Additive response to selection adjusted for effects of inbreeding in a closed dairy cattle nucleus assuming a large number of gametes per female

1994 ◽  
Vol 58 (2) ◽  
pp. 173-180 ◽  
Author(s):  
I. J. M. de Boer ◽  
J. A. M. van Arendonk
Keyword(s):  
Dairy Cattle ◽  
Inbreeding Depression ◽  
Variance Reduction ◽  
Optimal Number ◽  
Factorial Designs ◽  
Additive Effects ◽  
Base Population ◽  
Response To Selection ◽  
Additive Variance ◽  
Commercial Population

AbstractInbreeding leads to reduction of the additive variance, whereas inbreeding depression reduces the performance of milk producing cows in both the nucleus and the commercial population. In this study, the cumulative additive response to 30 years of selection corrected for variance reduction due to inbreeding and inbreeding depression in the commercial cow population (denoted as expected phenotypic level or P) was evaluated in a closed (1024 cows tested per year) dairy cattle nucleus scheme, assuming a large number of gametes available per female. No dominance effects were simulated nor estimated in the nucleus. Various hierarchical and factorial designs with fewer sires than dams, an equal number of sires and dams, or even a larger number of sires than dams were compared for P. The trait considered was overall economic merit for milk production with a heritability of the unselected base population of 0·30. Sires and dams were selected on their animal model estimated additive effect for the trait considered at either 15 or 27 months of age. All full-sibs were available for selection. In the absence of inbreeding depression, a complete factorial scheme with more sires than dams resulted in the highest P. With increasing inbreeding depression, the optimal number of sires increased relatively more than the optimal number of dams. Increasing the number of sires decreased inbreeding relatively more than increasing the number of dams, and resulted in a relatively higher P. This is due to the fact that correlations between estimated additive effects of male selection candidates are higher than between those of female selection candidates.

scholarly journals The contribution of dominance to the understanding of quantitative genetic variation

2011 ◽  
Vol 93 (2) ◽  
pp. 139-154 ◽  
Author(s):  
ROBIN WELLMANN ◽  
JÖRN BENNEWITZ
Keyword(s):  
Qtl Mapping ◽  
Inbreeding Depression ◽  
Quantitative Trait ◽  
Breeding Value ◽  
Additive Effects ◽  
Additive Variance ◽  
Dominance Variance ◽  
True Value ◽  
Value Estimation ◽  
Trait Locus

SummaryKnowledge of the genetic architecture of a quantitative trait is useful to adjust methods for the prediction of genomic breeding values and to discover the extent to which common assumptions in quantitative trait locus (QTL) mapping experiments and breeding value estimation are violated. It also affects our ability to predict the long-term response of selection. In this paper, we focus on additive and dominance effects of QTL. We derive formulae that can be used to estimate the number of QTLs that affect a quantitative trait and parameters of the distribution of their additive and dominance effects from variance components, inbreeding depression and results from QTL mapping experiments. It is shown that a lower bound for the number of QTLs depends on the ratio of squared inbreeding depression to dominance variance. That is, high inbreeding depression must be due to a sufficient number of QTLs because otherwise the dominance variance would exceed the true value. Moreover, the second moment of the dominance coefficient depends only on the ratio of dominance variance to additive variance and on the dependency between additive effects and dominance coefficients. This has implications on the relative frequency of overdominant alleles. It is also demonstrated how the expected number of large QTLs determines the shape of the distribution of additive effects. The formulae are applied to milk yield and productive life in Holstein cattle. Possible sources for a potential bias of the results are discussed.

scholarly journals The number of loci affecting a quantitative trait in Drosophila melanogaster revealed by artificial selection

1983 ◽  
Vol 42 (2) ◽  
pp. 137-149 ◽  
Author(s):  
Araceli Gallego ◽  
Carlos López-Fanjul
Keyword(s):  
Initial Response ◽  
Selection Method ◽  
Base Population ◽  
Response To Selection ◽  
Family Selection ◽  
Selected Lines ◽  
Additive Variance ◽  
Bristle Number ◽  
Selection Limit ◽  
Selection For

