Variation In Allele Frequencies Research Articles

Drug Metabolizing Enzymes: An Exclusive Guide into Latest Research in Pharmaco-genetic Dynamics in Arab Countries.

Drug metabolizing enzymes play a crucial role in the pharmacokinetics and pharmacodynamics of therapeutic drugs, influencing their efficacy and safety. This review explores the impact of genetic polymorphisms in drug-metabolizing genes on drug response within Arab populations. We examine the genetic diversity specific to Arab countries, focusing on the variations in key drug-metabolizing enzymes such as CYP450, GST, and UGT families. The review highlights recent research on polymorphisms in these genes and their implications for drug metabolism, including variations in allele frequencies and their effects on therapeutic outcomes. Additionally, the paper discusses how these genetic variations contribute to the variability in drug response and adverse drug reactions among individuals in Arab populations. By synthesizing current findings, this review aims to provide a comprehensive understanding of the pharmacogenetic landscape in Arab countries and offer insights into personalized medicine approaches tailored to genetic profiles. The findings underscore the importance of incorporating pharmacogenetic data into clinical practice to enhance drug efficacy and minimize adverse effects, ultimately paving the way for more effective and individualized treatment strategies in the region.

Biological Insights from Schizophrenia-associated Loci in Ancestral Populations.

Large-scale genome-wide association studies of schizophrenia have uncovered hundreds of associated loci but with extremely limited representation of African diaspora populations. We surveyed electronic health records of 200,000 individuals of African ancestry in the Million Veteran and All of Us Research Programs, and, coupled with genotype-level data from four case-control studies, realized a combined sample size of 13,012 affected and 54,266 unaffected persons. Three genome-wide significant signals - near PLXNA4, PMAIP1, and TRPA1 - are the first to be independently identified in populations of predominantly African ancestry. Joint analyses of African, European, and East Asian ancestries across 86,981 cases and 303,771 controls, yielded 376 distinct autosomal loci, which were refined to 708 putatively causal variants via multi-ancestry fine-mapping. Utilizing single-cell functional genomic data from human brain tissue and two complementary approaches, transcriptome-wide association studies and enhancer-promoter contact mapping, we identified a consensus set of 94 genes across ancestries and pinpointed the specific cell types in which they act. We identified reproducible associations of schizophrenia polygenic risk scores with schizophrenia diagnoses and a range of other mental and physical health problems. Our study addresses a longstanding gap in the generalizability of research findings for schizophrenia across ancestral populations, underlining shared biological underpinnings of schizophrenia across global populations in the presence of broadly divergent risk allele frequencies.

Estimation of genetic variation in vitiligo associated genes: Population genomics perspective

BackgroundVitiligo is an auto-immune progressive depigmentation disorder of the skin due to loss of melanocytes. Genetic risk is one of the important factors for development of vitiligo. Preponderance of vitiligo in certain ethnicities is known which can be analysed by understanding the distribution of allele frequencies across normal populations. Earlier GWAS identified 108 risk alleles for vitiligo in Europeans and East Asians. In this study, 64 of these risk alleles were used for analysing their enrichment and depletion across populations (1000 Genomes Project and IndiGen) with reference to 1000 Genomes dataset. Genetic risk scores were calculated and Fisher’s exact test was performed to understand statistical significance of their variation in each population with respect to 1000 Genomes dataset as reference. In addition to SNPs reported in GWAS, significant variation in allele frequencies of 1079 vitiligo-related genes were also analysed. Two-tailed Chi-square test and Bonferroni’s multiple adjustment values along with fixation index (≥ 0.5) and minimum allele frequency (≥ 0.05) were calculated and used to prioritise the variants based on pairwise comparison across populations.ResultsRisk alleles rs1043101 and rs10768122 belong to 3 prime UTR of glutamate receptor gene SLC1A2 are found to be highly enriched in the South Asian population when compared with the ‘global normal’ population. Intron variant rs4766578 (ATXN2) was found to be deleted in SAS, EAS and AFR and enriched in EUR and AMR1. This risk allele is found to be under positive selection in SAS, AMR1 and EUR. From the ancillary vitiligo gene list, nonsynonymous variant rs16891982 was found to be enriched in the European and the Admixed American populations and depleted in all others. rs2279238 and rs11039155 belonging to the LXR-α gene involved in regulation of metalloproteinase 2 and 9 (melanocyte precursors) were found to be associated with vitiligo in the North Indian population (in earlier study).ConclusionThe differential enrichment/depletion profile of the risk alleles provides insight into the underlying inter-population variations. This would provide clues towards prioritisation of SNPs associated with vitiligo thereby elucidating its preponderance in different ethnic groups.

