Using clonal replicates to explore genetic variation in a perennial plant species

Summary An experimental design is presented for estimating genetic parameters using a family structure with clonally replicated individuals. This experimental design provides a technique to quantify genetic variation in a population, with partial separation of additive, dominance and epistatic gene action. Our method is offered as an alternative to techniques for estimating epistatic gene action that require several generations and/or inbreeding. Such methods are not particularly useful for long-lived perennials with long generation cycles. An example of the analysis is given with a forest tree species, Populus deltoides Bartr., and parameter estimates are presented for traits measured over 8 years.     

Quantitative genetic analysis of bi-iliac breadth

Bi-iliac breadth, the frontal maximum diameter between right and left iliac crests, was measured in 1,547 male and 2,085 female residents of a rural area in Japan. All subjects were over 14 years of age. The bi-iliac breadth showed an increase related to age but little sex difference. Modification of age and sex variations from the measured value was obtained by calculation of the score, represented by arithmetical means and standard deviations. Distribution of these scores appeared to be binomial, and since binomial distribution approaches normal distribution when n is large, it is presumed that this trait gains normal distribution. Thus variation of bi-iliac breadth in subjects 20-79 years of age enables us to analyze inheritance. No significant difference was found between husband and wife in the correlation coefficients or between father and daughter (0.13 +/- 0.08). Significant differences were found as follows: father-son (0.35 +/- 0.05) (P less than 0.001), mother-son (0.28 +/- 0.05) (P less than 0.001), and mother-daughter (0.28 +/- 0.06) (P less than 0.001). There was no indication of maternal or paternal effects, since no significant difference was found in father-child and mother-child correlation coefficients. It is concluded that bi-iliac breadth is a quantitative genetic trait under control of polygenes on autosomes. Regression coefficient of child on midparental value was 0.55 +/- 0.05, approximately twice the means of four pairs of correlation coefficients between parent-offspring. Narrowly, heritability was estimated as 0.54 approximately 0.55. Contribution of dominance to total variance was small (VD = 0.11), in contrast to the larger additive genetic variance (VA = 0.54).     

Sex-specific genetic variances in life-history and morphological traits of the seed beetle Callosobruchus maculatus

Knowledge of heritability and genetic correlations are of central importance in the study of adaptive trait evolution and genetic constraints. We use a paternal half-sib-full-sib breeding design to investigate the genetic architecture of three life-history and morphological traits in the seed beetle, Callosobruchus maculatus. Heritability was significant for all traits under observation and genetic correlations between traits (r(A)) were low. Interestingly, we found substantial sex-specific genetic effects and low genetic correlations between sexes (r(MF)) in traits that are only moderately (weight at emergence) to slightly (longevity) sexually dimorphic. Furthermore, we found an increased sire ([Formula: see text]) compared to dam ([Formula: see text]) variance component within trait and sex. Our results highlight that the genetic architecture even of the same trait should not be assumed to be the same for males and females. Furthermore, it raises the issue of the presence of unnoticed environmental effects that may inflate estimates of heritability. Overall, our study stresses the fact that estimates of quantitative genetic parameters are not only population, time, environment, but also sex specific. Thus, extrapolation between sexes and studies should be treated with caution.     

Methods for the study of cytoplasmic effects on quantitative traits

Summary The methods used to study cytoplasmic effects in quantitative traits often do not measure quantitative genetic parameters, while those that do are either complicated or do not take into account situations where the expression of cytoplasmic effects does not persist, but decreases in advanced generations. We present two simple models that take cytoplasmic effects and the quantitative genetic parameters into account. One of the models (A) is for cases where cytoplasmic effects remain constant through successive generations, and the second model (B) is for traits where cytoplasm-genotype interactions are present. This model also takes into account the decreasing persistence of cytoplasmic effects with advancing generations, which is often reported in the literature.     

Genetic analysis of some seed quality characters in upland cotton (Gossypium hirsutum L.)

