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1.
Background
We investigate the power of heterogeneity LOD test to detect linkage when a trait is determined by several major genes using Genetic Analysis Workshop 13 simulated data. We consider three traits, two of which are disease-causing traits: 1) the rate of change in body mass index (BMI); and 2) the maximum BMI; and 3) the disease itself (hypertension). Of interest is the power of "HLOD2", the maximum heterogeneity LOD obtained upon maximizing over the two genetic models.Results
Using a trait phenotype Obesity Slope, we observe that the power to detect the two markers closest to the two genes (S1, S2) at the 0.05 level using HLOD2 is 13% and 10%. The power of HLOD2 for Max BMI phenotype is 12% and 9%. The corresponding values for the Hypertension phenotype are 8% and 6%.Conclusion
The power to detect linkage to the slope genes is quite low. But the power using disease-related traits as a phenotype is greater than the power using the disease (hypertension) phenotype.2.
Jiangbao Xia Jiayun Ren Ximei Zhao Fengjuan Zhao Hongjun Yang Junhua Liu 《Plant and Soil》2018,424(1-2):157-169
Background and aims
Functional traits may underlie differences in niches, which promote plant species co-existence, but also differences in competitive ability, which drive competitive exclusion. Empirical evidence concerning the contribution of different traits to niche differentiation and the ability to supress and tolerate competitors is very limited, particularly when considering belowground interactions.Methods
We grew 26 temperate grassland species along a density gradient of interspecific competitors to determine which belowground traits a) explain species’ ability to suppress and tolerate neighbours and b) contribute to niche differentiation, such that species with dissimilar trait values experience reduced competition.Results
We found that having larger root systems with extensive horizontal spread and lower root tissue density enabled efficient suppression of neighbours but did not significantly contribute to the ability to tolerate competition. Species with deeper root systems, lower specific root length and less branched roots were better at tolerating competition, but these traits did not significantly affect the ability to suppress neighbours. None of the measured traits contributed significantly to niche differentiation, either individually or in combination.Conclusions
This study provides little support for belowground traits contributing to species co-existence through niche differentiation. Instead, different sets of weakly correlated traits enable plants to either suppress or tolerate their competitors.3.
Background
The Framingham Heart Study has contributed a great deal to advances in medicine. Most of the phenotypes investigated have been univariate traits (quantitative or qualitative). The aims of this study are to derive multivariate traits by identifying homogeneous groups of people and assigning both qualitative and quantitative trait scores; to assess the heritability of the derived traits; and to conduct both qualitative and quantitative linkage analysis on one of the heritable traits.Methods
Multiple correspondence analysis, a nonparametric analogue of principal components analysis, was used for data reduction. Two-stage clustering, using both k-means and agglomerative hierarchical clustering, was used to cluster individuals based upon axes (factor) scores obtained from the data reduction. Probability of cluster membership was calculated using binary logistic regression. Heritability was calculated using SOLAR, which was also used for the quantitative trait analysis. GENEHUNTER-PLUS was used for the qualitative trait analysis.Results
We found four phenotypically distinct groups. Membership in the smallest group was heritable (38%, p < 1 × 10-6) and had characteristics consistent with atherogenic dyslipidemia. We found both qualitative and quantitative LOD scores above 3 on chromosomes 11 and 14 (11q13, 14q23, 14q31). There were two Kong &; Cox LOD scores above 1.0 on chromosome 6 (6p21) and chromosome 11 (11q23).Conclusion
This approach may be useful for the identification of genetic heterogeneity in complex phenotypes by clarifying the phenotype definition prior to linkage analysis. Some of our findings are in regions linked to elements of atherogenic dyslipidemia and related diagnoses, some may be novel, or may be false positives.4.
