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PubMed2005

The value of genetic information in selecting dairy replacements.

The objective of this study was to empirically determine the economic value of genetic information in the selection of dairy replacements, and assess whether this value was sufficient to prompt producers to select replacements on this basis. The data set consisted of 1982 Michigan Holstein replacements in 115 herds. Each herd had a minimum of 10 replacements that were born in the last 6 months of 1992 and calved within the last 6 months of 1994. The data for each replacement included the estimated breeding value (EBV) for milk at the beginning and end of the rearing period, and the estimated lifetime profit corrected for the opportunity cost of postponed replacement (ELPCOC). The replacement selection decision for a profit-maximizing dairy producer selecting 70 or 80% of the replacements was modeled. We modeled three methods of selection: genetic, random and ex poste. Genetic selection was evaluated using the EBV milk available at the beginning or end of the rearing period. For each herd, the profit associated with each of the three methods of selection was simulated. The value of the genetic information and perfect information were the differences in herd profits of genetic selection and ex poste selection relative to random selection, respectively. The difference in value of the genetic information between the end of the rearing period and the beginning of the rearing period was the increase in value of the genetic information due to updating. The value of information was calculated as the average herd profit per replacement. The value of the genetic information ranged from 22 dollars/replacement to 30 dollars/replacement and was statistically greater than zero at a 95% confidence level. It is unclear whether this value is sufficient to prompt producers to select replacements on the basis of EBV milk as has been recommended. The negative value of EBV milk (from the end of the rearing period when selecting 80% of the replacements) for 32 herds was consistent with the noisiness of the genetic estimates as messages of ELPCOC. The increased value of the genetic information due to updating was approximately 5 dollars/replacement. This increased value is likely insufficient to warrant delaying replacement selection decisions solely to obtain the updated information. The value of EBV milk was approximately 4 dollars/replacement higher when selecting 70% of the replacements versus 80%. The genetic information captured between 15% (selecting 70% at the beginning of the rearing period) and 20% (selecting 80% at the end of the rearing period) of the value of perfect information.

Animals↗

PubMed2006

Joint modeling of additive and non-additive genetic line effects in single field trials.

A statistical approach is presented for selection of best performing lines for commercial release and best parents for future breeding programs from standard agronomic trials. The method involves the partitioning of the genetic effect of a line into additive and non-additive effects using pedigree based inter-line relationships, in a similar manner to that used in animal breeding. A difference is the ability to estimate non-additive effects. Line performance can be assessed by an overall genetic line effect with greater accuracy than when ignoring pedigree information and the additive effects are predicted breeding values. A generalized definition of heritability is developed to account for the complex models presented.

Breeding↗

PubMed1990

The use of elite nucleus units in beef cattle breeding.

Simple plans for the formation and continuation of elite nucleus breeding units utilizing multiple ovulation and embryo transfer for the genetic improvement of beef cattle were investigated. Three policies of forming nucleus units were considered, each in relation to conventional breeding herds with a possible rate of annual genetic change of .17 phenotypic standard deviation (SD) units and also to breeding herds with no genetic improvement. The genetic improvement (as a genetic lift) from the formation schemes ranged from .43 to 1.38 SD units. Three policies for the continuation of the nucleus units were outlined. The best scheme resulted in almost double the total genetic change possible from conventional breeding herds over a 20-yr period. Transfer of these gains from nucleus to breeding herds and to the commercial herds also was considered. Some advantages and limitations to nucleus breeding schemes were discussed. The opportunity exists for progressive breeders, or groups, to make use of improved genetic evaluation systems (expected breeding values) and embryo transfer to greatly accelerate rates of genetic change in economic efficiency of beef cattle.

Animals↗

PubMed1992

Approximate accuracy of genetic evaluation under a single-trait animal model.

