Non-additive Genetic Parameters Research Articles

Additive and non-additive genetic parameters for multipurpose traits in a clonally replicated incomplete factorial test of Castanea spp.

Second-year traits of growth, stem form, terminal flushing, and survival were assessed in 1770 ramets from 295 clones of 16 full-sib families of Castanea spp. Additive, dominance, and epistatic genetic variances were estimated in a clonally replicated incomplete 5 × 4 factorial test. Parents of the mating design were selected mainly on their phenotypes for wood quality (Castanea sativa traditional varieties) and their proven resistance to Phytophthora spp. (Asiatic species and Castanea crenata × C. sativa hybrids). Additive genetic variances were estimated to be 1.7–9 times greater than the dominance components. Inferred epistatic variance components showed a significant role in controlling growth traits and branch length. Narrow- and broad-sense heritability estimates showed that terminal flushing date was the most heritable trait, followed by height. The high estimates of half-sib, full-sib, and clonal mean heritabilities for almost all traits suggest that different strategies of backwards and forwards selection could be proposed. The ranking of the breeding values of parents allow us to select the best parents for new crosses and extend the mating design. Favorable genetic correlations were found between growth traits and straightness, so multi-trait selection looks promising. Our results provide the first information on the partitioning of genetic variance in Castanea spp. and a starting point for devising new selection strategies.

Quantitative genetics of speciation: additive and non-additive genetic differentiation between Drosophila madeirensis and Drosophila subobscura

The role of dominance and epistasis in population divergence has been an issue of much debate ever since the neoDarwinian synthesis. One of the best ways to dissect the several genetic components affecting the genetic architecture of populations is line cross analysis. Here we present a study comparing generation means of several life history-traits in two closely related Drosophila species: Drosophila subobscura, D. madeirensis as well as their F1 and F2 hybrids. This study aims to determine the relative contributions of additive and non-additive genetic parameters to the differentiation of life-history traits between these two species. The results indicate that both negative dominance and epistatic effects are very important in the differentiation of most traits. We end with considerations about the relevance of these findings for the understanding of the role of non-additive effects in speciation.

Evaluation of the performance of the Kenya Dual Purpose Goat composites: Additive and non-additive genetic parameters

Growth data from 6800 progeny of straightbreds, intermediate crosses and the resulting Kenya Dual Purpose Goat (KDPG) composites from 1982 to 2004 were used to estimate additive and non-additive genetic parameters. The KDPG was developed by crossing Toggenburg (T), Anglo-Nubian (N), Small East African (E) and Galla (G) breeds in equal proportions. All parameters were simultaneously estimated for early growth traits by fitting an animal model using Derivative-Free-Restricted Maximum Likelihood (DFREML) procedures (Meyer, 1998). The model included sex, type of birth, period and season of birth, and age of dam classes as fixed effects; crossbreeding parameters were fitted as covariates. Relative to Small East African breed, Anglo-Nubian showed the highest breed effects for weaning weight (+1.69 kg), yearling weight (+1.74 kg) and pre-weaning average daily gains (+13.28 g/day). Between the indigenous breeds, breed differences were in favour of Galla breed except for yearling weight. Individual heterosis had a positive effect on birth weight (+0.05 kg), yearling weight (+0.36 kg) and post-weaning average daily gains (+3.04 g/day) but negative in pre-weaning traits. Maternal heterosis was favourable in the traits influenced by pre-weaning maternal environment (weaning weight and pre-weaning average daily gains). The effect of recombination was negative and, therefore, reduced performance in all traits. Heritability estimates were low with very narrow range between traits. These estimates were 0.13 ± 0.03, 0.16 ± 0.01 0.16 ± 0.04, 0.24 ± 0.01 and 0.10 ± 0.02 for birth weight, weaning weight, yearling weight, pre-weaning and post-weaning average daily gains, respectively. The study shows that the developed KDPG composites have not optimized on the positive dominance effects; an effect due to retained recombination loss caused by lack of selection during breed development. It was concluded therefore, that the KDPG composites are still segregating and have not stabilized into a new breed as was the aim of the breeding programme.

