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PubMed2003

Effects of including a quantitative trait locus in selection under different waiting plans of young bulls.

The advantage of using the genotype of a quantitative trait locus (QTL) in selection schemes of dairy cattle was quantified using stochastic simulation. Three selection plans were studied. In the first plan, young bulls waited for 3 yr until their sisters completed a lactation and then were evaluated and selected based on an animal model. In a second plan, young bulls waited for 5 yr until their daughters completed a lactation. An intermediate 4-yr waiting plan was also studied. Simulation was for 16 yr with overlapping generations. Population and model parameters were proportional to the U.S. Holstein population. The advantage of using a QTL was quantified as the percentage of superiority of QTL-assisted over QTL-free selection using cumulative genetic response. Percentage of superiority was reported for four selection pathways: active sires, young bulls, bull dams, and first lactation cows. A general trend was observed: low superiority in early years of selection that increased to a plateau in later years and then decreased. The superiority of the QTL information was greatest in the 3-yr waiting plan and least in the 4-yr waiting plan. Superiority at plateau for selection pathways ranged from 16 to 26% for the 3-yr waiting plan, from 3 to 12% for the 4-yr waiting plan, and from 5 to 13% for the 5-yr waiting plan. The contribution to selection response attributed to the QTL and the polygenes was quantified. The rate at which the favorable allele approached fixation and the accuracy of predicting breeding values on the percentage of superiority were studied.

Animals↗

PubMed2026

The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding.

Plant pan-genomics is entering a new phase beyond genome variation discovery, requiring a shift from cataloguing genomic diversity toward understanding how variation generates biological function and breeding value. Here, we propose that the future of plant pan-genomics will be shaped by three conceptual transitions. First, structural variation (SV), presence-absence variation (PAV), and haplotype diversity should be interpreted not merely as genomic differences, but as regulatory components that influence gene networks, chromatin organization, and complex traits. Second, the expansion from species-level pan-genomes to genus-level super pan-genomes provides an evolutionary framework for uncovering adaptive genetic modules preserved in wild relatives and overlooked during domestication. Third, integrating pan-genomes with pan-omics, three-dimensional genome analyses, and artificial intelligence will enable the transformation of genomic variation into predictive models for crop improvement. We further propose that the ultimate value of pan-genomes lies not in generating increasingly complete genome collections, but in establishing a mechanistic bridge between genome diversity, biological function, and breeding decisions. This transition will move crop improvement from empirical selection toward rational genome design, where evolutionary diversity can be systematically interpreted, predicted, and engineered.

Journal Article↗

PubMed1997

Genetic relationships among production traits and rebreeding performance.

We studied effects of selection for increased daily gain, reduced backfat, increased number of piglets born alive, and increased 21-d litter weight on interval from weaning to farrowing (IWF) of two commercial populations of purebred Large White (LW) and Landrace (LR) lines with each represented in two farms. The analysis took into account that normal and prolonged intervals could be distinguished. Distributions of IWF were described by a mixture of a normal and an exponential distribution. Observed intervals were transformed to the probability of being a prolonged interval, using the mixed density function. Incidence of normal intervals was less in LR than in LW sows and was least in first-litter sows. Heritability estimates of IWF ranged from zero to .24 across parities and farms. Genetic trend within breed and farm was different from zero (P < .05) for each trait under selection, except backfat on Farm 2. Genetic correlations between the traits under selection and IWF were inconsistent across farms. Differences in estimated breeding value for the traits under selection between sows with a normal and a prolonged interval were significant only on Farm 1 in the Large White breed, when only observed intervals were analyzed. Including culled sows in the analysis as sows with a prolonged interval yielded consistent differences for average daily gain and backfat, such that genetic selection for improved production would increase the liability for a prolonged interval. Culling sows for delayed estrus apparently overcame this problem on Farm 2 but not on Farm 1, on which a trend of increasing incidence of prolonged intervals was observed.

