QUANTITATIVE GENETIC MODELS FOR DEVELOPMENT,EPIGENETIC SELECTION,AND PHENOTYPIC EVOLUTION

Herein we describe a general multivariate quantitative genetic model that incorporates two potentially important developmental phenomena, maternal effects and epigenetic effects. Maternal and epigenetic effects are defined as partial regression coefficients and phenotypic variances are derived in terms of age-specific genetic and environmental variances. As a starting point, the traditional quantitative genetic model of additive gene effects and random environmental effects is cast in a developmental time framework. From this framework, we first extend a maternal effects model to include multiple developmental ages for the occurrence of maternal effects. An example of maternal effects occurring at multiple developmental ages is prenatal and postnatal maternal effects in mammals. Subsequently, a model of intrinsic and epigenetic effects in the absence of maternal effects is described. It is shown that genetic correlations can arise through epigenetic effects, and in the absence of other developmental effects, epigenetic effects are in general confounded with age-specific intrinsic genetic effects. Finally, the two effects are incorporated into the basic quantitative genetic model. For this more biologically realistic model combining maternal and epigenetic effects, it is shown that the phenotypic regressions of offspring on mother and offspring on father can be used in some cases to estimate simultaneously maternal effects and epigenetic effects.     

母体遗传效应对青海细毛羊生产性能遗传参数估计的影响

为了研究母体遗传效应对青海细毛羊生长性状、产毛性状的影响, 文章采用平均信息最大约束似然法应用不同混合动物模型估计青海细毛羊生产性状的遗传参数, 并采用似然比检验对不同模型进行比较分析。各模型中均包括固定效应、个体直接加性遗传效应、残差效应; 随机效应为：个体永久环境效应、母体遗传效应、母体永久环境效应。不同模型对随机效应作了不同考虑：模型1不考虑个体永久环境效应、母体遗传效应、母体永久环境效应; 模型2考虑母体永久环境效应; 模型3考虑母体遗传效应; 模型4考虑母体遗传效应和母体永久环境效应; 模型5考虑个体永久环境效应和母体遗传效应; 模型6考虑个体永久环境效应、母体遗传效应、母体永久环境效应。各模型估计的初生重遗传力为：0.1896~0.3781; 断奶重遗传力为：0.2537~0.2890; 周岁重遗传力范围：0.2244~0.3225; 成年羊体重遗传力范围：0.2205~0.3983; 产毛量遗传力为：0.1218~0.1490; 羊毛细度遗传力为：0.0983~0.4802; 羊毛长度遗传力为：0.1170~0.1311。与模型1相比, 模型3对于初生重、断奶重差异显著(P<0.01), 对于周岁重、成年羊体重各模型与模型1的似然比检验差异不显著(P>0.05); 与模型6相比, 模型4、5对于羊毛细度差异显著(P<0.01), 模型4对羊毛长度差异显著(P<0.05), 对于产毛量各模型与模型6似然比检验差异不显著(P>0.05)。生长性状中初生重、断奶重受母体遗传效应影响显著, 周岁重、成年羊体重受母体遗传效应影响不显著; 产毛性状中羊毛细度、长度受母体遗传效应影响显著, 产毛量受母体遗传效应影响较弱。     

Mapping reciprocal effects and interactions with plant density stress in Zea mays L

Reciprocal effects are due to genetic effects of the parents (i.e. maternal and paternal effects), cytoplasmic effects and parent-of-origin effects. However, in Zea mays L. the extent to which reciprocal effects exist, or can be attributed to specific underlying components, remains an area of interest and study. Reciprocal effects have been reported by several investigators for various agronomic characters in different types of maize materials for grain and silage usage. Maize geneticists and breeders have recognized reciprocal effects as one source of genetic variability, but the lack of consistency in the observation of these effects, particularly due to stress conditions, has prevented a systematic exploitation of these effects in practical breeding programs. There is mounting molecular evidence for underlying mechanisms in maize, which could be responsible for both the existence, and the instability of reciprocal effects. In this study, we developed population of reciprocal backcrosses based on an initial set of recombinant inbred lines. This population was used for dissecting reciprocal effects into the underlying components (maternal, cytoplasmic and parent-of-origin) effects. We also developed statistical framework to identify and map contributions of specific nuclear chromosomal regions to reciprocal effects. We showed that differences in maternal parents, endosperm DNA and maternally transmitted factors collectively influence reciprocal effects early during the season, and that their influence diluted at later stages. We also found evidence that parent-of-origin effects in the sporophyte DNA existed at all stages and played an important role in establishing differences between reciprocal backcrosses at later developmental stages.     

