Epistatic effects on grain yield of soybean [Glycine max (L.) Merrill]

Studies addressing the estimation of genetic parameters in soybean have not emphasized the epistatic effects. The purpose of this study was to estimate the significance of these effects on soybean grain yield, based on the Modified Triple Test Cross design. Thirty-two inbred lines derived from a cross between two contrasting lines were used, which were crossed with two testers (L1 and L2). The experiments were carried out at two locations, in 10 x 10 triple lattice designs with 9 replications, containing 32 lines (Pi ), 64 crosses (32 Pi x L1 and 32 Pi x L2 ) and controls. The variation between ( ͞L1i + ͞L2i - ͞Pi ) revealed the presence of epistasis, as well as an interaction of epistasis x environment. Since the predominant component of epistasis in autogamous species is additive x additive (i type), we suggest postponing the selection for grain yield to later generations of inbreeding in order to exploit the beneficial effects of additive x additive epistasis.

The Effects of Emotions and Distraction on Attention During a Perceptual Task

According to the broaden-and-build theory of positive emotions, positive emotions broaden while negative emotions narrow thought-action repertoires. These processes reflect changes in attentional scope, which is the focus of this research. The present study tested the hypothesis that participants in negative mood would be better able to focus on a target figure and separate it from its context in a perceptual task, and would also be better able to focus on the task amid a distracting environment than participants in a positive mood. An undergraduate sample of 77 participants watched video clips selected to induce either fear or amusement, and completed an Embedded Figures Test either in a quiet setting or in a noisy setting. A higher-order ANOVA revealed that Mood had a marginally significant effect on task performance, F(1, 73) = 3.94, p = .051, and that Distraction, F(1, 72) = 4.61, p = .035 and the Mood x Distraction interaction, F(1, 73) = 9.12, p = .003 did significantly affect task performance. However, contrary to the hypothesis, the effect of the distraction manipulation was greater for participants in a negative mood than it was for participants in a positive mood. The author suggests future directions to clarify the relationship between emotions, attentional scope, and susceptibility to environmental distraction.

A unifying approach for haplotype analysis of quantitative traits in family-based association studies: Testing and estimating gene-environment interactions with complex exposure variables

We propose robust and e±cient tests and estimators for gene-environment/gene-drug interactions in family-based association studies. The methodology is designed for studies in which haplotypes, quantitative pheno- types and complex exposure/treatment variables are analyzed. Using causal inference methodology, we derive family-based association tests and estimators for the genetic main effects and the interactions. The tests and estimators are robust against population admixture and strati¯cation without requiring adjustment for confounding variables. We illustrate the practical relevance of our approach by an application to a COPD study. The data analysis suggests a gene-environment interaction between a SNP in the Serpine gene and smok- ing status/pack years of smoking that reduces the FEV1 volume by about 0.02 liter per pack year of smoking. Simulation studies show that the pro- posed methodology is su±ciently powered for realistic sample sizes and that it provides valid tests and effect size estimators in the presence of admixture and stratification.

Genetics and epidemiology of gallbladder disease in New World native peoples.

Native peoples of the New World, including Amerindians and admixed Latin Americans such as Mexican-Americans, are highly susceptible to diseases of the gallbladder. These include cholesterol cholelithiasis (gallstones) and its complications, as well as cancer of the gallbladder. Although there is clearly some necessary dietary or other environmental risk factor involved, the pattern of disease prevalence is geographically associated with the distribution of genes of aboriginal Amerindian origin, and levels of risk generally correspond to the degree of Amerindian admixture. This pattern differs from that generally associated with Westernization, which suggests a gene-environment interaction, and that within an admixed population there is a subset whose risk is underestimated when admixture is ignored. The risk that an individual of a susceptible New World genotype will undergo a cholecystectomy by age 85 can approach 40% in Mexican-American females, and their risk of gallbladder cancer can reach several percent. These are heretofore unrecognized levels of risk, especially of the latter, because previous studies have not accounted for admixture or for the loss of at-risk individuals due to cholecystectomy. A genetic susceptibility may, thus, be as "carcinogenic" in New World peoples as any known major environmental exposure; yet, while the risk has a genetic basis, its expression as gallbladder cancer is so delayed as to lead only very rarely to multiply-affected families. Estimates in this paper are derived in part from two studies of Mexican-Americans in Starr County and Laredo, Texas.

