Heritability and genetic correlations explained by common SNPs for metabolic syndrome traits

We used a bivariate (multivariate) linear mixed-effects model to estimate the narrow-sense heritability (h(2)) and heritability explained by the common SNPs (h(g)(2)) for several metabolic syndrome (MetS) traits and the genetic correlation between pairs of traits for the Atherosclerosis Risk in Communities (ARIC) genome-wide association study (GWAS) population. MetS traits included body-mass index (BMI), waist-to-hip ratio (WHR), systolic blood pressure (SBP), fasting glucose (GLU), fasting insulin (INS), fasting trigylcerides (TG), and fasting high-density lipoprotein (HDL). We found the percentage of h(2) accounted for by common SNPs to be 58% of h(2) for height, 41% for BMI, 46% for WHR, 30% for GLU, 39% for INS, 34% for TG, 25% for HDL, and 80% for SBP. We confirmed prior reports for height and BMI using the ARIC population and independently in the Framingham Heart Study (FHS) population. We demonstrated that the multivariate model supported large genetic correlations between BMI and WHR and between TG and HDL. We also showed that the genetic correlations between the MetS traits are directly proportional to the phenotypic correlations.     

Heritability of the backtest response in piglets and its genetic correlations with production traits

The backtest response of a pig gives an indication of its coping style, that is, its preferred strategy to cope with stressful situations, which may in turn be related to production traits. The objective of this study was therefore to estimate the heritability of the backtest response and estimate genetic correlations with production traits (birth weight, growth, fat depth and loin depth). The backtest was performed by placing the piglet on its back for 60 s and the number of struggles (NrS) and vocalizations (NrV), and the latency to struggle and vocalize (LV) was recorded. In total, 992 piglets were subjected to the backtest. Heritability estimates for backtest traits were statistically moderate (although high for behavioral traits), with LV having the highest heritability estimate (0.56±0.10, P<0.001) and NrS having the lowest estimate (0.37±0.09, P<0.001). Backtest traits also had high genetic correlations with each other, with vocalization traits (NrV and LV) having the highest (−0.94±0.03, P<0.001), and NrS with NrV the lowest correlation (0.70±0.09, P<0.001). No significant correlations were found between backtest traits and production traits, but correlations between NrS and birth weight (−0.38±0.25), and NrV and loin depth (−0.28±0.19) approached significance (P=0.07). More research into genotype-by-environment interactions may be needed to assess possible connections between backtest traits and production traits, as this may depend on the circumstances (environment, experiences, etc.). In conclusion, heritability estimates of backtest traits are high and it would therefore be possible to select for them. The high genetic correlations between backtest traits indicate that it may be possible to only consider one or two traits for characterization and selection purposes. There were no significant genetic correlations found between backtest traits and production traits, although some of the correlations approached significance and hence warrant further research.     

Heritability and cross-sex genetic correlations of early-life circulating testosterone levels in a wild mammal

Testosterone is an important hormone that has been shown to have sex-specific links to fitness in numerous species. Although testosterone concentrations vary substantially between individuals in a population, little is known about its heritable genetic basis or between-sex genetic correlations that determine its evolutionary potential. We found circulating neonatal testosterone levels to be both heritable (0.160 ± 0.064 s.e.) and correlated between the sexes (0.942 ± 0.648 s.e.) in wild red deer calves (Cervus elaphus). This may have important evolutionary implications if, as in adults, the sexes have divergent optima for circulating testosterone levels.     

Factorial correspondence analysis of fear-related behaviour traits in Japanese quail

Factorial correspondence analysis was performed on 341 quails from a F2 cross between two lines divergently selected on the duration of tonic immobility over 29 generations. Several fear- or stress-related traits were recorded, i.e. tonic immobility duration, number of inductions needed to induce tonic immobility, open-field behaviour (time spent walking, latency before first movement and number of defecations), asymmetry of tibia lengths and corticosterone concentration after restraint stress. Variables were categorised in classes and analysed by factorial correspondence analysis. The first axis was mostly described by open-field behaviour, and the second by tonic immobility traits (duration of tonic immobility and number of inductions), which showed that these behaviours were almost independent. No relationship was found between axes of the factorial correspondence analysis and corticosterone concentration or asymmetry of tibia lengths, showing that these variables reflected other characteristics of stress susceptibility than those described by tonic immobility and open-field behaviour. These results show that reaction to stress of quails is a multidimensional trait and cannot be summarised by one trait.     

