scholarly journals Identity recognition in response to different levels of genetic relatedness in commercial soya bean

2017 ◽  
Vol 4 (1) ◽  
pp. 160879 ◽  
Author(s):  
Guillermo P. Murphy ◽  
Rene Van Acker ◽  
Istvan Rajcan ◽  
Clarence J. Swanton
Keyword(s):  
Genetic Relatedness ◽  
Glycine Soja ◽  
Soya Bean ◽  
Wild Progenitor ◽  
Crop Species ◽  
Identity Recognition ◽  
Crop Density ◽  
Recognition Systems ◽  
Species Specific ◽  
Different Levels

Identity recognition systems allow plants to tailor competitive phenotypes in response to the genetic relatedness of neighbours. There is limited evidence for the existence of recognition systems in crop species and whether they operate at a level that would allow for identification of different degrees of relatedness. Here, we test the responses of commercial soya bean cultivars to neighbours of varying genetic relatedness consisting of other commercial cultivars (intraspecific), its wild progenitor Glycine soja , and another leguminous species Phaseolus vulgaris (interspecific). We found, for the first time to our knowledge, that a commercial soya bean cultivar, OAC Wallace, showed identity recognition responses to neighbours at different levels of genetic relatedness. OAC Wallace showed no response when grown with other commercial soya bean cultivars (intra-specific neighbours), showed increased allocation to leaves compared with stems with wild soya beans (highly related wild progenitor species), and increased allocation to leaves compared with stems and roots with white beans (interspecific neighbours). Wild soya bean also responded to identity recognition but these responses involved changes in biomass allocation towards stems instead of leaves suggesting that identity recognition responses are species-specific and consistent with the ecology of the species. In conclusion, elucidating identity recognition in crops may provide further knowledge into mechanisms of crop competition and the relationship between crop density and yield.

scholarly journals Molecular Diversity and Genetic Relatedness of Candida albicans Isolates from Birds in Hungary

2021 ◽  
Vol 186 (2) ◽  
pp. 237-244
Author(s):  
M. Domán ◽  
L. Makrai ◽  
Gy. Lengyel ◽  
R. Kovács ◽  
L. Majoros ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Molecular Diversity ◽  
Genetic Relatedness ◽  
Group Method ◽  
Pair Group ◽  
Degree Of Separation ◽  
Avian Origin ◽  
Species Specific ◽  
Sequence Types ◽  
Unweighted Pair Group Method

AbstractThe molecular epidemiology of Candida albicans infections in animals has been rarely studied. In this study, multilocus sequence typing was used to characterise the genetic diversity and population structure of 24 avian origin C. albicans isolates collected from different birds with candidiasis and compared to human isolates. Fourteen diploid sequence types (DSTs) including six new DSTs were determined. Cluster analysis revealed that isolates grouped into 8 clades. Bird isolates mainly belonged to minor clades and Clade 15 with DST 172 was the most common (11 isolates; 45.8%). The remaining isolates were clustered into Clade 7 (5 isolates; 20.8%), Clade 10 (4 isolates; 16.6%), Clade 8 (2 isolates; 8.3%), Clade 4 (1 isolate; 4.2%) and Clade 16 (1 isolate; 4.2%). Unweighted pair group method with arithmetic averages (UPGMA) and eBURST analyses showed that the genetic construction of avian origin C. albicans population is fairly diverse. Although species-specific lineages were not found, some degree of separation in the evolution of bird and human strains could be observed.

scholarly journals LED light gradient as a screening tool for light quality responses in model plant species

2020 ◽  
Author(s):  
P. Lejeune ◽  
A. Fratamico ◽  
F. Bouché ◽  
S. Huerga Fernández ◽  
P. Tocquin ◽  
...  
Keyword(s):  
Brachypodium Distachyon ◽  
Production Costs ◽  
Fluorescent Light ◽  
Plant Responses ◽  
Light Spectrum ◽  
Crop Species ◽  
Phenotypic Data ◽  
Euphorbia Peplus ◽  
Light Gradient ◽  
Species Specific