GENETIC DETERMINANTS OF CARBOHYDRATE METABOLISM: INTRA- AND INTERETHNIC VARIABILITY OF THE LACTASE LCT, TREHALASE TREH AND SUCRASE-ISOMALTASE SI GENES IN THE EVENKI AND OTHER INDIGENOUS PEOPLES OF SIBERIA

Introduction. The authors consider the features of genetic determinants of disaccharide assimilation as the corollary of adaptation to the environment. The aim of the study was to assess the polymorphism of the genes that determine activity of disaccharidase enzymes lactase (LCT, rs4988235), trehalase (TREH, rs2276064) and sucrase-isomaltase (SI, rs781470490) in different territorial groups of Evenks. Materials and methods. Biomaterial samples from 1365 unrelated individuals representing 15 ethno-territorial population groups in European Russia, Siberia, and the Far East of the Russian Federation were genotyped. "Focus" groups include "Western" (N=65), "Transbaikal" (N=50), and "Okhotsk" (N=81) Evenks (Krasnoyarsk Krai, Northern Transbaikalia, Okhotsk-Aldan region). The other study groups allow us to assess the specificity of the distribution of genetic determinants of disaccharide assimilation in populations that differ from racial, ecological, and subsistence perspectives. Results. The Evenki territory subgroups do not differ from each other in terms of allele frequencies and genotype distribution of LCT (p>0.2) and TREH (p>0.8) and are similar to Yakuts, Buryats, Mongols, and populations of the Far East and Chukotka. The SI delAG deletion was not found in the Western Evenki subgroup. Discussion. A question of similarity between taiga hunters Evenks to cattle breeders Buryats, Mongols, and Yakuts in terms of C*LCT frequencies requires further elaboration. Possible explanations may include a weakening of selection for the T*LCT allele due to the shift in traditional diet toward replacement of fresh milk with fermented dairy products, high activity of specific intestinal microflora, or the existence of other lactase synthesis genetic determinants, besides LCT*C/T-13910. The evolutionary origins of the clinal variation in the TREH gene allele frequencies, which appears to be associated with the expression of the Mongoloid ancestral component in the gene pool of populations in Northern Eurasia, remain unclear. It seems appropriate to conduct genetic screening in the indigenous populations of the Russian Far East in order to assess the prevalence of SI delAG deletion as an inducer of the sucrase-isomaltase deficiency.

Environmental variation predicts patterns of genomic variation in an African tropical forest frog

Central African rainforests are predicted to be disproportionately affected by future climate change. How species will cope with these changes is unclear, but rapid environmental changes will likely impose strong selection pressures. Here we examined environmental drivers of genomic variation in the central African puddle frog (Phrynobatrachus auritus) to identify areas of elevated environmentally-associated turnover. We also compared current and future climate models to pinpoint areas of high genomic vulnerability where allele frequencies will have to shift the most in order to keep pace with future climate change. Neither physical landscape barriers nor the effects of past Pleistocene refugia influenced genomic differentiation. Alternatively, geographic distance and seasonal aspects of precipitation are the most important drivers of SNP allele frequency variation. Patterns of genomic differentiation coincided with key ecological gradients across the forest-savanna ecotone, montane areas, and a coastal to interior rainfall gradient. Areas of greatest vulnerability were found in the lower Sanaga basin, the southeastern region of Cameroon, and southwest Gabon. In contrast with past conservation efforts that have focused on hotspots of species richness or endemism, our findings highlight the importance of maintaining environmentally heterogeneous landscapes to preserve genomic variation and ongoing evolutionary processes in the face of climate change.

Frequency of the Main Human Leukocyte Antigen A, B, DR, and DQ Loci Known to Be Associated with the Clearance or Persistence of Hepatitis C Virus Infection in a Healthy Population from the Southern Region of Morocco: A Preliminary Study.