Dominance and the maintenance of polymorphism in multiallelic migration-selection models with two demes

The maintenance of genetic variation in a spatially heterogeneous environment has been one of the main research themes in theoretical population genetics. Despite considerable progress in understanding the consequences of spatially structured environments on genetic variation, many problems remain unsolved. One of them concerns the relationship between the number of demes, the degree of dominance, and the maximum number of alleles that can be maintained by selection in a subdivided population. In this work, we study the potential of maintaining genetic variation in a two-deme model with deme-independent degree of intermediate dominance, which includes absence of G x E interaction as a special case. We present a thorough numerical analysis of a two-deme three-allele model, which allows us to identify dominance and selection patterns that harbor the potential for stable triallelic equilibria. The information gained by this approach is then used to construct an example in which existence and asymptotic stability of a fully polymorphic equilibrium can be proved analytically. Noteworthy, in this example the parameter range in which three alleles can coexist is maximized for intermediate migration rates. Our results can be interpreted in a specialist-generalist context and (among others) show when two specialists can coexist with a generalist in two demes if the degree of dominance is deme independent and intermediate. The dominance relation between the generalist allele and the specialist alleles play a decisive role. We also discuss linear selection on a quantitative trait and show that G x E interaction is not necessary for the maintenance of more than two alleles in two demes.

Modifier genes and susceptibility to colorectal cancer in individuals with Lynch syndrome

Lynch syndrome, is caused by inherited germ-line mutations in the DNA mismatch repair genes resulting in cancers at an early age, predominantly colorectal (CRC) and endometrial cancers. Though the median age at onset for CRC is about 45 years, disease penetrance varies suggesting that cancer susceptibility may be modified by environmental or other low-penetrance genes. Genetic variation due to polymorphisms in genes encoding metabolic enzymes can influence carcinogenesis by alterations in the expression and activity level of the enzymes. Variation in MTHFR, an important folate metabolizing enzyme can affect DNA methylation and DNA synthesis and variation in xenobiotic-metabolizing enzymes can affect the metabolism and clearance of carcinogens, thus modifying cancer risk. ^ This study examined a retrospective cohort of 257 individuals with Lynch syndrome, for polymorphisms in genes encoding xenobiotic-metabolizing enzymes-- CYP1A1 (I462V and MspI), EPHX1 (H139R and Y113H), GSTP1 (I105V and A114V), GSTM1 and GSTT1 (deletions) and folate metabolizing enzyme--MTHFR (C677T and A1298C). In addition, a series of 786 cases of sporadic CRC were genotyped for CYP1A1 I462V and EPHX1 Y113H to assess gene-gene interaction and gene-environment interaction with smoking in a case-only analysis. ^ Prominent findings of this study were that the presence of an MTHFR C677T variant allele was associated with a 4 year later age at onset for CRC on average and a reduced age-associated risk for developing CRC (Hazard ratio: 0.55; 95% confidence interval: 0.36–0.85) compared to the absence of any variant allele in individuals with Lynch syndrome. Similarly, Lynch syndrome individuals heterozygous for CYP1A1 I462V A>G polymorphism developed CRC an average of 4 years earlier and were at a 78% increased age-associated risk (Hazard ratio for AG relative to AA: 1.78; 95% confidence interval: 1.16-2.74) than those with the homozygous wild-type genotype. Therefore these two polymorphisms may be additional susceptibility factors for CRC in Lynch syndrome. In the case-only analysis, evidence of gene-gene interaction was seen between CYP1A1 I462V and EPHX1 Y113H and between EPHX1 Y113H and smoking suggesting that genetic and environmental factors may interact to increase sporadic CRC risk. Implications of these findings are the ability to identify subsets of high-risk individuals for targeted prevention and intervention. ^

Gene by smoking interaction in blood pressure

Hypertension (HT) is mediated by the interaction of many genetic and environmental factors. Previous genome-wide linkage analysis studies have found many loci that show linkage to HT or blood pressure (BP) regulation, but the results were generally inconsistent. Gene by environment interaction is among the reasons that potentially explain these inconsistencies between studies. Here we investigate influences of gene by smoking (GxS) interaction on HT and BP in European American (EA), African American (AA) and Mexican American (MA) families from the GENOA study. A variance component-based method was utilized to perform genome-wide linkage analysis of systolic blood pressure (SBP), diastolic blood pressure (DBP), and HT status, as well as bivariate analysis for SBP and DBP for smokers, non-smokers, and combined groups. The most significant results were found for SBP in MA. The strongest signal was for chromosome 17q24 (LOD = 4.2), increased to (LOD = 4.7) in bivariate analysis but there was no evidence of GxS interaction at this locus (p = 0.48). Two signals were identified only in one group: on chromosome 15q26.2 (LOD = 3.37) in non-smokers and chromosome 7q21.11 (LOD = 1.4) in smokers, both of which had strong evidence for GxS interaction (p = 0.00039 and 0.009 respectively). There were also two other signals, one on chromosome 20q12 (LOD = 2.45) in smokers, which became much higher in the combined sample (LOD = 3.53), and one on chromosome 6p22.2 (LOD = 2.06) in non-smokers. Neither peak had very strong evidence for GxS interaction (p = 0.08 and 0.06 respectively). A fine mapping association study was performed using 200 SNPs in 30 genes located under the linkage signals on chromosomes 15 and 17. Under the chromosome 15 peak, the association analysis identified 6 SNPs accounting for a 7 mmHg increase in SBP in MA non-smokers. For the chromosome 17 linkage peak, the association analysis identified 3 SNPs accounting for a 6 mmHg increase in SBP in MA. However, none of these SNPs was significant after correcting for multiple testing, and accounting for them in the linkage analysis produced very small reductions in the linkage signal. ^ The linkage analysis of BP traits considering the smoking status produced very interesting signals for SBP in the MA population. The fine mapping association analysis gave some insight into the contribution of some SNPs to two of the identified signals, but since these SNPs did not remain significant after multiple testing correction and did not explain the linkage peaks, more work is needed to confirm these exploratory results and identify the culprit variations under these linkage peaks. ^

