Response to Selection Under Non-Random Mating I. Partitioning Genetic Variance

In analogy to the concept of breeding value defined for random mating equilibrium populations, the “transmittable genetic value” of an individual is defined as the average value of its expected progeny for any system of mating. The genotypic value is then characterised in terms of transmittable and residual genetic values and components of genetic variance redefined which can be estimated by the conventional procedure based on resemblance between relatives.     

Partition of Genetic Variance for Sub-Populations

The variance between and within backcrosses of two populations is partitioned on the base of (I) multinomially distributed numbers of effects of specific chromosomes taking (II) recombination into account and on the base of (III) normally distributed sums of gene effects. The method of estimation makes use of a specific structure of data with backcross parents taken from different generations of random mating reproduction of crosses between the two populations.     

Genetic Architecture of Two Fitness-related Traits in Drosophila melanogaster: Ovariole Number and Thorax Length

In Drosophila melanogaster, ovariole number and thorax length are morphological characters thought to be associated with fitness. Maximum daily egg production in females is positively correlated with ovariole number, while thorax length is correlated with male reproductive success and female fecundity. Though both traits are related to fitness, ovariole number is likely to be under stabilizing selection, while thorax length appears to be under directional selection. Current research has focused on examining the sources of variation for ovariole number in relation to fitness, with a view towards elucidating how segregating variation is maintained in natural populations. Here, we utilize a diallel design to explore the genetic architecture of ovariole number and thorax length in nine isogenic lines derived from a natural population. The full diallel design allows the estimation of general combining ability (GCA), specific combining ability (SCA), and also describes variation due to reciprocal effects (RGCA and RSCA). Ovariole number and thorax length differed with respect to their genetic architecture, reflective of the independent selective forces acting on the traits. For ovariole number, GCA accounted for the majority (67.3%) of variation segregating between the lines, with no evidence of reciprocal effects or inbreeding depression; SCA accounted for a small percentage (3.9%) of the variance, suggesting dominance variation; no reciprocal effects were observed. In contrast, for thorax length, the majority of the non-error variance was accounted for by SCA (17.9%), with only one third as much variance (6.2%) due to GCA. Interestingly, RSCA (nuclear–extranuclear interactions) accounted for slightly more variation (7.5%) than GCA in these data. Thus, genetic variation for thorax length is largely in accord with predictions for a fitness trait under directional selection: little additive genetic variation and substantial dominance variation (including a suggestion of inbreeding depression); while the mechanisms underlying the maintenance of variation for ovariole number are more complex.     

The Nature of Genetic Variation for Complex Traits Revealed by GWAS and Regional Heritability Mapping Analyses

We use computer simulations to investigate the amount of genetic variation for complex traits that can be revealed by single-SNP genome-wide association studies (GWAS) or regional heritability mapping (RHM) analyses based on full genome sequence data or SNP chips. We model a large population subject to mutation, recombination, selection, and drift, assuming a pleiotropic model of mutations sampled from a bivariate distribution of effects of mutations on a quantitative trait and fitness. The pleiotropic model investigated, in contrast to previous models, implies that common mutations of large effect are responsible for most of the genetic variation for quantitative traits, except when the trait is fitness itself. We show that GWAS applied to the full sequence increases the number of QTL detected by as much as 50% compared to the number found with SNP chips but only modestly increases the amount of additive genetic variance explained. Even with full sequence data, the total amount of additive variance explained is generally below 50%. Using RHM on the full sequence data, a slightly larger number of QTL are detected than by GWAS if the same probability threshold is assumed, but these QTL explain a slightly smaller amount of genetic variance. Our results also suggest that most of the missing heritability is due to the inability to detect variants of moderate effect (∼0.03–0.3 phenotypic SDs) segregating at substantial frequencies. Very rare variants, which are more difficult to detect by GWAS, are expected to contribute little genetic variation, so their eventual detection is less relevant for resolving the missing heritability problem.     