SUMMARYIndividual and within-full-sib family selection for low sternopleural bristle number was carried out for 17 generations, with six replicate lines for each selection method. Our results can be summarized as follows: (1) the response to selection was exhausted very quickly, (2) the additive variance of the selected lines declined rapidly, (3) the variation in response to selection decreased as selection progressed, (4) genetic differences among replicates at the selection limit were small, (5) individual selection resulted in a higher initial response than within-family selection, but similar limits were achieved with both procedures. These observations are consistent with the hypothesis that the pattern of response to selection is due to the segregation in the base population of only a few loci with large effects, at intermediate frequencies.

scholarly journals Genomic prediction with non-additive effects in beef cattle: stability of variance component and genetic effect estimates against population size

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Akio Onogi ◽  
Toshio Watanabe ◽  
Atsushi Ogino ◽  
Kazuhito Kurogi ◽  
Kenji Togashi
Keyword(s):  
Population Size ◽  
Genomic Prediction ◽  
Variance Components ◽  
Variance Component ◽  
Predictive Accuracy ◽  
Genetic Effect ◽  
Genetic Effects ◽  
Additive Effects ◽  
Additive Variance ◽  
Additive Genetic Effects

Abstract Background Genomic prediction is now an essential technology for genetic improvement in animal and plant breeding. Whereas emphasis has been placed on predicting the breeding values, the prediction of non-additive genetic effects has also been of interest. In this study, we assessed the potential of genomic prediction using non-additive effects for phenotypic prediction in Japanese Black, a beef cattle breed. In addition, we examined the stability of variance component and genetic effect estimates against population size by subsampling with different sample sizes. Results Records of six carcass traits, namely, carcass weight, rib eye area, rib thickness, subcutaneous fat thickness, yield rate and beef marbling score, for 9850 animals were used for analyses. As the non-additive genetic effects, dominance, additive-by-additive, additive-by-dominance and dominance-by-dominance effects were considered. The covariance structures of these genetic effects were defined using genome-wide SNPs. Using single-trait animal models with different combinations of genetic effects, it was found that 12.6–19.5 % of phenotypic variance were occupied by the additive-by-additive variance, whereas little dominance variance was observed. In cross-validation, adding the additive-by-additive effects had little influence on predictive accuracy and bias. Subsampling analyses showed that estimation of the additive-by-additive effects was highly variable when phenotypes were not available. On the other hand, the estimates of the additive-by-additive variance components were less affected by reduction of the population size. Conclusions The six carcass traits of Japanese Black cattle showed moderate or relatively high levels of additive-by-additive variance components, although incorporating the additive-by-additive effects did not improve the predictive accuracy. Subsampling analysis suggested that estimation of the additive-by-additive effects was highly reliant on the phenotypic values of the animals to be estimated, as supported by low off-diagonal values of the relationship matrix. On the other hand, estimates of the additive-by-additive variance components were relatively stable against reduction of the population size compared with the estimates of the corresponding genetic effects.

Additive and non-additive genetic effects of growth-curve parameters of Holstein, Ayrshire and crossbred females

1994 ◽  
Vol 74 (3) ◽  
pp. 401-409 ◽  
Author(s):  
D. Perotto ◽  
R. I. Cue ◽  
A. J. Lee ◽  
A. J. McAllister ◽  
J. R. Batra ◽  
...  
Keyword(s):  
Growth Rate ◽  
Dairy Cattle ◽  
Growth Curve ◽  
Growth Traits ◽  
Individual Performance ◽  
Breeding Value ◽  
Average Lifetime ◽  
Additive Effects ◽  
Positive Effects ◽  
Maternal Performance

