Indicators of genetic erosion in an endangered population: the Alentejana cattle breed in Portugal

A study was conducted to characterize genetic diversity in the Alentejana breed of cattle based on its demographic trends and to investigate the major factors affecting genetic erosion in this breed. Herdbook information collected between 1940 and 2004, including pedigree records on 100,562 animals in 155 herds, was used to estimate demographic parameters. The mean generation intervals were 6.0 +/- 2.4 yr and 6.8 +/- 3.2 yr for sires and dams of calves, respectively. Average inbreeding increased steadily over the period analyzed, with an annual rate of inbreeding of 0.33 +/- 0.004% (P < 0.01) and an effective population size of 23.3. In the reference population (28,531 calves born between 2000 and 2003) the average inbreeding was 8.35 +/- 9.02% and nearly 80% of the calves were inbred, whereas the average relationship among all animals was 0.026 +/- 0.040. Nevertheless, the mean relationship was 0.328 +/- 0.264 and 0.022 +/- 0.026 for animals born in the same and in different herds, respectively. The computed genetic contributions to the reference population resulted in estimates for the effective number of founders, ancestors, founding herds, and herds supplying sires of 121.6, 55.0, 17.1, and 26.9, respectively, the 2 most influential herds and ancestors contributing 24.2 and 15.1%, respectively, of the current genetic pool. Of the 671 founding sires, only 24 Y-chromosomes are currently represented, but 1 sire alone contributes nearly 60% of this representation, such that the effective number of Y-chromosomes is only 2.73. The observed inbreeding per herd was, on average, 0.053 +/- 0.071 lower than expected from the relationship among the generation of parents of calves in the reference population, indicating that producers have followed breeding strategies that have kept inbreeding at lower levels than anticipated with random selection and mating. When compared with other cattle breeds, Alentejana has some of the highest levels of mean inbreeding and annual rate of inbreeding, and an effective population size that is nearly half of the minimum recommended for maintenance of genetic variability. These critical indicators demonstrate the need to adopt strategies aimed at minimizing inbreeding to avoid further losses of genetic diversity.     

Breeding programme for Piétrain pigs in Bavaria with an estimation of genetic trends and effective population size

Population structure, performance testing and breeding scheme of the sire breed Piétrain in Bavaria were analyzed as a basis for further optimization studies of the breeding programme. To evaluate the current breeding programme, genetic trends and effective population size were estimated. Four data sets were used which contained breeding animals born between 1981 and 2005, estimated breeding values of traits in the breeding goal, records from young boars in field test and records from purebred and crossbred progeny on test stations. The population is subdivided in many small herds. That has disadvantages with respect to a uniform breeding goal used across herds and with respect to selection intensity and the avoidance of inbreeding. The idealized selection practice consists of three selection stages. On the first two stages information from half and full sibs on test stations is most important so that the risk of co-selecting related animals is increased. The breeding scheme is a mixture of a half sib design and a progeny testing design, but both have disadvantages. Nevertheless, genetic trends are in the desired directions. To improve accuracy and intensity of selection, only AI-boars should be used instead of natural service sires. Though the effective population size is high, the recent trend of inbreeding shows that the extensive use of popular AI-boars can lead to a rapid increase of inbreeding.     

Population structure and genetic variability in the Murrah dairy breed of water buffalo in Brazil accessed via pedigree analysis