A method to approximate breeding value accuracy under a single-trait animal model was developed. Meyer's method was extended to account explicitly for the covariance between contemporaries, the distribution of relatives across herds, exact relationships between animals, and some cases of close in-breeding. The procedure comprised five steps. The diagonal term of each animal in the mixed model equations was progressively adjusted for 1) the herd-year-season effect, 2) contemporaries, 3) progeny and contemporaries of progeny, 4) mates, and 5) parents and parents of contemporaries, before being inverted and expressed in term of repeatability. The efficiency of this method and Meyer's method was compared with two examples. The proposed method appeared to be more efficient, particularly when herds were small, progeny concentrated in a few herds, and animals inbred. Estimates of repeatability from both methods were biased upward and remained sensitive to the number of generations included in the analysis. However, because of its ease of use, Meyer's method, with simple adjustments for repeatability level and inbreeding, can be recommended.

Animals↗

PubMed2003

[Possible uses of genetic markers for improving fertility and health in swine production].

Selection with regard to breeding aims can take into consideration the genotype with its effects besides the phenotype--meaning the externally visible or measurable traits. The phenotype expression of a trait depends on the underlying genotype that is modulated by environmental influences. Selection using phenotypic traits leads inevitable to inaccuracies as the genotypic effects can only be distinguished from the environmental deviations by the means of simplified statistical models. The marker-assisted selection is a method that combines the genotypic information of single genes with breeding values predicted from phenotypic information. By including the genotypic information the accuracy and intensity of selection can be improved. The selection decision can take place early in life of an animal because the time to phenotypic expression of the traits of the breeding goals has not to be bided for. The possibility of realizing selection criteria on a molecular genetic level shortens the generation interval. Particularly for fertility and health traits, this is of greatest interest. Genotyping can be performed by using blood or tissue samples of new-born piglets; it is not necessary to wait for the first parities of a sow or the results obtained by the offspring of a boar. Thus, damages and suffering from diseases can be reduced in animals, because susceptible animals can be diagnosed prior to occurrence of a disease and appropriate actions for prophylaxis can be undertaken. In the following the possibilities for pig breeding connected with marker-assisted selection are pointed out. Besides, it is shown by some examples how genes become so called candidate genes because of the physiological importance of their transcription products within the scope of metabolism. Besides the representation of the physiology of a few transcription products involved in reproductive processes results of studies analysing the association of alleles of these candidate genes with fertility traits are given.

Animals↗

PubMed2006

Genetics of litter size in three maternal lines of rabbits: repeatability versus multiple-trait models.

Variance components were estimated in 3 lines of rabbits selected for litter size at weaning (A, Prat, and V) to test one of the assumptions of the models used for selection: that litter size data at different parities are repeated measurements of the same trait. Multiple-trait analyses were performed for the total number of kits born (TB), the number of kits born alive (BA), and the number of kits weaned (NW) per litter. Estimates were obtained by REML in multivariate analyses, including all of the information of the selection criteria, under a repeatability model or a multiple-trait model, considering litter size at the first, second, and subsequent parities as different traits. Models included the fixed effects of the physiological status of the female and the year-season of mating day, buck and doe random permanent environmental effects, and doe additive genetic effects. Results indicated that prolificacy was determined mainly by doe components and that the service sire had a very small effect. Heritabilities for the first and second parities were greater than the estimates obtained under the repeatability model (0.04 to 0.14 for the repeatability model). In the A and V lines, similar values of heritability were found at the first and second parities, but in the Prat line heritability at the second parity was always greater than at the first and greater parities (values of 0.21, 0.17, and 0.15 for TB, BA, and NW, respectively, in second parities of the Prat line). Genetic correlations between the same traits at different parities were approximately 0.8 for all traits in line A, but much lower in the other 2 lines. On average, the values were 0.64 for TB, 0.48 for BA, and 0.39 for NW between the first and second parities, and 0.65 for TB, 0.56 for BA, and 0.45 for NW between the first and third and greater parities. Genetic correlations between the second and greater parities showed the greatest values (approximately 0.8) in lines A and Prat for all traits, but they were lower in line V (0.63 for BA and 0.37 for NW). The heterogeneity of heritabilities and genetic correlations between parities lower than 0.9 suggests that litter size at different parities could be considered as different traits when genetic evaluations are performed. However, when the accuracies of predicted breeding values under a multiple-trait and a repeatability model were calculated, assuming the first to be the true model, the values obtained were nearly the same for all traits in all lines.

