scholarly journals On the importance of negative controls in viral landscape phylogeography

2018 ◽  
Vol 4 (2) ◽  
Author(s):  
Simon Dellicour ◽  
Bram Vrancken ◽  
Nídia S Trovão ◽  
Denis Fargette ◽  
Philippe Lemey
Keyword(s):  
Environmental Factors ◽  
Sequence Data ◽  
Rice Yellow Mottle Virus ◽  
Transition Rates ◽  
False Positive Result ◽  
Virus Spread ◽  
Yellow Mottle ◽  
Dispersal Velocity ◽  
Negative Controls ◽  
The Impact

Abstract Phylogeographic reconstructions are becoming an established procedure to evaluate the factors that could impact virus spread. While a discrete phylogeographic approach can be used to test predictors of transition rates among discrete locations, alternative continuous phylogeographic reconstructions can also be exploited to investigate the impact of underlying environmental layers on the dispersal velocity of a virus. The two approaches are complementary tools for studying pathogens' spread, but in both cases, care must be taken to avoid misinterpretations. Here, we analyse rice yellow mottle virus (RYMV) sequence data from West and East Africa to illustrate how both approaches can be used to study the impact of environmental factors on the virus’ dispersal frequency and velocity. While it was previously reported that host connectivity was a major determinant of RYMV spread, we show that this was a false positive result due to the lack of appropriate negative controls. We also discuss and compare the phylodynamic tools currently available for investigating the impact of environmental factors on virus spread.

scholarly journals Distribution, Pathogenicity, and Interactions of Two Strains of Rice yellow mottle virus in Forested and Savanna Zones of West Africa

Plant Disease ◽  
2001 ◽  
Vol 85 (1) ◽  
pp. 59-64 ◽  
Author(s):  
P. N'Guessan ◽  
A. Pinel ◽  
A. A. Sy ◽  
A. Ghesquière ◽  
D. Fargette
Keyword(s):  
Cote D'ivoire ◽  
Côte D’Ivoire ◽  
Mottle Virus ◽  
Rice Yellow Mottle Virus ◽  
Yield Losses ◽  
The West ◽  
Cote D’Ivoire ◽  
Côte D'ivoire ◽  
Yellow Mottle ◽  
The Impact

In Côte d'Ivoire, the S2 strain of Rice yellow mottle virus (RYMV) predominated in the forested zones, including the “rice belt” to the west, in each of the cropping systems where rice was grown. The S1 strain occurred more frequently in the northern Guinean savanna, and only S1 isolates were found further north in the Sahelo-Soudanian zones. In mixed infection, S2 dominated over S1 both in viral capsid and RNA contents under temperature regimes encompassing those observed in savanna and forested zones of Côte d'Ivoire. There was no evidence of interactions in virus accumulation between the West African strains S1 or S2 with the more distantly related East African strain S4. Field trials emphasized the impact of RYMV, which induced yield losses of 40 to 60% in several widely grown cultivars of Oryza sativa indica and O. sativa japonica. We report the high resistance of the O. indica cv. Gigante under field conditions which was apparent with all the S1 and S2 isolates tested. Responses to RYMV infection of several cultivars were isolate dependent. With most differential cultivars, responses were not strain specific, with the exception of the O. japonica cv. Idsa6, in which the S2 isolates always induced higher yield losses than the S1 isolates.

scholarly journals Rice yellow mottle virus genus Sobemovirus: a continental problem in africa

2010 ◽  
Vol 40 (No. 1) ◽  
pp. 26-36 ◽  
Author(s):  
O.O. Banwo ◽  
M.D. Alegbejo ◽  
M.E. Abo
Keyword(s):  
Management Strategies ◽  
Central Africa ◽  
Mottle Virus ◽  
Future Research ◽  
Limiting Factor ◽  
Rice Yellow Mottle Virus ◽  
Virus Spread ◽  
Yield Losses ◽  
African Countries ◽  
Yellow Mottle

