Categorical Trait Research Articles

Segregation GWAS to linearize a non-additive locus with incomplete penetrance: an example of horn status in sheep

BackgroundThe objective of this study was to introduce a genome-wide association study (GWAS) in conjunction with segregation analysis on monogenic categorical traits. Genotype probabilities calculated from phenotypes, mode of inheritance and pedigree information, are expressed as the expected allele count (EAC) (range 0 to 2), and are inherited additively, by definition, unlike the original phenotypes, which are non-additive and could be of incomplete penetrance. The EAC are regressed on the single nucleotide polymorphism (SNP) genotypes, similar to an additive GWAS. In this study, horn phenotypes in Merino sheep are used to illustrate the advantages of using the segregation GWAS, a trait believed to be monogenic, affected by dominance, sex-dependent expression and likely affected by incomplete penetrance. We also used simulation to investigate whether incomplete penetrance can cause prediction errors in Merino sheep for horn status.ResultsEstimated penetrance values differed between the sexes, where males showed almost complete penetrance, especially for horned and polled phenotypes, while females had low penetrance values for the horned status. This suggests that females homozygous for the ‘horned allele’ have a horned phenotype in only 22% of the cases while 78% will be knobbed or have scurs. The GWAS using EAC on 4001 animals and 510,174 SNP genotypes from the Illumina Ovine high-density (600k) chip gave a stronger association compared to using actual phenotypes. The correlation between the EAC and the allele count of the SNP with the highest –log10(p-value) was 0.73 in males and 0.67 in females. Simulations using penetrance values found by the segregation analyses resulted in higher correlations between the EAC and the causative mutation (0.95 for males and 0.89 for females, respectively), suggesting that the most predictive SNP is not in full LD with the causative mutation.ConclusionsOur results show clear differences in penetrance values between males and female Merino sheep for horn status. Segregation analysis for a trait with mutually exclusive phenotypes, non-additive inheritance, and/or incomplete penetrance can lead to considerably more power in a GWAS because the linearized genotype probabilities are additive and can accommodate incomplete penetrance. This method can be extended to any monogenic controlled categorical trait of which the phenotypes are mutually exclusive.

CoRRE Trait Data: A dataset of 17 categorical and continuous traits for 4079 grassland species worldwide

In our changing world, understanding plant community responses to global change drivers is critical for predicting future ecosystem composition and function. Plant functional traits promise to be a key predictive tool for many ecosystems, including grasslands; however, their use requires both complete plant community and functional trait data. Yet, representation of these data in global databases is sparse, particularly beyond a handful of most used traits and common species. Here we present the CoRRE Trait Data, spanning 17 traits (9 categorical, 8 continuous) anticipated to predict species’ responses to global change for 4,079 vascular plant species across 173 plant families present in 390 grassland experiments from around the world. The dataset contains complete categorical trait records for all 4,079 plant species obtained from a comprehensive literature search, as well as nearly complete coverage (99.97%) of imputed continuous trait values for a subset of 2,927 plant species. These data will shed light on mechanisms underlying population, community, and ecosystem responses to global change in grasslands worldwide.

Variability in spectral absorption within cryptophyte phycobiliprotein types.

Cryptophytes are known to vary widely in coloration among species. These differences in color arise primarily from the presence of phycobiliprotein accessory pigments. There are nine defined cryptophyte phycobiliprotein (Cr-PBP) types, named for their wavelength of maximal absorbance. Because Cr-PBP type has traditionally been regarded as a categorical trait, there is a paucity of information about how spectral absorption characteristics of Cr-PBPs vary among species. We investigated variability in primary and secondary peak absorbance wavelengths and full width at half max (FWHM) values of spectra of Cr-PBPs extracted from 75 cryptophyte strains (55 species) grown under full spectrum irradiance. We show that there may be substantial differences in spectral shapes within Cr-PBP types, with Cr-Phycoerythrin (Cr-PE) 545 showing the greatest variability with two, possibly three, subtypes, while Cr-PE 566 spectra were the least variable, with only ±1 nm of variance around the mean absorbance maximum of 565 nm. We provide additional criteria for classification in cases where the wavelength of maximum absorbance alone is not definitive. Variations in spectral characteristics among strains containing the same presumed Cr-PBP type may indicate differing chromophore composition and/or the presence of more than one Cr-PBP in a single cryptophyte species.

