Genetic parameters for growth traits of a Brazilian Bos taurus x Bos indicus beef composite

The genetic analysis of composite data is very complicated, mainly because it is necessary to adjust data to the effects of heterosis and breed complementarity, and because there is usually considerable confounding of these data with several other effects, such as contemporary group effects, breed composition of the animal and maternal breed composition, among others. Data on birth weight (n = 151,083), weaning weight adjusted to 205 days (n = 137,257), yearling weight adjusted to 390 days (n = 61,410), weight gain from weaning to yearling (n = 56,653), and scrotum circumference (n = 23,323) and muscle score (n = 54,770), both adjusted to 390 days, from Bos taurus x Bos indicus composite beef calves born from 1994 to 2003 were analyzed to estimate (co)variance components and genetic parameters of growth traits. The animals belonged to the Montana Tropical program. Estimation was made by three models that approach adjustment to heterozygosis in order to suggest the best model. The RM model included contemporary groups, class of age of dam, outcrossing percentages for direct and maternal effects, and direct and maternal additive genetic breed effects as covariates; the R model was the same as RM, but without additive maternal breed effects, and H was the same as RM, but not considering any additive breed effect. Both R2 values and consistency of genetic parameters indicate that the more complex model (RM), which considers maternal and individual additive genetic breed effect, produces the best estimates when compared to other models. The R model seems to overestimate (co)variance components. The magnitudes of direct and maternal heritability estimates, obtained in this study, would permit genetic improvement for weight and growth traits, as much by selection of direct genetic effects for weight and growth as for the improvement of maternal performance, but in different lineages. Therefore, the correlations between these effects were unfavorable.     

Mapping quantitative trait Loci interactions from the maternal and offspring genomes

The expression of most developmental or behavioral traits involves complex interactions between quantitative trait loci (QTL) from the maternal and offspring genomes. The maternal-offspring interactions play a pivotal role in shaping the direction and rate of evolution in terms of their substantial contribution to quantitative genetic (co)variation. To study the genetics and evolution of maternal-offspring interactions, a unifying statistical framework that embraces both the direct and indirect genetic effects of maternal and offspring QTL on any complex trait is developed. This model is derived for a simple backcross design within the maximum-likelihood context, implemented with the EM algorithm. Results from extensive simulations suggest that this model can provide reasonable estimation of additive and dominant effects of the QTL at different generations and their interaction effects derived from the maternal and offspring genomes. Although our model is framed to characterize the actions and interactions of maternal and offspring QTL affecting offspring traits, the idea can be readily extended to decipher the genetic machinery of maternal traits, such as maternal care. Our model provides a powerful means for studying the evolutionary significance of indirect genetic effects in any sexually reproductive organisms.     

Consequences of paternally inherited effects on the genetic evaluation of maternal effects

Background

Mixed models are commonly used for the estimation of variance components and genetic evaluation of livestock populations. Some evaluation models include two types of additive genetic effects, direct and maternal. Estimates of variance components obtained with models that account for maternal effects have been the subject of a long-standing controversy about strong negative estimates of the covariance between direct and maternal effects. Genomic imprinting is known to be in some cases statistically confounded with maternal effects. In this study, we analysed the consequences of ignoring paternally inherited effects on the partitioning of genetic variance.

Results

We showed that the existence of paternal parent-of-origin effects can bias the estimation of variance components when maternal effects are included in the evaluation model. Specifically, we demonstrated that adding a constraint on the genetic parameters of a maternal model resulted in correlations between relatives that were the same as those obtained with a model that fits only paternally inherited effects for most pairs of individuals, as in livestock pedigrees. The main consequence is an upward bias in the estimates of the direct and maternal additive genetic variances and a downward bias in the direct-maternal genetic covariance. This was confirmed by a simulation study that investigated five scenarios, with the trait affected by (1) only additive genetic effects, (2) only paternally inherited effects, (3) additive genetic and paternally inherited effects, (4) direct and maternal additive genetic effects and (5) direct and maternal additive genetic plus paternally inherited effects. For each scenario, the existence of a paternally inherited effect not accounted for by the estimation model resulted in a partitioning of the genetic variance according to the predicted pattern. In addition, a model comparison test confirmed that direct and maternal additive models and paternally inherited models provided an equivalent fit.