<I>Rice yellow mottle virus</I> genus <I>sobemovirus </I>(RYMV) was first reported in Kenya in 1966. The disease caused by this virus is fast becoming a major limiting factor in the rice production in Africa and neighbouring islands. It is known to occur in eastern, western and southern African countries and, since very recently, in Central Africa. It is transmitted by insect vectors such as <I>Chaectonema </I>spp., <I>Sesselia pusilla</I> Gerst. and <I>Trichispa sericea</I> Guerin (all <I>Coleoptera</I>) and also by mechanical means. About six strains of the virus now exist. Yield losses caused by the virus range from 20 to 100%. Integrated pest management has been suggested to minimise damage caused by this disease to rice. This paper reviews the characteristics of the virus, symptomatology, host range, distribution, strains, transmission, vector dynamics and virus spread, the economic importance, and management strategies. The need of future research of RYMV is also highlighted.

scholarly journals Variation among Tanzania Rice Germplasm Collections Based on Agronomic Traits and Resistance to Rice Yellow Mottle Virus

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 391
Author(s):  
William Titus Suvi ◽  
Hussein Shimelis ◽  
Mark Laing ◽  
Isack Mathew ◽  
Admire I. T. Shayanowako
Keyword(s):  
Grain Yield ◽  
Agronomic Traits ◽  
Genotypic Variation ◽  
Germplasm Collection ◽  
Mottle Virus ◽  
Rice Yellow Mottle Virus ◽  
Lattice Design ◽  
Rice Germplasm ◽  
Yellow Mottle ◽  
The Impact

Rice (Oryza species) is a commercial crop worldwide. Across Africa, the potential yield and quality of rice is diminished by a lack of high performance, locally adapted varieties, and the impact of rice yellow mottle virus (RYMV). The objective of this study was to assess the performance of a diverse collection of rice germplasm for RYMV resistance and agronomic traits, and to select promising lines for breeding for Tanzanian conditions. Fifty-four rice genotypes were field evaluated in two important rice production sites (Ifakara and Mkindo) in Tanzania, which are recognized as RYMV hotspots, using a 6 × 9 alpha lattice design with two replications. There was significant (p < 0.05) genotypic variation for agronomic traits and RYMV susceptibility in the tested germplasm. Seven genotypes with moderate to high RYMV resistance were identified, including Salama M-57, SSD1, IRAT 256, Salama M-55, Mwangaza, Lunyuki, and Salama M-19, which were identified as new sources of resistance genes. Positive and significant correlations were detected between grain yield and number of panicles per plant (NPP), panicle length (PL), number of grains per panicle (NGP), percentage-filled grains (PFG), and thousand-grain weight (TGW), which are useful traits for simultaneous selection for rice yield improvement. A principal component analysis allocated five principal components, accounting for 79.88% of the total variation present in the assessed germplasm collection. Traits that contributed most to variability included NPP, number of tillers/plant (NT), PL, grain yield (GY), and days to 50% flowering (DFL). The genotypes Rangimbili, Gigante, and SARO possess complementary agronomic traits and RYMV resistance, and can be recommended for further evaluation, genetic analysis, and breeding.

scholarly journals Expression of the Rice Yellow Mottle Virus P1 Proteinin Vitroandin Vivoand Its Involvement in Virus Spread

Virology ◽  
1998 ◽  
Vol 244 (1) ◽  
pp. 79-86 ◽  
Author(s):  
Caroline Bonneau ◽  
Christophe Brugidou ◽  
Lili Chen ◽  
Roger N. Beachy ◽  
Claude Fauquet
Keyword(s):  
Mottle Virus ◽  
Rice Yellow Mottle Virus ◽  
Virus Spread ◽  
Yellow Mottle

scholarly journals Rice Yellow Mottle Virus, an RNA Plant Virus, Evolves as Rapidly as Most RNA Animal Viruses

