scholarly journals Polygenic basis for adaptive morphological variation in a threatened Aotearoa | New Zealand bird, the hihi ( Notiomystis cincta )

2020 ◽  
Vol 287 (1933) ◽  
pp. 20200948
Author(s):  
Laura Duntsch ◽  
Barbara M. Tomotani ◽  
Pierre de Villemereuil ◽  
Patricia Brekke ◽  
Kate D. Lee ◽  
...  
Keyword(s):  
Body Mass ◽  
Morphological Traits ◽  
Nucleotide Polymorphisms ◽  
Tarsus Length ◽  
Effective Population ◽  
Chromosome Partitioning ◽  
Genome Wide ◽  
Small Effect Size ◽  
Bill Length ◽  
Notiomystis Cincta

To predict if a threatened species can adapt to changing selective pressures, it is crucial to understand the genetic basis of adaptive traits, especially in species historically affected by severe bottlenecks. We estimated the heritability of three hihi ( Notiomystis cincta ) morphological traits known to be under selection (nestling tarsus length, body mass and head–bill length) using 523 individuals and 39 699 single nucleotide polymorphisms (SNPs) from a 50 K Affymetrix SNP chip. We then examined the genetic architecture of the traits via chromosome partitioning analyses and genome-wide association scans (GWAS). Heritabilities estimated using pedigree relatedness or genomic relatedness were low. For tarsus length, the proportion of genetic variance explained by each chromosome was positively correlated with its size, and more than one chromosome explained significant variation for body mass and head–bill length. Finally, GWAS analyses suggested many loci of small effect contributing to trait variation for all three traits, although one locus (an SNP within an intron of the transcription factor HEY2 ) was tentatively associated with tarsus length. Our findings suggest a polygenic nature for the morphological traits, with many small effect size loci contributing to the majority of the variation, similar to results from many other wild populations. However, the small effective population size, polygenic architecture and already low heritabilities suggest that both the total response and rate of response to selection are likely to be limited in hihi.

scholarly journals Genome-Wide Association study Identifies a Novel Association Between a Cardiovascular Gene Polymorphism and Superior Athletic Performance

2020 ◽  
Author(s):  
Mohamed Elrayess ◽  
Fatima Al-Khelaifi ◽  
Noha Yousri ◽  
Omar Al-Bagha
Keyword(s):  
Athletic Performance ◽  
Genome Wide Association Study ◽  
Endurance Athlete ◽  
Meta Analysis ◽  
Significant Snps ◽  
Nucleotide Polymorphisms ◽  
Replication Studies ◽  
Genome Wide ◽  
Small Effect Size ◽  
Metabolomics Analysis

Research into the genetic predisposition to superior athletic performance has been a hindered by the underpowered studies and the small effect size of identified genetic variants. The aims of this study were to investigate the association of common single-nucleotide polymorphisms (SNPs) with endurance athlete status in a large cohort of elite European athletes using GWAS approach, followed by replication studies in Russian and Japanese elite athletes and functional validation using metabolomics analysis. Results: The association of 476,728 SNPs of Illumina DrugCore Gene chip and endurance athlete status was investigated in 796 European international-level athletes (645 males, 151 females) by comparing allelic frequencies between athletes specialized in sports with high (n=662) and low/moderate (n=134) aerobic component. Validation of results was performed by comparing the frequencies of the most significant SNPs between 242 and 168 elite Russian high and low/moderate aerobic athletes, respectively, and between 60 elite Japanese endurance athletes and 406 controls. A meta-analysis has identified rs1052373 (GG homozygotes) in Myosin Binding Protein (MYBPC3; implicated in cardiac hypertrophic myopathy) gene to be associated with endurance athlete status (P=1.43E-08, odd ratio 2.2). Homozygotes carriers of rs1052373 G allele in Russian athletes had significantly greater VO2max than carriers of the AA+AG (P = 0.005). Subsequent metabolomics analysis revealed several amino acids and lipids associated with rs1052373 G allele (1.82x10-05) including the testosterone precursor androstenediol (3beta, 17beta) disulfate. Conclusion: This is the first report of genome-wide significant SNP and related metabolites associated with elite athlete status. Further investigations of the functional relevance of the identified SNPs and metabolites in relation to enhanced athletic performance are warranted.

