Dynamics of GB-speckles with a small number of scatterers

A method for generating dynamic GB-speckles, formed during diffraction of focused Gaussian beams by moving virtual rough surfaces, obtained for two nucleotide sequences (the ompA genes of the Chlamydia psittaci GR9 and AMK-16 strains), is proposed. The statistical characteristics of the 1st- and 2nd-order statistics of GB-speckles, formed at a small number of scattering events, are studied. The difference in the manifestation of the Doppler effect in the dynamics of GB-speckles and for speckles, formed with a small number of scatterers, produced by light diffraction on physically-existing rough surfaces and in scattering micro-streams is revealed. The problems of interference of dynamic GB-speckles are considered. A new technique for detecting individual single nucleotide polymorphism in nucleotide sequences using the interference of dynamic GB-speckles is proposed.

Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle

A haplotype is defined as a combination of alleles at adjacent loci belonging to the same chromosome that can be transmitted as a unit. In this study, we used both the Illumina BovineHD chip (HD chip) and imputed whole-genome sequence (WGS) data to explore haploblocks and assess haplotype effects, and the haploblocks were defined based on the different LD thresholds. The accuracies of genomic prediction (GP) for dressing percentage (DP), meat percentage (MP), and rib eye roll weight (RERW) based on haplotype were investigated and compared for both data sets in Chinese Simmental beef cattle. The accuracies of GP using the entire imputed WGS data were lower than those using the HD chip data in all cases. For DP and MP, the accuracy of GP using haploblock approaches outperformed the individual single nucleotide polymorphism (SNP) approach (GBLUP_In_Block) at specific LD levels. Hotelling’s test confirmed that GP using LD-based haplotypes from WGS data can significantly increase the accuracies of GP for RERW, compared with the individual SNP approach (∼1.4 and 1.9% for GHBLUP and GHBLUP+GBLUP, respectively). We found that the accuracies using haploblock approach varied with different LD thresholds. The LD thresholds (r2 ≥ 0.5) were optimal for most scenarios. Our results suggested that LD-based haploblock approach can improve accuracy of genomic prediction for carcass traits using both HD chip and imputed WGS data under the optimal LD thresholds in Chinese Simmental beef cattle.