2008 ◽  
Vol 82 (7) ◽  
pp. 3584-3589 ◽  
Author(s):  
D. Fargette ◽  
A. Pinel ◽  
M. Rakotomalala ◽  
E. Sangu ◽  
O. Traoré ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Plant Virus ◽  
Sequence Data ◽  
Plant Viruses ◽  
Pairwise Distance ◽  
Mottle Virus ◽  
Evolution Rate ◽  
Rice Yellow Mottle Virus ◽  
Wide Range ◽  
Yellow Mottle

ABSTRACT The rate of evolution of an RNA plant virus has never been estimated using temporally spaced sequence data, by contrast to the information available on an increasing range of animal viruses. Accordingly, the evolution rate of Rice yellow mottle virus (RYMV) was calculated from sequences of the coat protein gene of isolates collected from rice over a 40-year period in different parts of Africa. The evolution rate of RYMV was estimated by pairwise distance linear regression on five phylogeographically defined groups comprising a total of 135 isolates. It was further assessed from 253 isolates collected all over Africa by Bayesian coalescent methods under strict and relaxed molecular clock models and under constant size and skyline population genetic models. Consistent estimates of the evolution rate between 4 × 10−4 and 8 × 10−4 nucleotides (nt)/site/year were obtained whatever method and model were applied. The synonymous evolution rate was between 8 × 10−4 and 11 × 10−4 nt/site/year. The overall and synonymous evolution rates of RYMV were within the range of the rates of 50 RNA animal viruses, below the average but above the distribution median. Experimentally, in host change studies, substitutions accumulated at an even higher rate. The results show that an RNA plant virus such as RYMV evolves as rapidly as most RNA animal viruses. Knowledge of the molecular clock of plant viruses provides methods for testing a wide range of biological hypotheses.

Assessing the sustainability of the Siberian Federal District regions

2020 ◽  
Vol 18 (5) ◽  
pp. 891-908
Author(s):  
T.A. Smirnova
Keyword(s):  
Sustainable Development ◽  
Environmental Factors ◽  
Regional Development ◽  
Federal District ◽  
Integrated Approach ◽  
Siberian Federal District ◽  
The Sustainable Development ◽  
The Impact ◽  
Empirical Analyses

Subject. This article deals with the issues of functioning of the region as a system. Objectives. The article aims to identify the problems of the region's functioning as a system, develop methodological tools to monitor the sustainable development of the Siberian Federal District territories, and determine the the impact of socio-economic and environmental factors on the sustainable development of the region as a whole. Methods. For the study, I used the methods of theoretical, statistical, and empirical analyses taking into account an integrated approach. Results. The article reveals the impact of some individual components of regional development on the sustainability of the territorial system as a whole. Relevance. The results of the study can be used to analyze the sustainability of regions' development.

Directions of Accounting Environmental Factors for Forecasting Formation of Agroecosystems

2020 ◽  
pp. 31-35
Author(s):  
L.Z. Khalishkhova ◽  
◽  
A. Kh. Temrokova ◽  
I.R. Guchapsheva ◽  
K.A. Bogаtyreva ◽  
...  
Keyword(s):  
Sustainable Development ◽  
Comparative Analysis ◽  
Environmental Factors ◽  
Environmental Safety ◽  
Logical Analysis ◽  
Management Decisions ◽  
The Sustainable Development ◽  
The Impact

Ensuring the sustainable development of agroecosystems requires research into the justification of the impact of environmental factors on the formation of territorial agroecosystems and identifies ways to take them into account in order to justify management decisions and ensure environmental safety. The main goal of the research within the article is to identify the most significant environmental factors in predicting the formation of agroecosystems. Provisions are devoted to the study of the laws governing the functioning of agroecosystems in order to increase their stability. The methods of comparative analysis, generalization, abstraction, logical analysis are applied. A number of provisions are formulated regarding ways to account for the influence of factors on the formation of key elements of agroecosystems.

scholarly journals PSI-40 Two mitochondrial lineages revealed in North American yak