Evolution of larval gregariousness is associated with host plant specialisation, but not host morphology, in Heliconiini butterflies.

Insect herbivores, such as lepidopteran larvae, often have close evolutionary relationships with their host plants, with which they may be locked in an evolutionary arms race. Larval grouping behaviour may be one behavioural adaptation that improves host plant feeding, but aggregation also comes with costs, such as higher competition and limited resource access. Here, we use the Heliconiini butterfly tribe to explore the impact of host plant traits on the evolution of larval gregariousness. Heliconiini almost exclusively utilise species from the Passifloraceae as larval host plants. Passifloraceae display incredible diversity in leaf shape and a range of anti-herbivore defences, suggesting they are responding to, and influencing, the evolution of Heliconiini larvae. By analysing larval social behaviour as both a binary (solitary or gregarious) and categorical (increasing larval group size) trait, we revisit the multiple origins of larval gregariousness across Heliconiini. We investigate whether host habitat, leaf defences and leaf size are important drivers of, or constraints on, larval gregariousness. Whereas our data do not reveal links between larval gregariousness and the host plant traits included in this study, we do find an interaction between host plant specialisation and larval behaviour, revealing gregarious larvae to be more likely to feed on a narrower range of host plant species than solitary larvae. We also find evidence that this increased specialisation typically precedes the evolutionary transition to gregarious behaviour. The comparatively greater host specialisation of gregarious larvae suggests that there are specific morphological and/or ecological features of their host plants that favour this behaviour.

Testing phylogenetic signal with categorical traits and tree uncertainty.

The phylogenetic signal, frequently used to identify signatures of adaptive evolution or important associations between genes and phenotypes, measures the tendency for recently diverged species to resemble each other more than distantly related species. An example of such a measure is the δ statistic, which uses Shannon entropy to measure the degree of phylogenetic signal between a categorical trait and a phylogeny. In this study, we refined this statistic to account for tree uncertainty, resulting in more accurate assessments of phylogenetic associations. Additionally, we provided a more accessible and computationally efficient implementation of the δ statistic that will facilitate its use by the evolutionary community. github.com/diogo-s-ribeiro/delta-statistic. Supplementary data are available at Bioinformatics online.

Evaluation of Respondent-Driven Sampling Prevalence Estimators Using Real-World Reported Network Degree.

Respondent-driven sampling (RDS) is used to measure trait or disease prevalence in populations that are difficult to reach and often marginalized. The authors evaluated the performance of RDS estimators under varying conditions of trait prevalence, homophily, and relative activity. They used large simulated networks (N = 20,000) derived from real-world RDS degree reports and an empirical Facebook network (N = 22,470) to evaluate estimators of binary and categorical trait prevalence. Variability in prevalence estimates is higher when network degree is drawn from real-world samples than from the commonly assumed Poisson distribution, resulting in lower coverage rates. Newer estimators perform well when the sample is a substantive proportion of the population, but bias is present when the population size is unknown. The choice of preferred RDS estimator needs to be study specific, considering both statistical properties and knowledge of the population under study.

Cross-walking personality disorder types to ICD-11 trait domains: An overview of current findings.

The ICD-11 has adopted a classification of Personality Disorders (PD) that abolishes the established categorical PD types in favor of global severity classification with specification of individual trait domains. To facilitate and guide this profound transition, an overview of current research on empirical associations between established PD types and ICD-11 trait domains seems warranted. We identified a total of 9 relevant studies from 2018 to 2022, which were based on both clinical and community samples from U.S., China, Brazil, Denmark, Spain, Korea, and Canada. The patterns of associations with ICD-11 trait domains were systematically synthesized and portrayed for each PD type. Findings overall showed expected and conceptually meaningful associations between categorical PD types and ICD-11 trait domains, with only few deviations. Based on these findings, we propose a cross-walk for translating categorical PD types into ICD-11 trait domains. More research is needed in order to further guide continuity and translation between ICD-10 and ICD-11 PD classification in mental healthcare, including facet-level ICD-11 trait information. Moreover, the nine reviewed studies only relied on self-reported ICD-11 trait domains, which should be expanded with clinician-rated trait domains in future research. Finally, future research should also take ICD-11's essential PD severity classification into account.