Aging↗

PubMed1989

Relationship of bull fertility with daughter fertility and production traits in Holstein dairy cattle.

The phenotypic and genetic correlations between fertility ratings of AI bulls for conception rate and their estimated breeding values for daughters' fertility and production traits were calculated. Genetic correlations between fertility ratings of bulls for conception and heifer fertility traits (age at first breeding, age at last breeding, and number of insemination per conception) were negative and ranged from -.04 to -.23, indicating daughters of bulls with high fertility ratings were younger at first breeding and required fewer services to conceive. In general, genetic correlations between fertility ratings of bulls for conception rate and cow fertility traits (days from calving to first breeding, days open, and number of inseminations per conception) and production traits (breed class average milk and fat and fat percentage) in the first two lactations were also moderate to high and in the favorable direction. Although heritability of both male and female fertility is low, these data indicate that heavy use of sires with high fertility ratings could have a mild positive effect on both male and female fertility. Evidence is also found to indicate that in this breed, selection for increased milk yield should not impair genetic ability of cows to reproduce.

Animals↗

PubMed1990

Restriction fragment length polymorphism of bovine lysozyme genes.

Genetic polymorphism of bovine lysozyme (LYZ) genes was investigated by analysing restriction fragment length polymorphism (RFLP). The analysis revealed three RFLP loci designated LYZ1, LYZ2 and LYZ2. Each system included two or three allelic variants. Evidence for close genetic linkage of the three loci was found. There was also a significant linkage disequilibrium among the three loci in a sample of about 200 breeding bulls from one breed. No statistically significant association was found between LYZ RFLPs and breeding values of bulls for disease or milk production traits.

Alleles↗

PubMed2005

Estimation of genetic effects in the presence of multicollinearity in multibreed beef cattle evaluation.

Breed additive, dominance, and epistatic loss effects are of concern in the genetic evaluation of a multibreed population. Multiple regression equations used for fitting these effects may show a high degree of multicollinearity among predictor variables. Typically, when strong linear relationships exist, the regression coefficients have large SE and are sensitive to changes in the data file and to the addition or deletion of variables in the model. Generalized ridge regression methods were applied to obtain stable estimates of direct and maternal breed additive, dominance, and epistatic loss effects in the presence of multicollinearity among predictor variables. Preweaning weight gains of beef calves in Ontario, Canada, from 1986 to 1999 were analyzed. The genetic model included fixed direct and maternal breed additive, dominance, and epistatic loss effects, fixed environmental effects of age of the calf, contemporary group, and age of the dam x sex of the calf, random additive direct and maternal genetic effects, and random maternal permanent environment effect. The degree and the nature of the multicollinearity were identified and ridge regression methods were used as an alternative to ordinary least squares (LS). Ridge parameters were obtained using two different objective methods: 1) generalized ridge estimator of Hoerl and Kennard (R1); and 2) bootstrap in combination with cross-validation (R2). Both ridge regression methods outperformed the LS estimator with respect to mean squared error of predictions (MSEP) and variance inflation factors (VIF) computed over 100 bootstrap samples. The MSEP of R1 and R2 were similar, and they were 3% less than the MSEP of LS. The average VIF of LS, R1, and R2 were equal to 26.81, 6.10, and 4.18, respectively. Ridge regression methods were particularly effective in decreasing the multicollinearity involving predictor variables of breed additive effects. Because of a high degree of confounding between estimates of maternal dominance and direct epistatic loss effects, it was not possible to compare the relative importance of these effects with a high level of confidence. The inclusion of epistatic loss effects in the additive-dominance model did not cause noticeable reranking of sires, dams, and calves based on across-breed EBV. More precise estimates of breed effects as a result of this study may result in more stable across-breed estimated breeding values over the years.

Animals↗

PubMed2006

Marker-assisted selection based on a multi-trait economic index in chicken: Experimental results and simulation.

