A classical setting for associations between markers and loci affecting quantitative traits

We examine the relationships between a genetic marker and a locus affecting a quantitative trait by decomposing the genetic effects of the marker locus into additive and dominance effects under a classical genetic model. We discuss the structure of the associations between the marker and the trait locus, paying attention to non-random union of gametes, multiple alleles at the marker and trait loci, and non-additivity of allelic effects at the trait locus. We consider that this greater-than-usual level of generality leads to additional insights, in a way reminiscent of Cockerham's decomposition of genetic variance into five terms: three terms in addition to the usual additive and dominance terms. Using our framework, we examine several common tests of association between a marker and a trait.     

Pervasive genetic associations between traits causing reproductive isolation in Heliconius butterflies

Ecological speciation proceeds through the accumulation of divergent traits that contribute to reproductive isolation, but in the face of gene flow traits that characterize incipient species may become disassociated through recombination. Heliconius butterflies are well known for bright mimetic warning patterns that are also used in mate recognition and cause both pre- and post-mating isolation between divergent taxa. Sympatric sister taxa representing the final stages of speciation, such as Heliconius cydno and Heliconius melpomene, also differ in ecology and hybrid fertility. We examine mate preference and sterility among offspring of crosses between these species and demonstrate the clustering of Mendelian colour pattern loci and behavioural loci that contribute to reproductive isolation. In particular, male preference for red patterns is associated with the locus responsible for the red forewing band. Two further colour pattern loci are associated, respectively, with female mating outcome and hybrid sterility. This genetic architecture in which ‘speciation genes’ are clustered in the genome can facilitate two controversial models of speciation, namely divergence in the face of gene flow and hybrid speciation.     

Developmental evolution: going beyond the 'just so'

Two new protocols for infecting non-mammalian embryos with viruses, together with RNA inhibition, have provided evolutionary developmental biologists with the tools to study the effects of manipulating gene activity in a wide range of species, allowing them to test hypotheses rather than rely on inference from similarity.     

Developmental biology: cell intercalation one step beyond

Formation of the primitive streak, the equivalent of the blastopore, is a critical step during the early development of amniote embryos. Medio-lateral cell intercalation and the planar cell polarity pathway play a role during this earliest step of gastrulation in the chick embryo.     

The design of complex sexual traits in male barn swallows: associations between signal attributes

Variation in the expression of sexually selected traits among individuals is widely investigated on the premise that these traits evolved to signal male quality. Significant repeatabilities of sexual signals and their associations with condition, mating success, survivorship and age may be the signatures of sexual selection. However, little is known about the relationship between these sexual attributes. Here we studied 28 acoustic and visual traits in the barn swallow, Hirundo rustica, that may potentially function in sexual selection. Based on effect sizes calculated at the between-individual level, we assessed the relationship between repeatability, condition-dependence, attractiveness, age-dependence and viability indicator value of sexual traits using sexual signals as the units of analyses. Those traits that showed high within-year repeatability also showed high between-year repeatability, indicating that between-individual variation is consistent within and among seasons. In addition, age-dependence of traits, probably causing between-year variation, was negatively related to between-year repeatability. Condition-dependence was negatively correlated with effect sizes for the extent to which traits predicted viability. Therefore, traits that are positively related to immediate condition are those that are negatively related to survival, which may be the signature of a trade-off between current and future reproductive success ultimately reflecting signal reliability. No other significant relationship was found between trait attributes. We conclude that multiple sexual signals reflect different aspects of male quality in the barn swallow.     

Factors affecting the reproductive success of the crab spider Misumenoides formosipes: the covariance between juvenile and adult traits

