GENETIC MODELS AND ANALYSIS METHODS FOR SEX-LINKED AND MATERNAL GENE EFFECTS

INTRODUCTIONInanimalbrce(lingexperilllents,sex--linkedandmaternaleff(3ctsaretheprimarysourcesofreciprocaleffects.Eiap1etal.(1966)presentedamodelcontainillgparametersforsex--linlcedan(lmaternaleffectsasxvellasautosomalgeneticeffects.Cockerhalllandacid(1977…     

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.).     

Analysis of cytoplasmic and maternal effects I. A genetic model for diploid plant seeds and animals

A genetic model for modified diallel crosses is proposed for estimating variance and covariance components of cytoplasmic, maternal additive and dominance effects, as well as direct additive and dominance effects. Monte Carlo simulations were conducted to compare the efficiencies of minimum norm quadratic unbiased estimation (MINQUE) methods. For both balanced and unbalanced mating designs, MINQUE (0/1), which has 0 for all the prior covariances and 1 for all the prior variances, has similar efficiency to MINQUE(), which has parameter values for the prior values. Unbiased estimates of variance and covariance components and their sampling variances could be obtained with MINQUE(0/1) and jackknifing. A t-test following jackknifing is applicable to test hypotheses for zero variance and covariance components. The genetic model is robust for estimating variance and covariance components under several situations of no specific effects. A MINQUE(0/1) procedure is suggested for unbiased estimation of covariance components between two traits with equal design matrices. Methods of unbiased prediction for random genetic effects are discussed. A linear unbiased prediction (LUP) method is shown to be efficient for the genetic model. An example is given for a demonstration of estimating variance and covariance components and predicting genetic effects.     

A remark on the notions of gene and gametic frequencies for sex-linked genes

Summary A general model describing the evolution of genotypic frequencies at a heterosomal locus with n alleles is introduced. The treatment includes as a special case the standard derivation for X-linked loci as well as different concepts encountered in the literature which seem to contradict this derivation. The disagreement, however, is easily solved by distinguishing between gene and gametic frequencies.     

The effects of selection for gain in mice on the direct-maternal genetic correlation

Components of genetic variation for postweaning growth traits were estimated for both control and growth stocks of mice. The effect of phenotypic selection for gain, which genetically combines selection for additive direct and maternal effects, on additive genetic variance components, heritability, and additive genetic correlationsis discussed. Quantitative genetic theory predicts that simultaneous selection for two metric traits in the same direction will cause the genetic correlation between the two traits to become more negative. The results presented in this paper conflict with this theory. The direct-maternal additive genetic correlation was more negative in the control line (with 356 mice) than in the growth-selected line (with 320 mice) for the three traits analyzed (0.310 vs 0.999 for 21-day weight, 0.316 vs 1.000 for 42-day weight, and 0.506 vs 1.000 for gain from 21–42 days). Estimates were obtained by restricted maximum likelihood (REML) computed under a derivative free algorithm (DFREML).     

Diallel analysis of androgenetic plant production in hexaploid Triticale (X. triticosecale,Wittmack)

Summary Studies were made on the genetic determination of androgenetic plant yield and its two components: embryo production and green plant regeneration. This involved the analysis of a complete 7×7 diallel cross of 4 androgenetic lines and 3 lines obtained by pedigree selection, one of them having the Triticum timopheevi cytoplasm. The three traits analysed are both heritable and environmentally influenced (by season and culture medium composition). The analysis of embryo production shows a mainly nuclear inheritance, with predominantly additive gene action, but also a favourable effect of Triticum timopheevi cytoplasm. Green plant regeneration has a more complex genetic determination, with additive as well as non-additive gene action and cytoplasmic influences. Hybrids appear superior to inbred lines for embryogenesis and green plant yield, but not for green plant regeneration. Androgenetic lines used as parents did not show superiority over other parents either in their own value or in the transmission of androgenetic abilities. Genetic improvement seems to be possible by recombination in progenies of hybrids between lines having complementary abilities.     