Crossbreeding parameters (line additive, dominance and additive × additive epistatic effects for individual and for maternal performance) on growth traits of females from a crossbreeding experiment between Holstein-based (HS) and Ayrshire-based (AS) lines were estimated by individual animal models, incorporating all known additive genetic relationships among animals, through restricted maximum likelihood and mixed-model methodologies. The growth traits [asymptotic weight (A), rate parameter (k), inflection parameter (m), average lifetime absolute growth rate (AGR), average lifetime absolute maturing rate (AMR) and average lifetime relative growth rate (RGR)] were estimated by fitting the Richards function to the observed growth curve of 3076 individuals. The statistical model included the random effect of the animal breeding value and the fixed effects of genetic group and station–year–season of birth. Results indicated that the HS exceeded (P < 0.001) the AS in additive effects for individual performance for both A and AGR. The HS exceeded (P < 0.05) the AS in additive effects for maternal performance for A. Individual heterosis was positive for A (P < 0.001) and for AGR (P < 0.01). Maternal heterosis was negative for A (P < 0.05) and positive for AMR (P < 0.05). Total heterosis (TH) had positive effects on both AGR and AMR (P < 0.05). Heterosis retained in advanced crossbred generations was not significant (P > 0.05) for any of the studied traits. The results suggest that crossbreeding designed to exploit TH can alter the shape of the growth curve of dairy cattle. Key words: Crossbreeding, dairy cattle, growth curve

scholarly journals Selection, Load and Inbreeding Depression in a Large Metapopulation

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 1191-1202 ◽  
Author(s):  
Michael C Whitlock
Keyword(s):  
Population Structure ◽  
Inbreeding Depression ◽  
Population Subdivision ◽  
Response To Selection ◽  
Mutation Load ◽  
Deleterious Alleles ◽  
Subdivided Population ◽  
Soft Selection ◽  
Mean Fitness ◽  
The Mean

Abstract The subdivision of a species into local populations causes its response to selection to change, even if selection is uniform across space. Population structure increases the frequency of homozygotes and therefore makes selection on homozygous effects more effective. However, population subdivision can increase the probability of competition among relatives, which may reduce the efficacy of selection. As a result, the response to selection can be either increased or decreased in a subdivided population relative to an undivided one, depending on the dominance coefficient FST and whether selection is hard or soft. Realistic levels of population structure tend to reduce the mean frequency of deleterious alleles. The mutation load tends to be decreased in a subdivided population for recessive alleles, as does the expected inbreeding depression. The magnitude of the effects of population subdivision tends to be greatest in species with hard selection rather than soft selection. Population structure can play an important role in determining the mean fitness of populations at equilibrium between mutation and selection.

scholarly journals A multivariate analysis with direct additive and inbreeding depression load effects

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Luis Varona ◽  
Juan Altarriba ◽  
Carlos Moreno ◽  
María Martínez-Castillero ◽  
Joaquim Casellas
Keyword(s):  
Beef Cattle ◽  
Inbreeding Depression ◽  
Negative Correlation ◽  
Simulated Data ◽  
Genetic Effects ◽  
Strong Negative Correlation ◽  
Additive Variance ◽  
Inbreeding Coefficients ◽  
Load Effects ◽  
Additive Genetic Effects

Abstract Background Inbreeding is caused by mating between related individuals and its most common consequence is inbreeding depression. Several studies have detected heterogeneity in inbreeding depression among founder individuals, and recently a procedure for predicting hidden inbreeding depression loads associated with founders and the Mendelian sampling of non-founders has been developed. The objectives of our study were to expand this model to predict the inbreeding loads for all individuals in the pedigree and to estimate the covariance between the inbreeding loads and the additive genetic effects for the trait of interest. We tested the proposed approach with simulated data and with two datasets of records on weaning weight from the Spanish Pirenaica and Rubia Gallega beef cattle breeds. Results The posterior estimates of the variance components with the simulated datasets did not differ significantly from the simulation parameters. In addition, the correlation between the predicted and simulated inbreeding loads were always positive and ranged from 0.27 to 0.82. The beef cattle datasets comprised 35,126 and 75,194 records on weights between 170 and 250 days of age, and pedigrees of 308,836 and 384,434 individual-sire-dam entries for the Pirenaica and Rubia Gallega breeds, respectively. The posterior mean estimates of the variance of inbreeding depression loads were 29,967.8 and 28,222.4 for the Pirenaica and Rubia Gallega breeds, respectively. They were larger than those of the additive variance (695.0 and 439.8 for Pirenaica and Rubia Gallega, respectively), because they should be understood as the variance of the inbreeding depression achieved by a fully inbred (100%) descendant. Therefore, the inbreeding loads have to be rescaled for smaller inbreeding coefficients. In addition, a strong negative correlation (− 0.43 ± 0.10) between additive effects and inbreeding loads was detected in the Pirenaica, but not in the Rubia Gallega breed. Conclusions The results of the simulation study confirmed the ability of the proposed procedure to predict inbreeding depression loads for all individuals in the populations. Furthermore, the results obtained from the two real datasets confirmed the variability in the inbreeding depression loads in both breeds and suggested a negative correlation of the inbreeding loads with the additive genetic effects in the Pirenaica breed.