Mapping and Validation of Alectra vogelii Resistance in the Cowpea Landrace B301

Cowpea is the most important food legume in West and Central Africa and a valuable economic commodity in the region. Among the major biotic constraints to cowpea production are root parasitic weeds of which Alectra vogelii (Benth.) is of increasing importance. The cowpea landrace B301 was previously identified as a source of Alectra resistance, but neither the genes nor genomic loci conferring this resistance have been mapped. Therefore, to map and identify genetic markers linked to Alectra resistance for use in the molecular improvement of cowpea, we developed an F2 population from a cross of the susceptible variety 524B with B301. The population was phenotyped for resistance to A. vogelii and genotyped with a cowpea high density single nucleotide polymorphism (SNP) microarray. Putative resistance loci were mapped in F2 populations by categorical trait–multiple interval mapping and validated by selective genotyping. Selective genotyping indicated that the resistance loci on Vu04 (Rav1) and Vu11 (Rav2) were significantly associated with resistance (p ≤ 0.01). Using marker assisted backcrossing, the two resistance loci were introgressed independently into the susceptible 524B genetic background. Phenotyping and genotyping of the segregating backcross families delineated Rav1 to a 10 cM on chromosome 4 and Rav2 to a 6.7 cM interval in chromosome 11. These two loci are desirable for breeding Alectra resistant cowpea varieties due to their simple inheritance and ability to independently confer complete immunity to the parasite.

MiCloud: A unified web platform for comprehensive microbiome data analysis.

The recent advance in massively parallel sequencing has enabled accurate microbiome profiling at a dramatically lowered cost. Then, the human microbiome has been the subject of intensive investigation in public health and medicine. In the meanwhile, researchers have developed lots of microbiome data analysis methods, protocols, and/or tools. Among those, especially, the web platforms can be highlighted because of the user-friendly interfaces and streamlined protocols for a long sequence of analytic procedures. However, existing web platforms can handle only a categorical trait of interest, cross-sectional study design, and the analysis with no covariate adjustment. We therefore introduce here a unified web platform, named MiCloud, for a binary or continuous trait of interest, cross-sectional or longitudinal/family-based study design, and with or without covariate adjustment. MiCloud handles all such types of analyses for both ecological measures (i.e., alpha and beta diversity indices) and microbial taxa in relative abundance on different taxonomic levels (i.e., phylum, class, order, family, genus and species). Importantly, MiCloud also provides a unified analytic protocol that streamlines data inputs, quality controls, data transformations, statistical methods and visualizations with vastly extended utility and flexibility that are suited to microbiome data analysis. We illustrate the use of MiCloud through the United Kingdom twin study on the association between gut microbiome and body mass index adjusting for age. MiCloud can be implemented on either the web server (http://micloud.kr) or the user's computer (https://github.com/wg99526/micloudgit).

Bayesian threshold analysis of litter size in sheep

Background: Litter size at birth (LSB) is one of the most important economic traits in sheep and could be used in genetic improvement schemes for meat production. LSB is inherently a categorical trait and should be analysed with threshold models. Objective: Bayesian threshold models were used to analyze sheep LSB to estimate genetic parameters. Methods: Data was based on 7,901 LSB records from 14,968 dams and 682 sires collected from 1986 to 2012 at Makouie Sheep Breeding Station in Iran. Means of posterior distributions (MPDs) of LSB's genetic parameters were estimated, and the best-fitted models were selected using the deviance information criterion. Results: In the repeated measurement analysis, the estimated direct and maternal heritabilities, and permanent environmental effect (±SE), according to the best-fitted model (model 5), were 0.01 (0.010), 0.02 (0.014), and 0.01 (0.011), respectively. In the univariate analysis, the best estimates of direct and maternal heritabilities were 0.12 (0.064) and 0.08 (0.045), respectively. An increasing trend for direct and maternal heritabilities was observed in parity 2 (0.15 (0.082) and 0.25 (0.083), respectively). In the bivariate analysis, the best estimates of direct and maternal heritabilities for LSB were 0.03 (0.027) and 0.22 (0.041), respectively. The direct and maternal genetic correlations among parities were 0.25 (0.054) and 0.12 (0.021), respectively. Conclusions: The results showed a considerable influence of environmental factors on LSB in each parity of sheep; also, statistically different genetic parameters (p<0.05) were obtained from one parity to another, indicating the different and large influences of genetic and environmental factors for each parity.