Conclusions

Ignoring paternally inherited effects in the maternal models for genetic evaluation can lead to a specific pattern of bias in variance component estimates, which may account for the unexpectedly strong negative direct-maternal genetic correlations that are typically reported in the literature.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0141-5) contains supplementary material, which is available to authorized users.     

Heritability of deciduous tooth size in Australian aboriginals

The contributions of genetic and evironmental influences to observed variability of deciduous tooth size were quantified in a group of Australian aboriginals. Phenotypic variability was partitioned into four components; between sides, between fathers, between mothers, and between offspring. Results suggested that about 58% of deciduous tooth-size variability was due to additive genetic variance and 15% to common environmental variance. It appears that additive genetic variance is similar in both deciduous and permanent dentitions, but that common maternal effects are more important in determining deciduous tooth-size variability.     

Estimates of direct and indirect effects for early juvenile survival in captive populations maintained for conservation purposes: the case of Cuvier's gazelle

Together with the avoidance of any negative impact of inbreeding, preservation of genetic variability for life‐history traits that could undergo future selective pressure is a major issue in endangered species management programmes. However, most of these programmes ignore that, apart from the direct action of genes on such traits, parents, as contributors of offspring environment, can influence offspring performance through indirect parental effects (when parental genotype and phenotype exerts environmental influences on offspring phenotype independently of additive genetic effects). Using quantitative genetic models, we estimated the additive genetic variance for juvenile survival in a population of the endangered Cuvier's gazelle kept in captivity since 1975. The dataset analyzed included performance recording for 700 calves and a total pedigree of 740 individuals. Results indicated that in this population juvenile survival harbors significant additive genetic variance. The estimates of heritability obtained were in general moderate (0.115–0.457) and not affected by the inclusion of inbreeding in the models. Maternal genetic contribution to juvenile survival seems to be of major importance in this gazelle's population as well. Indirect genetic and indirect environmental effects assigned to mothers (i.e., maternal genetic and maternal permanent environmental effects) roughly explain a quarter of the total variance estimated for the trait analyzed. These findings have major evolutionary consequences for the species as show that offspring phenotypes can evolve strictly through changes in the environment provided by mothers. They are also relevant for the captive breeding programme of the species. To take into account, the contribution that mothers have on offspring phenotype through indirect genetic effects when designing pairing strategies might serve to identify those females with better ability to recruit, and, additionally, to predict reliable responses to selection in the captive population.     

Estimation of maternal,sex-linked and additive x additive epistatic gene effects for body size of Tribolium

Summary The genetic structure of two quantitative traits, 13-day larval weight and pupal weight, in two unselected populations of Tribolium castaneum was investigated by the genetic model of Carbonell et al. (1983). The variability among two and three-way crosses was analyzed into components due to: general and specific combining abilities, maternal, sex-linkage, specific reciprocal and additive-by-additive epistasis. Also, indirect evidence of higher order epistasis was studied. It is concluded that the heterotic trait larval weight is highly affected by sex-linked genes and by non-additive gene action with additive-by-additive as well as higher order epistasis playing major roles. Pupal weight, on the other hand, is determined mostly by additive gene action although epistasis is also a significant source for genetic variability. Both traits are significantly influenced by maternal effects.Journal Paper No. 9033 from Purdue University Agricultural Experiment Station. Based in part on PhD Theses submitted by the first two authors at Purdue University     

Analysis of cytoplasmic and maternal effects. II. Genetic models for triploid endosperms