AbstractCurrent developments in light-emitting diodes (LEDs) technologies have opened new perspectives for sustainable and highly efficient indoor cultivation. The introduction of LEDs not only allows a reduction in the production costs on a quantitative level, it also offers opportunities to manipulate and optimise qualitative traits. Indeed, while plants respond strongest to red and blue lights for photosynthesis, the whole light spectrum has an effect on plant shape, development, and chemical composition. In order to evaluate LEDs as an alternative to traditional lighting sources, the species-specific plant responses to distinct wavelengths need to be evaluated under controlled conditions. Here, we tested the possibility to use light composition gradients in combination with semi-automated phenotyping to rapidly explore the phenotypic responses of different species to variations in the light spectrum provided by LED sources. Plants of seven different species (Arabidopsis thaliana, Ocimum basilicum, Solanum lycopersicum, Brachypodium distachyon, Oryza sativa, Euphorbia peplus, Setaria viridis) were grown under standard white fluorescent light for 30 days, then transferred to a Red:Blue gradient for another 30 days and finally returned to white light. In all species, differences in terms of dimension, shape, and color were rapidly observed across the gradient and the overall response was widely species-dependent. The experiment yielded large amounts of imaging-based phenotypic data and we suggest simple data analysis methods to aggregate the results and facilitate comparisons between species. Similar experimental setups will help achieve rapid environmental optimization, screen new crop species and genotypes, or develop new gene discovery strategies.

scholarly journals Estimation of Phoneme-Specific HMM Topologies for the Automatic Recognition of Dysarthric Speech

2013 ◽  
Vol 2013 ◽  
pp. 1-15 ◽  
Author(s):  
Santiago-Omar Caballero-Morales
Keyword(s):  
Neurological Diseases ◽  
Gaussian Mixture ◽  
Motor Speech ◽  
Motor Speech Disorder ◽  
Acoustic Modelling ◽  
Speech Database ◽  
Recognition Systems ◽  
Dysarthric Speech ◽  
Different Levels

Dysarthria is a frequently occurring motor speech disorder which can be caused by neurological trauma, cerebral palsy, or degenerative neurological diseases. Because dysarthria affects phonation, articulation, and prosody, spoken communication of dysarthric speakers gets seriously restricted, affecting their quality of life and confidence. Assistive technology has led to the development of speech applications to improve the spoken communication of dysarthric speakers. In this field, this paper presents an approach to improve the accuracy of HMM-based speech recognition systems. Because phonatory dysfunction is a main characteristic of dysarthric speech, the phonemes of a dysarthric speaker are affected at different levels. Thus, the approach consists in finding the most suitable type of HMM topology (Bakis, Ergodic) for each phoneme in the speaker’s phonetic repertoire. The topology is further refined with a suitable number of states and Gaussian mixture components for acoustic modelling. This represents a difference when compared with studies where a single topology is assumed for all phonemes. Finding the suitable parameters (topology and mixtures components) is performed with a Genetic Algorithm (GA). Experiments with a well-known dysarthric speech database showed statistically significant improvements of the proposed approach when compared with the single topology approach, even for speakers with severe dysarthria.