Hepatitis C Virus (HCV) infection represents a significant global health challenge, with its natural course largely influenced by the host's immune response. Human Leukocyte Antigen (HLA) molecules, particularly HLA class I and II, play a crucial role in the adaptive immune response against HCV. The polymorphism of HLA molecules contributes to the variability in immune response, affecting the outcomes of HCV infection. This study aims to investigate the frequency of HLA A, B, DR, and DQ alleles known to be associated with HCV clearance or persistence in a healthy Moroccan population. Conducted at the University Hospital Center Mohammed VI, Marrakech, this study spanned from 2015 to 2022 and included 703 healthy Moroccan individuals. HLA class I and II typing was performed using complement-dependent cytotoxicity and polymerase chain reaction-based methodologies. The results revealed the distinct patterns of HLA-A, B, DRB1, and DQB1 alleles in the Moroccan population. Notably, alleles linked to favorable HCV outcomes, such as HLA-DQB1*0301, DQB1*0501, and DRB1*1101, were more prevalent. Conversely, alleles associated with increased HCV susceptibility and persistence, such as HLA-DQB1*02 and DRB1*03, were also prominent. Gender-specific variations in allele frequencies were observed, providing insights into genetic influences on HCV infection outcomes. The findings align with global trends in HLA allele associations with HCV infection outcomes. The study emphasizes the role of host genetics in HCV infection, highlighting the need for further research in the Moroccan community, including HCV-infected individuals. The prevalence of certain HLA alleles, both protective and susceptibility-linked, underscores the potential for a national HLA data bank in Morocco.

Characterization of rice (Oryza sativa L.) landraces from Majuli and surrounding riverine ecologies in Assam: Assessment of morphogenetic variability and submergence tolerance

AbstractRice landraces from the fragile riverine ecosystems surrounding Majuli islands in Assam are pivotal for local livelihoods, as well as for their potential in developing flood tolerant varieties. We characterized 87 landraces from Majuli, Dhemaji, and North Lakhimpur districts in Assam by assessing 36 agro‐morphological traits, submergence tolerance, and microsatellite diversity. Multivariate analyses revealed that grain and leaf characteristics, plant height, and tillering are important traits differentiating the cultivar types. Sixty‐six SSR markers generated 271 alleles with an average of 4.1 alleles per marker with population structuring in two clusters having an allele frequency divergence of 0.124. The Bao or deep‐water landraces displayed the highest phenotypic and genetic diversity, with potential genetic links to the aus and wild species. Sali (winter rice) and bora (sticky rice) landraces were predominantly indica type. Nearly 47% of the germplasm exhibited tolerance to two‐week submergence at seedling stage. Surveying SUB1A and SNORKEL genes revealed the presence of SUB1A‐1 and SNORKEL genes in 64% and 57% of the tolerant accessions, respectively. This study highlights the untapped potential of rice landraces in a fragile ecological region, providing insights into their agronomical traits, submergence tolerance, and genetic diversity. The findings lay the foundation for improved germplasm management and developing flood‐resilient rice varieties, crucial for sustainable agriculture in riverine ecosystems.

Locally adaptive inversions in structured populations.

Inversions have been proposed to facilitate local adaptation, by linking together locally coadapted alleles at different loci. Prior work addressing this question theoretically has considered the spread of inversions in "continent-island" scenarios in which there is a unidirectional flow of maladapted migrants into the island population. In this setting, inversions capturing locally adaptive haplotypes are most likely to invade when selection is weak, because stronger local selection (i) more effectively purges maladaptive alleles and (ii) generates linkage disequilibrium between adaptive alleles, thus lessening the advantage of inversions. We show this finding only holds under limited conditions by studying the establishment of inversions in a more general two-deme model, which explicitly considers the dynamics of allele frequencies in both populations linked by bidirectional migration. In this model, the level of symmetry between demes can be varied from complete asymmetry (continent-island) to complete symmetry. For symmetric selection and migration, strong selection increases the allele frequency divergence between demes thereby increasing the frequency of maladaptive alleles in migrants, favoring inversions-the opposite of the pattern seen in the asymmetric continent-island scenario. We also account for the likelihood that a new inversion captures an adaptive haplotype in the first instance. When considering the combined process of capture and invasion in "continent island" and symmetric scenarios, relatively strong selection increases inversion establishment probability. Migration must also be low enough that the inversion is likely to capture an adaptive allele combination, but not so low as to eliminate the inversion's advantage. Overall, our analysis suggests that inversions are likely to harbor larger effect alleles that experience relatively strong selection.

