Cylindrical, periodic surface lattice — theory, dispersion analysis, and experiment

A two-dimensional surface lattice of cylindrical topology obtained via perturbing the inner surface of a cylinder is considered. Periodic perturbations of the surface lead to observation of high-impedance, dielectric-like media and resonant coupling of surface and non-propagating volume fields. This allows synthesis of tailored-for-purpose "coating" material with dispersion suitable, for instance, to mediate a Cherenkov type interaction. An analytical model of the lattice is discussed and coupled-wave equations are derived. Variations of the lattice dispersive properties with variation of parameters are shown, illustrating the tailoring of the structure's electromagnetic properties. Experimental results are presented showing agreement with the theoretical model

SNP associations and genetic-parameter estimation for nose and hoof pigmentation in Corriedale sheep

Published Online 7/6/23 OnlinePublContext. Quantity and quality of both meat and wool are important for selection programs of the dual-purpose Corriedale sheep. In Corriedales, black pigmentation of nose skin and hooves is preferred as part of the breed standard. However, within the breed, pigmentation can vary from none to complete pigmentation. Aims. The aim was to discover single-nucleotide polymorphisms (SNPs) and genes associated with nose and hoof pigmentation and to estimate genetic parameters of nose and hoof pigmentation, wool traits and meat traits. Methods. The phenotype and genotype data on Corriedale lambs (n = 764) produced from 44 sires (12 studs) and 300 ewes in 2017–2019 were used in this study. Lambs were slaughtered at 6–7 months of age. Nose pigmentation and hoof pigmentation were scored on a five-point scale, where no pigmentation was scored 0 and complete pigmentation was scored 5. Wool-and meat-quality traits were measured, including greasy fleece weight, fibre diameter, weaning weight, hot standard carcass weight and intramuscular fat percentage. The lambs were genotyped with the GGPOvine50K SNP chip. A genome-wide association study (GWAS) was conducted. Genetic parameters and bivariate analyses were estimated using ASReml-R. Results. The lambs had a mean nose-pigmentation score of 3.69 and hoof-pigmentation score of 4.12. The nose pigmentation (h2 = 0.58) and hoof pigmentation (h2 = 0.51) were highly heritable and highly correlated (rG = 0.73). The GWAS identified a genome-wide significant SNP (OAR19_33278780.1) associated with nose pigmentation (q-value = 0.04). This SNP is positioned in a known pigmentation gene, melanocyte-inducing transcription factor (MITF ). The same SNP was the sixth-most associated SNP for hoof pigmentation but did not reach significance level. OAR19_33278780.1 also had a significant effect on back conformation and weaning weight. Conclusions. The results of these analyses have provided information and an understanding of the genetics for pigmentation of nose and hooves in Corriedale sheep. Implications. Nose and hoof pigmentation are highly genetically correlated with each other, but with no negative effects on production traits.J. E. Aldersey, M. S. Khatkar, P. J. Blackwood, C. E. Blackwood, J. M. Pitchford, H. Gordon, S. C. Welsh and W. S. Pitchfor

The next wave in selective breeding: implementing genomic selection in aquaculture

Advanced animal breeding in aquaculture has reached a tipping point where the commercial implementation of genomic selection to improve productivity and disease resistance is becoming reality. However, the success of practical implementation of genomic selection depends on the specific aquaculture species, production system and available phenotyping and genetic resources. Using the experience learned from commercial programs for pearl oysters and marine shrimp, we highlight current benefits and options in cost-effective high-throughput genotyping and phenotyping technologies for genomic selection applications relevant to aquaculture species, followed by discussion of some of the lessons learnt when dealing with its practical implementation, including what is needed to build adequate genotype resources for non-model species; confounded breeding objective verse trait measurements; complex traits and unknown interactions; multi-family breeding schemes; multi-stage selection schemes, and transition to a genomic selection breeding program incorporating minimisation of inbreeding

Data and the associated R code used to estimate health and economic burden of neurocysticercosis in India