大豆粒形性状的遗传效应分析

采用双子叶植物种子数量性状的遗传模型,分析了大豆品种双列杂交F1和F2种子的粒重、粒宽、粒厚和粒长／粒宽、粒长／粒厚、粒宽／粒厚粒形性状的遗传效应。结果表明：7种粒形性状同时受制于种子直接遗传效应,而且还不同程度的受制于母体和细胞质效应。其中,百粒重、粒长、粒长／粒宽、粒长／粒厚和粒宽／粒厚的遗传以细胞质效应为主;粒宽和粒厚以母体遗传效应为主。粒重、粒长和粒长／粒宽、粒宽／粒厚的种子直接遗传率和细胞质遗传率均属中等,对其4个性状选择可以在较高世代单株和单粒选择均有效果。粒宽和粒厚母体遗传率数值较大,对其性状应以母体单株为单位早代选择,以增加粒宽和粒厚。P2和P7可作为增加百粒重、粒长／粒宽、粒长／粒厚和粒宽／粒厚的理想亲本;P1、P4和P6分别是提高粒长、粒厚和粒宽的理想亲本。     

On the Probabilities of Obtaining Negative Estimates of Genetic Variance Components

This paper derives the probabilities of obtaining negative estimates of additive and dominance genetic variances when one uses the traditional weighted least square method for estimating genetic variances as given in MATHER and JINKS (1971). The model considered involves P₁, P₂, F₂, B₁ (Backcross to P₁) and B₂ (Backcross to P₂). The results are derived under the ordinary assumptions as made in the genetic literatures. It is shown that unless the genetic effects are very large and environmental effects small, the probabilities of obtaining negative estimates of additive and dominance variances are in general quite large.     

果蝇心脏发育基因调控的研究进展

果蝇心脏的发育是一个受到一系列基因共同调控的复杂过程,这些基因在脊椎动物和无脊椎动物果蝇中具有惊人的相似性,对于它们功能的研究将有助于揭示人类心脏发育的过程及分子控制机理.通过将果蝇作为一种重要的模式动物,对心脏发育基因调控的研究进展作一综述.     

二棱大麦熟期性状的遗传研究

以甘木二条等7个二棱大麦品种进行不完全双列杂交,对其亲本、F1和F2的抽穗期,灌浆期和成熟期三个性状以1992和1995年（播种年份）的两年资料,采用加性-显性-上位性（ADAA）模型进行遗传分析．遗传方差分量的比率估算表明,三个性状都存在上位性作用．除灌浆期外,其余二性状还受显性和加性效应的作用,并以加性为主．显性效应和加性效应与环境的互作均达显著水平,基因效应的预测值表明采用P3（黔浙1号）和P4（浙农大3号）较易获得早熟后代．     

RAPD分析在绢丝昆虫亲缘关系研究中的应用：Ⅱ．柞蚕品种间的遗传差异

采用RAPD技术,对5个柞蚕品种的遗传差异进行比较研究,结果表明,所采用40个随机引物中,有27个引物扩增谱清晰且重复性较好,扩增总片段数253条,单个引物的扩增片段数在4－16之间,片段大小在0．33－3．0kb之间。不同柞蚕品种间的遗传差异较小,遗传距离（D）在0．066－0．1659之间,根据D值,由UPGMA聚类分析软件绘制了它们的分子进化树。     

西方蜜蜂产浆量的动态遗传研究

应用条件和非条件遗传效应分析方法对3个西方蜜蜂(Apis mellifera L.)品种的蜂群产浆量、台浆量和台基接受率进行了发育遗传研究。结果表明：蜂群产浆量、台浆量在各个时期均存在显著或极显著的基因型方差,台基接受率在大部分时期存在显著或极显著的基因型方差,说明这3个性状主要由遗传因素决定。条件遗传分析发现,在某些无法检测到非条件方差的时期存在显著水平的条件方差,证明在产浆期的不同阶段,3个性状都有基因的新表达。同一性状不同时期的遗传相关分析表明：蜂群产浆量以及台浆量在各个时期均检测到显著或极显著的基因型相关,台基接受率在大多时期存在显著的基因型相关,表明控制产浆量和台浆量早期表现的遗传效应总是以相同的方式调节后期的表现,而台基接受率则不然。成对性状之间的相关研究表明：蜂群产浆量和台浆量之间在各个时期存在显著或极显著的遗传相关,说明2性状基因效应之间的协同作用是一致的,而蜂群产浆量和台基接受率之间在大多时期存在显著的遗传相关,但在一些时期没有相关,2性状之间的基因效应协同作用较差。     

Comparative Studies on the Estimation of Genetic Variances by Several Variance Components Estimation Method

Using a quantitative genetic model, this paper compares four different methods for estimating genetic variance components. Given various genetic parameters, data were generated and estimates computed. The number of negative estimates, the sample mean, the sample variance, and the sample mean squared error were computed for each method. It is shown that, if the genetic values are not very small, the traditional MATHER -JINKS method is at least as good as any other method. The ML method might be preferable only if the genetic values are very small and the number of loci large.     

