Indirect Genetic Effects Research Articles

Direct and indirect genetic effects in life-history traits of flour beetles (Tribolium castaneum).

Indirect genetic effects (IGEs) are the basis of social interactions among conspecifics, and can affect genetic variation of nonsocial and social traits. We used flour beetles (Tribolium castaneum) of two phenotypically distinguishable populations to estimate genetic (co)variances and the effect of IGEs on three life-history traits: development time (DT), growth rate (GR), and pupal body mass (BM). We found that GR was strongly affected by social environment with IGEs accounting for 18% of the heritable variation. We also discovered a sex-specific social effect: male ratio in a group significantly affected both GR and BM; that is, beetles grew larger and faster in male-biased social environments. Such sex-specific IGEs have not previously been demonstrated in a nonsocial insect. Our results show that beetles that achieve a higher BM do so via a slower GR in response to social environment. Existing models of evolution in age-structured or stage-structured populations do not account for IGEs of social cohorts. It is likely that such IGEs have played a key role in the evolution of developmental plasticity shown by Tenebrionid larvae in response to density. Our results document an important source of genetic variation for GR, often overlooked in life-history theory.

M. Weinstein and M. A. Lane, Sociality, Hierarchy, Health: Comparative Biodemography: A Collection of Papers.

M. Weinstein and M. A. Lane, Sociality, Hierarchy, Health: Comparative Biodemography: A Collection of Papers.

On the effectiveness of multilevel selection.

Experimental studies of group selection show that higher levels of selection act on indirect genetic effects, making the response to group and community selection qualitatively different from that of individual selection. This suggests that multilevel selection plays a key role in the evolution of supersocial societies. Experiments showing the effectiveness of community selection indicate that we should consider the possibility that selection among communities may be important in the evolution of supersocial species.

Evolution of maternal effect senescence

Increased maternal age at reproduction is often associated with decreased offspring performance in numerous species of plants and animals (including humans). Current evolutionary theory considers such maternal effect senescence as part of a unified process of reproductive senescence, which is under identical age-specific selective pressures to fertility. We offer a novel theoretical perspective by combining William Hamilton's evolutionary model for aging with a quantitative genetic model of indirect genetic effects. We demonstrate that fertility and maternal effect senescence are likely to experience different patterns of age-specific selection and thus can evolve to take divergent forms. Applied to neonatal survival, we find that selection for maternal effects is the product of age-specific fertility and Hamilton's age-specific force of selection for fertility. Population genetic models show that senescence for these maternal effects can evolve in the absence of reproductive or actuarial senescence; this implies that maternal effect aging is a fundamentally distinct demographic manifestation of the evolution of aging. However, brief periods of increasingly beneficial maternal effects can evolve when fertility increases with age faster than cumulative survival declines. This is most likely to occur early in life. Our integration of theory provides a general framework with which to model, measure, and compare the evolutionary determinants of the social manifestations of aging. Extension of our maternal effects model to other ecological and social contexts could provide important insights into the drivers of the astonishing diversity of lifespans and aging patterns observed among species.

Early developmental processes limit socially mediated phenotypic plasticity in an ant

Caste determination in social insects has long been considered to exemplify socially mediated phenotypic plasticity: young larvae can develop into queens or workers depending on the social environment. However, recent studies have challenged this view by showing that, in some species, larval development can be biased early by factors such as larval genotype. We analyzed this issue in the ant species Aphaenogaster senilis. First, we found that the probability that a larva develops into a queen or a worker varies consistently among colonies. Next, we conducted a cross-fostering experiment in which larvae from colonies with relatively low queen production were transferred to colonies with relatively high queen production and vice versa. The results show a strong significant interaction between early determination and worker control of larval caste fate. Therefore, our study shows that socially mediated phenotypic plasticity is limited by processes occurring at an early developmental stage that possibly include direct or indirect genetic effects or non-genetic maternal effects.

An analysis of indirect genetic effects on adult body weight of the Pacific white shrimp Litopenaeus vannamei at low rearing density.