Summary A set of diallel crosses involving ten parents was evaluated over two locations to determine the genetic control of protein per cent, oil per cent, seed index, percentage of mature seeds and number of seeds per boll. The analysis of pooled data showed that percentage of mature seeds was controlled by additive (D) and non-additive (H₁ and H₂) genetic effects. Overdominance was noticed. For seed index the D component measuring additive, and the H₂ component measuring dominance, variation were significant. Protein content and oil content were primarily under the control of non-additive (H₁ and H₂) genetic effects, while for number of seeds per boll the variability was accounted for by dominance (H₁) effects only. The development of pure lines through appropriate methods is suggested.Part of the thesis of the senior author, submitted in partial fulfilment for the Ph.D. degree     

Hierarchical and factorial mating designs for quantitative genetic analysis in tetrasomic potato

Plant breeders need to quantify additive and non-additive components of genetic variance in order to determine appropriate selection methods to improve quantitative characteristics. Hierarchical and factorial mating designs (also known as North Carolina mating designs I and II, respectively) allow one to determine these variance components. The relative advantages of these two designs in the quantitative genetics of tuber yield in tetrasomic potato were investigated. Likewise, the number of female parents to include in design I was also investigated. Data were collected from two independent experiments at two contrasting Peruvian locations: La Molina in the dry coast and San Ramon in the humid mid-altitude. In the first experiment, although design I gave a negative digenic variance (σ² _D), this design provided almost the same estimate of narrow-sense heritability (h²) for tuber yield as that obtained in design II (0.291 and 0.260, respectively). Therefore, design I appears to be appropriate for quantitative genetics research in tetrasomic potato, a crop in which some clones are male sterile. The easy handling of crosses (distinct random females included in the crossing scheme) is another advantage of design I relative to design II. In the second experiment, 12 males were crossed with either two or four females following a design-I mating scheme. The additive genetic variance (σ² _A) was zero (or negative) when two females per male were included but was positive with four females. These results suggest that two females per male may not be enough for design I in tetrasomic potato. Four females per male are preferable to determine σ² _A in design I for this tetrasomic crop. Received: 19 March 2001 / Accepted: 3 July 2001     

A comparison of methods to estimate cross-environment genetic correlations

Advanced techniques for quantitative genetic parameter estimation may not always be necessary to answer broad genetic questions. However, simpler methods are often biased, and the extent of this determines their usefulness. In this study we compare family mean correlations to least squares and restricted error maximum likelihood (REML) variance component approaches to estimating cross-environment genetic correlations. We analysed empirical data from studies where both types of estimates were made, and from studies in our own laboratories. We found that the agreement between estimates was better when full-sib rather than half-sib estimates of cross-environment genetic correlations were used and when mean family size increased. We also note biases in REML estimation that may be especially important when testing to see if correlations differ from 0 or 1. We conclude that correlations calculated from family means can be used to test for the presence of genetic correlations across environments, which is sufficient for some research questions. Variance component approaches should be used when parameter estimation is the objective, or if the goal is anything other than determining broad patterns.     

A Genetic Basis Behind Combining Ability and Breeding Values in Mono- and Di-genic Systems

Combining ability and breeding values are concepts of crucial importance in practical breeding. However, in early literature, methods of partitioning the genetic value into additive and dominance effects were described mostly in single gene and under random mating. Though average effect and average excess of gene substitution were defined by Fisher and a practial method of obtaining breeding values outlined by Falconer, concerted attempts are scarce in integrating the concepts of combining ability, breeding value and additive effects. Only a few workers have reported the values of those parameters for inbred populations while published reports on those effects in digenic systems with linkage appear to be not readily available. Practical breeders continue to use those concepts as if they were independent. This paper is therefore an attempt at filling the research gaps and setting those concepts in proper practical perspective.     

Negative genetic correlation between diapause duration and fecundity after diapause in a spider mite

Abstract.  1. Recently, the costs of diapause, i.e. the reduction of fecundity after diapause, have been examined from an evolutionary perspective.
2. The evolution of this trade-off should be clarified by quantitative genetic approaches, as theoretical studies address the evolution of multiple traits. Nevertheless, previous studies on the costs of diapause have been based on phenotypic correlations or experimental manipulations, whereas the genetic background underlying this trade-off remains unclear.
3. In the present study, a half-sib breeding design was used to examine the quantitative genetic relationships between diapause duration and post-diapause fecundity in the Kanzawa spider mite Tetranychus kanzawai Kishida (Acari: Tetranychidae).
4. The heritability of diapause duration, post-diapause total fecundity, and post-diapause early fecundity were 0.37, 0.14, and 0.11 respectively. Genetic correlations between diapause duration and post-diapause total fecundity, and between diapause duration and early fecundity were both significantly negative (–0.70 and –0.90 respectively). These results suggest that the cost of prolonging diapause duration is genetically based, and that these life-history traits respond to natural selection acting on them simultaneously.     