The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability in the Murrah dairy breed of water buffalo (Bubalus bubalis) in Brazil. Pedigree analysis was performed on 5,061 animals born between 1972 and 2002. The effective number of founders (fe) was 60, representing 6.32?% of the potential number of founders. The effective number of ancestors (fa) was 36 and the genetic contribution of the 17 most influent ancestors explained 50?% of the genetic variability in the population. The ratio fe/fa (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.66. Completeness level for the whole pedigree was 76.8, 49.2, 27.7, and 12.8?% for, respectively, the first, second, third, and fourth known parental generations. The average inbreeding values for the whole analyzed pedigree and for inbreed animals were, respectively, 1.28 and 7.64?%. The average relatedness coefficient between individuals of the population was estimated to be 2.05?%??the highest individual coefficient was 10.31?%. The actual inbreeding and average relatedness coefficient are probably higher than estimated due to low levels of pedigree completeness. Moreover, the inbreeding coefficient increased with the addition of each generation to the pedigree, indicating that incomplete pedigrees tend to underestimate the level of inbreeding. Introduction of new sires with the lowest possible average relatedness coefficient and the use of appropriate mating strategies are recommended to keep inbreeding at acceptable levels and increase the genetic variability in this economically important species, which has relatively low numbers compared to other commercial cattle breeds. The inclusion of additional parameters, such as effective number of founders, effective number of ancestors, and fe/fa ratio, provides better resolution as compared to the inclusion of inbreeding coefficient and may help breeders and farmers adopt better precautionary measures against inbreeding depression and other deleterious genetic effects.     

Genetic aspects of productive and reproductive traits in a Murrah buffalo herd in São Paulo,Brazil

This study investigated genetic trends of some productive and reproductive traits in a herd of Murrah buffalo raised in São Paulo, Brazil. Variance components for milk production (MP), length of lactation (LL), calving interval (CI) and age of first calving (AFC) were estimated by the restricted maximum likelihood method, using an animal model. Estimated heritability values were 0.38; 0.01; 0.10 and 0.20 for MP, LL, CI and AFC, respectively. Estimated repeatability values were 0.50, 0.13 and 0.20 for MP, LL and CI, respectively. Means of predicted breeding values for cows, dams and sires according to calving year and the genetic correlations were presented.     

A review on breeding and genetic strategies in Iranian buffaloes (<Emphasis Type="Italic">Bubalus bubalis</Emphasis>)

The aim of current study was to review breeding progress and update information on genetic strategies in Iranian buffaloes. Iranian buffalo is one of the vital domestic animals throughout north, north-west, south and south-west of Iran with measurable characteristics both in milk and meat production. The species plays an important role in rural economy of the country due to its unique characteristics such as resistance to diseases and parasites, having long productive lifespan and showing higher capability of consuming low-quality forage. In Iran, total production of milk and meat devoted to buffaloes are 293,000 and 24,700 tons, respectively. Selection activities and milk yield recording are carrying out by the central government through the Animal Breeding Centre of Iran. The main breeding activities of Iranian buffaloes included the estimation of genetic parameters and genetic trends for performance traits using different models and methods, estimation of economic values and selection criteria and analysis of population structure. Incorporating different aspects of dairy buffalo management together with improved housing, nutrition, breeding and milking, is known to produce significant improvements in buffalo production. Therefore, identifying genetic potential of Iranian buffaloes, selection of superior breeds, improving nutritional management and reproduction and developing the education and increasing the skills of practical breeders can be useful in order to enhance the performance and profitability of Iranian buffaloes.     

Effect of culling on selection response using phenotypic selection or best linear unbiased prediction of breeding values in small, closed herds of swine.

Records from 7,200 separate closed herds with either 12 or 25 sows that were mated to either four or eight boars per year were simulated by computer. Effects of selection method, herd size, and contemporary group variability on average genetic change, genetic variance, and inbreeding over 10 yr of selection were analyzed for traits with heritabilities of .1, .3, and .6. Selection of replacement animals was on individual phenotype or BLUP of breeding value using a reduced animal model. For both of these selection methods, two culling schemes were imposed: 1) based only on involuntary culling because of losses due to conception rate and age and 2) when an available replacement animal was projected to be superior to an existing breeding animal in the herd in addition to the involuntary culling. The contemporary group standard deviation was set at either .1 or .5 of a phenotypic standard deviation. Selection with BLUP gave 72, 36, and 12% more genetic improvement for heritabilities of .1, .3, and .6, respectively, than selection on individual phenotype after 10 yr. However, inbreeding increased 20 to 52% more rapidly and there was a decrease in genetic variance. Culling based on Scheme 2 increased genetic improvement over Scheme 1 by about 75% with coincident increases in inbreeding level and decreases in genetic variance. The largest changes in inbreeding and genetic variance were associated with culling on BLUP. Culling when a superior animal was available with individual phenotype had little effect on inbreeding and genetic variance. Use of four boars rather than eight boars and 25 rather than 12 sows per herd increased genetic response. Use of four boars also increased inbreeding and decreased genetic variance. Genetic variance was higher in herds with 25 sows, but the size of the sow herd had little effect on inbreeding. Contemporary group variation influenced only the genetic response of individual phenotypic selection with culling.     

