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

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

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

QC analyses of SNP array data: experience from a large population of dairy sires with 23.8 million data points

The use of a high throughput SNP genotyping platform with 15,380 bovine SNP assays, across 1546 dairy bulls resulted in a data set of approximately 23.8 M SNP data points. Stringent control measures based around low polymorphic content, sample failure, deviation from HWE, low call rate, non-Mendelian inheritance, tri-allelic SNP, and incompatible clustering of data, resulted in removal of 4321 SNPs. The majority (2973) were due to low polymorphic content (MAF99%) across repeat samples, and between platforms. SNP technology has now matured where comprehensive genome-wide analyses can be conducted in cattle with a high degree of robustness

Genome based genetic evaluation and genome wide selection\ud 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\ud disequilibrium. A SNP ranking method was applied to select a subset of markers which have equal predictive power compared to using all SNP simultaneously

Whole-genome amplification of DNA extracted from cattle semen samples

The bovine genome sequence project and the discovery\ud of many thousands of bovine single nucleotide polymorphisms\ud has opened the door for large-scale genotyping studies to identify genes that contribute to economically important traits with relevance to the beef and dairy industries. Large amounts of DNA will be required for these research projects. This study reports the use of the whole-genome amplification (WGA) method to create an unlimited supply of DNA for use in genotyping studies and long-term storage for future gene discovery projects. Two commercial WGA kits (GenomiPhi, Amersham Biosciences, Sydney, Australia, and REPLI-g, Qiagen, Doncaster, Australia) were used to amplify DNA from straws of bull semen, resulting in an average of 7.2 and 67 g of DNA per reaction, respectively. The comparison of 3.5 kb of sequences from the amplified and unamplified DNA indicated no detectable DNA differences. Similarly, gene marker analysis conducted on genomic DNA and DNA after WGA indicated no difference in marker amplification or clarity and accuracy of scoring for approximately 10,000 single nucleotide polymorphism markers when compared with WGA samples genotyped in duplicate. These results illustrate that WGA is a suitable method for the amplification and recovery of DNA from bull semen samples for routine genomic investigations

Genome-wide selection in dairy cattle: use of genetic algorithms in the estimation of molecular breeding values

A procedure has been developed for the prediction of genetic merit and the simultaneous assessment of multiple genotypes for subsequent use in gene detection. The system utilises a large volume of genotype information but ignores pedigree. With a simple additive model of inheritance, high correlations between estimates of molecular breeding value and highly reliable progeny test estimated breeding values were observed (0.70–0.77)

Extent of linkage disequilibrium and haplotype blocks in bovine genome using high density SNP markers

A haplotype block map of the bovine genome was constructed based on the analysis of 15,036 SNPs on 1,000 un-related bulls. This map identified a total of 727 haplotype blocks consisting of three or more SNPs. These blocks have a mean length of 69.7 kb and cover 2.2 % of the length of all\ud autosomes. This analysis suggested that approximately 250,000 SNPs would be required to prepare a complete haplotype block map of the bovine genome with 75,000 tag SNPs