Animals↗

PubMed2002

[Research and application of animal genetic marker-assisted selection].

With the development of molecular and quantitative genetics and its related subjects, it made a great progress on the research about animal genetic marker-assisted selection (MAS). There were also some successful examples on the application of MAS to animal genetic improvement. The statistical method which using phenotypic, pedigree and genetic marker information to predict individual breeding values has already been developed. Many achievements were obtained from the researches, which carried on MAS relative efficiency and its affecting factors and selection schemes. The present paper reviewed some progresses of MAS research and discussed some problems about MAS application to animal breeding.

English Abstract↗

PubMed2005

Variance components and heritabilities for sow productivity traits estimated from purebred versus crossbred sows.

Genetic parameters were estimated for number of pigs born alive (NBA), adjusted litter weaning weight (ALWT), and the interval from weaning to first service (W2E) using 2002 purebred litter records and 14 583 crossbred litter records from a swine production unit with a defined great-grandparent, grandparent, and parent stock genetic system structure. Estimation of (co)variance components was carried out by REML methods. Heritability estimates from this study for NBA were 0.155, 0.146, 0.145 for the purebred, crossbred, and pooled data, respectively. Heritability estimates for ALWT were 0.162, 0.195, and 0.183 for the purebred, crossbred and pooled data, respectively. Heritability estimates for W2E were 0.205, 0.239 and 0.202 for the purebred, crossbred and pooled data, respectively. Genetic correlations between NBA and ALWT were weak and positive for the three groups. The genetic correlation between W2E and ALWT were -0.158 for the purebred Yorkshires, 0.031 for the crossbreds and 0.051 for the pooled data. The genetic correlation between W2E and NBA was -0.027 for the purebred Yorkshires, 0.310 for the crossbreds and 0.236 for the pooled data. These similarities suggest that pooling of purebred and crossbred data may be considered, which may potentially increase the accuracy of breeding value estimates, which would result in increased genetic progress.

Age Factors↗

PubMed1992

A bioeconomic simulation model for a hierarchical swine breeding structure.

A stochastic computer model was developed to simulate individual pigs in a hierarchical breeding system. The bioeconomic model was designed as a tool to facilitate the evaluation of selection, culling, and management strategies for a three-tiered breeding structure. Events such as mating, farrowing, and selection occurred weekly. Variables included number of pigs born alive, survival rate from birth to weaning, average daily gain and backfat at 110 kg, number of pigs weaned, feed per gain, days from weaning to 110 kg, age at puberty, and growth rate and weight of sows and service boars. Also included were probabilities of conception, return to estrus by week, survival, involuntary culling, male infertility, and unacceptable conformation. Variables important for selection were determined by breeding value, individual and maternal heterosis, parity, size of birth litter, sex, age of dam, genetic and environmental relationships between variables, and common litter, permanent, and random environmental effects. Variables derived from selection variables were computed by regression using phenotypic relationships between all variables. Also, a random environmental effect was added to predicted performance. Means and variances of variables differed between genetic lines. Production costs included feed, non-feed operating, fixed, and replacement stock costs. Income included market animals, culls, and replacements sold to lower tiers. Effects of changes in backfat on market value and sow maintenance feed costs were not modeled. An example is given to illustrate model output.

Animal Feed↗

PubMed2002

The genetic relationship between commencement of luteal activity and calving interval, body condition score, production, and linear type traits in Holstein-Friesian dairy cattle.