scholarly journals Patterns of Growth in Nestling Indian Barn-Owls

The Condor ◽  
2002 ◽  
Vol 104 (4) ◽  
pp. 885-890 ◽  
Author(s):  
Rajarathinavelu Nagarajan ◽  
Krishinamoorthy Thiyagesan ◽  
Rajagopalan Natarajan ◽  
Ramalingam Kanakasabai
Keyword(s):  
Body Mass ◽  
Body Length ◽  
Wing Length ◽  
Growth Patterns ◽  
The Body ◽  
Logistic Growth ◽  
Adult Size ◽  
Tyto Alba ◽  
Tarsus Length ◽  
Bill Length

Abstract We examined nestling growth patterns of the Indian Barn-Owl (Tyto alba stertens) in Tamilnadu, Southern India, with reference to body mass, body length, bill length, bill width, wing length, wingspan, tail length, tarsus length, and middle claw length. Body mass reached an asymptote of 447.0 ± 6.8 g during week 7, which was 10% higher than the adult mass. Then it significantly declined to 437.0 ± 10.9 g at fledging. At the end of week 4, the body length, bill length, bill width, tarsus length, and middle toe length had surpassed 50% of adult sizes. The wingspan and tarsus length reached almost adult size by the time of fledging. A logistic growth curve was found to be a good fit for all the growth variables and explained between 71% (wing length) and 86% (body length) of the variance. Patrones de Crecimiento en Polluelos de Tyto alba stertens Resumen. Examinamos los patrones de crecimiento de polluelos de Tyto alba stertens en Tamilnadu, sudoeste de India, en relación al peso y el largo del cuerpo, el largo y el ancho del pico, el largo del ala y su envergadura, y el largo de la cola, los tarsos y de la garra mediana. El peso corporal alcanzó una asíntota de 447.0 ± 6.8 g durante la séptima semana, el cual fue un 10% mayor que el peso de los adultos. Posteriormente, durante el período de volantones, el peso corporal disminuyó hasta 437.0 ± 10.9 g. Al final de la cuarta semana, el largo del cuerpo, el largo y el ancho del pico, y los largos del tarso y del dedo mediano habían sobrepasado el 50% de los tamaños adultos. La envergadura del ala y el largo del tarso casi alcanzaron tamaños adultos durante el período de volantones. Se encontró que una curva de crecimiento logístico se ajustó bien a todas las variables de crecimiento y explicó un 71% (largo del ala) y un 86% (largo del cuerpo) de la varianza.

scholarly journals Large differences in adiponectin levels have no clear effect on multiple sclerosis risk: A Mendelian randomization study

2016 ◽  
Vol 23 (11) ◽  
pp. 1461-1468 ◽  
Author(s):  
Julia Devorak ◽  
Lauren E Mokry ◽  
John A Morris ◽  
Vincenzo Forgetta ◽  
George Davey Smith ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Body Mass ◽  
Mendelian Randomization ◽  
Strong Support ◽  
Sensitivity Analyses ◽  
Nucleotide Polymorphisms ◽  
Standard Deviation Increase ◽  
Clear Effect ◽  
Genome Wide ◽  
Unit Increase

Background: Mendelian randomization (MR) studies have demonstrated strong support for an association between genetically increased body mass index and risk of multiple sclerosis (MS). The adipokine adiponectin may be a potential mechanism linking body mass to risk of MS. Objective: To evaluate whether genetically increased adiponectin levels influence risk of MS. Methods: Using genome-wide significant single nucleotide polymorphisms (SNPs) for adiponectin, we undertook an MR study to estimate the effect of adiponectin on MS. This method prevents bias due to reverse causation and minimizes bias due to confounding. Sensitivity analyses were performed to evaluate the assumptions of MR. Results: MR analyses did not support a role for genetically elevated adiponectin in risk of MS (odds ratio (OR) = 0.93 per unit increase in natural-log-transformed adiponectin, equivalent to a two-standard deviation increase in adiponectin on the absolute scale; 95% confidence interval (CI) = 0.66–1.33; p = 0.61). Further MR analysis suggested that genetic variation at the adiponectin gene, which influences adiponectin level, does not impact MS risk. Sensitivity analyses, including MR-Egger regression, suggested no bias due to pleiotropy. Conclusion: Lifelong genetically increased adiponectin levels in humans have no clear effect on risk of MS. Other biological factors driving the association between body mass and MS should be investigated.