Estimating the Extent of Parameter Bias in the Classical Twin Design: A Comparison of Parameter Estimates From Extended Twin-Family and Classical Twin Designs

AbstractTheclassical twin design(CTD) circumvents parameter indeterminacy by assuming (1) negligible higher-order epistasis; and (2) either nonadditive genetic or common environmental effects are nonexistent, creating two potential sources of bias (Eaves et al., 1978; Grayson, 1989). Because the extended twin-family design (ETFD) uses many more unique covariance observations to estimate parameters, common environmental and nonadditive genetic parameters can be simultaneously estimated. The ETFD thereby corrects for what is likely to be the largest of the two sources of bias in CTD parameter estimates (Keller & Coventry, 2005). In the current paper, we assess the extent of this and other potential sources of bias in the CTD by comparing all published ETFD parameter estimates to CTD parameter estimates derived from the same data. CTD estimates of the common environment were lower than ETFD estimates of the common environment for some phenotypes, but for other phenotypes (e.g., stature in females and certain social attitudes), what appeared as the common environment was resolved to be assortative mating in the ETFD. On average, CTD estimates of nonadditive genetic factors were 43% lower, and additive genetic factors 63% higher, than ETFD estimates. However, broad-sense heritability estimates from the CTD were only 18% higher than ETFD estimates, highlighting that the CTD is useful for estimating broad-sense but not narrow-sense heritability. These results suggest that CTD estimates can be misleading when interpreted literally, but useful, albeit coarse, when interpreted properly.

Estimating the Extent of Parameter Bias in the Classical Twin Design: A Comparison of Parameter Estimates From Extended Twin-Family and Classical Twin Designs

The classical twin design (CTD) circumvents parameter indeterminacy by assuming (1) negligible higher-order epistasis; and (2) either nonadditive genetic or common environmental effects are nonexistent, creating two potential sources of bias (Eaves et al., 1978; Grayson, 1989). Because the extended twin-family design (ETFD) uses many more unique covariance observations to estimate parameters, common environmental and nonadditive genetic parameters can be simultaneously estimated. The ETFD thereby corrects for what is likely to be the largest of the two sources of bias in CTD parameter estimates (Keller & Coventry, 2005). In the current paper, we assess the extent of this and other potential sources of bias in the CTD by comparing all published ETFD parameter estimates to CTD parameter estimates derived from the same data. CTD estimates of the common environment were lower than ETFD estimates of the common environment for some phenotypes, but for other phenotypes (e.g., stature in females and certain social attitudes), what appeared as the common environment was resolved to be assortative mating in the ETFD. On average, CTD estimates of nonadditive genetic factors were 43% lower, and additive genetic factors 63% higher, than ETFD estimates. However, broad-sense heritability estimates from the CTD were only 18% higher than ETFD estimates, highlighting that the CTD is useful for estimating broad-sense but not narrow-sense heritability. These results suggest that CTD estimates can be misleading when interpreted literally, but useful, albeit coarse, when interpreted properly.

Is Crossbreeding the Answer to Questions of Dairy Breed Utilization?

The current interest in crossbreeding in the commercial dairy industry, even though it is quite limited, raises questions of breed utilization. Fewer than 5% of US dairy cattle are other than purebred or grade Holsteins. The large advantage of Holsteins for additive genetic merit for lactation milk yield is apparently responsible for this trend. Why, then, this interest in crossbreeding? The economic importance of traits such as reproduction, health, and survival in dairy production systems is likely the basis for the interest in crossbreeding, even though these traits are secondary to milk yield. Several US studies and a Canadian study confirmed that while several crossbred groups were equivalent to Holsteins for lactation milk yield, none were superior. Two crossbred groups in the Canadian study had lifetime yields, milk value, and net returns equivalent to Holsteins. In the New Zealand study, Friesian-Jersey reciprocal crossbreds were predicted to exceed Friesians in first-lactation fat yield. Crossbred performance is dictated by a combination of additive and nonadditive genetic effects. Evidence exists for direct, maternal, heterosis, and cytoplasmic maternal effects. Heterosis of 15 to 20% for lifetime traits was found in two studies. Results from previous crossbreeding studies have something to recommend for inclusion of Holstein, Ayrshire, Brown Swiss, and Jersey breeds in a crossbreeding scheme. However, multiple-generation lifetime performance on an array of purebreds and crossbreds under US condition does not exist. Full unique identification of individual animals, including breed composition, would permit the use of DHIA data to estimate additive and nonadditive genetic parameters for the traits recorded therein. Survival data from birth and health data would need to be fully recorded to provide complete data on lifetime performance. Self-propagation of crossbred replacements is mandatory if any crossbreeding system is to be successful. Based on current empirical data, a two-breed rotational crossing system appears to be the most viable system to maximize economic merit. The theoretical advantages of a three-breed rotational crossing system are clear, but the data to recommend the third breed and this system in practice are limited. Full-scale long-term breeding experiments or analysis of field data paired with a comprehensive modeling of alternative breed utilization strategies for US conditions are recommended.