Summary To examine the importance of covariance between stages in traits related to foraging, we quantified the relationships between reproductive success and sizerelated variability in weight gain in juvenile and adult instars of the crab spider Misumenoides formosipes (Araneae: Thomisidae). Prereproductive weight and fecundity are both highly correlated with carapace width, a linear measure of size which does not change within an instar. In field populations, adult females with larger carapaces gain more weight and are more likely to reproduce than females with smaller carapaces. The growth rate of spiders fed ad libitum in the laboratory is unrelated to size, suggesting that size-related differences in the field are due to variation in prey-capture success. Adult females with a carapace width less than 3.4 mm comprised 22% of the population, but were never found to reproduce. Of the individuals that did reproduce, a 17% increase in carapace width resulted in a 100% increase in fecundity. Juvenile stages must be examined to understand adult foraging and reproductive success, because the net weight gained by juvenile instars determines adult size. The final weight gained by spiders in the antepenultimate and penultimate instars explained nearly all the variation in carapace width in the penultimate and adult instars, respectively. We found that constraints on foraging in late juvenile stages are different from the adult stage. Penultimate foraging behavior differs from that of adults, because of constraints on foraging in the period preceding ecdysis. Additionally, in both late juvenile instars, carapace width had little or no effect on the final weight gained within the instar suggesting that factors that affect foraging are different between the juvenile and adult stages. These analyses stress the fact that to fully understand the effects of foraging on reproductive success, we must examine stage-specific constraints throughout an organism's life history.     

The use of genetic correlations to evaluate associations between SNP markers and quantitative traits

Open-pollinated progeny of Corymbia citriodora established in replicated field trials were assessed for stem diameter, wood density, and pulp yield prior to genotyping single nucleotide polymorphisms (SNP) and testing the significance of associations between markers and assessment traits. Multiple individuals within each family were genotyped and phenotyped, which facilitated a comparison of standard association testing methods and an alternative method developed to relate markers to additive genetic effects. Narrow-sense heritability estimates indicated there was significant additive genetic variance within this population for assessment traits ( $ {\widehat{h}^{{2}}} = 0.{28}\;{\text{to}}\;0.{44} $ ) and genetic correlations between the three traits were negligible to moderate (r _G?=?0.08 to 0.50). The significance of association tests (p values) were compared for four different analyses based on two different approaches: (1) two software packages were used to fit standard univariate mixed models that include SNP-fixed effects, (2) bivariate and multivariate mixed models including each SNP as an additional selection trait were used. Within either the univariate or multivariate approach, correlations between the tests of significance approached +1; however, correspondence between the two approaches was less strong, although between-approach correlations remained significantly positive. Similar SNP markers would be selected using multivariate analyses and standard marker-trait association methods, where the former facilitates integration into the existing genetic analysis systems of applied breeding programs and may be used with either single markers or indices of markers created with genomic selection processes.     

Food and fitness: associations between crop yields and life-history traits in a longitudinally monitored pre-industrial human population

Severe food shortage is associated with increased mortality and reduced reproductive success in contemporary and historical human populations. Studies of wild animal populations have shown that subtle variation in environmental conditions can influence patterns of mortality, fecundity and natural selection, but the fitness implications of such subtle variation on human populations are unclear. Here, we use longitudinal data on local grain production, births, marriages and mortality so as to assess the impact of crop yield variation on individual age-specific mortality and fecundity in two pre-industrial Finnish populations. Although crop yields and fitness traits showed profound year-to-year variation across the 70-year study period, associations between crop yields and mortality or fecundity were generally weak. However, post-reproductive individuals of both sexes, and individuals of lower socio-economic status experienced higher mortality when crop yields were low. This is the first longitudinal, individual-based study of the associations between environmental variation and fitness traits in pre-industrial humans, which emphasizes the importance of a portfolio of mechanisms for coping with low food availability in such populations. The results are consistent with evolutionary ecological predictions that natural selection for resilience to food shortage is likely to weaken with age and be most severe on those with the fewest resources.     

Apolipoprotein A-II: beyond genetic associations with lipid disorders and insulin resistance

