Improving root characterisation for genomic prediction in cassava

Open Access Journal; Published online: 14 May 2020Cassava is cultivated due to its drought tolerance and high carbohydrate-containing storage roots. The lack of uniformity and irregular shape of storage roots poses constraints on harvesting and post-harvest processing. Here, we phenotyped the Genetic gain and offspring (C1) populations from the International Institute of Tropical Agriculture (IITA) breeding program using image analysis of storage root photographs taken in the field. In the genome-wide association analysis (GWAS), we detected for most shape and size-related traits, QTL on chromosomes 1 and 12. In a previous study, we found the QTL on chromosome 12 to be associated with cassava mosaic disease (CMD) resistance. Because the root uniformity is important for breeding, we calculated the standard deviation (SD) of individual root measurements per clone. With SD measurements we identified new significant QTL for Perimeter, Feret and Aspect Ratio on chromosomes 6, 9 and 16. Predictive accuracies of root size and shape image-extracted traits were mostly higher than yield trait prediction accuracies. This study aimed to evaluate the feasibility of the image phenotyping protocol and assess GWAS and genomic prediction for size and shape image-extracted traits. The methodology described and the results are promising and open up the opportunity to apply high-throughput methods in cassava

"QUALITY ASSESSMENT OF NUTRITION INFORMATION PUBLISHED WEEKLY IN THE SURROUNDING OF FOUR HOSPITALS IN LIMA, PERU"

"There is a growing demand from the general public regarding nutrition topics that has prompted social media such as magazines, newspapers, television, radio and the internet to include more nutritional content. The purpose of this study was to assess the quality of nutrition information published by health weeklies in the surroundings of four hospitals in Lima, Peru. A cross- sectional study was conducted using a mixed methodological design involving both quantitative and qualitative analyses. Thirtyseven hard copies of 4 health weeklies were purchased over the 10- week study period. Bivariate Logistic Regression was performed to examine all available journal characteristics associated with the quality of provided information. Logistic Regression Models were estimated for the independent variables that showed statistical significance in the bivariate analysis. Weekly publications with the highest percentage of pages dedicated to nutrition were “My Health” (41.67%), “Natural Health” (48.6%) and those with the lowest percentage were “Sun, medicine and beauty” (19.37%) and “Health, Money and Love” (18.34%). Collected publications included 185 articles that were classified into two groups regarding the validity of the nutrition information presented: supported 50.3% (93/185) and unsupported 49.7% (92/185). Statistical analysis for quality estimated that the “name of weekly” had a p value=0.000, the “topic” had a p value=0.035, and the “objective, source description, quarter of publications” had a p value >0.05. Multivariate logistic regression reports that only the variable “name of the weekly” had statistical significance with p values less than 0.05. The percentage of nutrition information suggests that editors may not be applying journalistic principles and shows the importance of interdisciplinary work, between nutritionists and health journalists, to improve health status of the general population. In the case of weekly health publications, editors responsible for this type of written press could benefit from including nutritionists in charge of providing nutritional information.

Three-dimensional stability of Burgers vortices

Burgers vortices are explicit stationary solutions of the Navier-Stokes equations which are often used to describe the vortex tubes observed in numerical simulations of three-dimensional turbulence. In this model, the velocity field is a two-dimensional perturbation of a linear straining flow with axial symmetry. The only free parameter is the Reynolds number $Re = \Gamma/\nu$, where $\Gamma$ is the total circulation of the vortex and $\nu$ is the kinematic viscosity. The purpose of this paper is to show that Burgers vortex is asymptotically stable with respect to general three-dimensional perturbations, for all values of the Reynolds number. This definitive result subsumes earlier studies by various authors, which were either restricted to small Reynolds numbers or to two-dimensional perturbations. Our proof relies on the crucial observation that the linearized operator at Burgers vortex has a simple and very specific dependence upon the axial variable. This allows to reduce the full linearized equations to a vectorial two-dimensional problem, which can be treated using an extension of the techniques developped in earlier works. Although Burgers vortices are found to be stable for all Reynolds numbers, the proof indicates that perturbations may undergo an important transient amplification if $Re$ is large, a phenomenon that was indeed observed in numerical simulations.Comment: 31 pages, no figur