On the Additive and Dominant Variance and Covariance of Individuals Within the Genomic Selection Scope

Genomic evaluation models can fit additive and dominant SNP effects. Under quantitative genetics theory, additive or “breeding” values of individuals are generated by substitution effects, which involve both “biological” additive and dominant effects of the markers. Dominance deviations include only a portion of the biological dominant effects of the markers. Additive variance includes variation due to the additive and dominant effects of the markers. We describe a matrix of dominant genomic relationships across individuals, D, which is similar to the G matrix used in genomic best linear unbiased prediction. This matrix can be used in a mixed-model context for genomic evaluations or to estimate dominant and additive variances in the population. From the “genotypic” value of individuals, an alternative parameterization defines additive and dominance as the parts attributable to the additive and dominant effect of the markers. This approach underestimates the additive genetic variance and overestimates the dominance variance. Transforming the variances from one model into the other is trivial if the distribution of allelic frequencies is known. We illustrate these results with mouse data (four traits, 1884 mice, and 10,946 markers) and simulated data (2100 individuals and 10,000 markers). Variance components were estimated correctly in the model, considering breeding values and dominance deviations. For the model considering genotypic values, the inclusion of dominant effects biased the estimate of additive variance. Genomic models were more accurate for the estimation of variance components than their pedigree-based counterparts.     

二棱大麦茎杆特性的ADAA模型的遗传研究

以二棱大麦(Hordeum,distichum L.)甘木二条等7个品种进行半双列杂交,对1992年和1997年的亲本、F     

Changes in Variance Components of Flanking Marker Genotypes Under Varying Selection Intensities

Selection is practically ubiquitous during marker-QTL linkage analysis with an experimental population. Thus, it is necessary to investigate the impacts of selection upon linkage analyses in order to obtain unbiased estimates of QTL position and effect. In this article, by exploiting flanking markers through the widely applied half-sib design, we have developed the structures of three variance components, i.e., variance component between marker genotypes, polygenic variance component and recombinant variance component within marker genotypes. Changes in these variance components under varying selection intensities were investigated in this study to formulate the effects of selection on various variance components. Results showed clearly that all variance components presented were quite sensitive to changes in selection intensity. As selection intensity increased, all variance components declined by differing extents in a quadratic fashion. Comparatively speaking, the variance between marker genotypes decreased most drastically, followed by the polygenic variance within marker genotypes and then the recombinant variance within marker genotypes, which suggested a decrease of power for QTL linkage analysis. Therefore, steps should be taken to avoid as much as possible the presence of selection in real populations, so as to further eliminate the negative effects of selection on QTL linkage analysis.     

侧翼标记基因型方差组分随不同选择强度的变化

从实际角度看,选择在用于标记-QTL连锁分析的实验群体中是较普遍存在的。为获得QTL位置及其效应的无偏估计,有必要研究选择对连锁分析实验所造成的影响。该文在侧翼标记情况下利用广泛使用的半同胞设计提出了3种方差组分,即标记组间方差、组内多基因方差和组内重组方差及其构成。着重从理论上研究了各方差组分在不同选择强度下的变化规律,阐明了选择对各方差组分的效应。结果表明,各方差组分对选择强度的变化很敏感。随着选择强度的增加,所有方差组分都以二次曲线方式有不同程度的下降。比较而言,标记组间方差组分下降最快,标记组内多基因方差下降较慢,组内重组方差下降最慢。这意味着QTL连锁分析功效的降低。所以在实际群体中应采取必要措施尽量避免选择的发生,从而消除选择对QTL连锁分析的负面效应。     

Genetic Variance and Correlation after Selection for Two Traits by Index, Independent Culling Levels and Extreme Selection

Three two-trait selection methods were analyzed for their effects on genetic variance and correlation by multivariate methods, two-locus methods and computer simulation. The two-trait selection methods studied were independent culling levels (ICL), index (IND) and extreme (EXT) selection. The effects of the selection methods on genetic variance and correlation were partitioned into permanent effects due to changes in gene frequencies and temporary effects due to nonrandom association of alleles at different loci. Multivariate methods were used to predict temporary effects from a single generation of selection by each method and from several generations of index selection. Two-locus theory was used to determine the stability and rank of temporary effects on genetic correlation for all three methods. Predictions were compared to computer simulation results. When selection increased the means of both traits, EXT had the lowest (closest to -1.0) genetic correlation and highest variances, while ICL tended to have the highest (closest to 1.0) genetic correlation. When selection increased the mean of one trait and decreased the mean of the other, EXT had the highest genetic variances and correlation, while ICL had the lowest genetic variances and correlation.     