scholarly journals Genomic analysis of a reef-building coral, Acropora digitifera, reveals complex population structure and a migration network in the Nansei Islands, Japan

2021 ◽  
Author(s):  
Kojin Tsuchiya ◽  
Yuna Zayasu ◽  
Yuichi Nakajima ◽  
Nana Arakaki ◽  
Go Suzuki ◽  
...  
Keyword(s):  
Population Structure ◽  
Marine Conservation ◽  
Ocean Currents ◽  
General Tendency ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Acropora Digitifera ◽  
Genome Wide ◽  
Nansei Islands ◽  
Migration Network

Understanding the structure and connectivity of coral populations is fundamental for developing marine conservation policies, especially in patchy environments such as archipelagos. The Nansei Islands, extending more than 1,000 km in southwestern Japan, are characterized by high levels of biodiversity and endemism, supported by coral reefs, although precise, detailed genetic attributes of corals are still largely unknown. In this study, we conducted population genomic analyses based on genome-wide, single-nucleotide polymorphisms (SNPs) of Acropora digitifera, a common species in the Nansei Islands, for which a complete genome is available. With ~24x sequencing coverage of entire genomes of 303 colonies collected at 21 locations, we identified more than four million genome-wide SNPs. While population structure analyses suggested weak genetic differentiation among sampled locations, the most southwestern location (the west end of the Yaeyama Islands) was genetically similar to the northernmost location (the Tanegashima Islands), separated by >1,000 km. Although examination of a migration network found a general tendency of northward migration along the Kuroshio Current, a substantial amount of southward migration was also detected, indicating important contributions of minor ocean currents to coral larval dispersal. Moreover, heterogeneity in the transition of effective population sizes among locations suggests different histories for individual subpopulations. The unexpected complexity of both past and present population dynamics in the Nansei Islands implies that heterogeneity of ocean currents and local environments, past and present, have influenced the population structure of this species, highlighting the importance of local scale assessments for effective coral restoration and management.

scholarly journals Genome-wide association study reveals novel genetic markers associated with endurance athlete status

2019 ◽  
Author(s):  
Fatima Al-Khelaifi ◽  
Noha Yousri ◽  
Omar Albagha ◽  
Ekaterina A. Semenova ◽  
Elena Kostryukova ◽  
...  
Keyword(s):  
Athletic Performance ◽  
Genome Wide Association Study ◽  
Performance Enhancement ◽  
Endurance Athlete ◽  
Significant Snps ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Small Effect Size ◽  
Level Of Significance ◽  
Metabolomics Analysis

Abstract Background: The genetic predisposition to elite athletic performance has been a controversial subject due to the underpowered studies and the small effect size of identified genetic variants. The aims of this study were to investigate the association of common single-nucleotide polymorphisms (SNPs) with endurance athlete status in a large cohort of elite athletes using GWAS approach, followed by a functional validation of significant SNPs by metabolomics analysis. Results: The association of 476,728 SNPs of Illumina DrugCore Gene chip and endurance athlete status was investigated in 753 European international-level athletes (594 males, 159 females) by comparing allelic frequencies between athletes specialized in sports with high (n=630) and low/moderate (n=123) aerobic component. Validation of results was performed by comparing the frequencies of the most significant SNPs between 176 elite Russian endurance athletes and 173 Russian controls or 43 sprinters. Two novel SNPs showed significant associations with endurance athlete status at Bonferroni level of significance (rs56330321 in ATP2B2, p=1.46E-7) and FDR level of significance (rs2635438 in SYNE1, p=2.54E-7), respectively. Replication study using Russian cohorts and a subsequent meta-analysis have confirmed the association of rs56330321 and rs2635438 SNPs with endurance athlete status at genome-wide significance (P= 5.13E-09 and 1.91E-08, respectively). Metabolomics analysis revealed several amino acids and lipids associated with the identified SNPs with potential roles in performance enhancement. Conclusions: This is the first report of GWAS significant SNPs and related metabolites associated with elite athlete status. Further investigations of the functional relevance of the identified SNPs and metabolites in relation to enhanced athletic performance are warranted.