Determination of Cardinal Temperatures of Flax-leaf Alyssum (Alyssum linifolium) in Response to Salinity, pH, and Drought Stress

Weed Science ◽  
2018 ◽  
Vol 66 (4) ◽  
pp. 470-476 ◽  
Author(s):  
Ahmadreza Mobli ◽  
Ali Ghanbari ◽  
Mehdi Rastgoo
Keyword(s):  
Germination Rate ◽  
Farming Systems ◽  
Quadratic Polynomial ◽  
Polynomial Model ◽  
Weed Species ◽  
Wide Range ◽  
Species Specific ◽  
Cardinal Temperatures ◽  
Different Levels

AbstractFlax-leaf alyssum (Alyssum linifoliumSteph. ex. Willd.) is a winter weed species in irrigated and dryland farming systems of Iran. Experiments were conducted to compare the cardinal temperatures ofA. linifoliumat different levels of drought, salt concentration, and pH. In all experiments, the dent-like model showed a better fit than the quadratic polynomial model.Alyssum linifoliumproduced the highest germination rates at pH 7 and a temperature of 20C in nonstress treatment. Minimum, optimum, and ceiling temperatures in the dent-like model were 4.1 (upper=26.8, lower=10.0) and 35C, and in the quadratic polynomial model were 3.3, 19.1, and 35.0C, respectively. At increased salinity and drought potential levels, the minimum temperature increased, while optimum and ceiling temperatures decreased. Seeds could germinate at up to 20 dS m−1and −1 MPa, respectively, but germination rate and percentage significantly decreased. The seeds of this weed germinated across a wide range of pH values (4≤pH≥8), but the temperature range at which seeds could germinate was reduced. These data serve as guidelines for species-specific propagation protocols and agricultural decision support systems.

A Bayesian hierarchical approach to improve model parameter estimates and predictions of silage maize phenology in Germany

2021 ◽  
Author(s):  
Michelle Viswanathan ◽  
Tobias KD Weber ◽  
Andreas Scheidegger ◽  
Thilo Streck
Keyword(s):  
Environmental Conditions ◽  
Plant Phenology ◽  
Parameter Estimates ◽  
Crop Species ◽  
Bayesian Hierarchical ◽  
Crop Models ◽  
Hierarchical Framework ◽  
Silage Maize ◽  
Parameterized Model ◽  
Species Specific

<p>Crop models are used to evaluate the impact of climate change on food security by simulating plant phenology, yield, biomass and leaf area index. Plant phenology defines the timing of crucial growth stages and physiological processes that influence organ appearance and assimilate partitioning. It is governed by environmental factors such as solar radiation, temperature and water availability. Plant phenology is not only specific for the crop species, but also depends on the cultivar. Additionally, growth of a cultivar could vary depending on the environment. Common crop models cannot fully capture the influence of the environment on phenology, resulting in cultivar-specific parameters that are environment-dependent. These parameter estimates may be unreliable in case of limited data. Moreover, crucial species-specific information is ignored. On the other hand, in large regional-scale models covering multiple cultivars and environments, information about the cultivars grown is generally not available. In this case, a shared set of parameters for the crop species would suppress within-species differences leading to unreliable predictions.</p><p>A Bayesian hierarchical framework enables us to alleviate these problems by honouring the multi-level data structure. Additionally, we can reflect the uncertainty from different sources, for example, model inputs and measurements. In this study we implement a Bayesian hierarchical framework to estimate parameters of the Soil-Plant-Atmosphere System Simulation (SPASS) model for simulating phenological development of different cultivars of silage maize grown over all the contrasting climatological regions of Germany.</p><p>We used data from the German weather service on the phenological development stages of silage maize grown across Germany between 2009 and 2019. During this period, silage maize was grown in over 3000 unique location-year combinations. Maize crops were differentiated into early, mid-early, mid-late and late ripening groups and were further classified into cultivars within each ripening group. Within the hierarchical framework, we estimate maize species-specific parameters as well as parameters per ripening group and cultivar, through Bayesian model calibration. We analyse the influence of environmental conditions on parameter estimates, to further develop the hierarchical structure. We perform cross-validation to assess the prediction quality of the parameterized model.</p><p>With this approach, we show that robust parameter estimates account for differences between cultivars, ripening groups as well as different environmental conditions. The parameterized model can be used for large-scale phenology predictions of silage maize grown across Germany. These parameter estimates may perform better than independent species- or cultivar-specific estimates, in predicting phenology of future cultivars where specific cultivar characteristics are not known.</p>

scholarly journals When science mirrors life: on the origins of the Price equation

