CRISPR/Cas9 Gene Drive: Growing Pains for a New Technology [Commentary]
(Source: Genetics)
Source: Genetics - March 6, 2017 Category: Genetics & Stem Cells Authors: Reed, F. A. Tags: Commentary Source Type: research
Molecular Population Genetics [Ecology and Evolution]
We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. (Source: Genetics)
Source: Genetics - March 6, 2017 Category: Genetics & Stem Cells Authors: Casillas, S., Barbadilla, A. Tags: Ecology and Evolution Source Type: research
ISSUE HIGHLIGHTS [Issue Highlights]
(Source: Genetics)
Source: Genetics - March 6, 2017 Category: Genetics & Stem Cells Tags: Issue Highlights Source Type: research
DNA Repair in Drosophila: Mutagens, Models, and Missing Genes [Repair, Recombination, and Cell Division]
The numerous processes that damage DNA are counterbalanced by a complex network of repair pathways that, collectively, can mend diverse types of damage. Insights into these pathways have come from studies in many different organisms, including Drosophila melanogaster. Indeed, the first ideas about chromosome and gene repair grew out of Drosophila research on the properties of mutations produced by ionizing radiation and mustard gas. Numerous methods have been developed to take advantage of Drosophila genetic tools to elucidate repair processes in whole animals, organs, tissues, and cells. These studies have led to the disc...
Source: Genetics - February 1, 2017 Category: Genetics & Stem Cells Authors: Sekelsky, J. Tags: Repair, Recombination, and Cell Division Source Type: research
Emergence of a Novel Chimeric Gene Underlying Grain Number in Rice [Genetics of Complex Traits]
In this study, we identified a novel functional chimeric gene and also provided information regarding the molecular mechanisms regulating rice grain number. (Source: Genetics)
Source: Genetics - February 1, 2017 Category: Genetics & Stem Cells Authors: Chen, H., Tang, Y., Liu, J., Tan, L., Jiang, J., Wang, M., Zhu, Z., Sun, X., Sun, C. Tags: Genetics of Complex Traits Source Type: research
Genetic Mechanisms Leading to Sex Differences Across Common Diseases and Anthropometric Traits [Genetics of Complex Traits]
Common diseases often show sex differences in prevalence, onset, symptomology, treatment, or prognosis. Although studies have been performed to evaluate sex differences at specific SNP associations, this work aims to comprehensively survey a number of complex heritable diseases and anthropometric traits. Potential genetically encoded sex differences we investigated include differential genetic liability thresholds or distributions, gene–sex interaction at autosomal loci, major contribution of the X-chromosome, or gene–environment interactions reflected in genes responsive to androgens or estrogens. Finally, we ...
Source: Genetics - February 1, 2017 Category: Genetics & Stem Cells Authors: Traglia, M., Bseiso, D., Gusev, A., Adviento, B., Park, D. S., Mefford, J. A., Zaitlen, N., Weiss, L. A. Tags: Genetics of Complex Traits Source Type: research
Human Facial Shape and Size Heritability and Genetic Correlations [Genetics of Complex Traits]
The human face is an array of variable physical features that together make each of us unique and distinguishable. Striking familial facial similarities underscore a genetic component, but little is known of the genes that underlie facial shape differences. Numerous studies have estimated facial shape heritability using various methods. Here, we used advanced three-dimensional imaging technology and quantitative human genetics analysis to estimate narrow-sense heritability, heritability explained by common genetic variation, and pairwise genetic correlations of 38 measures of facial shape and size in normal African Bantu c...
Source: Genetics - February 1, 2017 Category: Genetics & Stem Cells Authors: Cole, J. B., Manyama, M., Larson, J. R., Liberton, D. K., Ferrara, T. M., Riccardi, S. L., Li, M., Mio, W., Klein, O. D., Santorico, S. A., Hallgrimsson, B., Spritz, R. A. Tags: Genetics of Complex Traits Source Type: research
Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus [Genetics of Complex Traits]
The dwarf phenotype characterizes the smallest of rabbit breeds and is governed largely by the effects of a single dwarfing allele with an incompletely dominant effect on growth. Dwarf rabbits typically weigh under 1 kg and have altered craniofacial morphology. The dwarf allele is recessive lethal and dwarf homozygotes die within a few days of birth. The dwarf phenotype is expressed in heterozygous individuals and rabbits from dwarf breeds homozygous for the wild-type allele are normal, although smaller when compared to other breeds. Here, we show that the dwarf allele constitutes a ~12.1 kb deletion overlapping the promot...
Source: Genetics - February 1, 2017 Category: Genetics & Stem Cells Authors: Carneiro, M., Hu, D., Archer, J., Feng, C., Afonso, S., Chen, C., Blanco-Aguiar, J. A., Garreau, H., Boucher, S., Ferreira, P. G., Ferrand, N., Rubin, C.-J., Andersson, L. Tags: Genetics of Complex Traits Source Type: research
Evaluating Sequence-Based Genomic Prediction with an Efficient New Simulator [Genomic Selection]
The vast amount of sequence data generated to analyze complex traits is posing new challenges in terms of the analysis and interpretation of the results. Although simulation is a fundamental tool to investigate the reliability of genomic analyses and to optimize experimental design, existing software cannot realistically simulate complete genomes. To remedy this, we have developed a new strategy (Sequence-Based Virtual Breeding, SBVB) that uses real sequence data and simulates new offspring genomes and phenotypes in a very efficient and flexible manner. Using this tool, we studied the efficiency of full sequence in genomic...