scholarly journals Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 599 ◽  
Author(s):  
Morteza Bitaraf Sani ◽  
Javad Zare Harofte ◽  
Ahmad Bitaraf ◽  
Saeid Esmaeilkhanian ◽  
Mohammad Hossein Banabazi ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Balancing Selection ◽  
Demographic History ◽  
Genomic Analysis ◽  
Genotyping By Sequencing ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Genome Wide

The development of camel husbandry for good production in a desert climate is very important, thus we need to understand the genetic basis of camels and give attention to genomic analysis. We assessed genome-wide diversity, linkage disequilibrium (LD), effective population size (Ne) and relatedness in 96 dromedaries originating from five different regions of the central desert of Iran using genotyping-by-sequencing (GBS). A total of 14,522 Single Nucleotide Polymorphisms (SNPs) with an average minor allele frequency (MAF) of 0.19 passed quality control and filtering steps. The average observed heterozygosity in the population was estimated at 0.25 ± 0.03. The mean of LD at distances shorter than 40 kb was low (r2 = 0.089 ± 0.234). The camels sampled from the central desert of Iran exhibited higher relatedness than Sudanese and lower than Arabian Peninsula dromedaries. Recent Ne of Iran’s camels was estimated to be 89. Predicted Tajima’s D (1.28) suggested a bottleneck or balancing selection in dromedary camels in the central desert of Iran. A general decrease in effective and census population size poses a threat for Iran’s dromedaries. This report is the first SNP calling report on nearly the chromosome level and a first step towards understanding genomic diversity, population structure and demography in Iranian dromedaries.

scholarly journals A Genome-Wide Association Study of Self-Rated Health

2010 ◽  
Vol 13 (4) ◽  
pp. 398-403 ◽  
Author(s):  
Miriam A. Mosing ◽  
Karin J. H. Verweij ◽  
Sarah E. Medland ◽  
Jodie Painter ◽  
Scott D. Gordon ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Large Sample ◽  
Self Rated Health ◽  
Genome Wide ◽  
A Genome ◽  
Small Effect Size

AbstractSelf-rated health questions have been proven to be a highly reliable and valid measure of overall health as measured by other indicators in many population groups. It also has been shown to be a very good predictor of mortality, chronic or severe diseases, and the need for services, and is positively correlated with clinical assessments. Genetic factors have been estimated to account for 25–64% of the variance in the liability of self-rated health. The aim of the present study was to identify Single Nucleotide Polymorphisms (SNPs) underlying the heritability of self-rated health by conducting a genome-wide association analysis in a large sample of 6,706 Australian individuals aged 18–92. No genome wide significant SNPs associated with self-rated health could be identified, indicating that self-rated health may be influenced by a large number of SNPs with very small effect size. A very large sample will be needed to identify these SNPs.

scholarly journals Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Waldiodio Seck ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Root System ◽  
System Architecture ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Primary Root ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P < 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

EpiPen: An R Package to Investigate Two-Locus Epistatic Models

2014 ◽  
Vol 17 (4) ◽  
Author(s):  
Raymond K. Walters ◽  
Charles Laurin ◽  
Gitta H. Lubke
Keyword(s):  
Power Analysis ◽  
R Package ◽  
Simulation Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Epistatic Interactions ◽  
Model Interpretation ◽  
Genome Wide ◽  
Using Data ◽  
Power Analyses

Epistasis is a growing area of research in genome-wide studies, but the differences between alternative definitions of epistasis remain a source of confusion for many researchers. One problem is that models for epistasis are presented in a number of formats, some of which have difficult-to-interpret parameters. In addition, the relation between the different models is rarely explained. Existing software for testing epistatic interactions between single-nucleotide polymorphisms (SNPs) does not provide the flexibility to compare the available model parameterizations. For that reason we have developed an R package for investigating epistatic and penetrance models, EpiPen, to aid users who wish to easily compare, interpret, and utilize models for two-locus epistatic interactions. EpiPen facilitates research on SNP-SNP interactions by allowing the R user to easily convert between common parametric forms for two-locus interactions, generate data for simulation studies, and perform power analyses for the selected model with a continuous or dichotomous phenotype. The usefulness of the package for model interpretation and power analysis is illustrated using data on rheumatoid arthritis.

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