scholarly journals A study of Kibbutzim in Israel reveals risk factors for cardiometabolic traits and subtle population structure

2017 ◽  
Author(s):  
Einat Granot-Hershkovitz ◽  
David Karasik ◽  
Yechiel Friedlander ◽  
Laura Rodriguez-Murillo ◽  
Rajkumar Dorajoo ◽  
...  
Keyword(s):  
Social Stability ◽  
Genetic Determinants ◽  
Isolated Populations ◽  
Genetic Studies ◽  
Point Estimates ◽  
Genome Wide ◽  
Extensive Information ◽  
Cardiometabolic Traits ◽  
Homogeneous Environment

AbstractGenetic studies in isolated populations have provided increased power for identifying loci associated with complex diseases and traits. We present here the Kibbutzim Family Study (KFS), initiated for investigating environmental and genetic determinants of cardiometabolic traits in extended Israeli families living in communes characterized by long-term social stability and homogeneous environment. Extensive information on cardiometabolic traits, as well as genome-wide genetic data, was collected on 901 individuals, making this study, to the best of our knowledge, the largest of its kind in Israel. We have thoroughly characterized the KFS genetic structure, observing that most participants were of Ashkenazi Jewish (AJ) origin, and confirming a recent severe bottleneck in their recent history (point estimates: effective size ≈450 individuals, 23 generations ago). Focusing on genetic variants enriched in KFS compared with non-Finnish Europeans, we demonstrated that AJ-specific variants are largely involved in cancer-related pathways. Using linear mixed models, we conducted an association study of these enriched variants with 16 cardiometabolic traits. We found 24 variants to be significantly associated with cardiometabolic traits. The strongest association, which we also replicated, was between a variant upstream of the MSRA gene, ≈200-fold enriched in KFS, and weight (P=3.6·10−8). In summary, the KFS is a valuable resource for the study of the population genetics of Israel as well as the genetics of cardiometabolic traits in a homogeneous environment.

scholarly journals Drone phenotyping and machine learning enable discovery of loci regulating daily floral opening in lettuce

2021 ◽  
Vol 72 (8) ◽  
pp. 2979-2994 ◽  
Author(s):  
Rongkui Han ◽  
Andy J Y Wong ◽  
Zhehan Tang ◽  
Maria J Truco ◽  
Dean O Lavelle ◽  
...  
Keyword(s):  
Machine Learning ◽  
Time Course ◽  
Image Data ◽  
Support Vector ◽  
Genetic Determinants ◽  
Flower Opening ◽  
Genetic Studies ◽  
Marker Data ◽  
Genome Wide ◽  
Bayesian Inference Method

Abstract Flower opening and closure are traits of reproductive importance in all angiosperms because they determine the success of self- and cross-pollination. The temporal nature of this phenotype rendered it a difficult target for genetic studies. Cultivated and wild lettuce, Lactuca spp., have composite inflorescences that open only once. An L. serriola×L. sativa F6 recombinant inbred line (RIL) population differed markedly for daily floral opening time. This population was used to map the genetic determinants of this trait; the floral opening time of 236 RILs was scored using time-course image series obtained by drone-based phenotyping on two occasions. Floral pixels were identified from the images using a support vector machine with an accuracy >99%. A Bayesian inference method was developed to extract the peak floral opening time for individual genotypes from the time-stamped image data. Two independent quantitative trait loci (QTLs; Daily Floral Opening 2.1 and qDFO8.1) explaining >30% of the phenotypic variation in floral opening time were discovered. Candidate genes with non-synonymous polymorphisms in coding sequences were identified within the QTLs. This study demonstrates the power of combining remote sensing, machine learning, Bayesian statistics, and genome-wide marker data for studying the genetics of recalcitrant phenotypes.

scholarly journals Genomic signatures of inbreeding and genetic load in a threatened rattlesnake

2021 ◽  
Author(s):  
Alexander Ochoa ◽  
H. Lisle Gibbs
Keyword(s):  
Threatened Species ◽  
Empirical Studies ◽  
Genetic Load ◽  
Population History ◽  
Deleterious Mutations ◽  
Genetic Rescue ◽  
Isolated Populations ◽  
Genome Wide ◽  
The Impact

