A genome-wide association study of seed composition traits in wild soybean (Glycine soja).

BACKGROUND: Cultivated soybean (Glycine max) is a major agricultural crop that provides a crucial source of edible protein and oil. Decreased amounts of saturated palmitic acid and increased amounts of unsaturated oleic acid in soybean oil are considered optimal for human cardiovascular health and therefore there has considerable interest by breeders in discovering genes affecting the relative concentrations of these fatty acids. Using a genome-wide association (GWA) approach with nearly 30,000 single nucleotide polymorphisms (SNPs), we investigated the genetic basis of protein, oil and all five fatty acid levels in seeds from a sample of 570 wild soybeans (Glycine soja), the progenitor of domesticated soybean, to identify quantitative trait loci (QTLs) affecting these seed composition traits. RESULTS: We discovered 29 SNPs located on ten different chromosomes that are significantly associated with the seven seed composition traits in our wild soybean sample. Eight SNPs co-localized with QTLs previously uncovered in linkage or association mapping studies conducted with cultivated soybean samples, while the remaining SNPs appeared to be in novel locations. Twenty-four of the SNPs significantly associated with fatty acid variation, with the majority located on chromosomes 14 (6 SNPs) and seven (8 SNPs). Two SNPs were common for two or more fatty acids, suggesting loci with pleiotropic effects. We also identified some candidate genes that are involved in fatty acid metabolism and regulation. For each of the seven traits, most of the SNPs produced differences between the average phenotypic values of the two homozygotes of about one-half standard deviation and contributed over 3% of their total variability. CONCLUSIONS: This is the first GWA study conducted on seed composition traits solely in wild soybean populations, and a number of QTLs were found that have not been previously discovered. Some of these may be useful to breeders who select for increased protein/oil content or altered fatty acid ratios in the seeds. The results also provide additional insight into the genetic architecture of these traits in a large sample of wild soybean, and suggest some new candidate genes whose molecular effects on these traits need to be further studied.

Exercise and diet affect quantitative trait loci for body weight and composition traits in an advanced intercross population of mice.

Driven by the recent obesity epidemic, interest in understanding the complex genetic and environmental basis of body weight and composition is great. We investigated this by searching for quantitative trait loci (QTLs) affecting a number of weight and adiposity traits in a G(10) advanced intercross population produced from crosses of mice in inbred strain C57BL/6J with those in a strain selected for high voluntary wheel running. The mice in this population were fed either a high-fat or a control diet throughout the study and also measured for four exercise traits prior to death, allowing us to test for pre- and postexercise QTLs as well as QTL-by-diet and QTL-by-exercise interactions. Our genome scan uncovered a number of QTLs, of which 40% replicated QTLs previously found for similar traits in an earlier (G(4)) generation. For those replicated QTLs, the confidence intervals were reduced from an average of 19 Mb in the G(4) to 8 Mb in the G(10). Four QTLs on chromosomes 3, 8, 13, and 18 were especially prominent in affecting the percentage of fat in the mice. About of all QTLs showed interactions with diet, exercise, or both, their genotypic effects on the traits showing a variety of patterns depending on the diet or level of exercise. It was concluded that the indirect effects of these QTLs provide an underlying genetic basis for the considerable variability in weight or fat loss typically found among individuals on the same diet and/or exercise regimen.

Epistatic interactions of genes influence within-individual variation of physical activity traits in mice.

A number of quantitative trait loci (QTLs) recently have been discovered that affect various activity traits in mice, but their collective impact does not appear to explain the consistently moderate to high heritabilities for these traits. We previously suggested interactions of genes, or epistasis, might account for additional genetic variability of activity, and tested this for the average distance, duration and speed run by mice during a 3 week period. We found abundant evidence for epistasis affecting these traits, although, recognized that epistatic effects may well vary within individuals over time. We therefore conducted a full genome scan for epistatic interactions affecting these traits in each of seven three-day intervals. Our intent was to assess the extent and trends in epistasis affecting these traits in each of the intervals. We discovered a number of epistatic interactions of QTLs that influenced the activity traits in the mice, the majority of which were not previously found and appeared to affect the activity traits (especially distance and speed) primarily in the early or in the late age intervals. The overall impact of epistasis was considerable, its contribution to the total phenotypic variance varying from an average of 22-35% in the three traits across all age intervals. It was concluded that epistasis is more important than single-locus effects of genes on activity traits at specific ages and it is therefore an essential component of the genetic architecture of physical activity.