Heritability of shoulder ulcers and genetic correlations with mean piglet weight and sow body condition

The objective of this paper was to estimate the heritability for shoulder ulcers and the genetic correlations between shoulder ulcers, mean piglet weight and sow body condition. The analyses were based on information on 5549 Norwegian Landrace sows and their 7614 purebred litters. The genetic analysis was performed using the Gibbs sampling method. Shoulder ulcers were analyzed as a threshold trait. Sow body condition and mean piglet weight were analyzed as linear traits. The heritability of shoulder ulcers was estimated at 0.25 (s.d. = 0.03). The heritability for sow body condition was estimated at 0.14 (s.d. = 0.02) and that for mean piglet weight at 0.23 (s.d. = 0.02). The genetic correlation between shoulder ulcers and sow body condition was negative (-0.59, s.d. = 0.09). The genetic correlation between shoulder ulcers and mean piglet weight was positive (0.23, s.d. = 0.10) and the genetic correlation between sow body condition and mean piglet weight was negative (-0.24, s.d. = 0.10).     

Architectural evolution and its implications for domestication in grasses

BACKGROUND: The cereal crops domesticated from grasses provide a large percentage of the calories consumed by humans. Domestication and breeding in individual cereals has historically occurred in isolation, although this is rapidly changing with comparative genomics of the sequenced or soon-to-be sequenced genomes of rice, sorghum, maize and Brachypodium. Genetic information transferred through genomic comparisons is helping our understanding of genetically less tractable crops such as the hexaploid wheats and polyploid sugarcane, as well as the approx. 10 000 species of wild grasses. In turn, phylogenetic analysis helps put our knowledge of the morphology of cereal crops into an evolutionary context. GRASS ARCHITECTURE: Domestication often involves a change in the pattern and timing of branching, which affects both vegetative and inflorescence architecture, and ultimately yield. Cereal grasses exhibit two main forms of vegetative architecture: the pooid and erhartoid cereals such as wheat and rice have multiple basal tillers, while panicoid cereals such as maize, sorghum and the millets have few tillers or even only a single main stem. These differences are reflected in the differences between the wild species of pooid and some erhartoid grasses, which emphasize basal branching over axillary branching, and the panicoid grasses, where axillary branching is more frequently found. A combination of phylogenetic and genomic analysis is beginning to reveal the similarities and differences between different cereal crops, and relate these to the diversity of wild grasses to which they are related. Recent work on genes controlling branching emphasizes that developmental genetics needs to be viewed in both an evolutionary and ecological framework, if it is to be useful in understanding how morphology evolves. Increasingly, exploring the phylogenetic context of the crop grasses will suggest new ways to identify and create combinations of morphological traits that will best suit our future needs.     

Heritability and genetic correlations of metabolic disease-related phenotypes in Mexico: preliminary report from the GEMM Family Study

Cardiovascular disease (CVD) is a major cause of mortality in the Republic of Mexico, and metabolic syndrome, a complex of CVD risk factors, is increasingly prevalent. To date, however, there have been few studies of the genetic epidemiology of metabolic syndrome in Mexico. As a first step in implementing the GEMM Family Study, a large, multicenter collaborative study, we recruited 375 individuals in 21 extended families, without ascertainment on disease, at 9 medical institutions across Mexico. Participants were measured for anthropometric (stature, weight, waist circumference) and hemodynamic (blood pressure, heart rate) phenotypes; glucose, cholesterol, and triglyceride levels were measured in fasting blood. Variance components-based quantitative genetic analyses were performed using SOLAR. All phenotypes except diastolic blood pressure were significantly heritable. Consistent with the definition of metabolic syndrome, many phenotypes exhibited significant environmental correlation, and significant genetic correlations were found between measures of adiposity and fasting glucose and fasting triglyceride levels. These preliminary data represent the first heritability estimates for many of these phenotypes in the Republic of Mexico and indicate that this study design offers excellent power for future gene discovery relative to metabolic disease.     

