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Da Cruz V.A.R.,Sao Paulo State University | Schenkel F.S.,University of Guelph | Savegnago R.P.,Sao Paulo State University | Grupioni N.V.,Sao Paulo State University | And 6 more authors.
PLoS ONE | Year: 2015

Apolipoprotein B (APOB) and Adiponectin Receptor 1 (ADIPOR1) are related to the regulation of feed intake, fat metabolism and protein deposition and are candidate genes for genomic studies in birds. In this study, associations of two single nucleotide polymorphisms (SNPs) g.102A>T (APOB) and g.729C>T (ADIPOR1) with carcass, bone integrity and performance traits in broilers were investigated. Genotyping was performed on a paternal line of 1,454 broilers. The SNP detection was carried out by PCR-RFLP technique using the restriction enzymes HhaI for the SNP g.729C>T and MslI for the SNP g.102A>T. The association analyses of the two SNPs with 85 traits were performed using the restricted maximum likelihood (REML) and Generalized Quasi-Likelihood Score (GQLS) methods. For REML the model included the random additive genetic effect of animal and fixed effects of sex, hatch and SNP genotypes. In the GQLS method, a logistic regression was used to associate the genotypes with phenotypes adjusted for fixed effects of sex and hatch. The SNP g.729C>T in the ADIPOR1 gene was associated with thickness of the femur and breast skin yield. Thus, the ADIPOR1 gene seems implicated in the metabolism and/or fat deposition and bone integrity in broilers. © 2015 Cruz et al.


Forutan M.,Isfahan University of Technology | Ansari Mahyari S.,Isfahan University of Technology | Sargolzaei M.,Semex Alliance | Sargolzaei M.,University of Guelph
Journal of Animal Breeding and Genetics | Year: 2015

Calf and heifer survival are important traits in dairy cattle affecting profitability. This study was carried out to estimate genetic parameters of survival traits in female calves at different age periods, until nearly the first calving. Records of 49 583 female calves born during 1998 and 2009 were considered in five age periods as days 1-30, 31-180, 181-365, 366-760 and full period (day 1-760). Genetic components were estimated based on linear and threshold sire models and linear animal models. The models included both fixed effects (month of birth, dam's parity number, calving ease and twin/single) and random effects (herd-year, genetic effect of sire or animal and residual). Rates of death were 2.21, 3.37, 1.97, 4.14 and 12.4% for the above periods, respectively. Heritability estimates were very low ranging from 0.48 to 3.04, 0.62 to 3.51 and 0.50 to 4.24% for linear sire model, animal model and threshold sire model, respectively. Rank correlations between random effects of sires obtained with linear and threshold sire models and with linear animal and sire models were 0.82-0.95 and 0.61-0.83, respectively. The estimated genetic correlations between the five different periods were moderate and only significant for 31-180 and 181-365 (rg = 0.59), 31-180 and 366-760 (rg = 0.52), and 181-365 and 366-760 (rg = 0.42). The low genetic correlations in current study would suggest that survival at different periods may be affected by the same genes with different expression or by different genes. Even though the additive genetic variations of survival traits were small, it might be possible to improve these traits by traditional or genomic selection. © 2015 Blackwell Verlag GmbH.


Anzar M.,Agriculture and Agri Food Canada | Kroetsch T.,Semex Alliance | Boswall L.,Agriculture and Agri Food Canada
Animal Reproduction Science | Year: 2011

In the Canadian Animal Genetic Resource Program, bull semen is donated in frozen or fresh (diluted) states. This study was designed to assess the cryopreservation of diluted bull semen shipped at 4. °C overnight, and to determine the post-thaw quality of shipped semen using different straw volumes and freezing rates. Semen was collected from four breeding bulls (three ejaculates per bull). Semen was diluted in Tris-citric acid-egg yolk-glycerol (TEYG) extender, cooled to 4. °C and frozen as per routine (control semen). After cooling to 4. °C, a part of semen was removed and shipped overnight to the research laboratory via express courier (shipped semen). Semen was packaged in 0.25 or 0.5. ml straws and frozen in a programmable freezer using three freezing rates, i.e., -10, -25 or -40. °C/min. Control semen was also shipped to the research laboratory. Post-thaw sperm motility characteristics were assessed using CASA, and post-thaw sperm plasma membrane, mitochondrial membrane potential and normal acrosomes were assessed using flow cytometry. Post-thaw sperm quality was greater in shipped semen as compared to control (P<. 0.001). The shipped semen packaged in 0.25. ml straws had better post-thaw sperm quality than in 0.5. ml straws (P<. 0.001). Freezing rate had no effect on post-thaw sperm quality. In conclusion, bull semen can be shipped overnight for subsequent cryopreservation and gene banking. Overnight shipping of semen was found advantageous for bull semen cryopreservation. Semen packaging in 0.25. ml straws yielded better post-thaw quality than 0.5. ml straws. © 2011.