A search for quantitative trait loci controlling within-individual variation of physical activity traits in mice.

BACKGROUND: In recent years it has become increasingly apparent that physical inactivity can predispose individuals to a host of health problems. While many studies have analyzed the effect of various environmental factors on activity, we know much less about the genetic control of physical activity. Some studies in mice have discovered quantitative trait loci (QTL) influencing various physical activity traits, but mostly have analyzed inter-individual variation rather than variation in activity within individuals over time. We conducted a genome scan to identify QTLs controlling the distance, duration, and time run by mice over seven consecutive three-day intervals in an F2 population created by crossing two inbred strains (C57L/J and C3H/HeJ) that differed widely (average of nearly 300%) in their activity levels. Our objectives were (a) to see if we would find QTLs not originally discovered in a previous investigation that assessed these traits over the entire 21-day period and (b) to see if some of these QTLs discovered might affect the activity traits only in the early or in the late time intervals. RESULTS: This analysis uncovered 39 different QTLs, over half of which were new. Some QTLs affected the activity traits only in the early time intervals and typically exhibited significant dominance effects whereas others affected activity only in the later age intervals and exhibited less dominance. We also analyzed the regression slopes of the activity traits over the intervals, and found several QTLs affecting these traits that generally mapped to unique genomic locations. CONCLUSIONS: It was concluded that the genetic architecture of physical activity in mice is much more complicated than has previously been recognized, and may change considerably depending on the age at which various activity measures are assessed.

Genetic variation for body weight change in mice in response to physical exercise.

BACKGROUND: Physical activity is beneficial in reducing the weight gain and associated health problems often experienced by individuals as they age, but the association of weight change with physical activity remains complex. We tested for a possible genetic basis for this association between 9-12-week body weight change (WTC) and the distance, duration, and speed voluntarily run by 307 mice in an F2 population produced from an intercross of two inbred strains (C57L/J and C3H/HeJ) that differed dramatically in their physical activity levels. RESULTS: In this population WTC did show the expected negative association with the physical activity traits, but only the phenotypic correlation of WTC with speed (-0.18) reached statistical significance. Using an interval mapping approach with single-nucleotide polymorphism markers, we discovered five (four suggestive and one significant) quantitative trait loci (QTLs) affecting body weight change, only one of which appeared to show pleiotropic effects on the physical activity traits as well. Genome-wide epistasis scans also detected several pairwise interactions of QTLs with pleiotropic effects on WTC and the physical activity traits, but these effects made a significant contribution (51%) only to the covariance of WTC with speed. CONCLUSION: It was concluded that the genetic contribution to the phenotypic association between WTC and the physical activity traits in this population of mice was primarily epistatic in origin, restricted to one measure of physical activity, and could be quite variable among different populations depending on the genetic background, experimental design and traits assessed.

Genetic variation in the pleiotropic association between physical activity and body weight in mice.

BACKGROUND: A sedentary lifestyle is often assumed to lead to increases in body weight and potentially obesity and related diseases but in fact little is known about the genetic association between physical activity and body weight. We tested for such an association between body weight and the distance, duration, and speed voluntarily run by 310 mice from the F2 generation produced from an intercross of two inbred lines that differed dramatically in their physical activity levels. METHODS: We used a conventional interval mapping approach with SNP markers to search for QTLs that affected both body weight and activity traits. We also conducted a genome scan to search for relationship QTLs (relQTLs), or chromosomal regions that affected an activity trait variably depending on the phenotypic value of body weight. RESULTS: We uncovered seven quantitative trait loci (QTLs) affecting body weight, but only one co-localized with another QTL previously found for activity traits. We discovered 19 relQTLs that provided evidence for a genetic (pleiotropic) association of physical activity and body weight. The three genotypes at each of these loci typically exhibited a combination of negative, zero, and positive regressions of the activity traits on body weight, the net effect of which was to produce overall independence of body weight from physical activity. We also demonstrated that the relQTLs produced these varying associations through differential epistatic interactions with a number of other epistatic QTLs throughout the genome. CONCLUSION: It was concluded that individuals with specific combinations of genotypes at the relQTLs and epiQTLs might account for some of the variation typically seen in plots of the association of physical activity with body weight.