Background
Trait based functional and community ecology is en vogue. Most studies, however, ignore phenotypical diversity by characterizing entire species considering only trait means rather than their variability. Phenotypical variability may arise from genotypical differences or from ecological factors (e.g., nutritionally imbalanced diet), and these causes can usually not be separated in natural populations. We used a single genotype from a parthenogenetic model system (the oribatid mite Archegozetes longisetosus Aoki) to exclude genotypical differences. We investigated patterns of dietary (10 different food treatments) induced trait variation by measuring the response of nine different traits (relating to life history, morphology or exocrine gland chemistry).Results
Nutritional quality (approximated by carbon-to-nitrogen ratios) influenced all trait means and their variation. Some traits were more prone to variation than others. Furthermore, the “threshold elemental ratio”- rule of element stoichiometry applied to phenotypic trait variation. Imbalanced food (i.e. food not able to fully meet the nutritional demands of an animal) led to lower trait mean values, but also to a higher variation of traits.Conclusion
Imbalanced food led not only to lower trait value averages, but also to higher trait variability. There was a negative relationship between both parameters, indicating a direct link of both, average trait levels and trait variation to nutritional quality. Hence, variation of trait means may be a predictor for general food quality, and further indicate trade-offs in specific traits an animal must deal with while feeding on imbalanced diets.5.
Background and aims
Selection for deep roots to improve drought tolerance of maize (Zea mays L.) requires presence of genetic variation and suitable screening methods.Methods
We examined a diverse set of 33 tropical maize inbred lines that were grown in growth columns in the greenhouse up to the 2-, 4-, and 6-leaf stage and in the field in Mexico. To determine length of roots from different depths at high throughput, we tested an approach based on staining roots with methylene blue and measuring the amount of absorbed dye as proxy measure for root length.Results
Staining provided no advantage over root weights that are much easier to measure and therefore preferable. We found significant genotypic variation for all traits at the 6-leaf stage. For development rates between the 2-leaf and the 6-leaf stage, genotypes only differed for rooting depth and the number of crown roots. Positive correlations of leaf area with root length and rooting depth indicated a common effect of plant vigor. However, leaf area in growth columns was negatively related to grain yield under drought (r?=??0.50).Conclusion
The selection for deeper roots by an increase in plant vigor likely results in a poorer performance under drought conditions. The proportion of deep roots was independent of other traits but showed a low heritability and was not correlated to field performance. An improved screening protocol is proposed to increase throughput and heritability for this trait.6.
B. Gómez-Muñoz L. S. Jensen A. de Neergaard A. E. Richardson J. Magid 《Plant and Soil》2018,429(1-2):159-174
Background and aims
Functional traits are promising indicators of global changes and ecosystem processes. Trait responses to environmental conditions have been examined widely in vascular plants. In contrast, few studies have focused on soil lichens and mosses composing biocrusts. We aimed to evaluate the potential of biocrust tissue traits as indicators of changes in climate and soil properties.Methods
Isotope ratios and nutrient content in biocrust tissue were analyzed in 13 Mediterranean shrublands along an aridity gradient. Differences in tissue traits between biocrust groups (lichens and mosses), and relationships between tissue traits and climatic and soil variables were examined.Results
Lichens and mosses differed in δ13C, δ15N and N content, indicating distinct physical and physiological attributes. Tissue traits correlated strongly with numerous climatic variables, likely due to a modulator effect on biocrust water relations and metabolism. We found contrasting responses of lichen and moss traits to climate, although they responded similarly to soil properties. Overall, the most responsive trait was δ15N, suggesting this trait is the best to reflect integrated processes occurring in the atmosphere and soil.Conclusions
Biocrust tissue traits arise as cost-effective, integrative ecological indicators of global change drivers in Mediterranean ecosystems, with potential applications in response-effect trait frameworks.7.
Background
With the development of high-throughput genotyping and sequencing technology, there are growing evidences of association with genetic variants and complex traits. In spite of thousands of genetic variants discovered, such genetic markers have been shown to explain only a very small proportion of the underlying genetic variance of complex traits. Gene-gene interaction (GGI) analysis is expected to unveil a large portion of unexplained heritability of complex traits.Methods
In this work, we propose IGENT, Information theory-based GEnome-wide gene-gene iNTeraction method. IGENT is an efficient algorithm for identifying genome-wide gene-gene interactions (GGI) and gene-environment interaction (GEI). For detecting significant GGIs in genome-wide scale, it is important to reduce computational burden significantly. Our method uses information gain (IG) and evaluates its significance without resampling.Results
Through our simulation studies, the power of the IGENT is shown to be better than or equivalent to that of that of BOOST. The proposed method successfully detected GGI for bipolar disorder in the Wellcome Trust Case Control Consortium (WTCCC) and age-related macular degeneration (AMD).Conclusions
The proposed method is implemented by C++ and available on Windows, Linux and MacOSX.8.