Source: Genetics - February 1, 2017 Category: Genetics & Stem Cells Authors: Perez-Enciso, M., Forneris, N., de los Campos, G., Legarra, A. Tags: Genomic Selection Source Type: research
The Genomic Architecture of Interactions Between Natural Genetic Polymorphisms and Environments in Yeast Growth [Genetics of Complex Traits]
Gene-environment interaction (GxE) refers to the phenomenon that the same mutation has different phenotypic effects in different environments. Although quantitative trait loci (QTLs) exhibiting GxE have been reported, little is known about the general properties of GxE, and those of its underlying QTLs. Here, we use the genotypes of 1005 segregants from a cross between two Saccharomyces cerevisiae strains, and the growth rates of these segregants in 47 environments, to identify growth rate QTLs (gQTLs) in each environment, and QTLs that have different growth effects in each pair of environments (gxeQTLs) . The average numb...
Source: Genetics - February 1, 2017 Category: Genetics & Stem Cells Authors: Wei, X., Zhang, J. Tags: Genetics of Complex Traits Source Type: research
Recombinant Haplotypes Narrow the ARMS2/HTRA1 Association Signal for Age-Related Macular Degeneration [Genetics of Complex Traits]
In this study, we analyzed rare recombinant haplotypes in 16,144 AMD cases and 17,832 controls from the International AMD Genomics Consortium and identified variants in ARMS2 but not HTRA1 to exclusively carry the AMD risk with P-values between 1.0 x 10–773 and 6.7 x 10–5. This now allows prioritization of the gene of interest for subsequent functional studies. (Source: Genetics)
Source: Genetics - February 1, 2017 Category: Genetics & Stem Cells Authors: Grassmann, F., Heid, I. M., Weber, B. H. F., International AMD Genomics Consortium (IAMDGC) Tags: Genetics of Complex Traits Source Type: research
Correlated Mutations and Homologous Recombination Within Bacterial Populations [Population and Evolutionary Genetics]
Inferring the rate of homologous recombination within a bacterial population remains a key challenge in quantifying the basic parameters of bacterial evolution. Due to the high sequence similarity within a clonal population, and unique aspects of bacterial DNA transfer processes, detecting recombination events based on phylogenetic reconstruction is often difficult, and estimating recombination rates using coalescent model-based methods is computationally expensive, and often infeasible for large sequencing data sets. Here, we present an efficient solution by introducing a set of mutational correlation functions computed u...
Source: Genetics - February 1, 2017 Category: Genetics & Stem Cells Authors: Lin, M., Kussell, E. Tags: Population and Evolutionary Genetics Source Type: research
Genomic Trajectories to Desiccation Resistance: Convergence and Divergence Among Replicate Selected Drosophila Lines [Population and Evolutionary Genetics]
Adaptation to environmental stress is critical for long-term species persistence. With climate change and other anthropogenic stressors compounding natural selective pressures, understanding the nature of adaptation is as important as ever in evolutionary biology. In particular, the number of alternative molecular trajectories available for an organism to reach the same adaptive phenotype remains poorly understood. Here, we investigate this issue in a set of replicated Drosophila melanogaster lines selected for increased desiccation resistance—a classical physiological trait that has been closely linked to Drosophila...
Source: Genetics - February 1, 2017 Category: Genetics & Stem Cells Authors: Griffin, P. C., Hangartner, S. B., Fournier-Level, A., Hoffmann, A. A. Tags: Population and Evolutionary Genetics Source Type: research
Inferring Ancestral Recombination Graphs from Bacterial Genomic Data [Population and Evolutionary Genetics]
Homologous recombination is a central feature of bacterial evolution, yet it confounds traditional phylogenetic methods. While a number of methods specific to bacterial evolution have been developed, none of these permit joint inference of a bacterial recombination graph and associated parameters. In this article, we present a new method which addresses this shortcoming. Our method uses a novel Markov chain Monte Carlo algorithm to perform phylogenetic inference under the ClonalOrigin model. We demonstrate the utility of our method by applying it to ribosomal multilocus sequence typing data sequenced from pathogenic and no...
Source: Genetics - February 1, 2017 Category: Genetics & Stem Cells Authors: Vaughan, T. G., Welch, D., Drummond, A. J., Biggs, P. J., George, T., French, N. P. Tags: Population and Evolutionary Genetics Source Type: research
Statistical Methods for Identifying Sequence Motifs Affecting Point Mutations [Population and Evolutionary Genetics]
We present new log-linear models that allow explicit examination of these questions, along with sequence logo style visualization to enable identifying specific motifs. We demonstrate the performance of these methods by analyzing mutation processes in human germline and malignant melanoma. We recapitulate the known CpG effect, and identify novel motifs, including a highly significant motif associated with A$$\to $$G mutations. We show that major effects of neighbors on germline mutation lie within $$\pm 2$$ of the mutating base. Models are also presented for contrasting the entire mutation spectra (the distribution of the ...
Source: Genetics - February 1, 2017 Category: Genetics & Stem Cells Authors: Zhu, Y., Neeman, T., Yap, V. B., Huttley, G. A. Tags: Population and Evolutionary Genetics Source Type: research