Hybridization mediated range expansion and climate change resilience in two keystone tree species of boreal forests.

Current global climate change is expected to affect biodiversity negatively at all scales leading to mass biodiversity loss. Many studies have shown that the distribution of allele frequencies across a species' range is often influenced by specific genetic loci associated with local environmental variables. This association reflects local adaptation and allele changes at those loci could thereby contribute to the evolutionary response to climate change. However, predicting how species will adapt to climate change from this type of data alone remains challenging. In the present study, we combined exome capture sequences and environmental niche reconstruction, to test multiple methods for assessing local adaptation and climate resilience in two widely distributed conifers, Norway spruce and Siberian spruce. Both species are keystone species of the boreal forest and share a vast hybrid zone. We show that local adaptation in conifers can be detected through allele frequency variation, population-level ecological preferences, and historical niche movement. Moreover, we integrated genetic and ecological information into genetic offset predictive models to show that hybridization plays a central role in expanding the niche breadth of the two conifer species and may help both species to cope better with future changing climates. This joint genetic and ecological analysis also identified spruce populations that are at risk under current climate change.

Cross-pollination in seed-blended refuge and selection for Vip3A resistance in a lepidopteran pest as detected by genomic monitoring

The evolution of pest resistance to management tools reduces productivity and results in economic losses in agricultural systems. To slow its emergence and spread, monitoring and prevention practices are implemented in resistance management programs. Recent work suggests that genomic approaches can identify signs of emerging resistance to aid in resistance management. Here, we empirically examined the sensitivity of genomic monitoring for resistance management in transgenic Bt crops, a globally important agricultural innovation. Whole genome resequencing of wild North American Helicoverpa zea collected from non-expressing refuge and plants expressing Cry1Ab confirmed that resistance-associated signatures of selection were detectable after a single generation of exposure. Upon demonstrating its sensitivity, we applied genomic monitoring to wild H. zea that survived Vip3A exposure resulting from cross-pollination of refuge plants in seed-blended plots. Refuge seed interplanted with transgenic seed exposed H. zea to sublethal doses of Vip3A protein in corn ears and was associated with allele frequency divergence across the genome. Some of the greatest allele frequency divergence occurred in genomic regions adjacent to a previously described candidate gene for Vip3A resistance. Our work highlights the power of genomic monitoring to sensitively detect heritable changes associated with field exposure to Bt toxins and suggests that seed-blended refuge will likely hasten the evolution of resistance to Vip3A in lepidopteran pests.

Population structure and genetic diversity analysis in faba bean (Vicia faba L.) germplasm using SSR markers

In the present study, population structure and genetic diversity were studied among 100 faba bean germplasm lines along with three checks using 29 SSR (microsatellite) markers and morphological traits. ET218734, ET226572, and ET218734 genotypes exhibited maximum seed yield and high mean performance for various yield-attributing traits. The D2 statistics analysis grouped genotypes into five clusters. SSR marker analysis revealed, on average, 2 alleles per locus ranging from 2 to 3 among the studied genotypes. Polymorphic information content (PIC) for these markers ranged from 0.063 to 0.492 with an average of 0.37. Population structure analysis classified the studied genotypes into three major clusters. The Molecular Diversity Distance was found to be greatest among Cluster III and Cluster I (0.289), while the lowest was among Cluster II and Cluster I (0.148). The allele frequency divergence (expected heterozygosity) was found highest on Cluster II (0.164), and the lowest was on Cluster III (0.096).

Development of a novel five dye insertion/deletion (INDEL) panel for ancestry determination.

The use of genetic markers, specifically Short Tandem Repeats (STRs), has been a valuable tool for identifying persons of interest. However, the ability to analyze additional markers including Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletion (INDELs) polymorphisms allows laboratories to explore other investigative leads. INDELs were chosen in this study because large panels can be differentiated by size, allowing them to be genotyped by capillary electrophoresis. Moreover, these markers do not produce stutter and are smaller in size than STRs, facilitating the recovery of genetic information from degraded samples. The INDEL Ancestry Informative Markers (AIMs) in this study were selected from the 1000 Genomes Project based on a fixation index (FST) greater than 0.50, high allele frequency divergence, and genetic distance. A total of 25 INDEL-AIMs were optimized and validated according to SWGDAM guidelines in a five-dye multiplex. To validate the panel, genotyping was performed on 155 unrelated individuals from four ancestral groups (Caucasian, African, Hispanic, and East Asian). Bayesian clustering and principal component analysis (PCA) were performed revealing clear separation among three groups, with some observed overlap within the Hispanic group. Additionally, the PCA results were compared against a training set of 793 samples from the 1000 Genomes Project, demonstrating consistent results. Validation studies showed the assay to be reproducible, tolerant to common inhibitors, robust with challenging casework type samples, and sensitive down to 125 pg. In conclusion, our results demonstrated the robustness and effectiveness of a 25 loci INDEL system for ancestry inference of four ancestries commonly found in the United States.

