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Admixture mapping

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https://www.readbyqxmd.com/read/29674434/natural-selection-interacts-with-recombination-to-shape-the-evolution-of-hybrid-genomes
#1
Molly Schumer, Chenling Xu, Daniel L Powell, Arun Durvasula, Laurits Skov, Chris Holland, John C Blazier, Sriram Sankararaman, Peter Andolfatto, Gil G Rosenthal, Molly Przeworski
To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the "minor" parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human and archaic admixture...
April 19, 2018: Science
https://www.readbyqxmd.com/read/29644624/the-demographic-history-of-atlantic-salmon-salmo-salar-across-its-distribution-range-reconstructed-from-approximate-bayesian-computations
#2
Quentin Rougemont, Louis Bernatchez
Understanding the dual roles of demographic and selective processes in the buildup of population divergence is one of the most challenging tasks in evolutionary biology. Here, we investigated the demographic history of Atlantic Salmon across the entire species range using 2035 anadromous individuals from North America and Eurasia. By combining results from admixture graphs, geo-genetic maps and an Approximate Bayesian Computation (ABC) framework, we validated previous hypotheses pertaining to secondary contact between European and Northern American populations, but also identified secondary contacts in European populations from different glacial refugia...
April 12, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29531077/-ubd-modifies-apol1-induced-kidney-disease-risk
#3
Jia-Yue Zhang, Minxian Wang, Lei Tian, Giulio Genovese, Paul Yan, James G Wilson, Ravi Thadhani, Amy K Mottl, Gerald B Appel, Alexander G Bick, Matthew G Sampson, Seth L Alper, David J Friedman, Martin R Pollak
People of recent African ancestry develop kidney disease at much higher rates than most other groups. Two specific coding variants in the Apolipoprotein-L1 gene APOL1 termed G1 and G2 are the causal drivers of much of this difference in risk, following a recessive pattern of inheritance. However, most individuals with a high-risk APOL1 genotype do not develop overt kidney disease, prompting interest in identifying those factors that interact with APOL1 We performed an admixture mapping study to identify genetic modifiers of APOL1 -associated kidney disease...
March 27, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29484647/gene-based-evaluation-of-low-frequency-variation-and-genetically-predicted-gene-expression-impacting-risk-of-keloid-formation
#4
Jacklyn N Hellwege, Shirley B Russell, Scott M Williams, Todd L Edwards, Digna R Velez Edwards
Keloids are benign dermal tumors occurring approximately 20 times more often in individuals of African descent as compared to individuals of European descent. While most keloids occur sporadically, a genetic predisposition is supported by both familial aggregation of some keloids and large differences in risk among populations. Despite Africans and African Americans being at increased risk over lighter-skinned individuals, little genetic research exists into this phenotype. Using a combination of admixture mapping and exome analysis, we reported multiple common variants within chr15q21...
February 27, 2018: Annals of Human Genetics
https://www.readbyqxmd.com/read/29428798/analysis-of-population-structure-and-genetic-diversity-in-an-exotic-germplasm-collection-of-eleusine-coracana-l-gaertn-using-genic-ssr-markers
#5
Subramani Pandian, Lakkakula Satish, Ramakrishnan Rameshkumar, Pandiyan Muthuramalingam, Arockiam Sagina Rency, Periyasamy Rathinapriya, Manikandan Ramesh
Finger millet (Eleusine coracana (L.) Geartn.) is one of the important small millets serves as a food security crop because of its high nutritional values. The complex tetraploid genome of finger millet requires a large number of informative, functional DNA markers for different applications in genetics and breeding. Yet, less number of simple sequence repeat (SSR) markers have been developed from expressed sequence tags in finger millet. In the present study, 56 new genic SSR markers were developed from publicly available drought related ESTs...
February 8, 2018: Gene
https://www.readbyqxmd.com/read/29411878/the-breakdown-of-genomic-ancestry-blocks-in-hybrid-lineages-given-a-finite-number-of-recombination-sites
#6
Thijs Janzen, Arne W Nolte, Arne Traulsen
When a lineage originates from hybridization genomic blocks of contiguous ancestry from different ancestors are fragmented through genetic recombination. The resulting blocks are delineated by so called “junctions”, which accumulate with every generation that passes. Modeling the accumulation of ancestry block junctions can elucidate processes and timeframes of genomic admixture. Previous models have not addressed ancestry block dynamics for chromosomes that consist of a finite number of recombination sites...