Quantitative genetic approach for assessing invasiveness: geographic and genetic variation in life-history traits

Predicting the spread of invasive species is a challenge for modern ecology. Although many invasive species undergo genetic bottlenecks during introduction to new areas resulting in a loss of genetic diversity, successful invaders manage to flourish in novel environments either because of pre-adaptations or because important traits contain adaptive variation enabling rapid adaptation to changing conditions. To predict and understand invasion success, it is crucial to analyse these features. We assessed the potential of a well-known invader, the Colorado potato beetle (Leptinotarsa decemlineata), to expand north of its current range in Europe. A short growing season and harsh overwintering conditions are apparent limiting factors for this species’ range. By rearing full-sib families from four geographically distinct populations (Russia, Estonia, Poland, Italy) at two fluctuating temperature regimes, we investigated (a) possible differences in survival, development time, and body size among populations and (b) the amount of adaptive variation within populations in these traits. All populations were able to complete their development in cooler conditions than in their current range. A significant genotype–environment interaction for development time and body size suggests the presence of adaptive genetic variation, indicating potential to adapt to cooler conditions. The northernmost population had the highest survival rates and fastest development times on both temperature regimes, suggesting pre-adaptation to cooler temperatures. Other populations had minor differences in development times. Interestingly, this species lacks the classical trade-off between body size and development time which could have contributed to its invasion potential. This study demonstrates the importance of considering both ecological and evolutionary aspects when assessing invasion risk.     

Maintenance of genetic variation in sexual ornaments: a review of the mechanisms

Female preferences for elaborate male sexual traits have been documented in a number of species in which males contribute only genes to the next generation. In such systems, mate choice has been hypothesised to benefit females genetically. For the genetic benefits to be possible there must be additive genetic variation (V(A)) for sexual ornaments, such that highly ornamented males can pass fitter genes on to the progeny of choosy females. Here, I review the mechanisms that can contribute to the maintenance of this variation. The variation may be limited to sexual ornaments, resulting in Fisherian benefits in terms of the increased reproductive success of male progeny produced by choosy females. Alternatively, ornaments may capture V(A) in other life-history traits. In the latter case, "good genes" benefits may apply in terms of improved performance of the progeny of either sex. Some mechanisms, however, such as negative pleiotropy, sexually antagonistic variation or overdominance, can maintain V(A )in ornaments and other life-history traits with little variation in total fitness, leaving little room for any genetic benefits of mate choice. Distinguishing between these mechanisms has consequences not only for the theory of sexual selection, but also for evolution of sex and for biological conservation. I discuss how the traditional ways of testing for genetic benefits can usefully be supplemented by tests detecting benefits resulting from specific mechanisms maintaining V(A )in sexual ornaments.     

Comparing G: multivariate analysis of genetic variation in multiple populations

The additive genetic variance–covariance matrix (G) summarizes themultivariate genetic relationships among a set of traits. The geometry of Gdescribes the distribution of multivariate genetic variance, and generates geneticconstraints that bias the direction of evolution. Determining if and how the multivariategenetic variance evolves has been limited by a number of analytical challenges incomparing G-matrices. Current methods for the comparison of G typically shareseveral drawbacks: metrics that lack a direct relationship to evolutionary theory, theinability to be applied in conjunction with complex experimental designs, difficultieswith determining statistical confidence in inferred differences and an inherentlypair-wise focus. Here, we present a cohesive and general analytical framework for thecomparative analysis of G that addresses these issues, and that incorporates andextends current methods with a strong geometrical basis. We describe the application ofrandom skewers, common subspace analysis, the 4th-order genetic covariance tensor and thedecomposition of the multivariate breeders equation, all within a Bayesian framework. Weillustrate these methods using data from an artificial selection experiment on eighttraits in Drosophila serrata, where a multi-generational pedigree was availableto estimate G in each of six populations. One method, the tensor, elegantlycaptures all of the variation in genetic variance among populations, and allows theidentification of the trait combinations that differ most in genetic variance. The tensorapproach is likely to be the most generally applicable method to the comparison ofG-matrices from any sampling or experimental design.     