Caracterización de poblaciones nativas de maíz mediante Análisis de Procrustes Generalizado y Análisis Factorial Múltiple

El establecimiento de relaciones entre taxones es un paso esencial en el proceso de catalogación y evaluación del material conservado en un Banco de Germoplasma. Existen distintos métodos de evaluación en función del tipo de caracteres estudiados. Cuando el registro de caracteres se repite en el tiempo y en distintos ambientes, se debe separar la variabilidad intrínsecamente genética entre los taxones de aquella que se debe al ambiente, y más aún, de la posible variabilidad debida a la interacción genotipo*ambiente para el posterior establecimiento de relaciones puramente filogenéticas. En el presente trabajo se estudia comparativamente la factibilidad de aplicación de dos estrategias de análisis estadístico para dar solución a este problema. La primera corresponde al análisis tradicional donde se realiza un Análisis de Componentes Principales sobre los caracteres promedios a lo largo de los diferentes ambientes; y la segunda son métodos más complejos en los cuales cada dato es originado por tres modos: individuos, variables y condiciones ambientales, tales como el Análisis Factorial Múltiple y el Análisis de Procrustes Generalizado. Si bien las configuraciones resultantes fueron todas equivalentes, los métodos de tres vías permiten la interpretación de la interacción genotipo*ambiente.

Efecto de la interacción genotipo-ambiente sobre la expresión del contenido de allicina y ácido pirúvico en ajo (Allium sativum L.)

La expresión de la intensidad del flavor en los bulbos de ajo (Allium sativum L.), depende tanto de factores genéticos como ambientales. Las características organolépticas se manifiestan por la presencia de compuestos organoazufrados, específicamente tiosulfinatos, siendo el representante mayoritario la allicina (diallil tiosulfinato). El ácido pirúvico constituye un producto secundario de la reacción enzimática generadora del flavor, por lo que su medición se asocia a la intensidad de pungencia en ajo. El objetivo del presente trabajo fue estudiar si la variabilidad en el contenido de allicina y pirúvico está más asociada a las características genéticas o a la influencia de las regiones de cultivo. Se seleccionaron cuatro cultivares (Castaño INTA, Sureño INTA, Lican INTA y Unión) pertenecientes al banco de germoplasma del Instituto Nacional de Tecnología Agropecuaria (INTA) La Consulta, Mendoza, Argentina, cultivados en diferentes zonas geográficas: La Consulta (Dpto. San Carlos, Mendoza), Esquel (Chubut) y Ushuaia (Tierra del Fuego). Se cuantificó la allicina mediante Cromatografía Líquida de Alta Resolución (HPLC) y pungencia mediante espectrofotometría. A partir del análisis estadístico de los valores obtenidos se puede inferir que existen diferencias significativas en el contenido de allicina y pirúvico entre distintas cultivares de una misma zona y en el contenido de allicina y pirúvico para la misma cultivar en distintas zonas.

Impact of thermal stress on evolutionary trajectories of pathogen resistance in three-spined stickleback (Gasterosteus aculeatus), supplementary material