Testing hypotheses for maternal effects in Daphnia magna

Maternal effects are widely observed, but their adaptive nature remains difficult to describe and interpret. We investigated adaptive maternal effects in a clone of the crustacean Daphnia magna, experimentally varying both maternal age and maternal food and subsequently varying food available to offspring. We had two main predictions: that offspring in a food environment matched to their mothers should fare better than offspring in unmatched environments, and that offspring of older mothers would fare better in low food environments. We detected numerous maternal effects, for example offspring of poorly fed mothers were large, whereas offspring of older mothers were both large and showed an earlier age at first reproduction. However, these maternal effects did not clearly translate into the predicted differences in reproduction. Thus, our predictions about adaptive maternal effects in response to food variation were not met in this genotype of Daphnia magna.     

Missing Plot Technique in Diallel Crosses for Griffing Method-III

The method of combining ability analysis of diallel crosses for Griffing method-3 for one and two missing observations has been presented. The formulae for estimating the parameters, the variances of different estimates and the sum of squares for various effects have been presented. The given analysis can easily be extended for the case of missing of more than two observations. The procedure of analysis has been illustrated through an example.     

Genetic analysis of agronomic characters in chickpea

Summary Twenty-eight diallel trials over 8 years and two locations were analysed to estimate genetic variances for agronomic characters of chickpea (Cicer arietinum L.). The data were analysed according to Method 4 and Model I of Griffing (1956). Days to flowering, plant height, and seed size were found to be predominantly under additive inheritance and were highly predictable. Both additive and non-additive genetic components were important for seed yield, number of branches, pods per plant, and seeds per pod. Although both general combining ability (gca) and specific combining ability (sca) varied significantly with generation, components of gca mean squares were invariably much larger than gca x generation interaction components, indicating that either the F₁ or the F₂ generation can be used to estimate the gca components effectively. Combined diallel analysis of F₂s over locations revealed the importance of combining ability x location interactions and emphasized the need for testing over more than one location for the precise estimation of combining ability. The implications of these findings and those reported earlier in the literature on the breeding strategies/methods for the genetic improvement of agronomic characters in chickpea are discussed.ICRISAT journal article no. 1199     

A Study of Maternal and Maternal Interaction Effects in Diallel Crosses

The analysis of diallel crosses by including the components due to maternal effect and maternal interaction effects have been presented for Griffing method—1 (random effect model) and Griffing method—3 (fixed and random effect model). Wherever exact test of significance is not possible, testing procedure using Satterthwaite (1946) approximation has been presented.     

Multigenerational hybridisation and its consequences for maternal effects in Atlantic salmon

Outbreeding between segregating populations can be important from an evolutionary,conservation and economical-agricultural perspective. Whether and how outbreedinginfluences maternal effects in wild populations has rarely been studied, despite both theprominent maternal influence on early offspring survival and the known presence of fitnesseffects resulting from outbreeding in many taxa. We studied several traits during theyolk-feeding stage in multigenerational crosses between a wild and a domesticated Atlanticsalmon (Salmo salar) population up to their third-generation hybrid in a commonlaboratory environment. Using cross-means analysis, we inferred that maternal additiveoutbreeding effects underlie most offspring traits but that yolk mass also underliesmaternal dominant effects. As a consequence of the interplay between additive and dominantmaternally controlled traits, offspring from first-generation hybrid mothers expressed anexcessive proportion of residual yolk mass, relative to total mass, at the time of firstfeeding. Their residual yolk mass was 23–97% greater than those of othercrosses and 31% more than that predicted by a purely additive model. Offspringadditive, epistatic and epistatic offspring-by-maternal outbreeding effects appeared tofurther modify this largely maternally controlled cross-means pattern, resulting in anincrease in offspring size with the percentage of domesticated alleles. Fitnessimplications remain elusive because of unknown phenotype-by-environment interactions.However, these results suggest how mechanistically co-adapted genetic maternal control onearly offspring development can be disrupted by the effects of combining alleles fromdivergent populations. Complex outbreeding effects at both the maternal and offspringlevels make the prediction of hybrid phenotypes difficult.     