A method proposed herein allows simultaneous selection for several production traits, taking into consideration their marginal economic values (i.e. the economic value of a trait's additional unit). This economic index-marker assisted selection (EI-MAS) method is based on the calculation of the predicted economic breeding value (BV), using information on DNA markers that have previously been found to be associated with relevant quantitative trait loci. Based on the proposed method, results with real birds showed that sire progeny performance was significantly correlated with expected performance (r = 0.61-0.76; P = 0.03-0.01). Simulation analysis using a computer program written specifically for this purpose suggested that the relative advantage of EI-MAS would be large for traits with low heritability values. As expected, the response to EI-MAS was higher when the map distance between the marker and the quantitative trait gene was small, and vice versa. A large number of distantly located markers, spread 10 cM apart, yielded higher response to selection than a small number of closely located markers spread 3 cM apart. Additionally, the response to EI-MAS was higher when a large number (ca.150) of progeny was used for the prediction equation.

Animal Husbandry↗

PubMed1999

Controlling canine hip dysplasia in Finland.

The aim of the study was to evaluate the Finnish Kennel Club's hip-dysplasia screening and control programs. As a retrospective study, records of hip-dysplasia screening of 69,349 dogs in 22 breeds that were born in 1988-1995 were analyzed and compared to data from prior to 1988. In most breeds, no significant changes in dysplasia prevalence could be found. In English cocker spaniels, golden and Labrador retrievers and Rottweilers a significant decrease - but in boxers, Dobermans, German Shepherd dogs and rough collies a significant increase - in prevalence was detected. In flat-coated retrievers overall prevalence increased - but the prevalence of severe hip-dysplasia decreased significantly during the study period. The present control program has not resulted in fast progress. Selecting against hip-dysplasia cannot be expected to be very effective, when based only on mass selection on phenotypic observations. Predicted breeding values based on progeny testing would probably give better results. Also, breeders' compliance and commitment to programs is not always high and other selection criteria in breeding are thought to be more important. Modern society has high demands for animal welfare and consumer issues, and breeders and kennel societies should pay more attention to health issues in breeding pedigreed dogs.

Animals↗

PubMed1995

Calculation and use of inbreeding coefficients for genetic evaluation of United States dairy cattle.

Inbreeding coefficients are calculated routinely for all animals included in national genetic evaluations for yield traits. The base population for inbreeding is defined as animals born during 1960. Animals with unknown parents are assumed to have inbreeding coefficients that are equal to the mean of coefficients for animals with known parents born during the same year. Mean inbreeding coefficients reached .03 to .04 for recent years, and coefficients for some animals exceeded .50. The annual increase in level of inbreeding was highest for Milking Shorthorns, but the rate of change of that increase was greatest for Holsteins. Accounting for inbreeding in calculation of the inverse of the relationship matrix had only a small effect on evaluations. For Jersey, the maximum change in breeding value was 73 kg of milk for cows and 40 kg of milk for bulls with > or = 10 daughters. Estimates of inbreeding depression were similar across breeds for production traits and were -29.6 kg of milk, -1.08 kg of fat, and -.97 kg of protein per 1% of inbreeding for Holsteins. In January 1994, the USDA began considering the percentage of inbreeding when calculating inverses of relationship matrices, the largest matrix representing over 20 million Holsteins; this inbreeding percentage was released to the dairy industry for bulls.

Animals↗

PubMed1992

Genetic analysis of bovine respiratory disease in beef calves during the first year of life.