February 7, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29394082/a-genome-wide-association-study-in-hispanics-latinos-identifies-novel-signals-for-lung-function-the-hispanic-community-health-study-study-of-latinos
#7
Kristin M Burkart, Tamar Sofer, Stephanie J London, Ani Manichaikul, Fernando P Hartwig, Qi Yan, María Soler Artigas, Lydiana Avila, Wei Chen, Sonia Davis Thomas, Alejandro A Diaz, Ian P Hall, Bernardo L Horta, Robert C Kaplan, Cathy C Laurie, Ana M Menezes, Jean V Morrison, Elizabeth C Oelsner, Deepa Rastogi, Stephen S Rich, Manuel Soto-Quiros, Adrienne M Stilp, Martin D Tobin, Louise V Wain, Juan C Celedón, R Graham Barr
RATIONALE: Lung function and chronic obstructive pulmonary disease (COPD) are heritable traits. Genome-wide association studies (GWAS) have identified numerous pulmonary function and COPD loci, primarily in cohorts of European ancestry. OBJECTIVES: Perform a GWAS of COPD-phenotypes in Hispanic/Latino populations to identify loci not previously detected in European populations. METHODS: GWAS of lung function and COPD in Hispanic/Latino participants from a population-based cohort...
February 2, 2018: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/29297395/between-lake-baikal-and-the-baltic-sea-genomic-history-of-the-gateway-to-europe
#8
Petr Triska, Nikolay Chekanov, Vadim Stepanov, Elza K Khusnutdinova, Ganesh Prasad Arun Kumar, Vita Akhmetova, Konstantin Babalyan, Eugenia Boulygina, Vladimir Kharkov, Marina Gubina, Irina Khidiyatova, Irina Khitrinskaya, Ekaterina E Khrameeva, Rita Khusainova, Natalia Konovalova, Sergey Litvinov, Andrey Marusin, Alexandr M Mazur, Valery Puzyrev, Dinara Ivanoshchuk, Maria Spiridonova, Anton Teslyuk, Svetlana Tsygankova, Martin Triska, Natalya Trofimova, Edward Vajda, Oleg Balanovsky, Ancha Baranova, Konstantin Skryabin, Tatiana V Tatarinova, Egor Prokhortchouk
BACKGROUND: The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic-speaking migrants as well as eastward by Europeans. Unfortunately, the material records of history of this region are not dense enough to reconstruct details of population history. These considerations stimulate growing interest to obtain a genetic picture of the demographic history of migrations and admixture in Northern Eurasia...
December 28, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29288582/properties-of-global-and-local-ancestry-adjustments-in-genetic-association-tests-in-admixed-populations
#9
Eden R Martin, Ilker Tunc, Zhi Liu, Susan H Slifer, Ashley H Beecham, Gary W Beecham
Population substructure can lead to confounding in tests for genetic association, and failure to adjust properly can result in spurious findings. Here we address this issue of confounding by considering the impact of global ancestry (average ancestry across the genome) and local ancestry (ancestry at a specific chromosomal location) on regression parameters and relative power in ancestry-adjusted and -unadjusted models. We examine theoretical expectations under different scenarios for population substructure; applying different regression models, verifying and generalizing using simulations, and exploring the findings in real-world admixed populations...
March 2018: Genetic Epidemiology
https://www.readbyqxmd.com/read/29230682/association-of-functional-markers-with-flowering-time-in-lentil
#10
Jitendra Kumar, Sunanda Gupta, Revanappa S Biradar, Priyanka Gupta, Sonali Dubey, Narendra Pratap Singh
In the present study, a diverse panel of 96 accessions of lentil germplasm was used to study flowering time over environments and to identify simple sequence repeat markers associated with flowering time through association mapping. The study showed high broad sense heritability estimate (h2 bs=0.93) for flowering time in lentil. Screening of 534 SSR markers resulted in an identification of 75 SSR polymorphic markers (13.9%) across studied genotypes. These markers amplified 266 loci and generated 697 alleles ranging from two to 16 alleles per locus...