Гносеологічна категорія ознаки в англійській епізоотологічній термінології

The conceptual sphere of epizootology as a veterinary science is characterized by such epistemological categories as the categories of process and state, action, object, sign, space, time. One of the main categories for the terminology of all scientific fields is the category of trait. In conceptual and linguistic aspects, the category of trait in epizootology is one of the most complex epistemological categories. This is due to the variety of concepts of veterinary science, the number of manifestations of pathological processes, the evolution of medical knowledge, reflected in the semantics of terms, and the relative subjectivity of human thinking, able to create definitions of scientific concepts based on various analogies and personal associations. The purpose of the article is to determine the category of sign of epizootological terminology in English and to investigate their role in the classification of zoonotic diseases. Materials and methods of research. The source base of the work were the terms obtained by the method of continuous sampling from the texts of scientific literature in English (publications of scientific journals, materials of the Internet) and veterinary lexicographical sources. The main methods used in the study were systematization and categorical analysis of epizootological terms-zoonoses. Results of the research. The studied category is widely used in epizootological terminology, as it is one of the basic categories used to classify the concepts expressed by the terms zoonoses. In conceptual and linguistic aspects, the category of trait in epizootology is one of the most complex epistemological categories. This is due to the variety of concepts of veterinary science, the number of manifestations of pathological processes, the evolution of medical knowledge, reflected in the semantics of terms, and the relative subjectivity of human thinking, able to create definitions of scientific concepts based on various analogies and personal associations. The most striking category of the trait in epizootological terminology is represented in zoonoses, generalized names of natural focal infections, i.e. such infectious diseases that are usually common in animals, but can sometimes be transmitted from animals to humans. In epizootology, the category of the sign has a pragmatic significance, which is explained by the need for precise indication of specific signs of pathological processes. A number of epistemological category of sign are reflected in the studied terminology: temporal, spatial, color, causal, quantitative, etc. Dominant among the English terms were zoonoses, which have a temporal categorical feature, which indicates the specifics of the zoonotic disease, its duration, nature, age, and so on. The second categorical feature, which is often represented by the terms-zoonoses, is color, which plays an important role in establishing the diagnosis, stage of the disease and the degree of its spread. The causal categorical feature, according to which the English terms-zoonoses are structured, indicates a causal relationship. There are common terms in which the names of zoonotic diseases indicate the pathogenic microbes and viruses that caused the infectious disease. The spatial categorical feature, which is represented by zoonotic terms, is often represented by toponym terms. A less common categorical trait, which is represented by the terms zoonoses, is quantitative. Сonclusions. The studied category is widely used in epizootological terminology, as it is one of the basic categories used to classify the concepts expressed by the terms-zoonoses. We see the prospect of the study in identifying a set of language tools in English that are used in epizootological terminology to verbalize the category of trait.

A 44-kb deleted-type copy number variation is associated with decreasing complement component activity and calf mortality in Japanese Black cattle

BackgroundCalf mortality generally occurs in calves prior to weaning, which is a serious problem in cattle breeding. Several causative variants of monogenic Mendelian disorders in calf mortality have been identified, whereas genetic factors affecting the susceptibility of calves to death are not well known. To identify variants associated with calf mortality in Japanese Black cattle, we evaluated calf mortality as a categorical trait with a threshold model and performed a genome-wide copy number variation (CNV) association study on calf mortality.ResultsWe identified a 44-kb deleted-type CNV ranging from 103,317,687 to 103,361,802 bp on chromosome 5, which was associated with the mortality of 1–180-day-old calves. The CNV harbored C1RL, a pseudogene, and an IncRNA localized in the C1R and C1S gene cluster, which is a component of the classical complement activation pathway for immune complexes for infectious pathogens. The average complement activity in CNVR_221 homozygotes at postnatal day 7 was significantly lower than that of wild-type animals and heterozygotes. The frequency of the risk allele in dead calves suffering from diarrhea and pneumonia and in healthy cows was 0.35 and 0.28, respectively (odds ratio = 2.2, P = 0.016), suggesting that CNVR_221 was associated with the mortality of Japanese Black calves suffering from an infectious disease.ConclusionsThis study identified a deleted-type CNV associated with the mortality of 1–180-day-old calves. The complement activity in CNVR_221 homozygotes was significantly lower than that in heterozygotes and wild type animals. The frequency of the risk allele was higher in dead calves suffering from an infectious disease than in healthy cows. These results suggest that the existence of CNVR_221 in calves could be attributed to a reduction in complement activity, which in turn leads to susceptibility to infections. Thus, the risk allele could serve as a useful marker to reduce the mortality of infected Japanese Black calves.