Obscuration in AGNs: near-infrared luminosity relations and dust colors

We combine two approaches to isolate the AGN luminosity at near-infrared wavelengths and relate the near-IR pure AGN luminosity to other tracers of the AGN. Using integral-field spectroscopic data of an archival sample of 51 local AGNs, we estimate the fraction of non-stellar light by comparing the nuclear equivalent width of the stellar 2.3 micron CO absorption feature with the intrinsic value for each galaxy. We compare this fraction to that derived from a spectral decomposition of the integrated light in the central arc second and find them to be consistent with each other. Using our estimates of the near-IR AGN light, we find a strong correlation with presumably isotropic AGN tracers. We show that a significant offset exists between type 1 and type 2 sources in the sense that type 1 sources are 7 (10) times brighter in the near-IR at log L_MIR = 42.5 (log L_X = 42.5). These offsets only becomes clear when treating infrared type 1 sources as type 1 AGNs. All AGNs have very red near-to-mid-IR dust colors. This, as well as the range of observed near-IR temperatures, can be explained with a simple model with only two free parameters: the obscuration to the hot dust and the ratio between the warm and hot dust areas. We find obscurations of A_V (hot) = 5 - 15 mag for infrared type 1 sources and A_V (hot) = 15 - 35 mag for type 2 sources. The ratio of hot dust to warm dust areas of about 1000 is nicely consistent with the ratio of radii of the respective regions as found by infrared interferometry.Comment: 17 pages, 10 Figures, 3 Tables, accepted by A&

Reaction-Diffusion System in a Vesicle with Semi-Permeable Membrane

We study the Schloegl model in a vesicle with semi-permeable membrane. The diffusion constant takes a smaller value in the membrane region, which prevents the outflow of self-catalytic product. A nonequilibrium state is stably maintained inside of the vesicle. Nutrients are absorbed and waste materials are exhausted through the membrane by diffusion. It is interpreted as a model of primitive metabolism in a cell.Comment: 8 pages, 6 figure

On the relation of optical obscuration and X-ray absorption in Seyfert galaxies

The optical classification of a Seyfert galaxy and whether it is considered X-ray absorbed are often used interchangeably. But there are many borderline cases and also numerous examples where the optical and X-ray classifications appear to be in conflict. In this article we re-visit the relation between optical obscuration and X-ray absorption in AGNs. We make use of our "dust color" method (Burtscher et al. 2015) to derive the optical obscuration A_V and consistently estimated X-ray absorbing columns using 0.3--150 keV spectral energy distributions. We also take into account the variable nature of the neutral gas column N_H and derive the Seyfert sub-classes of all our objects in a consistent way. We show in a sample of 25 local, hard-X-ray detected Seyfert galaxies (log L_X / (erg/s) ~ 41.5 - 43.5) that there can actually be a good agreement between optical and X-ray classification. If Seyfert types 1.8 and 1.9 are considered unobscured, the threshold between X-ray unabsorbed and absorbed should be chosen at a column N_H = 10^22.3 / cm^2 to be consistent with the optical classification. We find that N_H is related to A_V and that the N_H/A_V ratio is approximately Galactic or higher in all sources, as indicated previously. But in several objects we also see that deviations from the Galactic ratio are only due to a variable X-ray column, showing that (1) deviations from the Galactic N_H/A_V can simply be explained by dust-free neutral gas within the broad line region in some sources, that (2) the dust properties in AGNs can be similar to Galactic dust and that (3) the dust color method is a robust way to estimate the optical extinction towards the sublimation radius in all but the most obscured AGNs.Comment: 7 pages, 3 figures, accepted for publication by A&A; updated PDF to include abstrac

Genome-wide association and prediction reveals genetic architecture of cassava mosaic disease resistance and prospects for rapid genetic improvement