Effects of food abundance on genetic and maternal variation in the growth rate of juvenile red squirrels

Sources of variation in growth in body mass were assessed in natural and experimental conditions of high and low food abundance using reciprocal cross-fostering techniques and long-term data (1987-2002) for a population of North American red squirrels (Tamiasciurus hudsonicus). Growth rates were significantly higher in naturally good and food supplemented conditions, than in poor conditions. Mother-offspring resemblance was higher in poor conditions as a result of large increases in both the direct genetic variance and direct-maternal genetic covariance and a smaller increase in the coefficient of maternal variation. Furthermore, the genetic correlation across environments was significantly less than one indicating that sources of heritable variation differed between the two environments. These results are consistent with the hypothesis that selection has eroded heritable variation for growth more in good conditions and indicate the potential for independent adaptation of growth rates in good and poor conditions.     

The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population

Appropriate selection of parents for the development of mapping populations is pivotal to maximizing the power of quantitative trait loci detection. Trait genotypic variation within a family is indicative of the family's informativeness for genetic studies. Accurate prediction of the most useful parental combinations within a species would help guide quantitative genetics studies. We tested the reliability of genotypic and phenotypic distance estimators between pairs of maize inbred lines to predict genotypic variation for quantitative traits within families derived from biparental crosses. We developed 25 families composed of ~200 random recombinant inbred lines each from crosses between a common reference parent inbred, B73, and 25 diverse maize inbreds. Parents and families were evaluated for 19 quantitative traits across up to 11 environments. Genetic distances (GDs) among parents were estimated with 44 simple sequence repeat and 2303 single-nucleotide polymorphism markers. GDs among parents had no predictive value for progeny variation, which is most likely due to the choice of neutral markers. In contrast, we observed for about half of the traits measured a positive correlation between phenotypic parental distances and within-family genetic variance estimates. Consequently, the choice of promising segregating populations can be based on selecting phenotypically diverse parents. These results are congruent with models of genetic architecture that posit numerous genes affecting quantitative traits, each segregating for allelic series, with dispersal of allelic effects across diverse genetic material. This architecture, common to many quantitative traits in maize, limits the predictive value of parental genotypic or phenotypic values on progeny variance.     

How to separate genetic and environmental causes of similarity between relatives

Related individuals often have similar phenotypes, but this similarity may be due to the effects of shared environments as much as to the effects of shared genes. We consider here alternative approaches to separating the relative contributions of these two sources to phenotypic covariances, comparing experimental approaches such as cross-fostering, traditional statistical techniques and more complex statistical models, specifically the 'animal model'. Using both simulation studies and empirical data from wild populations, we demonstrate the ability of the animal model to reduce bias due to shared environment effects such as maternal or brood effects, especially where pedigrees contain multiple generations and immigration rates are low. However, where common environment effects are strong, a combination of both cross-fostering and an animal model provides the best way to avoid bias. We illustrate ways of partitioning phenotypic variance into components of additive genetic, maternal genetic, maternal environment, common environment, permanent environment and temporal effects, but also show how substantial confounding between these different effects may occur. Whilst the flexibility of the mixed model approach is extremely useful for incorporating the spatial, temporal and social heterogeneity typical of natural populations, the advantages will inevitably be restricted by the quality of pedigree information and care needs to be taken in specifying models that are appropriate to the data.     

Genetic prenatal maternal effects on organ size in mice and their potential contribution to evolution

