central role in the evolutionary history of domesticated plants. Notably, several breeding programs relying on gene introgression from the wild compartment have been performed in fruit tree species within the genus Prunus but few studies investigated spontaneous gene flow among wild and domesticated Prunus species. Consequently, a comprehensive understanding of genetic relationships and levels of gene flow between domesticated and wild Prunus species is needed. Combining nuclear and chloroplastic microsatellites, we investigated the gene flow and hybridization among two key almond tree species, the cultivated Prunus dulcis and one of the most widespread wild relative Prunus orientalis in the Fertile Crescent. We detected high genetic diversity levels in both species along with substantial and symmetric gene flow between the domesticated P. dulcis and the wild P. orientalis. These results were discussed in light of the cultivated species diversity, by outlining the frequent spontaneous genetic contributions of wild species to the domesticated compartment. In addition, crop-to-wild gene flow suggests that ad hoc transgene containment strategies would be required if genetically modified cultivars were introduced in the northwestern Mediterranean. PMID:25568053

Mosquitoes of the rice agroecosystem of Malaysia: species composition and their abundance in relation to rice farming

International Nuclear Information System (INIS)

Abu Hassan Ahmad; Che Salmah Md Rawi

2002-01-01

Mosquito abundance in relation to rice farming was studied in the Muda and the Kerian Irrigation Schemes. Mosquito larvae were collected using dippers for several growing seasons. Adult mosquitoes were collected by using human bait and cow bait and net trap at nights. Culex, Mansonia and Anopheles were the three genera of mosquito found in the rice agroecosystem. Four species of Mansonia were found biting on human bait. Culex mosquitoes were caught biting on human and cow baits. Culex tritaeniorhynchus, C pseudovishnui, C vishnui, C gelidus and C bitaeniorhynchus were the most common Culex mosquitoes found. Anoheles sinensis and A. peditaeniatus were the most dominant panopheline mosquitoes. High abundance of larvae and adult mosquitoes were observed during ploughing, planting, and tillering stages of rice farming. (Author)

Spatial and seasonal diversity of wild food plants in home gardens of Northeast Thailand

NARCIS (Netherlands)

Cruz Garcia, G.S.; Struik, P.C.

2015-01-01

Wild food plants (WFPs) are major components of tropical home gardens, constituting an important resource for poor farmers. The spatial and seasonal diversity of WFPs was analyzed across multi-species spatial configurations occurring within home gardens in a rice farming village in northeast

Different localization patterns of anthocyanin species in the pericarp of black rice revealed by imaging mass spectrometry.

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Yukihiro Yoshimura

Full Text Available Black rice (Oryza sativa L. Japonica contains high levels of anthocyanins in the pericarp and is considered an effective health-promoting food. Several studies have identified the molecular species of anthocyanins in black rice, but information about the localization of each anthocyanin species is limited because methodologies for investigating the localization such as determining specific antibodies to anthocyanin, have not yet been developed Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS is a suitable tool for investigating the localization of metabolites. In this study, we identified 7 species of anthocyanin monoglycosides and 2 species of anthocyanin diglycosides in crude extracts from black rice by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS analysis. We also analyzed black rice sections by MALDI-IMS and found 2 additional species of anthocyanin pentosides and revealed different localization patterns of anthocyanin species composed of different sugar moieties. Anthocyanin species composed of a pentose moiety (cyanidin-3-O-pentoside and petunidin-3-O-pentoside were localized in the entire pericarp, whereas anthocyanin species composed of a hexose moiety (cyanidin-3-O-hexoside and peonidin-3-O-hexoside were focally localized in the dorsal pericarp. These results indicate that anthocyanin species composed of different sugar moieties exhibit different localization patterns in the pericarp of black rice. This is the first detailed investigation into the localization of molecular species of anthocyanins by MALDI-IMS.

A study on compatibilities on transgenic herbicide-resistant rice with wild relatives by using autoradiography of 32P labeled pollen

International Nuclear Information System (INIS)

Liu Linli; Qiang Sheng; Song Xiaoling

2004-01-01

To evaluate the possibility of gene flow through observation of the sexual compatibilities of transgenic herbicide-resistant rice with wild relative by using isotope tracer to label pollen grains, the experiments on radioactivity, tracer mode, autoradiography film and time were conducted. Better procedure was to label pollen grains of transgenic herbicide-resistant rice by culturing the rice in a 1.48 x 10 7 Bq/L 32 P nutrient liquid, to pollinate the labelled pollen grains on the stigmas of barnyard grass (Echinochloa crusgalli var. mitis), Oryza officinalis and weedy rice (Oryza sativa) respectively, and then 3 hour later, to fix these pistils on a piece of glass plate and cover the film of Luck 400 on it for autoradiography. The autoradiographs show that the tube of the transgenic rice's pollens cannot penetrate the stigma of barnyard grass and arrive at embryo sacs to fertilize, so that the possibility of gene flow between them is the lowest; the tube of the labelled pollens can penetrate the stigma of O officinalis and enter the style but can not arrive at embryo sacs to fertilize, so the possibility of gene flow between them is relatively low; and the pollen tube can arrive at the embryo sacs of the weedy rice, so that the possibility of gene flow is relatively high from transgenic herbicide-resistant rice to weedy rice. (authors)

Arsenic species in wheat, raw and cooked rice: Exposure and associated health implications.

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Rasheed, Hifza; Kay, Paul; Slack, Rebecca; Gong, Yun Yun

2018-09-01

Arsenic concentrations above 10μgL -1 were previously found in 89% of ground water sources in six villages of Pakistan. The present study has ascertained the health risks associated with exposure to total arsenic (tAs) and its species in most frequently consumed foods. Inorganic arsenic (iAs) concentrations were found to be 92.5±41.88μgkg -1 , 79.21±76.42μgkg -1 , and 116.38±51.38μgkg -1 for raw rice, cooked rice and wheat respectively. The mean tAs concentrations were 47.47±30.72μgkg -1 , 71.65±74.7μgkg -1 , 105±61.47μgkg -1 . Wheat is therefore demonstrated to be a significant source of arsenic exposure. Dimethylarsinic acid was the main organic species detected in rice, whilst monomethylarsonic acid was only found at trace levels. Total daily intake of iAs exceeded the provisional tolerable daily intake of 2.1μgkg -1 day -1 body weight in 74% of study participants due to concurrent intake from water (94%), wheat (5%) and raw rice (1%). A significant association between tAs in cooked rice and cooking water resulted in tAs intake 43% higher in cooked rice compared to raw rice. The study suggests that arsenic intake from food, particularly from wheat consumption, holds particular significance where iAs is relatively low in water. Chronic health risks were found to be significantly higher from wheat intake than rice, whilst the risk in terms of acute effects was below the USEPA's limit of 1.0. Children were at significantly higher health risk than adults due to iAs exposure from rice and/or wheat. The dietary exposure of participants to tAs was attributable to staple food intake with ground water iAs iAs in drinking water. Although the daily iAs intake from food was lower than total water intake, the potential health risk from exposure to arsenic and its species still exists and requires exposure control measures. Copyright © 2018 Elsevier B.V. All rights reserved.

[Determination of five arsenic species in rice by liquid chromatography-inductively coupled plasma-mass spectrometry].

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Gong, Jiadi; Cao, Xiaolin; Cao, Zhaoyun; Bian, Yingfang; Yu, Shasha; Chen, Mingxue

2014-07-01

A method was developed for the simultaneous determination of arsenic acid [As (V)], arsenious acid [As (III)], arsenobetaine (AsB), monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA) in rice by liquid chromatography-inductively coupled plasma-mass spectrometry (LC-ICP-MS). The extraction reagent was 0.3 mol/L nitric acid with heat-assistant condition for 1.5 h at 95 degrees C. Then, the five arsenic species were separated by an anion exchange column (Dionex IonPac AS19, 250 mm x 4 mm) and detected by ICP-MS. Four kinds of extracted solutions were compared through the extraction efficiency. The concentration of nitric acid, the temperature and the extraction time were optimized. The recoveries of the five arsenic species spiked in rice at two levels ranged from 89.6% to 99.5% with the relative standard deviations (RSDs, n = 5) of 0.6% - 3.6%. The measured values of the arsenic species in standard rice materials were consistent with their standard values. The linear ranges were 0.05 - 200 microg/L for AsB and DMA, 0.10-400 microg/L for As (III) and MMA, 0.15-600 microg/L for As (V). The limits of detection for the five arsenic species were 0.15-0.45 microg/kg. The results showed that the method is much more precise for the risk assessment of the rice. This method is simple, accurate and durable for the determination of arsenic species in rice.

Identification of heat-sensitive QTL derived from common wild rice (Oryza rufipogon Griff.).

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Lei, Dongyang; Tan, Lubin; Liu, Fengxia; Chen, Liyun; Sun, Chuanqing

2013-03-01

Understanding the responses of rice plants to heat-stress is a challenging, yet crucial, endeavor. A set of introgression lines was previously developed using an advanced backcrossing strategy that involved the elite indica cultivar Teqing as the recipient and an accession of common wild rice (Oryza rufipongon Griff.) as the donor. In this study, we evaluated the responses of 90 of these previously developed introgression lines to heat stress. Five quantitative trait loci (QTLs) related to heat response were detected. The phenotypic variances explained by these QTLs ranged from 6.83% to 14.63%, and O. rufipogon-derived alleles at one locus reduced sensitivity to heat. A heat-sensitive introgression line, YIL106, was identified and characterized. Genotypic analysis demonstrated that YIL106 contained four introgressed segments derived from O. rufipongon and two QTLs (qHTS1-1 and qHTS3) related to heat response. Physiological tests, including measurements of chlorophyll content, electrolyte leakage, malondialdehyde content, and soluble sugar content, were consistent with the heat sensitivity observed in YIL106. Ultrastructural analysis of YIL106 mesophyll cells showed that they were severely damaged following heat stress. This suggests that modification of the cell membrane system is a primary response to heat stress in plants. Identification and characterization of the heat-sensitive line YIL106 may facilitate the isolation of genes associated with the response of rice plants to heat stress. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

29 CFR 780.114 - Wild commodities.

Science.gov (United States)

2010-07-01

... Agricultural Or Horticultural Commodities § 780.114 Wild commodities. Employees engaged in the gathering or harvesting of wild commodities such as mosses, wild rice, burls and laurel plants, the trapping of wild... 29 Labor 3 2010-07-01 2010-07-01 false Wild commodities. 780.114 Section 780.114 Labor Regulations...

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

Science.gov (United States)

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. Copyright © 2014 Elsevier GmbH. All rights reserved.

Comparison of arsenic uptake ability of barnyard grass and rice species for arsenic phytoremediation.

Science.gov (United States)

Sultana, Razia; Kobayashi, Katsuichiro; Kim, Ki-Hyun

2015-01-01

In this research, the relative performance in arsenic (As) remediation was evaluated among some barnyard grass and rice species under hydroponic conditions. To this end, four barnyard grass varieties and two rice species were selected and tested for their remediation potential of arsenic. The plants were grown for 2 weeks in As-rich solutions up to 10 mg As L(-1) to measure their tolerance to As and their uptake capabilities. Among the varieties of plants tested in all treatment types, BR-29 rice absorbed the highest amount of As in the root, while Nipponbare translocated the maximum amount of As in the shoot. Himetainubie barnyard grass produced the highest biomass, irrespective of the quantity of As in the solution. In all As-treated solutions, the maximum uptake of As was found in BR-29 followed by Choto shama and Himetainubie. In contrast, while the bioaccumulation factor was found to be the highest in Nipponbare followed by BR-29 and Himetainubie. The results suggest that both Choto shama and Himetainubie barnyard grass varieties should exhibit a great potential for As removal, while BR-29 and Nipponbare rice species are the best option for arsenic phytoremediation.

Disentangling urban habitat and matrix effects on wild bee species.

Science.gov (United States)

Fischer, Leonie K; Eichfeld, Julia; Kowarik, Ingo; Buchholz, Sascha

2016-01-01

In face of a dramatic decline of wild bee species in many rural landscapes, potential conservation functions of urban areas gain importance. Yet effects of urbanization on pollinators, and in particular on wild bees, remain ambiguous and not comprehensively understood. This is especially true for amenity grassland and extensively managed wastelands within large-scale residential housing areas. Using Berlin as a study region, we aimed to investigate (a) if these greenspaces are accepted by wild bee assemblages as foraging habitats; (b) how assemblage structure of bees and individual bee species are affected by different habitat (e.g., management, flower density) and urban matrix variables (e.g., isolation, urbanization); and (c) to what extent grassland restoration can promote bees in urban environments. In summer 2012, we collected 62 bee species belonging to more than 20% of the taxa known for Berlin. Urbanization significantly affected species composition of bees; 18 species were affiliated to different levels of urbanization. Most bee species were not affected by any of the environmental variables tested, and urbanization had a negative effect only for one bee species. Further, we determined that restoration of diverse grasslands positively affected bee species richnesss in urban environments. We conclude that differently structured and managed greenspaces in large-scale housing areas can provide additional foraging habitats and refuges for pollinators. This supports approaches towards a biodiversity friendly management within urban regions and may be of particular importance given that anthropogenic pressure is increasing in many rural landscapes.

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

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Hepler Peter K

2011-01-01

Full Text Available Abstract 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

Morphological identification of Candida species on glucose agar, rice extract agar and corn meal agar with and without Tween-80.

Science.gov (United States)

Joshi, K R; Solanki, A; Prakash, P

1993-01-01

A comparative study for the identification of 32 known strains of Candida species on the basis of morphology on glucose agar, rice extract agar and corn meal agar with and without Tween 80 revealed that when Tween 80 is incorporated in the media identification is possible for 96.8% of the species within 48 hours on rice extract agar and for 96.8% of the species within 48 hours on rice extract agar and for 90.6% of the species on glucose agar. The germ tubes and chlamydospores were also produced more on rice extract agar than on 0.1% glucose agar. Rice extract agar with Tween 80 can be used as single medium for morphologic identification of Candida species. The inoculated medium is first incubated at 37 degrees C for 3 hours and examined for germ tube formation and then incubated at 25 degrees C for 24 to 72 hours and examined for appearance of chlamydospores and mycelial morphology.

Use of wild and semi-wild edible plants in nutrition and survival of people in 1430 days of siege of Sarajevo during the war in Bosnia and Herzegovina (1992-1995).

Science.gov (United States)

Redzić, Sulejman

2010-06-01

This study is a systematic overview of data on use of wild and semi-wild edible plants in nutrition of people in 1430 days of the siege of Sarajevo during aggression on Bosnia and Herzegovina (1992-1995). The author of this study spent all that time in Sarajevo. In 1993, the author prepared a survival program for people that included usage of edible wild plants. In addition, he conducted a detailed survey, including special interviews, on 630 people of average age 37.4 years (55% residential inhabitants, the rest were refuges), 310 males and the rest were females. According to survey, 91 species of mostly wild plants and three species of fungus were used: Küchneromyces mutabilis, Armillariella mellea and Coprinus comatus. Wild vegetables included 49 species, spices 24, wild fruits 16, and 2 species of bread-plants. They belong to 26 plants communities, and grew on 24 different habitats (urban surfaces, river coasts, low forest and scrubs, meadows and rocky grasslands). The 156 plant parts (leaves, young branches, fruit, flower, seed, root and rhizome) from 91 plant species were used. Vegetables were dominant category of use (soups, pottages, sauces) with 80 ways of preparation (30.53%), then salads 41 (15.65%), spices 39 (14.89%), different beverages 38 (14.50%), sweets 21 (8.02%), nutritive teas 15 (5.73%), and other preparations. In order to improve conventional food (war pasta, rice, lentils, old beans) people used spices made from different wild plants.

Disentangling urban habitat and matrix effects on wild bee species

Directory of Open Access Journals (Sweden)

Leonie K. Fischer

2016-11-01

Full Text Available In face of a dramatic decline of wild bee species in many rural landscapes, potential conservation functions of urban areas gain importance. Yet effects of urbanization on pollinators, and in particular on wild bees, remain ambiguous and not comprehensively understood. This is especially true for amenity grassland and extensively managed wastelands within large-scale residential housing areas. Using Berlin as a study region, we aimed to investigate (a if these greenspaces are accepted by wild bee assemblages as foraging habitats; (b how assemblage structure of bees and individual bee species are affected by different habitat (e.g., management, flower density and urban matrix variables (e.g., isolation, urbanization; and (c to what extent grassland restoration can promote bees in urban environments. In summer 2012, we collected 62 bee species belonging to more than 20% of the taxa known for Berlin. Urbanization significantly affected species composition of bees; 18 species were affiliated to different levels of urbanization. Most bee species were not affected by any of the environmental variables tested, and urbanization had a negative effect only for one bee species. Further, we determined that restoration of diverse grasslands positively affected bee species richnesss in urban environments. We conclude that differently structured and managed greenspaces in large-scale housing areas can provide additional foraging habitats and refuges for pollinators. This supports approaches towards a biodiversity friendly management within urban regions and may be of particular importance given that anthropogenic pressure is increasing in many rural landscapes.

An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice.

Science.gov (United States)

Chen, Guoxiong; Komatsuda, Takao; Ma, Jian Feng; Nawrath, Christiane; Pourkheirandish, Mohammad; Tagiri, Akemi; Hu, Yin-Gang; Sameri, Mohammad; Li, Xinrong; Zhao, Xin; Liu, Yubing; Li, Chao; Ma, Xiaoying; Wang, Aidong; Nair, Sudha; Wang, Ning; Miyao, Akio; Sakuma, Shun; Yamaji, Naoki; Zheng, Xiuting; Nevo, Eviatar

2011-07-26

Land plants have developed a cuticle preventing uncontrolled water loss. Here we report that an ATP-binding cassette (ABC) subfamily G (ABCG) full transporter is required for leaf water conservation in both wild barley and rice. A spontaneous mutation, eibi1.b, in wild barley has a low capacity to retain leaf water, a phenotype associated with reduced cutin deposition and a thin cuticle. Map-based cloning revealed that Eibi1 encodes an HvABCG31 full transporter. The gene was highly expressed in the elongation zone of a growing leaf (the site of cutin synthesis), and its gene product also was localized in developing, but not in mature tissue. A de novo wild barley mutant named "eibi1.c," along with two transposon insertion lines of rice mutated in the ortholog of HvABCG31 also were unable to restrict water loss from detached leaves. HvABCG31 is hypothesized to function as a transporter involved in cutin formation. Homologs of HvABCG31 were found in green algae, moss, and lycopods, indicating that this full transporter is highly conserved in the evolution of land plants.

Biological control of rice brown spot with native isolates of three Trichoderma species

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Elham Khalili

2012-03-01

Full Text Available Brown spot caused by Bipolaris oryzae is an important rice disease in Southern coast of Caspian Sea, the major rice growing region in Iran. A total of 45 Trichoderma isolates were obtained from rice paddy fields in Golestan and Mazandaran provinces which belonged to Trichoderma harzianum, T. virens and T. atroviride species. Initially, they were screened against B. oryzae by antagonism tests including dual culture, volatile and nonvolatile metabolites and hyperparasitism. Results showed that Trichoderma isolates can significantly inhibit mycelium growth of pathogen in vitro by producing volatile and nonvolatile metabolites Light microscopic observations showed no evidence of mycoparasitic behaviour of the tested isolates of Trichoderma spp. such as coiling around the B. oryzae. According to in vitro experiments, Trichoderma isolates were selected in order to evaluate their efficacy in controlling brown spot in glasshouse using seed treatment and foliar spray methods. Concerning the glasshouse tests, two strains of T. harzianum significantly controlled the disease and one strain of T. atroviride increased the seedling growth. It is the first time that the biological control of rice brown spot and increase of seedling growth with Trichoderma species have been studied in Iran.

Synthetic Hexaploids Derived from Wild Species Related to Sweet Potato

OpenAIRE

SHIOTANI, Itaru; KAWASE, Tsuneo; 塩谷, 格; 川瀬, 恒男

1987-01-01

The utilization of germplasm of the wild species in sweet-potato breeding has been conducted for the last three decades. Such attempts brought some remarkable achievments in improving root yield, starch content and resistance to the nematodes of sweet potato. Some wild plants in polyploid series may have many genes potentially important for further improvement of the agronomic traits. However, the genomic relationship between the wild relatives and hexaploid sweet potato (2n=6x=90) has been u...

Characterization of mercury species in brown and white rice (Oryza sativa L.) grown in water-saving paddies

Energy Technology Data Exchange (ETDEWEB)

Rothenberg, Sarah E., E-mail: rothenberg.sarah@gmail.com [State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, 46 Guanshui Lu, Guiyang 550002 (China); Feng Xinbin, E-mail: fengxinbin@vip.skleg.cn [State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, 46 Guanshui Lu, Guiyang 550002 (China); Dong Bin, E-mail: dongbin@whu.edu.cn [State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072 (China); Shang Lihai, E-mail: shanglihai@vip.gyig.ac.cn [State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, 46 Guanshui Lu, Guiyang 550002 (China); Yin Runsheng, E-mail: yinrunsheng2002@163.com [State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, 46 Guanshui Lu, Guiyang 550002 (China); Yuan Xiaobo, E-mail: xiantao_131@163.com [College of Resources and the Environment, Southwest University, Chongqing 400716 (China)

2011-05-15

In China, total Hg (Hg{sub T}) and methylmercury (MeHg) were quantified in rice grain grown in three sites using water-saving rice cultivation methods, and in one Hg-contaminated site, where rice was grown under flooded conditions. Polished white rice concentrations of Hg{sub T} (water-saving: 3.3 {+-} 1.6 ng/g; flooded: 110 {+-} 9.2 ng/g) and MeHg (water-saving 1.3 {+-} 0.56 ng/g; flooded: 12 {+-} 2.4 ng/g) were positively correlated with root-soil Hg{sub T} and MeHg contents (Hg{sub T}: r{sup 2} = 0.97, MeHg: r{sup 2} = 0.87, p < 0.05 for both), which suggested a portion of Hg species in rice grain was derived from the soil, and translocation of Hg species from soil to rice grain was independent of irrigation practices and Hg levels, although other factors may be important. Concentrations of Hg{sub T} and other trace elements were significantly higher in unmilled brown rice (p < 0.05), while MeHg content was similar (p > 0.20), indicating MeHg infiltrated the endosperm (i.e., white rice) more efficiently than inorganic Hg(II). - Highlights: > First time that Hg{sub T} and MeHg were characterized in both brown and white rice. > MeHg translocation into the endosperm was more efficient than inorganic Hg(II). > In this respect, MeHg behaved like dimethylarsinic acid and organic Se species. > In white rice, Hg{sub T} and MeHg were positively correlated with soil Hg{sub T} and MeHg. > Uptake rates of Hg{sub T} and MeHg were independent of irrigation methods and Hg content. - Methylmercury was more efficiently translocated to the endosperm than inorganic mercury.

Microbial Species and Functional Diversity in Rice Rhizosphere of High-yield Special Ecological Areas

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PAN Li-yuan

2016-11-01

Full Text Available Taoyuan, Yunnan Province is a special eco-site which keeps the highest yield records of rice cultivation in small planting areas. Soil microbial species and functional diversity were evaluated using cultivation method and BIOLOG ecoplates. The results showed that the microbial community of the high yield region was more abundant, and the total microbial population was 2 times of the control, furthermore, the areas belonged to the healthy "bacteria" soil, which was showed as bacteria > actinomycetes > fungi. Bacteria were the dominant populations in the rhizosphere of high yielding rice field, and the yield formation of rice was not correlated with the depth of soil layers. In order to obtain more species diversity information, Shannon diversity index H, Shannon evenness index E and Simpson index D were analyzed, and the results showed that microbial community diversity and evenness were not the main differences between the high and general yield areas. Then, the functional diversity of soil microbial community was investigated through the average well color development(AWCD and diversity index analyses. The results of AWCD analysis indicated that the metabolic activity of soil microbial community in high yield paddy soils were stronger than the control. Moreover, the difference range from large to small showed as tillering stage > harvest period > seedling period > rotation period, the stronger the rice growth, the greater the difference between the high yield region and the control. At tillering stage and harvest stage, due to the vigorous plant growth, the root exudates were rich, and the microbial communities of high yield paddy soils showed a strong metabolic activity and strong ability to use carbon sources. The results of Shannon, Simpson and McIntosh indices analysis indicated that common microbial species was not a key factor affecting the yield of rice. Tillering stage was a key period for the growth of high yield rice, and many

Wild Musa Species Collection of Purwodadi Botanic Garden: Inventory and Its Morpho - taxonomic Review

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Lia Hapsari

2014-01-01

Full Text Available Indonesia, being part of the center of origin of bananas (Musaceae, has a large number diversity of bananas both wild seeded species and edible seedless cultivated varieties. Inventory of wild Musa species in Purwodadi Botanic Garden has been conducted through compiling data records from PBG’s Registration section, field inspection and observation to living collections in the garden, herbarium specimens and literature studies. The results show that total 17 wild Musa accessions has been recorded planted in Purwodadi Botanic Garden since 1990 until 2012; comprises of 8 Musa acuminata sub species, 2 Musa balbisiana forms, 1 Musa ornata, 1 Musa troglodytarum, 1 Musa borneensis and 4 unidentified species Musa spp.; but only 8 living accessions remained in 2012. Morphotaxonomic review of those 8 wild Musa accessions remained will be discussed in this paper including their geographical distributions. According to its differentiated morphological characteristics observations, it is known that there are three accessions were resembled cultivars and one unidentified species have been determined its species level, so that their registration identity needs to be revised. It is important next to prioritize ex-situ conservation of wild Musa species not yet collected in Purwodadi Botanic Garden especially from Eastern Indonesia.

Dolce Vita in the Rice Paddy - Characterization of weedy rice groups in Northern Italy and investigation of their evolutionary origins

OpenAIRE

Grimm, Annabelle

2014-01-01

The thesis deals with the topic of the invasive rice form called weedy rice or red rice. Studies focused on the geographical area of Italy. Different populations of weedy rice in Italy were genetically characterized. The evolutionary origins of different weedy rice groups were investigated using molecular, morphological and physiological methods. Invasion of wild rice as well as de-domestication of cultivars could be identified as evolutionary sources of weedy rice in Northern Italy.

Broomrape (Orobanche cumana Wallr.) resistance breeding utilizing wild Helianthus species

Science.gov (United States)

Wild Helianthus species possess valuable resistance genes for sunflower broomrape (Orobanche cumana Wallr.), especially the 39 largely under-utilized perennial species. Resistance to race F has been transferred into cultivated background via bridging of interspecific amphiploids. More recently, a si...

Wild Prunus Fruit Species as a Rich Source of Bioactive Compounds.

Science.gov (United States)

Mikulic-Petkovsek, Maja; Stampar, Franci; Veberic, Robert; Sircelj, Helena

2016-08-01

Sugars, organic acids, carotenoids, tocopherols, chlorophylls, and phenolic compounds were quantified in fruit of 4 wild growing Prunus species (wild cherry, bird cherry, blackthorn, and mahaleb cherry) using HPLC-DAD-MSn. In wild Prunus, the major sugars were glucose and fructose, whereas malic and citric acids dominated among organic acids. The most abundant classes of phenolic compounds in the analyzed fruit species were anthocyanins, flavonols, derivatives of cinnamic acids, and flavanols. Two major groups of anthocyanins measured in Prunus fruits were cyanidin-3-rutinoside and cyanidin-3-glucoside. Flavonols were represented by 19 derivatives of quercetin, 10 derivatives of kaempferol, and 2 derivatives of isorhamnetin. The highest total flavonol content was measured in mahaleb cherry and bird cherry, followed by blackthorn and wild cherry fruit. Total phenolic content varied from 2373 (wild cherry) to 11053 mg GAE per kg (bird cherry) and ferric reducing antioxidant power antioxidant activity from 7.26 to 31.54 mM trolox equivalents per kg fruits. © 2016 Institute of Food Technologists®

Domesticated, Genetically Engineered, and Wild Plant Relatives Exhibit Unintended Phenotypic Differences: A Comparative Meta-Analysis Profiling Rice, Canola, Maize, Sunflower, and Pumpkin

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Alejandra Hernández-Terán

2017-12-01

Full Text Available Agronomic management of plants is a powerful evolutionary force acting on their populations. The management of cultivated plants is carried out by the traditional process of human selection or plant breeding and, more recently, by the technologies used in genetic engineering (GE. Even though crop modification through GE is aimed at specific traits, it is possible that other non-target traits can be affected by genetic modification due to the complex regulatory processes of plant metabolism and development. In this study, we conducted a meta-analysis profiling the phenotypic consequences of plant breeding and GE, and compared modified cultivars with wild relatives in five crops of global economic and cultural importance: rice, maize, canola, sunflower, and pumpkin. For these five species, we analyzed the literature with documentation of phenotypic traits that are potentially related to fitness for the same species in comparable conditions. The information was analyzed to evaluate whether the different processes of modification had influenced the phenotype in such a way as to cause statistical differences in the state of specific phenotypic traits or grouping of the organisms depending on their genetic origin [wild, domesticated with genetic engineering (domGE, and domesticated without genetic engineering (domNGE]. In addition, we tested the hypothesis that, given that transgenic plants are a construct designed to impact, in many cases, a single trait of the plant (e.g., lepidopteran resistance, the phenotypic differences between domGE and domNGE would be either less (or inexistent than between the wild and domesticated relatives (either domGE or domNGE. We conclude that (1 genetic modification (either by selective breeding or GE can be traced phenotypically when comparing wild relatives with their domesticated relatives (domGE and domNGE and (2 the existence and the magnitude of the phenotypic differences between domGE and domNGE of the same crop

Species integrity enhanced by a predation cost to hybrids in the wild

DEFF Research Database (Denmark)

Nilsson, P. A.; Hulthén, Kaj; Chapman, Ben B.

2017-01-01

Species integrity can be challenged, and even eroded, if closely related species can hybridize and produce fertile offspring of comparable fitness to that of parental species. The maintenance of newly diverged or closely related species therefore hinges on the establishment and effectiveness of pre...... barrier to gene flow in the wild. Cyprinid fishes commonly produce fertile, viable hybrid offspring and therefore make excellent study organisms to investigate ecological costs to hybrids. We electronically tagged two freshwater cyprinid fish species (roach Rutilus rutilus and bream Abramis brama...... to directly test for a predation cost to hybrids in the wild. Hybrid individuals were found significantly more susceptible to cormorant predation than individuals from either parental species. Such ecological selection against hybrids contributes to species integrity, and can enhance species diversification....

Occurrence and distribution of Giardia species in wild rodents in Germany.