"Get a Grip on Hypertension": EXPLORING THE USE OF ISOMETRIC HANDGRIP TRAINING IN CARDIOPULMONARY REHABILITATION PATIENTS.

PURPOSE: Isometric handgrip (IHG) training lowers systolic and diastolic blood pressure (SBP and DBP, respectively), but the efficacy of IHG training in cardiopulmonary rehabilitation patients is unknown. The purpose of this study was to determine if IHG decreases blood pressure in cardiopulmonary rehabilitation patients. METHODS: Cardiopulmonary rehabilitation program participants (n = 11; 50-80 yr old) were randomized to IHG (n = 6) or control (CON; no treatment; n = 5) groups. IHG participants completed an IHG training program at 30% maximal voluntary contraction, 3 d/wk for 6 wk. Resting SBP, DBP, and heart rate were assessed weekly. RESULTS: Mean regression for SBP following IHG was negative (-1.04 ± 0.80). Mean regression in the CON group was positive (0.50 ± 0.88), but there was no significant difference between groups. Separate analysis of weeks 1 to 7 yielded a negative mean regression (-1.12 ± 0.54) in the IHG group, but positive (1.2 ± 0.60) in the CON group. A Wilcoxon test of these differences yielded significance for SBP (P = .009). In 3 of 6 IHG participants, SBP was lower (mean ± SD: -16 ± 11 mm Hg; P = .12), and in 2 IHG participants, DBP was lower (-9 ± 1 mm Hg; P = .06) compared with baseline. In 2 of 5 CON participants, SBP was not significantly lower (-11 ± 7 mm Hg) and, in 3 of 5 CON participants, DBP was lower (-7 ± 4 mm Hg; P = .04). CONCLUSIONS: Our data suggest that standard IHG training may be inadequate for blood pressure management immediately following a major cardiac or pulmonary event. Future work with a larger cohort and more developed training protocol to determine the efficacy of IHG training in patients with cardiopulmonary disease is warranted.

Quantitative trait loci for physical activity traits in mice.

The genomic locations and identities of the genes that regulate voluntary physical activity are presently unknown. The purpose of this study was to search for quantitative trait loci (QTL) that are linked with daily mouse running wheel distance, duration, and speed of exercise. F(2) animals (n = 310) derived from high active C57L/J and low active C3H/HeJ inbred strains were phenotyped for 21 days. After phenotyping, genotyping with a fully informative single-nucleotide polymorphism panel with an average intermarker interval of 13.7 cM was used. On all three activity indexes, sex and strain were significant factors, with the F(2) animals similar to the high active C57L/J mice in both daily exercise distance and duration of exercise. In the F(2) cohort, female mice ran significantly farther, longer, and faster than male mice. QTL analysis revealed no sex-specific QTL but at the 5% experimentwise significance level did identify one QTL for duration, one QTL for distance, and two QTL for speed. The QTL for duration (DUR13.1) and distance (DIST13.1) colocalized with the QTL for speed (SPD13.1). Each of these QTL accounted for approximately 6% of the phenotypic variance, whereas SPD9.1 (chromosome 9, 7 cM) accounted for 11.3% of the phenotypic variation. DUR13.1, DIST13.1, SPD13.1, and SPD9.1 were subsequently replicated by haplotype association mapping. The results of this study suggest a genetic basis of voluntary activity in mice and provide a foundation for future candidate gene studies.

Sex dependent imprinting effects on complex traits in mice.

