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PubMed2005

Comparison of three models to estimate breeding values for percentage of loin intramuscular fat in Duroc swine.

Three selection models were evaluated to compare selection candidate rankings based on EBV and to evaluate subsequent effects of model-derived EBV on the selection differential and expected genetic response in the population. Data were collected from carcass- and ultrasound-derived estimates of loin i.m. fat percent (IMF) in a population of Duroc swine under selection to increase IMF. The models compared were Model 1, a two-trait animal model used in the selection experiment that included ultrasound IMF from all pigs scanned and carcass IMF from pigs slaughtered to estimate breeding values for both carcass (C1) and ultrasound IMF (U1); Model 2, a single-trait animal model that included ultrasound IMF values on all pigs scanned to estimate breeding values for ultrasound IMF (U2); and Model 3, a multiple-trait animal model including carcass IMF from slaughtered pigs and the first three principal components from a total of 10 image parameters averaged across four longitudinal ultrasound images to estimate breeding values for carcass IMF (C3). Rank correlations between breeding value estimates for U1 and C1, U1 and U2, and C1 and C3 were 0.95, 0.97, and 0.92, respectively. Other rank correlations were 0.86 or less. In the selection experiment, approximately the top 10% of boars and 50% of gilts were selected. Selection differentials for pigs in Generation 3 were greatest when ranking pigs based on C1, followed by U1, U2, and C3. In addition, selection differential and estimated response were evaluated when simulating selection of the top 1, 5, and 10% of sires and 50% of dams. Results of this analysis indicated the greatest selection differential was for selection based on C1. The greatest loss in selection differential was found for selection based on C3 when selecting the top 10 and 1% of boars and 50% of gilts. The loss in estimated response when selecting varying percentages of boars and the top 50% of gilts was greatest when selection was based on C3 (16.0 to 25.8%) and least for selection based on U1 (1.3 to 10.9%). Estimated genetic change from selection based on carcass IMF was greater than selection based on ultrasound IMF. Results show that selection based on a combination of ultrasonically predicted IMF and sib carcass IMF produced the greatest selection differentials and should lead to the greatest genetic change.

Adipose Tissue↗
PubMed2005

Selection for placental efficiency in swine: genetic parameters and trends.

The objectives of this study were to estimate response to divergent selection for an index of placental efficiency in swine, and to evaluate the effect of placental efficiency on litter size. The selection index (SI) included total born (TB), birth weight (BRWT), and placental weight (PW), and was designed to increase in the high line (H) or decrease in the low line (L) the efficiency of the placental function (PE), defined as the ratio BRWT:PW. (Co)variance components were estimated for direct and maternal additive effects by using an animal model with MTDFREML procedures. Estimated breeding values were calculated by using records on individual BRWT (n = 2,111), PW (n = 2,006), PE (n = 1,677), and SI (n = 1,677). Litter traits were evaluated using records on 193 litters. The model included the fixed effects of contemporary group for all traits, with the addition of sex for individual traits and parity for litter traits. Litter was fitted as an uncorrelated random effect for all traits, and TB was used as a linear and quadratic covariate for BRWT, PW, and PE. Direct heritability estimates from single-trait models were 0.03, 0.25, 0.18, 0.11, and 0.08 for BRWT, PW, PE, SI, and TB, respectively. Estimated breeding values were compared between lines by using a model including generation, line within generation, and replicate within line as the error term. Estimates of genetic divergence were 20.7 +/- 2.7 g, 0.24 +/- 0.03, 0.11 +/- 0.02, and 0.07 +/- 0.02 per generation for PW, PE, SI, and TB, respectively (P < 0.01), but divergence was not significant for BRWT. At Generation 4, direct EBV was higher in L than in H for PW (55.9 +/- 8.7 vs. -24.2 +/- 9.5 g, respectively; P < 0.01) and higher in H than in L for PE (0.58 +/- 0.10 vs. -0.35 +/- 0.09 g, respectively; P < 0.01). However, EBV was not different for BRWT, SI, or TB. These results indicate that PW and PE are susceptible to change by genetic selection; however, the correlated response in TB was an unexpected genetic trend toward a higher TB in L of 0.05 +/- 0.01 piglets per generation (P < 0.01).