2020 ◽  
Vol 375 (1797) ◽  
pp. 20190352 ◽  
Author(s):  
Oren Harman
Keyword(s):  
Population Genetics ◽  
Genetic Relatedness ◽  
Personal Life ◽  
Price Equation ◽  
Narrow Sense ◽  
Theme Issue ◽  
Young Girls ◽  
Link Type ◽  
Mother And Daughter ◽  
Different Levels

The Price equation was a piece of abstract mathematics. What kind of a connection could it possibly have had to George Price's personal life and biography? Here, I will argue that the initial impetus for Price's foray into mathematical population genetics stemmed from a preoccupation with the origins of family, one that was born following a divorce from his wife and the abandonment of their two young girls. What is special about the Price equation is the way in which it associates statistically between two groups, a ‘mother’ and ‘daughter’ population. The association need not mean genetic relatedness in the narrow sense of direct descent, and it allows us to see selection working at different levels simultaneously, a fact that was not lost on William Hamilton. Hamilton was one of the few friends who desperately tried to save Price from falling into the abyss of depression and homelessness in the period following the publication of ‘Selection and covariance’ (Price 1928 Nature 227 , 520–521 ( doi:10.1038/227520a0 )). Viewed in this light, the Price equation assumes new meaning. This article is part of the theme issue ‘Fifty years of the Price equation’.

Detection of intergenomic translocations with centromeric and noncentromeric breakpoints in Triticum araraticum: mechanism of origin and adaptive significance

Genome ◽  
1995 ◽  
Vol 38 (5) ◽  
pp. 976-981 ◽  
Author(s):  
Ekatherina D. Badaeva ◽  
Jiming Jiang ◽  
Bikram S. Gill
Keyword(s):  
Natural Populations ◽  
Chromosome Translocation ◽  
Adaptive Significance ◽  
Genomic In Situ Hybridization ◽  
Intraspecific Diversity ◽  
Wild Progenitor ◽  
Intergenomic Translocations ◽  
Species Specific ◽  
Triticum Araraticum

Triticum araraticum Jakubz. (2n = 4x = 28, AtAtGG), a wild progenitor of the polyploid cultivated wheat T. timopheevii, shows extensive chromosome translocation polymorphism in natural populations from the Middle East and Transcaucasia. From an extensive survey, eight intergenomic translocation types were observed and their breakpoints analyzed by genomic in situ hybridization. The previously reported species-specific 6At–1G–4G cyclic translocation was found in all accessions studied. In four translocation types, the breakpoints were in interstitial regions of chromosomes and the other four arose via centric–breakage–fusion. A model is presented on the mechanism of origin and the adaptive significance of translocations with centromeric and noncentromeric breakpoints.Key words: intraspecific diversity, intergenomic translocations, Triticum araraticum.

Isolation by distance in a hierarchically clustered population

1983 ◽  
Vol 20 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Stanley Sawyer ◽  
Joseph Felsenstein
Keyword(s):  
Total Population ◽  
Genetic Relatedness ◽  
Isolation By Distance ◽  
Random Mating ◽  
Physical Distance ◽  
Population Densities ◽  
Total Population Size ◽  
Biological Population ◽  
Equilibrium Probability ◽  
Different Levels

A biological population with local random mating, migration, and mutation is studied which exhibits clustering at several different levels. The migration is determined by the clustering rather than actual geographic or physical distance. Darwinian selection is assumed to be absent, and population densities are such that nearby individuals have a probability of being related. An expression is found for the equilibrium probability of genetic relatedness between any two individuals as a function of their clustering distance. Asymptotics for a small mutation rate u are discussed for both a finite number of clustering levels (and of total population size), and for an infinite number of levels. A natural example is discussed in which the probability of heterozygosity varies as u to a power times a periodic function of log(l/u).