BACKGROUND: Genomic imprinting is an epigenetic source of variation in quantitative traits that results from monoallelic gene expression, where commonly either only the paternally- or the maternally-derived allele is expressed. Imprinting has been shown to affect a diversity of complex traits in a variety of species. For several such quantitative traits sex-dependent genetic effects have been discovered, but whether imprinting effects also show such sex-dependence has yet to be explored. Moreover, theoretical work on the evolution of sex-dependent genomic imprinting effects makes specific predictions about the phenotypic patterns of such effects, which, however, have not been assessed empirically to date. RESULTS: Using a genome-scan for loci affecting a set of complex growth and body composition traits from an intercross between two divergent mouse strains, we investigated possible sex-dependent imprinting effects. Our results demonstrate for the first time the existence of genomic imprinting effects that depend on sex and are not related to sex-chromosome effects. We detected a total of 13 loci on 11 chromosomes that showed significant differences between the sexes in imprinting effects. Most loci showed imprinting effects in only one sex, with eight imprinted effects found in males and six in females. One locus showed sex-dependent imprinting effects in both sexes for different traits. The absence of an imprinting effect in one sex was not necessarily indicative of the overall inactivity of the locus in that sex, as for several loci a significant additive or dominance effect was detected. Moreover, three loci exhibited significant additive effects in both sexes but their imprinting effect was restricted to one sex. CONCLUSION: Our results clearly show that imprinting effects can be sex-dependent and also suggest that new candidate imprinted loci can be detected when taking account of sex-specific imprinting effects. However, predictions made about the evolution of sex-dependent imprinting effects and associated phenotypic patterns cannot be unequivocally supported at present and further research into the selection pressures applied to the strains of mice used in our study is required.

Genetic differences in sensitivity to alterations of mandible structure caused by the teratogen 2,3,7,8-tetrachlorodibenzo-p-dioxin.

The contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is an environmental pollutant and teratogen that has been shown to alter craniofacial development. Differences in sensitivity to TCDD are attributed primarily to differences in alleles at the Ahr locus coding for the aryl-hydrocarbon receptor (AHR) that binds TCDD and mediates its effects by altering gene expression. The authors used geometric morphometric methods to evaluate differences in the effects of small in utero exposures of TCDD on adult mandible size and shape in five different inbred mouse strains with the same Ahr alleles. Because of the known effects of this toxicant on bone and craniofacial structures, the authors hypothesized that TCDD would decrease mandible size and alter mandible shape, but that the effects of TCDD exposure would differ among the inbred strains. The authors found that TCDD did alter mandible size and shape, but these effects were limited to specific strains and also differed between the sexes. The relative sensitivity to TCDD's effects on mandibles did not correspond with the previously reported sensitivity to TCDD's effects on molars. The authors hypothesize that beyond Ahr-related effects, variation in response to TCDD reflects differences in the genetic architecture controlling the trait being evaluated, thus explaining the species, strain, and trait specificity of TCDD.

An epistatic genetic basis for physical activity traits in mice.

We recently identified several (4-8) quantitative trait loci (QTL) for 3 physical activity traits (daily distance, duration, and speed voluntarily run) in an F(2) population of mice derived from an original intercross of 2 strains that exhibited large differences in activity. These QTL cumulatively explained from 11% to 34% of the variation in these traits, but this was considerably less than their total genetic variability estimated from differences among inbred strains. We therefore decided to test whether epistatic interactions might account for additional genetic variation in these traits in this same population of mice. We conducted a full genome epistasis scan for all possible interactions of QTL between each pair of 20 chromosomes. The results of this scan revealed an abundance of epistasis, with QTL throughout the genome being involved in significant interactions. Overall, epistatic effects contributed an average of 26% of the total variation among the 3 activity traits. These results suggest that epistatic interactions of genes may play as important a role in the genetic architecture of physical activity traits as single-locus effects and need to be considered in future candidate gene identification studies.

Effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin on molar development among non-resistant inbred strains of mice: a geometric morphometric analysis.