Animal Husbandry↗
PubMed2005

Carcass composition, bone mechanical properties, and meat quality traits in relation to growth rate in rabbits.

The objective of this study was to characterize correlated responses in carcass composition, bone mechanical properties, and meat quality indicators to divergent selection for growth rate. Rabbits from low (LOW) or high (HIGH) lines divergently selected over five generations on 63-d BW and a control group (CONT) were used. Rabbits were slaughtered at an average BW of 2,306 +/- 65 g, corresponding to 63, 58, or 52 d of age in LOW (n = 41), CONT (n = 43), and HIGH (n = 44) groups, respectively. Postweaning ADG and G:F increased (P < 0.001) in the order LOW < CONT < HIGH groups. The lengths of the tibia and femur in rabbit legs decreased (P < 0.001) with increasing growth rate. Tibia and femur bone intrinsic stiffness, as assessed by a three-point flexure test, followed the order (P < 0.001) of HIGH < CONT < LOW groups. At the same BW, HIGH rabbits and CONT rabbits showed many similarities for dressing percent, carcass composition, and color and chemical composition of muscles or meat parts. In contrast, carcass yield and the relative proportion of hind part were 3% greater (P < 0.01) in LOW rabbits than in CONT and HIGH rabbits. The meat-to-bone ratio in the hind leg was 11% greater (P < 0.001) in the LOW group compared with the CONT and HIGH groups. Yellow color index and moisture content in LM, a fast-twitch glycolytic muscle, were lower (P < 0.05) in LOW rabbits than in HIGH rabbits, but ultimate pH, WHC, and cooking loss did not differ between the two growth-selected lines. Ultimate pH in semitendinosus, a mixed slow- and fast-twitch oxidoglycolytic muscle, was less (P < 0.001) in HIGH rabbits than in CONT and LOW rabbits. However, lactate dehydrogenase and isocitrate dehydrogenase activities in this muscle (n = 21 per group), assessed at the time of slaughter as markers of glycolytic and oxidative capacities, respectively, did not differ among groups. Growth rate did not modify mean cross-sectional area and type frequency of myofibers in semitendinosus muscle. Finally, Warner-Bratzler shear force and total energy needed to achieve rupture did not differ among groups in semitendinosus muscle (n = 21 per group), whereas they were the least (P < 0.001) in LM (n = 128) from HIGH rabbits. Results from this study indicate that improvement of growth rate by selection has little effect in rabbit carcass and meat quality traits.

Animals↗
PubMed2006

Correlated responses in maternal performance following divergent selection for heat loss in mice.

Divergent selection in mice was applied in 3 independent replicates for high (maintenance high; MH) and low (maintenance low; ML) heat loss for 16 generations. An unselected control (maintenance control; MC) was also maintained in all replicates. Selection ceased for 26 generations; heat-loss measurement and selection resumed at generation 42. Lactation performance, dam weight, dam feed intake, and efficiency of production of pup weight were recorded or calculated for MH and ML dams in all 3 replicates at generation 46 or 47 with the objective of determining whether selection for heat loss has created correlated responses in maternal performance. One-half of the dams reared their own litters, and one-half reared cross-fostered (across lines) litters. Between 10 and 12 litters were used from each replicate-line-rearing class. Litter size was recorded, and litters were standardized to 8 pups within 24 h of birth. For cross fostering, MH litters were matched to ML litters born within 24 h of each other, and MH-ML litter pairs were cross-fostered at 3 d of age. A weigh-suckle-weigh protocol was used to obtain milk production estimates over a 2-h suckling period at 6, 9, 12, and 15 d. Dam (plus litter) feed intake was also recorded at these times and was calculated as the disappearance of feed over 3-d intervals. Dams of the MH selection tended (P < 0.11) to have greater litter size than those of the ML selection; litter size of MC dams was intermediate. Line of dam affected milk production (P = 0.04) and dam feed intake (P < 0.03) as MH dams produced more milk and consumed more feed than ML dams. Average milk production for the 2-h measurement period was 1.70 +/- 0.07 and 1.41 +/- 0.07 g, and average 3-d feed consumption was 50.8 +/- 1.2 and 45.2 +/- 1.2 g for MH and ML dams, respectively. Cross-fostering had no effect (P > 0.86) on milk production. Line of dam tended to affect 21-d litter weight (P = 0.15) with litters reared by MH dams weighing more than those reared by ML dams, but there was no difference (P > 0.86) in 21-d dam weights. Efficiency of producing litter weight (litter 15-d weight: dam plus litter feed intake from d 6 to 15) was greater (0.49 vs. 0.46, SE = 0.009; P = 0.03) for ML than for MH dams. Selection for reduced heat loss (lower maintenance feed intake in the ML line) resulted in reduced milk production and feed intake in dams and greater efficiency of litter weight production.

