Estimation of variance components with dominance and inbreeding in dairy cattle

SUMMARY: The five variance components in the genetic (co)variance among inbred relatives for a quantitative trait with additive and dominance genetic variation were estimated by equating variances among and within different types of families of inbred cows to their expectations. The data used were milk and fat yields of 85,433 U.S. Holstein cows with inbreeding coefficients of 6.25% or higher. When all five parameters were estimated, unrealistic results were obtained. If all quantitative trait loci are biallelic, genetic (co)variance depends on only four parameters. More realistic estimates were obtained under this assumption. There was a substantial negative covariance among breeding values and dominance effects under inbreeding, and the dominance variance in inbred cows was larger than the dominance variance in the noninbred base population. ZUSAMMENFASSUNG: Varianzkomponenteneinsch?tzung bei Dominanz und Inzucht von Milchvieh Die fünf Varianzkomponenten in der genetischen (Ko)Varianz zwischen ingezüchteten Verwandten in einem quantitativen Merkmal wurden gesch?tzt durch Gleichsetzen von Varianzen zwischen und innerhalb verschiedener Familien von ingezüchteter Kühen zu ihren Erwartungswerten. Das Datenmaterial bestand aus den Milch- und Fettmengen von 85,433 U.S. Holstein Kühen mit Inzuchtkoeffizienten von 6.25% oder h?her. Die gleichzeitige Sch?tzung aller fünf Parameter führte zu unrealistischen Ergebnissen. Wenn an allen Genorten des quantitativen Merkmals nur zwei Allele vorkommen, gehen nur vier Parameter in die genetische (Ko)Varianz ein. Die Sch?tzwerte, die unter dieser Annahme berechnet wurden, waren plausibler. Eine betr?chtliche negative Kovarianz zwischen den Zuchtwerten und den Dominanzwerten bei Inzucht wurde gefunden, und die Dominanzvarianz war unter Inzucht gró?er als in der Basispopulation.     

Differences in feed intake between holstein Friesian,Dutch Red and White and Dutch Friesian cattle

In a comparison of Holstein Friesian (HF) from North America with Dutch Red and Whites (DRW) and Dutch Friesians (DF), the feed intake of 20 animals per breed was measured at different stages of lactation and at different ages. In the experiments with dairy cows, the animals were offered concentrates individually according to their milk yield. In all experiments roughage (silage or hay) was offered ad libitum.In all experiments the DRW animals ate less roughage than the HF and DF animals, although they ate the lowest amount of concentrates in nearly all experiments, due to their lower milk yield. The HF animals were offered more concentrates than the DF animals, but ate the same amount of roughage.     

Effects of inbreeding on fighting ability measured in Aosta Chestnut and Aosta Black Pied cattle

Aosta Black Pied (ABP) and Aosta Chestnut (AC) are dual-purpose cattle indigenous to the western Alps and famous for their fighting ability in traditional Italian Batailles de Reines. The present study aimed to investigate the influence of inbreeding on breeding values for fighting ability achieved in participants. Inbreeding (F) and average relatedness (AR) were obtained from the entire pedigree information available (19,554 and 87,967 records for ABP and AC, respectively). Data (n = 23,998) relating to 8,259 cows competing in years 2001-2009 were analyzed to obtain heritability (h(2)) estimates and breeding values for the trait. A placement score was chosen as a phenotype for fighting ability and both a classical quantitative model (NORM) and its implementation, used to identify its indirect genetic effects (COMP), were analyzed using the expectation maximization-REML (EM-REML) method. The F and AR trends in animals born between 1990 and 2009 were generally low and were greater for ABP (+0.06%/yr) than for AC (+0.03%/yr) populations, which also presented a greater mean F (about 2.8% ± 1.7% vs. 0.8% ± 1.5% for ABP and AC, respectively) and mean AR among individuals (about 1.0% ± 0.8% vs. 0.4% ± 0.3% for ABP and AC, respectively). Heritability estimates from 0.083 ± 0.036 to 0.120 ± 0.037 were obtained using the NORM model, accounting for or not accounting for F, respectively. Similar results were obtained also for the COMP model, with h(2) estimates of 0.12 ± 0.037, whether or not F was taken into consideration. Linear regression analyses carried out on the 33 major lineages to which most of participants belonged (n = 6,087) revealed an overall negative trend of EBV compared with the increase of either F (b = -21.3, P < 0.01) or AR (b = -50.1, P < 0.01). However, a great variability in the relationship between EBV and F or AR was found by analyzing data within lineages. Despite the variability, an unfavorable effect of inbreeding was detected in the fighting ability trait of both ABP and AC cattle, and this should be carefully considered in the breeding management of both breeds.     

