Population genomic structures and signatures of selection define the genetic uniqueness of several fancy and meat rabbit breeds

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Abstract

Following the recent domestication process of the European rabbit (Oryctolagus cuniculus), many different breeds and lines, distinguished primarily by exterior traits such as coat colour, fur structure and body size and shape, have been constituted. In this study, we genotyped, with a high-density single-nucleotide polymorphism panel, a total of 645 rabbits from 10 fancy breeds (Belgian Hare, Champagne d'Argent, Checkered Giant, Coloured Dwarf, Dwarf Lop, Ermine, Giant Grey, Giant White, Rex and Rhinelander) and three meat breeds (Italian White, Italian Spotted and Italian Silver). ADMIXTURE analysis indicated that breeds with similar phenotypic traits (e.g. coat colour and body size) shared common ancestries. Signatures of selection using two haplotype-based approaches (iHS and XP-EHH), combined with the results obtained with other methods previously reported that we applied to the same breeds, we identified a total of 5079 independent genomic regions with some signatures of selection, covering about 1777 Mb of the rabbit genome. These regions consistently encompassed many genes involved in pigmentation processes (ASIP, EDNRA, EDNRB, KIT, KITLG, MITF, OCA2, TYR and TYRP1), coat structure (LIPH) and body size, including two major genes (LCORL and HMGA2) among many others. This study revealed novel genomic regions under signatures of selection and further demonstrated that population structures and signatures of selection, left into the genome of these rabbit breeds, may contribute to understanding the genetic events that led to their constitution and the complex genetic mechanisms determining the broad phenotypic variability present in these untapped rabbit genetic resources.

Alternative SNP weighting for multi‐step and single‐step genomic BLUP in the presence of causative variants

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Abstract

The accuracy of genetic selection in dairy can be increased by the adoption of new technologies, such as the inclusion of sequence data. In simulation studies, assigning different weights to causative single-nucleotide polymorphism (SNP) markers led to better predictions depending on the genomic prediction method used. However, it is still not clear how the weights should be calculated. Our objective was to evaluate the accuracy of a multi-step method (GBLUP) and single-step GBLUP with simulated data using regular SNP, causatives variants (QTN) and the combination of both. Additionally, we compared the accuracies of all previous scenarios using alternatives for SNP weighting. The data were simulated assuming a single trait with a heritability of 0.3. The effective population size (Ne) was approximately 200. The pedigree contained 440,000 animals, and approximately 16,800 individuals were genotyped. A total of 49,974 SNP markers were evenly placed throughout the genome, and 100, 1000 and 2000 causative QTN were simulated. Both GBLUP and ssGBLUP were used in this study. We evaluated quadratic and nonlinear SNP weights in addition to the unweighted G. The inclusion of QTN to panels led to significant accuracy gains. Nonlinear A was demonstrated to be superior to quadratic weighting and unweighted approaches; however, results from Nonlinear A were dependent on the equation parameters. The unweighted approach was more suitable for less polygenic scenarios. Finally, SNP weighting might help elucidate trait architecture features based on changes in the accuracy of genomic prediction.

Ascertaining the genetic background of the Celtic‐Iberian pig strain: A signatures of selection approach