Science.gov (United States)

Helmy, Yosra A; Spierling, Nastasja G; Schmidt, Sabrina; Rosenfeld, Ulrike M; Reil, Daniela; Imholt, Christian; Jacob, Jens; Ulrich, Rainer G; Aebischer, Toni; Klotz, Christian

2018-03-27

Giardiasis is an important gastrointestinal parasitic disease in humans and other mammals caused by the protozoan Giardia duodenalis. This species complex is represented by genetically distinct groups (assemblages A-H) with varying zoonotic potential and host preferences. Wild rodents can harbor potentially zoonotic assemblages A and B, and the rodent-specific assemblage G. Other Giardia spp. found in these animals are Giardia muris and Giardia microti. For the latter, only limited information on genetic typing is available. It has been speculated that wild rodents might represent an important reservoir for parasites causing human giardiasis. The aim of this study was to investigate the occurrence and distribution of Giardia spp. and assemblage types in wild rodents from different study sites in Germany. Screening of 577 wild rodents of the genera Apodemus, Microtus and Myodes, sampled at eleven study sites in Germany, revealed a high overall Giardia prevalence. Giardia species determination at the SSU rDNA gene locus revealed that Apodemus mice, depending on species, were predominantly infected with one of two distinct G. muris sequence types. Giardia microti was the predominant parasite species found in voles of the genera Microtus and Myodes. Only a few animals were positive for potentially zoonotic G. duodenalis. Subtyping at the beta-giardin (bg) and glutamine dehydrogenase (gdh) genes strongly supported the existence of different phylogenetic subgroups of G. microti that are preferentially harbored by distinct host species. The present study highlights the preference of G. muris for Apodemus, and G. microti for Microtus and Myodes hosts and argues for a very low prevalence of zoonotic G. duodenalis assemblages in wild rodents in Germany. It also provides evidence that G. muris and G. microti subdivide into several phylogenetically distinguishable subgroups, each of which appears to be preferentially harbored by species of a particular rodent host genus

Signatures of adaptation in the weedy rice genome

Science.gov (United States)

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...

Photosynthetic Characteristics of Flag Leaves in Rice White Stripe Mutant 6001 During Senescence Process

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Xiao-hui ZHEN

2014-11-01

Full Text Available Physiological, biochemical and electron microscopy analyses were used to investigate the photosynthetic performance of flag leaves in rice white stripe mutant 6001 during the senescence process. Results showed that the chlorophyll content at the heading and milk-ripe stages in rice mutant 6001 were about 34.78% and 3.00% less than those in wild type 6028, respectively. However, the chlorophyll content at the fully-ripe stage in rice mutant 6001 was higher than that in wild type 6028. At the heading stage, the net photosynthetic rate (Pn in rice mutant 6001 was lower than that in wild type 6028. Rice mutant 6001 also exhibited a significantly slower decrease rate of Pn than wild type 6028 during the senescence progress, especially at the later stage. Furthermore, Ca2+-ATPase, Mg2+-ATPase and photophosphorylation activities exhibited the similar trends as the Pn. During the senescence process, the 68 kDa polypeptide concentrations in the thylakoid membrane proteins exhibited a significant change, which was one of the critical factors that contributed to the observed change in photosynthesis. We also observed that the chloroplasts of rice mutant 6001 exhibited higher integrity than those of wild type 6028, and the chloroplast membrane of rice mutant 6001 disintegrated more slow during the senescence process. In general, rice mutant 6001 had a relatively slower senescence rate than wild type 6028, and exhibited anti-senescence properties.

Natural and human dimensions of a quasi-wild species: The case of kudzu

Science.gov (United States)

Li, Z.; Dong, Q.; Albright, Thomas P.; Guo, Q.

2011-01-01

The human dimensions of biotic invasion are generally poorly understood, even among the most familiar invasive species. Kudzu (Pueraria montana (Lour.) Merr.) is a prominent invasive plant and an example of quasi-wild species, which has experienced repeated introduction, cultivation, and escape back to the wild. Here, we review a large body of primary scientific and historic records spanning thousands of years to characterize the complex relationships among kudzu, its natural enemies, and humans, and provide a synthesis and conceptual model relevant to the ecology and management of quasi-wild invasive species. We documented over 350, mostly insect, natural enemy species and their impacts on kudzu in its native East Asian range. These natural enemies play a minor role in limiting kudzu in its native range, rarely generating severe impacts on populations of wild kudzu. We identified a number of significant influences of humans including dispersal, diverse cultural selection, and facilitation through disturbances, which catalyzed the expansion and exuberance of kudzu. On the other hand, harvest by humans appears to be the major control mechanism in its native areas. Humans thus have a complex relationship with kudzu. They have acted as both friend and foe, affecting the distribution and abundance of kudzu in ways that vary across its range and over time. Our conceptual model of kudzu emphasizes the importance of multiple human dimensions in shaping the biogeography of a species and illustrates how kudzu and other quasi-wild species are more likely to be successful invaders. ?? 2011 Springer Science+Business Media B.V.(outside the USA).

Natural variation of rice blast resistance gene Pi-d2

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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 (...

Natural and human dimensions of a quasi-wild species:the case of kudzu

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Zhenyu Li; Quan Dong; Thomas Albright; Qinfeng Guo

2011-01-01

The human dimensions of biotic invasion are generally poorly understood, even among the most familiar invasive species. Kudzu (Pueraria montana (Lour.) Merr.) is a prominent invasive plant and an example of quasi-wild species, which has experienced repeated introduction, cultivation, and escape back to the wild. Here, we review a large body of primary scientific and...

Comparative metabolite profiling of Solanum tuberosum against six wild Solanum species with Colorado potato beetle resistance.

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Tai, Helen H; Worrall, Kraig; Pelletier, Yvan; De Koeyer, David; Calhoun, Larry A

2014-09-10

The Colorado potato beetle Leptinotarsa decemlineata (Say) (CPB) is a coleopteran herbivore that feeds on the foliage on Solanum species, in particular, potato. Six resistant wild Solanum species were identified, and two of these species had low levels of glycoalkaloids. Comparative analysis of the untargeted metabolite profiles of the foliage using UPLC-qTOF-MS was done to find metabolites shared between the wild species but not with Solanum tuberosum (L.) to identify resistance-related metabolites. It was found that only S. tuberosum produced the triose glycoalkaloids solanine and chaconine. Instead, the six wild species produced glycoalkaloids that shared in common tetrose sugar side chains. Additionally, there were non-glycoalkaloid metabolites associated with resistance including hydroxycoumarin and a phenylpropanoid, which were produced in all wild species but not in S. tuberosum.

Population genetics of foxtail millet and its wild ancestor

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Wang Yongfang

2010-10-01

Full Text Available Abstract Background Foxtail millet (Setaria italica (L. P. Beauv., one of the most ancient domesticated crops, is becoming a model system for studying biofuel crops and comparative genomics in the grasses. However, knowledge on the level of genetic diversity and linkage disequilibrium (LD is very limited in this crop and its wild ancestor, green foxtail (Setaria viridis (L. P. Beauv.. Such information would help us to understand the domestication process of cultivated species and will allow further research in these species, including association mapping and identification of agricultural significant genes involved in domestication. Results In this study, we surveyed DNA sequence for nine loci across 50 accessions of cultivated foxtail millet and 34 of its wild progenitor. We found a low level of genetic diversity in wild green foxtail (θ = 0.0059, θ means Watterson's estimator of θ. Despite of a 55% loss of its wild diversity, foxtail millet still harbored a considerable level of diversity (θ = 0.0027 when compared to rice and sorghum (θ = 0.0024 and 0.0034, respectively. The level of LD in the domesticated foxtail millet extends to 1 kb, while it decayed rapidly to a negligible level within 150 bp in wild green foxtail. Using coalescent simulation, we estimated the bottleneck severity at k = 0.6095 when ρ/θ = 1. These results indicated that the domestication bottleneck of foxtail millet was more severe than that of maize but slightly less pronounced than that of rice. Conclusions The results in this study establish a general framework for the domestication history of foxtail millet. The low level of genetic diversity and the increased level of LD in foxtail millet are mainly caused by a population bottleneck, although gene flow from foxtail millet to green foxtail is another factor that may have shaped the pattern of genetic diversity of these two related gene pools. The knowledge provided in this study will benefit future population

Effect of organic matter amendment, arsenic amendment and water management regime on rice grain arsenic species

International Nuclear Information System (INIS)

Norton, Gareth J.; Adomako, Eureka E.; Deacon, Claire M.; Carey, Anne-Marie; Price, Adam H.; Meharg, Andrew A.

2013-01-01

Arsenic accumulation in rice grain has been identified as a major problem in some regions of Asia. A study was conducted to investigate the effect of increased organic matter in the soil on the release of arsenic into soil pore water and accumulation of arsenic species within rice grain. It was observed that high concentrations of soil arsenic and organic matter caused a reduction in plant growth and delayed flowering time. Total grain arsenic accumulation was higher in the plants grown in high soil arsenic in combination with high organic matter, with an increase in the percentage of organic arsenic species observed. The results indicate that the application of organic matter should be done with caution in paddy soils which have high soil arsenic, as this may lead to an increase in accumulation of arsenic within rice grains. Results also confirm that flooding conditions substantially increase grain arsenic. -- Highlights: ► High soil arsenic and organic matter caused a reduction in plant growth. ► A delayed flowering time was observed in high arsenic and organic matter soil. ► Total grain arsenic increased in high arsenic and organic matter soil. ► Percentage organic arsenic in the grain altered in arsenic and organic matter soil. -- The addition of high amounts of organic matter to soils led to an increase in total rice grain arsenic, as well as alteration in the percentage arsenic species in the rice grains

Meiotic behavior of wild Caricaceae species potentially suitable for papaya improvement

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Emanuelli Narducci da Silva

2012-01-01

Full Text Available The purpose of this study was to evaluate the meiotic behavior and determine the meiotic index and pollen viability of representative plants of the wild species V. goudotiana, V. quercifolia and J. spinosa. Meiotic analysis confirmed that the species are diploid and have 18 chromosomes. Meiosis was partially normal, since some abnormalities, e.g, sticky and lagging chromosomes, precocious segregation, lack of synchrony, and disturbances in the spindle fibers were observed. These abnormalities resulted in post-meiotic products (monads, dyads, triads, and polyads that probably contributed to the meiotic index of 85.7 % (V. goudotiana to 95.9 % (J. spinosa; significant variation was observed in the species V. goudotiana. The pollen viability of 68.0% (V. goudotiana to 96.0 % (J. spinosa was reasonably good in these wild species. Crossings in breeding programs involving V. goudotiana should therefore be carefully planned, since part of the gametes of this species is unviable.

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

International Nuclear Information System (INIS)

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

2012-01-01

Highlights: ► We isolated a novel E2 ubiquitin-conjugating enzyme from leaves of wild rice plants. ► The OgUBC1 was highly expressed in leaves treated with SA and UV-B radiation. ► The recombinant OgUBC1 has an enzymatic activity of E2 in vitro. ► The OgUBC1 could protect disruption of plant cells by UV-B radiation. ► 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.

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

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Jeon, En Hee; Pak, Jung Hun; Kim, Mi Jin; Kim, Hye Jeong [Department of Genetic Engineering, Dong-A University, Busan 604-714 (Korea, Republic of); Shin, Sang Hyun [National Crop Experiment Station, Rural Development Administration, Suwon 441-100 (Korea, Republic of); Lee, Jai Heon; Kim, Doh Hoon; Oh, Ju Sung [Department of Genetic Engineering, Dong-A University, Busan 604-714 (Korea, Republic of); Oh, Boung-Jun [BioControl Center, Jeonnam 516-942 (Korea, Republic of); Jung, Ho Won, E-mail: hwjung@dau.ac.kr [Department of Genetic Engineering, Dong-A University, Busan 604-714 (Korea, Republic of); Chung, Young Soo, E-mail: chungys@dau.ac.kr [Department of Genetic Engineering, Dong-A University, Busan 604-714 (Korea, Republic of)

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.

Defensive Responses of Rice Genotypes for Resistance Against Rice Leaffolder Cnaphalocrocis medinalis

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M. PUNITHAVALLI

2013-09-01

Full Text Available The experiment was carried out to assess the reaction of different categories of rice genotypes viz., resistant, susceptible, hybrid, scented, popular and wild in response to the infestation by rice leaffolder (RLF, Cnaphalocrocis medinalis (Guenee and to explore the possible use of these genotypes in developing RLF-resistant rice varieties. The changes of various biochemical constituents such as leaf soluble protein, phenol, ortho-dihydroxy phenol, tannin and enzymes viz., peroxidase, phenyl alanine ammonia lyase (PAL were assessed spectrophotometrically in all the rice genotypes before and after RLF infestation. The protein profile was analyzed using sodium dodecyl sulphate-poly acrylamide gel electrophoresis (SDS-PAGE method. A significant constituent of biochemical content such as tannin, phenol and ortho-dihydroxy phenol has been increased along with enzyme activities of peroxidase and PAL in the infested resistant (Ptb 33, TKM6 and LFR831311 and wild rice genotypes (Oryza minuta and O. rhizomatis. A decrease in leaf protein content was evident invariably in all the infested rice genotypes. It is also evident that the contents of biochemicals such as phenol, ortho-dihydroxy phenol and tannin were negatively correlated with leaffolder damage. However, leaf protein content was positively correlated with the damage by rice leaffolder. SDS-PAGE analysis for total protein profiling of healthy and C. medinalis-infested genotypes revealed the enhanced expression of a high molecular weight (> 97 kDa protein in all the genotypes. Besides, there was also an increased induction of a 38 kDa protein in C. medinalis infested resistant genotypes, which was absent in uninfested plants. The present investigation proved that the elevated levels of biochemicals and enzymes may play a vital role in rice plants resistance to RLF.

Wild Allium species (Alliaceae used in folk medicine of Tajikistan and Uzbekistan

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Kurbonova Parvina A

2006-04-01

Full Text Available Abstract Background Hitherto available sources from literature mentioned several wild growing Allium species as "edible" or "medicinally used" but without any further specification. Methods New data were gained during recent research missions: Allium plants were collected and shown to the local population which was asked for names and usage of these plants. Results Information was collected about current medical applications of sixteen wild species, nine of which belong to different sections of Allium subgenus Melanocrommyum. These plants are used against headache, cold, and stomach problems, and are mostly applied fresh or after boiling. Conclusion Close taxonomic relatives of the common onion were used similar to cultivated onion species, but medical use like garlic was mostly reported for species taxonomically not related to garlic.

Ribosomal DNA variation in finger millet and wild species of Eleusine (Poaceae).

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Hilu, K W; Johnson, J L

1992-04-01

Finger millet is an important cereal crop in the semi-arid regions of Africa and India. The crop belongs to the grass genus Eleusine, which includes nine annual and perennial species native to Africa except for the New World species E. tristachya. Ribosomal DNA (rDNA) variation in finger millet and related wild species was used to provide information on the origin of the genomes of this tetraploid crop and point out genetic relationships of the crop to other species in the genus. The restriction endonucleases used revealed a lack of variability in the rDNA spacer region in domesticated finger millet. All the rDNA variants of the crop were found in the proposed direct tetraploid ancestor, E. coracana subsp. africana. Wild and domesticated finger millet displayed the phenotypes found in diploid E. indica. Diploid Eleusine tristachya showed some similarity to the crop in some restriction sites. The remaining species were quite distinct in rDNA fragment patterns. The study supports the direct origin of finger millet from subspecies africana shows E. indica to be one of the genome donors of the crop, and demonstrates that none of the other species examined could have donated the second genome of the crop. The rDNA data raise the possibility that wild and domesticated finger millet could have originated as infraspecific polyploid hybrids from different varieties of E. indica.

Karyotipic asymmetry of both wild and cultivated species of Pennisetum

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Vânia Helena Techio

2010-01-01

Full Text Available This study aimed the establishment of the relation between karyotipic asymmetry values obtained for different accessions of both wild and cultivated species of Pennisetum from Germplasm Bank of Embrapa Gado de Leite/Juiz de Fora-Minas Gerais State, Brazil. Conventional cell cycle synchronization protocols and Feulgen staining method were used to obtain metaphases plates. The wild-type accessions corresponded to the species P. setosum (2n=6x=54, P. nervosum (2n=4x=36, and P. orientale (2n=4x=36, and the cultivated to P. purpureum (2n=4x=28 and P. glaucum (2n=2x=14. No significant difference was found for the total length of chromosomes (p>0.05 among the species. The analysis of intra-chromosomal asymmetry (A1 and inter-chromosomal asymmetry (A2 has shown that P. setosum has a tendency to chromosome asymmetry. P. nervosum, P. orientale, and P. purpureum have presented an intermediary level of asymmetry and P. glaucum, low asymmetry. Considering Stebbins criteria, the karyotype of P. glaucum and those from the three wild species fitted into the category 1A-symmetrical. With regard to P. purpureum, karyotypes of the accessions BAGs 54, 65 and 91 fitted into the category 2B and the other two genotypes (BAGs 63 and 75 fitted into the 1A. Comparison between the karyotype classification according to the inter- and intra-chromosomal asymmetry and Stebbins methodologies revealed that this last one alone was not able to detect small variations between karyotypes of the taxa closely related.

Regulation of reactive oxygen and nitrogen species by salicylic acid in rice plants under salinity stress conditions

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Mun, Bong-Gyu; Khan, Abdul Latif; Waqas, Muhammad; Kim, Hyun-Ho; Shahzad, Raheem; Imran, Muhammad

2018-01-01

This study investigated the regulatory role of exogenous salicylic acid (SA) in rice and its effects on toxic reactive oxygen and nitrogen species during short-term salinity stress. SA application (0.5 and 1.0 mM) during salinity-induced stress (100 mM NaCl) resulted in significantly longer shoot length and higher chlorophyll and biomass accumulation than with salinity stress alone. NaCl-induced reactive oxygen species production led to increased levels of lipid peroxidation in rice plants, which were significantly reduced following SA application. A similar finding was observed for superoxide dismutase; however, catalase (CAT) and ascorbate peroxidase (APX) were significantly reduced in rice plants treated with SA and NaCl alone and in combination. The relative mRNA expression of OsCATA and OsAPX1 was lower in rice plants during SA stress. Regarding nitrogenous species, S-nitrosothiol (SNO) was significantly reduced initially (one day after treatment [DAT]) but then increased in plants subjected to single or combined stress conditions. Genes related to SNO biosynthesis, S-nitrosoglutathione reductase (GSNOR1), NO synthase-like activity (NOA), and nitrite reductase (NIR) were also assessed. The mRNA expression of GSNOR1 was increased relative to that of the control, whereas OsNOA was expressed at higher levels in plants treated with SA and NaCl alone relative to the control. The mRNA expression of OsNR was decreased in plants subjected to single or combination treatment, except at 2 DAT, compared to the control. In conclusion, the current findings suggest that SA can regulate the generation of NaCl-induced oxygen and nitrogen reactive species in rice plants. PMID:29558477

Characterization of the Cultivable Gut Microflora in Wild-Caught 
Mediterranean Fish Species.

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Jammal, Ahmad; Bariche, Michel; Zu Dohna, Heinrich; Kambris, Zakaria

2017-05-01

Microflora of the gastrointestinal tract plays important roles in food digestion, nutrient absorption and in host defense against ingested pathogens. Several studies have focused on the microflora of farmed fishes, but the gut flora of wild fishes remains poorly characterized. The aim of this work was to provide an overview of the bacteria colonizing the gut of wild-caught fishes and to determine whether some bacterial species can be pathogenic. We isolated cultivable bacteria from fifteen wild-caught Mediterranean fish species corresponding to different habitat, diet and origin. Bacterial species identity was determined by 16s rRNA gene sequencing for the 61 isolates. The potential pathogenicity of isolated bacteria was investigated using fruit fly (Drosophila melanogaster) and zebrafish (Danio rerio) as model organisms. Two bacterial strains (Serratia sp. and Aeromonas salmonicida) were lethal when microinjected to Drosophila, while zebrafish did not develop any disease when exposed to any of 34 isolated bacterial strains. However, it was interesting to note that two bacterial strains (Shewanella and Arthrobacter) isolated from marine fishes were able to colonize the guts of freshwater zebrafish. The results of this study give an overview of the bacterial species found in the guts of wild fishes living off Beirut seashore. It shows that some parameters believed to be limiting factors to host-gut colonization by bacteria can be overcome by some species. This pilot study could be extended by sampling a larger number of fish species with several specimens per fish species, and by identifying uncultivable bacteria that reside in the fish guts. Our results may have implications for the utilization of certain bacterial species in fish farming or their use as bio-indicators for water and/or food quality.

Geographic and Research Center Origins of Rice Resistance to Asian Planthoppers and Leafhoppers: Implications for Rice Breeding and Gene Deployment

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Finbarr G. Horgan

2017-09-01

Full Text Available This study examines aspects of virulence to resistant rice varieties among planthoppers and leafhoppers. Using a series of resistant varieties, brown planthopper, Nilaparvata lugens, virulence was assessed in seedlings and early-tillering plants at seven research centers in South and East Asia. Virulence of the whitebacked planthopper, Sogatella furcifera, in Taiwan and the Philippines was also assessed. Phylogenetic analysis of the varieties using single-nucleotide polymorphisms (SNPs indicated a clade of highly resistant varieties from South Asia with two further South Asian clades of moderate resistance. Greenhouse bioassays indicated that planthoppers can develop virulence against multiple resistance genes including genes introgressed from wild rice species. Nilaparvata lugens populations from Punjab (India and the Mekong Delta (Vietnam were highly virulent to a range of key resistance donors irrespective of variety origin. Sogatella furcifera populations were less virulent to donors than N. lugens; however, several genes for resistance to S. furcifera are now ineffective in East Asia. A clade of International Rice Research Institute (IRRI-bred varieties and breeding lines, without identified leafhopper-resistance genes, were highly resistant to the green leafhopper, Nephotettix virescens. Routine phenotyping during breeding programs likely maintains high levels of quantitative resistance to leafhoppers. We discuss these results in the light of breeding and deploying resistant rice in Asia.

The new species Enterobacter oryziphilus sp. nov. and Enterobacter oryzendophyticus sp. nov. are key inhabitants of the endosphere of rice

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2013-01-01

Background Six independent Gram-negative, facultatively anaerobic, non-spore-forming, nitrogen-fixing rod-shaped isolates were obtained from the root endosphere of rice grown at the International Rice Research Institute (IRRI) and investigated in a polyphasic taxonomic study. Results The strains produced fatty acid patterns typical for members of the family Enterobacteriaceae. Comparative sequence analyses of the 16S rRNA as well as rpoB genes allocated the strains to two well-defined groups within the genus Enterobacter, family Enterobacteriaceae. The analyses indicated Enterobacter radicincitans, Enterobacter arachidis and Enterobacter oryzae to be the closest related species. An RpoB (translated) protein comparison supported the placement in the genus Enterobacter and the relatedness of our isolates to the aforementioned species. Genomic DNA:DNA hybridization analyses and biochemical analyses provided further evidence that the novel strains belong to two new species within the genus Enterobacter. The two species can be differentiated from each other and from existing enteric species by acid production from L-rhamnose and D-melibiose, decarboxylation of ornithine and utilization of D-alanine, D-raffinose L-proline and L-aspartic acid, among other characteristics. Members of both species revealed capacities to colonise rice roots, including plant-growth-promoting capabilities such as an active supply of fixed nitrogen to the plant and solubilisation of inorganic phosphorus, next to traits allowing adaptation to the plant. Conclusions Two novel proposed enterobacterial species, denominated Enterobacter oryziphilus sp. nov. (type strain REICA_142T=LMG 26429T=NCCB 100393T) and Enterobacter oryzendophyticus sp. nov. (type strain REICA_082T=LMG 26432T =NCCB 100390T) were isolated from rice roots. Both species are capable of promoting rice growth by supplying nitrogen and phosphorus. PMID:23865888

Transgenic expression of an unedited mitochondrial orfB gene product from wild abortive (WA) cytoplasm of rice (Oryza sativa L.) generates male sterility in fertile rice lines.

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Chakraborty, Anirban; Mitra, Joy; Bhattacharyya, Jagannath; Pradhan, Subrata; Sikdar, Narattam; Das, Srirupa; Chakraborty, Saikat; Kumar, Sachin; Lakhanpaul, Suman; Sen, Soumitra K

2015-06-01

Over-expression of the unedited mitochondrial orfB gene product generates male sterility in fertile indica rice lines in a dose-dependent manner. Cytoplasmic male sterility (CMS) and nuclear-controlled fertility restoration are widespread developmental features in plant reproductive systems. In self-pollinated crop plants, these processes often provide useful tools to exploit hybrid vigour. The wild abortive CMS has been employed in the majority of the "three-line" hybrid rice production since 1970s. In the present study, we provide experimental evidence for a positive functional relationship between the 1.1-kb unedited orfB gene transcript, and its translated product in the mitochondria with male sterility. The generation of the 1.1-kb unedited orfB gene transcripts increased during flowering, resulting in low ATP synthase activity in sterile plants. Following insertion of the unedited orfB gene into the genome of male-fertile plants, the plants became male sterile in a dose-dependent manner with concomitant reduction of ATPase activity of F1F0-ATP synthase (complex V). Fertility of the transgenic lines and normal activity of ATP synthase were restored by down-regulation of the unedited orfB gene expression through RNAi-mediated silencing. The genetic elements deciphered in this study could further be tested for their use in hybrid rice development.

Human impact on wild firewood species in the rural Andes community of Apillapampa, Bolivia.

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Thomas, Evert; Douterlungne, David; Vandebroek, Ina; Heens, Frieke; Goetghebeur, Paul; Van Damme, Patrick

2011-07-01

Firewood is the basic fuel source in rural Bolivia. A study was conducted in an Andean village of subsistence farmers to investigate human impact on wild firewood species. A total of 114 different fuel species was inventoried during fieldtrips and transect sampling. Specific data on abundance and growth height of wild firewood species were collected in thirty-six transects of 50 ×2 m(2). Information on fuel uses of plants was obtained from 13 local Quechua key participants. To appraise the impact of fuel harvest, the extraction impact value (EIV) index was developed. This index takes into account local participants' appreciation of (1) decreasing plant abundance; (2) regeneration capacity of plants; (3) impact of root harvesting; and (4) quality of firewood. Results suggest that several (sub-)woody plant species are negatively affected by firewood harvesting. We found that anthropogenic pressure, expressed as EIV, covaried with density of firewood species, which could entail higher human pressure on more abundant and/or more accessible species. The apparent negative impact of anthropogenic pressure on populations of wild fuel species is corroborated by our finding that, in addition to altitude, several anthropogenic variables (i.e. site accessibility, cultivation of exotics and burning practices) explain part of the variation in height of firewood species in the surroundings of Apillapampa.

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

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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.

Monitoring potential geographical distribution of four wild bird species in China

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Dai, S.; Feng, D.; Xu, B.

2015-12-01

The outbreak of highly pathogenic avian influenza (HPAI) of the H5N1 subtype in wild birds and poultry have caught worldwide attention. To explore the association between wild bird migration and avian influenza virus transmission, we monitored potential geographical distribution of four wild bird species that might carry the avian influenza viruses in China. They are Bar-headed geese (Anser indicus), Ruddy Shelduck (Tadorna ferruginea), Whooper Swan (Cygnus cygnus) and Black-headed Gull (Larus ridibundus). They served as major reservoir of the avian influenza viruses. We used bird watching records with the precise latitude/longitude coordinates from January 2002 to August 2014, and environmental variables with a pixel resolution of 5 km × 5 km from 2002 to 2014. The study utilized maximum entropy (MaxEnt) model based on ecological niche model approaches, and got the following results: 1) MaxEnt model have good discriminatory ability with the area under the curve (AUC) of the receiver operating curve (ROC) of 0.86-0.97; 2) The four wild bird species were estimated to concentrate in the North China Plain, the middle and lower region of the Yangtze River, Qinghai Lake, Tianshan Mountain and Tarim Basin, part of Tibet Plateau, and Hengduan Mountains; 3) Radiation and the minimum temperature were found to provide the most significant information. Our findings will help to understand the spread of avian influenza viruses by wild bird migration in China, which benefits for effective monitoring strategies and prevention measures.

78 FR 13694 - Conference of the Parties to the Convention on International Trade in Endangered Species of Wild...

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2013-02-28

... Wild Fauna and Flora (CITES); Sixteenth Regular Meeting; Tentative U.S. Negotiating Positions for... Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), will attend the... . SUPPLEMENTARY INFORMATION: Background The Convention on International Trade in Endangered Species of Wild Fauna...

Determination of plant species for the phytoremediation of carbofuran residue in rice field soils

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Alissara Reungsang

2005-09-01

Full Text Available This study searched for plant species suitable for accumulating carbofuran residue in rice field soil. Three groups of plant, i.e. grass crops, upland crops, and vegetable crops, were grown in 8 inches diameter plastic pots filled with soil containing 5 mg/kg carbofuran. Parts of plants (stems and leaves, roots, fruits were harvested at day 120 and analyzed for carbofuran residue using HPLC. The results indicated that Helianthus annuus L. (sunflower was the most suitable species for phytoremediation of carbofuran residue in rice field soil because it highly accumulated carbofuran up to 93.4 μg/kg dry weight in its stems and leaves. In addition, H. annuus L. (sunflower could tolerate carbofuran since it showed similar physical appearance (circumference and height to control not receiving carbofuran.

A rice chloroplast transit peptide sequence does not alter the cytoplasmic localization of sheep serotonin N-acetyltransferase expressed in transgenic rice plants.

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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. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

IDENTIFICATION AND OCCURRENCE OF FUSARIUM SPECIES ON SEEDS OF COMMON WETCH, WHITE LUPINE AND SOME WILD LEGUMES

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Tihomir Miličević

2013-06-01

Full Text Available The presence and occurrence of Fusarium species was examined on the seeds of cultivated legumes – common vetch (Vicia sativa, white lupine (Lupinus albus, and wild legumes: bird’s-foot trefoil (Lotus corniculatus, wild alfalfa (Medicago sativa, black locust (Robinia pseudoacacia, honey locust (Gleditsia triacanthos, sweet clover (Melilotus officinalis, bird vetch (Vicia cracca and meadow vetchling (Lathyrus pratensis. Thirteen Fusarium species were identified - F. verticillioides, F. acuminatum, F. avenaceum, F. tricinctum F. oxysporum, F. scirpi, F. semitectum, F. culmorum, F. proliferatum, F. pseudograminearum, F. sporotrichioides, F. sambucinum and F. heterosporum. Species F. verticillioides and F. proliferatum were determined on seeds of the cultivated legumes (common vetch and white lupine. Other 11 Fusarium species were determined on seeds of wild legumes (bird’s-foot trefoil, wild alfalfa, sweet clover and bird vetch among which the most prevalent were species F. avenaceum and F. acuminatum.

Community-wise evaluation of rice beer prepared by some ethnic tribes of Tripura

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Sushanta Ghosh

2016-12-01

Full Text Available Tripura is inhabited by many indigenous communities having unique ethno-socio-cultural lifestyle with age-old rice beer brewing techniques using wild herbs and local rice varieties popularly known as chuwak or zu. The present study is focused on comparative evaluation of brewing methods and nutritional aspects of rice beer among Debbarma, Jamatia, Koloi, and Molsom tribes of Tripura. Sample ingredients and plant species are properly identified before reporting. Rice beer is also prepared in laboratory conditions for comparative studies of qualitative and quantitative aspects. Thirteen different plant species are used by these four tribes for preparation of starter cultures using soaked rice flour. Markhamia stipulate (Wall. Seem. is common to all communities for starter cake preparation. Litsea monopetala (Roxb. Pers. is used by all three communities except Jamatia. The use of Ananus comosus Mill. is common among Debbarma and Jamatia tribes, whereas that of Artocarpus heterophyllus Lam. is common among Molsom and Koloi tribes. However, Aporusa diocia (Roxb. Muell., Combretum indicum (L. DeFilipps., and Citrus sinensis (L. Osbeck. are used only by Debbarma tribe for unique tangy flavor. The physicochemical properties of rice beer varied within tribes for its moisture content, carbohydrate content, reducing sugar, and alcohol percentage. The concentration of alcohol increases with aging and prolonged fermentation. The plants reported here are also reported for having nutritional and medicinal benefits for the metabolic stability in humans, which make the process more prospective for commercialization if a standard for maintaining a quality and associated risk can be determined.

