Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching

Science ◽  
2020 ◽  
Vol 369 (6501) ◽  
pp. eaba4674 ◽  
Author(s):  
Zachary L. Fuller ◽  
Veronique J. L. Mocellin ◽  
Luke A. Morris ◽  
Neal Cantin ◽  
Jihanne Shepherd ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Conservation Strategies ◽  
Genome Sequences ◽  
Acropora Millepora ◽  
Genome Wide ◽  
A Genome ◽  
Bleaching Response ◽  
In The Wild

Although reef-building corals are declining worldwide, responses to bleaching vary within and across species and are partly heritable. Toward predicting bleaching response from genomic data, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We obtained whole-genome sequences for 237 phenotyped samples collected at 12 reefs along the Great Barrier Reef, among which we inferred little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We conducted a genome-wide association study of visual bleaching score for 213 samples, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for genomics-based approaches in conservation strategies.

scholarly journals Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching

2019 ◽  
Author(s):  
Zachary L. Fuller ◽  
Veronique J.L. Mocellin ◽  
Luke Morris ◽  
Neal Cantin ◽  
Jihanne Shepherd ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Genome Wide Association ◽  
Conservation Strategies ◽  
Genome Sequences ◽  
Acropora Millepora ◽  
Genome Wide ◽  
A Genome ◽  
In The Wild

AbstractAlthough reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

scholarly journals What do we learn from a Genome Wide Association Study performed on HIV-1 infected Long Term Non Progressors individuals?

Retrovirology ◽  
2009 ◽  
Vol 6 (S2) ◽  
Author(s):  
Julien Guergnon ◽  
◽  
Cyril Dalmasso ◽  
Ioannis Theodorou ◽  
Agostino Riva
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Hiv 1

scholarly journals Genome-wide sexually antagonistic variants reveal longstanding constraints on sexual dimorphism in the fruitfly

2017 ◽  
Author(s):  
Filip Ruzicka ◽  
Mark S. Hill ◽  
Tanya M. Pennell ◽  
Ilona Flis ◽  
Fiona C. Ingleby ◽  
...  
Keyword(s):  
Sexual Dimorphism ◽  
Evolutionary Dynamics ◽  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Sexual Antagonism ◽  
Protein Coding ◽  
Genome Wide ◽  
Genomic Location ◽  
Classic Theory ◽  
A Genome

The evolution of sexual dimorphism is constrained by a shared genome, leading to ‘sexual antagonism’ where different alleles at given loci are favoured by selection in males and females. Despite its wide taxonomic incidence, we know little about the identity, genomic location and evolutionary dynamics of antagonistic genetic variants. To address these deficits, we use sex-specific fitness data from 202 fully sequenced hemiclonal D. melanogaster fly lines to perform a genome-wide association study of sexual antagonism. We identify ~230 chromosomal clusters of candidate antagonistic SNPs. In contradiction to classic theory, we find no clear evidence that the X chromosome is a hotspot for sexually antagonistic variation. Characterising antagonistic SNPs functionally, we find a large excess of missense variants but little enrichment in terms of gene function. We also assess the evolutionary persistence of antagonistic variants by examining extant polymorphism in wild D. melanogaster populations. Remarkably, antagonistic variants are associated with multiple signatures of balancing selection across the D. melanogaster distribution range, indicating widespread and evolutionarily persistent (>10,000 years) genomic constraints. Based on our results, we propose that antagonistic variation accumulates due to constraints on the resolution of sexual conflict over protein coding sequences, thus contributing to the long-term maintenance of heritable fitness variation.

scholarly journals A Genome-wide Association Study to Identify Candidate Genes for Metabolic Disorders in Offspring by in Vitro Fertilization

2022 ◽  
Author(s):  
Lihong Liu ◽  
Siyao HA ◽  
MingQing Li ◽  
Zhiling Li
Keyword(s):  
Lipid Metabolism ◽  
Health Risks ◽  
Genome Wide Association Study ◽  
Vitro Fertilization ◽  
Genome Wide ◽  
A Genome ◽  
Offspring Health