Prenatal development is highly sensitive to the effects of environmental contaminants. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is an environmental toxicant that at very low levels causes teratogenic effects such as irregular tooth development. Variations in susceptibility to TCDD's effects have been attributed primarily to differences at the Ahr locus. There is some evidence, however, that genes at other loci may be involved in mediating TCDD's effects on various endpoints. Our hypothesis therefore was that the effect of TCDD on molar development would differ even among inbred mouse strains possessing similar Ahr alleles. To test this, geometric morphometric techniques were used to evaluate the effects of several different levels of TCDD on molar size, shape and asymmetry in the offspring of dosed females from five different inbred strains of mice bearing TCDD-sensitive Ahr alleles. The results indicated that a maternal dose of 1 microg TCDD/kg body weight on gestation day 13 altered the shape (but not the size or asymmetry) of the first two molars in mice from the C3H/HeJ and CBA/J strains of mice, but not in mice from the other strains. The C3H/HeJ and CBA/J strains appeared to be the most sensitive to the disruption of molar development via TCDD and the C57BL/6J strain appeared to be the least sensitive.

A comparison of blood pressure reductions following 12-weeks of isometric exercise training either in the laboratory or at home.

Isometric exercise training (IET)-induced reductions in resting blood pressure (RBP) have been achieved in laboratory environments, but data in support of IET outside the laboratory are scarce. The aim of this study was to compare 12 weeks of home-based (HOM) IET with laboratory-based, face-to-face (LAB) IET in hypertensive adults. Twenty-two hypertensive participants (24-60 years) were randomized to three conditions: HOM, LAB, or control (CON). IET involved isometric handgrip training (4 × 2 minutes at 30% maximum voluntary contraction, 3 days per week). RBP was measured every 6 weeks (0, 6, and 12 weeks) during training and 6 weeks after training (18 weeks). Clinically meaningful, but not statistically significant reductions in RBP were observed after 12 weeks of LAB IET (resting systolic blood pressure [SBP] -9.1 ± 4.1; resting diastolic blood pressure [DBP] -2.8 ± 2.1; P > .05), which was sustained for 6 weeks of detraining (SBP -8.2 ± 2.9; DBP -4 ± 2.9, P > .05). RBP was reduced in the HOM group after 12 weeks of training (SBP -9.7 ± 3.4; DBP -2.2 ± 2.0; P > .05), which was sustained for an additional 6 weeks of detraining (SBP -5.5 ± 3.4; DBP -4.6 ± 1.8; P > .05). Unsupervised home-based IET programs present an exciting opportunity for community-based strategies to combat hypertension, but additional work is needed if IET is to be used routinely outside the laboratory.

Quantitative trait loci associated with maximal exercise endurance in mice.

The role of genetics in the determination of maximal exercise endurance is unclear. Six- to nine-week-old F2 mice (n = 99; 60 female, 39 male), derived from an intercross of two inbred strains that had previously been phenotyped as having high maximal exercise endurance (Balb/cJ) and low maximal exercise endurance (DBA/2J), were treadmill tested to estimate exercise endurance. Selective genotyping of the F2 cohort (n = 12 high exercise endurance; n = 12 low exercise endurance) identified a significant quantitative trait locus (QTL) on chromosome X (53.7 cM, DXMit121) in the entire cohort and a suggestive QTL on chromosome 8 (36.1 cM, D8Mit359) in the female mice. Fine mapping with the entire F2 cohort and additional informative markers confirmed and narrowed the QTLs. The chromosome 8 QTL (EE8(F)) is homologous with two suggestive human QTLs and one significant rat QTL previously linked with exercise endurance. No effect of sex (P = 0.33) or body weight (P = 0.79) on exercise endurance was found in the F2 cohort. These data indicate that genetic factors in distinct chromosomal regions may affect maximal exercise endurance in the inbred mouse. Whereas multiple genes are located in the identified QTL that could functionally affect exercise endurance, this study serves as a foundation for further investigations delineating the identity of genetic factors influencing maximum exercise endurance.

The effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin on molar and mandible traits in congenic mice: a test of the role of the Ahr locus.