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.     

Milk production increase following treatment of Dutch dairy cattle with thiabendazole

Summary In a trial involving 542 dairy cattle on 28 farms, 276 were treated once with thiabendazole within two days of calving. The treated group showed an average increase in milk yielded over the non-return group of 229.8 kg during the subsequent lactation. In the treated group, total milk fat production was increased over that of the controls by 7.4 kg per cow; milk protein was increased by 6.9 kg per cow. All treatment parameter differences were highly significant at the 1% level of probability.     

Milk production increase following treatment of Dutch dairy cattle with thiabendazole

Summary

In a trial involving 542 dairy cattle on 28 farms, 276 were treated once with thiabendazole within two days of calving. The treated group showed an average increase in milk yielded over the non‐return group of 229.8 kg during the subsequent lactation.

In the treated group, total milk fat production was increased over that of the controls by 7.4 kg per cow; milk protein was increased by 6.9 kg per cow. All treatment parameter differences were highly significant at the 1% level of probability.     

Effects of diseases on reproductive performance in Swedish Red and White dairy cattle

The objectives of this study were to evaluate the effect of diseases on days open (DO), days to first breeding (DFB) and days from first breeding to conception (DFBC) using survival analysis models, and to assess the significance of the sire component and its possible confounding effect. The data consisted of a random sample of 20% of all herds enrolled in Swedish recording system and using 100% artificial insemination with at least 15 Swedish Red and White cows calving in 1991. The follow-up period was from 45 to 145 d after calving. After editing, the data sets had 23,927, 28,197, and 22,089 cows for days open, days to first breeding, and days from first breeding to conception, respectively. The Cox models included parity, calving season, cow milk production and age at first calving as fixed effects, and herd and sire as random effects. Ten disease groups were considered as possible risk factors for the reproductive traits. Disease groups were treated differently if they occurred before or after 45 d postpartum. Diseases occurring in the first 45 d after calving were treated as time-independent covariates and diseases occurring after day 45 were treated as time-dependent covariates for days open and days to first breeding. The percentages of censored cows were 35% for days open, 19% for days to first breeding, and 33% for days from first breeding to conception. Days open increased in cows with dystocia, stillbirth, retained placenta, metritis, or other diseases occurring in the first 45 d after calving, and in cows with metritis, mastitis, or other diseases occurring after 45 d. Days to first breeding increased in cows with stillbirth, retained placenta, milk fever, mastitis, foot and leg problems, or other diseases occurring before day 45, and in cows with metritis, mastitis, foot and leg problems, or other diseases occurring after 45 d. Days to first breeding decreased in cows treated for ovulatory dysfunctions either before or after 45 d. Days from first breeding to conception increased in cows with dystocia, stillbirth, retained placenta, metritis, or ovulatory dysfunctions occurring before first breeding, and in cows with mastitis occurring after first breeding. Although the additive genetic components were significant for all traits considered, the sires did not act as confounders because only a small amount of variability for the traits considered in this study was explained by the sires, with estimated heritabilities of 2% on the logarithmic scale and from 3 to 4% on the real scale.     

