The effect of prolactin (PRL), beta-lactoglobulin (beta-LG), and kappa-casein (CSN3) on milk yield was estimated in an East Friesian dairy sheep population from Old Chatham Sheepherding Company, New York. Genotypes were determined by PCR amplification followed by digestion with HaeIII and RsaI for PRL and beta-LG, respectively, and by PCR amplification for CSN3. Monthly milking records and pedigree information were used to evaluate the effect of each polymorphism on milk yield. Results indicated that PRL genotype had a significant effect on milk yield. Ewes carrying one A allele produced 110.6g more milk per day than ewes with no A alleles. There was no statistical difference between ewes with only one A allele and ewes with 2 A alleles. No association among polymorphisms at the beta-LG and CSN3 loci and milk yield was found. The results presented in this study indicate that the PRL gene is a potential marker that could be used in selection programs for improving milk yield in dairy sheep.

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The objective of this study was to estimate genetic parameters for intramuscular fatty acids from triacylglycerol (TAG) and phospholipid (PL) fractions in beef LM tissue. Longissimus muscle samples were obtained from 1,833 Angus cattle to determine the intramuscular fatty acid composition for 31 lipids and lipid classes from TAG and PL fractions and were classified by structure into saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), omega-3 (n-3), and omega-6 (n-6) fatty acids. An atherogenic index (AI) was also determined as a measure of the unsaturated fatty acid to SFA ratio. Restricted maximum likelihood methods combined with pedigree data were used to estimate variance components with the WOMBAT software package. Heritability estimates ranged from 0.00 to 0.63 for the major classes of fatty acids. Heritability estimates differed between the TAG and PL fractions, with higher estimates for TAG up to 0.64 and lower estimates for PL that ranged from 0.00 to 0.14. Phenotypic and genetic correlations among individual fatty acids were determined for the TAG fraction as well as among carcass traits, including rib eye area, numerical marbling score, yield grade, ether fat, and Warner-Bratzler shear force value. Strong negative or positive genetic correlations were observed among individual fatty acids in the TAG fraction, which ranged from -0.99 to 0.97 ( < 0.05). Moderate correlations between carcass traits and fatty acids from the TAG fraction ranged from -0.43 to 0.32 ( < 0.05). These results indicate that fatty acids prominent in beef tissues show significant genetic variation as well as genetic relationships with carcass traits.

Fatty acid profiles and intramuscular expression of genes involved in fatty acid metabolism were characterized in concentrate- (CO) and forage- (FO) based finishing systems. Intramuscular samples from the adductor were taken at slaughter from 99 heifers finished on a CO diet and 58 heifers finished on a FO diet. Strip loins were obtained at fabrication to evaluate fatty acid profiles of LM muscle for all 157 heifers by using gas chromatography fatty acid methyl ester analysis. Composition was analyzed for differences by using the General Linear Model (GLM) procedure in SAS. Differences in fatty acid profile included a greater atherogenic index, greater percentage total MUFA, decreased omega-3 to omega-6 ratio, decreased percentage total PUFA, and decreased percentage omega-3 fatty acids in CO- compared with FO-finished heifers (P<0.05). Fatty acid profiles from intramuscular samples were ranked by the atherogenic index, and 20 heifers with either a high (HAI; n=10) or low (LAI; n=10) atherogenic index were selected for gene expression analysis using real-time PCR (RT-PCR). Gene expression data for the 20 individuals were analyzed as a 2 by 2 factorial arrangement of treatments using the GLM procedure in SAS. There was no significant diet × atherogenic index interaction identified for any gene (P>0.05). Upregulation was observed for PPARγ, fatty acid synthase (FASN), and fatty acid binding protein 4 (FABP4) in FO-finished compared with CO-finished heifers in both atherogenic index categories (P<0.05). Upregulation of diglyceride acyl transferase 2 (DGAT2) was observed in FO-finished heifers with a HAI (P<0.05). Expression of steroyl Co-A desaturase (SCD) was upregulated in CO-finished heifers with a LAI, and downregulated in FO-finished heifers with a HAI (P<0.05). Expression of adiponectin (ADIPOQ) was significantly downregulated in CO-finished heifers with a HAI compared with all other categories (P<0.05). The genes identified in this study which exhibit differential regulation in response to diet or in animals with extreme fatty acid profiles may provide genetic markers for selecting desirable fatty acid profiles in future selection programs.