The prevalence of bovine respiratory disease (BRD) was assessed in a population of 10,142 beef calves representing nine pure breeds and three composite populations born in 1983 through 1988. Twenty-four percent of the calves experienced at least one episode of respiratory disease during the 1st yr of life; frequencies over the six birth years ranged from 14 to 38%. The timing of respiratory disease outbreaks differed among birth years; in 4 of the 6 yr, more illness occurred in the pasture before weaning than in the feedlot after weaning. Frequencies of BRD during preweaning and postweaning periods were analyzed separately. Pure breeds and composite populations within a single preweaning location differed in frequency of illness during the preweaning period. However, not all possible breed comparisons could be made because preweaning location differed for the breed groups, and preweaning location had a significant effect on the frequency of respiratory disease in the preweaning period. The preweaning location effect did not carry through to the postweaning period. Pinzgauers had the highest BRD frequency within the feedlot (24.6%). The heritability estimates of BRD during the preweaning and postweaning periods did not differ significantly from 0 (.10 +/- .02 and .06 +/- .07, respectively). Although it is likely that response to selection for resistance to BRD would be slight using the animal's history of BRD as the selection criterion, including information on relatives or additional immune traits may improve the accuracy of an estimated breeding value for BRD resistance.

Animals↗

PubMed2004

Genetic comparison of breeding schemes based on semen importation and local breeding schemes: framework and application to Costa Rica.

Local breeding schemes for Holstein cattle of Costa Rica were compared with the current practice based on continuous semen importation (SI) by deterministic simulation. Comparison was made on the basis of genetic response and correlation between breeding goals. A local breeding goal was defined on the basis of prevailing production circumstances and compared against a typical breeding goal for an exporting country. Differences in genetic response were <3%, and the correlation between breeding goals was 0.99. Therefore, difference between breeding objectives proved negligible. For the evaluation of genetic response, the current scheme based on SI was evaluated against a progeny testing (PT) scheme and a closed nucleus (CN) breeding scheme, both local. Selection intensities and accuracy of selection were defined according to current population size and reproduction efficiency parameters. When genotype x environment interaction (G x E) was ignored, SI was the strategy with the highest genetic response: 5.0% above the CN breeding scheme and 33.2% above PT. A correlation between breeding values in both countries lower than one was assumed to assess the effect of G x E. This resulted in permanent effects on the relative efficiencies of breeding strategies because of the reduction in the rate of genetic response when SI was used. When the genetic correlation was assumed equal to 0.75, the genetic response achieved with SI was reduced at the same level as local PT. When an initial difference in average genetic merit of the populations was assumed, this only had a temporal effect on the relative ranking of strategies, which is reverted after some years of selection because the rate of change in genetic responses remains unchanged. Given that the actual levels of genetic correlation between countries may be around 0.60, it was concluded that a local breeding scheme based on a nucleus herd could provide better results than the current strategy based on SI.

Animals↗

PubMed2004

[Maximum likelihood analysis for mapping dynamic trait QTL in outbred population. I . Methodology].

The quantitative traits whose phenotypic values change with time in life or other quantitative factors, were defined as dynamic traits. Based on the idea about random regression test-day model for estimating breeding values in animal evaluation, a mathematic model was constructed for mapping dynamic trait loci by using Legendre polynomials to model dynamic changes of each genetic effect. The Maximum likelihood analysis implemented via EM algorithm was used to estimate the parameters, including QTL position, fixed genetic regression effects for dynamic trait QTL mapping in outbred population. Compared with the existing method for dynamic trait mapping QTL, the new method presented here not only allowed to sample dynamic trait in disequillibrium way, but also can achieve to map dynamic traits QTL in any resource population by just one step. The further study on dynamic trait mapping QTL was theoretically discussed by incorporating genetic analysis of dynamic trait into general mapping QTL.

Likelihood Functions↗

PubMed2001

Parameters of glucose and lipid metabolism in the male Göttingen minipig: influence of age, body weight, and breeding family.