February 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29207956/a-microsatellite-diversity-analysis-and-the-development-of-core-set-germplasm-in-a-large-hulless-barley-hordeum-vulgare-l-collection
#11
Qijun Xu, Xingquan Zeng, Bin Lin, Zeqing Li, Hongjun Yuan, Yulin Wang, Zhasang, Nyima Tashi
BACKGROUND: Clarifying genetic diversity in a large germplasm resource plays important roles in experimental designs that provides flexible utility in fundamental research and breeding in crops. However, the work is limited due to small collections of barley that are insufficient representatives. RESULTS: In the present study, we collected 562 hulless barley (Hordeum vulgare L.) accessions with worldwide geographic origins and evaluated their genetic variability and relatedness based on 93 simple sequence repeat (SSR) markers...
December 6, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29202956/admixture-mapping-of-uterine-fibroid-size-and-number-in-african-american-women
#12
MULTICENTER STUDY
Michael J Bray, Todd L Edwards, Melissa F Wellons, Sarah H Jones, Katherine E Hartmann, Digna R Velez Edwards
OBJECTIVE: To evaluate the relationship between genetic ancestry and uterine fibroid characteristics. DESIGN: Cross-sectional study. SETTING: Not applicable. PATIENT(S): A total of 609 African American participants with image- or surgery-confirmed fibroids in a biorepository at Vanderbilt University electronic health record biorepository and the Coronary Artery Risk Development in Young Adults studies were included. INTERVENTION(S): None...
December 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/29155883/admixture-mapping-in-the-hispanic-community-health-study-study-of-latinos-reveals-regions-of-genetic-associations-with-blood-pressure-traits
#13
Tamar Sofer, Leslie J Baier, Sharon R Browning, Timothy A Thornton, Gregory A Talavera, Sylvia Wassertheil-Smoller, Martha L Daviglus, Robert Hanson, Sayuko Kobes, Richard S Cooper, Jianwen Cai, Daniel Levy, Alex P Reiner, Nora Franceschini
Admixture mapping can be used to detect genetic association regions in admixed populations, such as Hispanics/Latinos, by estimating associations between local ancestry allele counts and the trait of interest. We performed admixture mapping of the blood pressure traits systolic and diastolic blood pressure (SBP, DBP), mean arterial pressure (MAP), and pulse pressure (PP), in a dataset of 12,116 participants from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Hispanics/Latinos have three predominant ancestral populations (European, African, and Amerindian), for each of which we separately tested local ancestry intervals across the genome...
2017: PloS One
https://www.readbyqxmd.com/read/29124769/introgression-from-populus-balsamifera-underlies-adaptively-significant-variation-and-range-boundaries-in-p-trichocarpa
#14
Adriana Suarez-Gonzalez, Charles A Hefer, Christian Lexer, Carl J Douglas, Quentin C B Cronk
Introgression can be an important source of adaptive phenotypes, although conversely it can have deleterious effects. Evidence for adaptive introgression is accumulating but information on the genetic architecture of introgressed traits lags behind. Here we determine trait architecture in Populus trichocarpa under introgression from P. balsamifera using admixture mapping and phenotypic analyses. Our results reveal that admixture is a key driver of clinal adaptation and suggest that the northern range extension of P...
January 2018: New Phytologist
https://www.readbyqxmd.com/read/29118129/admixture-mapping-in-a-hybrid-zone-reveals-loci-associated-with-avian-feather-coloration
#15
Alan Brelsford, David P L Toews, Darren E Irwin
Identifying the genetic bases for colour patterns has provided important insights into the control and expression of pigmentation and how these characteristics influence fitness. However, much more is known about the genetic bases for traits based on melanin pigments than for traits based on another major class of pigments, carotenoids. Here, we use natural admixture in a hybrid zone between Audubon's and myrtle warblers ( Setophaga coronata auduboni / S. c. coronata ) to identify genomic regions associated with both types of pigmentation...