Benthic macroinvertebrates in Italian rice fields

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Daniela Lupi

2013-02-01

Full Text Available Rice fields can be considered man-managed temporary wetlands. Five rice fields handled with different management strategies, their adjacent channels, and a spring were analysed by their benthic macroinvertebrate community to i evaluate the role of rice agroe- cosystem in biodiversity conservation; ii find indicator species which can be used to compare the ecological status of natural wetlands with rice agroecosystems; and iii find the influence of environmental variables on biodiversity. Different methods of data analysis with increasing degree of complexity – from diversity index up to sophisticated multivariate analysis – were used. The investigation provided a picture of benthic macroinvertebrates inhabiting rice agroecosystems where 173 taxa were identified, 89 of which detected in rice paddies. Among them, 4 phyla (Mollusca, Annelida, Nematomorpha, and Arthropoda, 8 classes (Bivalvia, Gastropoda, Oligochaeta, Hirudinea, Gordioida, Insecta, Branchiopoda, and Malacostraca, 24 orders, 68 families, 127 genera and 159 species have been found. Ten threatened and 3 invasive species were detected in the habitats examined. The information obtained by the different methods of data analysis allowed a more comprehensive view on the value of the components of rice agroecosystems. Data analyses highlighted significant differences between habitats (feeding channel and rice field, with higher diversity observed in channels, and emphasised the role of the water chemical-physical parameters. The period of water permanence in rice fields resulted to be only one of the factors influencing the community of benthic macroinvertebrates. The presence of rare/endangered species allowed characterising some stations, but it was less informative about management strategies in rice paddies because most of these species were absent in rice fields.

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

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

OpenAIRE

Wei Tong; Qiang He; Yong-Jin Park

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 nucle...

Estimating radionuclide transfer to wild species-data requirements and availability for terrestrial ecosystems

International Nuclear Information System (INIS)

Beresford, N A; Broadley, M R; Howard, B J; Barnett, C L; White, P J

2004-01-01

Assessment of the transfer of radionuclides to wild species is an important component in the estimation of predicted doses to biota. Reviews of available data for the many potential radionuclide-biota combinations which may be required for environmental assessments highlight many data gaps for terrestrial species. Here, we discuss different approaches which have been suggested to compensate for these data gaps. All of the reviewed approaches have merit; however, there is a requirement for transparency in methodology and data provenance which in some instances is currently missing. Furthermore, there is a need to validate the various methodologies to enable their use with confidence. The requirements of improving our ability to predict radionuclide transfer to wild species are discussed and recommendations made

Improved stress tolerance and productivity in transgenic rice plants constitutively expressing the Oryza sativa glutathione synthetase OsGS under paddy field conditions.

Science.gov (United States)

Park, Seong-Im; Kim, Young-Saeng; Kim, Jin-Ju; Mok, Ji-Eun; Kim, Yul-Ho; Park, Hyang-Mi; Kim, Il-Sup; Yoon, Ho-Sung

2017-08-01

Reactive oxygen species, which increase under various environmental stresses, have deleterious effects on plants. An important antioxidant, glutathione, is used to detoxify reactive oxygen species in plant cells and is mainly produced by two enzymes: gamma-glutamylcysteine synthetase (γ-ECS) and glutathione synthetase (GS). To evaluate the functional roles of the glutathione synthetase gene (OsGS) in rice, we generated four independent transgenic rice plants (TG1-TG4) that overexpressed OsGS under the control of the constitutively expressed OsCc1 promoter. When grown under natural paddy field conditions, the TG rice plants exhibited greater growth development, higher chlorophyll content, and higher GSH/GSSH ratios than control wild-type (WT) rice plants. Subsequently, the TG rice plants enhanced redox homeostasis by preventing hydroperoxide-mediated membrane damage, which improved their adaptation to environmental stresses. As a result, TG rice plants improved rice grain yield and total biomass following increases in panicle number and number of spikelets per panicle, despite differences in climate during the cultivation periods of 2014 and 2015. Overall, our results indicate that OsGS overexpression improved redox homeostasis by enhancing the glutathione pool, which resulted in greater tolerance to environmental stresses in the paddy fields. Copyright © 2017. Published by Elsevier GmbH.

Babesia spp. in European wild ruminant species: parasite diversity and risk factors for infection.

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Michel, Adam O; Mathis, Alexander; Ryser-Degiorgis, Marie-Pierre

2014-06-13

Babesia are tick-borne parasites that are increasingly considered as a threat to animal and public health. We aimed to assess the role of European free-ranging wild ruminants as maintenance mammalian hosts for Babesia species and to determine risk factors for infection. EDTA blood was collected from 222 roe deer (Capreolus c. capreolus), 231 red deer (Cervus e. elaphus), 267 Alpine chamois (Rupicapra r. rupicapra) and 264 Alpine ibex (Capra i. ibex) from all over Switzerland and analysed by PCR with pan-Babesia primers targeting the 18S rRNA gene, primers specific for B. capreoli and Babesia sp. EU1, and by sequencing. Babesia species, including B. divergens, B. capreoli, Babesia sp. EU1, Babesia sp. CH1 and B. motasi, were detected in 10.7% of all samples. Five individuals were co-infected with two Babesia species. Infection with specific Babesia varied widely between host species. Cervidae were significantly more infected with Babesia spp. than Caprinae. Babesia capreoli and Babesia sp. EU1 were mostly found in roe deer (prevalences 17.1% and 7.7%, respectively) and B. divergens and Babesia sp. CH1 only in red deer. Factors significantly associated with infection were low altitude and young age. Identification of Babesia sp. CH1 in red deer, co-infection with multiple Babesia species and infection of wild Caprinae with B. motasi and Babesia sp. EU1 are novel findings. We propose wild Caprinae as spillover or accidental hosts for Babesia species but wild Cervidae as mammalian reservoir hosts for B. capreoli, possibly Babesia sp. EU1 and Babesia sp. CH1, whereas their role regarding B. divergens is more elusive.

The Caryopsis of Red-Grained Rice Has Enhanced Resistance to Fungal Attack

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Alberto Gianinetti

2018-06-01

Full Text Available Seed persistence in the soil is threatened by microorganisms, but the seed coat helps protect the seed from them. Although modern rice (Oryza sativa L. cultivars have a whitish caryopsis, some varieties have a red caryopsis coat, a trait typical of wild Oryza species. The red colour is due to the oxidation of proanthocyanidins, a class of flavonoids that is found in the outer layers of the seed in many species. We aimed to assess whether these natural compounds (proanthocyanidins and proanthocyanidin-derived pigment have some protective effect against microbial attacks. Dehulled caryopses of white-grained and red-grained rice genotypes were employed to assay fungal infection. Specifically, three white-grained rice cultivars (Perla, Augusto, and Koral and three red-grained rice varieties (Perla Rosso, Augusto Rosso, and Koral Rosso were used. In a first test, the caryopses were infected with Epicoccum nigrum at 10 °C, and seedling growth was then assessed at 30 °C. In a second test, the degree of infection by the mycotoxigenic fungus Fusarium sporotrichioides was assayed by measuring the accumulation of T-2/HT-2 toxins in the caryopses. Infection was performed at 10 °C to prevent rice germination while allowing fungal growth. In both the tests, red caryopses showed reduced, or delayed, infection with respect to white ones. One black-grained cultivar (Venere was assayed for the accumulation of T-2/HT-2 toxins as well, with results corresponding to those of the red-grained rice varieties. We argue that the red pigment accumulating in the caryopsis coat, and/or the proanthocyanidins associated with it, provides a protective barrier against challenging microorganisms.

Introduction of wild MAP species into the field culture

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Dušková, Elena

2016-07-01

Full Text Available Althea officinalis L., Dracocephalum moldavica L., Gentiana lutea L., Rhodiola rosea L., and Valeriana officinalis L. are the species of wild medicinal plants which are not very commonly grown in field culture. The methods and practical experiences of their multiplication and growing in a field nursery in Olomouc (the Czech Republic are explained and shown in the manuscript.

Little White Lies: Pericarp Color Provides Insights into the Origins and Evolution of Southeast Asian Weedy Rice

Science.gov (United States)

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

Development and characterization of japonica rice lines carrying the brown planthopper-resistance genes BPH12 and BPH6.

Science.gov (United States)

Qiu, Yongfu; Guo, Jianping; Jing, Shengli; Zhu, Lili; He, Guangcun

2012-02-01

The brown planthopper (Nilaparvata lugens Stål; BPH) has become a severe constraint on rice production. Identification and pyramiding BPH-resistance genes is an economical and effective solution to increase the resistance level of rice varieties. All the BPH-resistance genes identified to date have been from indica rice or wild species. The BPH12 gene in the indica rice accession B14 is derived from the wild species Oryza latifolia. Using an F(2) population from a cross between the indica cultivar 93-11 and B14, we mapped the BPH12 gene to a 1.9-cM region on chromosome 4, flanked by the markers RM16459 and RM1305. In this population, BPH12 appeared to be partially dominant and explained 73.8% of the phenotypic variance in BPH resistance. A near-isogenic line (NIL) containing the BPH12 locus in the background of the susceptible japonica variety Nipponbare was developed and crossed with a NIL carrying BPH6 to generate a pyramid line (PYL) with both genes. BPH insects showed significant differences in non-preference in comparisons between the lines harboring resistance genes (NILs and PYL) and Nipponbare. BPH growth and development were inhibited and survival rates were lower on the NIL-BPH12 and NIL-BPH6 plants compared to the recurrent parent Nipponbare. PYL-BPH6 + BPH12 exhibited 46.4, 26.8 and 72.1% reductions in population growth rates (PGR) compared to NIL-BPH12, NIL-BPH6 and Nipponbare, respectively. Furthermore, insect survival rates were the lowest on the PYL-BPH6 + BPH12 plants. These results demonstrated that pyramiding different BPH-resistance genes resulted in stronger antixenotic and antibiotic effects on the BPH insects. This gene pyramiding strategy should be of great benefit for the breeding of BPH-resistant japonica rice varieties.

Dispersal distance of rice ( Oryza Sativa L.) pollen at the Tana River ...

African Journals Online (AJOL)

Rice is a staple food in Kenya and its production needs to be increased. Genetically modified (GM) rice may be a solution, but before it can be introduced, potential ecological impacts, such as pollen mediated gene flow from GM rice to non-GM rice or to its wild indigenous relatives, need to be understood. Pollen dispersal in ...

Fatty Acid Compositions of Six Wild Edible Mushroom Species

Science.gov (United States)

Günç Ergönül, Pelin; Akata, Ilgaz; Kalyoncu, Fatih; Ergönül, Bülent

2013-01-01

The fatty acids of six wild edible mushroom species (Boletus reticulatus, Flammulina velutipes var. velutipes, Lactarius salmonicolor, Pleurotus ostreatus, Polyporus squamosus, and Russula anthracina) collected from different regions from Anatolia were determined. The fatty acids were identified and quantified by gas chromatography and studied using fruit bodies. Fatty acid composition varied among species. The dominant fatty acid in fruit bodies of all mushrooms was cis-linoleic acid (18 : 2). Percentage of cis-linoleic acid in species varied from 22.39% to 65.29%. The other major fatty acids were, respectively, cis-oleic, palmitic, and stearic acids. Fatty acids analysis of the mushrooms showed that the unsaturated fatty acids were at higher concentrations than saturated fatty acids. PMID:23844377

Fatty Acid Compositions of Six Wild Edible Mushroom Species

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Pelin Günç Ergönül

2013-01-01

Full Text Available The fatty acids of six wild edible mushroom species (Boletus reticulatus, Flammulina velutipes var. velutipes, Lactarius salmonicolor, Pleurotus ostreatus, Polyporus squamosus, and Russula anthracina collected from different regions from Anatolia were determined. The fatty acids were identified and quantified by gas chromatography and studied using fruit bodies. Fatty acid composition varied among species. The dominant fatty acid in fruit bodies of all mushrooms was cis-linoleic acid (18 : 2. Percentage of cis-linoleic acid in species varied from 22.39% to 65.29%. The other major fatty acids were, respectively, cis-oleic, palmitic, and stearic acids. Fatty acids analysis of the mushrooms showed that the unsaturated fatty acids were at higher concentrations than saturated fatty acids.

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.

Science.gov (United States)

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

Observation of Wild Seaweed Species in Labuhanbua Waters, Indonesia: a preliminary assessment for aquaculture development

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Erlania .

2017-05-01

Full Text Available Seaweed industry has been growing up and is supplied by either wild or cultivated seaweed crops. This study was aimed to present relevant information regarding ecological availability of wild seaweed in Labuhanbua coastal waters, Sumbawa Regency, West Nusa Tenggara and potential use of important species as candidate species for aquaculture. 46 sampling stations were determined along line transects perpendicular to coastal line; and seaweeds sampling were conducted during low tide by using 1 x 1 m2 quadrat transect. Field data consist of in-situ parameter including number of seaweed species and coverage area of each species; and ex-situ parameters consist of carbohydrate, protein, total C, total N, and total P content of seaweeds. The results showed that 33 species were found and three species has the most widely distribu tion, i.e. Padina sp., Dictyota dichotoma, and Gracilaria salicornia. Turbinaria, Dictyota, Padina, Stoechospermum, Hydroclathrus, Halimeda, and Chaetomorpha might be some important species that could be develop as aquaculture species candidates among other uncultivated species that were found along this study location. They have potencies as human food, livestock feed, neutraceuicals, cosmetics, pulp, textile, biofuel and any other industries; but conversely, they were found in lower density at Labuhanbua coastal waters. These species should be develop through aquaculture technology, involve genetic improvement and possibly genetic engineering. Commercial scale cultivation of those important seaweed species will contribute to industrial needs and prevent decreasing of wild seaweed availability in natural ecosystem.

Convention on International Trade in Endangered Species of Wild Fauna and Flora.

Science.gov (United States)

Supplement to IUCN Bulletin, 1973

1973-01-01

Concern for the endangered species of wild animals and plants of the world prompted the drafting of this international convention regulating the import, export, and re-export of such species. Nations signing this document are required to impose strict controls on the international trade of these plants and animals or their recognizable parts. The…

Genetic structure and diversity of indigenous rice (Oryza sativa) varieties in the Eastern Himalayan region of Northeast India.

Science.gov (United States)

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

Chemical, Bioactive, and Antioxidant Potential of Twenty Wild Culinary Mushroom Species

OpenAIRE

Sharma, S. K.; Gautam, N.

2015-01-01

The chemical, bioactive, and antioxidant potential of twenty wild culinary mushroom species being consumed by the people of northern Himalayan regions has been evaluated for the first time in the present study. Nutrients analyzed include protein, crude fat, fibres, carbohydrates, and monosaccharides. Besides, preliminary study on the detection of toxic compounds was done on these species. Bioactive compounds evaluated are fatty acids, amino acids, tocopherol content, carotenoids (β-carotene, ...

Drought Tolerance of Wild and Cultivated Species of Safflower and Assessment of Morphological Variation

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R Shiravand

2015-04-01

Full Text Available Wild species of crop plants carry useful genes which can be used for breeding programs. This study was performed to investigate genetic variation of 46 genotypes from five Carthamus species and to evaluate their drought tolerance under field conditions (normal and deficit moisture environments during 2011at Isfahan university of technology research farm. Results indicated that safflower species had different response to drought stress. Results showed that drought stress significantly reduced seed yield in C. tinctorius and C. palaestinus. The wild species of C. palaestinus had higher seed yield, its component and oil percent compared other species in both moisture conditions. Drought tolerance indice (STI showed that C. palaestinus had the highest drought tolerance. Cluster analysis based on agro-morphological traits indicated that three species C. tinctorius, C palaestinu and C. oxyacanthus had the most similarity among studied species. Finally in respect to high hybridization of two main safflower relatives C. palaestinus (because high STI and C. oxyacanthus (because high stability under drought condition are suitable source for transferring drought tolerance genes to cultivated species.

Heritability of Wing Size and Shape of the Rice and Corn Strains of Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae).

Science.gov (United States)

Cañas-Hoyos, N; Márquez, E J; Saldamando-Benjumea, C I

2016-08-01

Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) represents a pest of economic importance in all Western Hemisphere. This polyphagous species has diverged into two populations that have been mainly recognized with various mitochondrial and nuclear molecular markers and named "the rice" and "the corn" strains. In Colombia, both strains have evolved prezygotic and postzygotic isolation. They differ in tolerance to Bacillus thuringiensis (Cry1Ac and Cry1Ab endotoxins) and the insecticides lambda-cyhalothrin and methomyl. In 2014, a wing morphometric analysis made in 159 individuals from a colony showed that both strains significantly differ in wing shape. The species also exhibits sexual dimorphism in the rice strain as in females wing size is larger than in males. Here, we continued this work with another wing morphometric approach in laboratory-reared strains to calculate wing size and shape heritabilities using a full-sib design and in wild populations to determine if this method distinguishes these strains. Our results show that male heritabilities of both traits were higher than female ones. Wild populations were significantly different in wing shape and size. These results suggest that wing morphometrics can be used as an alternative method to molecular markers to differentiate adults from laboratory-reared populations and wild populations of this pest, particularly in males of this species. Finally, Q ST values obtained for wing size and shape further demonstrated that both strains are genetically differentiated in nature.

Insights into the Musa genome: Syntenic relationships to rice and between Musa species

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Althoff Ryan

2008-01-01

Full Text Available Abstract Background Musa species (Zingiberaceae, Zingiberales including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome. Results We produced 1.4 Mb of Musa sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for Musa-Zingiber (Zingiberaceae, Zingiberales orthologs and paralogs provide strong evidence for a large-scale duplication event in the Musa lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from M. acuminata and M. balbisiana revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya. Conclusion These results point to the utility of comparative analyses between distantly-related monocot species such as rice and Musa for improving our understanding of monocot genome evolution. Sequencing the genome of M. acuminata would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated Musa polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic

Extraction techniques for arsenic species in rice flour and their speciation by HPLC-ICP-MS.

Science.gov (United States)

Narukawa, Tomohiro; Suzuki, Toshihiro; Inagaki, Kazumi; Hioki, Akiharu

2014-12-01

The extraction of arsenic (As) species present in rice flour samples was investigated using different extracting solvents, and the concentration of each species was determined by HPLC-ICP-MS after heat-assisted extraction. The extraction efficiencies for total arsenic species and especially for arsenite [As(III)] and arsenate [As(V)] were investigated. As(III), As(V) and dimethylarsinic acid (DMAA) were found in the samples, and the concentration of DMAA did not vary with treatment conditions. However, the concentrations of extracted total arsenic and those of As(III) and As(V) depended on the extracting solvents. When an extracting solvent was highly acidic, the concentrations of extracted total arsenic were in good agreement with the total arsenic concentration determined by ICP-MS after microwave-assisted digestion, though a part of the As(V) was reduced to As(III) during the highly acidic extraction process. Extraction under neutral conditions increased the extracted As(V), but extracted total arsenic was decreased because a part of the As(III) could not be extracted. Optimum conditions for the extraction of As(III) and As(V) from rice flour samples are discussed to allow the accurate determinations of As(III), As(V) and DMAA in the rice flour samples. Heat block extraction techniques using 0.05 mol L(-1) HClO4 and silver-containing 0.15 mol L(-1) HNO3 were also developed. Copyright © 2014 Elsevier B.V. All rights reserved.

The role of Bh4 in parallel evolution of hull colour in domesticated and weedy rice.

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Vigueira, C C; Li, W; Olsen, K M

2013-08-01

The two independent domestication events in the genus Oryza that led to African and Asian rice offer an extremely useful system for studying the genetic basis of parallel evolution. This system is also characterized by parallel de-domestication events, with two genetically distinct weedy rice biotypes in the US derived from the Asian domesticate. One important trait that has been altered by rice domestication and de-domestication is hull colour. The wild progenitors of the two cultivated rice species have predominantly black-coloured hulls, as does one of the two U.S. weed biotypes; both cultivated species and one of the US weedy biotypes are characterized by straw-coloured hulls. Using Black hull 4 (Bh4) as a hull colour candidate gene, we examined DNA sequence variation at this locus to study the parallel evolution of hull colour variation in the domesticated and weedy rice system. We find that independent Bh4-coding mutations have arisen in African and Asian rice that are correlated with the straw hull phenotype, suggesting that the same gene is responsible for parallel trait evolution. For the U.S. weeds, Bh4 haplotype sequences support current hypotheses on the phylogenetic relationship between the two biotypes and domesticated Asian rice; straw hull weeds are most similar to indica crops, and black hull weeds are most similar to aus crops. Tests for selection indicate that Asian crops and straw hull weeds deviate from neutrality at this gene, suggesting possible selection on Bh4 during both rice domestication and de-domestication. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Species diversity and richness of wild birds in Dagona-Waterfowl ...

African Journals Online (AJOL)

The study of bird species diversity and richness in Dagona-Waterfowl Sanctuary was carried out during the midst of both early wet and late dry seasons, to provide comprehensive data on wild birds. Dagona Sanctuary is located within the Bade-Nguru Wetland sector. It is one of the important bird areas marked for the ...

The interaction of strigolactones with abscisic acid during the drought response in rice

KAUST Repository

Haider, Imran; Andreo-Jimenez, Beatriz; Bruno, Mark; Bimbo, Andrea; Floková , Kristý na; Abuauf, Haneen Waleed Hamza; Otang Ntui, Valentine; Guo, Xiujie; Charnikhova, Tatsiana; Al-Babili, Salim; Bouwmeester, Harro J; Ruyter-Spira, Carolien

2018-01-01

Both strigolactones (SLs) and abscisic acid (ABA) biosynthetically originate from carotenoids. Considering their common origin, the interaction of these two hormones at the biosynthetic and/or regulatory level may be anticipated. Here, we show in rice that drought simultaneously induces SL production in the root, and ABA production and the expression of SL biosynthetic genes in the shoot. Under control conditions, the ABA concentration was higher in shoots of the SL biosynthetic rice mutants dwarf10 (d10) and d17 than in wild-type plants, while a similar trend was observed for SL-perception mutant d3. These differences were enhanced under drought. However, drought did not result in an increase in leaf ABA content in rice mutant line d27, carrying a mutation in the gene encoding the first committed enzyme in SL biosynthesis, to the same extent as in the other SL mutants and the wild-type. Accordingly, d10, d17 and d3 lines were more drought tolerant than wild-type plants, whereas d27 displayed decreased tolerance. Finally, over-expression of OsD27 in rice resulted in increased levels of ABA when compared with wild-type plants. We conclude that the SL and ABA pathways are connected with each other through D27, which is playing a crucial role in determining ABA and SL content in rice.

The interaction of strigolactones with abscisic acid during the drought response in rice

KAUST Repository

Haider, Imran

2018-03-09

Both strigolactones (SLs) and abscisic acid (ABA) biosynthetically originate from carotenoids. Considering their common origin, the interaction of these two hormones at the biosynthetic and/or regulatory level may be anticipated. Here, we show in rice that drought simultaneously induces SL production in the root, and ABA production and the expression of SL biosynthetic genes in the shoot. Under control conditions, the ABA concentration was higher in shoots of the SL biosynthetic rice mutants dwarf10 (d10) and d17 than in wild-type plants, while a similar trend was observed for SL-perception mutant d3. These differences were enhanced under drought. However, drought did not result in an increase in leaf ABA content in rice mutant line d27, carrying a mutation in the gene encoding the first committed enzyme in SL biosynthesis, to the same extent as in the other SL mutants and the wild-type. Accordingly, d10, d17 and d3 lines were more drought tolerant than wild-type plants, whereas d27 displayed decreased tolerance. Finally, over-expression of OsD27 in rice resulted in increased levels of ABA when compared with wild-type plants. We conclude that the SL and ABA pathways are connected with each other through D27, which is playing a crucial role in determining ABA and SL content in rice.

HYR1-mediated detoxification of reactive oxygen species is required for full virulence in the rice blast fungus.

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Kun Huang

2011-04-01

Full Text Available During plant-pathogen interactions, the plant may mount several types of defense responses to either block the pathogen completely or ameliorate the amount of disease. Such responses include release of reactive oxygen species (ROS to attack the pathogen, as well as formation of cell wall appositions (CWAs to physically block pathogen penetration. A successful pathogen will likely have its own ROS detoxification mechanisms to cope with this inhospitable environment. Here, we report one such candidate mechanism in the rice blast fungus, Magnaporthe oryzae, governed by a gene we refer to as MoHYR1. This gene (MGG_07460 encodes a glutathione peroxidase (GSHPx domain, and its homologue in yeast was reported to specifically detoxify phospholipid peroxides. To characterize this gene in M. oryzae, we generated a deletion mutantΔhyr1 which showed growth inhibition with increased amounts of hydrogen peroxide (H₂O₂. Moreover, we observed that the fungal mutants had a decreased ability to tolerate ROS generated by a susceptible plant, including ROS found associated with CWAs. Ultimately, this resulted in significantly smaller lesion sizes on both barley and rice. In order to determine how this gene interacts with other (ROS scavenging-related genes in M. oryzae, we compared expression levels of ten genes in mutant versus wild type with and without H₂O₂. Our results indicated that the HYR1 gene was important for allowing the fungus to tolerate H₂O₂ in vitro and in planta and that this ability was directly related to fungal virulence.

FON2 SPARE1 redundantly regulates floral meristem maintenance with FLORAL ORGAN NUMBER2 in rice.

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Takuya Suzaki

2009-10-01

Full Text Available CLAVATA signaling restricts stem cell identity in the shoot apical meristem (SAM in Arabidopsis thaliana. In rice (Oryza sativa, FLORAL ORGAN NUMBER2 (FON2, closely related to CLV3, is involved as a signaling molecule in a similar pathway to negatively regulate stem cell proliferation in the floral meristem (FM. Here we show that the FON2 SPARE1 (FOS1 gene encoding a CLE protein functions along with FON2 in maintenance of the FM. In addition, FOS1 appears to be involved in maintenance of the SAM in the vegetative phase, because constitutive expression of FOS1 caused termination of the vegetative SAM. Genetic analysis revealed that FOS1 does not need FON1, the putative receptor of FON2, for its action, suggesting that FOS1 and FON2 may function in meristem maintenance as signaling molecules in independent pathways. Initially, we identified FOS1 as a suppressor that originates from O. sativa indica and suppresses the fon2 mutation in O. sativa japonica. FOS1 function in japonica appears to be compromised by a functional nucleotide polymorphism (FNP at the putative processing site of the signal peptide. Sequence comparison of FOS1 in about 150 domesticated rice and wild rice species indicates that this FNP is present only in japonica, suggesting that redundant regulation by FOS1 and FON2 is commonplace in species in the Oryza genus. Distribution of the FNP also suggests that this mutation may have occurred during the divergence of japonica from its wild ancestor. Stem cell maintenance may be regulated by at least three negative pathways in rice, and each pathway may contribute differently to this regulation depending on the type of the meristem. This situation contrasts with that in Arabidopsis, where CLV signaling is the major single pathway in all meristems.

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)

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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

Marker-assisted introgression of drought tolerance from wild ancestors into popular Indian rice varieties using a 7K Infinium SNP array

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Ravindra Donde

2017-10-01

Full Text Available Recent advances in the area of genomics have led to the development of high throughput genotyping platforms that have immensely contributed to molecular breeding programs. Custom-designed single nucleotide polymorphism (SNP arrays provide an efficient, cost effective, high throughput genotyping tool for QTL/gene mapping, variety identification, marker-assisted selection, etc. In the current study, two interspecific libraries of Chromosome Segment Substitution Lines (CSSLs were evaluated under both drought and control conditions to identify lines with superior yield under drought. The CSSL libraries consisted of 48 BC4F3 lines derived from O. sativa cv. Curinga (tropical japonica x O. rufipogon, and 32 BC4F3 lines derived from O. sativa cv. Curinga (tropical japonica x O. meridionalis. The phenotypic screening of these 80 CSSLs led to the identification of three lines, MER-20, RUF-16, and RUF-44, that yielded well under drought stress. This line was backcrossed with popular rice variety of India, Swarna-Sub1 to introgress wild chromosome segments responsible for reproductive stage drought tolerance. During backcrossing, tracking of wild introgressions and monitoring of recurrent parent genome recovery was facilitated by the use of the Cornell 6K and 7K Infinium rice SNP arrays. The 6K and 7K SNP arrays assayed 5275 SNPs and 7099 SNPs, respectively, distributed across the 12 chromosomes. In our populations of (MER-20X Swarna sub1 BC2F1 lines, 1775 SNPs were polymorphic using the 6K array. The percentage of recurrent parent genome in these backcrossed lines ranged from 33-92% and the percentage of wild donor genome ranged from 8-67%. Using genotypic selection, 5% of plants were identified for further marker assisted backcrossing, based on the presence of the target donor (wild segment and maximum recovery of recurrent parent background. In the next generation, BC3F1 lines were genotyped using the 7K SNP array, which identified 2521 polymorphic SNPs

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

Recent progress on the genetics and molecular breeding of brown planthopper resistance in rice.

Science.gov (United States)

Hu, Jie; Xiao, Cong; He, Yuqing

2016-12-01

Brown planthopper (BPH) is the most devastating pest of rice. Host-plant resistance is the most desirable and economic strategy in the management of BPH. To date, 29 major BPH resistance genes have been identified from indica cultivars and wild rice species, and more than ten genes have been fine mapped to chromosome regions of less than 200 kb. Four genes (Bph14, Bph26, Bph17 and bph29) have been cloned. The increasing number of fine-mapped and cloned genes provide a solid foundation for development of functional markers for use in breeding. Several BPH resistant introgression lines (ILs), near-isogenic lines (NILs) and pyramided lines (PLs) carrying single or multiple resistance genes were developed by marker assisted backcross breeding (MABC). Here we review recent progress on the genetics and molecular breeding of BPH resistance in rice. Prospect for developing cultivars with durable, broad-spectrum BPH resistance are discussed.

Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice.

Science.gov (United States)

Bessho-Uehara, Kanako; Wang, Diane R; Furuta, Tomoyuki; Minami, Anzu; Nagai, Keisuke; Gamuyao, Rico; Asano, Kenji; Angeles-Shim, Rosalyn B; Shimizu, Yoshihiro; Ayano, Madoka; Komeda, Norio; Doi, Kazuyuki; Miura, Kotaro; Toda, Yosuke; Kinoshita, Toshinori; Okuda, Satohiro; Higashiyama, Tetsuya; Nomoto, Mika; Tada, Yasuomi; Shinohara, Hidefumi; Matsubayashi, Yoshikatsu; Greenberg, Anthony; Wu, Jianzhong; Yasui, Hideshi; Yoshimura, Atsushi; Mori, Hitoshi; McCouch, Susan R; Ashikari, Motoyuki

2016-08-09

Domestication of crops based on artificial selection has contributed numerous beneficial traits for agriculture. Wild characteristics such as red pericarp and seed shattering were lost in both Asian (Oryza sativa) and African (Oryza glaberrima) cultivated rice species as a result of human selection on common genes. Awnedness, in contrast, is a trait that has been lost in both cultivated species due to selection on different sets of genes. In a previous report, we revealed that at least three loci regulate awn development in rice; however, the molecular mechanism underlying awnlessness remains unknown. Here we isolate and characterize a previously unidentified EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family member named REGULATOR OF AWN ELONGATION 2 (RAE2) and identify one of its requisite processing enzymes, SUBTILISIN-LIKE PROTEASE 1 (SLP1). The RAE2 precursor is specifically cleaved by SLP1 in the rice spikelet, where the mature RAE2 peptide subsequently induces awn elongation. Analysis of RAE2 sequence diversity identified a highly variable GC-rich region harboring multiple independent mutations underlying protein-length variation that disrupt the function of the RAE2 protein and condition the awnless phenotype in Asian rice. Cultivated African rice, on the other hand, retained the functional RAE2 allele despite its awnless phenotype. Our findings illuminate the molecular function of RAE2 in awn development and shed light on the independent domestication histories of Asian and African cultivated rice.