Two embryo transfer experiments were carried out in order to estimate the magnitude of prenatal maternal effects, independent of postnatal maternal factors, on the growth of internal organs and fat pads in mice. Reciprocal embryo transfers between the inbred mouse strains C3HeB/FeJ and SWR/J yielded three significant findings. First, all traits were not equally influenced by prenatal maternal factors. Genetic prenatal maternal factors, stemming from the genotype of the uterine mother, had a significant effect on testis weight, subcutaneous fat pad weight and epididymal fat pad weight in 21 day old progeny, but they had no effect on cranial capacity, an index of brain size, kidney weight, or liver weight. Prenatal litter size, defined as the sum of live and dead pups at birth, had a significant negative relationship with 21 day testis weight and kidney weight, and a significant positive association with subcutaneous and epididymal fat pad weights. Cranial capacity and liver weight at 21 days postnatally were not influenced by prenatal litter size. Second, the experiments demonstrated that there was ontogenetic variability in the strength of prenatal maternal effects. At 70 days of age, only subcutaneous fat pad weight was significantly influenced by genetic prenatal effects, and prenatal litter size had a significant negative relationship only with subcutaneous fat pad weight and body weight. Third, genetic prenatal effects had a significant influence on the among-trait covariances at 21 days postnatally, but not at 70 days. Because multivariate evolution involves covariances among characters, the latter results suggest that prenatal effects due to the mother's genotype can affect phenotypic evolution of mammals, especially for selection imposed early in life.     

The distribution of the effects of genes affecting quantitative traits in livestock

Meta-analysis of information from quantitative trait loci (QTL) mapping experiments was used to derive distributions of the effects of genes affecting quantitative traits. The two limitations of such information, that QTL effects as reported include experimental error, and that mapping experiments can only detect QTL above a certain size, were accounted for. Data from pig and dairy mapping experiments were used. Gamma distributions of QTL effects were fitted with maximum likelihood. The derived distributions were moderately leptokurtic, consistent with many genes of small effect and few of large effect. Seventeen percent and 35% of the leading QTL explained 90% of the genetic variance for the dairy and pig distributions respectively. The number of segregating genes affecting a quantitative trait in dairy populations was predicted assuming genes affecting a quantitative trait were neutral with respect to fitness. Between 50 and 100 genes were predicted, depending on the effective population size assumed. As data for the analysis included no QTL of small effect, the ability to estimate the number of QTL of small effect must inevitably be weak. It may be that there are more QTL of small effect than predicted by our gamma distributions. Nevertheless, the distributions have important implications for QTL mapping experiments and Marker Assisted Selection (MAS). Powerful mapping experiments, able to detect QTL of 0.1σ_p, will be required to detect enough QTL to explain 90% the genetic variance for a quantitative trait.     

Perspective: Here's to Fisher,additive genetic variance,and the fundamental theorem of natural selection

Fisher's fundamental theorem of natural selection, that the rate of change of fitness is given by the additive genetic variance of fitness, has generated much discussion since its appearance in 1930. Fisher tried to capture in the formula the change in population fitness attributable to changes of allele frequencies, when all else is not included. Lessard's formulation comes closest to Fisher's intention, as well as this can be judged. Additional terms can be added to account for other changes. The "theorem" as stated by Fisher is not exact, and therefore not a theorem, but it does encapsulate a great deal of evolutionary meaning in a simple statement. I also discuss the effectiveness of reproductive-value weighting and the theorem in integrated form. Finally, an optimum principle, analogous to least action and Hamilton's principle in physics, is discussed.     

Yolk testosterone and estradiol variation relative to clutch size, laying order and hatching asynchrony in Common Grackles

Maternal effects are typically thought to enhance rather than reduce offspring performance, but asynchronous hatching (ASH) in birds typically produces a size hierarchy within a clutch that frequently reduces the growth and survival of nestlings from eggs that hatch later. Given that yolk steroids can significantly affect offspring phenotype and that in many species the levels of yolk steroids have been found to increase with laying order, the maternal transfer of steroids to egg yolk has been proposed as a mechanism for females to offset the deleterious effects of ASH. To test this hypothesis, we determined whether yolk steroids varied with laying order or clutch size in Common Grackles (Quiscalus quiscula). Because ASH varies with clutch size (hatching span averages 48 h in five-egg clutches, 24 h in four-egg clutches) and regularly results in the starvation of later hatched nestlings, we predicted: (1) testosterone and 17?-estradiol levels should increase with laying order in both clutch sizes to mitigate the negative effects of ASH on last-hatched nestlings, and (2) the increase should be greater in five-egg clutches due to more pronounced hatching asynchrony. Using a competitive-binding steroid radioimmunoassay, we found no systematic variation in either testosterone or estradiol levels relative to laying order or clutch size. In the absence of evidence that yolk steroids interact adaptively with ASH, research must look elsewhere for potential benefits that might compensate for the costs these steroids impose on nestlings.