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 477-477
Author(s):  
Leah K Treffer ◽  
Edward S Rice ◽  
Anna M Fuller ◽  
Samuel Cutler ◽  
Jessica L Petersen
Keyword(s):  
Sequence Data ◽  
Haplotype Network ◽  
Ovis Aries ◽  
Similar Species ◽  
Nucleotide Polymorphisms ◽  
Mt Dna ◽  
Protein Coding ◽  
Sister Clade ◽  
Mtdna Sequence ◽  
The Impact

Abstract Domestic yak (Bos grunniens) are bovids native to the Asian Qinghai-Tibetan Plateau. Studies of Asian yak have revealed that introgression with domestic cattle has contributed to the evolution of the species. When imported to North America (NA), some hybridization with B. taurus did occur. The objective of this study was to use mitochondrial (mt) DNA sequence data to better understand the mtDNA origin of NA yak and their relationship to Asian yak and related species. The complete mtDNA sequence of 14 individuals (12 NA yak, 1 Tibetan yak, 1 Tibetan B. indicus) was generated and compared with sequences of similar species from GeneBank (B. indicus, B. grunniens (Chinese), B. taurus, B. gaurus, B. primigenius, B. frontalis, Bison bison, and Ovis aries). Individuals were aligned to the B. grunniens reference genome (ARS_UNL_BGru_maternal_1.0), which was also included in the analyses. The mtDNA genes were annotated using the ARS-UCD1.2 cattle sequence as a reference. Ten unique NA yak haplotypes were identified, which a haplotype network separated into two clusters. Variation among the NA haplotypes included 93 nonsynonymous single nucleotide polymorphisms. A maximum likelihood tree including all taxa was made using IQtree after the data were partitioned into twenty-two subgroups using PartitionFinder2. Notably, six NA yak haplotypes formed a clade with B. indicus; the other four haplotypes grouped with B. grunniens and fell as a sister clade to bison, gaur and gayal. These data demonstrate two mitochondrial origins of NA yak with genetic variation in protein coding genes. Although these data suggest yak introgression with B. indicus, it appears to date prior to importation into NA. In addition to contributing to our understanding of the species history, these results suggest the two major mtDNA haplotypes in NA yak may functionally differ. Characterization of the impact of these differences on cellular function is currently underway.

scholarly journals GPS Coordinates for Modelling Correlated Herd Effects in Genomic Prediction Models Applied to Hanwoo Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2050
Author(s):  
Beatriz Castro Dias Cuyabano ◽  
Gabriel Rovere ◽  
Dajeong Lim ◽  
Tae Hun Kim ◽  
Hak Kyo Lee ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Genomic Prediction ◽  
Prediction Models ◽  
Phenotypic Expression ◽  
Genetic Evaluation ◽  
Genomic Breeding ◽  
Breeding Values ◽  
Korean Cattle ◽  
Evaluation Programs ◽  
The Impact

It is widely known that the environment influences phenotypic expression and that its effects must be accounted for in genetic evaluation programs. The most used method to account for environmental effects is to add herd and contemporary group to the model. Although generally informative, the herd effect treats different farms as independent units. However, if two farms are located physically close to each other, they potentially share correlated environmental factors. We introduce a method to model herd effects that uses the physical distances between farms based on the Global Positioning System (GPS) coordinates as a proxy for the correlation matrix of these effects that aims to account for similarities and differences between farms due to environmental factors. A population of Hanwoo Korean cattle was used to evaluate the impact of modelling herd effects as correlated, in comparison to assuming the farms as completely independent units, on the variance components and genomic prediction. The main result was an increase in the reliabilities of the predicted genomic breeding values compared to reliabilities obtained with traditional models (across four traits evaluated, reliabilities of prediction presented increases that ranged from 0.05 ± 0.01 to 0.33 ± 0.03), suggesting that these models may overestimate heritabilities. Although little to no significant gain was obtained in phenotypic prediction, the increased reliability of the predicted genomic breeding values is of practical relevance for genetic evaluation programs.

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