Genetic models for quantitative traits of triploid endosperms are proposed for the analysis of direct gene effects, cytoplasmic effects, and maternal gene effects. The maternal effect is partitioned into maternal additive and dominance components. In the full genetic model, the direct effect is partitioned into direct additive and dominance components and high-order dominance component, which are the cumulative effects of three-allele interactions. If the high-order dominance effects are of no importance, a reduced genetic model can be used. Monte Carlo simulations were conducted in this study for demonstrating unbiasedness of estimated variance and covariance components from the MINQUE (0/1) procedure, which is a minimum norm quadratic unbiased estimation (MINQUE) method setting 0 for all the prior covariances and 1 for all the prior variances. Robustness of estimating variance and covariance components for the genetic models was tested by simulations. Both full and reduced genetic models are shown to be robust for estimating variance and covariance components under several situations of no specific effects. Efficiency of predicting random genetic effects for the genetic models by the MINQUE (0/1) procedure was compared with the best linear unbiased prediction (BLUP). A worked example is given to illustrate the use of the reduced genetic model for kernel growth characteristics in corn (Zea mays L.).     

Ontogeny of additive and maternal genetic effects: lessons from domestic mammals

Evolution of size and growth depends on heritable variation arising from additive and maternal genetic effects. Levels of heritable (and nonheritable) variation might change over ontogeny, increasing through "variance compounding" or decreasing through "compensatory growth." We test for these processes using a meta-analysis of age-specific weight traits in domestic ungulates. Generally, mean standardized variance components decrease with age, consistent with compensatory growth. Phenotypic convergence among adult sheep occurs through decreasing environmental and maternal genetic variation. Maternal variation similarly declines in cattle. Maternal genetic effects are thus reduced with age (both in absolute and relative terms). Significant trends in heritability (decreasing in cattle, increasing in sheep) result from declining maternal and environmental components rather than from changing additive variation. There was no evidence for increasing standardized variance components. Any compounding must therefore be masked by more important compensatory processes. While extrapolation of these patterns to processes in natural population is difficult, our results highlight the inadequacy of assuming constancy in genetic parameters over ontogeny. Negative covariance between direct and maternal genetic effects was common. Negative correlations with additive and maternal genetic variances indicate that antagonistic pleiotropy (between additive and maternal genetic effects) may maintain genetic variance and limit responses to selection.     

Generating data in models including direct and maternal dominance effects

Algorithms are presented to simulate multiple generations of animal data by a model including direct additive genetic, maternal additive genetic, direct dominance, maternal dominance and permanent environmental effects. Dominance effects were computed as parental subclasses. Testing involved five single trait models that included direct contemporary group and direct additive effects, and different combinations of maternal, permanent environmental, and dominance effects. Simulated populations included 5 generations of animals and 20 contemporary groups per generation. The base population contained 200 sires and 600 dams. Variance components were estimated by Average-Information Restricted Maximum Likelihood (AIREML). No significant bias was observed. The simulation algorithms can be used in research involving dominance models, such as evaluation of mating systems exploiting special combining abilities of prospective parents.     

Estimates of Genetic Parameters of Body Weight in Descendants of X-Irradiated Rat Spermatogonia

Effects of nine generations of 450r per generation of ancestral spermatogonial X irradiation of inbred rats on genetic parameters of body weight at 3, 6 and 10 weeks of age and of weight gains between these periods were studied. Covariances among relatives were estimated by mixed model and regression techniques in randomly selected lines with (R) and without (C) radiation history. Analyses of the data were based on five linear genetic models combining additive direct, additive indirect (maternal), dominance and environmental effects. Parameters in these models were estimated by generalized least-squares. A model including direct and indirect genetic effects fit more closely to the data in both R and C lines. Overdominance of induced mutations did not seem to be present. Ancestral irradiation increased maternal additive genetic variances of body weights and gains but not direct genetic variances. Theoretically, due to a negative direct-maternal genetic correlation, within full-sib family selection would be ineffective in increasing body weight at six weeks in both R and C lines. However, progress from mass selection would be expected to be faster in the R lines.     

