Hy-Line Cruises

Background Appreciable Linkage Disequilibrium (LD) is commonly found between pairs of loci close to one another, decreasing rapidly with distance between the loci. This provides the basis studies to map Quantitative Trait Loci Regions (QTLRs), where it is custom to assume that the closest sites to a significant markers are the prime candidate to be the causative mutation. Nevertheless, Long-Range LD (LRLD) can also be found among well-separated sites. LD blocks are runs of genomic sites all having appreciable LD with one another. High LD and LRLD are often separated by genomic sites with which they have practically no LD. Thus, not only can LD be found among distant loci, but also its pattern may be complex, comprised of fragmented blocks. Here, chicken LRLD and LD blocks, and their relationship with previously described Marek’s Disease (MD) QTLRs, were studied in an F 6 population from a full-sib advanced intercross line, and in eight commercial pure layer lines. Genome wide LRLD was studied in the F 6 population by random samples of non-syntenic and syntenic marker pairs. To illustrate the relationship with QTLRs, LRLD and LD blocks in and between the MD QTLRs were studied by all possible marker pairs. Results LRLD was defined as r 2 ≥ 0.7 over a distance ≥ 1 Mb, and 1.5% of all syntenic marker pairs were classified as LRLD. Complex fragmented and interdigitated LD blocks were found, ranging over distances from a few hundred to a few millions bases. Vast high, long-range, and complex LD was found between two of the MD QTLRs. Cross QTLRs STRING networks and gene interactions suggested possible origins of the exceptional LD between these two QTLRs. Conclusions All sites with high LD with a significant marker should be considered as candidate for the causative mutation, but, unlike the custom assumption, the causative mutation is not necessarily the one closest to the significant marker. Rather, the present results show that it can be located at a much larger distance from a significant marker than previously appreciated, beyond closer mutations. Thus, LRLD range and LD block complexity must be accounted for while interpreting genetic mapping studies.

Different genetic lines of laying hens may show varying levels of fearfulness in response to stressful events or situations. It is important to select appropriate genetic strains when keeping hens in alternative housing systems to minimize health and production issues caused by fear and stress. In this study, data were obtained from two strains of Rhode Island Red (RIR1-2), two strains of White Plymouth Rock (WPR1-2) and three strains of White Leghorn (WL1-3) breeds. One hundred hens from each strain were used to compare strain differences in fear and stress responses. Each hen was scored for fearfulness based on her responses to the following tests: novel object, physical restraint, pencil, human reaction, inversion, and tonic immobility (TI). Stress was assessed based on physical asymmetry (ASYM) of the metatarsal and middle toe, and on corticosterone (CORT) concentrations in blood plasma and egg albumen. Differences between brown (RIR; WPR) and white (WL) egg layers were observed for all measures: WL had more head movements and took more time to right themselves during TI (P < 0.001), but higher flapping intensity was observed in RIR and WPR (P < 0.001). Hens in the WL strains also scored lower than RIR and WPR on the struggle test (P < 0.001), and had lower ASYM scores (P = 0.002) and concentrations of albumen CORT (P = 0.0065) and plasma CORT (P = 0.002), but scored higher during the remaining fear tests (P < 0.001). Differences among WL strains were also observed for all measures: WL2 had the most head movements and took the longest to right during TI (P < 0.001). During inversion, WP2 and RIR2 had the highest flapping intensity (P < 0.001) whereas WL2 and WL3 had the lowest flapping intensity (P < 0.001). There was variation among strains in plasma CORT, albumen CORT, and scores for the struggle test and pencil test. Only the WPR2 strain showed significant differences in ASYM (P < 0.001). Genetic strains of laying hens show clear variation between brown and white shell color varieties regarding fear and stress responses. Brown hens tend to actively avoid perceived threats whereas white hens use passive avoidance. Using several methods to test fear and stress to better understand individual birds' responses to stressors will help to design breeding strategies to maximize hens' success in alternative housing systems.

The chicken major histocompatibility B complex (MHC-B) region is of great interest owing to its very strong association with resistance to many diseases. Variation in the MHC-B was initially identified by hemagglutination of red blood cells with specific alloantisera. New technologies, developed to identify variation in biological materials, have been applied to the chicken MHC. Protein variation encoded by the MHC genes was examined by immunoprecipitation and 2-dimensional gel electrophoresis. Increased availability of DNA probes, PCR, and sequencing resulted in the application of DNA-based methods for MHC detection. The chicken reference genome, completed in 2004, allowed further refinements in DNA methods that enabled more rapid examination of MHC variation and extended such analyses to include very diverse chicken populations. This review progresses from the inception of MHC-B identification to the present, describing multiple methods, plus their advantages and disadvantages.

SNP chips can be used to provide genomic information on copy number variations (CNV) in addition to information on the SNPs (single nucleotide polymorphism) for which they were originally designed. Although some CNVs may be missed compared to methods specifically designed for CVN detection, CNVs derived from SNP chips can contribute valuable information on additional genetic variation without additional cost.