New alleles in calpastatin gene are associated with meat quality traits in pigs

Suggestive QTL affecting raw firmness scores and average Instron force, tenderness, juiciness, and chewiness on cooked meat were mapped to pig chromosome 2 using a three-generation intercross between Berkshire and Yorkshire pigs. Based on its function and location, the calpastatin (CAST) gene was considered to be a good candidate for the observed effects. Several missense and silent mutations were identified in CAST and haplotypes covering most of the coding region were constructed and used for association analyses with meat quality traits. Results demonstrated that one CAST haplotype was significantly associated with lower Instron force and cooking loss and higher juiciness and, therefore, this haplotype is associated with higher eating quality. Some of the sequence variation identified may be associated with differences in phosphorylation of CAST by adenosine cyclic 3', 5'-monophosphate-dependent protein kinase and may in turn explain the meat quality phenotypic differences. The beneficial haplotype was present in all the commercial breeds tested and may provide significant improvements for the pig industry and consumers because it can be used in marker-assisted selection to produce naturally tender and juicy pork without additional processing steps.

Characterization of quantitative trait loci for growth and meat quality in a cross between commercial breeds of swine

A three-generation resource family was created by crossing two Berkshire grandsires with nine Yorkshire granddams to identify QTL affecting growth, body composition, and meat quality. A total of 512 F2 offspring were evaluated for 11 traits related to growth and body composition and 28 traits related to meat quality. All animals were initially genotyped for 125 markers across the genome. The objectives of this advanced phase of the project were to further identify and characterize QTL after genotyping for another 33 markers in special regions of interest, and to develop and apply methods for detecting QTL with parent-of-origin effects. New marker linkage maps were derived and used in QTL analysis based on line-cross least squares regression-interval mapping. A decision tree for identifying QTL with parent-of-origin effects was developed based on tests against the Mendelian mode of expression. Empirical significance thresholds were derived at chromosomewise and genomewise levels using specialized permutation strategies to create data under the null hypothesis appropriate for each test. Significance thresholds derived by the permutation tests were validated based on simulation of a pedigree and data structure similar to the Berkshire-Yorkshire population. The addition of 33 markers resulted in the discovery of 29 new QTL at the 5% chromosomewise level using the Mendelian model of analysis. Thirteen of the original QTL were no longer significant at the 5% chromosomewise level. A total of 33 QTL with parent-of-origin effects were identified, including QTL with paternal expression for backfat and loin muscle area on chromosome 2, near IGF2, and QTL with maternal expression for drip loss and reflectance on chromosome 9. Tests for imprinting against Mendelian expression identified much fewer QTL with parent-of-origin effects than tests based on significance of paternal and maternal alleles, which have been used in other studies. The detected QTL and their identified mode of expression will allow further research in these QTL regions and their utilization in marker-assisted improvement of meat quality.

Evaluation of strategies for selection for lean growth rate in pigs

Lean growth rate (LGR) in pigs is a nonlinear biological function of growth rate and lean quantity. According to animal breeding theory, genetic progress for LGR is maximized with selection on a linear index of its component traits, but selection on direct EBV for LGR is also common. In this study, the performance of five criteria for selection on estimated LGR in pigs was evaluated through simulation over five generations: linear indexes of multiple-trait EBV of component traits with or without updating index weights in each generation; a nonlinear index of multiple-trait EBV of component traits; and direct selection on EBV for LGR from a single-trait model or a multiple-trait model that included LGR and component traits. The nonlinear index yielded the highest response in LGR in Generation 5, but the linear index with updating performed almost as well. Not updating weights for the linear index reduced response in LGR by 1.1% in Generation 5 (P < 0.05). Direct selection on single-trait EBV for LGR yielded the lowest responses in Generation 5. Direct selection on EBV for LGR from a multiple-trait animal model yielded a 3.1% greater response in LGR in Generation 5 than direct selection on EBV for LGR based on a single-trait animal model (P < 0.05), but yielded a 1.9% lower response than the nonlinear index. Although differences in response in LGR were limited, alternative selection criteria resulted in substantially different responses in component traits. Linear index selection for LGR placed more emphasis on lean quantity, whereas direct selection for LGR emphasized growth rate. Based on the relative changes in the responses in LGR, selection for estimated LGR based on a nonlinear index or a linear index with updating is recommended for use in the swine industry.