Effect of sire mating patterns on future genetic merit and inbreeding in a closed beef cattle population

Summary Alternative breeding strategies were simulated based on the population structure of the Tajima strain of Japanese Black cattle. An analysis of the population structure revealed that some sires up to 20 years of age have been used in Tajima. In addition, 95% of newborn calves were the progeny of only 20 sires, and their mating frequencies were significantly skewed. The current average inbreeding coefficient and founder genome equivalents of the strain were estimated to be 0.199 and 2.25, respectively. Average inbreeding coefficient is expected to reach 0.394 within 27 years. Thus, different breeding strategies were assessed for their effect on the level of inbreeding and average genetic merit. We compared strategies that (1) halve the sire service period, (2) double the number of mating sires and (3) lower the skewed sire mating frequency and optimize the frequency for weighted genetic merit and diversity. Reducing the service period yielded a 7.0–12.0% reduction in the rate of inbreeding while maintaining almost the same genetic gain. Increasing the number of sires resulted in a 19.3–21.3% reduction in inbreeding with a corresponding 1.6–8.4% reduction in gain. The rates of inbreeding from the optimized strategies decreased as the weight on genetic diversity increased. However, a strategy that emphasized only genetic gain yielded lower gain than other strategies because the strategy allowed only one sire to mate, resulting in reduced genetic variance and low accuracy of genetic evaluation. In contrast, a strategy with no emphasis on genetic gain when determining mating frequency resulted in reductions of 16.0% and 63.2% in genetic gain and inbreeding, respectively. The strategies examined here are easily applicable and can be expected to reduce immediate loss of genetic diversity.     

Optimum contribution selection using traditional best linear unbiased prediction and genomic breeding values in aquaculture breeding schemes

The aim of this study was to compare genetic gain for a traditional aquaculture sib breeding scheme with breeding values based on phenotypic data (TBLUP) with a breeding scheme with genome-wide (GW) breeding values. Both breeding schemes were closed nuclei with discrete generations modeled by stochastic simulation. Optimum contribution selection was applied to restrict pedigree-based inbreeding to either 0.5 or 1% per generation. There were 1,000 selection candidates and a sib test group of either 4,000 or 8,000 fish. The number of selected dams and sires to create full sib families in each generation was determined from the optimum contribution selection method. True breeding values for a trait were simulated by summing the number of each QTL allele and the true effect of each of the 1,000 simulated QTL. Breeding values in TBLUP were predicted from phenotypic and pedigree information, whereas genomic breeding values were computed from genetic markers whose effects were estimated using a genomic BLUP model. In generation 5, genetic gain was 70 and 74% greater for the GW scheme than for the TBLUP scheme for inbreeding rates of 0.5 and 1%. The reduction in genetic variance was, however, greater for the GW scheme than for the TBLUP scheme due to fixation of some QTL. As expected, accuracy of selection increased with increasing heritability (e.g., from 0.77 with a heritability of 0.2 to 0.87 with a heritability of 0.6 for GW, and from 0.53 and 0.58 for TBLUP in generation 5 with sib information only). When the trait was measured on the selection candidate compared with only on sibs and the heritability was 0.4, accuracy increased from 0.55 to 0.69 for TBLUP and from 0.83 to 0.86 for GW. The number of selected sires to get the desired rate of inbreeding was in general less in GW than in TBLUP and was 33 for GW and 83 for TBLUP (rate of inbreeding 1% and heritability 0.4). With truncation selection, genetic gain for the scheme with GW breeding values was nearly twice as large as a scheme with traditional BLUP breeding values. The results indicate that the benefits of applying GW breeding values compared with TBLUP are reduced when contributions are optimized. In conclusion, genetic gain in aquaculture breeding schemes with optimized contributions can increase by as much as 81% by applying genome-wide breeding values compared with traditional BLUP breeding values.     