Variance components were estimated and relative economic importance of bovine respiratory disease (BRD) was derived from 3 yr of performance, morbidity, and mortality data collected from a single beef cattle finishing operation. One thousand one hundred eighty nine of 12,812 Charolais-sired calves were treated for BRD during the finishing period. Weaning weight (WW), DMI, days to harvest (D2H), HCW, yield grade (YG), and marbling score determined by image analysis (MARB) were collected to quantify the economic impact associated with treatment for BRD. Observed means and (co)variances for carcass and production traits were used to simulate populations of 10,000 healthy and 10,000 BRD treated calves. A bio-economic model was developed to derive the economic value associated with the incidence and number of treatments for BRD during the finishing period. Carcasses from healthy calves were worth $58.28 more on average compared to calves treated at least once for BRD. Heritability estimates for BRD were 0.15 when the trait was measured as number of treatments (0 to 4), and 0.14 when measured as incidence (0 or 1). The model indicated that D2H had the lowest relative economic importance in this system, with a cost of $1.91 per head for each additional day on feed. Furthermore, the relative economic value of BRD morbidity was approximately 10.65 greater than D2H when recording the BRD phenotype as the number of BRD treatments. The economic values of HCW, WW, and DMI were 11.47, 5.15, and 3.61 times more important than D2H, respectively. This indicates BRD morbidity has the second greatest relative economic value in this system, with a one percent increase in morbidity associated with an average loss of $2.08 per head. These results indicate that BRD morbidity can have an equal or greater economic importance when compared to carcass and production traits during the finishing period. Further, this indicates the opportunity exists to increase the genetic merit for profitability during the finishing period by incorporating BRD incidence into terminal-sire selection indexes.

The fatty acid profile of beef is a complex trait that can benefit from gene-interaction network analysis to understand relationships among loci that contribute to phenotypic variation. Phenotypic measures of fatty acid profile from triacylglycerol and phospholipid fractions of longissimus muscle, pedigree information, and Illumina 54 k bovine SNP genotypes were utilized to derive an annotated gene network associated with fatty acid composition in 1,833 Angus beef cattle. The Bayes-B statistical model was utilized to perform a genome wide association study to estimate associations between 54 k SNP genotypes and 39 individual fatty acid phenotypes within each fraction. Posterior means of the effects were estimated for each of the 54 k SNP and for the collective effects of all the SNP in every 1-Mb genomic window in terms of the proportion of genetic variance explained by the window. Windows that explained the largest proportions of genetic variance for individual lipids were found in the triacylglycerol fraction. There was almost no overlap in the genomic regions explaining variance between the triacylglycerol and phospholipid fractions. Partial correlations were used to identify correlated regions of the genome for the set of largest 1 Mb windows that explained up to 35% genetic variation in either fatty acid fraction. SNP were allocated to windows based on the bovine UMD3.1 assembly. Gene network clusters were generated utilizing a partial correlation and information theory algorithm. Results were used in conjunction with network scoring and visualization software to analyze correlated SNP across 39 fatty acid phenotypes to identify SNP of significance. Significant pathways implicated in fatty acid metabolism through GO term enrichment analysis included homeostasis of number of cells, homeostatic process, coenzyme/cofactor activity, and immunoglobulin. These results suggest different metabolic pathways regulate the development of different types of lipids found in bovine muscle tissues. Network analysis using partial correlations and annotation of significant SNPs can yield information about the genetic architecture of complex traits.