Yuki Motomura Yuka Egashira Takayuki Nishimura Yeon-kyu Kim Shigeki Watanuki 《Journal of physiological anthropology》2015,34(1):14
Background
Neuroimaging studies continue to indicate the major role the anterior cingulate cortex (ACC) plays in processing empathic responses. Error-related negativity (ERN), an event-related potential (ERP) thought to arise from the ACC, has been found to correlate with scores for individual empathic personality. This study investigated the relationship between empathic personality traits and the amplitude of feedback-related negativity (FRN), an ERP sourced from the ACC and similar to the ERN, using a task involving feedback of monetary gains or losses.Methods
Sixteen healthy participants answered an empathy trait questionnaire and performed a gambling task to elicit FRN. Because FRN amplitude is thought to be associated with attention, motivation, emotional state, and anxiety trait, we performed a partial correlation analysis between the empathic trait score and FRN amplitude while controlling for variables.Results
In partial correlation analysis, FRN amplitude was significantly inversely correlated with scores for personal distress and marginally correlated with scores for empathic concern and with total average score.Discussion
The study revealed for the first time an association between FRN and emotional empathic traits, after controlling for variables that can affect FRN amplitude. However, we also found a reversed directional correlation contrary to our expectations. This fronto-central brain activity may be associated with empathic properties via dopaminergic neuronal function. Future study using these electric potentials as experimental tools is expected to help elucidate the neurological mechanism of empathy.9.
Background
The purpose of this study was to determing which psychological traits of Japanese type 2 diabetes patients would provide reliability and validity to the Japanese version of the Acceptance and Action Diabetes Questionnaire (AADQ-J).Methods
Various questionnaires were administered to type 2 diabetes patients who were registered on the database of the research service provider; data from a total of 600 patients (mean?±?SD age was 57.50?±?9.87 years, female 21.83%) were analyzed.Results
Three items were excluded because of psychometric concerns related to the original 11-item AADQ. Confirmation factor analyses revealed that the eight-item version demonstrated the best indicators of a goodness of fit. The questionnaire showed adequate internal consistency. The questionnaire demonstrated high measurement accuracy in broad trait values by the test information function of Item Response Theory. The questionnaire showed stronger positive correlations with self-care activities and HbA1c than with diabetes distress and depressive mood.Conclusions
The eight-item Japanese version of AADQ has reliability and validity for type 2 diabetes patients.10.
Olusegun O. Osunkoya Olufemi A. Akinsanmi Layla S. A. Lim Christine Perrett Jason Callander Kunjithapatham Dhileepan 《Plant and Soil》2017,412(1-2):177-188
Background and aims
Competition from the annual grass Bromus tectorum threatens aridland perennial bunchgrass communities. Unlike annuals, perennials must allocate part of their first year nitrogen (N) budget to storage rather than growth, potentially placing them at a competitive disadvantage.Methods
We evaluated N acquisition and conservation for two perennial bunchgrasses, Agropyron desertorum and Pseudoroegneria spicata, at the seedling stage to investigate potential trade-offs between storage and growth when grown with and without B. tectorum under two levels of soil N.Results
Agropyron desertorum had higher growth rates, N uptake, and N productivity than P. spicata when grown without B. tectorum, but trait values were similarly low for both species under competition. Without competition, N resorption was poor under high soil N, but it was equally proficient among species under competition.Conclusions
A. desertorum had higher growth rates and N productivity than P. spicata without competition, suggesting these traits may in part promote its greater success in restoration programs. However, B. tectorum neighbors reduced its trait advantage. As plant traits become more integral to restoration ecology, understanding how N capture and conservation traits vary across candidate species and under competition may improve our ability to select species with the highest likelihood of establishing in arid, nutrient-limited systems.11.