Effects of a breeding scheme combined by genomic pre‐selection and progeny testing on annual genetic gain in a dairy cattle population

The effectiveness of the incorporation of genomic pre‐selection into dairy cattle progeny testing (GS‐PT) was compared with that of progeny testing (PT) where the fraction of dam to breed bull (DB) selected was 0.01. When the fraction of sires to breed bulls (SB) selected without being progeny tested to produce young bulls (YB) in the next generation was 0.2, the annual genetic gain from GS‐PT was 13% to 43% greater when h² = 0.3 and 16% to 53% greater when h² = 0.1 compared with that from PT. Given h² = 0.3, a selection accuracy of 0.8 for both YB and DB, and selected fractions of 0.117 for YB and 0.04 for DB, GS‐PT produced 40% to 43% greater annual genetic gain than PT. Given h² = 0.1, a selection accuracy of 0.6 for both YB and DB, and selected fractions of 0.117 for YB and 0.04 for DB, annual genetic gain from GS‐PT was 48% to 53% greater than that from PT. When h² = 0.3, progeny testing capacity had little effect on annual genetic gain from GS‐PT. However, when h² = 0.1, annual genetic gain from GS‐PT increased with increasing progeny testing capacity.     

Approaches to the management of inbreeding and relationship in the German Holstein dairy cattle population

The aim of this study was to estimate the current level of inbreeding in the German cow population and for bull dams born in Germany, to find out sires most related to different subsets of their breed and to demonstrate the negative effect of homozygosity in the case of complex vertebral malformation (CVM). Further on, the application of optimum genetic contribution (OGC) theory for the selection of bull dams and bull sires in different breeding scenarios was investigated. Levels of inbreeding for the cow population were in a low range from 0.97% to 1.70% evaluating birth years from 1996 to 1999 in a total dataset of 244,427 registered Holstein cows. The inbreeding coefficient of 8030 bull dams was much higher, i.e. 3.71%, for the birth year 1999. Increases in inbreeding of 0.19% per year indicated an effective population size of only 52 animals. Individual sires like R.O.R.A. Elevation and Hannoverhill Starbuck were highly related to potential bull dams with coefficients of relationship of 13.4% and 12.9%, respectively, whereas P.F. Arlinda Chief (16.3%) and Carlin-M Ivanhoe Bell (16.1%) were highest related to the best available AI sires. Coefficients of relationship were calculated by classes of estimated breeding values (EBV) for production traits showing highest values above 7% in the two highest EBV-classes. The optimum genetic contribution theory using official EBVs and approximative, for zero inbreeding corrected EBVs, was applied for elite matings in a breeding program embracing 30 young bulls per year to find the optimal allocations of bull sires and bull dams. Compared with the actual breeding program applied in practice, OGC-theory has the potential to increase genetic gain under the same constraint for the increase of average relationship by 13.1%. A more relaxed constraint on increase in inbreeding allowed even higher expected genetic gain whereas a more severe constraint resulted in more equal contributions of selected bull sires. Contributions from 21 selected bull sires and 30 selected bull dams for a scenario at 5% constrained relationship were used to develop a specific mating plan to minimise inbreeding in the short term in the following generation applying a simulated annealing algorithm. The expected coefficient of inbreeding of progeny was 66.3% less then the one resulting from random mating. Mating programs can address inbreeding concerns on the farm, at least in the short term, but long-term control of inbreeding in a dairy population requires consideration of relationships between young bulls entering AI progeny test programs. Significantly better EBVs of CVM-free bulls compared with CVM-carriers for the paternal fertility justify the application of OGC for elite matings.     