A genome-wide association study reveals a quantitative trait locus for calf mortality on chromosome 9 in Japanese Black cattle.

Calf mortality is a major problem affecting cattle production. To identify genetic variants associated with calf mortality in Japanese Black cattle, we evaluated calf mortality as a categorical trait using a threshold model and conducted a GWAS. We identified two SNPs between 32549 297 and 32606 924bp on bovine chromosome 9 that were significantly associated with calf mortality from 61 to 180days after birth. The SNP showing the highest association was localized at a region 624bp downstream of exon 4 of the anti-silencing function 1A histone chaperone gene (ASF1A) that promotes DNA damage repair, and the null mice, which exhibit pre- and postnatal lethality. This association was also detected using the breeding value of 334 sires. The frequency of the risk allele in Japanese Black cattle from locations across Japan was 0.013; although the frequency of ASF1A risk allele was low, it is widespread in the Japanese Black cattle population. Thus, it may be necessary to routinely monitor the cattle population for the presence of this allele.

Phenotypic and genomic relationships between vulva score categories and reproductive performance in first-parity sows

BackgroundOne of the biggest challenges in the swine industry is to increase female reproductive efficiency. Recently, vulva score categories (VSC), assessed prior to puberty, has been proposed as an indicator trait of efficient reproductive performance in sows. The objective of this study was to validate the use of VSC as an indicator trait for reproductive performance, and to perform genetic and genomic analyses for VSC.MethodsThe phenotypic relationship of VSC, using a three-point scale: small (VSC-S), medium (VSC-M), and large (VSC-L), on reproductive performance was evaluated on three farms. VSC was measured at 15 weeks of age, for farms 1 and 2, and at 14 weeks of age for farm 3 on 3981 Yorkshire gilts, in which 1083 had genotypes (~ 50 K SNPs). Genetic parameters for VSC with reproductive traits were estimated using ssGBLUP. A Genome-wide association study (GWAS) for VSC was performed using BayesB.ResultsFor the phenotypic analysis of VSC across datasets, differences in performance were identified there was a significant effect (P ≤ 0.05) for the interaction between Farm and VSC for total number dead (TND), and a trend (P < 0.10) for total number born (TNB). There were significant (P ≤ 0.05) pre-defined contrasts of VSC-S versus VSC-M + L on TNB, number born alive (NBA), TND, number of stillborn (NSB), and number of mummies (MUM). Heritability estimates for VSC as a categorical trait (VSCc) and a quantitative trait (VSCq) were 0.40 ± 0.02 and 0.83 ± 0.02, respectively, for across farm, 0.13 ± 0.07 and 0.20 ± 0.10, respectively, for Farm1, 0.07 ± 0.07 and 0.09 ± 0.09, respectively, for Farm2, and 0.20 ± 0.03 and 0.34 ± 0.05, respectively, for Farm3. For across farms, favorable genetic correlations estimates were found for TNB (0.28 ± 0.19) and NBA (0.26 ± 0.17). Within farms, moderate genetic correlations between VSC with reproductive traits were found for TNB (0.61 ± 0.47) and MUM (0.69 ± 0.47) for farm 1, for number of services until first farrow (NS; 0.69 ± 0.38) and unique service with successful first farrow (SFS; − 0.71 ± 0.38) for farm 3. Multiple genomic regions associated with VSCc were identified. Of these, a QTL located on chromosome 3 at 33–34 Mb accounted for about 7.1% of the genetic variance for VSCc and VSCq. This region harbors the gene PRM1 that has been associated with early embryonic development in pigs.ConclusionsThe results support potential of VSC for improved reproductive efficiency on first-parity performance, but the results might depend on the interaction between environmental factors and VSC, as well as potentially additive genetics.