Estimates of direct and maternal covariance functions for growth of Australian beef calves from birth to weaning

Records for birth and subsequent, monthly weights until weaning on beef calves of two breeds in a selection experiment were analysed fitting random regression models. Independent variables were orthogonal (Legendre) polynomials of age at weighing in days. Orders of polynomial fit up to 6 were considered. Analyses were carried out fitting sets of random regression coefficients due to animals'' direct and maternal, additive genetic and permanent environmental effects, with changes in variances due to temporary environmental effects modelled through a variance function, estimating up to 67 parameters. Results identified similar patterns of variation for both breeds, with maternal effects considerably more important in purebred Polled Herefords than a four-breed synthetic, the so-called Wokalups. Conversely, repeatabilities were higher for the latter. For both breeds, heritabilities decreased after birth, being lowest when maternal effects were most important around 100 days of age. Estimates at birth and weaning were consistent with previous, univariate results.     

Gene interactions from maternal effects

Theoretical analyses have demonstrated a potential role for epistasis in many of the most important processes in evolution. These analyses generally assume that an individual's genes map directly to its phenotype and epistasis results from interactions among loci that contribute to the same biochemical or developmental pathways (termed physiological, or within-genotype, epistasis). For many characters, particularly those expressed early in life, an individual's phenotype may also be affected by genes expressed by its parents. The presence of these parental effects allows for interactions between the genes present in the parental and offspring genomes. When the phenotypic effect of a locus in the offspring depends on the alleles possessed by its parents, genotype-by-genotype, or among-genotype, epistasis occurs. The among-genotype epistasis resulting from parental effects may contribute to ruggedness of adaptive landscapes because early mortality often accounts for much of the variance in fitness in populations. To demonstrate how parent-offspring interactions can result in among-genotype epistasis, I use a two-locus model, with one maternal effect locus and one direct effect locus, each with two alleles. Dynamical equations are presented for the two-locus model and are directly contrasted with the dynamical equations derived for a model for physiological epistasis. The relationship between the evolutionary dynamics resulting from these two forms of epistasis is discussed. Three scenarios are presented to illustrate systems in which maternal-offspring, genotype-by-genotype epistasis may occur. The implications of maternal-offspring epistasis for quantitative-trait-loci studies are also discussed.     

Additive and Non-additive Genetic Correlations. II. Application to Data Obtained from a 12 × 12 Diallel Cross

The proposed genetic correlation analysis, that involves the partitioning of the overall genetic correlation into an additive and a non-additive component, has been applied to data obtained from a diallel experiment involving 12 white modified opaque-2 maize inbred lines. The correlation analysis provided an insight into possible indirect selection strategies for the improvement of inferior kernel quality traits associated with the opaque-2 gene. Direct selection for high yield and low vitreousness rating would provide an efficient selection strategy for the development of high-yielding modified opaque-2 maize hybrids with desirable endosperm traits. It was concluded that it is not necessary to conduct the density, hardness and breakability determinations.     

Intergenerational effects of maternal birth season on offspring size in rural Gambia

Environmental conditions experienced in early life can influence an individual's growth and long-term health, and potentially also that of their offspring. However, such developmental effects on intergenerational outcomes have rarely been studied. Here we investigate intergenerational effects of early environment in humans using survey- and clinic-based data from rural Gambia, a population experiencing substantial seasonal stress that influences foetal growth and has long-term effects on first-generation survival. Using Fourier regression to model seasonality, we test whether (i) parental birth season has intergenerational consequences for offspring in utero growth (1982 neonates, born 1976-2009) and (ii) whether such effects have been reduced by improvements to population health in recent decades. Contrary to our predictions, we show effects of maternal birth season on offspring birth weight and head circumference only in recent maternal cohorts born after 1975. Offspring birth weight varied according to maternal birth season from 2.85 to 3.03 kg among women born during 1975-1984 and from 2.84 to 3.41 kg among those born after 1984, but the seasonality effect reversed between these cohorts. These results were not mediated by differences in maternal age or parity. Equivalent patterns were observed for offspring head circumference (statistically significant) and length (not significant), but not for ponderal index. No relationships were found between paternal birth season and offspring neonatal anthropometrics. Our results indicate that even in rural populations living under conditions of relative affluence, brief variation in environmental conditions during maternal early life may exert long-term intergenerational effects on offspring.     