Genetic analysis of sexual dimorphism of body weight in broilers

Variation in sexual dimorphism (SD) is particularly marked in meat-type chickens. This paper investigates the genetic basis of SD in an important economic trait, i.e. body weight (BW) at 35 days of age, in broilers by applying quantitative genetic analysis. A large dataset comprising 203,323 BW records of a commercial line of broiler chicken was used. First, a bivariate approach was employed treating BW as a sex-specific trait. During this approach, seven bivariate models were applied and variances due to direct additive genetic, maternal genetic and maternal environmental effects were estimated via the restricted maximum likelihood method. The best-fitting model included direct additive genetic, maternal genetic and maternal environmental effects with a direct–maternal genetic covariance. Differences between male and female direct heritabilities were non-significant (0.28 vs. 0.29 for males and females, respectively), implying no need for sex-specific selection strategies. The direct–maternal genetic correlation was more strongly negative in males than in females (?0.72 vs. ?0.56), implying a more profound antagonism between direct additive and maternal genetic effects in this particular gender. The direct genetic correlation of BW between the two sexes was as high as 0.91, i.e. only slightly lower than unity. Second, variance components and genetic parameters of two measures of SD, i.e. the weight difference (Δ) and the weight ratio (R), between the genders were estimated. Direct heritabilities for both measures were significantly different to 0 but of low magnitude (0.04). Apart from the additive–maternal covariance, no other random effects were found to be of importance for Δ and R. The results of the present study suggest that only minimal selection responses due to the selection of Δ and/or R and a small capacity for amplifying or reducing the BW differences between the sexes are to be expected in this specific population. Furthermore, selection pressure on BW is expected to amplify SD.     

籼型黑米粒形性状的遗传效应及其与矿质元素含量的遗传相关性

采用禾谷类作物种子数量性状的遗传模型,分析了灿型黑米稻品种双列杂交F1和F2种子的粒重,粒长,粒宽和粒长／粒宽等粒形性状的遗传效应及其与米粒中矿质元素Fe,Zn,Mn和P含量的遗传相关性,结果表明：4种粒形性状同时受制于种子直接遗传效应,母体效应和细胞质作用影响,其中种子直接遗传效应比母体效应和细胞质效应的作用更大,且种子直接遗传效应以加性效应占主导,粒重,粒宽和粒长／粒宽的种子直接遗传率较高,杂种早代单粒选择效果较好,粒长的种子直接遗传率和母体遗传率均属中等,较高世代的杂种进行单株选择和单粒选择均有一定效果,4种粒形性状与其米粒中矿质元素Fe,Zn,Mn和P含量表现较强的种子直接加性相关,直接显性相关,细胞质相关,母体加性相关和母体显性相关,在特种稻育种实践中,可以通过粒形性的间接选择,达到改良其矿质元素含量等营养品质性状的目标。     

玉米籽粒性状的遗传效应分析

采用二倍体胚和三倍体胚乳种子遗传模型及其分析方法,以5个玉米自交系及其配制的F1,F2,BC1,BC2世代为材料,研究5个玉米种子性状的胚直接效应、胚乳直接效应、母体效应和细胞质效应。分析结果表明,除粒宽外,各性状的遗传同时由细胞质效应和胚、胚乳、母体基因效应所控制,百粒重主要受胚乳和母体效应的影响,粒长的遗传以母体效应为主,粒宽和粒厚以胚乳效应为主。各部位籽粒百粒重的胚乳直接加性效应与母体加性效应的协方差达到显著或极显著水平,其余性状的胚、胚乳直接效应与母体效应间的协方差均不显著,通过母体植株的遗传表现可以对这些性状进行有效的选择。S22 是改良百粒重的优良亲本。 Abstract：The embryo,endosperm and cytoplasm effects of seven seed traits were studied by genetic model for diploid embryo and triploid endosperm plant seeds using five inbreds and their F1, F2, BC1 and BC2 generations. The estimates of genetic variance components indicated that the inheritance of all other kernel traits was controlled by the four effects except kernel width. The 100?kernel weight was mainly controlled by endosperm and maternal effects , and kernel length was controlled by the maternal effects,while endosperm conrrolled kernel width and kernel thickness. Except the significant or highly significant covariances between the endosperm direct additive and maternal additive effects for 100－kernel weight,all other traits between the embryo or endosperm direct effect and the maternal were not significant. So,maize inbreds could be developed by direct selection based on maternal plants for these traits. S22 was the best inbred of the improvement for kernel weight in this study.     