The pig is useful as a model for human physiology and pathophysiology and could be an important supplement to the many available rodent models of diabetes mellitus. Due to their small size, Göttingen minipigs are especially suitable for long-term studies. The aim of the study reported here was to establish reference values for a range of glucose and lipid homeostasis parameters of interest that could be used to identify possible diabetes-prone male Göttingen minipig individuals, families, or age groups. Plasma samples from nonfed animals were analyzed for glucose, leptin, fructosamine, insulin, C-peptide, triglyceride, free fatty acids, and total cholesterol values. Breeding family had significant effects only on plasma triglyceride concentrations (P < 0.001). Plasma concentrations of glucose (P = 0.012), fructosamine (P < 0.001) and triglycerides (P < 0.001) increased significantly with age, whereas total cholesterol concentration decreased significantly (P = 0.001) with age. Age did not influence other parameters. In conclusion, glycemia and insulinemia increased with age and body weight, possibly indicating a small deterioration in insulin sensitivity with age. It is, therefore, hypothesized that older, compared to younger animals may be more useful in the development of a model of type-2 diabetes mellitus. Furthermore, on the basis of decrease in cholesterol concentration with age, animals fed ad libitum with possibly a high calorie diet might be even more useful in the development of a type-2 diabetes mellitus model.

Aging↗

PubMed2006

From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding.

This article reviews methods of integration of transcriptomics (and equally proteomics and metabolomics), genetics, and genomics in the form of systems genetics into existing genome analyses and their potential use in animal breeding and quantitative genomic modeling of complex traits. Genetical genomics or the expression quantitative trait loci (eQTL) mapping method and key findings in this research are reviewed. Various procedures and potential uses of eQTL mapping, global linkage clustering, and systems genetics are illustrated using actual analysis on recombinant inbred lines of mice with data on gene expression (for diabetes- and obesity-related genes), pathway, and single nucleotide polymorphism (SNP) linkage maps. Experimental and bioinformatics difficulties and possible solutions are discussed. The main uses of this systems genetics approach in quantitative genomics were shown to be in refinement of the identified QTL, candidate gene and SNP discovery, understanding gene-environment and gene-gene interactions, detection of candidate regulator genes/eQTL, discriminating multiple QTL/eQTL, and detection of pleiotropic QTL/eQTL, in addition to its use in reconstructing regulatory networks. The potential uses in animal breeding are direct selection on heritable gene expression measures, termed "expression assisted selection," and genetical genomic selection of both QTL and eQTL based on breeding values of the respective genes, termed "expression-assisted evaluation."

Animals↗

PubMed2004

Open-nucleus breeding strategies compared with population-wide positive assortative mating: I. Equal distribution of testing efforts.

Positive assortative mating (PAM) can enhance the additive genetic variance in a breeding population(BP). This increases the potential for gains in the production population (PP, selected subset of the BP) for recurrent selection programs in forest trees. The assortment of mates can be either: (1) by individual tree rank across the whole BP (PAM), or (2) trees of similar rank can be merged into larger hierarchical groups and then mated randomly within group ("open"-nucleus breeding,NB). The objective of this study was to compare PAM and NB in quantitative terms. The NB simulation model assumed two tiers (nucleus, main) with unrestricted migration between the tiers. Clonal tests were used to predict breeding values and test resources per mate were kept constant for all mates. Both gain and diversity were combined into a single selection criterion, "group-merit selection." Alternatives were compared over five breeding cycles by considering genetic gain and diversity in a selected PP established in a seed orchard. The assortment of mates in both alternatives enhanced additive variance and increased the additive effect in the BP, leading to additional gain in the PP. Gains generated under PAM always exceeded gains under NB. Thus, the main message from this study is that PAM in both the short- and long-term results in more gain at any target level of diversity in the PP (the breeder's target) than is achieved by the NB alternative. The optimum size of the nucleus varies with the desired level of seed orchard diversity. At lower target diversity, smaller nucleus sizes are favorable, while larger sizes result in more gain when seed orchard diversity is considered more important.

Breeding↗

PubMedDate not supplied

[Repeatability and heredity in assessing the genotype of breeding bulls].