Development of a novel five-dye panel for human identification insertion/deletion (INDEL) polymorphisms.

DNA analysis of forensic case samples relies on short tandem repeats (STRs), a key component of the combined DNA index system (CODIS) used to identify individuals. However, limitations arise when dealing with challenging samples, prompting the exploration of alternative markers such as single nucleotide polymorphisms (SNPs) and insertion/deletion (INDELs) polymorphisms. Unlike SNPs, INDELs can be differentiated easily by size, making them compatible with electrophoresis methods. It is possible to design small INDEL amplicons (<200 bp) to enhance recovery from degraded samples. To this end, a set of INDEL Human Identification Markers (HID) was curated from the 1000 Genomes Project, employing criteria including a fixation index (FST) ≤ 0.06, minor allele frequency (MAF) >0.2, and high allele frequency divergence. A panel of 33 INDEL-HIDs was optimized and validated following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, utilizing a five-dye multiplex electrophoresis system. A small sample set (n = 79 unrelated individuals) was genotyped to assess the assay's performance. The validation studies exhibited reproducibility, inhibition tolerance, ability to detect a two-person mixture from a 4:1 to 1:6 ratio, robustness with challenging samples, and sensitivity down to 125 pg of DNA. In summary, the 33-loci INDEL-HID panel exhibited robust recovery with low-template and degraded samples and proved effective for individualization within a small sample set.

Genomic divergence and demographic history of Quercus aliena populations

BackgroundQuercus aliena is a major montane tree species of subtropical and temperate forests in China, with important ecological and economic value. In order to reveal the species’ population dynamics, genetic diversity, genetic structure, and association with mountain habitats during the evolutionary process, we re-sequenced the genomes of 72 Q. aliena individuals.ResultsThe whole chloroplast and nuclear genomes were used for this study. Phylogenetic analysis using the chloroplast genome dataset supported four clades of Q. aliena, while the nuclear dataset supported three major clades. Sex-biased dispersal had a critical role in causing discordance between the chloroplast and nuclear genomes. Population structure analysis showed two groups in Q. aliena. The effective population size sharply declined 1 Mya, coinciding with the Poyang Glaciation in Eastern China. Using genotype–climate association analyses, we found a positive correlation between allele frequency variation in SNPs and temperature, suggesting the species has the capacity to adapt to changing temperatures.ConclusionOverall, this study illustrates the genetic divergence, genomic variation, and evolutionary processes behind the demographic history of Q. aliena.

Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints.

The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would help understanding how adaptation happens over environmental clines. To bring new insights to this issue we set up a broad framework which aimed to compare the adaptive trajectories over environmental clines in two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at putatively adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the 430 candidate adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different putative mechanisms involved in local adaptation in these two closely related species. Interestingly, the genomes of the 2 species were impacted differently by the environment, genes related to signatures of selection were most related to altitude, slope and rainfall seasonality for sheep, and summer temperature and spring rainfall for goats. The diversity of candidate adaptive pathways may result from a high number of biological functions involved in the adaptations to multiple eco-climatic gradients, and a differential role of climatic drivers on the two species, despite their co-distribution along the same environmental gradients. This study describes empirical examples of clinal variation in putatively adaptive alleles with different patterns in allele frequency distributions over continuous environmental gradients, thus showing the diversity of genetic responses in adaptive landscapes and opening new horizons for understanding genomics of adaptation in mammalian species and beyond.