Age-specific genetic and maternal effects in fecundity of preindustrial Finnish women

A population's potential for evolutionary change depends on the amount of genetic variability expressed in traits under selection. Studies attempting to measure this variability typically do so over the life span of individuals, but theory suggests that the amount of additive genetic variance can change during the course of individuals' lives. Here we use pedigree data from historical Finns and a quantitative genetic framework to investigate how female fecundity, throughout an individual's reproductive life, is influenced by "maternal" versus additive genetic effects. We show that although maternal effects explain variation in female fecundity early in life, these effects wane with female age. Moreover, this decline in maternal effects is associated with a concomitant increase in additive genetic variance with age. Our results thus highlight that single over-lifetime estimates of trait heritability may give a misleading view of a trait's potential to respond to changing selection pressures.     

Host genetic architecture in single and multiple infections

Hosts are often target to multiple simultaneous infections by genetically diverse parasite strains. The interaction among these strains and the interaction of each strain with the host was shown to have profound effects on the evolution of parasite traits. Host factors like genetic architecture of resistance have so far been largely neglected. To see whether genetic architecture differs between different kinds of infections we used joint scaling analysis to compare the genetic components of resistance in the red flour beetle Tribolium castaneum exposed to single and multiple strains of the microsporidian Nosema whitei. Our results indicate that additive, dominance and epistatic components were more important in single infections whereas maternal components play a decisive role in multiple infections. In detail, parameter estimates of additive, dominance and epistatic components correlated positively between single and multiple infections, whereas maternal components correlated negatively. These findings may suggest that specificity of host–parasite interactions are mediated by genetic and especially epistatic components whereas maternal effects constitute a more general form of resistance.     

黑米中矿质元素铁、锌、锰、磷含量的遗传效应研究

采用禾谷类作物种子胚乳数量性状模型,分析黑米稻品种双列杂交Ｆ１和Ｆ２种子的Ｆｅ、Ｚｎ、Ｍｎ、Ｐ含量的遗传效应。结果表明,４种矿质元素含量同时受制于种子直接遗传效应、母体效应和细胞质作用影响。其中,Ｆｅ、Ｚｎ、Ｍｎ含量的种子直接效应比母体效应和细胞质效应的作用更大;Ｐ含量则主要受种子直接加性、母体加性和显性效应共同作用。Ｆｅ、Ｚｎ、Ｍｎ含量的种子直接遗传率较高,在杂种早代分别结合农艺性状选择单株上各     

Variance and covariance components for liability of piglet survival during different periods

Variance and covariance components for piglet survival in different periods were estimated from individual records of 133 004 Danish Landrace piglets and 89 928 Danish Yorkshire piglets, using a liability threshold model including both direct and maternal additive genetic effects. At the individual piglet level, the estimates of direct heritability in Landrace were 0.035, 0.057 and 0.027, and in Yorkshire the estimates were 0.012, 0.030 and 0.025 for liability of survival at farrowing (SVB), from birth to day 5 (SV5) and from day 6 to weaning (SVW), respectively. The estimates of maternal heritability for SVB, SV5 and SVW were, respectively, 0.057, 0.040 and 0.030 in Landrace, and 0.050, 0.038 and 0.019 in Yorkshire. Both direct and maternal genetic correlations between the three survival traits were low and not significantly different from zero, except for a moderate direct genetic correlation between SVB and SV5 and between SV5 and SVW in Landrace. Direct and maternal genetic correlations between piglet birth weight (BW) and SV5 were moderately high, but the correlations between BW and SVB and between BW and SVW were low and most of them were not significantly different from zero. These results suggest that effective genetic improvement in piglet survival before weaning by selection should be based on both direct and maternal additive genetic effects and treat survival in different periods as different traits.     