This article contains epidemiological, demographic and other data used for estimating health and economic burden of neurocysticercosis (NCC)-associated active epilepsy in India [1]. Most of the data are embedded in the R-code used for analyses so that the reader is able to replicate the results or adapt the code to their own data. However, data used to conduct sensitivity analyses to evaluate the effect of changing important input values such as prevalence and per capita income on health and economic impact of NCC in India are included in tables. Results from sensitivity analyses are also presented in tables and figures. The paper also includes three scenarios with different age weighting (k) and time discounting (r) values used to estimate health and economic burden of NCC in India. The data for the scenario without any age weighting and time discounting are presented in “Estimation of the health and economic burden of neurocysticercosis in India” [1]

Genome-wide genetic diversity of Holstein Friesian cattle reveals new insights into Australian and global population variability, including impact of selection

Past breeding strategies for dairy cattle have been very effective in producing rapid genetic gain to achieve industry targets and raise profitability. Such gains have been largely facilitated by intense selection of sires combined with the use of artificial insemination. However, this practice can potentially limit the level of genetic diversity through inbreeding and selection plateaus. The rate of inbreeding in Australia is increasing, primarily as a result of semen importation from a small number of prominent bulls from the USA. The effect of this genetic influx in the Australian dairy cattle population is poorly understood both in terms of diversity and local adaptation/divergence. This study uses 845 genome-wide SNP genetic markers and 431 bulls to characterize the level of genetic diversity and genetic divergence within the Australian and international Holstein Friesian dairy population. No significant differences in genetic diversity (as measured by heterozygosity [Ho] and allelic richness [A]) were observed over the 25-year time period (1975–1999) for bulls used in Australia. The importation of foreign semen into Australia has increased the effective population size until it was in effect a sub-sample of the global population. Our data indicate that most individuals are equally closely related to one another, regardless of country of origin and year of birth. In effect, the global population can be considered as one single population unit. These results indicate that inbreeding, genetic drift and selection has had little effect at reducing genetic diversity and differentiating the Australian Holstein Friesian population at a genome-wide level

Reconstruction of unknown donor genome from chimeric pearl sac tissue and host genotypes in pinctada maxima

Commercial pearl production involves two oysters, the seeded individual (host), and a sacrificed oyster (donor) from which a piece of tissue is utilised during the seeding process. During commercial seeding, it is often difficult to keep track of individual pairing information of host and donor oysters. Here we describe a method for reconstructing donor genotypes from host genotypes and allele frequencies generated from chimeric pearl sac tissue (a mixture of host and donor tissues) at pearl harvest. Using simulation of expected genotype frequencies and genotypes from true samples, we demonstrate that donor genotypes can be constructed with high accuracy. Best results were observed when the error rate of allele frequencies is low, SNPs have a high minor allelic frequency, and when the proportion of the donor tissue in the pearl sac tissue is greater than 20 percent

Developing a genomic selection breeding program for complex pearl colour traits within the silver-lipped pearl oyster

Selective breeding within the pearling industry is heavily confounded by the complexity of production traits and the ability to accurately measure these phenotypes. Pearls are produced by implanting a nucleus along with a small piece of donor tissue from a sacrificed oyster into a host oyster. Unravelling trait architecture for these complex pearl quality traits is integral if genomic selection is to be implemented into established selective breeding programs. By combining simulated and exploratory datasets, this study uses genome-wide loci to better understand the genetic architecture of pearl colour which provides insights into the optimal design and implementation for a genomic selection breeding program within the pearling industry

Developing a genomic selection breeding program for complex pearl colour traits within the silver-lipped pearl oyster

Selective breeding within the pearling industry is heavily confounded by the complexity of production traits and the ability to accurately measure these phenotypes. Pearls are produced by implanting a nucleus along with a small piece of donor tissue from a sacrificed oyster into a host oyster. Unravelling trait architecture for these complex pearl quality traits is integral if genomic selection is to be implemented into established selective breeding programs. By combining simulated and exploratory datasets, this study uses genome-wide loci to better understand the genetic architecture of pearl colour which provides insights into the optimal design and implementation for a genomic selection breeding program within the pearling industry

Genome based genetic evaluation and genome wide selection using supervised dimension reduction based on partial least squares

The method of partial least squares was applied to the prediction of genetic merit using whole genome scan data consisting of 10715 SNP. The method is particularly suited to data sets that have many more markers than observations and in which markers are collinear due to high linkage disequilibrium. A SNP ranking method was applied to select a subset of markers which have equal predictive power compared to using all SNP simultaneously