Heritability estimates and genetic correlations for body weight and scrotal circumference adjusted to 12 and 18 months of age for male Nellore cattle

Heritability estimates and genetic correlations were obtained for body weight and scrotal circumference, adjusted, respectively, to 12 (BW12 and SC12) and 18 (BW18 and SC18) months of age, for 10 742 male Nellore cattle. The adjustments to SC12 and SC18 were made using a nonlinear logistic function, while BW12 and BW18 were obtained by linear adjustment. The contemporary groups (CGs) were defined from animals born on the same farm, in the same year and birth season. The mean heritability estimates obtained using the restricted maximum likelihood method in bi-trait analysis were 0.25, 0.25, 0.29 and 0.42 for BW12, BW18, SC12 and SC18, respectively. The genetic correlations were 0.30 ± 0.11, 0.21 ± 0.13, 0.21 ± 0.11, -0.08 ± 0.15, 0.16 ± 0.12 and 0.89 ± 0.04 between the traits BW12 and BW18; BW12 and SC12; BW12 and SC18; BW18 and SC12; BW18 and SC18; and SC12 and SC18. The heritability for SC18 was considerably greater than for SC12, suggesting that this should be included as a selection criterion. The genetic correlation between BW18 and SC12 was close to zero, indicating that these traits did not influence each other. The contrary occurred between SC12 and SC18, indicating that selection using one of these could alter the other. Because of the mean magnitudes of heritabilities in the various measurements of weight and scrotal perimeter, it is suggested that the practice of individual selection for these traits is possible.     

Heritability of and correlations among genotype-by-environment stability statistics for grain yield in bread wheat

Several genotype-by-environment stability measures are in use, but little information exists about their inheritance or genetic inter-relationships. Among those measures in common use are the linear regression coefficient (b), deviations from regression (s_b), coefficient of determination (R²), coefficient of phenotypic variation (CPV) and, more recently, interaction principal components (IPCA) of the additive-main-effect-and-multiplicative-interaction (AMMI) model. Because of the factorial structure of the data, the diallel cross is well suited to study these parameters and their relationship to quantitative traits. For this study a complete diallel cross, derived by mating eight lines from a broad based bread wheat breeding population, was grown for several growing seasons at two Ugandan locations, one of which was prone to yellow rust. Stability parameters and grain yield were measured for each cross. CPV had the highest narrow-sense heritability (h²=0.522) followed by IPCA1 of the AMMI (h²=0.461). Lowest narrow-sense heritabilities were calculated for b and R² (h²=0.150 and 0.100 respectively). There were high additive genetic correlations (r_A) between grain yield and CPV (r_A=−0.933), grain yield and IPCA1 (r_A=0.707), and grain yield and IPCA2 (r_A=0.751). The genetic association between CPV and IPCA1 was also high and negative (r_A= −0.934). These results suggest that it may be possible to select simultaneously for high and stable grain yield in this broad-based bread wheat breeding pool by selecting outyielders that exhibit a low CPV. Received: 25 July 2000 / Accepted: 7 December 2000     

Potential genetic variance and the domestication of maize

Since Darwin, there has been a long and arduous struggle to understand the source and maintenance of natural genetic variation and its relationship to phenotype. The reason that this task is so difficult is that it requires integration of detailed, and as yet incomplete, knowledge from several biological disciplines, including evolutionary, population, and developmental genetics. In this 'post-genomic' era, it is relatively easy to identify differences in the DNA sequence between individuals. However, the task remains to delineate how this abundant genetic diversity actually contributes to phenotypic diversity. This necessitates tackling the problem of hidden genetic variation. Genetic polymorphisms can be conditionally cryptic, but have the potential to contribute to phenotypic variation in particular genetic backgrounds or under specific environmental conditions. A recent paper by Lauter and Doebley highlights the contribution of hidden genetic variation to traits characterizing the morphological evolution of modern maize from its wild grass-like progenitor teosinte.1 This work is the first to demonstrate hidden variance for selected (agronomically 'adaptive') traits in a well-characterized model for morphological evolution.     