Random regression analyses using B-spline functions to model growth of Nellore cattle

The objective of this study was to estimate (co)variance components using random regression on B-spline functions to weight records obtained from birth to adulthood. A total of 82 064 weight records of 8145 females obtained from the data bank of the Nellore Breeding Program (PMGRN/Nellore Brazil) which started in 1987, were used. The models included direct additive and maternal genetic effects and animal and maternal permanent environmental effects as random. Contemporary group and dam age at calving (linear and quadratic effect) were included as fixed effects, and orthogonal Legendre polynomials of age (cubic regression) were considered as random covariate. The random effects were modeled using B-spline functions considering linear, quadratic and cubic polynomials for each individual segment. Residual variances were grouped in five age classes. Direct additive genetic and animal permanent environmental effects were modeled using up to seven knots (six segments). A single segment with two knots at the end points of the curve was used for the estimation of maternal genetic and maternal permanent environmental effects. A total of 15 models were studied, with the number of parameters ranging from 17 to 81. The models that used B-splines were compared with multi-trait analyses with nine weight traits and to a random regression model that used orthogonal Legendre polynomials. A model fitting quadratic B-splines, with four knots or three segments for direct additive genetic effect and animal permanent environmental effect and two knots for maternal additive genetic effect and maternal permanent environmental effect, was the most appropriate and parsimonious model to describe the covariance structure of the data. Selection for higher weight, such as at young ages, should be performed taking into account an increase in mature cow weight. Particularly, this is important in most of Nellore beef cattle production systems, where the cow herd is maintained on range conditions. There is limited modification of the growth curve of Nellore cattle with respect to the aim of selecting them for rapid growth at young ages while maintaining constant adult weight.     

Genetic analysis of crossfostering data with sire and dam records

A method is presented for the analysis of data from crossfostering experiments in which parts of litters are reciprocally interchanged at birth. Observed variances and covariances of differently related individuals are expressed as functions of theoretical causal components of phenotypic variance (additive direct, dominance direct, additive maternal, dominance maternal, direct-maternal covariance, and environmental). Causal components are estimated by weighted least squares analysis of this system of equations, including a ridge-regression procedure to examine consequences of correlation between observed components. Ridge regression suggests that dominance direct genetic variance is generally underestimated, but that narrow-sense heritability estimates are reliable.     

Maternal genetic effects set the potential for evolution in a free-living vertebrate population

Heritable maternal effects have important consequences for the evolutionary dynamics of phenotypic traits under selection, but have only rarely been tested for or quantified in evolutionary studies. Here we estimate maternal effects on early-life traits in a feral population of Soay sheep (Ovis aries) from St Kilda, Scotland. We then partition the maternal effects into genetic and environmental components to obtain the first direct estimates of maternal genetic effects in a free-living population, and furthermore test for covariance between direct and maternal genetic effects. Using an animal model approach, direct heritabilities (h2) were low but maternal genetic effects (m2) represented a relatively large proportion of the total phenotypic variance for each trait (birth weight m2=0.119, birth date m2=0.197, natal litter size m2=0.211). A negative correlation between direct and maternal genetic effects was estimated for each trait, but was only statistically significant for natal litter size (ram= -0.714). Total heritabilities (incorporating variance from heritable maternal effects and the direct-maternal genetic covariance) were significant for birth weight and birth date but not for natal litter size. Inadequately specified models greatly overestimated additive genetic variance and hence direct h2 (by a factor of up to 6.45 in the case of birth date). We conclude that failure to model heritable maternal variance can result in over- or under-estimation of the potential for traits to respond to selection, and advocate an increased effort to explicitly measure maternal genetic effects in evolutionary studies.