PURPOSE OF REVIEW: Apolipoprotein A-II, the second major HDL apolipoprotein, was often considered of minor importance relatively to apolipoprotein A-I and its role was controversial. This picture is now rapidly changing, due to novel polymorphisms and mutations, to the outcome of clinical trials, and to studies with transgenic mice. RECENT FINDINGS: The -265 T/C polymorphism supports a role for apolipoprotein A-II in postprandial very-low-density lipoprotein metabolism. Fibrates, which increase apolipoprotein A-II synthesis, significantly decrease the incidence of major coronary artery disease events, particularly in subjects with low HDL cholesterol, high plasma triglyceride, and high body weight. The comparison of transgenic mice overexpressing human or murine apolipoprotein A-II has highlighted major structural differences between the two proteins; they have opposite effects on HDL size, apolipoprotein A-I content, plasma concentration, and protection from oxidation. Human apolipoprotein A-II is more hydrophobic, displaces apolipoprotein A-I from HDL, accelerates apolipoprotein A-I catabolism, and its plasma concentration is decreased by fasting. Apolipoprotein A-II stimulates ATP binding cassette transporter 1-mediated cholesterol efflux. Human and murine apolipoprotein A-II differently affect glucose metabolism and insulin resistance. A novel beneficial role for apolipoprotein A-II in the pathogenesis of hepatitis C virus has been shown. SUMMARY: The hydrophobicity of human apolipoprotein A-II is a key regulatory factor of HDL metabolism. Due to the lower plasma apolipoprotein A-II concentration during fasting, measurements of apolipoprotein A-II in fed subjects are more relevant. More clinical studies are necessary to clarify the role of apolipoprotein A-II in well-characterized subsets of patients and in the insulin resistance syndrome.     

A semiparametric test to detect associations between quantitative traits and candidate genes in structured populations

MOTIVATION: Although population-based association mapping may be subject to the bias caused by population stratification, alternative methods that are robust to population stratification such as family-based linkage analysis have lower mapping resolution. Recently, various statistical methods robust to population stratification were proposed for association studies, using unrelated individuals to identify associations between candidate genes and traits of interest. The association between a candidate gene and a quantitative trait is often evaluated via a regression model with inferred population structure variables as covariates, where the residual distribution is customarily assumed to be from a symmetric and unimodal parametric family, such as a Gaussian, although this may be inappropriate for the analysis of many real-life datasets. RESULTS: In this article, we proposed a new structured association (SA) test. Our method corrects for continuous population stratification by first deriving population structure and kinship matrices through a set of random genetic markers and then modeling the relationship between trait values, genotypic scores at a candidate marker and genetic background variables through a semiparametric model, where the error distribution is modeled as a mixture of Polya trees centered around a normal family of distributions. We compared our model to the existing SA tests in terms of model fit, type I error rate, power, precision and accuracy by application to a real dataset as well as simulated datasets.     

Symptom covariance accounts for behavioral approach associations across impulse control disorders

Behavioral approach system (BAS) dysfunction has been identified as a correlate of and a potential mechanism for attention-deficit/hyperactivity disorder (ADHD) and comorbid disorders. This study examined the role of symptom covariation in the relations among BAS dysfunction, ADHD symptoms, and comorbid impulsive personality disorder features. Undergraduates (N = 207) completed measures of BAS functioning, ADHD symptoms, and borderline and antisocial personality disorder symptoms, and associated features (i.e., relational aggression). Hierarchical regression suggested that age, impulsive ADHD symptoms, and relational aggression were associated with BAS functioning. Adding other ADHD symptom dimensions (inattention, hyperactivity) and antisocial and borderline scores to the model did not increase variance accounted for beyond that accounted for by ADHD impulsivity scores. Results highlight a role of symptom covariance in the previously demonstrated relation between BAS, impulsive presentations of ADHD, and comorbid impulsive personality pathology. Implications for etiological models of ADHD and its co-occurrence with other disorders are discussed.     

Parent-offspring transmission of adipocytokine levels and their associations with metabolic traits

Adipose tissue secreted cytokines (adipocytokines) have significant effects on the physiology and pathology of human metabolism relevant to diabetes and cardiovascular disease. We determined the relationship of the pattern of these circulating hormones with obesity-related phenotypes and whether such pattern is transmitted from parent to offspring. A combined total of 403 individuals from 156 consenting Saudi families divided into initial (119 families with 123 adults and 131 children) and replication (37 families with 58 adults and 91 children) cohorts were randomly selected from the RIYADH Cohort study. Anthropometrics were evaluated and metabolic measures such as fasting serum glucose, lipid profiles, insulin, leptin, adiponectin, resistin, tumor necrosis factor alpha (TNFα), activated plasminogen activator inhibitor 1 (aPAI1), high sensitivity C-reactive protein (hsCRP) and angiotensin II were also assessed. Parent-offspring regressions revealed that with the exception of hsCRP, all hormones measured showed evidence for significant inheritance. Principal component (PC) analysis of standardized hormone levels demonstrated surprising heritability of the three most common axes of variation. PC1, which explained 21% of the variation, was most strongly loaded on levels of leptin, TNFα, insulin, and aPAI1, and inversely with adiponectin. It was significantly associated with body mass index (BMI) and phenotypically stronger in children, and showed a heritability of ∼50%, after adjustment for age, gender and generational effects. We conclude that adipocytokines are highly heritable and their pattern of co-variation significantly influences BMI as early as the pre-teen years. Investigation at the genomic scale is required to determine the variants affecting the regulation of the hormones studied.     