Prevalence of Chlamydia psittaci and Other Chlamydia Species in Wild Birds in Poland.

Science.gov (United States)

Krawiec, Marta; Piasecki, Tomasz; Wieliczko, Alina

2015-11-01

Avian chlamydiosis is a zoonotic disease occurring in humans, poultry, and exotic birds. It has been suggested that some wild bird species play an important role as reservoirs for Chlamydia, especially Chlamydia psittaci. Whereas C. psittaci is the predominant chlamydial agent in birds, in the present study we have determined the prevalence of different species of Chlamydia among selected wild bird species in Poland using a rapid and sensitive real-time PCR method. In total, 369 free-living birds from 35 bird species and 15 orders were examined. Samples from 27 birds (7.3%) were positive for chlamydial DNA in the PCR; 22 positive samples (81.5%) belonged to C. psittaci, three to Chlamydia trachomatis (11.1%), and two (7.4%) classified only to the genus Chlamydia. Most of C. psittaci-positive samples belonged to five orders: Anseriformes, Columbiformes, Gruiformes, Phasianiformes, and Passeriformes. All C. trachomatis samples were obtained from Eurasian coots (Gruiformes). Two Chlamydia-positive samples not classified to any Chlamydia species were obtained from a common wood pigeon (Columbiformes) and a common buzzard (Accipitriformes). Detection of C. psittaci and C. trachomatis in free-living bird populations force to think on significance of birds as reservoir of varied Chlamydia species and their epidemiological importance.

Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles.

Science.gov (United States)

Labate, Joanne A; Robertson, Larry D

2012-08-07

Many highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions. Each marker was mapped with high confidence (etomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ± 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles. Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed genes within crop species such as S. lycopersicum will help

EVALUATION OF THREE WILD SPECIES OF ALMOND ON THE BASIS OF THEIR MORPHOLOGICAL CHARACTERS

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B BANINASAB

2007-07-01

Full Text Available Due to the suitable climatic conditions, Iran is one of the most important growing centre for wild and domesticated species/varieties of almond. Because of the adaptability of wild almond species to severe environmental conditions and resistance to drought, salinity and some pest and diseases, these can be used as rootstock for almond cultivars and in breeding programs for rootstock improvement in Iran. In this study, seeds of Amygdalous scoparia, A.webbii and A. orientalis were planted. The analysis of variance showed a significant difference between species. However, A. scoparia had highest stem height and leaf length. At the end of the experiment, the thickest stems were developed by A. scoparia, whereas the thinnest stems by A. orientalis. A. webbii produced more number and longer roots per seedling than the other two species. The correlation between various morphological traits showed that a few shoot characters were significantly correlated with root traits. However, leaf length, leaf width, leaf area, root number and root diameter for P. webbii, and leaf number, leaf length, leaf width, petiole length and root number characters for P.scoparia, and stem height, leaf number, leaf length, petiole length, internode length and root number for P. orientalis were found to be important morphological traits to evaluate seedling charactristics of wild almond genotypes before their nursery test.

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

Science.gov (United States)

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

A survey of wild plant species for food use in Sicily (Italy) - results of a 3-year study in four Regional Parks.

Science.gov (United States)

Licata, Mario; Tuttolomondo, Teresa; Leto, Claudio; Virga, Giuseppe; Bonsangue, Giuseppe; Cammalleri, Ignazio; Gennaro, Maria Cristina; La Bella, Salvatore

2016-02-09

This paper illustrates the results of a study carried out in four Regional Parks of Sicily (Italy), concerning traditional knowledge on food use of wild plant species. The main aims of the paper were: (i) to verify which wild plant species are used for food purpose in the local culture based on information provided by elderly inhabitants (ii) to verify the presence of wild plant species which have not been cited for food use in previous studies in the Mediterranean area (iii) to determine how many of the most frequently cited wild plant species are cultivated by the local population in the four Sicilian Parks. Semi-structured interviews were carried out in the local communities of the four Regional Parks between 2007 and 2010. A total of 802 people over the age of 60 were interviewed. Cultural Importance Index was used to evaluate the level of importance given to any wild plant species as a food in the local culture. The level of appreciation of the wild plant species and the possible effects of wild plants on human health were also investigated. Local communities currently use a total number of 119 wild species for food purposes. Asteraceae and Brassicaceae were the most represented botanical families. In each of the four Sicilian Parks, Cichorium intybus L. and Foeniculum vulgare Mill. obtained the highest Cultural Importance Index values. Sixty-four species were indicated as also having medicinal properties. Leaves and other aerial plant parts were the parts most-used for the preparation of traditional recipes. The research shows that the level of traditional knowledge on the food uses of wild plant species in the study area is poor. The food uses of plants which are most likely to survive over time are those at the interface of food and medicine. Further agronomic studies are needed for a number of species with a view to introducing them as a crop into non-intensive agricultural systems.

Why are There Indica Type and Japonica Type in Rice? — History of the Studies and a View for Origin of Two Types

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Hiroshi IKEHASHI

2009-03-01

Full Text Available On the bases of archaeological discoveries, the earliest domestication of rice has been confirmed in the middle and lower Changjiang River basin, while in the region wild rice populations are found in shallow swamps under a climate with freezing winter cold. These findings lead us re-examine the past ideas about domestication and differentiation of rice. Historically, in 1930s two sub-species, indica and japonica, were proposed on the basis of sterility in F1 hybrids between them. Soon after that, the two types were classified by the associations of a number of genetically independent traits. The characteristic associations of traits have been explained by the hybrid sterility or reproductive barriers which were assumed to comprise a set of duplicate recessive lethal genes and to be an inner genetic mechanism to lead to the varietal differentiations. In 1980s, the hybrid sterility between Indica and Japonica types was analyzed, and Indica, Japonica, and wide-compatibility type which gives fertile hybrids when cross to Indica and Japonica types, are proved to contain an allele, S5i, S5j and S5n, respectively at a locus on chromosome 6. And those gametes having S5j allele are found to be partially aborted in the hybrid genotypes of S5i/S5j while no gamete abortion occurs in S5i/S5n and S5j/S5n genotypes. Since then, the gene S5n has been used in hybrid rice breeding to obtain fertile and vigorous hybrids between subspecies, and the long-disputed problem of hybrid sterility has been solved. Also in such studies the characteristic association of traits found in each of varietal groups is better explained by founder effects. On the other hand, a large number of native cultivars of rice were surveyed with enzyme polymorphism in 1980s and later with molecular markers. As a result, profound genetic diversity is found in cultivated rice as well as in wild rice. These findings seem to lead us to the idea of multiple independent domestications of rice

Effects of drought stress on global gene expression profile in leaf and root samples of Dongxiang wild rice (Oryza rufipogon).

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Zhang, Fantao; Zhou, Yi; Zhang, Meng; Luo, Xiangdong; Xie, Jiankun

2017-06-30

Drought is a serious constraint to rice production throughout the world, and although Dongxiang wild rice ( Oryza rufipogon , DXWR) possesses a high degree of drought resistance, the underlying mechanisms of this trait remains unclear. In the present study, cDNA libraries were constructed from the leaf and root tissues of drought-stressed and untreated DXWR seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in drought-stress response. The results indicated that 11231 transcripts were differentially expressed in the leaves (4040 up-regulated and 7191 down-regulated) and 7025 transcripts were differentially expressed in the roots (3097 up-regulated and 3928 down-regulated). Among these differentially expressed genes (DEGs), the detection of many transcriptional factors and functional genes demonstrated that multiple regulatory pathways were involved in drought resistance. Meanwhile, the DEGs were also annotated with gene ontology (GO) terms and key pathways via functional classification and Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway mapping, respectively. A set of the most interesting candidate genes was then identified by combining the DEGs with previously identified drought-resistant quantitative trait loci (QTL). The present work provides abundant genomic information for functional dissection of the drought resistance of DXWR, and findings will further help the current understanding of the biological regulatory mechanisms of drought resistance in plants and facilitate the breeding of new drought-resistant rice cultivars. © 2017 The Author(s).

Culicoides Species Communities Associated with Wild Ruminant Ecosystems in Spain: Tracking the Way to Determine Potential Bridge Vectors for Arboviruses.

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Sandra Talavera

Full Text Available The genus Culicoides Latreille 1809 is a well-known vector for protozoa, filarial worms and, above all, numerous viruses. The Bluetongue virus (BTV and the recently emerged Schmallenberg virus (SBV are responsible for important infectious, non-contagious, insect-borne viral diseases found in domestic ruminants and transmitted by Culicoides spp. Both of these diseases have been detected in wild ruminants, but their role as reservoirs during the vector-free season still remains relatively unknown. In fact, we tend to ignore the possibility of wild ruminants acting as a source of disease (BTV, SBV and permitting its reintroduction to domestic ruminants during the following vector season. In this context, a knowledge of the composition of the Culicoides species communities that inhabit areas where there are wild ruminants is of major importance as the presence of a vector species is a prerequisite for disease transmission. In this study, samplings were conducted in areas inhabited by different wild ruminant species; samples were taken in both 2009 and 2010, on a monthly basis, during the peak season for midge activity (in summer and autumn. A total of 102,693 specimens of 40 different species of the genus Culicoides were trapped; these included major BTV and SBV vector species. The most abundant vector species were C. imicola and species of the Obsoletus group, which represented 15% and 11% of total numbers of specimens, respectively. At the local scale, the presence of major BTV and SBV vector species in areas with wild ruminants coincided with that of the nearest sentinel farms included in the Spanish Bluetongue Entomological Surveillance Programme, although their relative abundance varied. The data suggest that such species do not exhibit strong host specificity towards either domestic or wild ruminants and that they could consequently play a prominent role as bridge vectors for different pathogens between both types of ruminants. This finding

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

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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.

Community and species-specific responses of wild bees to insect pest control programs applied to a pollinator-dependent crop.

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Tuell, Julianna K; Isaacs, Rufus

2010-06-01

Wild bee conservation is regarded as essential for sustainable production of pollinator-dependent crops, yet little is known about the effects on wild bee communities of typical insect pest management programs used postbloom. We developed an insecticide program risk (IPR) index to quantify the relative risk to wild bees of insecticide programs applied to blueberry fields. This was used to determine the relationship between IPR and the abundance, diversity, and richness of wild bee communities sampled during three successive flowering seasons. In 2 of 3 yr, bee abundance and species richness declined with increasing IPR. Bee diversity declined with IPR in one of 3 yr. These results indicate that wild bee communities are negatively affected by increasingly intensive chemical pest management activities in crop fields and that interyear variability in bee populations has the potential to mask such effects in short-term studies. When several wild bee species were analyzed separately, two of three solitary and one of three social blueberry-foraging species declined with increasing IPR values, suggesting that different life histories and nesting habits may help some bee populations escape the negative effects of insecticides applied after bloom. Pollinator conservation programs aimed strictly at reducing insecticide use may have varying success, depending on the biology of the target bee species. The IPR index provides a standard method to compare pest management programs for their potential effect on wild bee communities, with broad application for use in other agricultural systems.

Chemical, Bioactive, and Antioxidant Potential of Twenty Wild Culinary Mushroom Species

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Sharma, S. K.; Gautam, N.

2015-01-01

The chemical, bioactive, and antioxidant potential of twenty wild culinary mushroom species being consumed by the people of northern Himalayan regions has been evaluated for the first time in the present study. Nutrients analyzed include protein, crude fat, fibres, carbohydrates, and monosaccharides. Besides, preliminary study on the detection of toxic compounds was done on these species. Bioactive compounds evaluated are fatty acids, amino acids, tocopherol content, carotenoids (β-carotene, lycopene), flavonoids, ascorbic acid, and anthocyanidins. Fruitbodies extract of all the species was tested for different types of antioxidant assays. Although differences were observed in the net values of individual species all the species were found to be rich in protein, and carbohydrates and low in fat. Glucose was found to be the major monosaccharide. Predominance of UFA (65–70%) over SFA (30–35%) was observed in all the species with considerable amounts of other bioactive compounds. All the species showed higher effectiveness for antioxidant capacities. PMID:26199938

Chemical, Bioactive, and Antioxidant Potential of Twenty Wild Culinary Mushroom Species

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S. K. Sharma

2015-01-01

Full Text Available The chemical, bioactive, and antioxidant potential of twenty wild culinary mushroom species being consumed by the people of northern Himalayan regions has been evaluated for the first time in the present study. Nutrients analyzed include protein, crude fat, fibres, carbohydrates, and monosaccharides. Besides, preliminary study on the detection of toxic compounds was done on these species. Bioactive compounds evaluated are fatty acids, amino acids, tocopherol content, carotenoids (β-carotene, lycopene, flavonoids, ascorbic acid, and anthocyanidins. Fruitbodies extract of all the species was tested for different types of antioxidant assays. Although differences were observed in the net values of individual species all the species were found to be rich in protein, and carbohydrates and low in fat. Glucose was found to be the major monosaccharide. Predominance of UFA (65–70% over SFA (30–35% was observed in all the species with considerable amounts of other bioactive compounds. All the species showed higher effectiveness for antioxidant capacities.

Chemical, Bioactive, and Antioxidant Potential of Twenty Wild Culinary Mushroom Species.

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Sharma, S K; Gautam, N

2015-01-01

The chemical, bioactive, and antioxidant potential of twenty wild culinary mushroom species being consumed by the people of northern Himalayan regions has been evaluated for the first time in the present study. Nutrients analyzed include protein, crude fat, fibres, carbohydrates, and monosaccharides. Besides, preliminary study on the detection of toxic compounds was done on these species. Bioactive compounds evaluated are fatty acids, amino acids, tocopherol content, carotenoids (β-carotene, lycopene), flavonoids, ascorbic acid, and anthocyanidins. Fruitbodies extract of all the species was tested for different types of antioxidant assays. Although differences were observed in the net values of individual species all the species were found to be rich in protein, and carbohydrates and low in fat. Glucose was found to be the major monosaccharide. Predominance of UFA (65-70%) over SFA (30-35%) was observed in all the species with considerable amounts of other bioactive compounds. All the species showed higher effectiveness for antioxidant capacities.

Detection and molecular characterization of feline hemoplasmas in wild felid species in Iran in the Middle East.

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Ghazisaeedi, Fereshteh; Atyabi, Nahid; Zahraei Salehi, Taghi; Tabatabaei, Saeid; Ashrafi Tamai, Iraj; Memarian, Iman; Tasker, Séverine

2017-10-01

Three feline hemoplasma species exist in felids: Mycoplasma haemofelis, 'Candidatus Mycoplasma haemominutum', and 'Candidatus Mycoplasma turicensis'. The aims of the study were to determine the presence of, and molecularly characterize, any hemoplasmas in wild felids, including the endangered Persian leopard in Iran, the Middle East. Blood samples were collected from 19 wild felids, including three Persian leopards. Using species-specific hemoplasma PCRs and ELISA serological testing for feline leukaemia virus and feline immunodeficiency virus (FIV), two Persian leopards were found to be infected with 'Ca. M. haemominutum' and were seropositive for FIV. Partial 16S rRNA gene sequences were generated for these 'Ca. M. haemominutum' species and subsequent phylogenetic analysis revealed 97.70% to 99.45% sequence identity with those found in domestic cats from Iran and other countries. This study confirms the presence of 'Ca. M. haemominutum' and concurrent FIV antibody in wild felids in Iran. This represents the first report of hemoplasma in wild felids in the Middle East as well as the first report of infection in Persian leopards. Copyright © 2017 Elsevier Ltd. All rights reserved.

Simultaneous determination of arsenic and mercury species in rice by ion-pairing reversed phase chromatography with inductively coupled plasma mass spectrometry.

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Fang, Yong; Pan, Yushi; Li, Peng; Xue, Mei; Pei, Fei; Yang, Wenjian; Ma, Ning; Hu, Qiuhui

2016-12-15

An analytical method using reversed phase chromatography-inductively coupled plasma mass spectrometry for arsenic and mercury speciation analysis was described. The effect of ion-pairing reagent on simultaneous separation of four arsenic (arsenite, arsenate, monomethlyarsonate and dimethylarsinate) and three mercury species (inorganic mercury (Hg(II)), methylmecury and ethylmercury) was investigated. Parameters including concentrations and pH of the mobile phase were optimized. The separation and re-equilibration time was attained within 20min. Meanwhile, a sequential extraction method for arsenic and mercury in rice was tested. Subsequently, 1% HNO3 microwave-assisted extraction was chosen. Calibration curves based on peak area measurements were linear with correlation coefficient greater than 0.9958 for each species in the range studied. The detection limits of the species were in the range of 0.84-2.41μg/L for arsenic and 0.01-0.04μg/L for mercury, respectively. The proposed method was then successfully applied for the simultaneous determination of arsenic and mercury species in rice flour standard material and two kinds of rice from local markets. Copyright © 2016 Elsevier Ltd. All rights reserved.

Differential iridoid production as revealed by a diversity panel of 84 cultivated and wild blueberry species.

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Courtney P Leisner

Full Text Available Cultivated blueberry (Vaccinium corymbosum, Vaccinium angustifolium, Vaccinium darrowii, and Vaccinium virgatum is an economically important fruit crop native to North America and a member of the Ericaceae family. Several species in the Ericaceae family including cranberry, lignonberry, bilberry, and neotropical blueberry species have been shown to produce iridoids, a class of pharmacologically important compounds present in over 15 plant families demonstrated to have a wide range of biological activities in humans including anti-cancer, anti-bacterial, and anti-inflammatory. While the antioxidant capacity of cultivated blueberry has been well studied, surveys of iridoid production in blueberry have been restricted to fruit of a very limited number of accessions of V. corymbosum, V. angustifolium and V. virgatum; none of these analyses have detected iridoids. To provide a broader survey of iridoid biosynthesis in cultivated blueberry, we constructed a panel of 84 accessions representing a wide range of cultivated market classes, as well as wild blueberry species, and surveyed these for the presence of iridoids. We identified the iridoid glycoside monotropein in fruits and leaves of all 13 wild Vaccinium species, yet only five of the 71 cultivars. Monotropein positive cultivars all had recent introgressions from wild species, suggesting that iridoid production can be targeted through breeding efforts that incorporate wild germplasm. A series of diverse developmental tissues was also surveyed in the diversity panel, demonstrating a wide range in iridoid content across tissues. Taken together, this data provides the foundation to dissect the molecular and genetic basis of iridoid production in blueberry.

Differential iridoid production as revealed by a diversity panel of 84 cultivated and wild blueberry species.

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Leisner, Courtney P; Kamileen, Mohamed O; Conway, Megan E; O'Connor, Sarah E; Buell, C Robin

2017-01-01

Cultivated blueberry (Vaccinium corymbosum, Vaccinium angustifolium, Vaccinium darrowii, and Vaccinium virgatum) is an economically important fruit crop native to North America and a member of the Ericaceae family. Several species in the Ericaceae family including cranberry, lignonberry, bilberry, and neotropical blueberry species have been shown to produce iridoids, a class of pharmacologically important compounds present in over 15 plant families demonstrated to have a wide range of biological activities in humans including anti-cancer, anti-bacterial, and anti-inflammatory. While the antioxidant capacity of cultivated blueberry has been well studied, surveys of iridoid production in blueberry have been restricted to fruit of a very limited number of accessions of V. corymbosum, V. angustifolium and V. virgatum; none of these analyses have detected iridoids. To provide a broader survey of iridoid biosynthesis in cultivated blueberry, we constructed a panel of 84 accessions representing a wide range of cultivated market classes, as well as wild blueberry species, and surveyed these for the presence of iridoids. We identified the iridoid glycoside monotropein in fruits and leaves of all 13 wild Vaccinium species, yet only five of the 71 cultivars. Monotropein positive cultivars all had recent introgressions from wild species, suggesting that iridoid production can be targeted through breeding efforts that incorporate wild germplasm. A series of diverse developmental tissues was also surveyed in the diversity panel, demonstrating a wide range in iridoid content across tissues. Taken together, this data provides the foundation to dissect the molecular and genetic basis of iridoid production in blueberry.

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

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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 ...

Identifications of Captive and Wild Tilapia Species Existing in Hawaii by Mitochondrial DNA Control Region Sequence

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Wu, Liang; Yang, Jinzeng

2012-01-01

Background The tilapia family of the Cichlidae includes many fish species, which live in freshwater and saltwater environments. Several species, such as O. niloticus, O. aureus, and O. mossambicus, are excellent for aquaculture because these fish are easily reproduced and readily adapt to diverse environments. Historically, tilapia species, including O. mossambicus, S. melanotheron, and O. aureus, were introduced to Hawaii many decades ago, and the state of Hawaii uses the import permit policy to prevent O. niloticus from coming into the islands. However, hybrids produced from O. niloticus may already be present in the freshwater and marine environments of the islands. The purpose of this study was to identify tilapia species that exist in Hawaii using mitochondrial DNA analysis. Methodology/Principal Findings In this study, we analyzed 382 samples collected from 13 farm (captive) and wild tilapia populations in Oahu and the Hawaii Islands. Comparison of intraspecies variation between the mitochondrial DNA control region (mtDNA CR) and cytochrome c oxidase I (COI) gene from five populations indicated that mtDNA CR had higher nucleotide diversity than COI. A phylogenetic tree of all sampled tilapia was generated using mtDNA CR sequences. The neighbor-joining tree analysis identified seven distinctive tilapia species: O. aureus, O. mossambicus, O. niloticus, S. melanotheron, O. urolepies, T. redalli, and a hybrid of O. massambicus and O. niloticus. Of all the populations examined, 10 populations consisting of O. aureus, O. mossambicus, O. urolepis, and O. niloticus from the farmed sites were relatively pure, whereas three wild populations showed some degree of introgression and hybridization. Conclusions/Significance This DNA-based tilapia species identification is the first report that confirmed tilapia species identities in the wild and captive populations in Hawaii. The DNA sequence comparisons of mtDNA CR appear to be a valid method for tilapia species

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

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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. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Engineered Dwarf Male-Sterile Rice: A Promising Genetic Tool for Facilitating Recurrent Selection in Rice.

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Ansari, Afsana; Wang, Chunlian; Wang, Jian; Wang, Fujun; Liu, Piqing; Gao, Ying; Tang, Yongchao; Zhao, Kaijun

2017-01-01

Rice is a crop feeding half of the world's population. With the continuous raise of yield potential via genetic improvement, rice breeding has entered an era where multiple genes conferring complex traits must be efficiently manipulated to increase rice yield further. Recurrent selection is a sound strategy for manipulating multiple genes and it has been successfully performed in allogamous crops. However, the difficulties in emasculation and hand pollination had obstructed efficient use of recurrent selection in autogamous rice. Here, we report development of the dwarf male-sterile rice that can facilitate recurrent selection in rice breeding. We adopted RNAi technology to synergistically regulate rice plant height and male fertility to create the dwarf male-sterile rice. The RNAi construct pTCK-EGGE, targeting the OsGA20ox2 and OsEAT1 genes, was constructed and used to transform rice via Agrobacterium -mediated transformation. The transgenic T0 plants showing largely reduced plant height and complete male-sterile phenotypes were designated as the dwarf male-sterile plants. Progenies of the dwarf male-sterile plants were obtained by pollinating them with pollens from the wild-type. In the T1 and T2 populations, half of the plants were still dwarf male-sterile; the other half displayed normal plant height and male fertility which were designated as tall and male-fertile plants. The tall and male-fertile plants are transgene-free and can be self-pollinated to generate new varieties. Since emasculation and hand pollination for dwarf male-sterile rice plants is no longer needed, the dwarf male-sterile rice can be used to perform recurrent selection in rice. A dwarf male-sterile rice-based recurrent selection model has been proposed.

Impact of Day Intervals on Sequential Infestations of the Rice Leaffolder (Guenée (Lepidoptera: Pyralidae and the White-Backed Rice Planthopper (Horváth on Rice Grain Damage

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Li-Ben Jiang

2014-01-01

Full Text Available The present study illustrates that different day intervals (DIs between the sequential infestations of two pest species, the rice leaffolder (RLF Cnaphalocrocis medinalis Guenée (Lepidoptera: Pyralidae and the white-backed rice planthopper (WBPH Sogatella furcifera Horváth (Hemiptera: Delphacidae, have a significant impact on the rice yield loss rate (YLR and on the carbohydrate contents of rice plants. For WBPH release after RLF release (WRARR, the YLR decreased with the increasing DIs, and the YLR at the 24 DI was significantly lower compared to that at the 6 and 12 DIs and had a minimum value for a simultaneous infestation of the two pest species (SITS. In contrast, for RLF release after WBPH release (RRAWR, the YLR at the 24 DI had a maximum value and was significantly higher compared to that at the 6 and 12 DIs and the SITS. These findings indicate that damaged rice plants gradually recover, with an increase in the DI for WRARR. The above results were demonstrated by biochemical tests. Therefore, the sequential infestation of the two pest species and their DIs should be considered for integrated pest management (IPM and control strategies for rice pests.

The puzzle of Italian rice origin and evolution: determining genetic divergence and affinity of rice germplasm from Italy and Asia.

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Xingxing Cai

Full Text Available 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 (H(e = 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.

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

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Ethel Sánchez

2006-06-01

Full Text Available 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. Rev. Biol. Trop. 54(2: 377-385. Epub 2006 Jun 01.El arroz silvestre Oryza grandiglumis es endémico de América. Se localiza en la zona norte de Costa Rica, principalmente en el humedal de Caño Negro y del Río Medio Queso. Es una planta vigorosa y grande. Su nombre deriva del gran tamaño de las lemas estériles (glumas. Presentamos una descripción ultraestructural de la lámina foliar, lígula, aurículas, espiguilla y cariópside, con énfasis en las estructuras de valor taxonómico, usando el microscopio electrónico de barrido. La lámina foliar se caracteriza por presentar un patrón de cera cuticular en forma de densos bastoncillos. Presenta estomas rodeados de papilas, células de sílice en forma crenada

Modelling seasonal habitat suitability for wide-ranging species: Invasive wild pigs in northern Australia.

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Jens G Froese

Full Text Available Invasive wildlife often causes serious damage to the economy and agriculture as well as environmental, human and animal health. Habitat models can fill knowledge gaps about species distributions and assist planning to mitigate impacts. Yet, model accuracy and utility may be compromised by small study areas and limited integration of species ecology or temporal variability. Here we modelled seasonal habitat suitability for wild pigs, a widespread and harmful invader, in northern Australia. We developed a resource-based, spatially-explicit and regional-scale approach using Bayesian networks and spatial pattern suitability analysis. We integrated important ecological factors such as variability in environmental conditions, breeding requirements and home range movements. The habitat model was parameterized during a structured, iterative expert elicitation process and applied to a wet season and a dry season scenario. Model performance and uncertainty was evaluated against independent distributional data sets. Validation results showed that an expert-averaged model accurately predicted empirical wild pig presences in northern Australia for both seasonal scenarios. Model uncertainty was largely associated with different expert assumptions about wild pigs' resource-seeking home range movements. Habitat suitability varied considerably between seasons, retracting to resource-abundant rainforest, wetland and agricultural refuge areas during the dry season and expanding widely into surrounding grassland floodplains, savanna woodlands and coastal shrubs during the wet season. Overall, our model suggested that suitable wild pig habitat is less widely available in northern Australia than previously thought. Mapped results may be used to quantify impacts, assess risks, justify management investments and target control activities. Our methods are applicable to other wide-ranging species, especially in data-poor situations.

Wild Nicotiana Species as a Source of Cytoplasmic Male Sterility in Nicotianatabacum

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Nikova V

2014-12-01

Full Text Available The results of our experiments executed to obtain tobacco male sterile lines through interspecific hybridization are summarized. Ten wild species from the genus Nicotiana: N. excelsior (exc, N. amplexicaulis (amp, N. rustica (rus, Nicotianaglauca (gla, N. velutina (vel, N. benthamiana (ben, N. maritima (mar, N. paniculata (pan, N. longiflora (lon and N. africana (afr were used as cytoplasmic donors and N. tabacum, cv. HarmanliiskaBasma (HB as a donor of the nucleus. Genetic effects of cytoplasmic-nuclear interaction of the studied species are discussed. Our results suggested that cytoplasmic male sterility (CMS was expressed when the cytoplasms of the above mentioned wild Nicotiana species were combined with the nucleus of N. tabacum. The 10 sources of CMS obtained in tobacco were characterized by altered flower phenotypes. Flowers are classified into types according the stamen, pistil and corolla modification. All these CMS sources were backcrossed to Oriental tobaccos, cvs. Tekne, Nevrokop B-12, Kroumovgrad 90 and Djebel 576, to develop corresponding CMS lines. The investigated cytoplasms produced compete male sterility in all those cultivars. The CMS lines preserved flower types, specific for every “sterile” cytoplasm. The extent of male organ modifications varied from apparently normal (but pollenless stamens in CMS (pan, (afr, some plants of (vel (mar through different degrees of malformations (shriveled anther on shortened filaments (lon, pinnate-like anthers on filaments of normal length (amp, petal - (ben, pistil- or stigma-like structures (rus, (gla to lack of male reproductive organs in (exc and in some plants of (vel, (mar, (rus and (gla. Most of the above mentioned cytoplasms had normal female gametophyte and good seed productivity. Alterations of the pistils were observed in CMS (rus, (exc and (ben causing reduction of the seed set. Electrophoresis of seed proteins of the tobacco cultivars and their CMS lines also suggested that

High altitude species, high profits: can the trade in wild harvested Fritillaria cirrhosa (Liliaceae) be sustained?