Animals↗
PubMed1987

Inherited immunoregulatory dysfunction in extrinsic bronchial asthma.

We studied 119 members of 22 asthmatic multiplex families. Included were: 44 parents (seven were asthmatics), 48 asthmatics (23 were undergoing an attack at the time of sampling), and 27 normal siblings. The following investigations were carried out on all subjects: 1) detection of total T lymphocytes, helper cells, and suppressor cells, using monoclonal antibodies (OKT3, OKT4, and OKT8), 2) study of nonspecific T-lymphocyte blast transformation induced by PHA, and 3) HLA-A, B, and DR antigen determination using the microcytotoxicity technique. The results were compared with normal ranges and data for a normal group and statistically and genetically analyzed. They indicate that: 1) the number of T cells was low in asymptomatic asthmatics and normal in asthmatics in attack; 2) there were fewer helper and normal suppressor cells (that is, a low H:S ratio) in asymptomatic asthmatics, and a normal amount of helper and suppressor cells (a normal H:S ratio) in those experiencing an attack; 3) there was a percentage of lymphocyte transformation in both groups of asthmatics; 4) whereas the T-helper cells increased, there was no change in the number of suppressor cells during an attack, which points to deficient function of suppressor cells; 5) the disorder is inherited and the gene controlling this dysfunction is HLA-linked and probably dominant.

Adolescent↗
PubMed2002

Producer breeding objectives and optimal sire selection.

Information from an online survey of dairy producers was used to determine how important producers perceived three different objectives in the breeding problem. The objectives were: maximizing expected net merit of the progeny, minimizing the expected progeny inbreeding coefficient, and minimizing semen expenditure. Producers were asked to rank the three objectives and then to weight the importance of each objective relative to the others. This information was then used to determine weights to be used in a multiple-objective integer program designed to select individual mates for a herd of 76 Jersey cows with known genetic background and cow net merit. The results of the multiple-objective models show that rank and relative importance of producer objectives can affect the portfolio of sires selected. Producers whose primary objective was to maximize expected net merit had a range of average expected progeny net merit of $306 to $310, but the level of expected progeny inbreeding was from 6.99 to 10.45%, with a semen cost per conception of $35 to $41. For producers who selected minimizing progeny inbreeding as the primary goal in their breeding programs, the range of inbreeding was from 6.11 to 6.60%, with lower net merit range of $274 to $301 and semen expenditure of $30 to $37 per conception. One producer selected minimizing semen cost as the primary objective. For that producer's portfolio, the semen cost was $27 per conception and net merit was $288, with a progeny inbreeding coefficient of 10.68%. The results of this research suggest that producer information and goals have a substantial impact on the portfolio of sires selected by that producer to attain these goals.

Animals↗
PubMed2006

Use of repeated measures analysis for evaluation of genetic background of dairy cattle behavior in automatic milking systems.

