Genome-Wide Association Studies for Methane Production in Dairy Cattle.

Genomic selection has been proposed for the mitigation of methane (CH4) emissions by cattle because there is considerable variability in CH4 emissions between individuals fed on the same diet. The genome-wide association study (GWAS) represents an important tool for the detection of candidate genes, haplotypes or single nucleotide polymorphisms (SNP) markers related to characteristics of economic interest. The present study included information for 280 cows in three dairy production systems in Mexico: 1) Dual Purpose (n = 100), 2) Specialized Tropical Dairy (n = 76), 3) Familiar Production System (n = 104). Concentrations of CH4 in a breath of individual cows at the time of milking (MEIm) were estimated through a system of infrared sensors. After quality control analyses, 21,958 SNPs were included. Associations of markers were made using a linear regression model, corrected with principal component analyses. In total, 46 SNPs were identified as significant for CH4 production. Several SNPs associated with CH4 production were found at regions previously described for quantitative trait loci of composition characteristics of meat, milk fatty acids and characteristics related to feed intake. It was concluded that the SNPs identified could be used in genomic selection programs in developing countries and combined with other datasets for global selection.

Looking at genetic structure and selection signatures of the Mexican chicken population using single nucleotide polymorphism markers.

Genetic variation enables both adaptive evolutionary changes and artificial selection. Genetic makeup of populations is the result of a long-term process of selection and adaptation to specific environments and ecosystems. The aim of this study was to characterize the genetic variability of México's chicken population to reveal any underlying population structure. A total of 213 chickens were sampled in different rural production units located in 25 states of México. Genotypes were obtained using the Affymetrix Axiom® 600 K Chicken Genotyping Array. The Identity by Descent (IBD) and the principal components analysis (PCA) were performed by SVS software on pruned single nucleotide polymorphisms (SNPs).ADMIXTURE analyses identified 3 ancestors and the proportion of the genetic contribution of each of them has been determined in each individual. The results of the Neighbor-Joining (NJ) analysis resulted consistent with those obtained by the PCA. All methods utilized in this study did not allow a classification of Mexican chicken in distinct clusters or groups. A total of 3,059 run of homozygosity (ROH) were identified and, being mainly short in length (<4 Mb), these regions are indicative of a low inbreeding level in the population. Finally, findings from the ROH analysis indicated the presence of natural selective pressure in the population of Mexican chicken.The study indicates that the Mexican chicken clearly appear to be a unique creole chicken population that was not subjected to a specific artificial selection. Results provide a genetic knowledge that can be used as a basis for the genetic management of a unique and very large creole population, especially in the view of using it in production of hybrids to increase the productivity and economic revenue of family farming agriculture, which is widely present in México.

Genomic variability in Mexican chicken population using copy number variants.

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.

Season of the year influences testosterone secretion in bulls administered luteinizing honrmone.

The objective of the present study was to evaluate the secretion of testosterone (T) in bulls in response to the administration of varying doses of bovine LH (bLH) during the four seasons of the year. Five adult bulls (4 yr of age) were treated with an amount of bLH that was estimated to induce a 5 ng/mL amplitude pulse of LH in blood serum on five consecutive days around the spring equinox, summer solstice, fall equinox, and winter solstice. Five hours after this dose, bulls were treated with bLH in amounts that were estimated to induce a 0.25, 0.5, 1, 2, or 4 ng/mL amplitude LH pulse in blood serum in a Latin square design. Blood samples were collected for 5 h after administration of a dose of bLH that was estimated to induce the 5-ng amplitude LH pulse, and for 3 h after administration of the variable doses of bLH, and were then assayed for concentrations of T. Average concentrations and amplitude of T release after doses of bLH that were estimated to induce the 5-ng amplitude LH pulses were greater during the spring and summer than during the winter (P < 0.05). The area under the release curve (AUC) was greater during the spring than during the winter (P < 0.05). During the 3 h after treatment with the variable doses of bLH, T response was affected by dose (P < 0.001) and season (P < 0.001), but there was no dose x season interaction. Testosterone response increased in a dose-dependent fashion for all variables studied. The greatest average concentrations of T and AUC were observed in the spring compared with the fall and winter (P < 0.05). These data support our working hypothesis that testes of bulls are more responsive in releasing T in response to bLH stimulation in the spring and summer compared with the winter; however, there were no changes in sensitivity of the testes to LH during different seasons of the year as indicated by the lack of a dose of bLH x season interaction.

Laying hen behavior 2. Cage type preference and heterophil to lymphocyte ratios.

Studies were conducted to determine hen preference for and stress response to cage type. By using a plywood (1.25 cm) test apparatus with open- and solid-sided compartments and a plexiglass divider at the entrance for controlling passage, birds (n = 20) were evaluated as to their choice of compartment after training and acclimation. For each test, after training, an individual bird was placed in the start box and given 1 min to acclimate before making a choice. The experiment was repeated after rotating the apparatus 180 degrees. In Experiment 1, the open-sided compartment was chosen by 45% of the hens, and the solid-sided compartment by 25% (P = 0.02); 30% chose neither. In Experiment 2, the compartment with open sides was chosen by 70% of the hens, and that with solid sides was chosen by 15% (P = 0.004); 15% chose neither. The length of time required to choose one compartment over the other did not differ in either experiment (P = 0.29; P = 0.76). In Experiment 3, tests were videotaped from 0830 h to 1330 h, and tapes were scored for time spent in each compartment. Birds were observed to spend more time in open- compared with solid-sided compartments (P = 0.02). To assess stress level of birds exposed to each type of enclosure, blood was collected from 24 commercial Hy-Line W36 hens housed long-term in either open (n = 12) or solid (n = 12) cages, and heterophil:lymphocyte (H:L) ratios were determined. Birds in solid cages had higher H:L ratios than did birds in open cages (P = 0.02), indicating a greater stress response. These data would suggest that hens may prefer greater visual access to their surroundings afforded by open cages.