Estimation of Variances and Covariances of Milk Traits by REML with an Individual Animal Model

Abstract

Records form Finnish Ayrshire cattle were used to estimate variances and covariances of milk traits by the restricted maximum likelihood (REML) method using the individual animal model (IAM). Two data sets were analyzed. The first data set consisted of 1423 sires and 16363 cows, of which 11911 had records on first lactation. The heritabilities estimated from this data set for milk yield, protein yield, protein content and fat content were 0.40, 0.31, 0.63 and 0.68, respectively. The second data set was a subset of first data set with herds with less than ten observations excluded and consisted of 1335 sires and 11262 cows with 8140 first, 5688 second and 3717 third lactation records. The heritability estimates from the second data set under a repeatability model for milk yield, protein yield, protein content and fat content were 0.30, 0.26, 0.59 and 0.66, respectively. The repeatability estimates for the same traits were 0.53, 0.51, 0.67 and 0.76, respectively. The second data set was also used to estimate genetic and phenotypic correlations among milk traits in first lactation. Both genetic and phenotypic correlations among protein yield and protein and fat content traits were small. The genetic correlation between milk yield and protein content was -0.61, between milk yield and fat content -0.50 and between protein content and fat content 0.67. Absolute values of phenotypic correlations for the same pairs of traits were somewhat smaller than respective genetic correlations.     

Marker-assisted selection for commercial crossbred performance

Several studies have shown that selection of purebreds for increased performance of their crossbred descendants under field conditions is hampered by low genetic correlations between purebred and commercial crossbred (CC) performance. Although this can be addressed by including phenotypic data from CC relatives for selection of purebreds through combined crossbred and purebred selection (CCPS), this also increases rates of inbreeding and requires comprehensive systems for collection of phenotypic data and pedigrees at the CC level. This study shows that both these limitations can be overcome with marker-assisted selection (MAS) by using estimates of the effects of markers on CC performance. To evaluate the potential benefits of CC-MAS, a model to incorporate marker information in selection strategies was developed based on selection index theory, which allows prediction of responses and rates of inbreeding by using standard deterministic selection theory. Assuming a genetic correlation between purebred and CC performance of 0.7 for a breeding program representing a terminal sire line in pigs, CC-MAS was shown to substantially increase rates of response and reduce rates of inbreeding compared with purebred selection and CCPS, with 60 CC half sibs available for each purebred selection candidate. When the accuracy of marker-based EBV was 0.6, CC-MAS resulted in 34 and 10% greater responses in CC performance than purebred selection and CCPS. Corresponding rates of inbreeding were 1.4% per generation for CC-MAS, compared with 2.1% for purebred selection and 3.0% for CCPS. For marker-based EBV with an accuracy of 0.9, CC-MAS resulted in 75 and 43% greater responses than purebred selection and CCPS, and further reduced rates of inbreeding to 1.0% per generation. Selection on marker-based EBV derived from purebred phenotypes resulted in substantially less response in CC performance than in CC-MAS. In conclusion, effective use of MAS requires estimates of the effect on CC performance, and MAS based on such estimates enables more effective selection for CC performance without the need for extensive pedigree recording and while reducing rates of inbreeding.     

Relationships of first lactation yields with lifetime performance traits in Holstein cows