Estimation of additive and non-additive genetic parameters for carcass traits on bulls in dairy, dual purpose and beef cattle breeds

Carcass records on 4749 bulls (from 153 sires) slaughtered at an average age of 20 months were collected from slaughter houses in the Netherlands. Bulls had a variable proportion of genes from Dutch Black and White (DBW), Dutch Red and White (DRW) and Pimontese (PIM). Additive genetic and crossbreeding parameters were estimated for fleshiness score (FLESH), fat covering score (FAT) and carcass weight (CWT) using three fixed models (additive breed, Dickerson and Kinghorn model) and the corresponding three mixed models with random sire effects. These models involved additive breed, heterosis (or dominance), and recombination loss (or epistatic loss) effects (i.e., crossbreeding parameters) as regression covariates. In addition, an additive sire group model was used as a mixed model. FLESH and FAT were defined numerical values ranging from 1 (poorly muscled; very much fat) to 15 (very muscled; very little fat). When comparing models, estimates of crossbreeding parameters over breeds and breed combinations showed similar patterns, although absolute values between the same parameters differed up to a standard error between fixed and mixed models and between Dickerson and Kinghorn models. Mixed models showed larger standard errors relative to fixed models. Relative to DBW, PIM showed significantly positive favorable breed effects for FLESH (ranging from 5.8 to 6.3 for different models) and CWT (62.6 to 111.8 kg), and unfavorable for FAT (−1.7 to −2.6). DRW showed favorable, but smaller than PIM, additive genetic effects for all three traits (2.2 to 2.3 for FLESH, 0.1 to 0.3 for FAT and 18.1 to 24.2 kg for CWT). Significant heterosis was only found for FAT (0.4 to 0.7) and for CWT (12 to 14 kg) in the cross DBW×DRW. Significant recombination and epistatic effects were obtained for CWT in the Dickerson and the Kinghorn models. Models not including non-additive effects over-estimated genetic variances and heritabilities for FLESH and FAT.

Estimation of non-additive genetic parameters for lactations 1 to 5 and for survival in Holstein-Friesian dairy cattle

First lactation production records of 275188 Holstein-Friesian dairy cows, progeny of 708 sires, and the second to fifth lactation records of survivors were analysed in order to estimate the regression coefficients of milk, fat and protein yield in lactations 1 to 5 on heterosis and recombination loss. Coefficients were fairly consistent over lactations. For milk yield in lactations 1 to 5 respectively, the regression coefficients were 100 kg, 111 kg, 155 kg, 124 kg and 118 kg for heterosis and −156 kg, −227 kg, −256 kg, −304 kg and −218 for recombination loss. There was negligible change in the proportion of Holstein over lactations. The regression coefficients of survival to complete lactations 2 to 5 on heterosis and recombination loss were mainly positive. After fitting first lactation yield in the model and compared to a pure Friesian, there is an increased chance of survival to third lactation of 3.6% for a pure Holstein, 3.8% for an F1 and an F2, and 2.4% for a Friesian backcross.

LISREL modeling: Genetic and environmental influences on IQ revisited

This article reports a model-fitting analysis of the covariance structure of the world's IQ data as reviewed by Bouchard and McGue (1981). A model is used which includes additive and nonadditive genetic parameters, and shared and nonshared environment parameters that permit different estimates for different types of relatives. The opportunity is taken here to explicate the use of LISREL for such purposes. The results indicate that, when assortative mating is included in the model, nonadditive, as well as additive genetic variance, is important for IQ. Broad heritability is estimated to be .51. Another interesting result is that the influence of shared environment differs in a reasonable way for different types of relatives: twins > siblings > parents and their offspring > cousins.