Genetic parameters and trends for litter traits in U.S. Yorkshire, Duroc, Hampshire, and Landrace pigs

Records on 251,296 Yorkshire, 75,262 Duroc, 83,338 Hampshire, and 53,234 Landrace litters born between 1984 and April of 1999 in herds on the National Swine Registry Swine Testing and Genetic Evaluation System were analyzed. Animal model and restricted maximum likelihood procedures were used to estimate variances of animal genetic (a), maternal genetic (m), permanent environmental, and service sire, and the covariances between a and m for number born alive (NBA), litter weight at 21 d (L21WT), and number weaned (NW). Fixed effects of contemporary groups were included in the analysis. Based on a single-trait model, estimates of heritabilities were 0.10, 0.09, 0.08, and 0.08 for NBA; 0.08, 0.07, 0.08, and 0.09 for L21WT; and 0.05, 0.07, 0.05, and 0.05 for NW in the Yorkshire, Duroc, Hampshire, and Landrace breeds, respectively. Estimates of maternal genetic effects were low and ranged from 0.00 to 0.02 for all traits and all breeds. Estimates of permanent environmental effects ranged from 0.03 to 0.08. Estimates of service sire effects ranged from 0.02 to 0.05. A bivariate analysis was used to estimate the genetic correlations among traits. Average genetic correlations over the four breeds were 0.13, 0.15, and 0.71 for NBA with L21WT, NBA with NW, and L21WT with NW, respectively. Average genetic trends were 0.018 pigs/yr, 0.114 kg/yr, and 0.004 pigs/yr for NBA, L21WT, and NW, respectively. Although estimates of heritabilities for litter traits were low and similar across breeds, genetic variances for litter traits were sufficiently large to indicate that litter traits could be improved through selection. This study presents the first set of breed-specific estimates of genetic parameters available from large numbers of field records. It provides information for use in national genetic evaluations.

The relationship between milk production and antibody response to ovalbumin during the peripartum period

Suboptimal innate and immune mechanisms of host resistance during the peripartum period may contribute to increased incidence of mastitis. To evaluate associations between antibody response to ovalbumin and milk production during the peripartum period, 136 Holstein cows and heifers from three herds with known antibody response profiles, were evaluated for projected 305-d milk, protein, and fat yield. Using a previously described index (Wagter et al., 2000), cows were quantitatively classified based on their profile of antibody response to ovalbumin into high, average, or low antibody response groups. The single-effect antibody response group contributed significantly to variation in fat and protein yield, but not milk yield. The interaction between antibody response and parity significantly contributed to the variation in milk, fat, and protein yields; therefore the effects of group were reported on a within-parity basis. Among first-parity cows, low responders had a higher fat and protein yield than high or average antibody responder animals. Among older cows (parity 3 or greater) milk yield was significantly higher for those in the high antibody response group compared with average and low response groups. However, no significant differences in fat or protein yields were observed between high and low antibody response groups. These results suggest the possibility to select cows for enhanced immune response with no adverse effects on yield. That first-parity cows with low antibody response produce more fat and protein may be offset by the fact that mastitis occurrence was highest in this group in two out of three herds investigated. Selection for high immune response may prove beneficial to herd life by maintaining optimal yield, yet minimizing occurrence of disease.