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Abstract

Celtic-Iberian pig breeds were majority in Spain and Portugal until the first half of the 20th century. In the 1990s, they were nearly extinct as a result of the introduction of foreign improved pig breeds. Despite its historical importance, the genetic background of the Celtic-Iberian pig strain is poorly documented. In this study, we have identified genomic regions that might contain signatures of selection peculiar of the Celtic-Iberian genetic lineage. A total of 153 DNA samples of Celtic-Iberian pigs (Spanish Gochu Asturcelta and Portuguese Bísara breeds), Iberian pigs (Spanish Iberian and Portuguese Alentejano breeds), Cinta Senese pig, Korean local pig and Cosmopolitan pig (Hampshire, Landrace and Large White individuals) were analysed. A pairwise-comparison approach was applied: the Gochu Asturcelta and the Bísara samples as test populations and the five other pig populations as reference populations. Three different statistics (XP-EHH, F ST and ΔDAF) were computed on each comparison. Strict criteria were used to identify selection sweeps in order to reduce the noise brought on by the Gochu Asturcelta and Bísara breeds' severe population bottlenecks. Within test population, SNPs used to construct potential candidate genomic areas under selection were only considered if they were identified in four of ten two-by-two pairwise comparisons and in at least two of three statistics. Genomic regions under selection constructed within test population were subsequently overlapped to construct candidate regions under selection putatively unique to the Celtic-Iberian pig strain. These genomic regions were finally used for enrichment analyses. A total of 39 candidate regions, mainly located on SSC5 and SSC9 and covering 3130.5 kb, were identified and could be considered representative of the ancient genomic background of the Celtic-Iberian strain. Enrichment analysis allowed to identify a total of seven candidate genes (NOL12, LGALS1, PDXP, SH3BP1, GGA1, WIF1, and LYPD6). Other studies reported that the WIF1 gene is associated with ear size, one of the characteristic traits of the Celtic-Iberian pig strain. The function of the other candidate genes could be related to reproduction, adaptation and immunity traits, indirectly fitting with the rusticity of a non-improved pig strain traditionally exploited under semi-extensive conditions.

Phenological description and thermal time requirements for the seedling phase of three Brazilian native forest species

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Phenological description and thermal time requirements for the seedling phase of three Brazilian native forest species

Morphology of the germination process (epigeal) and seedlings development stages of Libidibia ferrea (co: cotyledon; e1-e2: first pair of eophylls; in: embryo; ep: epicotyl; fr: fruit; hp: hypocotyl; me: metaphyll; pr: primary root; se: seed). Drawings made by Bruna Oliveira Borges.


Abstract

Understanding the phenological stages and thermal requirements of the seedling phase of forest species is crucial for sustainable nursery management. This study proposed an adaptation of a phenological scale based on the basic Biologische Bundesanstalt, Bundessortenamt, and Chemical industry, associated with the thermal requirement to describe the phenological stages during the seedling phase of three forest species: Cybistax antisyphilitica, Libidibia ferrea, and Platycyamus regnellii. The phenological scale of C. antisyphilitica and L. ferrea was defined and described through 22 seedling development stages ranging from dry seed to 20th visible leaf emitted on the main stem (from 00 to 120) and P. regnellii for 12 leaf development stages, from dry seed to 10th visible leaf emitted on the main stem (from 00 to 110). In addition, the duration (days) and thermal time (°C day) were determined for each seedling development stage. C. antisyphilitica needs to accumulate more energy (and days) to finish the seedling phase (1551.9°C day or 261 days) compared to L. ferrea (1127°C day or 175 days) and P. regnellii (1109.7°C day or 193 days). However, the three forest species exhibit similar energy demands throughout most stages of seedling development, except code 09–12 for C. antisyphilitica. This study provides important information for optimizing silvicultural techniques, evaluating the response of temperature on phenological stages, and assessing the impacts of global warming on forest seedling development.

Effect of in ovo feeding of folic acid on Disabled‐1 and gga‐miR‐182‐5p expression in the cerebral cortex of chick embryo