Published: 13 May 2016Cassava (Manihot esculenta Crantz) is a crucial, under-researched crop feeding millions worldwide, especially in Africa. Cassava mosaic disease (CMD) has plagued production in Africa for over a century. Biparental mapping studies suggest primarily a single major gene mediates resistance. To investigate this genetic architecture, we conducted the first genome-wide association mapping study in cassava with up to 6128 genotyping-by-sequenced African breeding lines and 42,113 reference genome-mapped single-nucleotide polymorphism (SNP) markers. We found a single region on chromosome 8 that accounts for 30 to 66% of genetic resistance in the African cassava germplasm. Thirteen additional regions with small effects were also identified. Further dissection of the major quantitative trait locus (QTL) on chromosome 8 revealed the presence of two possibly epistatic loci and/or multiple resistance alleles, which may account for the difference between moderate and strong disease resistances in the germplasm. Search of potential candidate genes in the major QTL region identified two peroxidases and one thioredoxin. Finally, we found genomic prediction accuracy of 0.53 to 0.58 suggesting that genomic selection (GS) will be effective both for improving resistance in breeding populations and identifying highly resistant clones as varieties

Asymptotic expansions of the solutions of the Cauchy problem for nonlinear parabolic equations

Let $u$ be a solution of the Cauchy problem for the nonlinear parabolic equation $$\partial_t u=\Delta u+F(x,t,u,\nabla u) \quad in \quad{\bf R}^N\times(0,\infty), \quad u(x,0)=\varphi(x)\quad in \quad{\bf R}^N,$$ and assume that the solution $u$ behaves like the Gauss kernel as $t\to\infty$. In this paper, under suitable assumptions of the reaction term $F$ and the initial function $\varphi$, we establish the method of obtaining higher order asymptotic expansions of the solution $u$ as $t\to\infty$. This paper is a generalization of our previous paper, and our arguments are applicable to the large class of nonlinear parabolic equations

Energy Landscape and Global Optimization for a Frustrated Model Protein

The three-color (BLN) 69-residue model protein was designed to exhibit frustrated folding. We investigate the energy landscape of this protein using disconnectivity graphs and compare it to a Go model, which is designed to reduce the frustration by removing all non-native attractive interactions. Finding the global minimum on a frustrated energy landscape is a good test of global optimization techniques, and we present calculations evaluating the performance of basin-hopping and genetic algorithms for this system.Comparisons are made with the widely studied 46-residue BLN protein.We show that the energy landscape of the 69-residue BLN protein contains several deep funnels, each of which corresponds to a different β-barrel structure

Prospects for Genomic Selection in Cassava Breeding

Article purchased; Published online: 28 Sept 2017Cassava (Manihot esculenta Crantz) is a clonally propagated staple food crop in the tropics. Genomic selection (GS) has been implemented at three breeding institutions in Africa to reduce cycle times. Initial studies provided promising estimates of predictive abilities. Here, we expand on previous analyses by assessing the accuracy of seven prediction models for seven traits in three prediction scenarios: cross-validation within populations, cross-population prediction and cross-generation prediction. We also evaluated the impact of increasing the training population (TP) size by phenotyping progenies selected either at random or with a genetic algorithm. Cross-validation results were mostly consistent across programs, with nonadditive models predicting of 10% better on average. Cross-population accuracy was generally low (mean = 0.18) but prediction of cassava mosaic disease increased up to 57% in one Nigerian population when data from another related population were combined. Accuracy across generations was poorer than within-generation accuracy, as expected, but accuracy for dry matter content and mosaic disease severity should be sufficient for rapid-cycling GS. Selection of a prediction model made some difference across generations, but increasing TP size was more important. With a genetic algorithm, selection of one-third of progeny could achieve an accuracy equivalent to phenotyping all progeny. We are in the early stages of GS for this crop but the results are promising for some traits. General guidelines that are emerging are that TPs need to continue to grow but phenotyping can be done on a cleverly selected subset of individuals, reducing the overall phenotyping burden.Bill & Melinda Gates FoundationUKaidCGIAR Research Program on Roots, Tubers and BananasPeer Revie