Background
Obtaining atomic-scale information about large-amplitude conformational transitions in proteins is a challenging problem for both experimental and computational methods. Such information is, however, important for understanding the mechanisms of interaction of many proteins.Methods
This paper presents a computationally efficient approach, combining methods originating from robotics and computational biophysics, to model protein conformational transitions. The ability of normal mode analysis to predict directions of collective, large-amplitude motions is applied to bias the conformational exploration performed by a motion planning algorithm. To reduce the dimension of the problem, normal modes are computed for a coarse-grained elastic network model built on short fragments of three residues. Nevertheless, the validity of intermediate conformations is checked using the all-atom model, which is accurately reconstructed from the coarse-grained one using closed-form inverse kinematics.Results
Tests on a set of ten proteins demonstrate the ability of the method to model conformational transitions of proteins within a few hours of computing time on a single processor. These results also show that the computing time scales linearly with the protein size, independently of the protein topology. Further experiments on adenylate kinase show that main features of the transition between the open and closed conformations of this protein are well captured in the computed path.Conclusions
The proposed method enables the simulation of large-amplitude conformational transitions in proteins using very few computational resources. The resulting paths are a first approximation that can directly provide important information on the molecular mechanisms involved in the conformational transition. This approximation can be subsequently refined and analyzed using state-of-the-art energy models and molecular modeling methods.12.
13.
Background
Hypovitaminosis D is prevalent worldwide. It is more prevalent in Eastern Asia region, including Korea. In addition to various environmental factors that influence serum 25-hydroxyvitamin D (25(OH)D) concentration, genetic influence also plays a significant role based on studies estimating the heritability of 25(OH)D in non-Asian populations. The objective of this study was to determine the genetic influence on serum 25(OH)D concentration in Korean men using the twin and family data.Methods
A total of 1126 Korean male adult twins and family members from the Healthy Twin Study with serum 25(OH)D measurement were included in this cross-sectional study. Intraclass correlation coefficients (ICCs) and heritability were calculated by mixed linear regression analysis and quantitative genetic analysis after adjusting for environmental and lifestyle factors.Results
Mean (±?standard deviation; SD) of serum 25(OH)D concentration was 15.34?±?6.18?ng/ml. The prevalence of vitamin D insufficiency was 19.8% and that of vitamin D deficiency was 77.9%. After adjusting for age, the highest ICC (0.61) was observed for monozygotic twin pairs while the lowest ICC (0.31) was found for father-son pairs. Age-adjusted heritability was estimated to be 58%. When physical activity, multivitamin intake and season of blood sampling were further considered, the ICC and heritability did not materially change. In the sensitivity analysis after excluding known multivitamin users, age-adjusted heritability was reduced to 44%.Conclusions
In our study of Korean male twins and family members, heritability of 25(OH)D was moderately high. This supports the finding that genetic factors have significant influence on vitamin D status.14.
Background
Genomic analyses have the potential to impact selective breeding programs by identifying markers that serve as proxies for traits which are expensive or difficult to measure. Also, identifying genes affecting traits of interest enhances our understanding of their underlying biochemical pathways. To this end we conducted genome scans of seven rainbow trout families from a single broodstock population to identify quantitative trait loci (QTL) having an effect on stress response to crowding as measured by plasma cortisol concentration. Our goal was to estimate the number of major genes having large effects on this trait in our broodstock population through the identification of QTL.Results
A genome scan including 380 microsatellite markers representing 29 chromosomes resulted in the de novo construction of genetic maps which were in good agreement with the NCCCWA genetic map. Unique sets of QTL were detected for two traits which were defined after observing a low correlation between repeated measurements of plasma cortisol concentration in response to stress. A highly significant QTL was detected in three independent analyses on Omy16, many additional suggestive and significant QTL were also identified. With linkage-based methods of QTL analysis such as half-sib regression interval mapping and a variance component method, we determined that the significant and suggestive QTL explain about 40-43% and 13-27% of the phenotypic trait variation, respectively.Conclusions
The cortisol response to crowding stress is a complex trait controlled in a sub-sample of our broodstock population by multiple QTL on at least 8 chromosomes. These QTL are largely different from others previously identified for a similar trait, documenting that population specific genetic variants independently affect cortisol response in ways that may result in different impacts on growth. Also, mapping QTL for multiple traits associated with stress response detected trait specific QTL which indicate the significance of the first plasma cortisol measurement in defining the trait. Fine mapping these QTL can lead towards the identification of genes affecting stress response and may influence approaches to selection for this economically important stress response trait.15.