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Abstract

Folate (vitamin B9) has been shown to reduce the prevalence of neural tube defects (NTDs). Many genes comprising Disabled-1 (DAB1) and miRNAs have been shown to play important role in normal brain development. Reelin-signalling has been shown to play key role in regulating of neuronal migration during brain development. The aim of this study was to evaluate the effects of in ovo administration of folic acid (FA) on DAB1 and gga-miR-182-5p expression in the cerebral cortex of chick embryo. A total number of 30 hatching eggs were used in this study. The number of 10 eggs were injected into the yolk sac with FA (150 µg/egg), 10 eggs by normal saline (sham group) on embryonic day 11 and 10 eggs were left without injection as control. Then the cerebral cortices were collected on E19 and the expression of DAB1 and gga-miR-182-5p was studied by Real-Time PCR. The results showed that DAB1 expression in the cerebral cortex of FA-treated, sham and control were 2.51 ± 0.13, 1.01 ± 0.04 and 1.03 ± 0.04 fold changes, respectively, and this amount for gga-miR-182-5p were 0.54 ± 0.03, 1.09 ± 0.07 and 1.00 ± 0.06-fold change respectively. Statistical analysis showed that there is a significant increase in DAB1 and a decrease in gga-miR-182-5p expression in FA injected cerebral cortex as compared either with either SHAM or control (p < 0.0001). But, no significant change in DAB1 and gga-miR-182-5p expression was observed between sham and the control group (p = 0.99 and p = 0.57 respectively). It is concluded that in ovo feeding of FA increases DAB1 and decreases gga-miR-182-5p expression in the developing chick cerebral cortex.

Scaffold, mechanics and functions of nuclear lamins

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Scaffold, mechanics and functions of nuclear lamins

Nuclear lamins, constituents of the nuclear lamina, bridge the gap between the nuclear membranes and chromatin. Here we discuss the lamins’ structure, assembly dynamics and their interactions with chromatin. We focus on the mechanical roles of lamins, from molecular to network scales, and finalize by linking the structural, mechanical, and molecular properties of lamins with biological function and disease.


Nuclear lamins are type-V intermediate filaments that are involved in many nuclear processes. In mammals, A- and B-type lamins assemble into separate physical meshwork underneath the inner nuclear membrane, the nuclear lamina, with some residual fraction localized within the nucleoplasm. Lamins are the major part of the nucleoskeleton, providing mechanical strength and flexibility to protect the genome and allow nuclear deformability, whilst also contributing to gene regulation via interactions with chromatin. While lamins are the evolutionary ancestors of all intermediate filament family proteins, their ultimate filamentous assembly is markedly different from their cytoplasmic counterparts. Interestingly, hundreds of genetic mutations in the lamina proteins have been causally linked with a broad range of human pathologies, termed laminopathies. These include muscular, neurological and metabolic disorders, as well as premature aging diseases. Recent technological advances have contributed to resolving the filamentous structure of lamins and the corresponding lamina organization. In this review we revisit the multiscale lamin organization and discuss its implications on nuclear mechanics and chromatin organization within lamina associated domains.

Impact of pubertal timing and socioeconomic status on adult height and body proportions in Igbo ethnicity

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Abstract

Objectives

Age at menarche is a marker of pubertal timing that may influence adult height and body proportions. Previous studies have shown that socioeconomic status can affect age at menarche and growth patterns in different populations. This study aims to examine the associations between age at menarche, socioeconomic status, height, and leg length in a sample of Igbo ethnicity.

Methods

The study used data from questionnaires and anthropometric measurements of 300 female students aged 18–25 years. Study tested the hypotheses that earlier menarche is associated with shorter stature and shorter leg length, and that these associations are modified by socioeconomic status using nonparametric analysis.

Results

Mean age at menarche was fluctuating around 12.84 ± 1.40 and 13.59 ± 1.41 years with school girls and grew 3.0 cm taller per year birth cohort. The study also found that girls with earlier menarche were shorter adult height (162.51 ± 6.00) compared with girls who have menarche at a later age. The linear regression coefficients (bs) ranged from 0.37–0.49 in later year birth cohort and 0.37–0.44 in early year birth cohort for height. The effect of age at menarche on leg length was similar to the relation between age at menarche and birth cohort height.

Conclusion

The study will contribute to the understanding of how pubertal timing and socioeconomic status interact to shape adult health outcomes in a transitioning population.

Community food environment and childhood obesity in a medium‐sized Brazilian city: An approach to school and neighborhood environments

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Abstract

Objective

We aimed to analyze the relationship of community food environments with childhood obesity in a medium-sized Brazilian city.