Genetic parameters and trends for lean growth rate and its comvonents in U.S. Yorkshire, Duroc, Hampshire, and Landrace pigs

Records on 361,300 Yorkshire, 154,833 Duroc, 99,311 Hampshire, and 71,097 Landrace pigs collected between 1985 and April of 2000 in herds on the National Swine Registry Swine Testing and Genetic Evaluation System were analyzed. Animal model and REML procedures were used to estimate random effects of animal genetic, common litter, maternal genetic, and the covariances between animal and maternal for lean growth rate (LGR), days to 113.5 kg (DAYS), backfat adjusted to 113.5 kg (BF), and loin eye area adjusted to 113.5 kg (LEA). Fixed effects of contemporary group and sex were also in the statistical model. Based on the single-trait model, estimates of heritabilities were 0.44, 0.44, 0.46, and 0.39 for LGR; 0.35, 0.40, 0.44, and 0.40 for DAYS; 0.48, 0.48, 0.49, and 0.48 for BF; and 0.33, 0.32, 0.35, and 0.31 for LEA in the Yorkshire, Duroc, Hampshire, and Landrace breeds, respectively. Estimates of maternal genetic effects were low and ranged from 0.01 to 0.05 for all traits across breeds. Estimates of common litter effects ranged from 0.07 to 0.16. A bivariate analysis was used to estimate the genetic correlations between lean growth traits. Average genetic correlations over four breeds were -0.83, -0.37, 0.44, -0.07, 0.08, and -0.37 for LGR with DAYS, BF, and LEA, DAYS with BF and LEA, and BF with LEA, respectively. Average genetic trends were 2.35 g/yr, -0.40 d/yr, -0.39 mm/yr, and 0.37 cm2/yr for LGR, DAYS, BF, and LEA, respectively. Results indicate that selection based on LGR can improve leanness and growth rate simultaneously and can be a useful biological selection criterion.

Correlations among selected pork quality traits

Establishing relationships among specific quality traits is important if significant progress toward developing improved pork quality is to be realized. As part of a study to examine the individual effects of genes on meat quality traits in pigs, a three-generation resource family was developed. Two Berkshire sires and nine Yorkshire dams were used to produce nine F1 litters. Sixty-five matings were made from the F1 litters to produce four sets of F2 offspring, for a total of 525 F2 animals used in the study. These F2 animals were slaughtered at a commercial facility upon reaching approximately 110 kg. Carcass composition traits, pH measurements, and subjective quality scores were made at 24 h postmortem. Loin samples (n = 525) were collected at 48 h postmortem, and meat quality traits were evaluated. These traits included pH (48 h), Hunter L-values, drip loss, glycolytic potential, ratio of type IIa/IIb myosin heavy chains (IIa/IIb), total lipid, instrumental measures of tenderness using the Star Probe attachment of the Instron, cook loss measurements, and sensory evaluations. Significant phenotypic correlations were found between many carcass, instrumental, and biochemical measurements, and sensory quality traits. Star Probe measurements were significantly correlated with drip loss (0.29), glycolytic potential (0.30), pH (-0.29), total lipid (-0.14), and Hunter L-values (0.28). Drip loss was significantly correlated with glycolytic potential (0.36), pH (-0.28), IIa/IIb (-0.10), and Hunter L-values (0.33). Hunter L-values were also significantly correlated with total lipid (0.33) and IIa/ IIb (-0.11). Sensory tenderness, flavor, and off-flavor scores were significantly correlated with drip loss, pH, and glycolytic potential measurements. Marbling score, total lipid, and drip loss were not significantly correlated with sensory juiciness scores, but cooking loss was. Marbling and total lipid were significantly correlated with firmness scores (0.37 and 0.31, respectively). Taken together, the data in this study suggest that changes in some meat quality traits can affect many other meat quality attributes. The correlations yield information that could aid in directing future studies aimed at understanding the underlying biological mechanisms behind the development of many quality traits.

Selection for lean growth rate and correlated responses in litter traits in a synthetic line of Yorkshire-Meishan pigs

