scholarly journals Medaka population genome structure and demographic history described via genotyping-by-sequencing

2017 ◽  
Author(s):  
Takafumi Katsumura ◽  
Shoji Oda ◽  
Mitani Hiroshi ◽  
Hiroki Oota
Keyword(s):  
Population Structure ◽  
Disease Risk ◽  
Association Studies ◽  
Demographic History ◽  
Genotyping By Sequencing ◽  
Genetic Population Structure ◽  
Genome Wide Association Studies ◽  
Genetic Population ◽  
Genome Wide ◽  
Genomic Study

AbstractMedaka is a model organism in medicine, genetics, developmental biology and population genetics. Lab stocks composed of more than 100 local wild populations are available for research in these fields. Thus, medaka represents a potentially excellent bioresource for screening disease-risk- and adaptation-related genes in genome-wide association studies. Although the genetic population structure should be known before performing such an analysis, a comprehensive study on the genome-wide diversity of wild medaka populations has not been performed. Here, we performed genotyping-by-sequencing (GBS) for 81 and 12 medakas captured from a bioresource and the wild, respectively. Based on the GBS data, we evaluated the genetic population structure and estimated the demographic parameters using an approximate Bayesian computation (ABC) framework. The autosomal data confirmed that there were substantial differences between local populations and supported our previously proposed hypothesis on medaka dispersal based on mitochondrial genome (mtDNA) data. A new finding was that a local group that was thought to be a hybrid between the northern and the southern Japanese groups was actually a sister group of the northern Japanese group. Thus, this paper presents the first population-genomic study of medaka and reveals its population structure and history based on autosomal diversity.

scholarly journals Genetic substructure and complex demographic history of South African Bantu speakers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dhriti Sengupta ◽  
◽  
Ananyo Choudhury ◽  
Cesar Fortes-Lima ◽  
Shaun Aron ◽  
...  
Keyword(s):  
South Africa ◽  
Population Structure ◽  
Iron Age ◽  
Association Studies ◽  
Demographic History ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Scale Population ◽  
Genome Wide Data ◽  
Genetic Substructure

AbstractSouth Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ~400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa.

scholarly journals Genome-wide patterns of population structure and linkage disequilibrium in farmed Nile tilapia (Oreochromis niloticus)

2019 ◽  
Author(s):  
Grazyella M. Yoshida ◽  
Agustín Barria ◽  
Katharina Correa ◽  
Giovanna Cáceres ◽  
Ana Jedlicki ◽  
...  
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Genomic Selection ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Population Genomics ◽  
Association Studies ◽  
Demographic History ◽  
Genome Wide Association Studies ◽  
Genome Wide

AbstractNile tilapia (Oreochromis niloticus) is one of the most produced farmed fish in the world and represents an important source of protein for human consumption. Farmed Nile tilapia populations are increasingly based on genetically improved stocks, which have been established from admixed populations. To date, there is scarce information about the population genomics of farmed Nile tilapia, assessed by dense single nucleotide polymorphism (SNP) panels. The patterns of linkage disequilibrium (LD) may affect the success of genome-wide association studies (GWAS) and genomic selection and can also provide key information about demographic history of farmed Nile tilapia populations. The objectives of this study were to provide further knowledge about the population structure and LD patterns, as well as, estimate the effective population size (Ne) for three farmed Nile tilapia populations, one from Brazil (POP A) and two from Costa Rica (POP B and POP C). A total of 55, 56 and 57 individuals from POP A, POP B and POP C, respectively, were genotyped using a 50K SNP panel selected from a whole-genome sequencing (WGS) experiment. Two principal components explained about 20% of the total variation and clearly discriminated between the three populations. Population genetic structure analysis showed evidence of admixture, especially for POP C. The contemporary Ne values calculated based to LD values, ranged from 71 to 141. No differences were observed in the LD decay among populations, with a rapid decrease of r2 when increasing inter-marker distance. Average r2 between adjacent SNP pairs ranged from 0.03 to 0.18, 0.03 to 0.17 and 0.03 to 0.16 for POP A, POP B and POP C, respectively. Based on the number of independent chromosome segments in the Nile tilapia genome, at least 4.2 K SNP are required for the implementation of GWAS and genomic selection in farmed Nile tilapia populations.

scholarly journals Genetic-substructure and complex demographic history of South African Bantu speakers

2020 ◽  
Author(s):  
Dhriti Sengupta ◽  
Ananyo Choudhury ◽  
Cesar Fortes-Lima ◽  
Shaun Aron ◽  
Gavin Whitelaw ◽  
...  
Keyword(s):  
South Africa ◽  
Population Structure ◽  
Iron Age ◽  
Association Studies ◽  
Demographic History ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Scale Population ◽  
Genome Wide Data ◽  
Genetic Substructure

AbstractSouth Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ∼400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa.