Allelic frequency variation of ACKR1 in three Algerian populations: Zenata, Reguibat, and Oran

IntroductionThe discovery of the Duffy antigen is of great significance, given its essential role in immune response and various physiological processes. Genetic mutations in the Duffy gene not only affect antigen expression but also result in different antigen types. This underscores the importance of genetic characterization for clinical studies and exploring genetic diversity within the population. This study primarily aims to genetically characterize the Duffy blood group within three Algerian populations: the Zenata, Reguibat, and Oran populations. MethodsThe genetic polymorphism of the Duffy erythrocyte group was examined, focusing on five allelic versions of the ACKR1 locus: FY*01, FY*02, FY*X, and silent alleles FY*01 N.01 and FY*02 N.01. A total of 223 Algerian individuals, including 90 from the Oran population, 66 from the Zenata population, and 67 from the Reguibat population, were analyzed using the polymerase chain reaction with sequence-specific primer (PCR-SSP) method.The results revealed the presence of the silent alleles (FY*01 N.01 and FY*02 N.01) in all three populations, with a total frequency of 78.03% in the Zenata population. Additionally, the FY*X allele was exclusively detected in the Reguibat population, with a frequency of 0.75% ConclusionThis study provides valuable insights into the allele and genotypic frequencies of the Duffy system in the Zenata, Reguibat and Oranpopulations, contributing to our understanding of the genetic history and origins of the Algerian population. Further research incorporating additional genetic markers and establishing a comprehensive database would enhance our knowledge in this area.

Evaluation of SOCS5 mRNA and its association with serum IL-12 levels and rs41379147 SNP in various subsets of allergic disorders: A case control study

BackgroundThe SOCS proteins act as suppressors of cytokine signaling by impeding certain signaling pathways. SOCS5, a constituent of the SOCS family, has been associated with the management of allergic reactions, primarily by impeding the signaling of interleukin-4 (IL-4), which is known to have a cardinal function in accelerating the development of an allergic reaction. The key goal of our research was to explore the probable ramifications of the SOCS5 single nucleotide polymorphism (SNP) namely rs41379147 on the expression of SOCS5 mRNA and serum IL-12 levels, as well as to analyze the interaction between SOCS5 genotypes and various clinicopathological parameters in atopic diseases. MethodsThe study involved the enrollment of 314 subjects comprising 154 atopic individuals and 160 healthy controls. PCR-RFLP was employed to conduct SNP analysis. Real-Time PCR was employed to quantify SOCS5 mRNA. The enzyme-linked immunosorbent assay (ELISA) technique was used for the quantification of interleukin-12 and total IgE levels in the serum while as chemiluminescence was used to determine Vitamin D levels. ResultsThe PCR-RFLP analysis indicated a lack of statistically significant variation in genotypic and allelic frequencies between the cases and controls (p > 0.05) for − 9147 C/T SNP either in total atopy (OR-0.70, 95% CI=0.43-1.12, p =0.15), and on subgroup stratifications of chronic urticaria (OR-0.81, 95 % CI = 0.42–1.59, p = 0.61), allergic rhinitis (OR-0.63, 95 % CI = 0.33–1.19, p = 0.16) and bronchial asthma (OR-0.66,95% CI = 0.29–1.4, p=0.32). There was reduced mRNA expression of SOCS5 in total atopic cases, allergic rhinitis, bronchial asthma and chronic urticaria in comparison to controls which advocates the fact that SOCS5 has a protective role in allergic disease development. Despite the reduced amounts of IL-12 in total atopic cases and different allergic disorders in comparison to controls, IL-12 showed significant positive correlation with SOCS5 mRNA expression (p < 0.05). ConclusionSOCS5 SNP rs41379147(C/T) does not pose any significant risk towards the development of any allergic disorder and has no impact on the expression of SOCS5 and IL-12. Our study has shown the reduced mRNA expression of SOCS5 among individuals diagnosed with chronic urticaria, allergic rhinitis and bronchial asthma and the expression of SOCS5 showed complete dependence on the cytokine milieu of IL12. The modulation of SOCS5 and IL-12 may represent potential curative targets for treating the menace of allergic diseases and present promising avenues for future investigation.

The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich.