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Cunningham, A B; Brinckmann, J A; Pei, S-J; Luo, P; Schippmann, U; Long, X; Bi, Y-F

2018-05-08

Fritillaria cirrhosa D. Don bulbs contain alkaloids and are one of the most intensively exploited alpine Himalayan medicinal species. In terms of proprietary medicines, our study shows that 210 F. cirrhosa products are offered by 46 suppliers, most of which (44) are situated in China and two in Nepal. A widepread commercial use is as one of the main ingredients in cough syrups. A well known example is "Nin Jiom Pei Pa Koa Herbal Cough & Throat Syrup", which typically contains more F. cirrhosa than any other herbal ingredient in the formulation. The biggest market for F. cirrhosa bulbs is China, where demand exceeds supply of this wild harvested species for use in traditional Chinese medicine (TCM). Cross-border trade from Nepal to China occurs in significant quantities. Bhutan also imports F. cirrhosa bulbs from Nepal. In addition, F. cirrhosa is registered as an active ingredient in traditional herbal medicinal preparations in Australia, Canada, Hong Kong SAR, Malaysia, Republic of Korea, Singapore and Taiwan. There is also an export trade in F. cirrhosa to Europe. Assessing how much F. cirrhosa is traded is complex, however, due to a "look-alike" challenge, as nine Chinese Fritillaria species are traded in Europe (Fritillaria cirrhosa, F. delavayi, F. hupehensis, F. pallidiflora, F. przewalskii, F. thunbergii, F. unibracteata, F. ussuriensis and F. walujewii). The aims of this review were to assess the scale of the global trade in F. cirrhosa, and to synthesise studies of the impacts of wild harvest on F. cirrhosa populations and on the extent of emerging cultivation initiatives as an alternative to wild harvest. Firstly, we reviewed published information on studies on impacts of wild F. cirrhosa harvest from across the geographic range of this species. Secondly, global trade data for F. cirrhosa were analysed. The principal demand for F. cirrhosa bulbs is in China, where hundreds of different companies produce Fritillaria preparations. Trade data also show that

Investigation of wild species potential to increase genetic diversity useful for apple breeding

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Dan Catalina

2015-01-01

Full Text Available The potential of testing new apple cultivars and the possibility to induce valuable traits is directly dependent on the availability of sufficient genetic diversity, while apple breeding has narrowed the genetic ground of commercial cultivars. Wild species were studied in regard to their influence upon progenies and their capacity to enlarge apple genetic diversity. The interspecific seedlings were framed in five biparental mating (paired crosses, in which Malus species were crossed with different cultivars, obtaining half-sib families. The number of F1 progenies per combination varied from 31 (Cluj 218/2 × M. floribunda up to 142 (Reinette Baumann × M. floribunda, with a total of 1650 hybrids F1. The influences upon vigour and juvenile period and possible correlation among fruit size and taste were analyzed. Juvenile period varied from 6.00 (M. zumi × Jonathan to 9.31 years (Cluj 218/2 × M. floribunda. Data based on correlation coefficient illustrated that the fructification year was not influenced by the vigour of trees. The highest value of correlation for fruit’s size and taste was obtained among M. coronaria hybrids. This result might suggest that once the fruit are larger, there is a high chance the taste is also more appreciative and fruit quality for mouth feels increase. Depending on the parental formula, additive effects may be inferior compared to genetic effects of dominance and epistasis. Although M. zumi and M. floribunda achieved the same genetic gain (0.31, M. zumi had a higher expected selection response for fruit size. The difficulty of obtaining seedlings with tasty and large fruit when wild Malus species are used as genitors is resulting from the values of expected selection response data, but in the same time results confirm that wild Malus species are suitable resources for genetic variability, both for dessert and ornamental apple cultivars.

Identification of molecular species of acylglycerols of Philippine wild edible mushroom, Ganoderma lucidum

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Wild edible mushrooms are widely consumed in many countries. We successfully cultivated four edible, medicinal Philippine mushrooms in liquid culture. Recently, we identified the molecular species of acylglycerols in the lipid extract of mushroom G. lucidum NRRL66208. One hundred and three molecular...

Ethanol production from rice on radioactively contaminated field toward sustainable rice farming

International Nuclear Information System (INIS)

Yokoyama, Shinya; Izumi, Bintaro; Oki, Kazuo

2011-01-01

Radioactive species such as 137 Cs were discharged from Fukushima Daiichi Nuclear Power Plant which was severely damaged by the enormous earthquake and tsunami. Cropland has been radioactively contaminated by 137 Cs etc. and it seems impossible to plant rice due to the non-suitability for food. According to the reports, 137 Cs transferred into the rice from soil is less than 1% on the average. Therefore, it is expected that the concentration of 137 Cs in bioethanol will be well below the tentative restriction value even if bioethanol could be produced from the rice. It is proposed that the rice field should be filled with water to avoid the flow of runoff contaminated by radioactive cesium compounds because they are insoluble in aqueous phase and that bioethanol should be produced from the rice in order to maintain the multifunction of rice field and to continue the agriculture. If rice farming is halted and neglected, agricultural function of rice field as well as local community will be permanently destroyed. (author)

RPAN: rice pan-genome browser for ∼3000 rice genomes.

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Sun, Chen; Hu, Zhiqiang; Zheng, Tianqing; Lu, Kuangchen; Zhao, Yue; Wang, Wensheng; Shi, Jianxin; Wang, Chunchao; Lu, Jinyuan; Zhang, Dabing; Li, Zhikang; Wei, Chaochun

2017-01-25

A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Methylobacterium Species Promoting Rice and Barley Growth and Interaction Specificity Revealed with Whole-Cell Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF/MS Analysis.

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Akio Tani

Full Text Available Methylobacterium species frequently inhabit plant surfaces and are able to utilize the methanol emitted from plants as carbon and energy sources. As some of the Methylobacterium species are known to promote plant growth, significant attention has been paid to the mechanism of growth promotion and the specificity of plant-microbe interactions. By screening our Methylobacterium isolate collection for the high growth promotion effect in vitro, we selected some candidates for field and pot growth tests for rice and barley, respectively. We found that inoculation resulted in better ripening of rice seeds, and increased the size of barley grains but not the total yield. In addition, using whole-cell matrix-assister laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS analysis, we identified and classified Methylobacterium isolates from Methylobacterium-inoculated rice plants. The inoculated species could not be recovered from the rice plants, and in some cases, the Methylobacterium community structure was affected by the inoculation, but not with predomination of the inoculated species. The isolates from non-inoculated barley of various cultivars grown in the same field fell into just two species. These results suggest that there is a strong selection pressure at the species level of Methylobacterium residing on a given plant species, and that selection of appropriate species that can persist on the plant is important to achieve growth promotion.

The mitochondrial gene orfH79 plays a critical role in impairing both male gametophyte development and root growth in CMS-Honglian rice.

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Peng, Xiaojue; Wang, Kun; Hu, Chaofeng; Zhu, Youlin; Wang, Ting; Yang, Jing; Tong, Jiping; Li, Shaoqing; Zhu, Yingguo

2010-06-24

Cytoplasmic male sterility (CMS) has often been associated with abnormal mitochondrial open reading frames. The mitochondrial gene orfH79 is a candidate gene for causing the CMS trait in CMS-Honglian (CMS-HL) rice. However, whether the orfH79 expression can actually induce CMS in rice remains unclear. Western blot analysis revealed that the ORFH79 protein is mainly present in mitochondria of CMS-HL rice and is absent in the fertile line. To investigate the function of ORFH79 protein in mitochondria, this gene was fused to a mitochondrial transit peptide sequence and used to transform wild type rice, where its expression induced the gametophytic male sterile phenotype. In addition, excessive accumulation of reactive oxygen species (ROS) in the microspore, a reduced ATP/ADP ratio, decreased mitochondrial membrane potential and a lower respiration rate in the transgenic plants were found to be similar to those in CMS-HL rice. Moreover, retarded growth of primary and lateral roots accompanied by abnormal accumulation of ROS in the root tip was observed in both transgenic rice and CMS-HL rice (YTA). These results suggest that the expression of orfH79 in mitochondria impairs mitochondrial function, which affects the development of both male gametophytes and the roots of CMS-HL rice.

A selfish genetic element confers non-Mendelian inheritance in rice.

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Yu, Xiaowen; Zhao, Zhigang; Zheng, Xiaoming; Zhou, Jiawu; Kong, Weiyi; Wang, Peiran; Bai, Wenting; Zheng, Hai; Zhang, Huan; Li, Jing; Liu, Jiafan; Wang, Qiming; Zhang, Long; Liu, Kai; Yu, Yang; Guo, Xiuping; Wang, Jiulin; Lin, Qibing; Wu, Fuqing; Ren, Yulong; Zhu, Shanshan; Zhang, Xin; Cheng, Zhijun; Lei, Cailin; Liu, Shijia; Liu, Xi; Tian, Yunlu; Jiang, Ling; Ge, Song; Wu, Chuanyin; Tao, Dayun; Wang, Haiyang; Wan, Jianmin

2018-06-08

Selfish genetic elements are pervasive in eukaryote genomes, but their role remains controversial. We show that qHMS7 , a major quantitative genetic locus for hybrid male sterility between wild rice ( Oryza meridionalis ) and Asian cultivated rice ( O. sativa ), contains two tightly linked genes [ Open Reading Frame 2 ( ORF2 ) and ORF3 ]. ORF2 encodes a toxic genetic element that aborts pollen in a sporophytic manner, whereas ORF3 encodes an antidote that protects pollen in a gametophytic manner. Pollens lacking ORF3 are selectively eliminated, leading to segregation distortion in the progeny. Analysis of the genetic sequence suggests that ORF3 arose first, followed by gradual functionalization of ORF2 Furthermore, this toxin-antidote system may have promoted the differentiation and/or maintained the genome stability of wild and cultivated rice. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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

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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.

Viral Encephalopathy and Retinopathy in groupers (Epinephelus spp. in southern Italy: a threat for wild endangered species?

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Vendramin Niccolò

2013-01-01

Full Text Available Abstract Background Betanodaviruses are the causative agents of Viral Encephalopathy and Retinopathy (VER. To date, more than 50 species have proved to be susceptible and among them, those found in genus Epinephelus are highly represented. Clinical disease outbreaks are generally characterized by typical nervous signs and significant mortalities mainly associated with aquaculture activities, although some concerns for the impact of this infection in wild fish have been raised. In this study, the authors present the first documented report describing an outbreak of VER in wild species in the Mediterranean basin. Case presentation In late summer - early winter 2011 (September-December, significant mortalities affecting wild Dusky grouper (Epinephelus marginatus, Golden grouper (Epinephelus costae and European sea bass (Dicentrarchus labrax were reported in the municipality of Santa Maria di Leuca (Northern Ionian Sea, Italy. The affected fish showed an abnormal swimming behavior and swollen abdomens. During this epizootic, five moribund fish showing clear neurological signs were captured and underwent laboratory investigations. Analytical results confirmed the diagnosis of VER in all the specimens. Genetic characterization classified all betanodavirus isolates as belonging to the RGNNV genotype, revealing a close genetic relationship with viral sequences obtained from diseased farmed fish reared in the same area in previous years. Conclusion The close relationship of the viral sequences between the isolates collected in wild affected fish and those isolated during clinical disease outbreaks in farmed fish in the same area in previous years suggests a persistent circulation of betanodaviruses and transmission between wild and farmed stocks. Further investigations are necessary to assess the risk of viral transmission between wild and farmed fish populations, particularly in marine protected areas where endangered species are present.

Some effects of aldrin-treated rice on Gulf Coast wildlife

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Flickinger, Edward L.; King, K.A.

1972-01-01

Wildlife casualties from aldrin-dieldrin poisoning are associated with the planting of aldrin-treated rice seed along the Texas Gulf Coast. The fulvous tree duck (Dendrocygna bicolor), which depends on the rice field habitats and is highly susceptible to aldrin-dieldrin poisoning, is suffering a serious population decline in that area. Dead waterfowl, shorebirds, and passerines were collected on study areas in Wharton, Brazoria, and Chambers counties, Texas, from 1967 through 1971. Residues of aldrin or dieldrin were found in all samples of bird casualties and in all eggs, scavengers, predators, fish, frogs, invertebrates, and soils. Fulvous tree ducks appeared to be less resistant to aldrin than other ducks. Dieldrin residues in brains of dead fulvous tree ducks were low, but whole-body residues were as high as 16 ppm. Brains of other dead ducks and geese averaged 10 ppm dieldrin. Some dead birds were exposed by eating treated rice seed, but many dead birds with high dieldrin residues were species that feed largely on invertebrates. Although soil residues were low, snails and crayfish contained enough aldrin and dieldrin (average 9.5 ppm) to account for deaths in birds that fed heavily on these invertebrates over a period of time. When fulvous tree ducks were penned for 3 days in fields aerially planted with treated seed, 3 of 10 birds died with brain residues of 2.5, 2.9, and 6.8 ppm dieldrin, and others were intoxicated. None of eight died, and some gained weight, when penned in fields planted with untreated seed. This study adds further evidence for the suspected lethal effects of aldrin-treated rice seed on wild birds and other wildlife in rice field habitats.

Molecular characterization of Babesia and Cytauxzoon species in wild South-African meerkats.

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Leclaire, Sarah; Menard, Sandie; Berry, Antoine

2015-04-01

Piroplasms, including Babesia, Cytauxzoon and Theileria species, frequently infect domestic and wild mammals. At present, there is no information on the occurrence and molecular identity of these tick-borne blood parasites in the meerkat, one of South Africa's most endearing wildlife celebrities. Meerkats live in territorial groups, which may occur on ranchland in close proximity to humans, pets and livestock. Blood collected from 46 healthy meerkats living in the South-African Kalahari desert was screened by microscopy and molecular methods, using PCR and DNA sequencing of 18S rRNA and ITS1 genes. We found that meerkats were infected by 2 species: one species related to Babesia sp. and one species related to Cytauxzoon sp. Ninety one percent of the meerkats were infected by the Cytauxzoon and/or the Babesia species. Co-infection occurred in 46% of meerkats. The pathogenicity and vectors of these two piroplasm species remains to be determined.

Differentiation of Meat Samples from Domestic Horses ( Equus caballus and Asiatic Wild Asses ( Equus hemionus Using a Species-Speci fi c Restriction Site in the Mitochondrial Cytochrome b Region

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Ralph Kuehn

2006-12-01

Full Text Available Recent studies suggest that Asiatic wild asses ( Equus hemionus are being increasingly poached in a commercial fashion. Part of the meat is believed to reach the meat markets in the capital Ulaanbaatar. To test this hypothesis, we collected 500 meat samples between February and May 2006. To differentiate between domestic horse ( Equus caballus and wild ass meat, we developed a restriction fragment length polymorphism (RFLP assay based on the polymerase chain reaction (PCR. We ampli fi ed and sequenced a cytochrome b fragment (335 bp and carried out a multialignment of the generated sequences for the domestic horse, the Asiatic wild ass, the domestic donkey ( Equus asinus and the Przewalski’s horse ( Equus ferus przewalskii . We detected a species-speci fi c restriction site (AatII for the Asiatic wild ass, resulting in a speci fi c restriction fragment length polymorphism (RFLP band pattern. This RFLP assay represents a rapid and cost-effective method to detect wild ass meat. All of the 500 meat samples we collected and analysed within this pilot project proved to be domestic horsemeat as declared by the sales people. Thus, either the assumption that wild ass meat is sold as “cheap horse meat” is wrong, or we picked the wrong markets, products or season.

Transcriptome Sequencing of Diverse Peanut (Arachis Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability

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Ratan Chopra

2016-12-01

Full Text Available To test the hypothesis that the cultivated peanut species possesses almost no molecular variability, we sequenced a diverse panel of 22 Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species. RNASeq was performed on pools of three tissues, and de novo assembly was performed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 biallelic SNPs. Among 10 naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs. In eight diploid accessions, 291,115 unique SNPs were identified in 26,320 contigs. The average SNP rate among the 10 cultivated tetraploids was 0.5, and among eight diploids was 9.2 per 1000 bp. Diversity analysis indicated grouping of diploids according to genome classification, and cultivated tetraploids by subspecies. Cluster analysis of variants indicated that sequences of B genome species were the most similar to the tetraploids, and the next closest diploid accession belonged to the A genome species. A subset of 66 SNPs selected from the dataset was validated; of 782 SNP calls, 636 (81.32% were confirmed using an allele-specific discrimination assay. We conclude that substantial genetic variability exists among wild species. Additionally, significant but lesser variability at the molecular level occurs among accessions of the cultivated species. This survey is the first to report significant SNP level diversity among transcripts, and may explain some of the phenotypic differences observed in germplasm surveys. Understanding SNP variants in the Arachis accessions will benefit in developing markers for selection.

Diversity and population dynamics of pests and predators in irrigated rice fields with treated and untreated pesticide.

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Rattanapun, W

2012-01-01

The monitoring of rice pests and their predators in pesticide untreated and treated rice fields was conducted at the southern of Thailand. Twenty-two species in 15 families and 6 orders of rice pests were sampled from untreated rice field. For treated rice field, 22 species in 14 families and 5 orders of rice pest were collected. Regardless of treatment type, dominant species and individual number of rice pest varied to physiological stage of rice. Lepidopteran pests had highest infestation during the vegetative stage of rice growth, while hemipteran pests composed of hopper species (Hemipetra: Auchenorrhyncha) and heteropteran species (Hemiptera: Heteroptera) were dominant groups during the reproductive stage and grain formation and ripening stage of rice growth. In contrast, dominant species of predator did not change throughout rice growing season. There were 35 species in 25 families and seven orders and 40 species in 29 families and seven orders of predators collected from untreated and treated rice field, respectively. Major predators of both rice fields were Micraspis discolor (Fabricius) (Coleoptera: Coccinellidae), Tetragnatha sp. (Araneae: Tetragnathidae) and Agriocnemis pygmaea Rambur (Odonata: Agrionidae). The population dynamic of predators were not related with rice pest population in both treatments. However, the fluctuation of population pattern of rice pests in the untreated treatment were more distinctly synchronized with their predators than that of the treated treatment. There were no significant differences in the total number of rice pest and predator between two treatments at vegetative and reproductive stages of rice growth. Untreated rice field had a higher population number of predator and a lower population number of rice pest than that of treated rice field during grain formation and ripening stages. These results indicated the ago-ecosystem balance in rice fields could be produced through minimal pesticide application, in order to allow

From Early Domesticated Rice of the Middle Yangtze Basin to Millet, Rice and Wheat Agriculture: Archaeobotanical Macro-Remains from Baligang, Nanyang Basin, Central China (6700-500 BC.

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Zhenhua Deng

Full Text Available Baligang is a Neolithic site on a northern tributary of the middle Yangtze and provides a long archaeobotanical sequence from the Seventh Millennium BC upto the First Millennium BC. It provides evidence for developments in rice and millet agriculture influenced by shifting cultural affiliation with the north (Yangshao and Longshan and south (Qujialing and Shijiahe between 4300 and 1800 BC. This paper reports on plant macro-remains (seeds, from systematic flotation of 123 samples (1700 litres, producing more than 10,000 identifiable remains. The earliest Pre-Yangshao occupation of the sites provide evidence for cultivation of rice (Oryza sativa between 6300-6700 BC. This rice appears already domesticated in on the basis of a dominance of non-shattering spikelet bases. However, in terms of grain size changes has not yet finished, as grains are still thinner than more recent domesaticated rice and are closer in grain shape to wild rices. This early rice was cultivated alongside collection of wild staple foods, especially acorns (Quercus/Lithicarpus sensu lato. In later periods the sites has evidence for mixed farming of both rice and millets (Setaria italica and Panicum miliaceum. Soybean appears on the site in the Shijiahe period (ca.2500 BC and wheat (Triticum cf. aestivum in the Late Longshan levels (2200-1800 BC. Weed flora suggests an intensification of rice agriculture over time with increasing evidence of wetland weeds. We interpret these data as indicating early opportunistic cultivation of alluvial floodplains and some rainfed rice, developing into more systematic and probably irrigated cultivation starting in the Yangshao period, which intensified in the Qujialing and Shijiahe period, before a shift back to an emphasis on millets with the Late Longshan cultural influence from the north.

MORPHOLOGICAL AND AGRONOMICAL CHARACTERISTICS OF SOME WILD AND CULTIVATED ISATIS SPECIES

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Süleyman KIZIL

2007-04-01

Full Text Available The study evaluated Isatis tinctoria, I. constricta, I. glauca, I. cochlearis, I. aucheri and I. demiriziana during 2002-03 and 2003-04 growing seasons for different agronomic characteristics affecting the percentage of dye in them. The results showed wide variations in the agronomic characteristics of Isatis constricta, Isatis cochlearis, Isatis aucheri, Isatis demiriziana collected from wild; compared to culture Isatis tinctoria and Isatis glauca. I. tinctoria showed early emergence (36 day compared to other species, and I. glauca was determined as late fl owering (512 day species. Among Isatis species, I. glauca showed the maximum plant height (113.4 cm, stem diameter (10.84 mm seed yield per plant (103.0 g . Whereas, I. tinctoria produced the largest number of branches per plant (16.8 plant-1 and the maximum number of seeds (17918 per plant.

Fungal diversity of rice straw for meju fermentation.

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Kim, Dae-Ho; Kim, Seon-Hwa; Kwon, Soon-Wo; Lee, Jong-Kyu; Hong, Seung-Beom

2013-12-01

Rice straw is closely associated with meju fermentation and it is generally known that the rice straw provides meju with many kinds of microorganisms. In order to elucidate the origin of meju fungi, the fungal diversity of rice straw was examined. Rice straw was collected from 12 Jang factories where meju are produced, and were incubated under nine different conditions by altering the media (MEA, DRBC, and DG18), and temperature (15°C, 25°C, and 35°C). In total, 937 strains were isolated and identified as belonging to 39 genera and 103 species. Among these, Aspergillus, Cladosporium, Eurotium, Fusarium, and Penicillium were the dominant genera. Fusarium asiaticum (56.3%), Cladosporium cladosporioides (48.6%), Aspergillus tubingensis (37.5%), A. oryzae (31.9%), Eurotium repens (27.1%), and E. chevalieri (25.0%) were frequently isolated from the rice straw obtained from many factories. Twelve genera and 40 species of fungi that were isolated in the rice straw in this study were also isolated from meju. Specifically, A. oryzae, C. cladosporioides, E. chevalieri, E. repens, F. asiaticum, and Penicillium polonicum (11.8%), which are abundant species in meju, were also isolated frequently from rice straw. C. cladosporioides, F. asiaticum, and P. polonicum, which are abundant in the low temperature fermentation process of meju fermentation, were frequently isolated from rice straw incubated at 15°C and 25°C, whereas A. oryzae, E. repens, and E. chevalieri, which are abundant in the high temperature fermentation process of meju fermentation, were frequently isolated from rice straw incubated at 25°C and 35°C. This suggests that the mycobiota of rice straw has a large influence in the mycobiota of meju. The influence of fungi on the rice straw as feed and silage for livestock, and as plant pathogens for rice, are discussed as well.

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

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

2017-12-01

High water use efficiency is essential to water-saving cropping. Morphological traits that affect photosynthetic water use efficiency are not well known. We examined whether leaf hairiness improves photosynthetic water use efficiency in rice. A chromosome segment introgression line (IL-hairy) of wild Oryza nivara (Acc. IRGC105715) with the genetic background of Oryza sativa cultivar 'IR24' had high leaf pubescence (hair). The leaf hairs developed along small vascular bundles. Linkage analysis in BC 5 F 2 and F 3 populations showed that the trait was governed by a single gene, designated BLANKET LEAF (BKL), on chromosome 6. IL-hairy plants had a warmer leaf surface in sunlight, probably due to increased boundary layer resistance. They had a lower transpiration rate under moderate and high light intensities, resulting in higher photosynthetic water use efficiency. Introgression of BKL on chromosome 6 from O. nivara improved photosynthetic water use efficiency in the genetic background of IR24.

Constitutive expression of CaPLA1 conferred enhanced growth and grain yield in transgenic rice plants.

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Park, Ki Youl; Kim, Eun Yu; Seo, Young Sam; Kim, Woo Taek

2016-03-01

Phospholipids are not only important components of cell membranes, but participate in diverse processes in higher plants. In this study, we generated Capsicum annuum phospholipiase A1 (CaPLA1) overexpressing transgenic rice (Oryza sativa L.) plants under the control of the maize ubiquitin promoter. The T4 CaPLA1-overexpressing rice plants (Ubi:CaPLA1) had a higher root:shoot mass ratio than the wild-type plants in the vegetative stage. Leaf epidermal cells from transgenic plants had more cells than wild-type plants. Genes that code for cyclin and lipid metabolic enzymes were up-regulated in the transgenic lines. When grown under typical paddy field conditions, the transgenic plants produced more tillers, longer panicles and more branches per panicle than the wild-type plants, all of which resulted in greater grain yield. Microarray analysis suggests that gene expressions that are related with cell proliferation, lipid metabolism, and redox state were widely altered in CaPLA1-overexpressing transgenic rice plants. Ubi:CaPLA1 plants had a reduced membrane peroxidation state, as determined by malondialdehyde and conjugated diene levels and higher peroxidase activity than wild-type rice plants. Furthermore, three isoprenoid synthetic genes encoding terpenoid synthase, hydroxysteroid dehydrogenase and 3-hydroxy-3-methyl-glutaryl-CoA reductase were up-regulated in CaPLA1-overexpressing plants. We suggest that constitutive expression of CaPLA1 conferred increased grain yield with enhanced growth in transgenic rice plants by alteration of gene activities related with cell proliferation, lipid metabolism, membrane peroxidation state and isoprenoid biosynthesis.

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

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

2014-06-01

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

Cadmium Accumulation and Its Toxicity in Brittle Culm 1 (bc1, a Fragile Rice Mutant

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Guo-sheng SHAO

2007-09-01

Full Text Available Cadmium (Cd accumulation and toxicity in rice plants were characterized and identified by using brittle culm 1 (bc1, a fragile rice mutant and its wild type (Shuangkezao, an indica rice as materials by hydroponics. The low Cd level didn't obviously affect the growth parameters in both rice genotypes, but under high Cd levels (1.0 and 5.0 μmol/L, the growth of both rice plants were substantially inhibited. Moreover, bc1 tended to suffer more seriously from Cd toxicity than Shuangkezao. Cd accumulation in both rice plants increased with the increase of Cd levels. There was a significant difference in Cd accumulation between the two rice genotypes with constantly higher Cd concentration in bc1, which also accumulated more Cd at 0, 0.1, and 1.0 μmol/L Cd levels. The same case was found in the two rice plants grown on Cd-contaminated soil. This suggested that cell wall might play an important role in Cd accumulation in rice plants by the physiological mechanisms. The malondialdehyde (MDA content, superoxide dismutase (SOD and peroxidase (POD activities in rice plants were affected differently under Cd treatments, and which implied that POD might play the main role in detoxifying active oxygen free radical. A significant difference in antioxidative system between the two rice genotypes was found with constantly higher MDA content, SOD and POD activities in bc1. In summary, bc1 accumulated more Cd and appeared to be more sensitive to Cd stress compared with its wild type.

Blast resistance of space-induced variants derived from rice cultivar Hanghui 7

International Nuclear Information System (INIS)

Zhang Jingxin; Yang Qiyun; Zhu Xiaoyuan; Wang Hui; Zeng Liexian; Liu Yongzhu; Guo Tao; Chen Zhiqiang

2010-01-01

To screen the resistance lines to rice blast, the blast resistance of SP 3 and SP 4 progenies derived from rice variety Hanghui 7 were evaluated after satellite flight, and the genomic DNA polymorphism of the resistant variants selected from SP 3 was compared with the wild type by microsatellite markers. The results indicated that the SP 3 Variant line H24, which was selected from the 250 space-induced lines ( SP 3 ) with excellent agronomic and economical characters, showed resistance segregation (119R : 108S) against blast isolate GD3286. It was demonstrated that the resistance of H24 might be controlled by two dominant and complementary resistance genes. The resistance of H24 was still segregated in SP 4 , but the resistance spectrum of H24 was 84. 4% in SP 5 , much higher than the wild type, 40. 6%, and H24 especially showed resistant against some blast isolates of broad pathogenic spectrum or specialized pathogenicity; further more, the DNA polymorphism wasn't detected between H24 and its wild type by 229 SSR (simple sequence repeat) markers covering the rice genome equally. (authors)

Heat-assisted aqueous extraction of rice flour for arsenic speciation analysis.

Science.gov (United States)

Narukawa, Tomohiro; Chiba, Koichi

2010-07-28

A versatile heat-assisted pretreatment aqueous extraction method for the analysis of arsenic species in rice was developed. Rice flour certified reference materials NIST SRM1568a and NMIJ CRM 7503-a and a flour made from polished rice were used as samples, and HPLC-ICP-MS was employed for the determination of arsenic species. Arsenite [As(III)], arsenate [As(V)], monomethylarsonic acid (MMAA) and dimethylarsinic acid (DMAA) were detected in NIST SRM, and As(III), As(V) and DMAA were found in NMIJ CRM and the prepared polished rice flour. The sums of the concentrations of all species in each rice flour sample were 97-102% of the total arsenic concentration in each sample.

Genetic control of a transition from black to straw-white seed hull in rice domestication.

Science.gov (United States)

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.

Clostridium difficile and Clostridium perfringens from wild carnivore species in Brazil.

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Silva, Rodrigo Otávio Silveira; D'Elia, Mirella Lauria; Tostes Teixeira, Erika Procópio; Pereira, Pedro Lúcio Lithg; de Magalhães Soares, Danielle Ferreira; Cavalcanti, Álvaro Roberto; Kocuvan, Aleksander; Rupnik, Maja; Santos, André Luiz Quagliatto; Junior, Carlos Augusto Oliveira; Lobato, Francisco Carlos Faria

2014-08-01

Despite some case reports, the importance of Clostridium perfringens and Clostridium difficile for wild carnivores remains unclear. Thus, the objective of this study was to identify C. perfringens and C. difficile strains in stool samples from wild carnivore species in Brazil. A total of 34 stool samples were collected and subjected to C. perfringens and C. difficile isolation. Suggestive colonies of C. perfringens were then analyzed for genes encoding the major C. perfringens toxins (alpha, beta, epsilon and iota) and the beta-2 toxin (cpb2), enterotoxin (cpe) and NetB (netb) genes. C. difficile strains were analyzed by multiplex-PCR for toxins A (tcdA) and B (tcdB) and a binary toxin gene (cdtB) and also submitted to a PCR ribotyping. Unthawed aliquots of samples positive for C. difficile isolation were subjected to the detection of A/B toxins by a cytotoxicity assay (CTA). C. perfringens was isolated from 26 samples (76.5%), all of which were genotyped as type A. The netb gene was not detected, whereas the cpb2 and cpe genes were found in nine and three C. perfringens strains, respectively. C. difficile was isolated from two (5.9%) samples. A non-toxigenic strain was recovered from a non-diarrheic maned wolf (Chrysocyon brachyurus). Conversely, a toxigenic strain was found in the sample of a diarrheic ocelot (Leopardus pardallis); an unthawed stool sample was also positive for A/B toxins by CTA, indicating a diagnosis of C. difficile-associated diarrhea in this animal. The present work suggests that wild carnivore species could carry C. difficile strains and that they could be susceptible to C. difficile infection. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

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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.

From Early Domesticated Rice of the Middle Yangtze Basin to Millet, Rice and Wheat Agriculture: Archaeobotanical Macro-Remains from Baligang, Nanyang Basin, Central China (6700–500 BC)

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Deng, Zhenhua; Qin, Ling; Gao, Yu; Weisskopf, Alison Ruth; Zhang, Chi; Fuller, Dorian Q.

2015-01-01

Baligang is a Neolithic site on a northern tributary of the middle Yangtze and provides a long archaeobotanical sequence from the Seventh Millennium BC upto the First Millennium BC. It provides evidence for developments in rice and millet agriculture influenced by shifting cultural affiliation with the north (Yangshao and Longshan) and south (Qujialing and Shijiahe) between 4300 and 1800 BC. This paper reports on plant macro-remains (seeds), from systematic flotation of 123 samples (1700 litres), producing more than 10,000 identifiable remains. The earliest Pre-Yangshao occupation of the sites provide evidence for cultivation of rice (Oryza sativa) between 6300–6700 BC. This rice appears already domesticated in on the basis of a dominance of non-shattering spikelet bases. However, in terms of grain size changes has not yet finished, as grains are still thinner than more recent domesaticated rice and are closer in grain shape to wild rices. This early rice was cultivated alongside collection of wild staple foods, especially acorns (Quercus/Lithicarpus sensu lato). In later periods the sites has evidence for mixed farming of both rice and millets (Setaria italica and Panicum miliaceum). Soybean appears on the site in the Shijiahe period (ca.2500 BC) and wheat (Triticum cf. aestivum) in the Late Longshan levels (2200–1800 BC). Weed flora suggests an intensification of rice agriculture over time with increasing evidence of wetland weeds. We interpret these data as indicating early opportunistic cultivation of alluvial floodplains and some rainfed rice, developing into more systematic and probably irrigated cultivation starting in the Yangshao period, which intensified in the Qujialing and Shijiahe period, before a shift back to an emphasis on millets with the Late Longshan cultural influence from the north. PMID:26460975

Herbicidal and antioxidant responses of transgenic rice overexpressing Myxococcus xanthus protoporphyrinogen oxidase.