The decline of fertility in the UK dairy herd and the unfavorable genetic correlation (r(a)) between fertility and milk yield has necessitated the broadening of breeding goals to include fertility. The coefficient of genetic variation present in fertility is of similar magnitude to that present in production traits; however, traditional measurements of fertility (such as calving interval, days open, nonreturn rate) have low heritability (h2 < 0.05), and recording is often poor, hindering identification of genetically superior animals. An alternative approach is to use endocrine measurements of fertility such as interval to commencement of luteal activity postpartum (CLA), which has a higher h2 (0.16 to 0.23) and is free from management bias. Although CLA has favorable phenotypic correlations with traditional measures of fertility, if it is to be used in a selection index, the genetic correlation (ra) of this trait with fertility and other components of the index must be estimated. The aim of the analyses reported here was to obtain information on the ra between lnCLA and calving interval (CI), average body condition score (BCS; one to nine, an indicator of energy balance estimated from records taken at different months of lactation), production and a number of linear type traits. Genetic models were fitted using ASREML, and r(a) were inferred from genetic regression of lnCLA on sire-predicted transmitting abilities (PTA) for the trait concerned by multiplying the regression coefficient (b) by the ratio of the genetic standard deviations. The inferred r(a) between lnCLA and CI and average BCS were 0.36 and -0.84, respectively. Genetic correlations between InCLA and milk fat and protein yields were all positive and ranged between 0.33 and 0.69. Genetic correlations between InCLA and linear type traits reflecting body structure ranged from -0.25 to 0.15, and between udder characteristics they ranged from -0.16 to 0.05. Thus, incorporation of endocrine parameters of fertility, such as CIA, into a fertility index may offer the potential to improve the accuracy of breeding value prediction for fertility, thus allowing producers to make more informed selection decisions.

Animals↗

PubMed1991

[Analysis of environmentally-conditioned and genetic influences on the frequency of hip joint dysplasia in German Shepherd dogs].

The importance of environmental and genetic influences on the frequency of hip dysplasia was studied in 10,595 German shepherd dogs. Systematic effects were analysed using mixed linear and mixed nonlinear threshold models. Following effects were regarded in the models applied: sire and mother of the dog as random effects, age at x-raying, sex, birth year and season of the x-rayed dogs, litter size, percentage of x-rayed dogs in each litter and sex ratio of the litter as fixed effects. Sire, mother, sex and age at x-raying showed significant influence on the occurrence of hip dysplasia. The heritability estimates in a hierarchical data design (sire, mother within sire) for the polychotomous trait hip dysplasia were for full sibs h2 = 0.30, for maternal half sibs h2 = 0, 48, and for paternal half sibs h2 = 0.11. Only the heritability estimates of the paternal half sibs seem to be reliable because kennel and breeder effects are confounded with the mother effect. Analysing the frequency of hip dysplasia as all-or-none traits, the heritability estimates were usually lowered by 50%. Selection programmes to reduce frequency of hip dysplasia can be improved if the estimation of breeding values with respect to environmental effects and frequency of hip dysplasia in all relatives will be implemented.

Analysis of Variance↗

PubMed2003

Genetic and plastic responses of a northern mammal to climate change.

Climate change is predicted to be most severe in northern regions and there has been much interest in to what extent organisms can cope with these changes through phenotypic plasticity or microevolutionary processes. A red squirrel population in the southwest Yukon, Canada, faced with increasing spring temperatures and food supply has advanced the timing of breeding by 18 days over the last 10 years (6 days per generation). Longitudinal analysis of females breeding in multiple years suggests that much of this change in parturition date can be explained by a plastic response to increased food abundance (3.7 days per generation). Significant changes in breeding values (0.8 days per generation), were in concordance with predictions from the breeder's equation (0.6 days per generation), and indicated that an evolutionary response to strong selection favouring earlier breeders also contributed to the observed advancement of this heritable trait. The timing of breeding in this population of squirrels, therefore, has advanced as a result of both phenotypic changes within generations, and genetic changes among generations in response to a rapidly changing environment.

Acclimatization↗

PubMed2005

Incidence, risk factors, and heritability estimates of hind limb lameness caused by hip dysplasia in a birth cohort of boxers.