Methods

This is a cross-sectional study with 366 schoolchildren aged 8 and 9 years. Children's body mass index (BMI), waist circumference and concentrations of total cholesterol (TC), high cholesterol density lipoprotein (HDL-c), low cholesterol density lipoprotein (LDL-c) and triglycerides (TG) were measured. The parent's nutritional status was assessed by calculating the BMI. All food stores within a 200- and 400-m radius buffers of schools and households were evaluated. The food stores were classified as healthy, unhealthy, and mixed according to the predominance of foods commercialized. Binary logistic regression models were proposed for each category.

Results

Over seventy percent (70.2%) of the food stores were categorized as “unhealthy”. The prevalence of obesity was 15.6%. In the 200-m buffer around schools, there was an inverse and direct association between obesity and the presence of healthy food stores and unhealthy food stores, respectively. Around the households, there was an inverse association between the presence of healthy food stores and obesity in both buffers.

Conclusion

The community food environment may be protective or potentiating childhood obesity, depending on the access and types of food sold.

A comparative study of different sleep assessment methods for preschool children

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Abstract

Purpose

This study aimed to examine the differences between different sleep assessment methods for preschool children.

Methods

Preschool children (n = 54, mean age: 4.6 years) were recruited from kindergarten. Data were collected using an accelerometer, a sleep log, and sleep questionnaire. Furthermore, correlation analysis, Bland–Altman analysis, and repeated measures ANOVA were performed.

Results

(1) The sleep duration evaluated by different sleep assessment methods were all significantly correlated, among which the sleep log and Sadeh algorithm showed the highest correlation (r = 0.972, p < .001), while the Tudor-Locke algorithm and the sleep questionnaire demonstrated the lowest correlation (r = 0.383, p < .01); (2) The points between different sleep assessment methods were all within 95% LoA, except for the sleep log and Tudor-Locke algorithm; (3) In various methods of sleep assessment, significant differences were observed in sleep onset (F2 (1.6,85.0) = 32.8, p < .001, η2: 0.38), while no significant differences were observed in sleep offset (F2 (1.5,80.1) = 32.8, p = .05, η2: 0.05); (4) In addition, no significant difference in sleep onset was observed between the sleep questionnaire and sleep log (p > .05), and there was also no significant difference in sleep onset between the Sadeh algorithm and the Tudor-Locke algorithm (p > .05).

Conclusions

Both the Sadeh algorithm and the Tudor-Locke algorithm can be used as effective algorithms for sleep duration assessment of Chinese preschool children, with the latter having obvious advantages in large sample surveys. Future research should pay attention to the differences between different sleep assessment methods when using these algorithms.

Mapping spatial morbidity patterns for bronchiolitis related to socioeconomic estimators: A spatial epidemiology approach to identify health disparities in Puerto Madryn, Argentina

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Abstract

Objectives

To describe the frequency of hospitalizations of infants under 1 year of age with bronchiolitis in Puerto Madryn, Argentina, and to study the spatial distribution of cases throughout the city in relation to socioeconomic indicators. To visualize and better understand the underlying processes behind the local manifestation of the disease by creating a vulnerability map of the city.

Methods

We performed a cross-sectional study of all patients discharged for bronchiolitis from the local public Hospital in 2017, considering length of hospital stay, readmission rate, patient age, home address and socioeconomic indicators (household overcrowding). To understand the local spatial distribution of the disease and its relationship to overcrowding, we used GIS and Moran's global and local spatial autocorrelation indices.

Results

The spatial distribution of bronchiolitis cases was not random, but significantly aggregated. Of the 120 hospitalized children, 100 infants (83.33%) live in areas identified as having at least one unsatisfied basic need (UBN). We found a positive and statistically significant relationship between frequency of cases and percentage of overcrowded housing by census radius.

Conclusions

A clear association was found between bronchiolitis and neighborhoods with UBNs, and overcrowding is likely to be a particularly important explanatory factor in this association. By combining GIS tools, spatial statistics, geo-referenced epidemiological data, and population-level information, vulnerability maps can be created to facilitate visualization of priority areas for development and implementation of more effective health interventions. Incorporating the spatial and syndemic perspective into health studies makes important contributions to the understanding of local health-disease processes.