SUMMARY: Genetic and phenotypic correlations between the first lactation and lifetime yields of milk, fat and protein, herdlife, productive life and number of lactations initiated in the herd were estimated from records of 24,231 progeny of 234 young and 119 proven Holstein sires in 1791 herds using a multivariate REML technique to fit a sire model with relationships among young sires. Proven sires were fitted as fixed effects. Genetic correlations between first lactation and lifetime yields were highest for milk (0.666) followed by fat (0.660) and protein (0.512). Genetic as well as phenotypic correlations of herdlife, productive life and number of lactations were higher with first lactation milk yield than with first lactation fat and protein yields. Direct selection for higher lifetime yields would not be effective because of low heritabilities. However the high, positive genetic correlations of lifetime yields of milk and fat with first lactation yields suggested that first lactation yields might be used for indirect selection for higher lifetime yields. ZUSAMMENFASSUNG: Beziehung zwischen Erstlaktations- und Lebensleistung bei Holstein-Kühen Zwischen Erstlaktations- und Lebensleistung für Milch, Fett, Protein, Verbleibedauer, produktiver Lebensdauer und Zahl von Laktationen in der Herde wurden von 24.291 T?chtern, 234 Jung- und 119 geprüften Holsteintieren in 1.791 Herden genetische Beziehungen gesch?tzt, wobei eine multivariate REML-Technik zur Analyse eines Stiermodells mit Verwandtschaft zwischen jungen Stieren angewendet worden ist. Die geprüften Stiere wurden als fixe Effekte angesehen. Genetische Korrelationen zwischen Erstlaktation und Lebensleistung war am h?chsten für Milch (0,666), gefolgt von Fett (0,660) und Protein (0,512). Genetische und ph?notypische Korrelationen mit Verbleibedauer, produktiver Lebensdauer und Zahl der Laktationen waren ebenfalls für Erstlaktations-milchmenge h?her als bei Fett und Protein. Direkte Selektion auf h?here Lebensleistung würde wegen der niedrigen Heritabilit?t nicht wirksam sein. Allerdings k?nnten die hohen positiven genetischen Korrelationen des Merkmals mit Erstlaktationsleistungen diese als geeignetes indirektes Selektionskriterium für h?here Lebensleistung anzeigen.     

中国荷斯坦牛乳房性状、体型总分与产奶性状的相关分析

研究利用武汉市58头公牛的971头女儿2006—2007年间的体型性状鉴定记录及2001—2007年间的生产性能测定记录,配合动物模型,采用REML方法进行参数估计,探讨了乳房性状、体型总分与产奶性状之间的关系。结果表明:乳房性状与产奶性状之间的表型相关较小。后乳房宽度与产奶性状之间存在强的遗传正相关(0.44～0.89)。后乳房高度与305 d产奶量(0.27)、305 d乳脂量(0.16)存在遗传正相关,而与305 d乳蛋白量(-0.32)存在遗传负相关。前乳房附着与产奶性状基本不存在相关。悬韧带与305 d产奶量存在遗传正相关(0.79)。乳房深度与305 d产奶量存在遗传负相关(-0.20)。体型总分与305 d产奶量、305 d乳脂量、305 d乳蛋白量存在较强的遗传正相关,故加强乳房性状和体型总分的选择对提高奶牛的生产性能有益。     

Genetic parameters of lifetime performance traits in Holstein cows

SUMMARY: Heritabilities, genetic and phenotypic correlations among lifetime yields of milk, fat and protein, herdlife, productive life and number of lactations initiated in the herd were estimated from records of 44,933 progeny of 427 young and 119 proven Holstein sires in 1949 herds using a multivariate Reml technique to fit a sire model with relationships among young sires. Proven sires were fitted as fixed effects. Heritabilities of lifetime traits ranged from 0.005 to 0.030, suggesting little scope for direct selection for lifetime performance traits. Productive life had highest genetic correlation with lifetime fat yield (0.934), but correlations with lifetime milk and protein yields were smaller and similar (0.773 and 0.772). The number of lactations also had highest genetic correlation with lifetime fat yield. ZUSAMMENFASSUNG: Genetische Parameter von Lebensleistungsmerkmalen bei Holsteinkühen Heritabilit?tswerte, genetische und ph?notypische Korrelationen zwischen Lebensleistungsmerkmalen für Milch, Fett und Protein, Lebensdauer, produktive Zeit und Zahl Laktationen wurden won 44933 Nachkommen von 427 jungen und 119 nachkommenschaftsgeprüften Holsteinstieren in 1949 Herden mittels einer multivariablen REML-Technik gesch?tzt, die auf einem Vatertiermodell mit Verwandtschaft zwischen den jungen Stieren beruhte. Geprüfte Stiere wurden als fixe Effekte im Modell berücksichtigt. Heritabilit?tswerte dieser Merkmale rangieren von 0.005 bis 0.03, so da? wenig Aussichten für Erfolg direkter Selektion auf Lebensleistungsmerkmale besteht. Die L?nge des produktiven Lebens hatte die h?chste genetische Korrelation mit Lebensfettmenge (0.934), aber die Korrelationen mit Milch- und Protein-Lebensleistung waren kleiner und ?hnlich (0.773 und 0.772). Die Zahl der Laktationen hatte die h?chste genetische Korrelation mit der Lebensfettmenge.     