Theory predicts that threatened species living in small populations will experience high levels of inbreeding that will increase their negative genetic load but recent work suggests that the impact of load may be minimized by purging resulting from long term population bottlenecks. Empirical studies that examine this idea using genome-wide estimates of inbreeding and genetic load in threatened species are limited. Here we use genome resequencing data to compare levels of inbreeding, levels of genetic load and population history in threatened Eastern massasauga rattlesnakes (Sistrurus catenatus) which exist in small isolated populations and closely-related yet outbred Western massasauga rattlesnakes (S. tergeminus). In terms of inbreeding, S. catenatus genomes had a greater number of ROHs of varying sizes indicating sustained inbreeding through repeated bottlenecks when compared to S. tergeminus. At the species level, outbred S. tergeminus had higher genome-wide levels of genetic load in the form of greater numbers of derived deleterious mutations compared to S. catenatus presumably due to long-term purging of deleterious mutations in S. catenatus. In contrast, mutations that escaped the “drift sieve” and were polymorphic within S. catenatus populations were more abundant and more often found in homozygote genotypes than in S. tergeminus suggesting a reduced efficiency of purifying selection in smaller S. catenatus populations. Our results support an emerging idea that the historical demography of a threatened species has a significant impact on the type of genetic load present which impacts implementation of conservation actions such as genetic rescue.

scholarly journals Genomic Consequences of Long-Term Population Decline in Brown Eared Pheasant

2020 ◽  
Vol 38 (1) ◽  
pp. 263-273
Author(s):  
Pengcheng Wang ◽  
John T Burley ◽  
Yang Liu ◽  
Jiang Chang ◽  
De Chen ◽  
...  
Keyword(s):  
Natural Selection ◽  
Population Size ◽  
Population Decline ◽  
Deleterious Mutations ◽  
Loss Of Function ◽  
Wild Populations ◽  
Effective Population ◽  
Isolated Populations ◽  
Genome Wide

Abstract Population genetic theory and empirical evidence indicate that deleterious alleles can be purged in small populations. However, this viewpoint remains controversial. It is unclear whether natural selection is powerful enough to purge deleterious mutations when wild populations continue to decline. Pheasants are terrestrial birds facing a long-term risk of extinction as a result of anthropogenic perturbations and exploitation. Nevertheless, there are scant genomics resources available for conservation management and planning. Here, we analyzed comparative population genomic data for the three extant isolated populations of Brown eared pheasant (Crossoptilon mantchuricum) in China. We showed that C. mantchuricum has low genome-wide diversity and a contracting effective population size because of persistent declines over the past 100,000 years. We compared genome-wide variation in C. mantchuricum with that of its closely related sister species, the Blue eared pheasant (C. auritum) for which the conservation concern is low. There were detrimental genetic consequences across all C. mantchuricum genomes including extended runs of homozygous sequences, slow rates of linkage disequilibrium decay, excessive loss-of-function mutations, and loss of adaptive genetic diversity at the major histocompatibility complex region. To the best of our knowledge, this study is the first to perform a comprehensive conservation genomic analysis on this threatened pheasant species. Moreover, we demonstrated that natural selection may not suffice to purge deleterious mutations in wild populations undergoing long-term decline. The findings of this study could facilitate conservation planning for threatened species and help recover their population size.

scholarly journals Multidimensional Heritability Analysis of Neuroanatomical Shape

2015 ◽  
Author(s):  
Tian Ge ◽  
Martin Reuter ◽  
Anderson M. Winkler ◽  
Avram J. Holmes ◽  
Phil H. Lee ◽  
...  
Keyword(s):  
Brain Structure ◽  
Large Scale ◽  
Brain Mri ◽  
Brain Structures ◽  
Biomedical Data ◽  
Genetic Determinants ◽  
Genetic Studies ◽  
Genome Wide ◽  
Human Connectome Project ◽  
Mri Scans