Testing Pollination Syndromes in &lt;i&gt;Oenothera&lt;/i&gt; (Onagraceae)

Pollinators are considered a major selective force in shaping the diversification of angiosperms. It has been hypothesized that convergent evolution of floral form has resulted in “pollination syndromes” - i.e. suites of floral traits that correspond to attraction of particular pollinator functional groups. Across the literature, the pollination syndrome concept has received mixed support. This may be due to studies using different methods to describe floral traits and/or the pollination syndrome concept being supported more often in species highly reliant on pollinators for reproduction. Here, we assess the predictive ability of pollination syndromes in Oenothera, a species rich clade with pollination systems existing on a gradient of specialization, and in which species are either self-compatible or self-incompatible. We ask the following questions: Do Oenothera species follow the pollination syndrome concept using traditional, categorical floral trait descriptions and/or quantitative floral trait measurements? And, are floral traits more predictive of primary pollinators in species with specialized pollination systems and/or species that are self-incompatible? Mapping floral traits of 54 Oenothera species into morphospace, we do not find support for the pollination syndrome concept using either categorical or quantitative floral trait descriptions. We do not find support for specialization or breeding system influencing the prediction of primary pollinators. However, we find pollination syndromes were more predictive in Oenothera species with moth pollination systems. Collectively, these results suggest that the pollination syndrome concept cannot be generally applied across taxa and that evolutionary history is important to consider when evaluating the relationship between floral form and contemporary pollinators.

Single-step genomic evaluation of lambing ease in Australian terminal sire breed sheep

Context Australian sheep breeding values (ASBVs) for the categorical trait of lambing ease are routinely estimated by Sheep Genetics via a threshold model. This has been pedigree-only, and has not utilised genomic information. Aim The present study aimed to update the genetic evaluation model and parameters for lambing ease for terminal sire sheep (dominated by White Suffolk and Poll Dorset breeds). The model includes correlations with birthweight and gestation length. Cross-validation was used to determine the value of the improved models and the inclusion of genomic information. Methods New data-preparation pipelines were developed to accommodate improved data-filtering methods and contemporary group construction. Genetic parameters, including correlations among traits, were estimated using continuous and threshold models, with various combinations of effects in mixed animal models. Cross-validation of breeding values was performed against progeny performance, by using forward prediction. Key results The increased volume of data, improved data preparation steps and enhanced evaluation software now allow a more complex model to be fitted, including maternal, sire by flock-year and genetic group effects, which were significant for all traits, along with the inclusion of multiple sire groups in the pedigree. However, the inclusion of the direct-maternal covariance and sire by flock-year terms resulted in unrealistically inflated estimates of some components, and thus the final covariance matrices required some adjustments. Cross-validation of breeding values was performed against progeny performance using forward prediction. For all traits, the phenotype accuracies and estimated breeding value correlations were higher from the new model without genomics than were those from the current routine evaluation. The benefit from including genomic information based on cross-validation is minimal currently but is expected to improve as the size of the reference population grows. Further work is required to define acceptable data-quality thresholds for the construction of datasets for routine breeding value estimation. Conclusions The new model and parameters resulted in ASBVs with an improved predictive ability, with increased accuracy and reduced bias compared with the current analysis. Furthermore, a small increase in accuracy was observed for all traits from utilising genomic information in the model. Implications The new genetic evaluation procedures and models will be used to update those being applied in the routine Sheep Genetics evaluation system and also support further index development for the terminal sire breeds in Australia.

Model comparisons for genetic evaluation of gait type in Mangalarga Marchador horses

Mangalarga Marchador (MM) is a very important Brazilian gaited horse breed. These animals show two gait types, differing in proportion of lateral or diagonal movements. Thus, it is possible to consider the gait type as a binary categorical trait in our statistical models. Threshold models (TM) are strongly recommended to handle binary traits for genetic evaluation purposes. However, TM are susceptible to the extreme categorical problem (ECP). ECP is usually observed due to the absence of variation within subclasses for a given systematic effect and can be avoided after handling this effect as random or by combining different systematic effects in the model. In this context, we aimed to find the most suitable systematic effect (based on goodness-of-fit and predictive ability) to be included in Bayesian threshold model for the genetic evaluation of gait type in MM horses. The dataset consisted of 1,231 gait type records and 3,172 animals in the pedigree file. Phenotypic record associated with gait type was treated as a categorical trait (MP = 0 and MB = 1). In summary, models with small complexity were benefited by smaller bias and average prediction errors. Additionally, these models showed higher heritability estimates. ECP was an important issue, and should always be approached when using threshold models for genetic evaluation.