母体遗传效应对青海细毛羊生产性能遗传参数估计的影响

为了研究母体遗传效应对青海细毛羊生长性状、产毛性状的影响,文章采用平均信息最大约束似然法应用不同混合动物模型估计青海细毛羊生产性状的遗传参数,并采用似然比检验对不同模型进行比较分析。各模型中均包括固定效应、个体直接加性遗传效应、残差效应;随机效应为:个体永久环境效应、母体遗传效应、母体永久环境效应。不同模型对随机效应作了不同考虑:模型1不考虑个体永久环境效应、母体遗传效应、母体永久环境效应;模型2考虑母体永久环境效应;模型3考虑母体遗传效应;模型4考虑母体遗传效应和母体永久环境效应;模型5考虑个体永久环境效应和母体遗传效应;模型6考虑个体永久环境效应、母体遗传效应、母体永久环境效应。各模型估计的初生重遗传力为:0.1896~0.3781;断奶重遗传力为:0.2537~0.2890;周岁重遗传力范围:0.2244~0.3225;成年羊体重遗传力范围:0.2205~0.3983;产毛量遗传力为:0.1218~0.1490;羊毛细度遗传力为:0.0983~0.4802;羊毛长度遗传力为:0.1170~0.1311。与模型1相比,模型3对于初生重、断奶重差异显著(P<0.01),对于周岁重、成年羊体重各模型与模型1的似然比检验差异不显著(P>0.05);与模型6相比,模型4、5对于羊毛细度差异显著(P<0.01),模型4对羊毛长度差异显著(P<0.05),对于产毛量各模型与模型6似然比检验差异不显著(P>0.05)。生长性状中初生重、断奶重受母体遗传效应影响显著,周岁重、成年羊体重受母体遗传效应影响不显著;产毛性状中羊毛细度、长度受母体遗传效应影响显著,产毛量受母体遗传效应影响较弱。     

When to rely on maternal effects and when on phenotypic plasticity?

Existing insight suggests that maternal effects have a substantial impact on evolution, yet these predictions assume that maternal effects themselves are evolutionarily constant. Hence, it is poorly understood how natural selection shapes maternal effects in different ecological circumstances. To overcome this, the current study derives an evolutionary model of maternal effects in a quantitative genetics context. In constant environments, we show that maternal effects evolve to slight negative values that result in a reduction of the phenotypic variance (canalization). By contrast, in populations experiencing abrupt change, maternal effects transiently evolve to positive values for many generations, facilitating the transmission of beneficial maternal phenotypes to offspring. In periodically fluctuating environments, maternal effects evolve according to the autocorrelation between maternal and offspring environments, favoring positive maternal effects when change is slow, and negative maternal effects when change is rapid. Generally, the strongest maternal effects occur for traits that experience very strong selection and for which plasticity is severely constrained. By contrast, for traits experiencing weak selection, phenotypic plasticity enhances the evolutionary scope of maternal effects, although maternal effects attain much smaller values throughout. As weak selection is common, finding substantial maternal influences on offspring phenotypes may be more challenging than anticipated.     

Developmental Genetic Analysis of Brown Rice Weight Under Different Environmental Conditions in indica Rice

Analysis of genetic main effects and genotype×environment (GE) interaction effects for brown rice weight (BRW) at four different filling stages in indica rice ( Oryza sativa L.) was conducted for two-year experimental data by using developmental genetic models and corresponding statistical approaches for quantitative traits of seeds in cereal crops. It was indicated that the genetic main effects and their GE interaction effects of triploid endosperm, cytoplasmic and diploid maternal plant genes were important for BRW at different filling stages of rice, especially for endosperm or maternal additive main effects and their additive interaction effects. Because of the higher additive effects and additive interaction effects for BRW at different filling stages, the better improving effects for this trait could be expected by selection in rice breeding. The results of conditional genetic variance components showed that the new expression of quantitative genes in endosperm and maternal plant for BRW was mostly found at all different filling stages of rice. The gene expression, however, was most active at the early filling stages especially for the first (1-7 d) and the second filling stages (8-14 d after flowering). The phenomena that some genes were spasmodically expressible among filling stages of rice were detected for some genetic effects especially for net cytoplasmic main effects or its interaction effects and net dominance main effects. Predicted genetic effects at different filling stages of rice showed that some parents such as V20 and Zuo 5 were better than others for improving the BRW.     