Selection for lean growth rate (LGR) was conducted for four generations in a synthetic line of Yorkshire-Meishan pigs to study the effectiveness of selection for LGR and correlated responses in litter traits. Lean growth rate was estimated from ultrasound measurements of 10th-rib backfat thickness and longissimus muscle area. In the selection line, 7 boars and 20 gilts with the highest LGR were selected to produce the next generation. The generation interval was 13 mo and the average selection differential per generation was 1.1 phenotypic standard deviation units. A contemporaneous control line was maintained by randomly selecting 5 boars and 15 gilts. Data from a total of 1057 pigs sired by 58 boars and out of 133 sows were available from the two lines. Selection responses were estimated from deviations of the selection line from the control line using least squares (LS) and by multiple trait derivative-free restricted maximum likelihood analysis using an animal model (AM). The estimate of response to selection per generation using LS was 9.4 ± 0.95 g d–1 for LGR. The corresponding estimate from the AM was 9.8 ± 0.51 g d–1. Correlated responses in litter traits were regressed on generation. For the LS method, regression coefficients were negative but not significant (P > 0.05) for total number born, number born alive, and number at 21 d and at 42 d. Significant, positive correlated responses occurred in 42-d litter weight and 21-d piglet weight (P < 0.05). For the AM method, the regression coefficients were also negative, but were not significant (P > 0.05) for numberalive at birth, at 21 d, and at 42 d. A significant positive correlated response occurred only for 42-d litter weight (P < 0.05). Although results are based on a population of limited size, it can be concluded that selection for LGR in a synthetic line is effective and should have little effect on litter traits. Key words: Pigs, selection, lean growth rate, correlated response

Genetic and phenotypic parameter estimates between production, feed intake, feed efficiency, body weight and linear type traits in first lactation Holsteins

Production and feed intake data on 36 115 first lactation Holstein cows obtained from Quebec Dairy Herd Analysis Service were combined with conformation data from the Holstein Association of Canada to estimate genetic correlations among production, energy intake, and conformation traits. Traits considered were 305-d milk yield, 305-d grain energy and total energy intake, feed efficiency (fat corrected milk yield/total energy intake), body weight at calving, capacity, size, stature, rump width and final score. Genetic and phenotypic parameters were estimated using Restricted Maximum Likelihood based on two-trait animal mixed model analyses. The model contained fixed effects of herd-year, season of calving, age of calving, sire group and a random animal genetic effect. Estimates of heritability were within the published range for all traits. Of the conformation traits examined, capacity, size and stature had the highest correlations with body weight, with phenotypic correlations between 0.36 and 0.43, and genetic correlations between 0.61 and 0.79. Feed efficiency was negatively correlated to all body size measures, both phenotypically (−0.01 to −0.29) and genetically (−0.31 to −0.53), but most significantly with body weight, capacity, size, and stature. Fat-corrected milk yield showed negligible phenotypic and low to moderately negative genetic (−0.07 to −0.29) correlations with body weight and related type traits. Total energy intake was positively related to all measures of body size, most notably body weight, while grain energy intake had moderately negative genetic correlations (−0.20 to −0.40) with the same body size traits. Because of their detrimental relationships with feed efficiency, negative selection emphasis should be placed on body weight and the related type traits capacity, size and stature. Capacity, size and stature are of moderate utility when selecting indirectly for body weight, total energy intake and feed efficiency. Key words: Dairy cattle, genetics, production, conformation, feed efficiency

Expected genetic responses from selection indexes for Canadian dairy cattle under present and future milk pricing systems

Expected selection responses and profit under alternative milk pricing scenarios for various selection indexes were compared: Lifetime Profit Index (LPI) with 60:40:0:0 emphasis on production:type:herdlife:somatic cell score and 9:2:0 relative weights on Protein:fat:milk, and Total Economic Value (TEV) reflecting the present pricing system, Neutral Total Economic Value (NTEV) and Future Total Economic Value (FTEV) reflecting future milk prices, each with 64:0:26:10 emphasis on production:type:herdlife:somatic cell score and 9:2:0, 1:0:0 and 18:–2:–5 relative weights, respectively, on protein:fat:milk and Large Herd Operator Index (LHO) with 83:17:0:0 emphasis and 13.5:–1.5:0 relative weights. Among the correlations between indexes the lowest was.93 (correlation of LPI with NTEV and FTEV) and the highest was 0.99 (between TEV and NTEV). For present and probable future milk pricing the most profitable sire selection indexes were TEV and FTEV in both whole and grade-only populations. When selection intensity and number of daughters per sire were equal to 1.0 and 50, respectively, profit expressed in Canadian dollars in net present value of lifetime profit of a milking daughter were 231.75 (226.62 in grade population) and 234.89 (229.89 in grade population) from TEV and FTEV respectively. The choice of sire selection indexes depends on individual farmer goals. However, if the total economic merit resulting from typical dairy production is the goal, then TEV and FTEV are advised for short-term and long term selection, respectively. Key words: Index, selection, genetic response, profit, milk pricing