Background: Pathogens are a major regulatory force for host populations, especially under stressful conditions. Elevated temperatures may enhance the development of pathogens, increase the number of transmission stages, and can negatively influence host susceptibility depending on host thermal tolerance. As a net result, this can lead to a higher prevalence of epidemics during summer months. These conditions also apply to marine ecosystems, where possible ecological impacts and the population-specific potential for evolutionary responses to changing environments and increasing disease prevalence are, however, less known. Therefore, we investigated the influence of thermal stress on the evolutionary trajectories of disease resistance in three marine populations of three-spined sticklebacks Gasterosteus aculeatus by combining the effects of elevated temperature and infection with a bacterial strain of Vibrio sp. using a common garden experiment. Results: We found that thermal stress had an impact on fish weight and especially on survival after infection after only short periods of thermal acclimation. Environmental stress reduced genetic differentiation (QST) between populations by releasing cryptic within-population variation. While life history traits displayed positive genetic correlations across environments with relatively weak genotype by environment interactions (GxE), environmental stress led to negative genetic correlations across environments in pathogen resistance. This reversal of genetic effects governing resistance is probably attributable to changing environment-dependent virulence mechanisms of the pathogen interacting differently with host genotypes, i.e. GPathogenxGHostxE or (GPathogenxE)x(GHostxE) interactions, rather than to pure host genetic effects, i.e. GHostxE interactions. Conclusion: To cope with climatic changes and the associated increase in pathogen virulence, host species require wide thermal tolerances and pathogen-resistant genotypes. The higher resistance we found for some families at elevated temperatures showed that there is evolutionary potential for resistance to Vibrio sp. in both thermal environments. The negative genetic correlation of pathogen resistance between thermal environments, on the other hand, indicates that adaptation to current conditions can be a weak predictor for performance in changing environments. The observed feedback on selective gradients exerted on life history traits may exacerbate this effect, as it can also modify the response to selection for other vital components of fitness.

Intentions: a confident-based interaction design for smart spaces

The paradigm of ubiquitous computing has become a reference for the design of Smart Spaces. Current trends in Ambient Intelligence are increasingly related to the scope of Internet of Things. This paradigm has the potential to support cost-effective solutions in the fields of telecare, e-health and Ambient Assisted Living. Nevertheless, ubiquitous computing does not provide end users with a role for proactive interactions with the environment. Thus, the deployment of smart health care services at a private space like the home is still unsolved. This PhD dissertation aims to define a person-environment interaction model to foster acceptability and users confidence in private spaces by applying the concept of user-centred security and the human performance model of seven stages of action.

One Hundred Years of Grain Omics: Identifying the Glutens That Feed the World.

Glutens, the storage proteins in wheat grains, are a major source of protein in human nutrition. The protein composition of wheat has therefore been an important focus of cereal research. Proteomic tools have been used to describe the genetic diversity of wheat germplasms from different origins at the level of polymorphisms in alleles encoding glutenin and gliadin, the two main proteins of gluten. More recently, proteomics has been used to understand the impact of specific gluten proteins on wheat quality. Here we review the impact of proteomics on the study of gluten proteins as it has evolved from fractionation and electrophoretic techniques to advanced mass spectrometry. In the postgenome era, proteomics is proving to be essential in the effort to identify and understand the interactions between different gluten proteins. This is helping to fill in gaps in our knowledge of how the technological quality of wheat is determined by the interaction between genotype and environment. We also collate information on the various storage protein alleles identified and their prevalence, which makes it possible to infer the effects of wheat selection on grain protein content. We conclude by reviewing the more recent use of transgenesis aimed at improving the quality of gluten.

Genetic and environmental factors modify bovine spongiform encephalopathy incubation period in mice

The incubation period (IP) and the neuropathology of transmissible spongiform encephalopathies (TSEs) have been extensively used to distinguish prion isolates (or strains) inoculated into panels of inbred mouse strains. Such studies have shown that the bovine spongiform encephalopathy (BSE) agent is indistinguishable from the agent causing variant Creutzfeldt–Jakob disease (vCJD), but differs from isolates of sporadic CJD, reinforcing the idea that the vCJD epidemic in Britain results from consumption of contaminated beef products. We present a mouse model for genetic and environmental factors that modify the incubation period of BSE cross-species transmission. We have used two mouse strains that carry the same prion protein (PrP) allele, but display a 100-day difference in their mean IP following intracerebral inoculation with primary BSE isolate. We report genetic effects on IP that map to four chromosomal regions, and in addition we find significant factors of host environment, namely the age of the host's mother, the age of the host at infection, and an X-cytoplasm interaction in the host.

High frequency of sex and equal frequencies of mating types in natural populations of the ciliate Tetrahymena thermophila.

In ciliate protists, sex involves the temporary joining of two cells of compatible mating type, followed by meiosis and exchange of gametic nuclei between conjugants. Reproduction is by asexual binary fission following conjugation. For the many ciliates with fixed multiple mating types, frequency-dependent sex-ratio theory predicts equal frequencies of mating types, if sex is common in nature. Here, we report that in natural populations of Tetrahymena thermophila sexually immature cells, indicative of recent conjugation, are found from spring through fall. In addition, the seven mating types occur in approximately equal frequencies, and these frequencies appear to be maintained by interaction between complex, multiple mat alleles and environmental conditions during conjugation. Such genotype-environment interaction determining mating type frequency is rare among ciliates.