BackgroundOur aim was to estimate the genetic parameters for the direct genetic effect (DGE) and indirect genetic effects (IGE) on adult body weight in the Pacific white shrimp. IGE is the heritable effect of an individual on the trait values of its group mates.MethodsTo examine IGE on body weight, 4725 shrimp from 105 tagged families were tested in multiple small test groups (MSTG). Each family was separated into three groups (15 shrimp per group) that were randomly assigned to 105 concrete tanks with shrimp from two other families. To estimate breeding values, one large test group (OLTG) in a 300 m2 circular concrete tank was used for the communal rearing of 8398 individuals from 105 families. Body weight was measured after a growth-test period of more than 200 days. Variance components for body weight in the MSTG programs were estimated using an animal model excluding or including IGE whereas variance components in the OLTG programs were estimated using a conventional animal model that included only DGE. The correlation of DGE between MSTG and OLTG programs was estimated by a two-trait animal model that included or excluded IGE.ResultsHeritability estimates for body weight from the conventional animal model in MSTG and OLTG programs were 0.26 ± 0.13 and 0.40 ± 0.06, respectively. The log likelihood ratio test revealed significant IGE on body weight. Total heritable variance was the sum of direct genetic variance (43.5 %), direct–indirect genetic covariance (2.1 %), and indirect genetic variance (54.4 %). It represented 73 % of the phenotypic variance and was more than two-fold greater than that (32 %) obtained by using a classical heritability model for body weight. Correlations of DGE on body weight between MSTG and OLTG programs were intermediate regardless of whether IGE were included or not in the model.ConclusionsOur results suggest that social interactions contributed to a large part of the heritable variation in body weight. Small and non-significant direct–indirect genetic correlations implied that neutral or slightly cooperative heritable interactions, rather than competition, were dominant in this population but this may be due to the low rearing density.

Predicting direct and indirect breeding values for survival time in laying hens using repeated measures.

BackgroundMinimizing bird losses is important in the commercial layer industry. Selection against mortality is challenging because heritability is low, censoring is high, and individual survival depends on social interactions among cage members. With cannibalism, mortality depends not only on an individual’s own genes (direct genetic effects; DGE) but also on genes of its cage mates (indirect genetic effects; IGE). To date, studies using DGE–IGE models have focussed on survival time but their shortcomings are that censored records were considered as exact lengths of life and models assumed that IGE were continuously expressed by all cage members even after death. However, since dead animals no longer express IGE, IGE should ideally be time-dependent in the model. Neglecting censoring and timing of IGE expression may reduce accuracy of estimated breeding values (EBV). Thus, our aim was to improve prediction of breeding values for survival time in layers that present cannibalism.MethodsWe considered four DGE–IGE models to predict survival time in layers. One model was an analysis of survival time and the three others treated survival in consecutive months as a repeated binomial trait (repeated measures models). We also tested whether EBV were improved by including timing of IGE expression in the analyses. Approximate EBV accuracies were calculated by cross-validation. The models were fitted to survival data on two purebred White Leghorn layer lines W1 and WB, each having monthly survival records over 13 months.ResultsIncluding the timing of IGE expression in the DGE–IGE model reduced EBV accuracy compared to analysing survival time. EBV accuracy was higher when repeated measures models were used. However, there was no universal best model. Using repeated measures instead of analysing survival time increased EBV accuracy by 10 to 21 and 2 to 12 % for W1 and WB, respectively. We showed how EBV and variance components estimated with repeated measures models can be translated into survival time.ConclusionsOur results suggest that prediction of breeding values for survival time in laying hens can be improved using repeated measures models. This is an important result since more accurate EBV contribute to higher rates of genetic gain.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0152-2) contains supplementary material, which is available to authorized users.

Comparison of designs for estimating genetic parameters and obtaining response to selection for social interaction traits in aquaculture