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     

A comparison of maternal effects and current environment on vital rates of Aphis nerii, the milkweed–oleander aphid

Abstract.  1. Non-Mendelian maternal effects, the effects of maternal phenotype or environment on offspring phenotype, have been documented in numerous taxa. By affecting offspring vital rates (birth, death, and movement), maternal effects have the potential to influence population dynamics. However, relatively few studies have directly linked maternal phenotype or environment to offspring vital rates. Additionally, even fewer studies have compared the magnitude of across-generation effects (i.e. maternal effects) to within-generation effects.
2. Because of their telescoping generations, aphids can be strongly influenced by maternal effects. The effects of maternal density and maternal host-plant species on offspring survival, fecundity, and alate formation were investigated experimentally in Aphis nerii , the milkweed–oleander aphid.
3. Additionally, the relative strength of maternal effects were compared with those operating within a generation. Therefore, in another set of experiments, the effects of current density and host-plant species (within-generation effects) on aphid vital rates were examined.
4. While maternal effects were present, within-generation effects were much stronger and more strongly influenced aphid vital rates. Within a generation, aphids exhibited density-dependent survival, fecundity, and alate formation and these effects varied among host-plant species.
5. These results indicate that while maternal effects have the potential to affect population dynamics, this potential is not always met. Additionally, the current environment, not the environment of previous generations, more strongly impacts population dynamics.     

Additive genetic variation and the distribution of QTN effects among sites

Early quantitative genetic theories emphasize the distribution of gene effects at individual loci or the distribution of mutant effects in maintaining quantitative genetic variation, but infrequently stress the distribution of gene effects among loci. In this study, we analyse the effects of the distribution of quantitative trait nucleotides (QTN) effects among sites under artificial and stabilizing selection. Wright's formula is applied to describing the density distribution of allele frequencies of multiple diallelic QTN at the equilibrium of mutation-drift-selection. Our results demonstrate that the distribution of QTN effects among sites can affect additive genetic variation in terms of total additive variance, average gene diversity, per-class contribution of QTN effects and per-QTN contribution. When the distribution of QTN effects among sites is changed from L-shaped to bell-shaped or to be a flatter, both the total additive variance and the average gene diversity are changed. Per-class and per-QTN contributions exhibit different distribution patterns. The L-shaped distribution indicates the predominant role of the aggregative effects from the QTN of small finite effects. The bell-shaped or flatter distributions indicate the predominance of the QTN of intermediate and large effects. These predictions highlight the significance of the distribution of QTN effects among sites in interpreting the maintenance of quantitative genetic variation at the fine genome scale.     

A single climate driver has direct and indirect effects on insect population dynamics

Weather drives population dynamics directly, through effects on vital rates, or indirectly, through effects on the population's competitors, predators or prey and thence on vital rates. Indirect effects may include non-additive interactions with density dependence. Detection of climate drivers is critical to predicting climate change effects, but identification of potential drivers may depend on knowing the underlying mechanisms. For the butterfly Speyeria mormonia, one climate driver, snow melt date, has multiple effects on population growth. Snow melt date in year t has density-dependent indirect effects. Through frost effects, early snow melt decreases floral resources, thence per-capita nectar availability, which determines fecundity in the lab. Snow melt date in year t?+?1 has density-independent direct effects. These effects explain 84% of the variation in population growth rate. One climate parameter thus has multiple effects on the dynamics of a species with non-overlapping generations, with one effect not detectable without understanding the underlying mechanism.     

Analysis of genetic effects on nutrient quality traits in indica rice

Nine cytoplasmic male-sterile lines and five restorer lines were used in an incomplete diallel cross to analyze seed effects, cytoplasmic effects, and maternal gene effects on nutrient quality traits of indica rice (Oryza sauva L.). The results indicated that nutrient quality traits were controlled by cytoplasmic and maternal effects as well as by seed direct effects. Maternal effects for lysine content (LC), lysine index (LI), and the ratio of lysine content to protein content (RLP) were more important than seed direct effects, while protein content (PC) and protein index (PI) were mainly affected by seed direct effects. Cytoplasmic effects accounted for 2.41–20.80% of the total genetic variation and were significant for all nutrient quality traits. Additive genetic effects were much more important than dominance effects for all of the traits studied, so that selection could be applied for these traits in early generations.     

Pièges et artéfacts en imagerie TEP/TDM : intérêts des post-traitements

In PET imaging, quantification of the acquired data can be achieved by using a series of correction techniques to minimize the effects inherent in the imaging process of emission tomography. Quantitative images can be reconstructed after correcting the detected emission data for the presence of random and scattered coincidences, attenuation effects, effects associated with the variable detectors sensitivity, effects related to the geometry of the device and the effects of dead-time. All these effects are well accounted for in the PET imaging market. However, other effects can degrade the quality of the PET images, such as the finite spatial resolution generating partial volume effects, or the patient movements including respiratory and cardiac physiological movements. In the thoracic field, the effects of respiratory motion on PET images are characterized by a loss of detection sensitivity due to the associated blur. Several methods have been developed to correct for these effects, but still without a wide acceptance in clinical routine. These research areas are therefore still very active.     