Abstract 1443: Systems-Based Analysis of HDL Metabolism in a Mouse Intercross between Strains CAST and C57BL6/J (CxB)

Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Margarete Mehrabian ◽  
Charles Farber ◽  
Peter Langfelder ◽  
Anatole Ghazalpour ◽  
Zhiqiang Zhou ◽  
...  
Keyword(s):  
Complex Traits ◽  
Association Studies ◽  
Plasma Lipid ◽  
Heart Association ◽  
Hdl Cholesterol ◽  
Chow Diet ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Genomic Study ◽  
Hdl Metabolism

A recent meta-analysis of three large genome-wide association studies for HDL cholesterol levels revealed several highly significant associations, but altogether these explained less than 10% of the population variance of HDL. Since HDL levels are highly heritable, with heritability estimated at 50–70% in many studies, there are clearly many additional genes, and probably complex genetic and environmental interactions, involved in HDL metabolism. Thus, if “personalized medicine” is to become a reality, these complex factors must be addressed. Combined genetic-genomic approaches have rejuvenated the analysis of complex traits using mouse models, and here report an integrative genomic study of HDL in a large mouse cross. We previously reported the identification of loci associated with HDL cholesterol concentrations using a CXB F2 intercross. We have now generated a much larger CXB cross, consisting of 438 mice, and have integrated genome wide gene expression analysis of liver and adipose with quantitative trait locus (QTL) mapping and causality modeling. These studies were carried out on mice fed a low fat, chow diet and then switched to a high fat, ’Western’ diet. QTL analysis on the clinical traits using R/QTL (http://cran.r-project.org/) revealed a complex inheritance pattern with significant LOD scores at 9 loci, on chromosomes 1,2,4,5,8,9,10,16,18. Of these loci, 6 (chr: 1,4,5,10,16,18) were seen to be involved in genetic-dietary regulation of HDL cholesterol. Expression QTLs (eQTL) were determined using Agilent microarrays for 23,624 transcripts. Genes expressed within a 1-LOD support interval or correlated with HDL (p<2.7E-11) in both adipose and liver were identified. Using Network Edge Orienting (NEO) methods, causal relationships between the identified genes, related QTL peak markers and HDL levels were accessed. The genes were then ranked based on the NEO scores. In liver the highest ranked genes were associated with mitochondrial, ER and golgi trafficking. In adipose, on the other hand, pathways associated with cell signaling, transcription regulation and protein ubiquitation were predicted to be causal for HDL levels. In conclusion, our results reveal a large number of novel pathways and candidate genes for plasma lipid metabolism. This research has received full or partial funding support from the American Heart Association, AHA Western States Affiliate (California, Nevada & Utah).

scholarly journals CONVERGENT AGING LOCI: PATHWAYS THAT TRANSCEND INDIVIDUAL DISEASES

2019 ◽  
Vol 3 (Supplement_1) ◽  
pp. S221-S221
Author(s):  
Luke C Pilling ◽  
Luigi Ferrucci ◽  
David Melzer
Keyword(s):  
Disease Risk ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Telomere Shortening ◽  
Chronic Disease Risk ◽  
Trade Offs ◽  
Age Related ◽  
Genome Wide ◽  
Artery Disease

Abstract Thousands of loci across the genome have been identified for specific diseases in genome-wide association studies (GWAS), yet very few are associated with lifespan itself. We hypothesized that specific biological pathways transcend individual diseases and affect health and lifespan more broadly. Using the published results for the most recent GWAS for 10 key age-related diseases (including coronary artery disease, type-2 diabetes, and several cancers) we identified 22 loci with a strong genetic association with at least three of the diseases. These multi-trait aging loci include known genes affecting multiple diverse health end points, such as CDKN2A/B (9p21.3) and APOE. There are also novel multi-trait genes including SH2B3 and CASC8, likely involved in hallmark pathways of aging biology, including telomere shortening and inflammation. Several of these loci involve trade-offs between chronic disease risk and cancer.

scholarly journals Sex Differences in Urate Handling

2020 ◽  
Vol 21 (12) ◽  
pp. 4269 ◽  
Author(s):  
Victoria L. Halperin Kuhns ◽  
Owen M. Woodward
Keyword(s):  
Sex Differences ◽  
Disease Risk ◽  
Association Studies ◽  
Elevated Serum ◽  
Serum Urate ◽  
Genome Wide Association Studies ◽  
Renal Handling ◽  
Physiological Regulation ◽  
Genome Wide

Hyperuricemia, or elevated serum urate, causes urate kidney stones and gout and also increases the incidence of many other conditions including renal disease, cardiovascular disease, and metabolic syndrome. As we gain mechanistic insight into how urate contributes to human disease, a clear sex difference has emerged in the physiological regulation of urate homeostasis. This review summarizes our current understanding of urate as a disease risk factor and how being of the female sex appears protective. Further, we review the mechanisms of renal handling of urate and the significant contributions from powerful genome-wide association studies of serum urate. We also explore the role of sex in the regulation of specific renal urate transporters and the power of new animal models of hyperuricemia to inform on the role of sex and hyperuricemia in disease pathogenesis. Finally, we advocate the use of sex differences in urate handling as a potent tool in gaining a further understanding of physiological regulation of urate homeostasis and for presenting new avenues for treating the constellation of urate related pathologies.

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