Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

Abstract\ud \ud Background\ud Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection.\ud \ud \ud Results\ud A total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development.\ud \ud \ud Conclusions\ud In this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry.CB received a fellowship from the program Science Without Borders - National Council for Scientific and Technological Development (CNPq, grant 370620/2013–5). GCMM and TFG received fellowships from São Paulo Research Foundation (FAPESP, grants 14/21380–9 and 15/00616–7). LLC is recipient of productivity fellowship from CNPq. This project was funded by São Paulo Research Foundation (FAPESP) - thematic project (2014/08704–0)

Thickness and conductivity determination of thin coatings on ferromagnetic substrates in the case of cylindrical symmetry

An eddy current method allowing the determination of parameters of a thin nonmagnetic conductive coating on a ferromagnetic conductive substrate is reported. At a single operating frequency, two independent quantities can be determined: a permeability-to-conductivity ratio of the substrate and a thickness-conductivity product of the coating. Thus, thickness or conductivity of the coating can be determined independent of variations of the substrate magnetic and electrical parameters. A simple theoretical formula for the normalized electrical impedance of the test coil is obtained using asymptotic expansions of Bessel functions. The method was applied to the evaluation of electrogalvanized wires in the frequency range 100 kHz-1 MHz. A set of low carbon steel wires with diameter around 2.2 mm, coated with zinc layers having thicknesses in the range 2.7-64.6 mu m, was investigated using two long coils. Experimental data of the electrical impedance were compared to those predicted. Agreement between theory and experiment is excellent for coatings thicker than 12 mu m. Despite discrepancies between theory and experiment for very thin layers arising from various imperfections of the coating and interfaces, the method was applied successfully in the thickness range below 12 mu m. To do this, two parameters: an apparent conductivity of the coating and a thickness offset, were introduced. The mathematical inversion of the experimental data with the two-variable Newton-Raphson method and the asymptotic formula is extremely fast. The technique developed has an extremely low sensitivity to variations of the ferromagnetic substrate conductivity and magnetic permeability. A magnetizing field of 0-23 000 A/m, producing large variations in the substrate magnetic permeability, does not significantly influence results of the coating thickness determination. The agreement between measured thickness and that obtained by a chemical method is excellent, typically within 0.5 mu m. An uncertainty of the thickness or conductivity determination better than 1% is obtained. (C) 1997 American Institute of Physics