Milking frequencies measured at official test days were used with repeated measurement analysis to reveal the environmental and genetic impact on the milking frequency of cows in automatic milking systems. Repeated measurements were 3 test-day observations per cow within days in milk (DIM) classes, with 1,216 cows in DIM class 1 (d 0 to 99), from 1,112 cows in DIM class 2 (d 100 to 199), and from 1,004 cows in DIM class 3 (d 200 to 299) kept in 15 farms. Selection criteria for models analyzing repeated measurements were Akaike and Schwarz Bayesian values, which favored the autoregressive [AR(1)] covariance structure over the compound symmetry model. Results from the AR(1) model indicated a significant impact of fixed herd and parity effects. Milking frequencies decreased with increasing parities and were greatest for first-parity cows. High daily milk yield was associated with higher milking frequencies. Heritabilities for milking frequency were 0.16, 0.19, and 0.22 in DIM classes 1, 2, and 3, respectively, from the AR(1) model. Higher heritabilities in the later stage of lactation were due to a substantial reduction of the residual variance. Genetic correlations between test-day milk yield and daily milking frequency were in the range of 0.46 to 0.57 for all DIM classes and between milking frequency and somatic cell score were near zero. For verification of results, milking frequencies of the same cows obtained from herd management programs were averaged within DIM classes. Heritabilities were slightly above the values from the AR(1) model. In conclusion, heritabilities for milking frequency in automatic milking systems are moderate enough to incorporate this behavioral trait in a combined breeding goal. The inevitable improvement of labor efficiency in dairy cattle farming demands such cows going easily and voluntarily in automatic milking systems.

Analysis of Variance↗
PubMed2006

Genetic analysis of number of mastitis cases and number of services to conception using a censored threshold model.

The objective of this study was to infer genetic parameters and genetic change for number of clinical mastitis cases (NCM) and number of services to conception (STC) in first-lactation Norwegian Red (NRF) cows. Records on 620,492 daughters of 3,064 NRF sires, with first calving from 1980 through 2004, were analyzed with a bivariate threshold liability model that takes censoring into account. Posterior mean (SD) of heritability of liability was 0.08 (0.004) for NCM and 0.03 (0.002) for STC. The mean (SD) of the posterior distribution of the genetic correlation between the 2 traits was 0.21 (0.04). Posterior means of the correlation between herd-5-yr effects, and between residuals for NCM and STC were 0.17 and 0.05, respectively. To evaluate effects of taking censoring into account, the data were also analyzed with a bivariate ordered threshold model ignoring censoring. The genetic correlation between NCM and STC was lower than in the censored threshold model (0.09 vs. 0.21). Heritability of liability to NCM and STC from this model was also slightly lower, whereas the point estimates of herd-5-yr and residual correlations were 0.15, and -0.01, respectively. These results suggest that genetic (co)variance may be understated in models ignoring censoring. For comparison purposes, the data were analyzed with a bivariate linear sire model and standard REML-BLUP procedures. The correlation (rank correlation) between sire evaluations from the censored threshold model and sire predicted transmitting abilities from the linear model was 0.90 (0.90) for NCM and 0.87 (0.86) for STC. The evolution of average sire posterior means by birth year of daughters was used to assess genetic change, and results indicated genetic reduction (i.e., genetic improvement) of NCM and little or no genetic change for STC in the NRF population.

Animals↗
PubMed2006

Selection for female fertility using censored fertility traits and investigation of the relationship with milk production.

