Objective: This study aimed to determine the effects of stress during slaughter of beef cattle on physiological parameters, carcass, and meat quality at a Federal Inspection Type slaughterhouse located in the southeast of Mexico.Methods: A total of 448 carcasses of male Zebu×European steers with an average age of 36 months were included. Carcass assessment of presence of bruises and bruise characteristics was carried out on each half-carcass. Blood variable indicators of stress (packed cell volume, neutrophil to lymphocyte ratio, glucose, cortisol concentration) and meat quality parameters (pH, color, shear force, drip loss) were evaluated.Results: Of the 448 carcasses evaluated, 81% of the carcasses showed at least one bruise; one bruise was detected in 36.6% and two bruises in 27.0% of animals. Of the 775 bruises found, 69.2% of the bruises were grade 1 in region 3. Of the 448 carcasses studied, 69.6% showed hyperglycemia (6.91 mmol/L); 44.3% and 22.7% showed high (74.7 ng/mL) and extremely high (108.8 ng/mL) cortisol levels, respectively, indicative of inadequate handling of animals during preslaughter and slaughter. Of the carcasses evaluated, 90.4% had a pH ≥5.8 with an average of pH 6.3. In both pH groups, meat samples showed L* values >37.0 (81.6%) and a shear force >54.3 N; meat pH≥5.8 group showed a drip loss of 2.5%. These findings were indicative of dark, firm, and dry (DFD) meat. According to principal component analysis, grades 1 and 2 bruises in region 3 and grade 1 bruises in region 5 were highly associated with cortisol, drip loss, and color parameters b* and h* and were negatively associated with L*, a*, and C*.Conclusion: The bruises probably caused by stress-inducing situations triggered DFD meat. Appropriate changes in handling routines in operating conditions should be made to minimize stress to animals during the slaughter process to improve animal welfare and meat quality.

Copy number variations are genome polymorphism that influence phenotypic variation and are an important source of genetic variation in populations. The aim of this study was to investigate genetic variability in the Mexican Creole chicken population using CNVs. The Hidden Markov Model of the PennCNV software detected a total of 1924 CNVs in the genome of the 256 samples processed with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix). The mapped CNVs comprised 1538 gains and 386 losses, resulting at population level in 1216 CNV regions (CNVRs), of which 959 gains, 226 losses and 31 complex (i.e. containing both losses and gains). The CNVRs covered a total of 47 Mb of the whole genome sequence length, corresponding to 5.12% of the chicken galGal4 autosome assembly. This study allowed a deep insight into the structural variation in the genome of unselected Mexican chicken population, which up to now has not been genetically characterized. The genomic study disclosed that the population, even if presenting extreme morphological variation, cannot be organized in differentiated genetic subpopulations. Finally this study provides a chicken CNV map based on the 600 K SNP chip array jointly with a genome-wide gene copy number estimates in a native unselected for more than 500 years chicken population.

• Beef cattle production in Latin America is very important worldwide. The region accounts for 29% of the world's cattle population and beef production. • Genomics allows the estimation of breeding values for young animals from DNA samples through the use of panels of single nucleotide polymorphisms (a type of DNA genetic marker). This information is used to increase the accuracy of estimated breeding values. More accurate estimates for young animals should increase the rates of improvement for economically important traits. • To implement these evaluations, the effects of single nucleotide polymorphisms on the traits need to be estimated in a training population. The cost of running a training population depends on the number and types of measured traits and also on the number of phenotypes and genotypes. • Several beef cattle populations in Latin America undergo traditional genetic programs for genetic evaluation. Opportunities exist for increasing the improvement rates by using genomic selection. • Not all populations are suitable for short-term implementation of the methodology owing to the small numbers of sires with genetic evaluations and small numbers of progeny per sire. Another short-term consideration is cost, although genotyping costs are decreasing. • Longer term reasons to consider using genomic selection are to increase the competitive position of a breed in the market, to select for a larger number of traits more closely related to the economic performance of the animals in specific environments, and to detect the genes associated with variations in productivity so that genetic improvement can become more efficient. Copyright © 2012. . © 2012 Montaldo, Casas, Bento Sterman Ferraz, Vega-Murillo, and Román-Ponce.

This study aims at investigating genomic diversity of several turkey populations using Copy Number Variants (CNVs). A total of 115 individuals from six Italian breeds (Colle Euganei, Bronzato Comune Italiano, Parma e Piacenza, Brianzolo, Nero d’Italia, and Ermellinato di Rovigo), seven Narragansett, 38 commercial hybrids, and 30 Mexican turkeys, were genotyped with the Affymetrix 600K single nucleotide polymorphism (SNP) turkey array. The CNV calling was performed with the Hidden Markov Model of PennCNV software and with the Copy Number Analysis Module of SVS 8.4 by Golden Helix^®. CNV were summarized into CNV regions (CNVRs) at population level using BEDTools. Variability among populations has been addressed by hierarchical clustering (pvclust R package) and by principal component analysis (PCA). A total of 2,987 CNVs were identified covering 4.65% of the autosomes of the Turkey_5.0/melGal5 assembly. The CNVRs identified in at least two individuals were 362—189 gains, 116 losses, and 57 complexes. Among these regions the 51% contain annotated genes. This study is the first CNV mapping of turkey population using 600K chip. CNVs clustered the individuals according to population and their geographical origin. CNVs are known to be indicators also of adaptation, as some researches in different species are suggesting.

Genetic variation enables both adaptive evolutionary changes and artificial selection. Genetic makeup of populations is the result of a long-term pro