2,3,7,8-Tetracholorodibenzo-p-dioxin is a highly toxic substance that can cause a variety of adverse effects on organisms. While it has been shown that TCDD acts mainly through the aryl-hydrocarbon receptor (AHR), the mechanism of toxicity is not completely clear. To test the role of the AHR in mediating the effects of TCDD, we exposed two congenic strains of mice differing only at the Ahr locus (Ahr(b)/Ahr(b) and Ahr(d)/Ahr(d)) to TCDD (0, 0.01, 0, or 1 microg/kg body weight) in utero on gestation day 13 and examined the developmental effects on mandible and mandibular tooth row size and shape. Our hypothesis was that TCDD would significantly affect one or more of these endpoints in Ahr(b)/Ahr(b) mice, previously shown to be sensitive to the effects of TCDD, while causing little or no effect in mice carrying the less sensitive Ahr(d) allele. At the doses used in this study, TCDD did not alter the size of mandibles or molars in either Ahr(b)/Ahr(b) or Ahr(d)/Ahr(d) mice. However, we did find that the highest dose of TCDD altered mandible shape, but only in Ahr(b)/Ahr(b) (not Ahr(d)/Ahr(d)) male mice. Similarly, the highest dose of TCDD significantly altered molar shape in Ahr(b)/Ahr(b) but not Ahr(d)/Ahr(d) male mice, although females in both congenic strains were affected. These results suggest that the effects of TCDD on molar and mandible shape are influenced by the Ahr genotype but that males and females differ in sensitivity to both of these effects.

Back into the wild-Apply untapped genetic diversity of wild relatives for crop improvement.

Deleterious effects of climate change and human activities, as well as diverse environmental stresses, present critical challenges to food production and the maintenance of natural diversity. These challenges may be met by the development of novel crop varieties with increased biotic or abiotic resistance that enables them to thrive in marginal lands. However, considering the diverse interactions between crops and environmental factors, it is surprising that evolutionary principles have been underexploited in addressing these food and environmental challenges. Compared with domesticated cultivars, crop wild relatives (CWRs) have been challenged in natural environments for thousands of years and maintain a much higher level of genetic diversity. In this review, we highlight the significance of CWRs for crop improvement by providing examples of CWRs that have been used to increase biotic and abiotic stress resistance/tolerance and overall yield in various crop species. We also discuss the surge of advanced biotechnologies, such as next-generation sequencing technologies and omics, with particular emphasis on how they have facilitated gene discovery in CWRs. We end the review by discussing the available resources and conservation of CWRs, including the urgent need for CWR prioritization and collection to ensure continuous crop improvement for food sustainability.

Epistatic pleiotropy and the genetic architecture of covariation within early and late-developing skull trait complexes in mice.

The role of epistasis as a source of trait variation is well established, but its role as a source of covariation among traits (i.e., as a source of "epistatic pleiotropy") is rarely considered. In this study we examine the relative importance of epistatic pleiotropy in producing covariation within early and late-developing skull trait complexes in a population of mice derived from an intercross of the Large and Small inbred strains. Significant epistasis was found for several pairwise combinations of the 21 quantitative trait loci (QTL) affecting early developing traits and among the 20 QTL affecting late-developing traits. The majority of the epistatic effects were restricted to single traits but epistatic pleiotropy still contributed significantly to covariances. Because of their proportionally larger effects on variances than on covariances, epistatic effects tended to reduce within-group correlations of traits and reduce their overall degree of integration. The expected contributions of single-locus and two-locus epistatic pleiotropic QTL effects to the genetic covariance between traits were analyzed using a two-locus population genetic model. The model demonstrates that, for single-locus or epistatic pleiotropy to contribute to trait covariances in the study population, both traits must show the same pattern of single-locus or epistatic effects. As a result, a large number of the cases where loci show pleiotropic effects do not contribute to the covariance between traits in this population because the loci show a different pattern of effect on the different traits. In general, covariance patterns produced by single-locus and epistatic pleiotropy predicted by the model agreed well with actual values calculated from the QTL analysis. Nearly all single-locus and epistatic pleiotropic effects contributed positive components to covariances between traits, suggesting that genetic integration in the skull is achieved by a complex combination of pleiotropic effects.

Differential Expression of Inflammatory Cytokines and Stress Genes in Male and Female Mice in Response to a Lipopolysaccharide Challenge.