Sheng Qin Wei-Wei Feng Tian-Tian Wang Peng Ding Ke Xing Ji-Hong Jiang 《Plant and Soil》2017,415(1-2):117-130
Background and aims
Xylem-tapping mistletoes may experience relaxed selective pressure to use water efficiently during photosynthesis because of lower per-unit costs for water acquisition than experienced by host plants. As a result, we hypothesised that mistletoes would exhibit parallel but dampened leaf-level adaptations and responses to aridity, compared to those seen in hosts.Methods
Photosynthetic traits, leaf dark respiration, nutrient concentrations and specific leaf area (SLA) were measured on 42 mistletoe-host species-pairs sampled from five sites in Australia and Brazil that vary widely in aridity.Results
Mistletoes exhibited similar trait-shifts to hosts in relation to site aridity. In both groups, arid-site species showed stronger control over stomatal water loss, larger drawdown of CO2 during photosynthesis (lower ci: ca), higher leaf N and P concentrations per unit leaf area, and lower SLA. Nevertheless, mistletoes were profligate water users compared to their hosts and showed substantially less efficient use of water during photosynthesis. On average, mistletoes showed twice higher leaf dark respiration rates at a given photosynthetic capacity, suggesting relatively higher leaf maintenance costs for these parasitic plants.Conclusions
Despite fundamental differences in lifestyle and in photosynthetic traits, mistletoes exhibit trait responses and adaptations to site aridity in parallel and to approximately the same extent as their hosts.16.
Plant-soil feedbacks and root responses of two Mediterranean oaks along a precipitation gradient 总被引：1，自引：0，他引：1
Aims
Plant-soil feedbacks (PSFs) have been shown to be relevant drivers of forest community dynamics. However, few studies have explored variation of PSFs along environmental gradients. In a framework of climate change, there is a great need to understand how interactions between plants and soil microbes respond along climatic gradients. Therefore, we compared PSFs along a precipitation gradient in Mediterranean oak forests and included trait responses. Following the Stress Gradient Hypothesis (SGH), we expected less negative or even positive PSFs in the physically harsh dry end of our gradient and more negative PSFs in the wettest end.Methods
We grew Quercus ilex and Quercus suber acorns on soil inoculated with microbes sampled under adults of both species in six sites ranging in annual precipitation. After 4 months, we measured shoot biomass and allocation and morphological traits above and belowground.Results
We found negative PSFs for Q. ilex independent of precipitation, whereas for Q. suber PSFs ranged from positive in dry sites to negative in wet sites, in agreement with the SGH. The leaf allocation showed patterns similar to shoot biomass, but belowground allocation and morphological traits revealed responses which could not be detected aboveground.Conclusions
We provide first evidence for context-dependent PSFs along a precipitation gradient. Moreover, we show that measuring root traits can help improve our understanding of climate-dependent PSFs. Such understanding helps to predict plant soil microbe interactions, and their role as drivers of plant community dynamics under ongoing climate change.17.
Fern&#;ndez-Rhodes Lindsay Howard Annie Green Tao Ran Young Kristin L. Graff Mariaelisa Aiello Allison E. North Kari E. Justice Anne E. 《BMC genetics》2018,19(1):69-14
Background
Transgenerational epigenetic inheritance has been posited as a possible contributor to the observed heritability of metabolic syndrome (MetS). Yet the extent to which estimates of epigenetic inheritance for DNA methylation sites are inflated by environmental and genetic covariance within families is still unclear. We applied current methods to quantify the environmental and genetic contributors to the observed heritability and familial correlations of four previously associated MetS methylation sites at three genes (CPT1A, SOCS3 and ABCG1) using real data made available through the GAW20.Results
Our findings support the role of both shared environment and genetic variation in explaining the heritability of MetS and the four MetS cytosine-phosphate-guanine (CpG) sites, although the resulting heritability estimates were indistinguishable from one another. Familial correlations by type of relative pair generally followed our expectation based on relatedness, but in the case of sister and parent pairs we observed nonsignificant trends toward greater correlation than expected, as would be consistent with the role of shared environmental factors in the inflation of our estimated correlations.Conclusions
Our work provides an interesting and flexible statistical framework for testing models of epigenetic inheritance in the context of human family studies. Future work should endeavor to replicate our findings and advance these methods to more robustly describe epigenetic inheritance patterns in human populations.18.