Social interactions among individuals may affect individual productivity and welfare in aquaculture. Since social effects may have a genetic component, known as an indirect genetic effect (IGE), genetic selection may be a promising tool to simultaneously improve welfare and productivity in aquaculture. Here we compare two experimental designs that have been previously proposed for the genetic improvement of socially affected traits. We used stochastic simulations to compare a design where each group consisted of members of two families (2-FAM) with a design where each group consisted of members of three families (3-FAM). The 2-FAM and 3-FAM designs were compared using an equal number of groups (96 groups). The group size, i.e., number of individuals within each group, was either 30 or 60 individuals. Both designs were compared for the precision of estimated direct and social genetic parameters and for response to selection, either with or without a restriction on the rate of inbreeding. Four different schemes with a low variance (heritability for social effects or hS2=0.1), a moderate variance (hS2=0.3), or a high variance (hS2=0.5) of the social genetic effects, and a negative correlation between direct and social genetic effects (rAD,S=−0.6) were compared. The negative rAD,S indicates competition between group mates. Differences in precision of estimated genetic parameters between both designs were small. At low hS2 and group size of 30, the 2-FAM design was superior with respect to precision of social additive genetic variance. When the social genetic variance was small, a larger group size, e.g. 60 is recommended. The 2-FAM design resulted in a higher accuracy of selection for social and total genetic effects, but also in a higher rate of inbreeding compared to the 3-FAM design. When the rate of inbreeding was restricted to ~2%, the total response to selection was significantly higher for the 3-FAM design. In conclusion, the 2-FAM and 3-FAM designs differ little in accuracy of the direct and social genetic parameter estimates, while the 3-FAM design is superior with respect to the response to selection at a fixed rate of inbreeding. This study is particularly important for making decisions regarding experimental design when breeding for social genetic effects in aquaculture. Statement of relevanceCommunal or family rearing with a large number of animals in a group is common practice in aquaculture. Large variation in body size, which may inflate competition for feed, is generally observed in the communal rearing tank. In addition, cannibalistic or aggressive behaviour is frequently observed in a large variety of fish species. So far, the issue is addressed by management measures, such as size grading, which may be labour intensive. Sustainable solutions through selective breeding have not been tested.Previous studies compared two experimental designs for social interaction traits; groups composed of two families (2-FAM) and three families (3-FAM) with groups composed at random and found that the 2-FAM and 3-FAM designs were better with respect to genetic parameter estimates than designs with groups composed at random. It is however still unknown whether the 2-FAM or the 3-FAM design is better. Previous studies did not consider the rate of inbreeding when studying the designs. This paper describes the results from a comparison of the two experimental designs for estimating genetic parameters and obtaining response to selection, taking into account the rate of inbreeding. As such, this paper should be of interest to a broad readership including those interested in aquaculture genetics.

Genetic and non-genetic indirect effects for harvest weight in the GIFT strain of Nile tilapia (Oreochromis niloticus)

Trait values of individuals are affected not only by their genetic makeup, but also by environmental factors and interactions with other individuals. The heritable effect of an individual on the trait values of other individuals it interacts with is known as an indirect genetic effect (IGE). Such IGEs may affect response to selection. Fish selected for high growth rate, for example, have been shown to be more aggressive and competitive, which may reduce the observed response in growth rate. The main objective of this study is to quantify the genetic and non-genetic indirect effects for harvest weight in the GIFT strain of Nile tilapia. A total of 6330 fish with harvest weight information were used to estimate genetic and non-genetic parameters. A bivariate analysis of harvest weight and survival was conducted by fitting different mixed models to investigate the presence of IGEs and other non-genetic effects. The full set of genetic parameters could not be estimated simultaneously with the inclusion of maternal common environmental effects. A confounding between maternal common environmental effects and direct genetic effects resulted from the mating strategy, where one sire was mated to only one or two dams. A 1 male to 2 females mating design is common in aquaculture, but it has limited power to estimate genetic parameters. Models without maternal common environmental effects showed significant IGE on harvest weight, which contributed 48% of total heritable variance. Models with maternal common environmental effects suggested the presence of IGE. The direct–indirect genetic correlation for harvest weight was negative (−0.38±0.19), indicating that traditional selection, if performed in an environment where the fish have to compete with each other for the resources, will increase competition. A strongly negative genetic correlation between direct effects on survival and indirect effects on harvest weight (−0.79±0.30) showed that individuals with better genes for survival suppressed growth rate of their social partners. Our results suggest that heritable competitive interactions affect harvest weight in Nile tilapia. Hence, breeding schemes may need to be adapted to avoid an increase in aggressiveness due to selection for growth rate in a competitive environment. Further studies are required to investigate the relevance of IGE and its implications on different systems of commercial aquaculture production. Statement of relevanceSociable fish will help to improve aquaculture production.

Indirect genetic effects and the dynamics of social interactions.

BackgroundIndirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves.ResultsIn our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.