Bivariate models (censored linear-linear and censored threshold-linear) were used to estimate genetic parameters for production and fertility traits in the Spanish Holstein population. Records on 71,217 lactations from 41,515 cows were used: 30 and 36% of lactations were censored for days open (DO) and number of inseminations to conception (INS), respectively. Heritability estimates for production traits (milk, fat, protein) ranged between 0.18 and 0.25. Heritability of days to first service (DFS) and DO was 0.05; heritability of INS on the liability scale was 0.04. Genetic correlations between fertility traits were 0.41, 0.71, and 0.87 for DFS-INS, DO-INS, and DO-DFS, respectively. Days open had a larger genetic correlation (ranging from 0.63 to 0.76) with production traits than did DFS (0.47 to 0.59) or INS (0.16 to 0.23). Greater antagonism between production and DO may be due to voluntary management decisions for high-yielding cows, resulting in longer lactation lengths. Inseminations to conception appeared to be less correlated with milk production than were the other 2 female fertility traits. Including INS in a total merit index would be expected to increase genetic gain in terms of profit, but profit would decrease if either DO or DO and DFS were included in the index. Thus, INS is the trait to be preferred when selecting for female fertility. The genetic correlation between actual milk yield and 305-d standardized milk yield was 0.96 in the present study, suggesting that some reranking of sires could occur. Because the target of attaining a 12-mo calving interval, as implied by a 305-d standardized lactation length, is changing in the dairy industry, routine genetic evaluation of actual total lactation milk yield should be considered.

Animals↗
PubMed1991

C. R. Henderson: contributions to predicting genetic merit.

The contributions of C. R. Henderson to the genetic evaluation of livestock have been widely accepted, utilized, and enhanced by animal breeders and statisticians. Not well known are the possible alternatives to BLUP that have been suggested by Henderson, such as biased predictors and Bayesian methodology to incorporate prior information. A search for rapid methods of inverting dominance and additive by additive genetic relationship matrices has taken place since Henderson first described his method for computing the inverse of the additive genetic relationship matrix. Accounting for inbreeding and selected base populations continues to be a problem. There is a need to derive accurate descriptions of selection processes and the appropriate selection model in order to solve the problems of cow culling, nonrandom association of sires with herd-year-seasons, and preferential treatment. Henderson solved many animal breeding problems and left hints for solving others, but there are still many difficult problems to be tackled that will have to be resolved without the availability of his generous advice.

Animals↗
PubMed1994

Maximizing genetic response in breeding schemes of dairy cattle with constraints on variance of response.

Predicted genetic progress in dairy cattle breeding schemes was maximized with the variances of selection responses constrained, i.e., restricted effective population sizes. This restriction would also lead to schemes with acceptable rates of inbreeding (< .5%/yr). If the required coefficient of variation of the annual selection response was reduced from .32 to .16, numbers of animals selected, openness of schemes, and generation intervals increased. When elite cows produced 8 offspring annually, this reduction of the coefficient of variation tended toward a conventional progeny-testing scheme. If the number of donor cows was optimized, responses increased < or = 2%, and the breeding schemes became virtually closed. Variances of responses were reduced by selecting fewer, but proven, bulls, as is done in hybrid multiple ovulation and embryo transfer schemes, which select progeny-tested bulls and young elite cows. In spite of the constrained coefficients of variation, maximized genetic gains were high and were only reduced from .300 to .293 genetic standard deviations per year, when coefficients of variation were reduced from .32 to .16. Adoption of breeding schemes with low coefficients of variation is recommended, because responses are high and coefficients of variation are sensitive to accidental changes in the breeding structure.

Algorithms↗
PubMed1998

Generalized linear mixed models in dairy cattle breeding.

Fitness and fertility traits of dairy cattle are of increasing importance and are often measured on a discrete scale. The development and application of generalized linear mixed models to the genetic analysis of these traits are reviewed. Because current genetic evaluation systems are predominantly based on animal models, the inferential challenges of highly parameterized generalized linear mixed models are discussed. Development and adoption of new methods for drawing appropriate inferences on dispersion parameters are essential. Recent hierarchical extensions have been proposed for generalized linear mixed models, allowing for complex dispersion patterns that accommodate heteroscedasticity and outlier robustness. Steady advances in available computing power have facilitated multiple-trait analyses involving continuous and discrete measures. Full Bayesian inference via the development of Markov Chain Monte Carlo methods will continue to allow even greater generality and dimensions in the genetic model.

Animals↗