Science.gov (United States)

Jung, Sunyo; Back, Kyoungwhan

2005-05-01

We analyzed the herbicidal and antioxidant defense responses of transgenic rice plants that overexpressed the Myxococcus xanthus protoporphyrinogen oxidase gene. Leaf squares of the wild-type incubated with oxyfluorfen were characterized by necrotic leaf lesions and increases in conductivity and malonyldialdehyde levels, whereas transgenic lines M4 and M7 did not show any change with up to 100 microM oxyfluorfen. The wild-type had decreased F(v)/F(m) and produced a high level of H(2)O(2) at 18 h after foliar application of oxyfluorfen, whereas transgenic lines M4 and M7 were unaffected. In response to oxyfluorfen, violaxanthin, beta-carotene, and chlorophylls (Chls) decreased in wild-type plants, whereas antheraxanthin and zeaxanthin increased. Only a slight decline in Chls was observed in transgenic lines at 48 h after oxyfluorfen treatment. Noticeable increases of cytosolic Cu/Zn-superoxide dismutase, peroxidase isozymes 1 and 2, and catalase were observed after at 48 h of oxyfluorfen treatment in the wild-type. Non-enzymatic antioxidants appeared to respond faster to oxyfluorfen-induced photodynamic stress than did enzymatic antioxidants. Protective responses for the detoxification of active oxygen species were induced to counteract photodynamic stress in oxyfluorfen-treated, wild-type plants. However, oxyfluorfen-treated, transgenic plants suffered less oxidative stress, confirming increased herbicidal resistance resulted from dual expression of M. xanthus Protox in chloroplasts and mitochondria.

Toxocara cati (Nematoda, Ascarididae in different wild feline species in Brazil: new host records

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Moisés Gallas

2013-05-01

Full Text Available http://dx.doi.org/10.5007/2175-7925.2013v26n3p117 This is the first detailed description of Toxocara cati parasitizing felines in South America. Seventeen run over wild felines (Leopardus colocolo, Leopardus geoffroyi, Leopardus tigrinus, and Puma yagouaroundi were collected from different towns in the State of Rio Grande do Sul, Brazil. The morphometry of males and females allowed the identification of specimens as being T. cati. The helminths were found in the stomach and intestine of hosts with prevalences of 66.6% in L. colocolo, L. geoffroyi, and L. tigrinus; and 60% in P. yagouaroundi. The ecological parameters were calculated for each host and L. colocolo had the highest infection intensity (22.5 helminths/ host. This is the first report of T. cati parasitizing four wild felines species in southern Brazil, besides a new record of this parasite for two host species.

Genetic mapping of the rice resistance-breaking gene of the brown planthopper Nilaparvata lugens

OpenAIRE

Kobayashi, Tetsuya; Yamamoto, Kimiko; Suetsugu, Yoshitaka; Kuwazaki, Seigo; Hattori, Makoto; Jairin, Jirapong; Sanada-Morimura, Sachiyo; Matsumura, Masaya

2014-01-01

Host plant resistance has been widely used for controlling the major rice pest brown planthopper (BPH, Nilaparvata lugens). However, adaptation of the wild BPH population to resistance limits the effective use of resistant rice varieties. Quantitative trait locus (QTL) analysis was conducted to identify resistance-breaking genes against the anti-feeding mechanism mediated by the rice resistance gene Bph1. QTL analysis in iso-female BPH lines with single-nucleotide polymorphism (SNP) markers d...

γ-Oryzanol, tocol and mineral compositions in different grain fractions of giant embryo rice mutants.

Science.gov (United States)

Jeng, Toong Long; Shih, Yi Ju; Ho, Pei Tzu; Lai, Chia Chi; Lin, Yu Wen; Wang, Chang Sheng; Sung, Jih Min

2012-05-01

Rice embryo is concentrated with lipid, protein and some bioactive chemicals. Two rice mutants IR64-GE and TNG71-GE (M7 generation) were characterised by an enlarged embryo compared with their wild types. In the present study, distributions of protein, lipid, total phenolics, γ-oryzanol, tocols and some essential minerals in these two giant embryo mutants and their respective normal embryo wild types IR64 and TNG71 were compared. The embryo dry weights of giant embryo mutants IR64-GE and TNG71-GE were 0.92 and 1.32 mg per seed respectively. These values were higher than those of their respective normal embryo genotypes (0.50 and 0.62 mg per seed). Large variations in protein, lipid, phenolic, γ-oryzanol, tocol and minerals levels were found between mutant and wild-type pairs. The brown rice of TNG71-GE had higher total γ-oryzanol (average of 24% increase) and total tocol (average of 75% increase) levels than TNG71, IR64 and IR64-GE. The embryo and bran parts of giant embryo mutant TNG71-GE were found to be good sources of vitamin E and γ-oryzanol. Therefore it could be used to produce high-value by-products from milled embryo and bran parts and as a genetic resource for rice improvement programmes. TNG71-GE can also be used as a nutrient-fortified rice cultivar. Copyright © 2011 Society of Chemical Industry.

Comparative analysis of the transcriptional responses to low and high temperatures in three rice planthopper species.

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Huang, Hai-Jian; Xue, Jian; Zhuo, Ji-Chong; Cheng, Ruo-Lin; Xu, Hai-Jun; Zhang, Chuan-Xi

2017-05-01

The brown planthopper (Nilaparvata lugens, BPH), white-backed planthopper (Sogatella furcifera, WBPH) and small brown planthopper (Laodelphax striatellus, SBPH) are important rice pests in Asia. These three species differ in thermal tolerance and exhibit quite different migration and overwintering strategies. To understand the underlying mechanisms, we sequenced and compared the transcriptome of the three species under different temperature treatments. We found that metabolism-, exoskeleton- and chemosensory-related genes were modulated. In high temperature (37 °C), heat shock protein (HSP) genes were the most co-regulated; other genes related with fatty acid metabolism, amino acid metabolism and transportation were also differentially expressed. In low temperature (5 °C), the differences in gene expression of the genes for fatty acid synthesis, transport proteins and cytochrome P450 might explain why SBPH can overwinter in high latitudes, while BPH and WBPH cannot. In addition, other genes related with moulting, and membrane lipid composition might also play roles in resistance to low and high temperatures. Our study illustrates the common responses and different tolerance mechanisms of three rice planthoppers in coping with temperature change, and provides a potential strategy for pest management. © 2017 John Wiley & Sons Ltd.

Polyphenol composition, antioxidant activity and cytotoxicity of seeds from two underexploited wild Licania species

NARCIS (Netherlands)

Pessoa, Igor Parra; Neto, José Joaquim Lopes; Almeida, De Thiago Silva; Farias, Davi Felipe; Vieira, Leonardo Rogério; Medeiros, De Jackeline Lima; Boligon, Aline Augusti; Peijnenburg, Ad; Castelar, Ivan; Carvalho, Ana Fontenele Urano

2016-01-01

Studies have shown the benefit of antioxidants in the prevention or treatment of human diseases and promoted a growing interest in new sources of plant antioxidants for pharmacological use. This study aimed to add value to two underexploited wild plant species (Licania rigida) and L. tomentosa) from

Molecular evolution of shattering loci in U.S. weedy rice.

Science.gov (United States)

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

2010-08-01

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.

Characterization and genetic improvement of two wild species blueberry from Costa Rica (Vaccinium consanguineum y V. poasanum)

International Nuclear Information System (INIS)

Soto Valverde, Rebeca de los Angeles

2015-01-01

Accessions of two wild species blueberry from Costa Rica were characterized for use in the genetic improvement of this crop. A collection of accessions of two wild species blueberry (Vaccinium consanguineum and V. poasanum) were georeferenced and collected in the highlands of the provinces of Alajuela, San Jose and Cartago. The bushes collected were transplanted in the subestacion Fraijanes of the Estacion Experimental Fabio Baudrit Moreno of the Universidad de Costa Rica. Quantitative and qualitative descriptors were evaluated to morphologically characterize in situ and ex situ the accessions collected from each of the two species. The effect of two antimitotic agents, colchicine and oryzalin was determined on the chromosomal duplication of accessions of V. consanguineum and V. poasanum established in vitro. The gibberellic acid was used to promote in vitro germination of the seeds of V. consanguineum and V. poasanum, but reduces the percentage of germination in the latter species if it is used in high doses. The effect of antimitotic agents on the ploidy of both species was determined by flow cytometry [es

The New Transgenic cry1Ab/vip3H Rice Poses No Unexpected Ecological Risks to Arthropod Communities in Rice Agroecosystems.

Science.gov (United States)

Lu, Zengbin; Dang, Cong; Han, Naishun; Shen, Zhicheng; Peng, Yufa; Stanley, David; Ye, Gongyin

2016-04-01

The ecological risks to nontarget organisms should be rigorously assessed before Bt crops are released. Here, the impacts of a new Cry1Ab/Vip3H rice line on arthropod communities in rice agroecosystems were evaluated across 3 yr. Arthropods collected via vacuum were sorted into five guilds. The abundance and proportion of each guild as well as community-level parameters were determined in Cry1Ab/Vip3H and control rice fields. Changes in arthropod species assemblage over sampling dates were investigated by principal response curves (PRCs). Cry1Ab/Vip3H rice did not exert significant impacts on the seasonal density and proportion of each guild, except parasitoids. Detritivore seasonal density, but not its relative abundance, was significantly affected by Cry1Ab/Vip3H rice. Four community indices (species richness S, Shannon-Wiener index H', Simpson index D, and evenness index J') were similar between rice types. PRCs revealed a slight community difference between rice types in the past two tested years, with rice types accounting for 1.0-3.5% of the variance among arthropod communities. However, sampling dates explain 32.1-67.6% for these community differences. Of the 46 taxa with higher species weights, 26.1% of the taxa were significantly different, including seven taxa with higher abundance and five with lower density in Cry1Ab/Vip3H rice fields. These differences may be attributed to change in abundance of prey or hosts but not to direct effects of Bt proteins. We infer that this new Cry1Ab/Vip3H rice line poses no unintended ecological risks to the arthropod community. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Can rice field channels contribute to biodiversity conservation in Southern Brazilian wetlands?

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Maltchik, Leonardo; Rolon, Ana Silvia; Stenert, Cristina; Machado, Iberê Farina; Rocha, Odete

2011-12-01

Conservation of species in agroecosystems has attracted attention. Irrigation channels can improve habitats and offer conditions for freshwater species conservation. Two questions from biodiversity conservation point of view are: 1) Can the irrigated channels maintain a rich diversity of macrophytes, macroinvertebrates and amphibians over the cultivation cycle? 2) Do richness, abundance and composition of aquatic species change over the rice cultivation cycle? For this, a set of four rice field channels was randomly selected in Southern Brazilian wetlands. In each channel, six sample collection events were carried out over the rice cultivation cycle (June 2005 to June 2006). A total of 160 taxa were identified in irrigated channels, including 59 macrophyte species, 91 taxa of macroinvertebrate and 10 amphibian species. The richness and abundance of macrophytes, macroinvertebrates and amphibians did not change significantly over the rice cultivation cycle. However, the species composition of these groups in the irrigation channels varied between uncultivated and cultivated periods. Our results showed that the species diversity found in the irrigation channels, together with the permanence of water enables these man-made aquatic networks to function as important systems that can contribute to the conservation of biodiversity in regions where the wetlands were converted into rice fields. The conservation of the species in agriculture, such as rice field channels, may be an important alternative for biodiversity conservation in Southern Brazil, where more than 90% of wetland systems have already been lost and the remaining ones are still at high risk due to the expansion of rice production.

Diversification of Cercopithifilaria species (Nematoda: Filarioidea in Japanese wild ruminants with description of two new species

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Uni S.

2002-12-01

Full Text Available Twelve of the 17 Cervus nippon nippon deer from Kyushu Island, Japan, that we examined were infected with one or two Cercopithifilaria species. C. longa n. sp. adults were in the subcutaneous tissues of limbs and the abdomen, and C. crassa n. sp. adults were in the skin, mainly in the anterior part of the back ; the distribution of the dermal microfilariae generally matched that of the adult worms. The two new species were assigned to the group of primitive Cercopithifilaria species that parasitize ruminants (bovids and cervids, but the new species could readily be distinguished from others morphologically. C. longa was more primitive and resembled C. bulboidea, one of the five species from the serow Capricornis crispus, a Japanese member of the Caprinae, and species from Bovidae in Africa. C. crassa had a thick body and large spicules like C. rugosicauda from Capreolus capreolus in Europe, the only previously known Cercopithifilaria species from cervids, but it also had one or two hypertrophied pairs of caudal papillae, an unusual character found so far only in Japanese parasites. Among the 12 species known from ruminants, four are African, one is European and more highly evolved, and seven are Japanese, with some being primitive and some more evolved. The great diversity of Cercopithifilaria species in the two wild ruminants that live in Japan seems to have resulted from local speciation, which occurred during the Pleistocene, from a primitive form of the C. longa type derived from Eurasiatic ancestors, which has disappeared or, more probably, not yet been discovered.

Testing of Rice Stocks for Their Survival of Winter Cold

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Hiroshi Ikehashi

2018-03-01

Full Text Available Rice cultivation is considered to be initiated by vegetative propagation of sprout from wild perennial stocks. To test whether any presently cultivated rice cultivar can survive the winter cold or not, rice stocks of several cultivars including indica and japonica types were placed in a shallow pool from October to April in 2015–2016 and 2016–2017. During the coldest period of the winter, the bases of the stocks were placed 5–6 cm below the surface of water, where temperatures ranged from 3 °C to 5 °C, while the surface was frozen for two or three times and covered with snow for a day. Only one cultivar, Nipponbare, a japonica type, survived the winter cold and regenerated sprouts in the end of April or early May. A possibility to develop perennial cultivation of rice or perennial hybrid rice is discussed.

Indica rice (Oryza sativa, BR29 and IR64).

Science.gov (United States)

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.

Discrimination and similarity evaluation of tissue-cultured and wild Dendrobium species using Fourier transform infrared spectroscopy

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Chen, Nai-dong; Chen, Han; Li, Jun; Sang, Mang-mang; Ding, Shen; Yu, Hao

2015-04-01

The FTIR method was applied to evaluate the similarity of tissue-cultured and wild Dendrobium huoshanense C.Z. Tang et S.J. Cheng, Dendrobium officinale Kimura et Migo and Dendrobium moniliforme (Linn.) Sw and discriminate different Dendrobium species, especially D. huoshanense and its main goldbrick Dendrobium henanense J.L. Lu et L.X. Gao. Despite the general pattern of the IR spectra, different intensities, shapes and peak positions were found in the IR spectra of these samples, especially in the range of 1800-600 cm-1, which could be used to discriminate them. The methanol, aqueous extracting procedure and the second derivative transformation obviously enlarged the tiny spectral differences among these samples. The similarity evaluation based on the IR spectra and the second derivative IR spectrum revealed that the similarity of the methanol extracts between tissue-cultured and wild Dendrobiums might be lower than that between different Dendrobium species. The similarities of the powders and aqueous extracts between tissue-cultured and wild Dendrobiums were higher than those between different Dendrobium species. The further principal component analysis showed that the first three components explained 99.7%, 87.7% and 85.1% of data variance for powder, methanol extract and aqueous extract, respectively, demonstrating a good discrimination between samples. Our research suggested that the variations of secondary metabolites between different origins of the investigated Dendrobiums might be higher than what we had supposed. Tissue culture techniques were widely used in the conversation of rare and endangered medicinal amedica, however, our study suggested that the chemical constituents of tissue-cultured plants might be quite different from their wild correspondences.

Overexpression of rice serotonin N-acetyltransferase 1 in transgenic rice plants confers resistance to cadmium and senescence and increases grain yield.

Science.gov (United States)

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. T 2 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.

Trans-sialidase inhibition assay detects Trypanosoma cruzi infection in different wild mammal species.

Science.gov (United States)

Sartor, Paula A; Ceballos, Leonardo A; Orozco, Marcela M; Cardinal, Marta V; Gürtler, Ricardo E; Leguizamón, María S

2013-08-01

The detection of Trypanosoma cruzi infection in mammals is crucial for understanding the eco-epidemiological role of the different species involved in parasite transmission cycles. Xenodiagnosis (XD) and hemoculture (HC) are routinely used to detect T. cruzi in wild mammals. Serological methods are much more limited because they require the use of specific antibodies to immunoglobulins of each mammalian species susceptible to T. cruzi. In this study we detected T. cruzi infection by trans-sialidase (TS) inhibition assay (TIA). TIA is based on the antibody neutralization of a recombinant TS that avoids the use of anti-immunoglobulins. TS activity is not detected in the co-endemic protozoan parasites Leishmania spp and T. rangeli. In the current study, serum samples from 158 individuals of nine wild mammalian species, previously tested by XD, were evaluated by TIA. They were collected from two endemic areas in northern Argentina. The overall TIA versus XD co-reactivity was 98.7% (156/158). All 18 samples from XD-positive mammals were TIA-positive (co-positivity, 100%) and co-negativity was 98.5% (138/140). Two XD-negative samples from a marsupial (Didelphis albiventris) and an edentate (Dasypus novemcinctus) were detected by TIA. TIA could be used as a novel tool for serological detection of Trypanosoma cruzi in a wide variety of sylvatic reservoir hosts.

Secondary Metabolite Profiles and Mating Populations of Fusarium species in Section Liseola Associated with Bakanae Disease of Rice

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Nur Ain Izzati, M. Z.

2008-01-01

Full Text Available A total of 25 strains of Fusarium species that belong to F. fujikuroi (a pathogen of bakanae disease, F. proliferatum, F. sacchari, F. subglutinans and F. verticillioides were isolated from rice plants showing typical bakanae symptoms in Malaysia and Indonesia and screened for their secondary metabolites. The objectives of the studies were to determine the physiological variability based on production of moniliformin (MON, fumonisin (FB1, gibberellic acid (GA3 and fusaric acid (FA as well as to ascertain the mating populations (MPs within the Gibberella fujikuroi species complex based on their ability to produce perithecia and viable ascospores. Production of GA3 could be used to separate F. fujikuroi that belongs to MP-C from other species. In crosses with seven standard testers of MPs, 76% of strains could be assigned to at least one of the G. fujikuroi species complex namely MP-A (G. moniliformis, MP-B (G. sacchari, MP-C (G. fujikuroi and MP-D (G. intermedia. Single strain (M3237P that was assigned as MP-C, and has also been identified morphologically as F. fujikuroi was also crossed-fertile with MP-D tester. The secondary metabolites profiles and the presence of MP-A, MP-B, MP-C and MP-D strains on samples of bakanae-infected rice plants are new records in Malaysia.

Investigating Pigment Radicals in Black Rice Using HPLC and Multi-EPR.

Science.gov (United States)

Nakagawa, Kouichi; Maeda, Hayato

2017-01-01

We investigated the location and distribution of paramagnetic species in black and white rice using electron paramagnetic resonance (EPR), X-band (9 GHz) EPR imaging (EPRI), and HPLC. EPR primarily detected two paramagnetic species in black rice, which were identified as a stable radical and Mn 2+ species, based on the g values and hyperfine components of the EPR signals. The signal from the stable radical appeared at g ≈ 2.00 and was relatively strong and stable. Subsequent noninvasive two-dimensional (2D) EPRI revealed that this stable radical was primarily located in the pigmented region of black rice, while very few radicals were observed in the rice interior. Pigments extracted from black rice were analyzed using HPLC; the major compound was found to be cyanidin-3-glucoside. EPR and HPLC results indicate that the stable radical was only found within the pigmented region of the rice, and that it could either be cyanidin-3-glucoside, or one of its oxidative decomposition products.

Sampling wild species to conserve genetic diversity

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Sampling seed from natural populations of crop wild relatives requires choice of the locations to sample from and the amount of seed to sample. While this may seem like a simple choice, in fact careful planning of a collector’s sampling strategy is needed to ensure that a crop wild collection will ...

Genetic Analysis of Seed Yield Components and its Association with Forage Production in Wild and Cultivated Species of Sainfoin

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A. Najafipoor

2017-02-01

Full Text Available Little is known about genetic variation of seed related traits and their association with forage characters in sainfoin. In order to investigate the variation and relationship among seed yield and its components, 93 genotypes from 21 wild and cultivated species of genus Onobrychis were evaluated using a randomized complete block design with four replications at Isfahan University of Technology Research Farm, Isfahan, Iran. Analysis of variance showed that there was significant difference among genotypes, indicating existence of considerable genetic variation in this germplasm. Panicle fertility and panicle length had the most variation in cultivated and the wild genotypes, respectively. Results of correlation analysis showed that seed yield was positively correlated with number of stems per plant and number of seeds per panicle and negatively correlated with panicle length and days to 50% flowering. Seed yield had positive correlation with forage yield in wild species while this correlation was not significant in cultivated one. Cluster analysis classified the genotypes into three groups which separate wild and cultivated species. Based on principal component analysis the first component was related to seed yield and the second one was related to components of forage yield which can be used for selection of high forage and seed yielding genotypes.

Discrimination of Transgenic Rice Based on Near Infrared Reflectance Spectroscopy and Partial Least Squares Regression Discriminant Analysis

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ZHANG Long

2015-09-01

Full Text Available Near infrared reflectance spectroscopy (NIRS, a non-destructive measurement technique, was combined with partial least squares regression discrimiant analysis (PLS-DA to discriminate the transgenic (TCTP and mi166 and wild type (Zhonghua 11 rice. Furthermore, rice lines transformed with protein gene (OsTCTP and regulation gene (Osmi166 were also discriminated by the NIRS method. The performances of PLS-DA in spectral ranges of 4 000–8 000 cm-1 and 4 000–10 000 cm-1 were compared to obtain the optimal spectral range. As a result, the transgenic and wild type rice were distinguished from each other in the range of 4 000–10 000 cm-1, and the correct classification rate was 100.0% in the validation test. The transgenic rice TCTP and mi166 were also distinguished from each other in the range of 4 000–10 000 cm-1, and the correct classification rate was also 100.0%. In conclusion, NIRS combined with PLS-DA can be used for the discrimination of transgenic rice.

Evaluation of Wild Lentil Species as Genetic Resources to Improve Drought Tolerance in Cultivated Lentil

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Linda Y. Gorim

2017-06-01

Full Text Available Increasingly unpredictable annual rainfall amounts and distribution patterns have far reaching implications for pulse crop biology. Seedling and whole plant survival will be affected given that water is a key factor in plant photosynthesis and also influences the evolving disease spectrum that affects crops. The wild relatives of cultivated lentil are native to drought prone areas, making them good candidates for the evaluation of drought tolerance traits. We evaluated root and shoot traits of genotypes of cultivated lentil and five wild species grown under two water deficit regimes as well as fully watered conditions over a 13 week period indoors. Plants were grown in sectioned polyvinyl chloride (PVC tubes containing field soil from the A, B, and C horizons. We found that root distribution into different soil horizons varied among wild lentil genotypes. Secondly, wild lentil genotypes employed diverse strategies such as delayed flowering, reduced transpiration rates, reduced plant height, and deep root systems to either escape, evade or tolerate drought conditions. In some cases, more than one drought strategy was observed within the same genotype. Sequence based classification of wild and cultivated genotypes did not explain patterns of drought response. The environmental conditions at their centers of origin may explain the patterns of drought strategies observed in wild lentils. The production of numerous small seeds by wild lentil genotypes may have implications for yield improvement in lentil breeding programs.

Arsenic biotransformation and volatilization in transgenic rice

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Meng, Xiang-Yan; Qin, Jie; Wang, Li-Hong; Duan, Gui-Lan; Sun, Guo-Xin; Wu, Hui-Lan; Chu, Cheng-Cai; Ling, Hong-Qing; Rosen, Barry P.; Zhu, Yong-Guan

2011-01-01

Summary Biotransformation of arsenic includes oxidation, reduction, methylation and conversion to more complex organic arsenicals. Members of the class of arsenite [As(III)] S-adenosylmethyltransferase enzymes catalyze As(III) methylation to a variety of mono-, di- and trimethylated species, some of which are less toxic than As(III) itself. However, no methyltransferase gene has been identified in plants. Here, an arsM gene from the soil bacterium Rhodopseudomonas palustris was expressed in Japonica rice (Oryza sativa L.) cultivar Nipponbare, and the transgenic rice produced methylated arsenic species, which were measured by inductively coupled plasma mass spectrometry (ICP-MS) and high performance liquid chromatography-inductively coupled plasma-mass spectrometry (HPLC-ICP-MS). Both monomethylarsenate [MAs(V)] and dimethylarsenate [DMAs(V)] were detected in the root and shoot of transgenic rice. After 12-d exposure to As(III), the transgenic rice gave off 10-fold more volatile arsenicals. The present study demonstrates that expression of an arsM gene in rice induces arsenic methylation and volatilization, providing a potential stratagem for phytoremediation theoretically. PMID:21517874

ANALYSIS ON THE DYNAMICS OF SPATIAL DISTRIBUTION PATTERN OF MIXED SPIDER POPULATION IN RICE FIELD

Institute of Scientific and Technical Information of China (English)

ZhiWang; Zhe-mingYuan; Da-xiangSong; Ming-shengZhu

2004-01-01

The results make it clear that there are total 11 families, 29 genera and 43 species of spiders in the rice field of Dong Fang Hong Farm. Among them, there are 8 families, 19 genera and 28 species in the early rice field, and 10 families, 27 genera and 36 species in the late rice field. The spatial distribution pattern of mixed spider populations in rice fields was different during different development stages of rice plant. During the prophase, metaphase and anaphase of early rice plant development, the spatial distribution pattern of mixed spider populations was aggregative, random and aggregative respectively. During the prophase, metaphase and anaphase of late rice plant development, the spatial distribution pattern was uniform, aggregative and uniform respectively.

Immediate Genetic and Epigenetic Changes in F1 Hybrids Parented by Species with Divergent Genomes in the Rice Genus (Oryza.

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Ying Wu

Full Text Available Inter-specific hybridization occurs frequently in higher plants, and represents a driving force of evolution and speciation. Inter-specific hybridization often induces genetic and epigenetic instabilities in the resultant homoploid hybrids or allopolyploids, a phenomenon known as genome shock. Although genetic and epigenetic consequences of hybridizations between rice subspecies (e.g., japonica and indica and closely related species sharing the same AA genome have been extensively investigated, those of inter-specific hybridizations between more remote species with different genomes in the rice genus, Oryza, remain largely unknown.We investigated the immediate chromosomal and molecular genetic/epigenetic instability of three triploid F1 hybrids produced by inter-specific crossing between species with divergent genomes of Oryza by genomic in situ hybridization (GISH and molecular marker analysis. Transcriptional and transpositional activity of several transposable elements (TEs and methylation stability of their flanking regions were also assessed. We made the following principle findings: (i all three triploid hybrids are stable in both chromosome number and gross structure; (ii stochastic changes in both DNA sequence and methylation occurred in individual plants of all three triploid hybrids, but in general methylation changes occurred at lower frequencies than genetic changes; (iii alteration in DNA methylation occurred to a greater extent in genomic loci flanking potentially active TEs than in randomly sampled loci; (iv transcriptional activation of several TEs commonly occurred in all three hybrids but transpositional events were detected in a genetic context-dependent manner.Artificially constructed inter-specific hybrids of remotely related species with divergent genomes in genus Oryza are chromosomally stable but show immediate and highly stochastic genetic and epigenetic instabilities at the molecular level. These novel hybrids might

Molecular identification of infective larvae of three species of Onchocerca found in wild-caught females of Simulium bidentatum in Japan

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Fukuda M.

2010-03-01

Full Text Available Wild female black flies attracted to a man or an idling automobile were collected at Oita, Japan where five cases of zoonotic onchocerciasis had occurred. Among the five Simulium species captured, 2% of Simulium bidentatum, the predominant species, were infected with filarial larvae. There were at least two types of infective larvae, types A and B, based on morphometric observation. Moreover, molecular analysis of the mitochondrial cytochrome c oxidase subunit 1 (CO1 gene revealed that types A and B were represented by a single unknown species of Onchocerca and two species, i.e., Onchocerca dewittei japonica from wild boar, the causative agent of zoonotic onchocerciasis in Japan, and an undescribed Onchocerca sp. from wild boar, respectively. Phylogenetic analysis based on the sequences of the mitochondrial 12S ribosomal RNA (12S rRNA gene also showed that type A is likely to be an unknown species of Onchocerca. Natural infection of black flies with infective larvae of O. dewittei japonica and O. sp. was demonstrated for the first time. The present study strongly suggests that S. bidentatum plays a role as a vector in the transmission of zoonotic onchocerciasis due to O. dewittei japonica in Japan.

Toxocara cati (Schrank, 1788 (Nematoda, Ascarididae in different wild feline species in Brazil: new host records

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Moisés Gallas

2013-09-01

Full Text Available This is the first detailed description of Toxocara cati parasitizing felines in South America. Seventeen run over wild felines (Leopardus colocolo, Leopardus geoffroyi, Leopardus tigrinus, and Puma yagouaroundi were collected from different towns in the State of Rio Grande do Sul, Brazil. The morphometry of males and females allowed the identification of specimens as being T. cati. The helminths were found in the stomach and intestine of hosts with prevalences of 66.6% in L. colocolo, L. geoffroyi, and L. tigrinus; and 60% in P. yagouaroundi. The ecological parameters were calculated for each host and L. colocolo had the highest infection intensity (22.5 helminths/host. This is the first report of T. cati parasitizing four wild felines species in southern Brazil, besides a new record of this parasite for two host species.

Wild plant food in agricultural environments: a study of occurrence, management, and gathering rights in Northeast Thailand.

NARCIS (Netherlands)

Price, L.L.

1997-01-01

This article examines the gathering of wild plant foods in agricultural environments and utilizes research conducted among rice cultivators in northeast Thailand as the case study. The management of wild food plants and gathering rights on agricultural land are closely linked to women's roles as

Comparison of aquatic macrophyte community structure between natural wetlands and rice fields with different cultivation ages

OpenAIRE

Rolon, A. S.; Godoy, R. S.; Maltchik, L.

2017-01-01

Abstract Recent studies indicate that rice fields contribute to the conservation of aquatic plants, however, repeated cultivation can reduce the species diversity harbored by rice fields. Repeated tillage, agrochemical application and environmental homogeneity can reduce plant diversity and select for species more tolerant to disturbance. Our hypotheses were: 1) macrophyte richness and biomass decrease with increased rice crop age; and 2) macrophyte species of rice fields are a subsample of n...

Comparative study on free amino acid composition of wild edible mushroom species.