A pedigreed population containing 71 calves and 8 sires was used to compare sire qualification using three genotyping platforms [14 microsatellite, real-time quantitative PCR, and 100, 200, 500, and 1000 single nucleotide polymorphism (SNP) arrays]. Parentage was also qualified in an unknown-pedigree population containing 8480 calves with 460 sires using SNP arrays. The three platforms qualified the true sire in the known-pedigree population with zero mismatches. The 100 and 200 SNP arrays yielded specificities of 0.92 and 0.99 with a 1% mismatch rate in the knownpedigree population, respectively. In the larger population, SNP panels of the 500 and 1000 highest minor allele frequency SNPs were also evaluated. The 1000 SNP panel qualified paternity to a single sire for 82.1% of calves with 1% or 2% mismatches. Not all commercial sires were genotyped, which accounts for missing paternity for some calves. In this larger population, the 100 SNP array qualified multiple sires to 0.42% of calves and single sires to 80.84% of calves without mismatches. The 200 SNP array assigned unique paternity, and 79.8% of calves were qualified to a sire without mismatches. With a 2% mismatch rate, sire qualifications agreed with the 1000 SNP array. This study highlights the interplay among population size, genotyping error rates, and the specificity and sensitivity of parentage platforms.Key words: SNP parentage panel, sensitivity (parentage), specificity (parentage), Charolais, cattle (beef).Résumé : Une population à pedigree contenant 71 veaux et 8 géniteurs mâles a été utilisée pour comparer la qualification des géniteurs mâles au moyen de trois plateformes de génotypage (14 microsatellites, PCR quantitative en temps réel, ainsi que des réseaux de 100, 200, 500, et 1000 SNPs). La parenté a aussi été qualifiée dans une population de pedigree inconnu contenant 8480 veaux et 460 géniteurs mâles au moyen des réseaux de SNPs. Les trois plateformes ont qualifié le véritable géniteur dans la population à pedigree connu avec aucun écart. Les réseaux à 100 et 200 SNPs ont rendu des spécificités de 0,92 et 0,99 avec un taux d'écart de 1 % dans la population à pedigree connu, respectivement. Dans la plus grande population, les panels de SNPs de 500 et 1000 SNPs de fréquence d'allèles mineurs les plus élevés ont aussi été évalués. Le panel de 1000 SNPs a qualifié la paternité à un seul géniteur pour 82,1 % des veaux avec seulement 1 % à 2 % d'écarts. Tous les géniteurs mâles commerciaux n'ont pas été génotypés ce qui explique la paternité manquante pour certains veaux. Dans cette population plus grande, le réseau à 100 SNPs a qualifié de multiples géniteurs à 0,42 % des veaux et un seul géniteur à 80,84 % des veaux sans écarts. Le réseau à 200 SNPs a assigné une paternité unique et 79,8 % des veaux ont été qualifiés à un géniteur sans écart. Avec un taux d'écart de 2 %, la qualification des géniteurs était en accord avec le réseau de 1000 SNPs. Cette étude souligne l'interdépendance entre la taille de la population, les taux d'éca...

The objective of this study was to evaluate the effects of various data structures on the genetic evaluation for the binary phenotype of reproductive success. The data were simulated based on an existing pedigree and an underlying fertility phenotype with a heritability of 0.10. A data set of complete observations was generated for all cows. This data set was then modified mimicking the culling of cows when they first failed to reproduce, cows having a missing observation at either their second or fifth opportunity to reproduce as if they had been selected as donors for embryo transfer, and censoring records following the sixth opportunity to reproduce as in a cull-for-age strategy. The data were analyzed using a third order polynomial random regression model. The EBV of interest for each animal was the sum of the age-specific EBV over the first 10 observations (reproductive success at ages 2-11). Thus, the EBV might be interpreted as the genetic expectation of number of calves produced when a female is given ten opportunities to calve. Culling open cows resulted in the EBV for 3 year-old cows being reduced from 8.27 ± 0.03 when open cows were retained to 7.60 ± 0.02 when they were culled. The magnitude of this effect decreased as cows grew older when they first failed to reproduce and were subsequently culled. Cows that did not fail over the 11 years of simulated data had an EBV of 9.43 ± 0.01 and 9.35 ± 0.01 based on analyses of the complete data and the data in which cows that failed to reproduce were culled, respectively. Cows that had a missing observation for their second record had a significantly reduced EBV, but the corresponding effect at the fifth record was negligible. The current study illustrates that culling and management decisions, and particularly those that impact the beginning of the trajectory of sustained reproductive success, can influence both the magnitude and accuracy of resulting EBV.