Phenotypic correlations between the breeding value of bulls and the level of lactation of their mothers as well as the results of the assessment of their fathers were calculated on the basis of the data of tests and assessments of 1687 diary bulls for quality of their progeny. A relatively weak correlation was detected for the paternal side of the pedigree. This was due to a low efficiency of genotype assessments. A functional relationship between the repetition value and the number of daughters and the number of herds, in which they were used, was determined.

Animals↗

PubMed2007

Genetic relationships among calving ease, calving interval, birth weight, and weaning weight in the Asturiana de los Valles beef cattle breed.

The aim of this paper was to estimate direct and maternal genetic parameters for calving ease (CE), birth weight (BrW), weaning weight (WW), and calving interval (CI) to assess the possibility of including this information in beef cattle improvement programs. Field data, including a total of 59,813 animals (1,390 sires and 1,147 maternal grand sires) from the Asturiana de los Valles beef cattle breed, were analyzed with a multivariate linear model. Estimates of heritability for direct genetic effects (CED, CID, BrWD, and WWD) were 0.191 +/- 0.019, 0.121 +/- 0.013, 0.390 +/- 0.030, and 0.453 +/- 0.035, respectively, whereas those for maternal genetic effects (CEM, BrWM, and WWM) were 0.140 +/- 0.015, 0.208 +/- 0.020, and 0.138 +/- 0.022, respectively. Genetic correlations between direct or maternal genetic effects across traits were, in general, positive and moderate to low. However, genetic correlation for the pair CED-BrWD was positive and high (0.604 +/- 0.064). Genetic correlations between the direct and maternal genetic effects within a trait were negative and moderate (-0.219 +/- 0.097 for CE, -0.337 +/- 0.080 for BrW, and -0.440 +/- 0.102 for WW). Genetic correlations for CED-BrWM and CED-WWM were -0.121 +/- 0.090 and -0.097 +/- 0.113, respectively. The genetic correlation for CEM-CID was unfavorable (0.485 +/- 0.078), and those for CEM-BrWD (-0.094 +/- 0.079) and CEM-WWD (-0.125 +/- 0.082) were low and negative. The genetic correlation between CID and WWM was favorable (-0.148 +/- 0.106). Overall, the data presented here support the hypothesis that maternal effects for CE and BrW are not the same and that the genetic relationships between CI and maternal effects for WW in beef cattle follow a similar pattern to that reported between CI and milk yield in dairy cattle. Moreover, the need to include direct and maternal breeding values in beef cattle selection programs is suggested.

Animals↗

PubMed2003

Genetic analysis of body condition score in first-parity Danish Holstein cows.

The aim of this study was to test whether genetic components for body condition score (BCS) changed during lactation in first-parity Danish Holsteins. Data were extracted from the national conformation scoring system and consisted of 28,948 records from 3894 herds. Cows were scored once during lactation for BCS on a scale from 1 to 9 with increments of 1. The majority of records were made from d 30 to 150 of lactation. Mean BCS was 4.28 +/- 0.98. Body condition score was lowest in wk 8 to 10 from calving. A multivariate sire model with BCS recordings in six lactation stages treated as different traits was used to analyze the data. In addition, a random regression sire model was used to evaluate the changes in BCS as continuous functions of lactation stage. Estimates of heritability from the multivariate approach ranged from 0.14 to 0.29, and the estimated genetic correlations between BCS at different lactation stages were all higher than 0.82. The random regression model was based on Legendre polynomials (LP) specified on days in milk at scoring. To evaluate the change in mean BCS during lactation, the fixed part of the model included a fifth-order LP on the effect of days in milk at scoring. The highest order of fit used for the sire effect was a third-order LP, but based on likelihood ratio tests this could be reduced to a 0 order, i.e., a model with only the intercept term for the sire effect. This means that the genetic variation is constant over the investigated part of the lactation. Therefore, BCS can be considered the same trait during lactation, and a simple sire model can be used for prediction of breeding values.

Adipose Tissue↗