Science.gov (United States)

Ribeiro, Bárbara; Andrade, Paula B; Silva, Branca M; Baptista, Paula; Seabra, Rosa M; Valentão, Patrícia

2008-11-26

A comparative study on the amino acid composition of 11 wild edible mushroom species (Suillus bellini, Suillus luteus, Suillus granulatus, Tricholomopsis rutilans, Hygrophorus agathosmus, Amanita rubescens, Russula cyanoxantha, Boletus edulis, Tricholoma equestre, Fistulina hepatica, and Cantharellus cibarius) was developed. To define the qualitative and quantitative profiles, a derivatization procedure with dabsyl chloride was performed, followed by HPLC-UV-vis analysis. Twenty free amino acids (aspartic acid, glutamic acid, asparagine, glutamine, serine, threonine, glycine, alanine, valine, proline, arginine, isoleucine, leucine, tryptophan, phenylalanine, cysteine, ornithine, lysine, histidine, and tyrosine) were determined. B. edulis and T. equestre were revealed to be the most nutritional species, whereas F. hepatica was the poorest. The different species exhibited distinct free amino acid profiles. The quantification of the identified compounds indicated that, in a general way, alanine was the major amino acid. The results show that the analyzed mushroom species possess moderate amino acid contents, which may be relevant from a nutritional point of view because these compounds are indispensable for human health. A combination of different mushroom species in the diet would offer good amounts of amino acids and a great diversity of palatable sensations.

Chloroplast overexpression of rice caffeic acid O-methyltransferase increases melatonin production in chloroplasts via the 5-methoxytryptamine pathway in transgenic rice plants.

Science.gov (United States)

Choi, Geun-Hee; Lee, Hyoung Yool; Back, Kyoungwhan

2017-08-01

Recent analyses of the enzymatic features of various melatonin biosynthetic genes from bacteria, animals, and plants have led to the hypothesis that melatonin could be synthesized via the 5-methoxytryptamine (5-MT) pathway. 5-MT is known to be synthesized in vitro from serotonin by the enzymatic action of O-methyltransferases, including N-acetylserotonin methyltransferase (ASMT) and caffeic acid O-methyltransferase (COMT), leading to melatonin synthesis by the subsequent enzymatic reaction with serotonin N-acetyltransferase (SNAT). Here, we show that 5-MT was produced and served as a precursor for melatonin synthesis in plants. When rice seedlings were challenged with senescence treatment, 5-MT levels and melatonin production were increased in transgenic rice seedlings overexpressing the rice COMT in chloroplasts, while no such increases were observed in wild-type or transgenic seedlings overexpressing the rice COMT in the cytosol, suggesting a 5-MT transport limitation from the cytosol to chloroplasts. In contrast, cadmium treatment led to results different from those in senescence. The enhanced melatonin production was not observed in the chloroplast COMT lines relative over the cytosol COMT lines although 5-MT levels were equally induced in all genotypes upon cadmium treatment. The transgenic seedlings with enhanced melatonin in their chloroplasts exhibited improved seedling growth vs the wild type under continuous light conditions. This is the first report describing enhanced melatonin production in chloroplasts via the 5-MT pathway with the ectopic overexpression of COMT in chloroplasts in plants. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Responses of sri lankan traditional rice to photoperiod at early vegetative stage

International Nuclear Information System (INIS)

Rathnathunga, U.U.E.; Geekiyanage, S.

2017-01-01

Rice is a photoperiod sensitive plant for flowering initiation. Effect of photoperiod can be important in vegetative growth and yield determination in rice. The objective of the research was to determine the effect of photoperiod on the vegetative responses of Sri Lankan traditional rice germplasm (SLTRG). Forty five traditional rice accessions (TRA), 5 improved rice varieties (IR), Sri Lankan wild rice (Oryza nivara and Oryza rufipogan) and Oryza japonica accessions 6782 and 6752 were grown in short day (SD), day neutral (DN) and long day (LD) conditions. Days to reach the fifth leaf stage (DFL), plant height (PH) and tiller number (TN) at the fifth leaf stage were recorded. Twenty three genotypes including 21 TRA, Oryza japonica 6752 and Oryza nivara did not respond to photoperiod having non-significant values for DFL, PH and TN among photoperiods. The DFL was affected in 25 genotypes; among them both DFL and PH were affected in 7 genotypes. DFL was significantly increased during LD in 4 TRA while DFL was significantly reduced in all 5 IR and 5 TRA. DFL was significantly increased in Oryza japonica 6782 and 5 TRA under SD. In 4 TRA, DFL was reduced under SD. The TN was affected in Oryza japonica 6782 only under SD with increased DFL. The DFL was significantly increased under DN in Oryza rufipogan, 5 TRA and 2 IR. Both SD and LD photoperiods differently affected the interaction between DFL and PH in TRA while only LD affected that of IR. DN had an effect on the interaction between DFL and PH only in wild rice Oryza rufipogon. Variation of vegetative growth response to photoperiod may depict the wide genetic basis of SLTRG. (author)

Adaptive management for improving species conservation across the captive-wild spectrum

Science.gov (United States)

Canessa, Stefano; Guillera-Arroita, Gurutzeta; Lahoz-Monfort, José J.; Southwell, Darren M; Armstrong, Doug P.; Chadès, Iadine; Lacy, Robert C; Converse, Sarah J.

2016-01-01

Conservation of endangered species increasingly envisages complex strategies that integrate captive and wild management actions. Management decisions in this context must be made in the face of uncertainty, often with limited capacity to collect information. Adaptive management (AM) combines management and monitoring, with the aim of updating knowledge and improving decision-making over time. We provide a guide for managers who may realize the potential of AM, but are unsure where to start. The urgent need for iterative management decisions, the existence of uncertainty, and the opportunity for learning offered by often highly-controlled captive environments create favorable conditions for AM. However, experiments and monitoring may be complicated by small sample sizes, and the ability to control the system, including stochasticity and observability, may be limited toward the wild end of the spectrum. We illustrate the key steps to implementing AM in threatened species management using four case studies, including the management of captive programs for cheetah (Acinonyx jubatus) and whooping cranes (Grus americana), of a translocation protocol for Arizona cliffroses Purshia subintegra and of ongoing supplementary feeding of reintroduced hihi (Notiomystis cincta) populations. For each case study, we explain (1) how to clarify whether the decision can be improved by learning (i.e. it is iterative and complicated by uncertainty) and what the management objectives are; (2) how to articulate uncertainty via alternative, testable hypotheses such as competing models or parameter distributions; (3) how to formally define how additional information can be collected and incorporated in future management decisions.

Use of the p-SINE1-r2 in inferring evolutionary relationships of Thai rice varieties with AA genome

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Preecha Prathepha

2006-01-01

Full Text Available In a previous study we described the prevalence and distribution in Thailand of the retroposon p- SINE1-r2, in the intron 10 of the waxy gene in cultivated and wild rice with the AA genome. In this study, additional varieties of rice were collected and sequencing was used to further characterize p-SINE1-r2. It was found that the length of the p-SINE1-r2 nucleotide sequences was about 125 bp, flanked by identical direct repeats of a 14 bp sequence. These sequences were compared and found to be similar to the sequences of p- SINE1-r2 found in Nipponbare, a rice strain discussed in a separate study. However, when compared the 48 DNA sequences identified in this study, much dissimilarity was found within the nucleotide sequences of p- SINE1-r2, in the form of base substitution mutations. Phylogenetic relationships inferred from the nucleotide sequences of these elements in cultivated rice (O. sativa and wild rice (O. nivara. It was found that rice accessions collected from the same geographical distribution have been placed in the same clade. The phylogenetic tree supports the origin and distribution of these rice strains.

Seed dormancy alleviation of grewia tenax (forssk.): a wild fruit tree species of pakistan

International Nuclear Information System (INIS)

Sohail, M.; Saied, A.S.

2015-01-01

Grewia tenax (Forssk.) Fiori is a fruit shrub and grows wild in arid and semi-arid tropics of Asia and Africa. The species is highly valuable for the rural populations because of its edible fruit and fodder for livestock. Species has immense potential for re-vegetation of degraded lands, as it has ability to withstand soil salinity and drought. Wild stands of the species are sparse which is supposed to have some kind of seed dormancy. Seeds of G. tenax were subjected to different combinations of heat and cold seed stratification treatments in two consecutive experiments. A positive correlation (r2 = 0.97) was observed between total emergence and weeks of seed exposure to constant dry heat at 40 degree C from 0 to 4 weeks. Maximum germination (70%) was achieved, when seeds were exposed to dry heat at 40 degree C for 4 weeks as compared to control (20%). Seeds exposed to constant heat for 4 weeks also took only 4 and 5 days to reach 1st and 50% emergence, respectively as compared to untreated seeds, which took 10 and 14 days to reach 1st and 50% emergence, respectively. Moreover, emergence spread lasted only 4 days as compared to untreated seeds with 21 days. Our results indicate that seeds of G. tenax possess a limited physiological dormancy which can be overcome by heat stratification. (author)

Wild species of interest for tourism in Manabí and Guayas, Ecuador

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Sonia Rosete Blandariz

2018-01-01

Full Text Available Ethnobotany is the discipline that studies the relationships between man and plants. The purpose of the study was to identify the uses of wild species of interest for tourism in Manabí and Guayas. Interviews, walks and field observations were carried out in areas with little disturbed vegetation. Seventeen species were reported with at least one recognized use, some used for the manufacture of artisanal, ornamental objects, and the majority in danger of extinction due to the degradation of their habitat. The species of greatest interest for tourism due to their beauty and degree of scarcity are Attalea colenda (O.F.Cook Balslev & A.J.Hend. (Arecaceae, Brassia jipijapensis Dodson & N.H.Williams (Orchidaceae, Ceiba trischistandra (A. Gray Bakhuisen (Malvaceae, Erythrina megistophylla Diels (Fabaceae, Erythrina smithiana Krukoff Fabaceae, Macroclinium manabinum (Dodson Dodson (Orchidaceae, Passiflora sprucei Mast. (Passifloraceae, Phytelephas aequatorialis Spruce (Arecaceae and Prestoea acuminata (Willd. H.E.Moore var. acuminata (Arecaceae.

Wild felid species richness affected by a corridor in the Lacandona forest, Mexico

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Gil–Fernández, M.

2017-02-01

Full Text Available Wild felids are one of the most vulnerable species due to habitat loss caused by fragmentation of ecosystems. We analyzed the effect of a structural corridor, defined as a strip of vegetation connecting two habitat patches, on the richness and habitat occupancy of felids on three sites in Marqués de Comillas, Chiapas, one with two isolated forest patches, the second with a structural corridor, and the third inside the Montes Azules Biosphere Reserve. We found only two species (L. pardalis and H. yagouaroundi in the isolated forest patches, five species in the structural corridor, and four species inside the Reserve. The corridor did not significantly affect occupancy, but due to the low detection rates, further investigation is needed to rule out differences. Our results highlight the need to manage habitat connectivity in the remaining forests in order to preserve the felid community of Marqués de Comillas, Chiapas, México.

THE BIOMINERAL CONCENTRATIONS AND ACCUMULATION IN SOME WILD GROWING EDIBLE SPECIES OF MUSHROOMS

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Carmen Cristina Elekes

2010-01-01

Full Text Available Many mushrooms species are known to accumulate metals to a higher level than the plants and are considered as a source of proteins, vitamins – riboflavin, biotin and thiamine, fats, carbohydrates, amino acids and minerals. The trace metals concentrations were established by Inductively Coupled Plasma - Atomic Emission Spectrometry method. The aim of this paper is to determinate the minerals content of some wild growing mushrooms, which may be useful in the phytopharmaceutical biotechnologies in order to obtain important quantities of biominerals accessible for the human body. The results are varying with the analyzed species of mushrooms between 11869.85 and 32088.68 mg/kg for potassium, 240.81 to 716.98 mg/kg for calcium and between 0 to 5350 mg/kg for phosphorus. The highest concentration if potassium was founded in B. griseus species, 32088.68 mg/kg. Only two species, Hygrophorus virgineus and Marasmius oreades show a phosphorus concentration in the fruiting body higher than in soil, indicating the accumulation capacity.

Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication1[C][W][OA

Science.gov (United States)

Zhu, Bo-Feng; Si, Lizhen; Wang, Zixuan; Jingjie Zhu, Yan Zhou; Shangguan, Yingying; Lu, Danfeng; Fan, Danlin; Li, Canyang; Lin, Hongxuan; Qian, Qian; Sang, Tao; Zhou, Bo; Minobe, Yuzo; Han, Bin

2011-01-01

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. PMID:21263038

Amino Acid Levels in Muscle Tissue of Six Wild Feathered Species

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Eva Straková

2016-01-01

Full Text Available The objective of this study was to determine and compare the levels of amino acids (AAs in breast and thigh muscles of six species of feathered game of the same age. The experiment involved the following species: wild turkey (Meleagris gallopavo, guinea fowl (Numida meleagris, chukar partridge (Alectoris chucar, Japanese quail (Coturnix coturnix japonica, common pheasant (Phasianus colchicus and grey partridge (Perdix perdix. The highest content of AAs was found in the chukar partridge (breast: 815.7 ± 47.71 g/kg; thigh: 771.4 ± 107.0 g/kg, on a dry matter basis, the lowest levels of AAs were found in Japanese quail (breast: 734.2 ± 45.07 g/kg and grey partridge (thigh: 614.9 ± 49.66 g/kg. In all examined species, the level of histidine in breast muscles differed (P ≤ 0.01 from that in thigh muscles. In all investigated species, the levels of essential AAs in breast muscles were higher (P ≤ 0.01 than those in thigh muscles, whereas the levels of non-essential AAs in breast muscles were lower (P ≤ 0.01 than those in thigh muscles. Breast muscles are therefore more valuable than thigh muscles because of the content of essential AAs.

Photosynthetic /sup 14/CO/sub 2/ fixation in the leaves of rice and some other species

Energy Technology Data Exchange (ETDEWEB)

Ishii, R; Samejima, M; Murata, Y [Tokyo Univ. (Japan). Faculty of Agriculture

1977-03-01

The activity of CO/sub 2/-fixing enzymes and the initial products of photosynthetic /sup 14/CO/sub 2/ fixation in two rice varieties, the one japonica and the other indica, were examined, comparing with those in several C/sub 3/ and C/sub 4/ crop species. Corn and barnyard grass as C/sub 4/ plants and barley and wheat as C/sub 3/ plants were used as comparison materials. The plants were cultured at 25 deg. C in daytime and 20 deg. C in night under natural light in a phytotron. After about a month from sowing, the fully expanded leaf blades were subjected to the experiments. The fresh leaf blades of one gram were homogenized in 5 ml of 50 mM Tris-H/sub 2/SO/sub 4/ buffer (pH 7.7) containing 4 mM EDTA, 10 mM dithiothreitol and 50 mg of polyamide powder. After filtration, the supernatant was used as the crude enzyme extract for assaying the activity of RuDP carboxylase and PEP carboxylase. The experiments revealed that (1) in C/sub 3/ plants, the RuDP carboxylase activity was higher, and the PEP carboxylase activity was lower than those in C/sub 4/ plants; (2) the initial products of photosynthetic /sup 14/CO/sub 2/ fixation in the japonica rice variety were mainly PGA and other sugar phosphates as in barley, whereas in corn, they were malic and aspartic acids; (3) the /sup 14/C incorporation into glycine and serine was high in the japonica rice and barley, whereas low in corn. From these results, rice could be regarded as C/sub 3/ plant.

Bt rice in China - focusing the nontarget risk assessment.

Science.gov (United States)

Li, Yunhe; Zhang, Qingling; Liu, Qingsong; Meissle, Michael; Yang, Yan; Wang, Yanan; Hua, Hongxia; Chen, Xiuping; Peng, Yufa; Romeis, Jörg

2017-10-01

Bt rice can control yield losses caused by lepidopteran pests but may also harm nontarget species and reduce important ecosystem services. A comprehensive data set on herbivores, natural enemies, and their interactions in Chinese rice fields was compiled. This together with an analysis of the Cry protein content in arthropods collected from Bt rice in China indicated which nontarget species are most exposed to the insecticidal protein and should be the focus of regulatory risk assessment. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Full establishment of arbuscular mycorrhizal symbiosis in rice occurs independently of enzymatic jasmonate biosynthesis.

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Caroline Gutjahr

Full Text Available Development of the mutualistic arbuscular mycorrhiza (AM symbiosis between most land plants and fungi of the Glomeromycota is regulated by phytohormones. The role of jasmonate (JA in AM colonization has been investigated in the dicotyledons Medicago truncatula, tomato and Nicotiana attenuata and contradicting results have been obtained with respect to a neutral, promotive or inhibitory effect of JA on AM colonization. Furthermore, it is currently unknown whether JA plays a role in AM colonization of monocotyledonous roots. Therefore we examined whether JA biosynthesis is required for AM colonization of the monocot rice. To this end we employed the rice mutant constitutive photomorphogenesis 2 (cpm2, which is deficient in JA biosynthesis. Through a time course experiment the amount and morphology of fungal colonization did not differ between wild-type and cpm2 roots. Furthermore, no significant difference in the expression of AM marker genes was detected between wild type and cpm2. However, treatment of wild-type roots with 50 μM JA lead to a decrease of AM colonization and this was correlated with induction of the defense gene PR4. These results indicate that JA is not required for AM colonization of rice but high levels of JA in the roots suppress AM development likely through the induction of defense.

Exome-wide DNA capture and next generation sequencing in domestic and wild species

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Ng Sarah B

2011-07-01

Full Text Available Abstract Background Gene-targeted and genome-wide markers are crucial to advance evolutionary biology, agriculture, and biodiversity conservation by improving our understanding of genetic processes underlying adaptation and speciation. Unfortunately, for eukaryotic species with large genomes it remains costly to obtain genome sequences and to develop genome resources such as genome-wide SNPs. A method is needed to allow gene-targeted, next-generation sequencing that is flexible enough to include any gene or number of genes, unlike transcriptome sequencing. Such a method would allow sequencing of many individuals, avoiding ascertainment bias in subsequent population genetic analyses. We demonstrate the usefulness of a recent technology, exon capture, for genome-wide, gene-targeted marker discovery in species with no genome resources. We use coding gene sequences from the domestic cow genome sequence (Bos taurus to capture (enrich for, and subsequently sequence, thousands of exons of B. taurus, B. indicus, and Bison bison (wild bison. Our capture array has probes for 16,131 exons in 2,570 genes, including 203 candidate genes with known function and of interest for their association with disease and other fitness traits. Results We successfully sequenced and mapped exon sequences from across the 29 autosomes and X chromosome in the B. taurus genome sequence. Exon capture and high-throughput sequencing identified thousands of putative SNPs spread evenly across all reference chromosomes, in all three individuals, including hundreds of SNPs in our targeted candidate genes. Conclusions This study shows exon capture can be customized for SNP discovery in many individuals and for non-model species without genomic resources. Our captured exome subset was small enough for affordable next-generation sequencing, and successfully captured exons from a divergent wild species using the domestic cow genome as reference.

Exome-wide DNA capture and next generation sequencing in domestic and wild species.

Science.gov (United States)

Cosart, Ted; Beja-Pereira, Albano; Chen, Shanyuan; Ng, Sarah B; Shendure, Jay; Luikart, Gordon

2011-07-05

Gene-targeted and genome-wide markers are crucial to advance evolutionary biology, agriculture, and biodiversity conservation by improving our understanding of genetic processes underlying adaptation and speciation. Unfortunately, for eukaryotic species with large genomes it remains costly to obtain genome sequences and to develop genome resources such as genome-wide SNPs. A method is needed to allow gene-targeted, next-generation sequencing that is flexible enough to include any gene or number of genes, unlike transcriptome sequencing. Such a method would allow sequencing of many individuals, avoiding ascertainment bias in subsequent population genetic analyses.We demonstrate the usefulness of a recent technology, exon capture, for genome-wide, gene-targeted marker discovery in species with no genome resources. We use coding gene sequences from the domestic cow genome sequence (Bos taurus) to capture (enrich for), and subsequently sequence, thousands of exons of B. taurus, B. indicus, and Bison bison (wild bison). Our capture array has probes for 16,131 exons in 2,570 genes, including 203 candidate genes with known function and of interest for their association with disease and other fitness traits. We successfully sequenced and mapped exon sequences from across the 29 autosomes and X chromosome in the B. taurus genome sequence. Exon capture and high-throughput sequencing identified thousands of putative SNPs spread evenly across all reference chromosomes, in all three individuals, including hundreds of SNPs in our targeted candidate genes. This study shows exon capture can be customized for SNP discovery in many individuals and for non-model species without genomic resources. Our captured exome subset was small enough for affordable next-generation sequencing, and successfully captured exons from a divergent wild species using the domestic cow genome as reference.

Weed populations and their buried seeds in rice fields of the MUDA area

International Nuclear Information System (INIS)

Ismail Sahid; Noor Faezah Zainuddin; Ho Nai Kin

2002-01-01

A total of 25 weed species belonging to 15 families were found in rice fields near Kampung Tandop, in the Muda Irrigation Scheme, Kedah, Malaysia. The dominant weeds in dry-seeded rice were Utricularia aurea Lour., Fimbristylis miliacea (L.) vahl., Echinochloa crusgalli (L.) Beauv., Monochoria vaginalis (Burm. Q Presl. and Najas graminea (Del.) Redl. In wet-seeded rice, the dominant species were N. graminea, Lemna minor L., Sphenoclea zeylanica Gaertn., U. aured, and Sagittaria guayanensis H. B. K., while in volunteer seedling rice fields, the dominant species were Echinochloa colonum (L.) Link., Fimbristylis alboviridis C. B. Clarke, E miliacea, Cyperus babakan Steud. and Fuirena umbellata Rottb. Dry-seeded rice fields contained the highest number of weed seeds (930 910/m 2 in the top 15 cm of soil); volunteer seedling rice fields contained 793.162/m 2 and wet-seeded rice fields 712 228/m 2 . In general, the seed numbers declined with increasing soil depth. At 1015 cm depth, seeds of U aurea and S. zeylanica were the most abundant in dry and wet-seeded rice fields, whilst seeds of Scirpusjuncoides Roxb. and E miliacea were most abundant in volunteer seedling fields. (Author)

The potential of wild vegetation species of Eleusine indica L., and Sonchus arvensis L. for phytoremediation of Cd-contaminated soil

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Amir Hamzah

2017-04-01

Full Text Available Phytoremediation has been intensively studied due its costs effectiveness and environmentally sound. Studies of heavy metal pollution phytoremediation has been done in develop countries, but still limited in Indonesia. This study aims to explore the potential of wild plant species Eleusine indica L. and Sonchus arvensis L. as an agent of phytoremediation on Cd-contaminated soil. This study was done descriptively in Pujon, Malang, Indonesia, to test the ability of two species of wild plants E. indica and S. arvensis in absorbing Cd. Along this research, plant growth and the concentration of Cd in roots, stems and leaves, was monitored. Plant growth was measured every week for three months. The plant roots, stems, and leaves collected separately, then analyzed its Cd levels. The results showed that both of two species of wild plants grew well on soil contaminated Cd. Plant roots can accumulate higher Cd than the stem part. In addition, E indica has the ability to accumulate Cd higher than S. arvensis, i.e. 57.11% and 35.84%, respectively

Selection of gamma-ray induced salt tolerant rice mutants by in vitro mutagenesis

International Nuclear Information System (INIS)

Kim, Dong Sub; Chun, Jae Beom; Lee, Kyung Jun; Kim, Jin Baek; Kim, Sang Hoon; Yun, Song Jong; Kang, Si Yong

2010-01-01

The present study had been performed to select the salt tolerant rice mutant lines through an in vivo and in vitro mutagenesis with a gamma-ray. The physiological responses such as MDA and chlorophyll of the selected salt mutant lines were investigated under salt stress. For the selection of the salt tolerant rice mutants by in vitro mutagenesis with gamma-ray, we conducted a second selection procedure with 1,500 mutant lines induced from the original cv. Dongan (wild-type, WT): Ist, selection under a nutrient solution with 171 mM NaCI: 2nd, selection under in vitro conditions. Based on a growth comparison of the entries, out of mutant lines, the putative 2 salt tolerant rice mutant lines, ST-495 and ST-532, were selected. The 2 ST-lines had a lower malonaldehyde (MDA) contents than wild-type (WT) during salt stress. The survival rate of the WT, ST-495 and ST-532 were 36.6%, 70% and 50% in 171 mM NaCI, respectively. The chlorophyll and carotenoid contents were decreased more in a WT plant than the two selected mutant lines. These rice mutant lines will be released for cultivation at the reclaimed land and used as a control plot for genetic research about salt tolerance

Selection of gamma-ray induced salt tolerant rice mutants by in vitro mutagenesis

Energy Technology Data Exchange (ETDEWEB)

Kim, Dong Sub; Chun, Jae Beom; Lee, Kyung Jun; Kim, Jin Baek; Kim, Sang Hoon; Yun, Song Jong; Kang, Si Yong [Korea Atomic Energy Research Institute, Jeongeup (Korea, Republic of)

2010-06-15

The present study had been performed to select the salt tolerant rice mutant lines through an in vivo and in vitro mutagenesis with a gamma-ray. The physiological responses such as MDA and chlorophyll of the selected salt mutant lines were investigated under salt stress. For the selection of the salt tolerant rice mutants by in vitro mutagenesis with gamma-ray, we conducted a second selection procedure with 1,500 mutant lines induced from the original cv. Dongan (wild-type, WT): Ist, selection under a nutrient solution with 171 mM NaCI: 2nd, selection under in vitro conditions. Based on a growth comparison of the entries, out of mutant lines, the putative 2 salt tolerant rice mutant lines, ST-495 and ST-532, were selected. The 2 ST-lines had a lower malonaldehyde (MDA) contents than wild-type (WT) during salt stress. The survival rate of the WT, ST-495 and ST-532 were 36.6%, 70% and 50% in 171 mM NaCI, respectively. The chlorophyll and carotenoid contents were decreased more in a WT plant than the two selected mutant lines. These rice mutant lines will be released for cultivation at the reclaimed land and used as a control plot for genetic research about salt tolerance.

Toxicity of essential oils from leaves of Piperaceae species in rice stalk stink bug eggs, Tibraca limbativentris (Hemiptera: Pentatomidae

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Diones Krinski

Full Text Available ABSTRACT Tibraca limbativentris to is an important rice pest and occurs in all rice-growing regions of Latin America. The control this insect is accomplished with synthetic chemical insecticides, however, new approaches are needed to reduce risks to the environment, to the natural enemies and also to avoid the onset of insecticides resistance. This study was designed to assess the toxicity of essential oils (EOs from leaves of Piper aduncum, P. gaudichaudianum, P. malacophyllum, P. marginatum and P. tuberculatum (Piperaceae on rice stalk stink bug eggs, T. limbativentris. Essential oils were extracted with steam distillation and dilutions were made for bioassays at concentrations of 0.25; 0.5; 1.0; 2.0 and 4.0%. Essential oils from all species of Piperaceae displayed ovicidal activity. The LC50 values indicated that both younger and older eggs were susceptible to these oils. Ovicidal activity is related to the potential toxicity of several compounds, especially dilapiolle, myristicin, cubebene, α-guaiene, longifolene, prezizane, spathulenol, sabinene and δ-2-carene. Thus, EOs tested showed promising results for use as biorational botanical insecticides.

The deposition of radioiodine onto rice plant from atmosphere

International Nuclear Information System (INIS)

Uchida, Shigeo; Muramatsu, Yasuyuki; Yoshida, Satoshi; Sumiya, Misako; Ohmomo, Yoichiro.

1994-01-01

Radiation dose estimations are usually made with the aid of assessment models in which model parameters such as the transfer factors of radionuclides from one environmental compartment to another are involved. In simple models the parameters are often described as the concentration ratio of a radionuclide between two compartments, when the system is under equilibrium condition. In this paper, the authors introduce the values of the parameters of radioiodine obtained by tracer experiments. Laboratory experiments on the transfer parameters of radionuclides from the atmosphere to rice plant were carried out in the atmosphere-to-crops system (deposition pathway). It is known that the typical chemical species of gaseous iodine in the atmosphere are elemental iodine (I 2 ) and methyliodide (CH 3 I). The deposition characteristics of both chemical species of gaseous iodine to rice grains were obtained. Mass normalized deposition velocity (V D ) and grain number normalized deposition velocity (V S ) of gaseous elemental iodine (I 2 ) and also methyliodide (CH 3 I) on unhulled rice were measured. Both V D and V S of methyliodide were about one percent of those of elemental iodine. Distribution pattern of methyliodide between unhulled rice and brown rice was significantly lower than that of elemental one. For wet deposition, we investigated the retention of radioiodines (iodide [I - ] and iodate [IO 3 - ] on rice grains and their translocation from the surface of the grains to brown rice. Though the ears were dipped into the solution containing 125 I - or 125 IO 3 - more than 15 min., both iodine species in the solutions were hardly taken up to the rice grains. The transfer rates of iodide and iodate, which are defined as 'the amount of the iodine in brown rice' divided by 'the amount of iodide in unhulled rice' were about 0.015 and 0.04, respectively. The rates were not changed with time after the radioiodine application. (author)

Structural and Functional Diversity of Weed Species in Organic and Conventional Rice Agro-Ecosystems

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S. Y. Mousawi Toghani

2016-02-01

Full Text Available Introduction Diversity reflects the complexity of a system and can maintain its sustainability. Higherdiversity, results in higher inherent complexity of agro-ecosystems and strengthen their processes. It is necessary to realize the spatial distribution and temporal properties of the biodiversity components in agro-ecosystems, for the conservation and optimal utilization. Since weeds as a complementary component of agro-ecosystems and are inseparable, so the study of species, their functional and structural diversity of them can play an important role in weed management and balance in ecological systems. Materials and Methods This study was performed to determine the effects of different management systems on structural, and functional diversity of paddy weeds in Mazandaran province. Three rice fields, ranged from 0.3 to 0.5 ha, were chosen for each management system. Samples were collected from three fields running under each selected management system (organic and conventional. Data (number of weed species and their density were randomly gathered from 9 quadrates (1m×1m per each field in four stages (tillering, stem elongation, grain filling and after harvest. The diversity, evenness, frequency and similarity indices for weeds were determined at genera and species level. Data analysis carried out through T-test and grouping performed via cluster analysis as hierarchy. Results and Discussion All monitored weeds can be classified into four plant family including cereals (Poaceae, sedges (Cyperaceae, plantain (Plantaginaceae and chicory (Asteraceae.Under conventional systems the values of weed diversity indices were higher during tillering and stem elongation compared with organic ones, and were lower during grain filling and after harvest stages. However indices of weed evenness showed contrary tendency. Both Sympson and Shanon-Wiener diversity indices, consist of two clusters in 76% similarity. Evenness indices of Kamargo and Smith

Molecular detection and characterization of potentially new Babesia and Theileria species/variants in wild felids from Kenya.

Science.gov (United States)

Githaka, Naftaly; Konnai, Satoru; Kariuki, Edward; Kanduma, Esther; Murata, Shiro; Ohashi, Kazuhiko

2012-10-01

Piroplasms frequently infect domestic and wild carnivores. At present, there is limited information on the occurrence and molecular identity of these tick-borne parasites in wild felids in Kenya. In 2009, a pair of captive lions (Panthare leo) was diagnosed with suspected babesiosis and mineral deficiency at an animal orphanage on the outskirts of Nairobi, Kenya. Blood smears indicated presences of haemoparasites in the erythrocytes, however, no further investigations were conducted to identify the infecting agent. The animals recovered completely following diet supplementation and treatment with anti-parasite drug. In this report, we extracted and detected parasite DNA from the two lions and seven other asymptomatic feline samples; two leopards (Panthera pardus) and five cheetahs (Acinonyx jubatus). Reverse line blot with probes specific for Babesia spp. of felines indicated the presence of new Babesia species or genotypes in the lions and leopards, and unknown Theileria sp. in the cheetahs. Phylogenetic analyses using partial sequences of 18S ribosomal RNA (18S rRNA) gene showed that the parasite infecting the lions belong to the Babesia canis complex, and the parasite variant detected in the leopards clusters in a clade bearing other Babesia spp. reported in wild felids from Africa. The cheetah isolates falls in the Theileria sensu stricto group. Our findings indicate the occurrence of potentially new species or genotypes of piroplams in all three feline species. Copyright © 2012 Elsevier B.V. All rights reserved.