Inbreeding and its effects on some economic traits in Raeini cashmere goats

2003 ◽  
Vol 2003 ◽  
pp. 147-147 ◽  
Author(s):  
M. Moradi-Shaharbabak ◽  
A. Mohammadi ◽  
S. R. Miraei-Ashtiani
Keyword(s):  
Body Weight ◽  
Inbreeding Depression ◽  
Fiber Length ◽  
Inbreeding Coefficient ◽  
Base Population ◽  
Economic Traits ◽  
Breeding Center ◽  
Cashmere Goats ◽  
Fleece Weight ◽  
The Impact

The Breeding Center of Raeini (BCR) cashmere goats was established in 1965 in Kerman province, with a base population of 120, 8 and 42 does, bucks, and kids respectively. Some new animals have been introduced to the BCR population in some periods of time, and selected males have been sold out to the local breeders each year. Animals have been selected based on their phenotypic performance for fleece weight (FW) and fleece color (FC-white), and body weight (BW). Mating system has been planned based on non-relative mating, but some relative mating has been occurred. Inbreeding depression is one of the most important empact of having inbreeding in a population (Miglior and Burnside 1995). A decrease of 0.8% in fiber length and 6.3% in longevity per 10% increase of inbreeding coefficient in cashmere goats has been reported (Deb 1998). The objective of this study was to estimate the animals inbreeding coefficient and to explore the impact of inbreeding on some economic traits in Raeini cashmere goats.

scholarly journals The effects of inbreeding on the components of litter size in mice

1967 ◽  
Vol 10 (1) ◽  
pp. 73-80 ◽  
Author(s):  
J. C. McCarthy
Keyword(s):  
Litter Size ◽  
Inbreeding Depression ◽  
First Generation ◽  
Inbreeding Coefficient ◽  
Ovulation Rate ◽  
Corpora Lutea ◽  
Base Population ◽  
Pregnant Females ◽  
Sib Mating ◽  
Size At Birth

Twenty-four lines were bred from a base population of outbred Q mice by continued full-sib mating. Inbreeding depression in litter size at birth was observed. This decline in litter size was analysed in terms of ovulation rate, the incidence of preimplantation mortality and the incidence of postimplantation mortality. Pregnant females were dissected at 17½ days' gestation and the numbers of corpora lutea, or eggs, and of live and dead embryos were counted. Matings were arranged so that separate estimates of the effects of inbreeding in the mother and in the litter on the components of litter size could be obtained.In the first generation of inbreeding when the inbreeding coefficient of the litter was raised from 0 to 25% decline in litter size was attributable to an increased incidence of preimplantation mortality.In the second and fourth generations decline in litter size was attributable to (1) a reduction in the number of eggs ovulated by the inbred mothers, (2) an increased incidence of preimplantation mortality which resulted from inbreeding in the mother. No evidence of significant effects on mortality of inbreeding in the litter was obtained in the later generation of inbreeding.These findings are discussed in the context of previous work on the effects of inbreeding and crossing on litter size and its components in mice and pigs.

scholarly journals Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle

2014 ◽  
Vol 46 (1) ◽  
Author(s):  
Jennie E Pryce ◽  
Mekonnen Haile-Mariam ◽  
Michael E Goddard ◽  
Ben J Hayes
Keyword(s):  
Dairy Cattle ◽  
Inbreeding Depression ◽  
Genomic Regions
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