Abstract BackgroundIn vitro fertilization (IVF) processes increase offspring's short-term and long-term health risks, but their mechanisms remain unclear. MethodsWe conducted a bibliometric analysis to determine the landscape of IVF offspring health. Subsequently, a bioinformatics method was utilized to identify the co-genes properties and biological function mechanisms of IVF and type 2 diabetes mellitus (T2DM). Finally, we predicted compounds against key targets and performed multiple validations of the mechanisms underlying IVF offspring health risks. ResultsWe identified 15 genes associated with T2DM, and their biological functions are primarily associated with lipid metabolism. We also identified the properties of co-genes, modified characteristics, identified 3 SNPs sites, and determined the three core genes, APOA1, APOB, and APOE, which were mainly correlated with metabolic and cardiovascular diseases. In addition, we predicted drugs that may improve metabolic abnormalities in IVF offspring. ConclusionsThe impact of aberrant lipid metabolism in offspring after IVF therapy warrants additional investigation, particularly in terms of long-term health consequences and possible mechanisms.

scholarly journals A regulatory variant of CHRM3 is associated with cannabis-induced hallucinations in European Americans

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Zhongshan Cheng ◽  
Chureerat Phokaew ◽  
Yi-Ling Chou ◽  
Dongbing Lai ◽  
Jacquelyn L. Meyers ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Collaborative Study ◽  
Risk Genes ◽  
European Americans ◽  
Genome Wide ◽  
Nominal Significance ◽  
A Genome ◽  
Regulatory Variant

AbstractCannabis, the most widely used illicit drug, can induce hallucinations. Our understanding of the biology of cannabis-induced hallucinations (Ca-HL) is limited. We used the Semi-Structured Assessment for Drug Dependence and Alcoholism (SSADDA) to identify cannabis-induced hallucinations (Ca-HL) among long-term cannabis users (used cannabis ≥1 year and ≥100 times). A genome-wide association study (GWAS) was conducted by analyzing European Americans (EAs) and African Americans (AAs) in Yale-Penn 1 and 2 cohorts individually, then meta-analyzing the two cohorts within population. In the meta-analysis of Yale-Penn EAs (n = 1917), one genome-wide significant (GWS) signal emerged at the CHRM3 locus, represented by rs115455482 (P = 1.66 × 10−10), rs74722579 (P = 2.81 × 10−9), and rs1938228 (P = 1.57 × 10−8); signals were GWS in Yale-Penn 1 EAs (n = 1092) and nominally significant in Yale-Penn 2 EAs (n = 825). Two SNPs, rs115455482 and rs74722579, were available from the Collaborative Study on the Genetics of Alcoholism data (COGA; 3630 long-term cannabis users). The signals did not replicate, but when meta-analyzing Yale-Penn and COGA EAs, the two SNPs’ association signals were increased (meta-P-values 1.32 × 10−10 and 2.60 × 10−9, respectively; n = 4291). There were no significant findings in AAs, but in the AA meta-analysis (n = 3624), nominal significance was seen for rs74722579. The rs115455482*T risk allele was associated with lower CHRM3 expression in the thalamus. CHRM3 was co-expressed with three psychosis risk genes (GABAG2, CHRNA4, and HRH3) in the thalamus and other human brain tissues and mouse GABAergic neurons. This work provides strong evidence for the association of CHRM3 with Ca-HL and provides insight into the potential involvement of thalamus for this trait.

scholarly journals Circulating Chemerin Levels, but not the RARRES2 Polymorphisms, Predict the Long-Term Outcome of Angiographically Confirmed Coronary Artery Disease

2019 ◽  
Vol 20 (5) ◽  
pp. 1174 ◽  
Author(s):  
Leay Er ◽  
Lung-An Hsu ◽  
Jyh-Ming Juang ◽  
Fu-Tien Chiang ◽  
Ming-Sheng Teng ◽  
...  
Keyword(s):  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Genome Wide Association Study ◽  
Outcome Analysis ◽  
Term Outcome ◽  
Long Term Outcome ◽  
Genome Wide ◽  
A Genome ◽  
Artery Disease