BACKGROUND: Sex plays a key role in an individual's immune response against pathogenic challenges such that females fare better when infected with certain pathogens. It is thought that sex hormones impact gene expression in immune cells and lead to sexually dimorphic responses to pathogens. We predicted that, in the presence of E. coli gram-negative lipopolysaccharide (LPS), there would be a sexually dimorphic response in proinflammatory cytokine production and acute phase stress gene expression and that these responses might vary among different mouse strains and times in a pattern opposite to that of body temperature associated with LPS-induced shock. MATERIALS AND METHODS: Interleukin-6 (IL-6), macrophage inflammatory protein-Iß (MIP-1ß), tumor necrosis factor alpha (TNF-α) and interleukin-1ß (IL-1ß) as well as beta-fibrinogen (Fgb) and metallothionein-1 (Mt-1) mRNA expression were measured at four time points (0, 2, 4 and 7 hours) after injection of E. coli LPS in mice from three inbred strains. RESULTS: Statistical analysis using analyses of variance (ANOVAs) showed that the levels of the all six traits changed over time, generally peaking at 2 hours after LPS injection. Mt-1, Fgb, and IL-6 showed differences among strains, although these were time-specific. Sexual dimorphism was seen for Fgb and IL6, and was most pronounced at the latest time period (7 hours) where male levels exceeded those for females. Trends for all six cytokine/gene expression traits were negatively correlated with those for body temperatures. DISCUSSION: The higher levels of expression of Fgb and IL6 in males compared with females are consistent with the greater vulnerability of males to infection and subsequent inflammation. Temperature appears to be a useful proxy for mortality in endotoxic shock, but sexual dimorphism in cytokine and stress gene expression levels may persist after an LPS challenge even if temperatures in the two sexes are similar and have begun to stabilize.

Environmental versus geographical effects on genomic variation in wild soybean (Glycine soja) across its native range in northeast Asia.

A fundamental goal in evolutionary biology is to understand how various evolutionary factors interact to affect the population structure of diverse species, especially those of ecological and/or agricultural importance such as wild soybean (Glycine soja). G. soja, from which domesticated soybeans (Glycine max) were derived, is widely distributed throughout diverse habitats in East Asia (Russia, Japan, Korea, and China). Here, we utilize over 39,000 single nucleotide polymorphisms genotyped in 99 ecotypes of wild soybean sampled across their native geographic range in northeast Asia, to understand population structure and the relative contribution of environment versus geography to population differentiation in this species. A STRUCTURE analysis identified four genetic groups that largely corresponded to the geographic regions of central China, northern China, Korea, and Japan, with high levels of admixture between genetic groups. A canonical correlation and redundancy analysis showed that environmental factors contributed 23.6% to population differentiation, much more than that for geographic factors (6.6%). Precipitation variables largely explained divergence of the groups along longitudinal axes, whereas temperature variables contributed more to latitudinal divergence. This study provides a foundation for further understanding of the genetic basis of climatic adaptation in this ecologically and agriculturally important species.

Integration and modularity of quantitative trait locus effects on geometric shape in the mouse mandible.

The mouse mandible has long served as a model system for complex morphological structures. Here we use new methodology based on geometric morphometrics to test the hypothesis that the mandible consists of two main modules, the alveolar region and the ascending ramus, and that this modularity is reflected in the effects of quantitative trait loci (QTL). The shape of each mandible was analyzed by the positions of 16 morphological landmarks and these data were analyzed using Procrustes analysis. Interval mapping in the F(2) generation from intercrosses of the LG/J and SM/J strains revealed 33 QTL affecting mandible shape. The QTL effects corresponded to a variety of shape changes, but ordination or a parametric bootstrap test of clustering did not reveal any distinct groups of QTL that would affect primarily one module or the other. The correlations of landmark positions between the two modules tended to be lower than the correlations between arbitrary subsets of landmarks, indicating that the modules were relatively independent of each other and confirming the hypothesized location of the boundary between them. While these results are in agreement with the hypothesis of modularity, they also underscore that modularity is a question of the relative degrees to which QTL contribute to different traits, rather than a question of discrete sets of QTL contributing to discrete sets of traits.