Analysis of genotype by environment interaction for milk yield traits in first lactation of Simmental cattle

The breeding goal for Simmental cattle is derived for intensively managed dairy farms. Its suitability for extensive farms was addressed by analysing possible genotype by environment interaction (G × E) between the management levels for first lactation milk yield traits. A first analysis was performed with the data collected from 300 000 purebred daughters of 278 second crop bulls born in Bavaria in 1993 and 1994. The farms were classified by herd‐year‐effect, using the sum of fat and protein yields into two levels of management, either with 33 or 10% quantiles, corresponding to approximately 100 000 cows and 30 000 cows, respectively. The comparison was based on ‘daughter yield’ deviations (DYD). Correlations between DYD of extensive and intensive environments were 0.90, 0.91 and 0.87 for milk, fat and protein yield (kg) for 33% quantiles, respectively. Corresponding correlations for 10% quantiles were 0.85, 0.83 and 0.77. Despite high correlations, 50 out of 149 sires showed significant differences between DYD in different environments. Bulls with higher DYD for milk yield on intensive farms were superior in all environments. For the second analysis extensive and intensive farms in northern and southern Bavaria were chosen at random. Approximately 20 000 cows in each management class were used for the estimation of genetic parameters. In both regions phenotypic and additive‐genetic variances were higher in the intensively managed herds. Likewise heritabilities were higher for fat and protein yield, but not for milk where higher heritabilities were observed in 33% quantiles. Genetic correlations between extensive and intensive environments were 0.97 and above (33% quantiles). Ten per cent quantiles led to lower genetic correlations (0.90–0.95). Although no serious re‐ranking effects of sires were evident, the scale effect and the differences in genetic parameters should be taken into consideration in practical breeding.     

Bayesian inference for genetic parameter estimation on growth traits for Nelore cattle in Brazil,using the Gibbs sampler

This data set consisted of over 29 245 field records from 24 herds of registered Nelore cattle born between 1980 and 1993, with calves sires by 657 sires and 12 151 dams. The records were collected in south‐eastern and midwestern Brazil and animals were raised on pasture in a tropical climate. Three growth traits were included in these analyses: 205‐ (W205), 365‐ (W365) and 550‐day (W550) weight. The linear model included fixed effects for contemporary groups (herd‐year‐season‐sex) and age of dam at calving. The model also included random effects for direct genetic, maternal genetic and maternal permanent environmental (MPE) contributions to observations. The analyses were conducted using single‐trait and multiple‐trait animal models. Variance and covariance components were estimated by restricted maximum likelihood (REML) using a derivative‐free algorithm (DFREML) for multiple traits (MTDFREML). Bayesian inference was obtained by a multiple trait Gibbs sampling algorithm (GS) for (co)variance component inference in animal models (MTGSAM). Three different sets of prior distributions for the (co)variance components were used: flat, symmetric, and sharp. The shape parameters (ν) were 0, 5 and 9, respectively. The results suggested that the shape of the prior distributions did not affect the estimates of (co)variance components. From the REML analyses, for all traits, direct heritabilities obtained from single trait analyses were smaller than those obtained from bivariate analyses and by the GS method. Estimates of genetic correlations between direct and maternal effects obtained using REML were positive but very low, indicating that genetic selection programs should consider both components jointly. GS produced similar but slightly higher estimates of genetic parameters than REML, however, the greater robustness of GS makes it the method of choice for many applications.     