Sex chromosomes have evolved repeatedly across the tree of life and often exhibit extreme size dimorphism due to genetic degeneration of the sex-limited chromosome (e.g. the W chromosome of some birds and Y chromosome of mammals). However, in some lineages, ancient sex-limited chromosomes have escaped degeneration. Here, we study the evolutionary maintenance of sex chromosomes in the ostrich (Struthio camelus), where the W remains 65% the size of the Z chromosome, despite being more than 100 million years old. Using genome-wide resequencing data, we show that the population scaled recombination rate of the pseudoautosomal region (PAR) is higher than similar sized autosomes and is correlated with pedigree-based recombination rate in the heterogametic females, but not homogametic males. Genetic variation within the sex-linked region (SLR) (π = 0.001) was significantly lower than in the PAR, consistent with recombination cessation. Conversely, genetic variation across the PAR (π = 0.0016) was similar to that of autosomes and dependent on local recombination rates, GC content and to a lesser extent, gene density. In particular, the region close to the SLR was as genetically diverse as autosomes, likely due to high recombination rates around the PAR boundary restricting genetic linkage with the SLR to only ~50Kb. The potential for alleles with antagonistic fitness effects in males and females to drive chromosome degeneration is therefore limited. While some regions of the PAR had divergent male-female allele frequencies, suggestive of sexually antagonistic alleles, coalescent simulations showed this was broadly consistent with neutral genetic processes. Our results indicate that the degeneration of the large and ancient sex chromosomes of the ostrich may have been slowed by high recombination in the female PAR, reducing the scope for the accumulation of sexually antagonistic variation to generate selection for recombination cessation.

Robustness of Hill's overlapping-generation method for calculating Ne to extreme patterns of reproductive success.

For species with overlapping generations, the most widely used method to calculate effective population size (Ne) is Hill's, the key parameter for which is lifetime variance in offspring number ([Formula: see text]). Hill's model assumes a stable age structure and constant abundance, and sensitivity to those assumptions has been evaluated previously. Here I evaluate the robustness of Hill's model to extreme patterns of reproductive success, whose effects have not been previously examined: (1) very strong reproductive skew; (2) strong temporal autocorrelations in individual reproductive success; and (3) strong covariance of individual reproduction and survival. Genetic drift (loss of heterozygosity and increase in allele frequency variance) was simulated in age-structured populations using methods that generated no autocorrelations or covariances (Model NoCor); or created strong positive (Model Positive) or strong negative (Model Negative) temporal autocorrelations in reproduction and covariances between reproduction and survival. Compared to Model NoCor, the other models led to greatly elevated or reduced [Formula: see text], and hence greatly reduced or elevated Ne, respectively. A new index is introduced (ρα,α+), which is the correlation between (1) the number of offspring produced by each individual at the age at maturity (α), and (2) the total number of offspring produced during the rest of their lifetimes. Mean ρα,α+ was ≈0 under Model NoCor, strongly positive under Model Positive, and strongly negative under Model Negative. Even under the most extreme reproductive scenarios in Models Positive and Negative, when [Formula: see text] was calculated from the realized population pedigree and used to calculate Ne in Hill's model, the result accurately predicted the rate of genetic drift in simulated populations. These results held for scenarios where age-specific reproductive skew was random (variance ≈ mean) and highly overdispersed (variance up to 20 times the mean). Collectively, these results are good news for researchers as they demonstrate the robustness of Hill's model even in extreme reproductive scenarios.

Comparative genomic analysis uncovers candidate genes related with milk production and adaptive traits in goat breeds

During the process of animal domestication, both natural and artificial selection cause variation in allele frequencies among populations. Identifying genomic areas of selection in domestic animals may aid in the detection of genomic areas linked to ecological and economic traits. We studied genomic variation in 140 worldwide goat individuals, including 75 Asian, 30 African and 35 European goats. We further carried out comparative population genomics to detect genomic regions under selection for adaptability to harsh conditions in local Asian ecotypes and also milk production traits in European commercial breeds. In addition, we estimated the genetic distances among 140 goat individuals. The results showed that among all studied goat groups, local breeds from West and South Asia emerged as an independent group. Our search for selection signatures in local goats from West and South Asia revealed candidate genes related to adaptation to hot climate (HSPB6, HSF4, VPS13A and NBEA genes) and immune response (IL7, IL5, IL23A and LRFN5) traits. Furthermore, selection signatures in European commercial goats involved several milk production related genes, such as VPS13C, NCAM2, TMPRSS15, CSN3 and ABCG2. The identified candidate genes could be the fundamental genetic resource for enhancement of goat production and environmental-adaptive traits, and as such they should be used in goat breeding programs to select more efficient breeds.