Genome-wide identification of conserved microRNA and their response to drought stress in Dongxiang wild rice (Oryza rufipogon Griff.).

Science.gov (United States)

Zhang, Fantao; Luo, Xiangdong; Zhou, Yi; Xie, Jiankun

2016-04-01

To identify drought stress-responsive conserved microRNA (miRNA) from Dongxiang wild rice (Oryza rufipogon Griff., DXWR) on a genome-wide scale, high-throughput sequencing technology was used to sequence libraries of DXWR samples, treated with and without drought stress. 505 conserved miRNAs corresponding to 215 families were identified. 17 were significantly down-regulated and 16 were up-regulated under drought stress. Stem-loop qRT-PCR revealed the same expression patterns as high-throughput sequencing, suggesting the accuracy of the sequencing result was high. Potential target genes of the drought-responsive miRNA were predicted to be involved in diverse biological processes. Furthermore, 16 miRNA families were first identified to be involved in drought stress response from plants. These results present a comprehensive view of the conserved miRNA and their expression patterns under drought stress for DXWR, which will provide valuable information and sequence resources for future basis studies.

Arsenic accumulation in rice: Consequences of rice genotypes and management practices to reduce human health risk.

Science.gov (United States)

Islam, Shofiqul; Rahman, Mohammad Mahmudur; Islam, M R; Naidu, Ravi

2016-11-01

Rice is an essential staple food and feeds over half of the world's population. Consumption of rice has increased from limited intake in Western countries some 50years ago to major dietary intake now. Rice consumption represents a major route for inorganic arsenic (As) exposure in many countries, especially for people with a large proportion of rice in their daily diet as much as 60%. Rice plants are more efficient in assimilating As into its grains than other cereal crops and the accumulation may also adversely affect the quality of rice and their nutrition. Rice is generally grown as a lowland crop in flooded soils under reducing conditions. Under these conditions the bioavailability of As is greatly enhanced leading to excessive As bioaccumulation compared to that under oxidizing upland conditions. Inorganic As species are carcinogenic to humans and even at low levels in the diet pose a considerable risk to humans. There is a substantial genetic variation among the rice genotypes in grain-As accumulation as well as speciation. Identifying the extent of genetic variation in grain-As concentration and speciation of As compounds are crucial to determining the rice varieties which accumulate low inorganic As. Varietal selection, irrigation water management, use of fertilizer and soil amendments, cooking practices etc. play a vital role in reducing As exposure from rice grains. In the meantime assessing the bioavailability of As from rice is crucial to understanding human health exposure and reducing the risk. Copyright © 2016 Elsevier Ltd. All rights reserved.

Long-term occurrence of Trichuris species in wild ruminants in the Czech Republic.

Science.gov (United States)

Nechybová, Stanislava; Vejl, Pavel; Hart, Vlastimil; Melounová, Martina; Čílová, Daniela; Vašek, Jakub; Jankovská, Ivana; Vadlejch, Jaroslav; Langrová, Iva

2018-05-02

The aim of this study was to identify Trichuris species in wild ruminants from 32 localities in the Czech Republic using morphological and molecular methods (ITS1-5.8S RNA-ITS2 region polymorphisms). Trichurids were obtained from 176 wild ruminants (roe deer, sika deer, red deer, fallow deer and mouflons) that were culled between 2009 and 2017. Trichuris discolor is the predominant trichurid of all of the above-mentioned wild ruminants, whereas Trichuris ovis was identified less frequently in roe deer, fallow deer, sika deer and mouflons. Red deer were parasitised exclusively by T. discolor. Young hosts under 1 year of age were more intensively infected by trichurids than were adults (χ 2  = 32.02, p = 0.00). Trichurid prevalence results obtained through coprological methods and those based on parasitological dissections differed significantly (χ 2  = 16.26, p = 0.00). The regression analysis indicated that the eggs per gram (EPG) threshold (20 EPG) was exceeded only if the host was parasitised by more than 7 trichurid females. Full concordance between the positive results obtained by the coprological methods and those obtained via direct dissections was achieved when the number of trichurid females per host exceeded 51.

Speciation and monitoring test for inorganic arsenic in white rice flour.

Science.gov (United States)

Narukawa, Tomohiro; Hioki, Akiharu; Chiba, Koichi

2012-02-01

A monitoring test for arsenic species in white rice flour was developed and applied to flours made from 20 samples of polished rice collected from locations all over Japan. The arsenic species in white rice flour made from five samples each of four types of rice were analyzed by HPLC-ICP-MS after a heat-assisted aqueous extraction. The total arsenic and major and minor element concentrations in the white rice flours were measured by ICP-MS and ICP-OES after microwave-assisted digestion. 91 ± 1% of the arsenic in the flours was extractable. Concentrations of arsenite [As(III)], arsenate [As(V)], and dimethylarsinic acid (DMAA) were closely positively correlated with the total arsenic concentrations. The total arsenic concentration in flours made from rice collected around Japan was 0.15 ± 0.07 mg kg(-1) (highest, 0.32 mg kg(-1)), which is very low. It was thus confirmed that the white rice flour samples collected in this experiment were not suffered from noticeable As contamination.

Black-bellied whistling duck (Dendrocygna autumnalis) brain cholinesterase characterization and diagnosis of anticholinesterase pesticide exposure in wild populations from Mexico.

Science.gov (United States)

Osten, Jaime Rendón-von; Soares, Amadeu M V M; Guilhermino, Lucia

2005-02-01

Rice is the main crop in the subbasin of the fluvial lagoon system of Palizada River (FLSPR) in the state of Campeche, Mexico. The pesticides used to control pests of this crop mainly are carbofuran, chlorpyrifos, and glyphosate. Black-bellied whistling duck (Dendrocygna autumnalis) is an ecologically and economically important species in the area. This duck is consumed by local inhabitants throughout the year, despite its potential exposure to pesticides. Due to its feeding habits, abundance, and nutritional value, D. autumnalis is a good indicator of environmental contamination and a potential route of human exposure to organophosphate and carbamate pesticides. In this study, the brain cholinesterase (ChE) in the frontal cerebral cortex of autochthonous ducks was characterized. In addition, the potential of the three locally used pesticides and mixtures to inhibit ChE activity was investigated and the exposure of the wild duck population during intensive pesticide applications in rice fields was evaluated. We found that acetylcholinesterase (AChE) seems to be the predominant ChE form in the biological fraction analyzed. Carbofuran was the most potent ChE inhibitor of D. autumnalis brain ChE activity from the three pesticides analyzed. Cholinesterase inhibition after exposure to pesticide mixtures predominantly was due to carbofuran. A decrease (p 30%) was apparent in wild ducks compared to reference ducks, with recovery of ChE inhibition in wild ducks occurring months later when no pesticides were applied in the field. Dendrocygna autumnalis brain ChE is a suitable parameter for inclusion in biomonitoring programs for both environmental protection and human safety.

Analysis of Powdery Mildew Resistance in Wild Melon MLO Mutants

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Cheng Hong

2015-11-01

Full Text Available Wild species have a potential value in crop breeding. Explore MLO gene which related with powdery mildew natural resistance is very important for improving the quality of melon. Resistance to powdery mildew was examined in cultivar and wild species by leaf inoculation. The wild germplasms showed resistance to powdery mildew Race1. Cloning and sequence analysis of the CmMLO2 gene identified an 85 bp difference between the wild and cultivated species. The CmMLO2 gene was expressed in the wild germplasm after fluorescence-labeled Agrobacterium-mediated transformation. A positive transgenic plant showed successful invasion by powdery mildew Race1. These results suggested that the wild species might have failed to encode the MLO protein, thereby resulting in the MLO-negative regulation of powdery mildew, which in turn resulted in the broad-spectrum resistance of the wild species to powdery mildew.

Photosynthetic characterization of a rolled leaf mutant of rice ( Oryza ...

African Journals Online (AJOL)

A new rolling leaf rice mutant was identified which showed an apparently straighter longitudinal shape normal transverse rolling characters at all developing stages. The chlorophyll contents per fresh weight of this mutant leaves were lower than those of wild-type. The electron transfer rate (ETR) and photochemical ...

Testing projected wild bee distributions in agricultural habitats: predictive power depends on species traits and habitat type.

Science.gov (United States)

Marshall, Leon; Carvalheiro, Luísa G; Aguirre-Gutiérrez, Jesús; Bos, Merijn; de Groot, G Arjen; Kleijn, David; Potts, Simon G; Reemer, Menno; Roberts, Stuart; Scheper, Jeroen; Biesmeijer, Jacobus C

2015-10-01

Species distribution models (SDM) are increasingly used to understand the factors that regulate variation in biodiversity patterns and to help plan conservation strategies. However, these models are rarely validated with independently collected data and it is unclear whether SDM performance is maintained across distinct habitats and for species with different functional traits. Highly mobile species, such as bees, can be particularly challenging to model. Here, we use independent sets of occurrence data collected systematically in several agricultural habitats to test how the predictive performance of SDMs for wild bee species depends on species traits, habitat type, and sampling technique. We used a species distribution modeling approach parametrized for the Netherlands, with presence records from 1990 to 2010 for 193 Dutch wild bees. For each species, we built a Maxent model based on 13 climate and landscape variables. We tested the predictive performance of the SDMs with independent datasets collected from orchards and arable fields across the Netherlands from 2010 to 2013, using transect surveys or pan traps. Model predictive performance depended on species traits and habitat type. Occurrence of bee species specialized in habitat and diet was better predicted than generalist bees. Predictions of habitat suitability were also more precise for habitats that are temporally more stable (orchards) than for habitats that suffer regular alterations (arable), particularly for small, solitary bees. As a conservation tool, SDMs are best suited to modeling rarer, specialist species than more generalist and will work best in long-term stable habitats. The variability of complex, short-term habitats is difficult to capture in such models and historical land use generally has low thematic resolution. To improve SDMs' usefulness, models require explanatory variables and collection data that include detailed landscape characteristics, for example, variability of crops and

Fungi and some mycotoxins contaminating rice ( Oryza Sativa ) in ...

African Journals Online (AJOL)

The major fungal genera contaminating rice were Aspergillus, Penicillium, Fusarium, Alternaria, Mucor, Rhizopus, Trichoderma, Curvularia, elminthosporium and Cladosporium. The most prevalent fungal species on rice were .Penicillium spp., A. flavus, A. parasiticus, A. niger, Mucor spp., Rhizopus spp. and Alternaria spp.

Adapting weed management in rice to changing climates

NARCIS (Netherlands)

Rodenburg, J.; Meinke, H.B.

2011-01-01

This paper provides some of the scientific background on how projected environmental conditions could affect weeds and weed management in rice in Africa. Elevated CO2 levels may have positive effects on rice competitiveness with C4 weeds, but these are generally outnumbered by C3 species in weed

Reactive Oxygen Species Generated by NADPH Oxidases Promote Radicle Protrusion and Root Elongation during Rice Seed Germination

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Wen-Yan Li

2017-01-01

Full Text Available Seed germination is a complicated biological process that requires regulation through various enzymatic and non-enzymatic mechanisms. Although it has been recognized that reactive oxygen species (ROS regulate radicle emergence and root elongation in a non-enzymatic manner during dicot seed germination, the role of ROS in monocot seed germination remains unknown. NADPH oxidases (NOXs are the major ROS producers in plants; however, whether and how NOXs regulate rice seed germination through ROS generation remains unclear. Here, we report that diphenyleneiodinium (DPI, a specific NOX inhibitor, potently inhibited embryo and seedling growth—especially that of the radicle and of root elongation—in a dose-dependent manner. Notably, the DPI-mediated inhibition of radicle and root growth could be eliminated by transferring seedlings from DPI to water. Furthermore, ROS production/accumulation during rice seed germination was quantified via histochemistry. Superoxide radicals (O2−, hydrogen peroxide (H2O2 and hydroxyl radicals (•OH accumulated steadily in the coleorhiza, radicle and seedling root of germinating rice seeds. Expression profiles of the nine typical NOX genes were also investigated. According to quantitative PCR, OsNOX5, 7 and 9 were expressed relatively higher. When seeds were incubated in water, OsNOX5 expression progressively increased in the embryo from 12 to 48 h, whereas OsNOX7 and 9 expressions increased from 12 to 24 h and decreased thereafter. As expected, DPI inhibits the expression at predetermined time points for each of these genes. Taken together, these results suggest that ROS produced by NOXs are involved in radicle and root elongation during rice seed germination, and OsNOX5, 7 and 9 could play crucial roles in rice seed germination. These findings will facilitate further studies of the roles of ROS generated by NOXs during seed germination and seedling establishment and also provide valuable information for the

Dietary cladode powder from wild type and domesticated Opuntia species reduces atherogenesis in apoE knock-out mice.

Science.gov (United States)

Garoby-Salom, Sandra; Guéraud, Françoise; Camaré, Caroline; de la Rosa, Ana-Paulina Barba; Rossignol, Michel; Santos Díaz, María del Socorro; Salvayre, Robert; Negre-Salvayre, Anne

2016-03-01

Dietary intake of Opuntia species may prevent the development of cardiovascular diseases. The present study was designed to characterize the biological antioxidant and anti-inflammatory properties of Opuntia species and to investigate whether Opuntia cladodes prevent the development of atherosclerosis in vivo, in apoE(-)KO mice. The effects of the two Opuntia species, the wild Opuntia streptacantha and the domesticated Opuntia ficus-indica, were tested on the generation of intra- and extracellular reactive oxygen species (ROS) production and kinetics of the LDL oxidation by murine CRL2181 endothelial cells and on the subsequent inflammatory signaling leading to the adhesion of monocytes on the activated endothelium and the formation of foam cells. Opuntia species blocked the extracellular ROS (superoxide anion) generation and LDL oxidation by CRL2181, as well as the intracellular ROS rise and signaling evoked by the oxidized LDL, including the nuclear translocation of the transcription factor NFκB, the expression of ICAM-1 and VCAM-1 adhesion molecules, and the adhesion of monocytes to CRL2181. In vivo, Opuntia significantly reduced the formation of atherosclerotic lesions and the accumulation of 4-hydroxynonenal adducts in the vascular wall of apoE-KO mice, indicating that Opuntia cladodes prevent lipid oxidation in the vascular wall. In conclusion, wild and domesticated Opuntia species exhibit antioxidant, anti-inflammatory, and antiatherogenic properties which emphasize their nutritional benefit for preventing cardiovascular diseases.

Herbicide resistance-endowing ACCase gene mutations in hexaploid wild oat (Avena fatua): insights into resistance evolution in a hexaploid species

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Yu, Q; Ahmad-Hamdani, M S; Han, H; Christoffers, M J; Powles, S B

2013-01-01

Many herbicide-resistant weed species are polyploids, but far too little about the evolution of resistance mutations in polyploids is understood. Hexaploid wild oat (Avena fatua) is a global crop weed and many populations have evolved herbicide resistance. We studied plastidic acetyl-coenzyme A carboxylase (ACCase)-inhibiting herbicide resistance in hexaploid wild oat and revealed that resistant individuals can express one, two or three different plastidic ACCase gene resistance mutations (Ile-1781-Leu, Asp-2078-Gly and Cys-2088-Arg). Using ACCase resistance mutations as molecular markers, combined with genetic, molecular and biochemical approaches, we found in individual resistant wild-oat plants that (1) up to three unlinked ACCase gene loci assort independently following Mendelian laws for disomic inheritance, (2) all three of these homoeologous ACCase genes were transcribed, with each able to carry its own mutation and (3) in a hexaploid background, each individual ACCase resistance mutation confers relatively low-level herbicide resistance, in contrast to high-level resistance conferred by the same mutations in unrelated diploid weed species of the Poaceae (grass) family. Low resistance conferred by individual ACCase resistance mutations is likely due to a dilution effect by susceptible ACCase expressed by homoeologs in hexaploid wild oat and/or differential expression of homoeologous ACCase gene copies. Thus, polyploidy in hexaploid wild oat may slow resistance evolution. Evidence of coexisting non-target-site resistance mechanisms among wild-oat populations was also revealed. In all, these results demonstrate that herbicide resistance and its evolution can be more complex in hexaploid wild oat than in unrelated diploid grass weeds. Our data provide a starting point for the daunting task of understanding resistance evolution in polyploids. PMID:23047200

Assessment of mammal reproduction for hunting sustainability through community-based sampling of species in the wild.

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Mayor, Pedro; El Bizri, Hani; Bodmer, Richard E; Bowler, Mark

2017-08-01

Wildlife subsistence hunting is a major source of protein for tropical rural populations and a prominent conservation issue. The intrinsic rate of natural increase. (r max ) of populations is a key reproductive parameter in the most used assessments of hunting sustainability. However, researchers face severe difficulties in obtaining reproductive data in the wild, so these assessments often rely on classic reproductive rates calculated mostly from studies of captive animals conducted 30 years ago. The result is a flaw in almost 50% of studies, which hampers management decision making. We conducted a 15-year study in the Amazon in which we used reproductive data from the genitalia of 950 hunted female mammals. Genitalia were collected by local hunters. We examined tissue from these samples to estimate birthrates for wild populations of the 10 most hunted mammals. We compared our estimates with classic measures and considered the utility of the use of r max in sustainability assessments. For woolly monkey (Lagothrix poeppigii) and tapir (Tapirus terrestris), wild birthrates were similar to those from captive populations, whereas birthrates for other ungulates and lowland-paca (Cuniculus paca) were significantly lower than previous estimates. Conversely, for capuchin monkeys (Sapajus macrocephalus), agoutis (Dasyprocta sp.), and coatis (Nasua nasua), our calculated reproductive rates greatly exceeded often-used values. Researchers could keep applying classic measures compatible with our estimates, but for other species previous estimates of r max may not be appropriate. We suggest that data from local studies be used to set hunting quotas. Our maximum rates of population growth in the wild correlated with body weight, which suggests that our method is consistent and reliable. Integration of this method into community-based wildlife management and the training of local hunters to record pregnancies in hunted animals could efficiently generate useful information of life

Characterization of Agronomy, Grain Physicochemical Quality, and Nutritional Property of High-Lysine 35R Transgenic Rice with Simultaneous Modification of Lysine Biosynthesis and Catabolism.

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Yang, Qingqing; Wu, Hongyu; Li, Qianfeng; Duan, Ruxu; Zhang, Changquan; Sun, Samuel Saiming; Liu, Qiaoquan

2017-05-31

Lysine is the first limiting essential amino acid in rice. We previously constructed a series of transgenic rice lines to enhance lysine biosynthesis (35S), down-regulate its catabolism (Ri), or simultaneously achieve both metabolic effects (35R). In this study, nine transgenic lines, three from each group, were selected for both field and animal feeding trials. The results showed that the transgene(s) caused no obvious effects on field performance and main agronomic traits. Mature seeds of transgenic line 35R-17 contained 48-60-fold more free lysine than in wild type and had slightly lower apparent amylose content and softer gel consistency. Moreover, a 35-day feeding experiment showed that the body weight gain, food efficiency, and protein efficiency ratio of rats fed the 35R-17 transgenic rice diet were improved when compared with those fed wild-type rice diet. These data will be useful for further evaluation and potential commercialization of 35R high-lysine transgenic rice.

Overexpression of Rat Neurons Nitric Oxide Synthase in Rice Enhances Drought and Salt Tolerance.

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Wei Cai

Full Text Available Nitric oxide (NO has been shown to play an important role in the plant response to biotic and abiotic stresses in Arabidopsis mutants with lower or higher levels of endogenous NO. The exogenous application of NO donors or scavengers has also suggested an important role for NO in plant defense against environmental stress. In this study, rice plants under drought and high salinity conditions showed increased nitric oxide synthase (NOS activity and NO levels. Overexpression of rat neuronal NO synthase (nNOS in rice increased both NOS activity and NO accumulation, resulting in improved tolerance of the transgenic plants to both drought and salt stresses. nNOS-overexpressing plants exhibited stronger water-holding capability, higher proline accumulation, less lipid peroxidation and reduced electrolyte leakage under drought and salt conditions than wild rice. Moreover, nNOS-overexpressing plants accumulated less H2O2, due to the observed up-regulation of OsCATA, OsCATB and OsPOX1. In agreement, the activities of CAT and POX were higher in transgenic rice than wild type. Additionally, the expression of six tested stress-responsive genes including OsDREB2A, OsDREB2B, OsSNAC1, OsSNAC2, OsLEA3 and OsRD29A, in nNOS-overexpressing plants was higher than that in the wild type under drought and high salinity conditions. Taken together, our results suggest that nNOS overexpression suppresses the stress-enhanced electrolyte leakage, lipid peroxidation and H2O2 accumulation, and promotes proline accumulation and the expression of stress-responsive genes under stress conditions, thereby promoting increased tolerance to drought and salt stresses.

Some wild-growing plant species from Serbia and Montenegro as the potential sources of drugs.

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Aljancić, I S; Vajs, V E; Tesević, V V; Milosavljević, S M

2008-01-01

The results of phytochemical investigation, over the last decade, of some wild-growing plant species from Serbia and Montenegro belonging to the families Asteraceae, Guttiferae and Gentianaceae are reported. Most of the investigated species are endemites and the emphasis in this report is on those exhibiting biological activities that could be regarded as the potential sources of drugs. This review comprises 154 compounds, e.g. sesquiterpene lactones and flavonoids (Asteraceae), xanthones, secoiridoids and C-glucoflavonoids (Gentanaceae) and prenylated phloroglucinols (Guttiferae) as well as some other secondary metabolites, produced by the above families, which could be of pharmacological interest.

Susceptibility of various Japanese freshwater fish species to an isolate of viral haemorrhagic septicaemia virus (VHSV) genotype IVb

DEFF Research Database (Denmark)

Ito, Takafumi; Olesen, Niels Jørgen

2013-01-01

Genotype IVb of viral haemorrhagic septicaemia virus (VHSV) was isolated for the first time in the Great Lakes basin in 2003, where it spread and caused mass mortalities in several wild fish species throughout the basin. In order to prevent further spreading of the disease and to assess risks...... mortalities in bluegill Lepomis macrochirus used as positive controls, Japanese fluvial sculpin Cottus pollux, and iwana Salvelinus leucomaenis pluvius were 50, 80 and 0%, respectively. In Expt 2, cumulative mortalities of 100, 100 and 10% were observed in Japanese fluvial sculpin C. pollux, Japanese rice......-isolation by cell culture was successful from all dead fish. We detected the virus in the brain from a few surviving bluegill 50 d post exposure by both cell culture and RT-PCR. These results revealed that VHSV IVb could become a serious threat to wild freshwater fish species in Japan, and that some surviving fish...

Use of Wild Relatives and Closely Related Species to Adapt Common Bean to Climate Change

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James D. Kelly

2013-05-01

Full Text Available Common bean (Phaseolus vulgaris L. is an important legume crop worldwide. However, abiotic and biotic stress limits bean yields to <600 kg ha−1 in low-income countries. Current low yields result in food insecurity, while demands for increased yields to match the rate of population growth combined with the threat of climate change are significant. Novel and significant advances in genetic improvement using untapped genetic diversity available in crop wild relatives and closely related species must be further explored. A meeting was organized by the Global Crop Diversity Trust to consider strategies for common bean improvement. This review resulted from that meeting and considers our current understanding of the genetic resources available for common bean improvement and the progress that has been achieved thus far through introgression of genetic diversity from wild relatives of common bean, and from closely related species, including: P. acutifolius, P. coccineus, P. costaricensis and P. dumosus. Newly developed genomic tools and their potential applications are presented. A broad outline of research for use of these genetic resources for common bean improvement in a ten-year multi-disciplinary effort is presented.

[Exposure degree of important non-target arthropods to Cry2Aa in Bt rice fields].

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Zhang, Qing-Ling; Li, Yun-He; Hua, Hong-Xia; Yang, Chang-Ju; Wu, Hong-Jin; Peng, Yu-Fa

2013-06-01

Based on the principle of "risk = hazard x exposure", the selected representative nontarget organisms in the assessment of the potential effects of insect-resistant genetically modified (GM) crops on non-target arthropods in laboratory are generally the arthropod species highly exposed to the insecticidal proteins expressed by the GM crops in farmland ecosystem. In order to understand the exposure degree of the important arthropod species to Cry proteins in Bt rice fields, and to select the appropriate non-target arthropods in the risk assessment of insect-resistant GM crops, the enzyme-linked immunosorbent assay (ELISA) was conducted to measure the Cry2Aa protein concentration in the arthropods collected from the cry2Aa rice fields at different rice growth stages. The results showed that there was a significant difference in the Cry2Aa content protein concentration in different arthropod species. Some species did not contain Cry2Aa protein, while some species contained larger amounts of Cry2Aa protein. Relative to the arthropods colleted after rice anthesis, the arthropods colleted in rice anthesis contained relative higher concentrations of Cry2Aa protein, especially for the predacious arthropods. No Cry proteins were detected in parasitic arthropods. This study provided references for the laboratory assessment of the effects of GM rice on nontarget arthropods.

Ehd4 encodes a novel and Oryza-genus-specific regulator of photoperiodic flowering in rice.

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He Gao

Full Text Available Land plants have evolved increasingly complex regulatory modes of their flowering time (or heading date in crops. Rice (Oryza sativa L. is a short-day plant that flowers more rapidly in short-day but delays under long-day conditions. Previous studies have shown that the CO-FT module initially identified in long-day plants (Arabidopsis is evolutionary conserved in short-day plants (Hd1-Hd3a in rice. However, in rice, there is a unique Ehd1-dependent flowering pathway that is Hd1-independent. Here, we report isolation and characterization of a positive regulator of Ehd1, Early heading date 4 (Ehd4. ehd4 mutants showed a never flowering phenotype under natural long-day conditions. Map-based cloning revealed that Ehd4 encodes a novel CCCH-type zinc finger protein, which is localized to the nucleus and is able to bind to nucleic acids in vitro and transactivate transcription in yeast, suggesting that it likely functions as a transcriptional regulator. Ehd4 expression is most active in young leaves with a diurnal expression pattern similar to that of Ehd1 under both short-day and long-day conditions. We show that Ehd4 up-regulates the expression of the "florigen" genes Hd3a and RFT1 through Ehd1, but it acts independently of other known Ehd1 regulators. Strikingly, Ehd4 is highly conserved in the Oryza genus including wild and cultivated rice, but has no homologs in other species, suggesting that Ehd4 is originated along with the diversification of the Oryza genus from the grass family during evolution. We conclude that Ehd4 is a novel Oryza-genus-specific regulator of Ehd1, and it plays an essential role in photoperiodic control of flowering time in rice.

Microbial-driven arsenic cycling in rice paddies amended with monosodium methanearsonate

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Maguffin, S. C.; McClung, A.; Rohila, J. S.; Derry, L. A.; Huang, R.; Reid, M. C.

2017-12-01

Rice consumption is the second largest contributor to human arsenic exposure worldwide and is linked to many serious diseases. Because rice is uniquely adapted for agricultural production under flooded soils, arsenic species solubilized in such environments can be effectively transported into plant tissue via root transporters. Through this process, both inorganic and organic (methylated) arsenic species can accumulate to problematic concentrations and may affect grain yield as well as crop value. The distribution of these species in plant tissue is determined by arsenic sources, as well as enzymatic redox and methylation-demethylation reactions in soils and pore water. Historic use of organoarsenic-based pesticides in US agriculture may provide an enduring source of arsenic in rice paddies. However, it is unclear how persistent these organic species are in the adsorbed phase or how available they remain to rice cultivars throughout the growing season. We conducted a field experiment in a 2x2 factorial design examining the effects of irrigation methods (continuous flooding and alternate wetting and drying) and monosodium methanearsonate (MSMA) application on the abundance and speciation of arsenic in pore water, soil, and rice plant tissues. We monitored arsenic speciation and partitioning between these reservoirs at semi-weekly to semi-monthly frequencies. Pore water arsenic speciation was determined using LC-ICP-MS, and X-ray absorption near-edge structure (XANES) analysis was employed to speciate the arsenic within solid-phase soil and plant tissue throughout the growing season. These data help clarify the role of two irrigation methods and MSMA amendments for arsenic bioavailability and speciation in rice. Furthermore, the study illuminates the significance of microbial metabolism in the reapportionment of arsenic within the soil-plant-water system and its impact on arsenic levels in rice grains.

Overexpression of a Pathogenesis-Related Protein 10 Enhances Biotic and Abiotic Stress Tolerance in Rice

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Jingni Wu

2016-12-01

Full Text Available Pathogenesis-related proteins play multiple roles in plant development and biotic and abiotic stress tolerance. Here, we characterize a rice defense related gene named “jasmonic acid inducible pathogenesis-related class 10” (JIOsPR10 to gain an insight into its functional properties. Semi-quantitative RT-PCR analysis showed up-regulation of JIOsPR10 under salt and drought stress conditions. Constitutive over-expression JIOsPR10 in rice promoted shoot and root development in transgenic plants, however, their productivity was unaltered. Further experiments exhibited that the transgenic plants showed reduced susceptibility to rice blast fungus, and enhanced salt and drought stress tolerance as compared to the wild type. A comparative proteomic profiling of wild type and transgenic plants showed that overexpression of JIOsPR10 led to the differential modulation of several proteins mainly related with oxidative stresses, carbohydrate metabolism, and plant defense. Taken together, our findings suggest that JIOsPR10 plays important roles in biotic and abiotic stresses tolerance probably by activation of stress related proteins.

Phylogenetic analysis and protein structure modelling identifies distinct Ca(2+)/Cation antiporters and conservation of gene family structure within Arabidopsis and rice species.

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Pittman, Jon K; Hirschi, Kendal D

2016-12-01

The Ca(2+)/Cation Antiporter (CaCA) superfamily is an ancient and widespread family of ion-coupled cation transporters found in nearly all kingdoms of life. In animals, K(+)-dependent and K(+)-indendent Na(+)/Ca(2+) exchangers (NCKX and NCX) are important CaCA members. Recently it was proposed that all rice and Arabidopsis CaCA proteins should be classified as NCX proteins. Here we performed phylogenetic analysis of CaCA genes and protein structure homology modelling to further characterise members of this transporter superfamily. Phylogenetic analysis of rice and Arabidopsis CaCAs in comparison with selected CaCA members from non-plant species demonstrated that these genes form clearly distinct families, with the H(+)/Cation exchanger (CAX) and cation/Ca(2+) exchanger (CCX) families dominant in higher plants but the NCKX and NCX families absent. NCX-related Mg(2+)/H(+) exchanger (MHX) and CAX-related Na(+)/Ca(2+) exchanger-like (NCL) proteins are instead present. Analysis of genomes of ten closely-related rice species and four Arabidopsis-related species found that CaCA gene family structures are highly conserved within related plants, apart from minor variation. Protein structures were modelled for OsCAX1a and OsMHX1. Despite exhibiting broad structural conservation, there are clear structural differences observed between the different CaCA types. Members of the CaCA superfamily form clearly distinct families with different phylogenetic, structural and functional characteristics, and therefore should not be simply classified as NCX proteins, which should remain as a separate gene family.

Molecular identification of Aspergillus and Eurotium species isolated from rice and their toxin-producing ability.