Chemerin, a novel adipokine, has been associated with metabolic, inflammatory, and atherosclerotic diseases. We aimed to determine the genetic basis of chemerin levels by conducting a genome-wide association study (GWAS) and to investigate the role of RARRES2 polymorphisms and circulating chemerin levels in the long-term outcome of coronary artery disease (CAD). A total of 2197 participants from the Taiwan Biobank (TWB) were recruited for the GWAS analysis, and 481 patients with angiographically confirmed CAD were enrolled for long-term outcome analysis. One locus of genome-wide significance with a single independent association signal was identified in the GWAS for chemerin levels with the peak association at the RARRES2 gene promoter region polymorphism rs3735167 (p = 2.35 × 10−21). In the CAD population, borderline significance was noted between RARRES2 polymorphisms and chemerin levels, whereas high chemerin levels were associated with obesity, female sex, diabetes mellitus, hypertension, current smoking, high platelet and leukocyte counts, anemia, impaired renal function, high C-reactive protein (CRP) levels, and multi-vessel disease. Kaplan–Meier survival curves indicated that the patients with high chemerin and CRP levels, but not those with RARRES2 polymorphisms, had a lower survival rate and higher combined cerebral and cardiovascular event rates. Combined chemerin and CRP levels further revealed a stepwise increase in poor clinical outcomes from low- to high-risk subgroups. In conclusion, rs3735167 is the lead RARRES2 polymorphism for chemerin levels in Taiwanese. Chemerin levels, but not the rs3735167 genotypes, predicted the long-term outcome of CAD, especially when combined with CRP levels.

scholarly journals Natural variation in insect egg-induced cell death uncovers a role for L-type LECTIN RECEPTOR KINASE-I.1 in Arabidopsis

2020 ◽  
Author(s):  
Raphaël Groux ◽  
Caroline Gouhier-Darimont ◽  
Envel Kerdaffrec ◽  
Philippe Reymond
Keyword(s):  
Signaling Pathway ◽  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Pieris Brassicae ◽  
Receptor Kinase ◽  
Large White ◽  
Lectin Receptor ◽  
Genome Wide ◽  
A Genome ◽  
Close Homolog

AbstractIn Arabidopsis thaliana, a hypersensitive-like response (HR-like) is triggered underneath the eggs of the large white butterfly Pieris brassicae, and this response is dependent on salicylic acid (SA) accumulation and signaling. Previous reports indicate that the clade I L-type lectin receptor kinase LecRK-I.8 is involved in early steps of egg recognition. A genome-wide association study (GWAS) was used to better characterize the genetic structure of HR-like and discover loci that contribute to this response. We report here the identification of LecRK-I.1, a close homolog of LecRK-I.8, and show that two main haplotypes that explain part of the variation in HR-like segregate amongst natural Arabidopsis accessions. In addition, signatures of balancing selection at this locus suggest that it may be ecologically important. Disruption of LecRK-I.1 resulted in decreased HR-like and SA signaling, indicating that this protein is important for the observed responses. Furthermore, we provide evidence that LecRK-I.1 functions in the same signaling pathway as LecRK-I.8. Altogether, our results show that the response to eggs of P. brassicae is controlled by LecRKs that operate at various steps of the signaling pathway.

scholarly journals Genetic associations and architecture of asthma-chronic obstructive pulmonary disease overlap

2020 ◽  
Author(s):  
C. John ◽  
A.L. Guyatt ◽  
N. Shrine ◽  
R. Packer ◽  
T.A. Olafsdottir ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Meta Analysis ◽  
European Ancestry ◽  
Chronic Obstructive ◽  
Genetic Associations ◽  
Obstructive Pulmonary Disease ◽  
Genome Wide ◽  
A Genome ◽  
Stage 1

AbstractSome individuals have characteristics of both asthma and COPD (asthma-COPD overlap, ACO), and evidence suggests they experience worse outcomes than those with either condition alone. Improved knowledge of the genetic architecture would contribute to understanding whether determinants of risk in this group differ from those in COPD or asthma.We conducted a genome-wide association study in 8,068 cases and 40,360 controls of European ancestry from UK Biobank (stage 1). After excluding variants only associated with asthma or COPD we selected 31 variants for further investigation in 12 additional cohorts (stage 2), and discovered eight novel signals for ACO in a meta-analysis of stage 1 and 2 studies.Our signals include an intergenic signal on chromosome 5 not previously associated with asthma, COPD or lung function, and suggest a spectrum of shared and distinct genetic influences in asthma, COPD and ACO. A number of signals may represent loci that predispose to serious long-term consequences in people with asthma.

scholarly journals Choosing the optimal population for a genome‐wide association study: A simulation of whole‐genome sequences from rice

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Kosuke Hamazaki ◽  
Hiromi Kajiya‐Kanegae ◽  
Masanori Yamasaki ◽  
Kaworu Ebana ◽  
Shiori Yabe ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genome Wide ◽  
A Genome ◽  
Optimal Population
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