Rob van Treuren Henriette D. L. M. van Eekelen Ron Wehrens Ric C. H. de Vos 《Metabolomics : Official journal of the Metabolomic Society》2018,14(11):146
Introduction
Lettuce (Lactuca sativa L.) is generally not specifically acknowledged for its taste and nutritional value, while its cultivation suffers from limited resistance against several pests and diseases. Such key traits are known to be largely dependent on the ability of varieties to produce specific phytochemicals.Objectives
We aimed to identify promising genetic resources for the improvement of phytochemical composition of lettuce varieties.Methods
Phytochemical variation was investigated using 150 Lactuca genebank accessions, comprising a core set of the lettuce gene pool, and resulting data were related to available phenotypic information.Results
A hierarchical cluster analysis of the variation in relative abundance of 2026 phytochemicals, revealed by untargeted metabolic profiling, strongly resembled the known lettuce gene pool structure, indicating that the observed variation was to a large extent genetically determined. Many phytochemicals appeared species-specific, of which several are generally related to traits that are associated with plant health or nutritional value. For a large number of phytochemicals the relative abundance was either positively or negatively correlated with available phenotypic data on resistances against pests and diseases, indicating their potential role in plant resistance. Particularly the more primitive lettuces and the closely related wild relatives showed high levels of (poly)phenols and vitamin C, thus representing potential genetic resources for improving nutritional traits in modern crop types.Conclusion
Our large-scale analysis of phytochemical variation is unprecedented in lettuce and demonstrated the ample availability of suitable genetic resources for the development of improved lettuce varieties with higher nutritional quality and more sustainable production.19.
Incorporating pleiotropic quantitative trait loci in dissection of complex traits: seed yield in rapeseed as an example 总被引：1，自引：0，他引：1
Ziliang Luo Meng Wang Yan Long Yongju Huang Lei Shi Chunyu Zhang Xiang Liu Bruce D. L. Fitt Jinxia Xiang Annaliese S. Mason Rod J. Snowdon Peifa Liu Jinling Meng Jun Zou 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2017,130(8):1569-1585
Key message
A comprehensive linkage atlas for seed yield in rapeseed.Abstract
Most agronomic traits of interest for crop improvement (including seed yield) are highly complex quantitative traits controlled by numerous genetic loci, which brings challenges for comprehensively capturing associated markers/genes. We propose that multiple trait interactions underlie complex traits such as seed yield, and that considering these component traits and their interactions can dissect individual quantitative trait loci (QTL) effects more effectively and improve yield predictions. Using a segregating rapeseed (Brassica napus) population, we analyzed a large set of trait data generated in 19 independent experiments to investigate correlations between seed yield and other complex traits, and further identified QTL in this population with a SNP-based genetic bin map. A total of 1904 consensus QTL accounting for 22 traits, including 80 QTL directly affecting seed yield, were anchored to the B. napus reference sequence. Through trait association analysis and QTL meta-analysis, we identified a total of 525 indivisible QTL that either directly or indirectly contributed to seed yield, of which 295 QTL were detected across multiple environments. A majority (81.5%) of the 525 QTL were pleiotropic. By considering associations between traits, we identified 25 yield-related QTL previously ignored due to contrasting genetic effects, as well as 31 QTL with minor complementary effects. Implementation of the 525 QTL in genomic prediction models improved seed yield prediction accuracy. Dissecting the genetic and phenotypic interrelationships underlying complex quantitative traits using this method will provide valuable insights for genomics-based crop improvement.20.
Hugues de Verdal Marc Vandeputte Wagdy Mekkawy Béatrice Chatain John A. H. Benzie 《BMC genetics》2018,19(1):105