Implications of domestication and rearing conditions for the behaviour of cultivated fishes

Farmed fishes are often selectively bred for desirable production traits, such as rapid growth, that brings with them behavioural differences. In addition, the striking differences in the environment experienced by wild and cultured fishes offers considerable scope both for unplanned, natural selection for different inherited behavioural phenotypes and for behavioural differences arising from differential experience. In this paper, the evidence that such processes have produced behavioural differences between wild and cultured fishes is reviewed in relation to feeding, antipredator responses, aggression and reproductive behaviour. The reported findings are discussed in relation to the concept of 'behavioural syndromes', or suites of co‐varying behavioural traits that adapt individuals of the same population to spatial and temporal variation in selection regimes. The implications of the behaviour of cultured fishes for their welfare in production cages, for the environmental impact of escapees on wild stocks and for the success of hatchery‐based restocking programmes are considered. The review inevitably concentrates on salmonids, in which such phenomena have been intensively researched.     

Heritability and genetic correlations of personality traits in a wild population of yellow‐bellied marmots (Marmota flaviventris)

Describing and quantifying animal personality is now an integral part of behavioural studies because individually distinctive behaviours have ecological and evolutionary consequences. Yet, to fully understand how personality traits may respond to selection, one must understand the underlying heritability and genetic correlations between traits. Previous studies have reported a moderate degree of heritability of personality traits, but few of these studies have either been conducted in the wild or estimated the genetic correlations between personality traits. Estimating the additive genetic variance and covariance in the wild is crucial to understand the evolutionary potential of behavioural traits. Enhanced environmental variation could reduce heritability and genetic correlations, thus leading to different evolutionary predictions. We estimated the additive genetic variance and covariance of docility in the trap, sociability (mirror image stimulation), and exploration and activity in two different contexts (open‐field and mirror image simulation experiments) in a wild population of yellow‐bellied marmots (Marmota flaviventris). We estimated both heritability of behaviours and of personality traits and found nonzero additive genetic variance in these traits. We also found nonzero maternal, permanent environment and year effects. Finally, we found four phenotypic correlations between traits, and one positive genetic correlation between activity in the open‐field test and sociability. We also found permanent environment correlations between activity in both tests and docility and exploration in the MIS test. This is one of a handful of studies to adopt a quantitative genetic approach to explain variation in personality traits in the wild and, thus, provides important insights into the potential variance available for selection.     

Wheat genetic diversity trends during domestication and breeding

It has been claimed that plant breeding reduces genetic diversity in elite germplasm which could seriously jeopardize the continued ability to improve crops. The main objective of this study was to examine the loss of genetic diversity in spring bread wheat during (1) its domestication, (2) the change from traditional landrace cultivars (LCs) to modern breeding varieties, and (3) 50 years of international breeding. We studied 253 CIMMYT or CIMMYT-related modern wheat cultivars, LCs, and Triticum tauschii accessions, the D-genome donor of wheat, with 90 simple sequence repeat (SSR) markers dispersed across the wheat genome. A loss of genetic diversity was observed from T. tauschii to the LCs, and from the LCs to the elite breeding germplasm. Wheats genetic diversity was narrowed from 1950 to 1989, but was enhanced from 1990 to 1997. Our results indicate that breeders averted the narrowing of the wheat germplasm base and subsequently increased the genetic diversity through the introgression of novel materials. The LCs and T. tauschii contain numerous unique alleles that were absent in modern spring bread wheat cultivars. Consequently, both the LCs and T. tauschii represent useful sources for broadening the genetic base of elite wheat breeding germplasm.     

Heritability of selectively advantageous foraging behaviour in a small passerine

Summary I measured the heritability of foraging patch choice in a laboratory population of zebra finches (Taeniopygia guttata). Mothers and offspring were tested for their ability to discriminate between four foraging patches which provided four different rates of energy gain. Use of a foraging patch with a high rate of energy gain has been shown to confer a selective advantage on zebra finches in a similar experimental system. In this population of zebra finches there was a large amount of variation in foraging patch choice behaviour both within and among individuals. I determined that foraging patch choice was a phenotypically labile trait with a degree of stereotypy or repeatability, much lower than those typically recorded for morphological traits. The mating behaviour of zebra finches required that heritability be determined from a mother—offspring regression, which showed that narrow sense heritability of foraging patch choice was approximately 0.346. This heritability was significantly different than zero, as was heritability when it was limited by repeatability to 0.246. Foraging patch choice, a behaviour that has a demonstrated fitness consequence, had a heritable component in this laboratory population of zebra finches.