Genetic and phenotypic trends in canine hip dysplasia in the German population of German shepherd dogs

Phenotypic and genetic trends were examined in 157,455 German shepherd dogs of the German population born between 1985 and 2003 which were Xrayed for canine hip dysplasia (CHD). A subset of 40,270 dogs born between 1998 and 2003 was examined for which information was available on age at examination and X-raying veterinary practitioner. Relative breeding values were predicted using best linear unbiased prediction methods (BLUP) and Gibbs Sampling. There was an almost linear and significant decline in both phenotypic and genetic trends for CHD scores (scale 1 to 5 for CHD free to severe CHD) over a period of 19 years, with b = -0.021 +/- 0.002, and b = -1.69 +/- 0.05, respectively. After introduction in 1999 of a selection scheme based on relative breeding values (RBVs, mean 100, standard deviation 20) of a linear animal model, phenotypic and genetic trends declined less than before 1999, with b = -0.019 +/- 0.011 and b = -1.43 +/- 0.29. Analysis of the effects of RBVs of parental combinations among sires and dams on the percentage of non-affected progeny showed that lower RBVs were associated with a higher percentage of non-affected progeny than were higher RBVs. In addition, it was also shown that selection procedures based on RBVs are more efficient than selection schemes based on phenotypic records of parents. When the maternal RBV was above 100, the proportion of non-affected progeny was between 10% and 20% lower than when the maternal RBV was below or equal to 100. There was a significant relationship between higher inbreeding coefficients and higher RBVs of the animal.     

Random regression models to estimate genetic parameters for test‐day milk yield in Brazilian Murrah buffaloes

The objective of this work was to estimate covariance functions for additive genetic and permanent environmental effects and, subsequently, to obtain genetic parameters for buffalo’s test‐day milk production using random regression models on Legendre polynomials (LPs). A total of 17 935 test‐day milk yield (TDMY) from 1433 first lactations of Murrah buffaloes, calving from 1985 to 2005 and belonging to 12 herds located in São Paulo state, Brazil, were analysed. Contemporary groups (CGs) were defined by herd, year and month of milk test. Residual variances were modelled through variance functions, from second to fourth order and also by a step function with 1, 4, 6, 22 and 42 classes. The model of analyses included the fixed effect of CGs, number of milking, age of cow at calving as a covariable (linear and quadratic) and the mean trend of the population. As random effects were included the additive genetic and permanent environmental effects. The additive genetic and permanent environmental random effects were modelled by LP of days in milk from quadratic to seventh degree polynomial functions. The model with additive genetic and animal permanent environmental effects adjusted by quintic and sixth order LP, respectively, and residual variance modelled through a step function with six classes was the most adequate model to describe the covariance structure of the data. Heritability estimates decreased from 0.44 (first week) to 0.18 (fourth week). Unexpected negative genetic correlation estimates were obtained between TDMY records at first weeks with records from middle to the end of lactation, being the values varied from ?0.07 (second with eighth week) to ?0.34 (1st with 42nd week). TDMY heritability estimates were moderate in the course of the lactation, suggesting that this trait could be applied as selection criteria in milking buffaloes.     

Use of partial budgeting to determine the economic outcome of Staphylococcus aureus intramammary infection reduction strategies in three Ohio dairy herds

Efforts to reduce the prevalence of Staphylococcus aureus intramammary infection were monitored in 3 Ohio dairy herds. Bacteriologic culturing of milk from all lactating cows in each herd was completed multiple times to identify infected cows and monitor reduction. Partial budgeting techniques were used to determine the economic outcome of the reduction program. Of particular emphasis was the economic impact of culling to maintain or achieve milk quality premium payments on the basis of bulk tank somatic cell counts. The prevalence of S aureusinfected cows was reduced in each herd. Culturing of milk from all lactating cows appeared to be an effective method to identify infected cows. Although numbers were limited, it also appeared that culturing of composite quarter samples was effective as a herd screening test to identify S aureus-infected cows. Bacteriologic culturing had a negative financial impact in all 3 herds. Using partial budgeting to assess the economic impact of the programs, it was determined that 2 herds experienced negative financial impacts as a result of an excess culling rate when compared with a 12-month baseline period prior to the initiation of the project. All herds had increased milk production per cow during the study as measured by the mature-equivalent method. However, when actual production was considered, increased milk production in each herd was not as great as that of other Ohio herds enrolled on Dairy Herd Improvement Association testing programs.(ABSTRACT TRUNCATED AT 250 WORDS)