AGHR polymorphism and its associations with carcass traits in Harrwoo cattle

The growth hormone receptor (GHR) is a membrane transmitter for the growth hormone signal transduction pathway that regulates various metabolic activities, including cell growth and expressions of cytokine genes. The presence or absence of a genetic polymorphism for the LINE-1 retroposon in the PI promoter, which specifically regulates theGHR gene expression in the liver, was screened by a novel detection method and examined for its relationships with carcass traits in Hanwoo cattle. Han woo cattle had taurine type LINE-1 present (alleleI) as well as incidine type LINE-1 absent (alleleA) promoter sequences. Three genotypes,I/I, I/A andA/A, showed frequencies of 49.1, 36.7 and 14.2%, respectively. The effects of allele A were significant on mean differences for final weight, eye muscle area, marbling score and fat color (p<0.05), but not for carcass weight, backfat thickness, final meat quality grade or meat color (p>0.05). Most 30-month old Hanwoo steers bearing the LINE-1 absent promoter had whiter fat color, heavier live weight and higher marbling score, reflecting intramuscular fat deposition inM. longissimus dorsi, compared to animals bearing a LINE-1 present promoter. This suggests that aGHR polymorphism could be a potential genetic marker for improving beef production of Hanwoo cattle.     

Genetic variations of ANGPTL6 gene and their associations with growth traits and slaughter traits in Qinchuan cattle

Angiopoietin-like protein 6 (ANGPTL6), which plays an important role in angiogenesis and energy metabolism as a circulating orphan peptide secreted by liver, could produce a potential effect on growth and development of animals. The objective of this study was to detect genetic variations of ANGPTL6 gene in 732 Qinchuan cattle, as well as to analyze their associations with growth traits and carcass weight. Herein, three novel mutations (T2359C, C2403A and G3258T) were identified in cattle for the first time. Chi-square test showed T2359C and C2403A loci were in Hardy-Weinberg equilibrium except G3258T locus. Haplotype with TCG (wild type) was dominant with frequency of 40.0 % among eight different haplotypes. Statistical analysis showed body height (BH) and hucklebone width (HW) of individuals with genotype CC were significant higher than other genotypes in T2359C locus (P < 0.05). In the C2403A locus, chest girth (CG), chest depth (CD), and chest breadth (CB) of individuals with genotype CA were all extremely significant higher (P < 0.01) while BH was significant higher (P < 0.05) than genotype CC. The association analysis of combined sites showed BH, CG, CB and HW of individuals with combined genotype TC-CA were significant higher than other combined genotypes (P < 0.05) in ScaI-VspI site. BH, CG and CB of individuals with genotype CA-GG were significant higher (P < 0.05) as well as CD was extremely significant higher (P < 0.01) than other genotypes in VspI-RsaI site. For ScaI-VspI-RsaI site, CD and HW of individuals with genotype TC-CA-GG were significant higher (P < 0.05) than those of other combined genotypes. Slaughter test also revealed that the effect of the combined genotypes was extremely significant on the carcass weight. Carcass weight of individuals with genotype TT-CA and TT-CA-GT were extremely significant heavier than other combined genotypes (P < 0.01) in the ScaI-VspI and ScaI-VspI-RsaI sites. And those with genotype TT-GT of ScaI-RsaI were significantly heavy (P < 0.05) as well as the individuals with genotype CA-GT of VspI-RsaI. In conclusion, the present results provided evidence that polymorphisms of ANGPTL6 gene were associated with growth and slaughter traits, and may apply to Qinchuan cattle breeding program as a possible candidate for marker-assisted selection (MAS).     