OBJECTIVE: To determine incidence, risk factors, and heritability estimates of hind limb lameness caused by hip dysplasia in a birth cohort of Boxers. ANIMALS: 1733 Boxers from 325 litters. PROCEDURE: Status of Boxers with respect to clinical signs of canine hip dysplasia (cCHD) was registered during an 8-year period. Survival analysis accounted for dogs lost to follow-up. Effective heritability for developing cCHD was estimated by use of a proportional hazard model on the basis of the Weibull distribution. Parametric survival models were developed to identify the influence of potential risk factors. RESULTS: Cumulative hazard rate for cCHD from 7 weeks to 8 years of age was 8.5%. Dogs that were kept on a floor covered with a slippery material were 1.6 times as likely to develop cCHD, compared with dogs kept on a nonslippery floor. Risk of cCHD doubled in dogs from litters with a high preweaning mortality rate. Dogs that were neutered at 6 months prior to a diagnosis of CHD were 1.5 times as likely to develop cCHD, compared with sexually intact dogs. Dogs >5 years of age were 1.8 times as likely to develop cCHD, compared with younger dogs. Estimated effective heritability of cCHD was 0.11. In terms of the risk of cCHD in progeny, mean estimated breeding value (EBV) of the 10 best and 10 worst sires was -0.32 and 0.42, respectively. CONCLUSIONS AND CLINICAL RELEVANCE: Registration of Boxers that develop cCHD may provide a strategy for disease prevention. In addition to diagnostic evaluation of radiographs, sire EBVs provide useful information for breeding selection decisions.

Animals↗

PubMed2002

Estimation of pedigree errors in the UK dairy population using microsatellite markers and the impact on selection.

The proportion of cows in the UK dairy herd whose sires were misidentified was estimated using DNA markers. Genetic marker genotypes were determined on 568 cows (from 168 milk samples and 400 hair samples) and 96 putative sires (from semen samples). The estimated pedigree error rate from the hair samples was 8.8%, and from the milk samples, 13.1%, giving an overall estimate of the error rate of 10%. This level of pedigree errors will have a relatively large impact on the efficiency of progeny testing and the accuracy of cow predicted breeding values. We predict a loss of response to selection of approximately 2 to 3% given this error rate.

Animals↗

PubMed2001

Breeding for improved disease resistance in organic farming--possibilities and constraints.

Lowered incidences of disease may be reached in several ways: management and rearing measures, vaccination programmes and preventive medications as well as breeding for improved disease resistance. Here the focus is on breeding for improved resistance to infectious diseases. In comparison to conventional farming, one has to acknowledge that the spectrum of diseases in animals reared under organic conditions is different and that the proportion of the breeding stock of animals in organic farming is considerably smaller. There are at least four different approaches that may be used in breeding towards resistance to infectious diseases. The most obvious is to record disease incidence in the progeny and select those parents that produce the progeny with the lowest incidences of disease. Another approach is to use breeders possessing certain major histocompatibility complex antigens suggested being associated with resistance to certain infections. A third approach is to analyse the heritability of a set of immune functions or related traits crucial for resistance to infections and then use the traits with high heritability in breeding programmes. Finally, one may genetically select animals for high immune response using an index that combines estimated breeding values for several immunological traits. Examples of these various approaches are given and the feasibility for using these in organic farming are discussed.

Animal Diseases↗

PubMed2003

Relationships among milk yield, body condition, cow weight, and reproduction in spring-calved Holstein-Friesians.