Diallel analysis for some quantitative characters in Petunia hybrida Hort

Summary Flowering time, plant height and flower size in Petunia hybrida Hort. (multiflora type) have been genetically analysed by means of a 5 × 5 diallel cross. The results indicated that: (1) the three characters are controlled by additive-dominance polygenic systems. The contribution of the additive gene actions to the genetic variance of flowering time was relatively higher than that of dominance. The reverse situation was found for plant height and flower size. (2) Dominance is ambi-directional for the three characters. Ratios of average dominance were in the range of partial for flowering-time, complete for plant height and overdominance for flower size. (3) Number of genes (or gene groups) controlling the characters are about 3, 3 and 5 for flowering time, plant height and flower size: respectively, (4) Heritability estimates are 0.84, 0.88 and 0.89 in the broad-sense and 0.40, 0.49 and 0.37 in the narrow-sense, for flowering time, plant height and flower size; respectively. (5) Heterosis as percent increase of the mean F₁-hybrid above the higher parent, or decrease below the lower parent, was observed for flowering time (+ 9.7% to +13.3%), for plant height (–13.6% to –20.3%) and for flower size (+2.5% to +16.0%).     

Additive and Non-additive Genetic Correlations. I. Properties of Sampling Distributions

The sampling distributions of additive and non-additive genetic correlations estimated from a diallel experiment were determined through a computer simulation study. The properties of the sampling distributions were investigated in terms of the effect of varying the magnitude of the relevant variance components and the true correlation coefficient (Q), as well as the size of the diallel experiment. It was found that there was a high incidence of Q falling outside the range ?1 ≦Q≦1 when Q was close to 1 or -1, and the variance components were small. The degrees of freedom of the correlation components were shown to affect the variability of Q, and it was shown that a diallel experiment, that is to be used for a correlation analysis, should not be smaller than a 12 × 12 half diallel. Use of the Z transformation as a means of testing the significance of Q has been verified in this study and improvements on the degrees of freedom used for the transformation have been discussed.     

Viviparous mothers impose stronger glucocorticoid‐mediated maternal stress effects on their offspring than oviparous mothers

Maternal stress during gestation has the potential to affect offspring development via changes in maternal physiology, such as increases in circulating levels of glucocorticoid hormones that are typical after exposure to a stressor. While the effects of elevated maternal glucocorticoids on offspring phenotype (i.e., “glucocorticoid‐mediated maternal effects”) have been relatively well established in laboratory studies, it remains poorly understood how strong and consistent such effects are in natural populations. Using a meta‐analysis of studies of wild mammals, birds, and reptiles, we investigate the evidence for effects of elevated maternal glucocorticoids on offspring phenotype and investigate key moderators that might influence the strength and direction of these effects. In particular, we investigate the potential importance of reproductive mode (viviparity vs. oviparity). We show that glucocorticoid‐mediated maternal effects are stronger, and likely more deleterious, in mammals and viviparous squamate reptiles compared with birds, turtles, and oviparous squamates. No other moderators (timing and type of manipulation, age at offspring measurement, or type of trait measured) were significant predictors of the strength or direction of the phenotypic effects on offspring. These results provide evidence that the evolution of a prolonged physiological association between embryo and mother sets the stage for maladaptive, or adaptive, prenatal stress effects in vertebrates driven by glucocorticoid elevation.     

Context-dependent sex allocation: constraints on the expression and evolution of maternal effects

Despite decades of research, whether vertebrates can and do adaptively adjust the sex ratio of their offspring is still highly debated. However, this may have resulted from the failure of empirical tests to identify large and predictable fitness returns to females from strategic adjustment. Here, we test the effect of diet quality and maternal condition on facultative sex ratio adjustment in the color polymorphic Gouldian finch (Erythrura gouldiae), a species that exhibits extreme maternal allocation in response to severe and predictable (genetically-determined) fitness costs. On high-quality diets, females produced a relatively equal sex ratio, but over-produced sons in poor dietary conditions. Despite the lack of sexual size dimorphism, nutritionally stressed foster sons were healthier, grew faster, and were more likely to survive than daughters. Although these findings are in line with predictions from sex allocation theory, the extent of adjustment is considerably lower than previously reported for this species. Females therefore have strong facultative control over sex allocation, but the extent of adjustment is likely determined by the relative magnitude of fitness gains and the ability to reliably predict sex-specific benefits from environmental (vs. genetic) variables. These findings may help explain the often inconsistent, weak, or inconclusive empirical evidence for adaptive sex ratio adjustment in vertebrates.