Estimation of ancestral inbreeding effects on stillbirth,calving ease and birthweight in German Holstein dairy cattle

In this study, the effect of different measurements of ancestral inbreeding on birthweight, calving ease and stillbirth were analysed. Three models were used to estimate the effect of ancestral inbreeding, and the estimated regression coefficient of phenotypic data on different measurements of ancestral inbreeding was used to quantify the effect of ancestral inbreeding. The first model included only one measurement of inbreeding, whereas the second model included the classical inbreeding coefficients and one alternative inbreeding coefficient. The third model included the classical inbreeding coefficients, the interaction between classical inbreeding and ancestral inbreeding, and the classical inbreeding coefficients of the dam. Phenotypic data for this study were collected from February 1998 to December 2008 on three large commercial milk farms. During this time, 36 477 calving events were recorded. All calves were weighed after birth, and 8.08% of the calves died within 48 h after calving. Calving ease was recorded on a scale between 1 and 4 (1 = easy birth, 4 = surgery), and 69.95, 20.91, 8.92 and 0.21% of the calvings were scored with 1, 2, 3 and 4, respectively. The average inbreeding coefficient of inbred animals was 0.03, and average ancestral inbreeding coefficients were 0.08 and 0.01, depending on how ancestral inbreeding was calculated. Approximately 26% of classically non‐inbred animals showed ancestral inbreeding. Correlations between different inbreeding coefficients ranged between 0.46 and 0.99. No significant effect of ancestral inbreeding was found for calving ease, because the number of animals with reasonable high level of ancestral inbreeding was too low. Significant effects of ancestral inbreeding were estimated for birthweight and stillbirth. Unfavourable effects of ancestral inbreeding were observed for birthweight. However, favourable purging effects were estimated for stillbirth, indicating that purging could be partly beneficial for genetic improvement of stillbirth.     

Age and weight at first calving and subsequent performance in Dutch dairy cattle from rearing farms

Calf-cow records from 1081 replacement heifers raised on 42 specialised rearing farms in the province of Noord-Brabant have been analysed. The predominant breed was Meuse-Rhine-Yssel (MRY). The objective was to study the relationship between weight and age at first calving and milk production in subsequent lactations, herd life span, dystocia and first calving interval. Weight appeared to be a better predictor for first lactation Fat and Protein Corrected Milk production (FPCM-1) than age. First lactation FPCM had a significant and positive effect on herd life FPCM. First lactation FPCM was significantly associated with first calving interval.     

Age and weight at first calving and subsequent performance in Dutch dairy cattle from rearing farms

Summary

Calf‐cow records from 1081 replacement heifers raised on 42 specialised rearing farms in the province of Noord‐Brabant have been analysed. The predominant breed was Meuse‐Rhine‐Yssel (MRY). The objective was to study the relationship between weight and age at first calving and milk production in subsequent lactations, herd life span, dystocia and first calving interval.

Weight appeared to be a better predictor for first lactation Fat and Protein Corrected Milk production (FPCM‐1) than age. First lactation FPCM had a significant and positive effect on herd life FPCM. First lactation FPCM was significantly associated with first calving interval.     

MIM: an indirect method to assess inbreeding and coancestry in large incomplete pedigrees of selected dairy cattle

In real data, inbreeding is usually underestimated because of missing pedigree information. A method adapted to the dairy cattle situation is presented to approximate inbreeding when the stored population pedigree is incomplete. Missing parents in incomplete pedigrees were given a dummy identification and assigned to groups (up to nine for a given birth date of progeny). These groups were linked to contemporary reference groups with known parents. An explicit model considered that polygenic breeding values in a censored group were centred on a function of the average breeding value in the corresponding reference group and deviated independently. Inbreeding coefficients were obtained progressively over birth dates starting from founders. For each date considered, the parameters pertaining to its groups were computed using the parameters already obtained from groups belonging to the previous dates. The updating algorithms were given in detail. An indirect method was implemented to expedite mass computations of the relationship coefficients involved (MIM). MIM was compared to Van Raden's (VR) method using simulated populations with 20 overlapping generations and different rates of missing sires and dams. In the situation of random matings, the average inbreeding coefficients by date obtained by MIM were close to true values, whereas they were strongly underestimated by VR. In the situation of assortative matings, MIM gave average inbreeding coefficients moderately underestimated, whereas those of VR's method were still strongly underestimated. The main conclusion of this study adapted to the situation of dairy cattle with incomplete pedigrees was that corrections for inbreeding and coancestry coefficients are more efficient with an explicit appropriate genetic model than without.     