Sargolzaei M.,University of Guelph | Chesnais J.P.,Semex Alliance | Schenkel F.S.,University of Guelph
BMC Genomics | Year: 2014

Background: Genotype imputation can help reduce genotyping costs particularly for implementation of genomic selection. In applications entailing large populations, recovering the genotypes of untyped loci using information from reference individuals that were genotyped with a higher density panel is computationally challenging. Popular imputation methods are based upon the Hidden Markov model and have computational constraints due to an intensive sampling process. A fast, deterministic approach, which makes use of both family and population information, is presented here. All individuals are related and, therefore, share haplotypes which may differ in length and frequency based on their relationships. The method starts with family imputation if pedigree information is available, and then exploits close relationships by searching for long haplotype matches in the reference group using overlapping sliding windows. The search continues as the window size is shrunk in each chromosome sweep in order to capture more distant relationships.Results: The proposed method gave higher or similar imputation accuracy than Beagle and Impute2 in cattle data sets when all available information was used. When close relatives of target individuals were present in the reference group, the method resulted in higher accuracy compared to the other two methods even when the pedigree was not used. Rare variants were also imputed with higher accuracy. Finally, computing requirements were considerably lower than those of Beagle and Impute2. The presented method took 28 minutes to impute from 6 k to 50 k genotypes for 2,000 individuals with a reference size of 64,429 individuals.Conclusions: The proposed method efficiently makes use of information from close and distant relatives for accurate genotype imputation. In addition to its high imputation accuracy, the method is fast, owing to its deterministic nature and, therefore, it can easily be used in large data sets where the use of other methods is impractical. © 2014 Sargolzaei et al.; licensee BioMed Central Ltd.


Kumar A.,Agriculture and Agri Food Canada | Kumar A.,University of Saskatchewan | Kumar A.,Guru Angad Dev Veterinary and Animal Sciences University | Kroetsch T.,Semex Alliance | And 3 more authors.
Molecular Reproduction and Development | Year: 2015

Early estimation of bull fertility is highly desirable for the conservation of male genetics of endangered species and for the exploitation of genetically superior sires in artificial insemination programs. The present work was conducted as a proof-of-principle study to identify fertility-associated metabolites in dairy bull seminal plasma and blood serum using proton nuclear magnetic resonance (1H NMR). Semen and blood samples were collected from high- and low-fertility breeding bulls (n=5 each), stationed at Semex, Guelph, Canada. NMR spectra of serum and seminal plasma were recorded at a resonance frequency of 500.13MHz on a Bruker Avance-500 spectrometer equipped with an inverse triple resonance probe (TXI, 5mm). Spectra were phased manually, baseline corrected, and calibrated against 3-(trimethylsilyl) propionic-2,2,3,3-d4 acid at 0.0 parts per million (ppm). Spectra were converted to an appropriate format for analysis using Prometab software running within MATLAB. Principal component analysis was used to examine intrinsic variation in the NMR data set, and to identify trends and to exclude outliers. Partial least square-discriminant analysis was performed to identify the significant features between fertility groups. The fertility-associated metabolites with variable importance in projections (VIP) scores >2 were citrate (2.50ppm), tryptamine/taurine (3.34-3.38ppm), isoleucine (0.74ppm), and leucine (0.78ppm) in the seminal plasma; and isoleucine (1.14ppm), asparagine (2.90-2.94ppm), glycogen (3.98ppm), and citrulline (1.54ppm) in the serum. These metabolites showed identifiable peaks, and thus can be used as biomarkers of fertility in breeding bulls. Mol. Reprod. Dev. 82: 123-131, 2015. © 2015 Wiley Periodicals, Inc.

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