Relationships between direct predation and risk effects

Risk effects arise when prey alter their behavior in response to predators, and these responses carry costs. Empirical studies have found that risk effects can be large. Nonetheless, studies of predation in vertebrate conservation and management usually consider only direct predation. Given the ubiquity and strength of behavioral responses to predators by vertebrate prey, it is not safe to assume that risk effects on dynamics can be ignored. Risk effects can be larger than direct effects. Risk effects can exist even when the direct rate of predation is zero. Risk effects and direct effects do not necessarily change in parallel. When risk effects reduce reproduction rather than survival, they are easily mistaken for limitation by food supply.     

Genetic and heterosis analysis for cooking quality traits of indica rice in different environments

Genetic effects and genotype×environment (GE) interaction effects on the cooking quality traits of indica rice (Oryza sativa L.) were analyzed based on a genetic model for quantitative traits of triploid endosperm in cereal crops. Nine cytoplasmic male-sterile lines as females and 5 restoring lines as males were used in an incomplete diallel cross over 2 years. The cooking quality traits studied were observed to be mainly controlled by genetic effects, but GE interaction effects, especially for amylose content (AC) and alkali spreading score (ASS), were also indicated. Among the genetic effects, seed direct effects and maternal effects were the main components of AC and ASS, respectively; cytoplasmic effects were the main components of gel consistency (GC). Among the GE interaction effects, AC and ASS were mainly affected by maternal interaction effects and GC by direct interaction effects. Additive effects and/or additive interaction effects were the main factors controlling the performance of rice cooking quality traits except for GC which was affected by dominant interaction effects. For AC and GC, there were seed heterosis and/or maternal heterosis. The predicated genetic effects indicated that four parents were better than the others in improving the rice cooking quality traits of the progenies. It was shown that genetic heterosis and GE interaction heterosis were important, especially for amylose content trait in early season indica rice.     

短季棉早熟不早衰生化性状的遗传分析

用5个早熟不早衰的短季棉品种和5个早衰的短季棉品种进行双列杂交,并对亲本、F1和F2代于2001年和2002年田间试验研究与短季棉早熟不早衰有关的抗氧化系统保护酶(SOD、POD和CAT)、叶绿素及激素(生长素和脱落酸)的遗传特性。结果表明：抗氧化系统保护酶CAT、POD和SOD存在着不同的遗传特性,CAT酶以加性上位性效应为主,其次为显性效应;POD酶以加性效应为主,其次为加性上位性效应;SOD酶活以显性效应为主,其次为加性上位性效应;IAA以显性效应为主,其次为加性效应;ABA以加性效应为主,其次为显性效应。且这些生化性状的遗传率较高,在后代能稳定遗传;同时棉株在不同发育时期体内生化性状表达不同,在花铃期CAT、POD和SOD酶以显性效应为主,其次为加性上位性效应,加性效应表达量很小;棉株体内生化性状的表达也是相互联系、相互制约,CAT酶与POD酶存在着遗传和表型负相关,与SOD酶存在着遗传和表型正相关;POD酶与SOD酶存在着遗传和表型负相关;抗氧化系统保护酶与激素之间存在着复杂的遗传关系。因此,研究生化性状的遗传特性和表达特征,为选育短季棉早熟不早衰新品种和生化性状的QTLs定位提供理论依据。     

食物、捕食和种间竞争对东方田鼠种群动态的作用

采用2×2×2析因实验设计,在野外围栏条件下,测定食物、捕食和竞争物种黑线姬鼠(Apodemus agrarius)对东方田鼠(Microtus fortis)种群动态作用的格局.食物可利用性、捕食及种间竞争的独立作用对种群最小存活数均具有极显著的效应,除捕食与种间竞争的交互作用接近显著水平外,食物与种间竞争、食物与捕食者以及三者间的交互作用均不显著;三类外部因子对种群补充量的独立作用效应均达到极显著水平,且对种群补充量的作用具有累加效应;食物可利用性、捕食及种间竞争对种群繁殖成体的比例具有极显著的作用;三类外部因子对种群幼体与成体的比例具有极显著的作用.对种群年龄结构而言,与捕食者及种间竞争比较,食物可利用性是相对较弱的影响因子,在任何捕食与种间竞争交互作用条件下,食物的作用均不显著;三类外部因子均能显著地影响东方田鼠的体重增长率,但三者的交互作用对其影响不显著;MANOVA结果表明,捕食对成体存活率的作用最强烈,其次,为食物可利用性,种间竞争的作用最弱,但三者的交互作用效应不显著.对幼体的存活时间,除捕食的作用接近显著水平外,食物可利用性及种间竞争的作用均不显著.结果提供了食物可利用性、捕食和种间竞争对东方田鼠种群动态作用的充分证据,验证了食物、捕食和种间竞争对田鼠类种群动态具有独立或累加效应的总假设.     