In the dawning era of large-scale biomedical data, multidimensional phenotype vectors will play an increasing role in examining the genetic underpinnings of brain features, behavior and disease. For example, shape measurements derived from brain MRI scans are multidimensional geometric descriptions of brain structure and provide an alternate class of phenotypes that remains largely unexplored in genetic studies. Here we extend the concept of heritability to multidimensional traits, and present the first comprehensive analysis of the heritability of neuroanatomical shape measurements across an ensemble of brain structures based on genome-wide SNP and MRI data from 1,320 unrelated, young and healthy individuals. We replicate our findings in an extended twin sample from the Human Connectome Project (HCP). Our results demonstrate that neuroanatomical shape can be significantly heritable, above and beyond volume, and can serve as a complementary phenotype to study the genetic determinants and clinical relevance of brain structure.

scholarly journals Searching for the human genetic factors standing in the way of universally effective vaccines

2015 ◽  
Vol 370 (1671) ◽  
pp. 20140341 ◽  
Author(s):  
Alexander J. Mentzer ◽  
Daniel O'Connor ◽  
Andrew J. Pollard ◽  
Adrian V. S. Hill
Keyword(s):  
Association Studies ◽  
Significant Proportion ◽  
Cost Effective ◽  
Genome Wide Association Studies ◽  
Genetic Determinants ◽  
Vaccine Response ◽  
Genetic Studies ◽  
Genome Wide ◽  
Effective Manner ◽  
Genetic Techniques

Vaccines have revolutionized modern public health. The effectiveness of some vaccines is limited by the variation in response observed between individuals and across populations. There is compelling evidence that a significant proportion of this variability can be attributed to human genetic variation, especially for those vaccines administered in early life. Identifying and understanding the determinants of this variation could have a far-reaching influence upon future methods of vaccine design and deployment. In this review, we summarize the genetic studies that have been undertaken attempting to identify the genetic determinants of response heterogeneity for the vaccines against hepatitis B, measles and rubella. We offer a critical appraisal of these studies and make a series of suggestions about how modern genetic techniques, including genome-wide association studies, could be used to characterize the genetic architecture of vaccine response heterogeneity. We conclude by suggesting how the findings from such studies could be translated to improve vaccine effectiveness and target vaccination in a more cost-effective manner.

scholarly journals Eating Disorders: From Twin Studies to Candidate Genes and Beyond

2005 ◽  
Vol 8 (5) ◽  
pp. 467-482 ◽  
Author(s):  
Margarita C. T. Slof-Op ‘t Landt ◽  
Eric F. van Furth ◽  
Ingrid Meulenbelt ◽  
P. Eline Slagboom ◽  
Meike Bartels ◽  
...  
Keyword(s):  
Eating Disorders ◽  
Candidate Genes ◽  
Genetic Association ◽  
Association Studies ◽  
Molecular Genetic ◽  
Twin Studies ◽  
Genetic Association Studies ◽  
Genetic Determinants ◽  
Genetic Studies ◽  
Genome Wide

AbstractSubstantial effort has been put into the exploration of the biological background of eating disorders, through family, twin and molecular genetic studies. Family studies have shown that anorexia (AN) and bulimia nervosa (BN) are strongly familial, and that familial etiologic factors appear to be shared by both disorders. Twin studies often focus on broader phenotypes or subthreshold eating disorders. These studies consistently yielded moderate to substantial heritabilities. In addition, there has been a proliferation of molecular genetic studies that focused on Diagnostic and Statistical Manual of Mental Disorders (4th ed.; DSM-IV; American Psychiatric Association, 1994) AN and BN. Seven linkage regions have been identified in genome-wide screens. Many genetic association studies have been performed, but no consistent association between a candidate gene and AN or BN has been reported. Larger genetic association studies and collaborations are needed to examine the involvement of several candidate genes and biological pathways in eating disorders. In addition, twin studies should be designed to assist the molecular work by further exploring genetic determinants of endophenotypes, evaluating the magnitude of contribution to liability of measured genotypes as well as environmental risk factors related to eating disorders. In this manner twin and molecular studies can move the field forward in a mutually informative way.

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