Estimation of indirect genetic effects in group‐housed mink (Neovison vison) should account for systematic interactions either due to kin or sex

Social interactions among individuals are abundant, both in wild and in domestic populations. With social interactions, the genes of an individual may affect the trait values of other individuals, a phenomenon known as indirect genetic effects (IGEs). IGEs can be estimated using linear mixed models. Most IGE models assume that individuals interact equally to all group mates irrespective of relatedness. Kin selection theory, however, predicts that an individual will interact differently with family members versus non-family members. Here, we investigate kin- and sex-specific non-genetic social interactions in group-housed mink. Furthermore, we investigated whether systematic non-genetic interactions between kin or individuals of the same sex influence the estimates of genetic parameters. As a second objective, we clarify the relationship between estimates of the traditional IGE model and a family-based IGE model proposed in a previous study. Our results indicate that male siblings in mink show different non-genetic interactions than female siblings in mink and that this may impact the estimation of genetic parameters. Moreover, we have shown how estimates from a family-based IGE model can be translated to the ordinary direct-indirect model and vice versa. We find no evidence for genetic differences in interactions among related versus unrelated mink.

The genetics of intra‐ and interspecific competitive response and effect in a local population of an annual plant species

Summary While competition is recognized as a major factor responsible for plant community dynamics, the genetics of intra‐ and interspecific competitive ability of a target species (i.e. level of intra‐population genetic variation, identity of phenotypic traits under selection and genetic bases) still deserves a deeper investigation at the local spatial scale by considering both numerous genotypes and several interacting species. In this study, we tested whether the genetics of competitive response and effect in Arabidopsis thaliana was dependent on the competitive environment at both the intraspecific and interspecific levels. We used a mapping population of 48 accessions (i) that maximize the genetic diversity of a local population of A. thaliana and (ii) that have been genotyped for 168 503 single nucleotide polymorphisms. In a common garden experiment, those 48 accessions were grown in six competitive environments: the absence of competition, intraspecific competition and interspecific competition with four species frequently associated with A. thaliana in natural plant communities (i.e. Poa annua, Stellaria media, Trifolium repens and Veronica arvensis). A suite of nine phenotypic traits, including a proxy of fitness, were scored on each target A. thaliana plant and the above‐ground dry biomass of its corresponding competitor was estimated. We first showed that crossing reaction norms of competitive response (A. thaliana performance) and effect (competitor biomass) might promote maintenance of genetic variation in a local population of A. thaliana and species coexistence at a fine spatial scale. By estimating genotypic gradients of selection, we then demonstrated that the optimal phenotypic strategies in response to competition depend on the identity of the competitor species. Finally, a genomewide association mapping approach highlighted that genomic regions associated with direct genetic effects were (i) dependent on the competitor species and (ii) different from genomic regions associated with interspecific indirect genetic effects. While a first step, this study highlighted the power of adding ecology to genomics in A. thaliana to identify genetic bases underlying micro‐geographic adaptation to competition. Next‐generation sequencing technologies will undoubtedly facilitate the discovery of molecular and genetic mechanisms underlying competitive ability in other plant species, and thereby the prediction of evolutionary trajectories of plant communities.

Methods to address poultry robustness and welfare issues through breeding and associated ethical considerations.

As consumers and society in general become more aware of ethical and moral dilemmas associated with intensive rearing systems, pressure is put on the animal and poultry industries to adopt alternative forms of housing. This presents challenges especially regarding managing competitive social interactions between animals. However, selective breeding programs are rapidly advancing, enhanced by both genomics and new quantitative genetic theory that offer potential solutions by improving adaptation of the bird to existing and proposed production environments. The outcomes of adaptation could lead to improvement of animal welfare by increasing fitness of the animal for the given environments, which might lead to increased contentment and decreased distress of birds in those systems. Genomic selection, based on dense genetic markers, will allow for more rapid improvement of traits that are expensive or difficult to measure, or have a low heritability, such as pecking, cannibalism, robustness, mortality, leg score, bone strength, disease resistance, and thus has the potential to address many poultry welfare concerns. Recently selection programs to include social effects, known as associative or indirect genetic effects (IGEs), have received much attention. Group, kin, multi-level, and multi-trait selection including IGEs have all been shown to be highly effective in reducing mortality while increasing productivity of poultry layers and reduce or eliminate the need for beak trimming. Multi-level selection was shown to increases robustness as indicated by the greater ability of birds to cope with stressors. Kin selection has been shown to be easy to implement and improve both productivity and animal well-being. Management practices and rearing conditions employed for domestic animal production will continue to change based on ethical and scientific results. However, the animal breeding tools necessary to provide an animal that is best adapted to these changing conditions are readily available and should be used, which will ultimately lead to the best possible outcomes for all impacted.