Феномен влечения к алкоголю и фибриноген

Введение. Фибриноген, как и многие белки системы гемостаза и фибринолиза, участвует во многих физиологических процессах, при этом его содержание может увеличиваться или уменьшаться при различных патологических состояниях, и эти модуляции часто служат диагностическим признаком заболевания. Цель исследования: определить уровень фибриногена и время лизиса эуглобулиновой фракции плазмы крови в зависимости от степени влечения к этанолу у крыс. Материалы и методы. Работа выполнена на 300 крысах-самцах линии Вистар весом 250–350 г, у которых после двух-недельного периода акклиматизации ежедневно в течение 7 дней проводили тестирование потребления 10% раствора этанола и воды в индивидуальных боксах. Эти жидкости были доступны в течение 23 часов без доступа к пище. Позиции 2 питьевых пипеток объемом 50 мл случайным образом менялись местами через каждые 24 часа. Результаты. Установлено, что чем выраженнее была исходная степень влечения к этанолу, тем выше оказывалось содержание фибриногена и ниже фибринолитическая активность. Заключение. Случаи повышенного содержания фибриногена у исходно отвергающих, не имевших контакта с этанолом крыс указывает на возможность генетически обусловленной гиперфибриногенемии, которая может стать источником предтромбозных состояний в случае предрасположенности к потреблению алкоголя в качестве энергетической самокоррекции. Introduction. Fibrinogen, like many proteins of hemostasis and fi brinolysis system, participates in many physiological processes, and its content may increase or decrease under various pathological conditions, and these modulations often serve as a diagnostic sign of the disease. Aim: to determine fi brinogen level and euglobulin lysis time as function of attraction degree to ethanol in rats. Materials and methods. The work was performed on male Wistar rats (n = 300) weighing 250–350 g. After 2 weeks of acclimatization the consumption of 10% ethanol and water in individual boxes was daily tested for 7 days. These fl uids were available for 23 hours without access to food. Positions of 2 drinking pipettes of 50 ml volume randomly changed every 24 hours. Results. It was found that fi brinogen content was higher but fi brinolytic activity was lower in rats with more expressed initial degree of attraction to ethanol. Conclusion. The cases of increased fi brinogen content in initially refused rats that did not contact with ethanol indicate the possibility of genetically determined hyperfi brinogenemia that can become a source of prethrombotic conditions in case of predisposition to alcohol consumption as an energy self-correction.

General retrospective mega‐analysis framework for rare variant association tests

Here, we describe a retrospective mega-analysis framework for gene- or region-based multimarker rare variant association tests. Our proposed mega-analysis association tests allow investigators to combine longitudinal and cross-sectional family- and/or population-based studies. This framework can be applied to a continuous, categorical, or survival trait. In addition to autosomal variants, the tests can be applied to conduct mega-analyses on X-chromosome variants. Tests were built on study-specific region- or gene-level quasiscore statistics and, therefore, do not require estimates of effects of individual rare variants. We used the generalized estimating equation approach to account for complex multiple correlation structures between family members, repeated measurements, and genetic markers. While accounting for multilevel correlations and heterogeneity across studies, the test statistics were computationally efficient and feasible for large-scale sequencing studies. The retrospective aspect of association tests helps alleviate bias due to phenotype-related sampling and type I errors due to misspecification of phenotypic distribution. We evaluated our developed mega-analysis methods through comprehensive simulations with varying sample sizes, covariates, population stratification structures, and study designs across multiple studies. To illustrate application of the proposed framework, we conducted a mega-association analysis combining a longitudinal family study and a cross-sectional case-control study from Genetic Analysis Workshop 19.

Relationship between Acropora millepora juvenile fluorescence and composition of newly established Symbiodinium assemblage.

Coral-dinoflagellate symbiosis is the key biological interaction enabling existence of modern-type coral reefs, but the mechanisms regulating initial host–symbiont attraction, recognition and symbiont proliferation thus far remain largely unclear. A common reef-building coral, Acropora millepora, displays conspicuous fluorescent polymorphism during all phases of its life cycle, due to the differential expression of fluorescent proteins (FPs) of the green fluorescent protein family. In this study, we examine whether fluorescent variation in young coral juveniles exposed to natural sediments is associated with the uptake of disparate Symbiodinium assemblages determined using ITS-2 deep sequencing. We found that Symbiodinium assemblages varied significantly when redness values varied, specifically in regards to abundances of clades A and C. Whether fluorescence was quantified as a categorical or continuous trait, clade A was found at higher abundances in redder juveniles. These preliminary results suggest juvenile fluorescence may be associated with Symbiodinium uptake, potentially acting as either an attractant to ecologically specific types or as a mechanism to modulate the internal light environment to control Symbiodinium physiology within the host.