Lifetime profitability measures for dairy cows and their relationships to lifetime performance traits

The objectives of this study were to evaluate and compare alternative measures of individual cow lifetime profitability and to determine what lifetime traits are significantly related to profitability of dairy cattle. Profitability measures considered were: 1) lifetime milk revenue minus lifetime feed costs (MMF); 2) lifetime profit (LP); 3) discounted lifetime profit (DLP); 4) annualized DLP per year of total life (ADLPLTL); 5) annualized DLP per year of productive life (ADLPLPL); 6) DLP adjusted for opportunity cost of postponed replacement (DLPOC), and 7) economic efficiency (EF). Data for this study consisted of 1112 lifetime performance records of Holstein cows from the National Cooperative Dairy Cattle Breeding Project, which was implemented by Agriculture Canada in 1972. Correlations were highest among MMF, LP, and DLP. EF had slightly lower correlations with MMF, LP, and DLP, but higher with ADLPLTL and ADLPLPL. ADLPLPL and DLPOC had low correlations with all other measures. DLPOC was recommended as the best because it considered the opportunity costs of postponed replacement.For DLPOC, average milk revenue per lactation was found to be the most important income trait, followed by length of productive life. Days dry (average over completed lactations) had the greatest negative impact on profitability. Age at first calving and average number of veterinary treatments for reproductive diseases over lactations were both negative contributions to profit. Lifetime traits accounted for 65% of variation in DLPOC. Key words: Dairy cow, profitability, lifetime traits

Relationships of early performance traits to lifetime profitability in Holstein cows

Relationships of first lactation traits to lifetime profitability were studied based on data of 1112 lifetime performance records of purebred Holstein cows from the National Cooperative Dairy Cattle Breeding Project, which was implemented by Agriculture Canada in 1972. Lifetime profit was defined based on milk production, body weight, reproductive performance, herdlife, and prices for feed energy, milk, calves, salvage value, and fixed costs. First lactation traits with significant relationships to lifetime profitability were identified using the backward elimination procedure for least squares. Relative weights of each prediction trait were expressed as standard partial regression coefficients. Milk revenue in first lactation was the most important trait, followed by 3 min yield, and udder height. First lactation survival was found to be significant. Increasing age at first calving, number of days from first breeding to conception in first lactation, and teat diameter had significant negative effects on profit. Health traits in first lactation were not significant. The significant traits explained 35% of total variation in lifetime profitability. Key words: Dairy cow, lifetime profitability, early indicator traits

Comparison of rebreeding policies for Ontario dairy herds

Net-revenues of rebreeding policies that differed in the maximum allowable days after calving for breeding were compared using data generated by a dynamic stochastic simulation model of Ontario dairy herds. Such comparisons benefit farmer decision support, as rebreeding decisions are important management choices. Rebreeding up to 168 d after calving only was least optimal. Hence, the rebreeding period should not be too short. At average and high herd fertility, a rebreeding policy under which cows with a mature equivalent milk production level lower than 80%, between 80 and 100%, and greater than 100% of the herd average were not rebred, bred up to 168 d after calving, and bred up to 250 d after calving, respectively, resulted in higher net-revenue than rebreeding policies that used a single cut-off for all cows. Differences in net-revenue between the optimal and the least optimal policy were $217.90 and $114.40 per cow per year for the lowest and highest simulated reproductive performance, respectively. At low herd fertility, rebreeding up to 364 d postpartum was optimal. However, at this level of performance emphasis should be given to improving fertility, rather than choice of rebreeding policy. Key words: Dairy cattle, simulation, economics, insemination policy, rebreeding policy