The prospects of selection for social genetic effects to improve welfare and productivity in livestock.

Social interactions between individuals living in a group can have both positive and negative effects on welfare, productivity, and health of these individuals. Negative effects of social interactions in livestock are easier to observe than positive effects. For example, laying hens may develop feather pecking, which can cause mortality due to cannibalism, and pigs may develop tail biting or excessive aggression. Several studies have shown that social interactions affect the genetic variation in a trait. Genetic improvement of socially-affected traits, however, has proven to be difficult until relatively recently. The use of classical selection methods, like individual selection, may result in selection responses opposite to expected, because these methods neglect the effect of an individual on its group mates (social genetic effects). It has become clear that improvement of socially-affected traits requires selection methods that take into account not only the direct effect of an individual on its own phenotype but also the social genetic effects, also known as indirect genetic effects, of an individual on the phenotypes of its group mates. Here, we review the theoretical and empirical work on social genetic effects, with a focus on livestock. First, we present the theory of social genetic effects. Subsequently, we evaluate the evidence for social genetic effects in livestock and other species, by reviewing estimates of genetic parameters for direct and social genetic effects. Then we describe the results of different selection experiments. Finally, we discuss issues concerning the implementation of social genetic effects in livestock breeding programs. This review demonstrates that selection for socially-affected traits, using methods that target both the direct and social genetic effects, is a promising, but sometimes difficult to use in practice, tool to simultaneously improve production and welfare in livestock.

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

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

Selection based on indirect genetic effects for growth, environmental enrichment and coping style affect the immune status of pigs.

Pigs living in intensive husbandry systems may experience both acute and chronic stress through standard management procedures and limitations in their physical and social environment, which may have implications for their immune status. Here, the effect of a new breeding method where pigs were selected on their heritable influence on their pen mates' growth, and environmental enrichment on the immune status of pigs was investigated. Hereto, 240 pigs with a relatively positive genetic effect on the growth of their pen mates (+SBV) and 240 pigs with a relatively negative genetic effect on the growth of their pen mates (−SBV) were housed in barren or straw-enriched pens from 4 to 23 weeks of age (n = 80 pens in total). A blood sample was taken from the pigs before, three days after a 24 h regrouping test, and at week 22. In addition, effects of coping style, as assessed in a backtest, and gender were also investigated. Mainly, +SBV were found to have lower leukocyte, lymphocyte and haptoglobin concentrations than -SBV pigs. Enriched housed pigs had a lower neutrophil to lymphocyte (N:L) ratio and lower haptoglobin concentrations, but had higher antibody titers specific for Keyhole Limpet Hemocyanin (KLH) than barren housed pigs. No interactions were found between SBV class and housing. Furthermore, pigs with a proactive coping style had higher alternative complement activity and, in the enriched pens, higher antibody titers specific for KLH than pigs with a reactive coping style. Lastly, females tended to have lower leukocyte, but higher haptoglobin concentrations than castrated males. Overall, these results suggest that +SBV pigs and enriched housed pigs were less affected by stress than -SBV and barren housed pigs, respectively. Moreover, immune activation might be differently organized in individuals with different coping styles and to a lesser extent in individuals of opposite genders.

Indirect genetic effects for growth rate in domestic pigs alter aggressive and manipulative biting behaviour.

Indirect genetic effects (IGEs) are heritable effects of an individual on phenotypic values of others, and may result from social interactions. We determined the behavioural consequences of selection for IGEs for growth (IGEg) in pigs in a G × E treatment design. Pigs (n = 480) were selected for high versus low IGEg with a contrast of 14 g average daily gain and were housed in either barren or straw-enriched pens (n = 80). High IGEg pigs showed from 8 to 23 weeks age 40 % less aggressive biting (P = 0.006), 27 % less ear biting (P = 0.03), and 40 % less biting on enrichment material (P = 0.005). High IGEg pigs had a lower tail damage score (high 2.0; low 2.2; P = 0.004), and consumed 30 % less jute sacks (P = 0.002). Selection on high IGEg reduced biting behaviours additive to the, generally much larger, effects of straw-bedding (P < 0.01), with no G × E interactions. These results show opportunities to reduce harmful biting behaviours in pigs.