November 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29073141/genomic-regions-associated-with-susceptibility-to-barrett-s-esophagus-and-esophageal-adenocarcinoma-in-african-americans-the-cross-betrnet-admixture-study
#16
Xiangqing Sun, Apoorva K Chandar, Marcia I Canto, Prashanthi N Thota, Malcom Brock, Nicholas J Shaheen, David G Beer, Jean S Wang, Gary W Falk, Prasad G Iyer, Julian A Abrams, Medha Venkat-Ramani, Martina Veigl, Alexander Miron, Joseph Willis, Deepa T Patil, Ilke Nalbantoglu, Kishore Guda, Sanford D Markowitz, Xiaofeng Zhu, Robert Elston, Amitabh Chak
BACKGROUND: Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) are far more prevalent in European Americans than in African Americans. Hypothesizing that this racial disparity in prevalence might represent a genetic susceptibility, we used an admixture mapping approach to interrogate disease association with genomic differences between European and African ancestry. METHODS: Formalin fixed paraffin embedded samples were identified from 54 African Americans with BE or EAC through review of surgical pathology databases at participating Barrett's Esophagus Translational Research Network (BETRNet) institutions...
2017: PloS One
https://www.readbyqxmd.com/read/29037167/ancestry-inference-using-principal-component-analysis-and-spatial-analysis-a-distance-based-analysis-to-account-for-population-substructure
#17
Jinyoung Byun, Younghun Han, Ivan P Gorlov, Jonathan A Busam, Michael F Seldin, Christopher I Amos
BACKGROUND: Accurate inference of genetic ancestry is of fundamental interest to many biomedical, forensic, and anthropological research areas. Genetic ancestry memberships may relate to genetic disease risks. In a genome association study, failing to account for differences in genetic ancestry between cases and controls may also lead to false-positive results. Although a number of strategies for inferring and taking into account the confounding effects of genetic ancestry are available, applying them to large studies (tens thousands samples) is challenging...
October 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29016599/coronary-collateralization-shows-sex-and-racial-ethnic-differences-in-obstructive-artery-disease-patients
#18
Zhi Liu, Margaret A Pericak-Vance, Pascal Goldschmidt-Clermont, David Seo, Liyong Wang, Tatjana Rundek, Gary W Beecham
BACKGROUND: Coronary collateral circulation protects cardiac tissues from myocardial infarction damage and decreases sudden cardiac death. So far, it is unclear how coronary collateralization varies by race-ethnicity groups and by sex. METHODS: We assessed 868 patients with obstructive CAD. Patients were assessed for collateral grades based on Rentrop grading system, as well as other covariates. DNA samples were genotyped using the Affymetrix 6.0 genotyping array...
2017: PloS One
https://www.readbyqxmd.com/read/28980262/the-analysis-of-ethnic-mixtures
#19
Xiaofeng Zhu, Heming Wang
Population of ethnic mixtures can be useful in genetic studies. Admixture mapping, or mapping by admixture linkage disequilibrium (MALD), is specially developed for admixed populations and can supplement traditional genome-wide association analyses in the search for genetic variants underlying complex traits. Admixture mapping tests the association between a trait and locus-specific ancestries. The locus-specific ancestries are in linkage disequilibrium (LD), which is generated by an admixture process between genetically distinct ancestral populations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28955604/genetic-diversity-and-population-structure-of-cucumis-sativus-l-by-using-ssr-markers
#20
Aejaz Ahmad Dar, Reetika Mahajan, Padma Lay, Susheel Sharma
The genetic variation, marker attributes and population structure was assessed in 104 genotypes of cucumber using 23 SSR primer pairs. The total number of alleles produced was 67 with an average of 2.91 per locus. Allele frequency was in the range of 0.215 to 0.561 with mean value of 0.403, polymorphic information content ranged from 0.158 to 0.495 with the mean of 0.333, marker index ranged from 0.316 to 1.54 with an average value of 0.954 and resolving power ranged from 0.346 to 2.692 with mean of 1.392...
October 2017: 3 Biotech
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