Environmental and sibling resemblance components of variance and covariance in traits of early child development

The multiple regression analyses were undertaken to elucidate the significance and relative importance of different potential determinants of several child development traits (i.e. age at which child 1. turns himself over; 2. sits up; 3. stands up; 4. walks, and 5. cuts his first tooth). Despite the fact that we used a relatively wide gamut of potential determinants (such as parental age, geographic origin, occupation, current residence, or family size) of trait variability, the results of multiple regression analysis (N = 300 families) indicate an almost complete absence of significant factors and studied variables of development. Sibling resemblance component of variance and covariance for five mentioned traits of development and some morphological characters (weight, length and head circumference at day of birth and at 16 months) were studied in 66 families. The transmissibility ("heritability") values for the development traits were small, ranging from 0 ("Turn") to 0.42 ("Walked"). The Findings suggest that there are significant inverse relationship between some of the developmental traits and inborn morphological characters.     

Life-history traits display strong associations to genome size in annelids

Hydrobiologia - Genome size, known also as the C-value, has been proposed as an important determinant of life-history variation in numerous animal taxa. We assessed the relationships between genome...     

Analysis of the associations between polymorphisms in GNAS complex locus and growth, carcass and meat quality traits in pigs

Imprinted genes are interesting candidates for marker assisted selection in farm animals. One of them—GNAS complex locus is engaged in obesity pathogenesis in humans and mice. In our study, we identified new polymorphism in porcine GNAS gene (variable number of CT repeats, accession number: rs196952953) and found that this polymorphism is in linkage disequilibrum with GNAS AM490165:g.324C>T. Statistical analysis (GLM procedure), performed on 552 animals (Large White n = 258 and Landrace n = 269), revealed that deduced haplotypes and GNAS AM490165:g.324C>T are associated with growth performance and a few carcass traits, but not with feed intake. We observed significant additive effects of GNAS AM490165:g.324C>T genotype and haplotype 2 (C/278 bp) on test daily gain (TDG), average daily gain (ADG), number of days on test, age of the slaughter (P < 0.01) and FCR ratio (P < 0.05). Animals with two copies of C/278 haplotype had significantly higher: TDG, ADG, lower feed:gain ratio and faster reached the weight of 100 kg. When carcass traits were considered, significant associations between GNAS AM490165:g.324C>T polymorphism, haplotype 2 (C/278) and weight of ham with and without backfat and skin (WH) (WH2), length of the carcass, height and the width of the loin, meat percentage, weight of the main cuts were identified. The significant dominance effects of GNAS AM490165:g.324C>T polymorphism and haplotype 2 on WH and WH2 were observed (P < 0.05). When the two breeds were analyzed separately significant associations were observed for most of the traits in Landrace while in Large White the same trends were present but the differences were mostly not significant. Among meat quality traits we found significant association between haplotype and IMF content in Landrace (P < 0.03). Our results show for the first time that GNAS complex locus may modulate economically important traits in pigs.     

Exploring the generality of associations between plant functional traits: evidence within ecological groups along an altitudinal gradient in Hyrcanian forest

We hypothesized that associations among plant functional traits may differ within different ecological assemblages and plant communities. Association among plant traits including plant maximum height, seed weight, fruit type, pollination mode, mean leaf area, and leaf type were explored within life forms, plant strategy groups along with lowland and montane forest vegetation. In total, 83 sampling plots of 400 m² were placed along a 2400 m altitudinal gradient in Hyrcanian forest. Importance‐values of species within vegetation types were used for weighting data and trait associations were explored using categorical principal component analysis. A G‐test and Fisher's exact test of independence were used to retest significance of the correlations. Different paired trait associations (association lines) including height–leaf, height–seed, height–pollination, leaf–seed, seed–fruit and fruit–pollination were observed and their ecological or physiological basis was discussed. Life forms, strategy types and vegetation types differed based on association lines. Some of the well‐known trade‐offs appear by increasing scale from ecological groups to vegetation types in Hyrcanian forest. The observed patterns of trait associations in Hyrcanian forest and several other ecosystems of the world call the generality of previously accepted trait correlations into question.     

Developmental evolution: Going beyond the ‘just so’

Two new protocols for infecting non-mammalian embryos with viruses, together with RNA inhibition, have provided evolutionary developmental biologists with the tools to study the effects of manipulating gene activity in a wide range of species, allowing them to test hypotheses rather than rely on inference from similarity.