Genotype by environment interaction for length of productive life in Swedish Red and White dairy cattle

In this study the amount of genotype by environment interaction (G×E) for length of productive life of Swedish Red and White dairy cattle was studied. The environmental variables used were the herd-year averages of number of first parity cows, peak yield, protein yield, and productive life. Data were analysed using multi-trait models (using low and high quartile herds) and reaction norm models (using the whole continuous scale). Considerable G×E was found for the trait productive life between environments (herds) with short or long average productive life, and a genetic correlation of 0.74 was found. For productive life in relation to herd size, G×E was negligible, and the genetic correlation was 0.95. For productive life in relation to herd-year average of peak yield or protein yield some G×E was indicated by the reaction norm model, especially between extreme environments. The G×E between herds with short or long average productive life should be studied further and might need to be considered in breeding programmes for dairy cattle.     

Evaluation of the long-term immune response in cattle after vaccination against paratuberculosis in two Dutch dairy herds

In the past decades, vaccination against paratuberculosis in cattle was performed in The Netherlands only on a limited scale. Because of its interference with the diagnosis of bovine tuberculosis, vaccination was restricted to herds with a high prevalence of clinical cases of paratuberculosis and was meant to aid in the economical survival of the farm. Recently, a voluntary paratuberculosis certification program has started, based in part on serological screening of cattle of at least 3 years of age. Herds that have been vaccinated against paratuberculosis are, therefore, likely to encounter problems when entering this program.The aim of this study was to evaluate the immune response resulting from vaccination with a heat-killed paratuberculosis vaccine. Over a period of 12-14 years, new-born calves were vaccinated in two herds. The B-cell response was evaluated using both the complement-fixation test (CFT) and an enzyme-linked immunosorbent assay (ELISA) and the cell-mediated immune response was evaluated using the gamma-interferon assay. Data obtained show a marked and prolonged effect of the vaccination on both cellular and humoral immune responses, in particular to the paratuberculosis antigen but also to the bovine tuberculosis antigen, using the respective tests. These responses were detected rapidly after vaccination. The individual responses were highly variable between animals with respect to both the level and to the duration of the evoked immune response. No relation between the results obtained with the ELISA and the CFT was observed. In conclusion, for a large number of vaccinated cattle, a long lasting interference is to be expected with the presently available immunodiagnostic methods for both bovine tuberculosis and paratuberculosis.     

Comparison of the disease incidences of Finnish Ayrshire and Finnish Black and White dairy cows

Finnish Ayrshire and Finnish Black and White cows were compared regarding the incidences of early and late mastitis, parturient paresis, ketosis, ovarian disorders, metritis and the risk of having a test-day somatic-cell count >200,000 cells ml⁻¹ at any of the first three monthly test days in lactation. In a retrospective cohort study 101,793 cows from 5844 tie stalls and 11,811 cows from 437 loose-housing systems from all over Finland were followed from calving in 2000 until the end of lactation. The observed incidences of those cows were then analysed using generalised linear mixed models. Finnish Black and White cows had higher incidences of all diseases except ovarian disorders. Although the differences were statistically significant in all models except metritis and early mastitis in loose-housing systems, they were, in our view, only important on the national level (for the breeding organisations), and of little importance for the farmers.     

Selenium poisoning in dairy cattle

An outbreak of chronic selenium poisoning occurred in a mob of 30 Friesian dairy cows. These cows were all autumn calvers on a well-managed dairy farm.     

Digital dermatitis in dairy cattle

A condition of digital dermatitis causing lameness in a dairy herd is described. The lesion was a small circumscribed area of epidermal inflammation in the skin immediately above the coronet between the bulbs of the heel. Topical treatment, consisting of excoriation and application of a gentian violet and tetracycline aerosol spray, was effective. Although the high incidence and rapid onset of the condition suggested an infectious cause, no organism was isolated consistently.