Indirect genetic effects from competition in the clonal herb Sedum album (Crassulaceae).

Recent years have seen increasing interest in indirect genetic effects, i.e. influences on the phenotype that depend on the genotype of other conspecific individuals; however, the empirical evidence for such effects is still limited, especially in wild plant species. The present study of the clonal herb Sedum album assessed direct and indirect genetic effects on performance-related traits in a 4-year experiment with clonally replicated genotypes, grown in pairs and differing in anthocyanin pigmentation to allow separation of individuals during data collection. In agreement with the existence of indirect genetic effects, the experimentally-paired plants not only expressed their own genotype but were also affected by the genotype of their pair mate. The effect of neighbour genotype explained up to one-fourth of the variation in performance and most likely resulted from competition, imposed by the close physical contact between paired individuals and the limiting conditions used in the garden environment. Indirect genetic effects from competition have the potential to enhance the efficacy of group-level selection relative to individual selection, given the nutrient-poor and spatially-confined substrate available to plants of S. album in the natural habitat.

Boar taint in entire male pigs: a genomewide association study for direct and indirect genetic effects on androstenone.

Androstenone is one of the compounds causing boar taint of pork and is highly heritable (approximately 0.6). Recently, indirect genetic effects (IGE; also known as associative effects or social genetic effects) were found for androstenone, meaning that pen mates (boars) affect each other's androstenone level genetically. Similar to estimating variance components with a direct-indirect animal model, direct and indirect genetic SNP effects can be estimated for androstenone. This study aims to detect SNP with significant direct genetic effects and IGE on androstenone. The dataset consisted of 1,282 noncastrated boars (993 boars genotyped) from 184 groups of pen members. After quality control, 46,421 SNP were included in the analysis. One model for single-SNP regression was fitted, where both the direct SNP effect of the individual itself and the indirect SNP effects of its pen mates were included. None of the SNP (direct or indirect) were found genomewide significant. One QTL on SSC6 was chromosome-wide significant for the direct effect. A single SNP on SSC9 and 2 regions and a single SNP on SSC14 were found for the indirect effect. A backwards elimination method and haplotype analysis were used to quantify the variance explained by the SNP. The backwards elimination method identified 4 independent regions affecting androstenone. The QTL on SSC6 explained 2.1 and 2.6% of the phenotypic variance using the backwards elimination method or the haplotype analysis. The QTL on SSC14 explained 3.4 and 2.7% of the phenotypic variance using the backwards elimination method or the haplotype analysis. The single association on SSC9 explained 2.2% of the phenotypic variance. All significant QTL together explained 7 to 8% of phenotypic variance and 40 to 44% of the total genetic variance available for response to selection. Besides the newly discovered QTL and the confirmation of known QTL, this study also presents a methodology to model SNP for IGE.

Indirect genetic effects underlie oxygen-limited thermal tolerance within a coastal population of chinook salmon.

With global temperatures projected to surpass the limits of thermal tolerance for many species, evaluating the heritable variation underlying thermal tolerance is critical for understanding the potential for adaptation to climate change. We examined the evolutionary potential of thermal tolerance within a population of chinook salmon (Oncorhynchus tshawytscha) by conducting a full-factorial breeding design and measuring the thermal performance of cardiac function and the critical thermal maximum (CTmax) of offspring from each family. Additive genetic variation in offspring phenotype was mostly negligible, although these direct genetic effects explained 53% of the variation in resting heart rate (fH). Conversely, maternal effects had a significant influence on resting fH, scope for fH, cardiac arrhythmia temperature and CTmax. These maternal effects were associated with egg size, as indicated by strong relationships between the mean egg diameter of mothers and offspring thermal tolerance. Because egg size can be highly heritable in chinook salmon, our finding indicates that the maternal effects of egg size constitute an indirect genetic effect contributing to thermal tolerance. Such indirect genetic effects could accelerate evolutionary responses to the selection imposed by rising temperatures and could contribute to the population-specific thermal tolerance that has recently been uncovered among Pacific salmon populations.