Effects of residual smoothing on the posterior of the fixed effects in disease-mapping models

Disease-mapping models for areal data often have fixed effects to measure the effect of spatially varying covariates and random effects with a conditionally autoregressive (CAR) prior to account for spatial clustering. In such spatial regressions, the objective may be to estimate the fixed effects while accounting for the spatial correlation. But adding the CAR random effects can cause large changes in the posterior mean and variance of fixed effects compared to the nonspatial regression model. This article explores the impact of adding spatial random effects on fixed effect estimates and posterior variance. Diagnostics are proposed to measure posterior variance inflation from collinearity between the fixed effect covariates and the CAR random effects and to measure each region's influence on the change in the fixed effect's estimates by adding the CAR random effects. A new model that alleviates the collinearity between the fixed effect covariates and the CAR random effects is developed and extensions of these methods to point-referenced data models are discussed.     

Cohort effects and population dynamics

Cohort effects originate from environmental conditions, and can have long‐term consequences for the cohort's performance. It has been proposed that cohort effects tend to increase population fluctuations. However, differences among individuals, which cohort effects introduce into a population, usually have stabilizing effects. There are thus two different predictions regarding the impact of cohort effects on population fluctuations. We argue that it is important to distinguish between environmental variability and its long‐term effects on individual quality, and approach the question with a population model that can include or exclude such effects. We show that the influence of cohort effects depends on the inherent dynamics: cohort effects can have stabilizing effects if dynamics are inherently unstable. However, the most common outcome is destabilization whenever cohort effects act on top of inherently stable dynamics. Intriguingly, both alternatives are due to individual differences affecting the structure of density dependence in a similar way.     

Fitness consequences of maternal and grandmaternal effects

Transgenerational effects are broader than only parental relationships. Despite mounting evidence that multigenerational effects alter phenotypic and life‐history traits, our understanding of how they combine to determine fitness is not well developed because of the added complexity necessary to study them. Here, we derive a quantitative genetic model of adaptation to an extraordinary new environment by an additive genetic component, phenotypic plasticity, maternal and grandmaternal effects. We show how, at equilibrium, negative maternal and negative grandmaternal effects maximize expected population mean fitness. We define negative transgenerational effects as those that have a negative effect on trait expression in the subsequent generation, that is, they slow, or potentially reverse, the expected evolutionary dynamic. When maternal effects are positive, negative grandmaternal effects are preferred. As expected under Mendelian inheritance, the grandmaternal effects have a lower impact on fitness than the maternal effects, but this dual inheritance model predicts a more complex relationship between maternal and grandmaternal effects to constrain phenotypic variance and so maximize expected population mean fitness in the offspring.     

RELATIVE CONTRIBUTION OF ADDITIVE, DOMINANCE, AND IMPRINTING EFFECTS TO PHENOTYPIC VARIATION IN BODY SIZE AND GROWTH BETWEEN DIVERGENT SELECTION LINES OF MICE

Epigenetic effects attributed to genomic imprinting are increasingly recognized as an important source of variation in quantitative traits. However, little is known about their relative contribution to phenotypic variation compared to those of additive and dominance effects, and almost nothing about their role in phenotypic evolution. Here we address these questions by investigating the relative contribution of additive, dominance, and imprinting effects of quantitative trait loci (QTL) to variation in "early" and "late" body weight in an intercross of mice selected for divergent adult body weight. We identified 18 loci on 13 chromosomes; additive effects accounted for most of the phenotypic variation throughout development, and imprinting effects were always small. Genetic effects on early weight showed more dominance, less additive, and, surprisingly, less imprinting variation than that of late weight. The predominance of additivity of QTL effects on body weight follows the expectation that additive effects account for the evolutionary divergence between selection lines. We hypothesize that the appearance of more imprinting effects on late body weight may be a consequence of divergent selection on adult body weight, which may have indirectly selected for alleles showing partial imprinting effects due to their associated additive effects, highlighting a potential role of genomic imprinting in the response to selection.