Evolutionary experiments on mate recognition in the Drosophila serrata species complex

It is becoming increasingly apparent that at least some aspects of the evolution of mate recognition may be amenable to manipulation in evolutionary experiments. Quantitative genetic analyses that focus on the genetic consequences of evolutionary processes that result in mate recognition evolution may eventually provide an understanding of the genetic basis of the process of speciation. We review a series of experiments that have attempted to determine the genetic basis of the response to natural and sexual selection on mate recognition in the Drosophila serrata species complex. The genetic basis of mate recognition has been investigated at three levels: (1) between the species of D. serrata and D. birchii using interspecific hybrids, (2) between populations of D. serrata that are sympatric and allopatric with respect to D. birchii, and (3) within populations of D. serrata. These experiments suggest that it may be possible to use evolutionary experiments to observe important events such as the reinforcement of mate recognition, or the generation of the genetic associations that are central to many sexual selection models.     

Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation

When polygenic traits are under stabilizing selection, many different combinations of alleles allow close adaptation to the optimum. If alleles have equal effects, all combinations that result in the same deviation from the optimum are equivalent. Furthermore, the genetic variance that is maintained by mutation–selection balance is 2μ/S per locus, where μ is the mutation rate and S the strength of stabilizing selection. In reality, alleles vary in their effects, making the fitness landscape asymmetric and complicating analysis of the equilibria. We show that that the resulting genetic variance depends on the fraction of alleles near fixation, which contribute by 2μ/S, and on the total mutational effects of alleles that are at intermediate frequency. The interplay between stabilizing selection and mutation leads to a sharp transition: alleles with effects smaller than a threshold value of 2μ/S remain polymorphic, whereas those with larger effects are fixed. The genetic load in equilibrium is less than for traits of equal effects, and the fitness equilibria are more similar. We find that if the optimum is displaced, alleles with effects close to the threshold value sweep first, and their rate of increase is bounded by μS. Long-term response leads in general to well-adapted traits, unlike the case of equal effects that often end up at a suboptimal fitness peak. However, the particular peaks to which the populations converge are extremely sensitive to the initial states and to the speed of the shift of the optimum trait value.     

Natural selection on the genetical component of variance in body condition in a wild bird population

Although there is substantial evidence that skeletal measures of body size are heritable in wild animal populations, it is frequently assumed that the nonskeletal component of body weight (or ‘condition’) is determined primarily by environmental factors, in particular nutritional state. We tested this assumption by quantifying the genetic and environmental components of variance in fledgling body condition index (=relative body weight) in a natural population of collared flycatchers (Ficedula albicollis), and compared the strength of natural selection on individual breeding values with that on phenotypic values. A mixed model analysis of the components of variance, based on an ‘animal model’ and using 18 years of data on 17 717 nestlings, revealed a significant additive genetic component of variance in body condition, which corresponded to a narrow sense heritability (h²) of 0.30 (SE=0.03). Nongenetic contributions to variation in body condition were large, but there was no evidence of dominance variance nor of contributions from early maternal or common environment effects (pre‐manipulation environment) in condition at fledging. Comparison of pre‐ and post‐selection samples revealed virtually identical h² of body condition index, despite the fact that there was a significant decrease (35%) in the levels of additive genetic variance from fledging to breeding. The similar h² in the two samples occurred because the environmental component of variance was also reduced by selection, suggesting that natural selection was acting on both genotypic and environmental variation. The effects of selection on genetic variance were confirmed by calculation of the selection differentials for both phenotypic values and best linear unbiased predictor (BLUP) estimates of breeding values: there was positive directional selection on condition index both at the phenotypic and the genotypic level. The significant h² of body condition index is consistent with data from human and rodent populations showing significant additive genetic variance in relative body mass and adiposity, but contrasts with the common assumption in ecology that body condition reflects an individual’s nongenetic nutritional state. Furthermore, the substantial reduction in the additive genetic component of variance in body condition index suggests that selection on environmental deviations cannot alone explain the maintenance of additive genetic variation in heritable traits, but that other mechanisms are needed to explain the moderate to high heritabilities of traits under consistent and strong directional selection.