scholarly journals Differential CYP 2D6 Metabolism Alters Primaquine Pharmacokinetics

2015 ◽  
Vol 59 (4) ◽  
pp. 2380-2387 ◽  
Author(s):  
Brittney M. J. Potter ◽  
Lisa H. Xie ◽  
Chau Vuong ◽  
Jing Zhang ◽  
Ping Zhang ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Antimalarial Activity ◽  
Wild Type ◽  
Phenolic Metabolites ◽  
Species Specific ◽  
Human And Mouse ◽  
Different Levels ◽  
Cyp 2D6

ABSTRACTPrimaquine (PQ) metabolism by the cytochrome P450 (CYP) 2D family of enzymes is required for antimalarial activity in both humans (2D6) and mice (2D). Human CYP 2D6 is highly polymorphic, and decreased CYP 2D6 enzyme activity has been linked to decreased PQ antimalarial activity. Despite the importance of CYP 2D metabolism in PQ efficacy, the exact role that these enzymes play in PQ metabolism and pharmacokinetics has not been extensively studiedin vivo. In this study, a series of PQ pharmacokinetic experiments were conducted in mice with differential CYP 2D metabolism characteristics, including wild-type (WT), CYP 2D knockout (KO), and humanized CYP 2D6 (KO/knock-in [KO/KI]) mice. Plasma and liver pharmacokinetic profiles from a single PQ dose (20 mg/kg of body weight) differed significantly among the strains for PQ and carboxy-PQ. Additionally, due to the suspected role of phenolic metabolites in PQ efficacy, these were probed using reference standards. Levels of phenolic metabolites were highest in mice capable of metabolizing CYP 2D6 substrates (WT and KO/KI 2D6 mice). PQ phenolic metabolites were present in different quantities in the two strains, illustrating species-specific differences in PQ metabolism between the human and mouse enzymes. Taking the data together, this report furthers understanding of PQ pharmacokinetics in the context of differential CYP 2D metabolism and has important implications for PQ administration in humans with different levels of CYP 2D6 enzyme activity.

scholarly journals Effects of seed dispersal on spatial genetic structure in populations of Rutidosis leptorrhychoides with different levels of correlated paternity

2002 ◽  
Vol 79 (3) ◽  
pp. 219-226 ◽  
Author(s):  
GUDRUN P. WELLS ◽  
ANDREW G. YOUNG
Keyword(s):  
Genetic Structure ◽  
Seed Dispersal ◽  
Genetic Relatedness ◽  
Spatial Genetic Structure ◽  
Dispersal Distance ◽  
Self Incompatibility ◽  
Southeastern Australia ◽  
Incompatibility System ◽  
Significant Patterns ◽  
Different Levels

Rutidosis leptorrynchoides is a perennial forb endemic to grasslands and grassy woodlands in southeastern Australia. Studies of seed dispersal, spatial genetic structure and clonality were carried out in four populations around the Canberra region that varied in levels of correlated paternity to examine: (1) whether R. leptorrhynchoides populations exhibit fine-scale spatial genetic structure and whether this varies between populations as a function of correlated paternity; (2) whether there is a correlation between seed dispersal distance and genetic relatedness within populations; and (3) whether clonal reproduction occurs in this species and to what degree this could account for the observed spatial genetic structure. The results show that there is variation in the magnitude and extent of spatial genetic structure between R. leptorrhynchoides populations. The three larger populations, with low to moderate full-sib proportions, showed significant patterns of coancestry between plants over scales of up to one metre, whereas the smallest population, with a high full-sib proportion, had erratically high but non-significant coancestry values. The observed patterns of genetic clumping could be explained by a combination of limited seed dispersal and correlated mating owing to limited mate availability resulting from the species' sporophytic self-incompatibility system. Clonality does not appear to be an important factor contributing to genetic structure in this species.

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