Relationships among milk production, body condition score (BCS), body weight (BW), and reproduction were studied using logistic regression on data from 6433 spring-calving Holstein-Friesian dairy cows in 74 commercial herds. Multivariate models were adjusted for herd, breeding value for milk yield, proportion of Holstein-Friesian genes, lactation number, calving period, and degree of calving assistance. Significant associations between reproductive measures and components of energy balance were identified. Higher 200-d milk protein content and higher protein-to-fat ratio at start of breeding were associated with increased likelihood of submission for breeding in the first 21 d of the breeding season (SR21). High 100-d cumulative milk yield as a proportion of estimated 305-d milk yield (low persistency) was associated with a lower likelihood of pregnancy to first service (PREG1), whereas cows reaching peak milk yields earlier tended to have higher PREG1. Cows that reached nadir milk protein content relatively late in lactation had lower PREG1. Milk yield at first service and 305-d milk protein content were positively associated with the likelihood of pregnancy after 42 d of breeding (PR42). Higher 305-d milk lactose content was associated with increased PREG1 and PR42. Mean BCS at 60 to 100 d of lactation was positively associated with both SR21 and PR42, whereas nadir BCS was positively associated with PREG1. Cows with precalving BCS > 3.0 that also lost > 0.5 BCS unit by first service had lower PR42. More BW gain for 90 d after start of breeding was associated with higher SR21 and PREG1; more BW gain for 90 d after first service was associated with higher PR42. Milk protein and lactose content, BCS, and BW changes are important tools to identify cows at risk of poor reproduction.

Animals↗

PubMed2004

The use of a genetic-counselling program by Dutch breeders for four hereditary health problems in boxer dogs.

Our group developed a genetic-counselling program for boxer-dog breeders in The Netherlands, using data for cryptorchidism (uni- and/or bilateral), epilepsy, knee-problems (including ligament rupture, fractured or ruptured meniscus, severe osteo-arthrosis of the knee, or a combination of these disorders), and schisis (including cheiloschisis, palatoschisis, or cheilopalatoschisis). We transformed the estimated breeding values (EBVs) into odds ratios (ORs), to enable the breeder to compare the risk for each of the traits for a certain dam-sire combination with the average population risk (set at 1). The goal of the study was to evaluate the use of our genetic-counselling program by Dutch breeders of boxer dogs. We asked breeders of the Dutch Boxer Club to send in an application form for genetic-counselling from June 1 to December 1, 2000. Breeders indicated on this application form three desirable sires for their dam (sire 1, sire 2, sire 3) in random order. On the basis of this information, a counselling report was produced which included ORs for the four diseases in litters of the dam-sire combinations indicated on the application form. Together with the counselling report, the breeders received an evaluation form. We received 129 application forms from 70 breeders, and collected 125 evaluations. Of these evaluations, 96 were informative about the influence of the counselling report on sire choice. The most-important criteria used by breeders to select sires were: the exterior characteristics (60%) and known progeny (52%). Although it was the first time breeders could make use of genetic-counselling, 32% of the breeders indicated that the genetic-counselling played a major role in their sire selection. Breeders expressed little difference in importance for the four genetic traits, but there was a tendency to consider epilepsy more than the others. Breeders hesitated to put long-term population interest above short-term personal interest. Nevertheless, the general conclusion of this study is that breeders acknowledge the value of counselling, especially to reduce the frequency of a threatening disease such as epilepsy.

Animals↗

PubMed2005

[Genetic potentiality of utilizing Yugoslavia maize inbred lines to improve Chinese elite hybrids].

In this study, 107 crosses were made using 9 Yugoslavia maize inbred line as female and 13 parent lines of 8 Chinese elite hybrids, belonging to different heterotic groups, as male. Though Dudley's method the genetic potentiality of 9 Yugoslavia maize inbred lines were analyzed for the improvement in the yield of 8 Chinese elite hybrids and main ear -kernel characters, and for their proper applications. The results showed that the introduced Yugoslavia inbreds had broad genetic basis and high breeding value in indirect utilization. Almost all Yugoslavia inbreds, including 9801, 9802, 9803, 9805, 9807, 9808, and 9809, could improve the yield of Yuyu15, GailiangYuyu20, Yuyu22, Yuyu23, Yuyu24, Shendn10 and Nongda 108 through different parents and ear-kernel characters, while the real improving effects should be proved in further practical breeding.

Alleles↗