scholarly journals Transgenic tools for targeted chromosome rearrangements allow construction of balancer chromosomes in non-melanogaster Drosophila species

2021 ◽  
Author(s):  
David L. Stern
Keyword(s):  
Reporter Genes ◽  
Drosophila Species ◽  
Chromosome Rearrangements ◽  
Genetic Studies ◽  
Fluorescent Reporter ◽  
Body Regions ◽  
Deleterious Alleles ◽  
Genomic Regions ◽  
Transgenic Tools ◽  
Balancer Chromosomes

Perhaps the most valuable single set of resources for genetic studies of Drosophila melanogaster is the collection of multiply-inverted chromosomes commonly known as balancer chromosomes. Balancers prevent the recovery of recombination exchange products within genomic regions included in inversions and allow perpetual maintenance of deleterious alleles in living stocks and the execution of complex genetic crosses. Balancer chromosomes have been generated traditionally by exposing animals to ionizing radiation and screening for altered chromosome structure or for unusual marker segregation patterns. These approaches are tedious and unpredictable, and have failed to produce the desired products in some species. Here I describe transgenic tools that allow targeted chromosome rearrangements in Drosophila species. The key new resources are engineered reporter genes containing introns with yeast recombination sites and enhancers that drive fluorescent reporter genes in multiple body regions. These tools were used to generate a doubly-inverted chromosome 3R in D. simulans that serves as an effective balancer chromosome.

scholarly journals K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology

Plant Methods ◽  
2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Peio Ziarsolo ◽  
Tomas Hasing ◽  
Rebeca Hilario ◽  
Victor Garcia-Carpintero ◽  
Jose Blanca ◽  
...  
Keyword(s):  
Cost Effective ◽  
Genetic Distances ◽  
Set Design ◽  
Special Equipment ◽  
Genetic Studies ◽  
Set Up ◽  
Genomic Regions ◽  
Biology Laboratory ◽  
Genotyping Technology ◽  
Genetic Results

Abstract Background K-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. Results As the first examples, K-seq in species as diverse as tomato, dog and wheat was developed. K-seq provided genetic distances similar to those based on WGS in dogs. Experiments comparing K-seq and GBS in tomato showed similar genetic results, although K-seq had the advantage of finding more SNPs for the same number of Illumina reads. The technology reproducibility was tested with two independent runs of the tomato samples, and the correlation coefficient of the SNP coverages between samples was 0.8 and the genotype match was above 94%. K-seq also proved to be useful in polyploid species. The wheat samples generated specific markers for all subgenomes, and the SNPs generated from the diploid ancestors were located in the expected subgenome with accuracies greater than 80%. Conclusion K-seq is an open, patent-unencumbered, easy-to-set-up, cost-effective and reliable technology ready to be used by any molecular biology laboratory without special equipment in many genetic studies.

scholarly journals Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Prasun Dutta ◽  
Andrea Talenti ◽  
Rachel Young ◽  
Siddharth Jayaraman ◽  
Rebecca Callaby ◽  
...  
Keyword(s):  
Water Buffalo ◽  
Whole Genome ◽  
Selective Sweeps ◽  
Whole Genome Analysis ◽  
Genetic Studies ◽  
Cattle Breeds ◽  
Functional Variants ◽  
Species Comparisons ◽  
Disproportionate Number ◽  
Genomic Regions

Abstract More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here, we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.

Variation I: Genetics

Mate Choice ◽  
2017 ◽  
Author(s):  
Gil G. Rosenthal
Keyword(s):  
Genetic Variation ◽  
Gene Structure ◽  
Infinite Number ◽  
Reverse Genetics ◽  
Forward Genetics ◽  
Genetic Models ◽  
Genetic Studies ◽  
Quantitative Genetic ◽  
Negative Effect ◽  
Genomic Regions

This chapter reviews the main approaches for characterizing preference genetics. Approaches to understanding the genetics underlying preferences (or any other phenotype) take two broad forms. The first approach consists of attempts to identify particular genes or genomic regions associated with preference variation; for preferences, this is typically done using so-called forward genetics, whereby variation in phenotype is correlated with variation in genotype. Alternatively, the effects of candidate genes on preference can be characterized using reverse genetics, whereby gene structure or function is altered to test its effect on phenotype. The second approach encompasses quantitative genetic studies that assume that the underlying genetic variation is continuous and additive. Quantitative genetic models often assume an infinite number of loci each contributing infinitely small positive or negative effect, summing to determine trait value.

scholarly journals The UMOD Locus: Insights into the Pathogenesis and Prognosis of Kidney Disease

2017 ◽  
Vol 29 (3) ◽  
pp. 713-726 ◽  
Author(s):  
Olivier Devuyst ◽  
Cristian Pattaro
Keyword(s):  
Kidney Disease ◽  
Kidney Diseases ◽  
Association Studies ◽  
Biochemical Properties ◽  
Genome Wide Association Studies ◽  
Genetic Studies ◽  
Rare Mutations ◽  
Genome Wide ◽  
Genomic Regions ◽  
Insight Into

The identification of genetic factors associated with kidney disease has the potential to provide critical insights into disease mechanisms. Genome-wide association studies have uncovered genomic regions associated with renal function metrics and risk of CKD. UMOD is among the most outstanding loci associated with CKD in the general population, because it has a large effect on eGFR and CKD risk that is consistent across different ethnic groups. The relevance of UMOD for CKD is clear, because the encoded protein, uromodulin (Tamm–Horsfall protein), is exclusively produced by the kidney tubule and has specific biochemical properties that mediate important functions in the kidney and urine. Rare mutations in UMOD are the major cause of autosomal dominant tubulointerstitial kidney disease, a condition that leads to CKD and ESRD. In this brief review, we use the UMOD paradigm to describe how population genetic studies can yield insight into the pathogenesis and prognosis of kidney diseases.

Use of fluorescent reporter genes in olive (Olea europaea L.) transformation

2019 ◽  
Vol 41 (4) ◽  
Author(s):  
Sergio Cerezo ◽  
Elena Palomo-Ríos ◽  
Sinda Ben Mariem ◽  
José A. Mercado ◽  
Fernando Pliego-Alfaro
Keyword(s):  
Olea Europaea ◽  
Reporter Genes ◽  
Fluorescent Reporter ◽  
Olea Europaea L ◽  
Fluorescent Reporter Genes ◽  
Olea Europaéa

scholarly journals Highly efficient scarless knock-in of reporter genes into human and mouse pluripotent stem cells via transient antibiotic selection

2018 ◽  
Author(s):  
Valentin M. Sluch ◽  
Xitiz Chamling ◽  
Claire Wenger ◽  
Yukan Duan ◽  
Dennis S. Rice ◽  
...  
Keyword(s):  
Stem Cells ◽  
Pluripotent Stem Cells ◽  
Low Frequency ◽  
Reporter Genes ◽  
Specific Cell ◽  
Fluorescent Reporter ◽  
Antibiotic Selection ◽  
Homology Directed Repair ◽  
Human And Mouse ◽  
Fluorescent Reporter Genes

AbstractPluripotent stem cells (PSCs) edited with genetic reporters are useful tools for differentiation analysis and for isolation of specific cell populations for study. Reporter integration into the genome is now commonly achieved by targeted DNA nuclease-enhanced homology directed repair (HDR). However, human PSCs are known to have a low frequency of gene knock-in (KI) by HDR, making reporter line generation an arduous process. Here, we report a methodology for scarless KI of large fluorescent reporter genes into PSCs by transient selection with puromycin or zeocin. With this method, we can perform targeted KI of a single reporter gene with up to 65% efficiency, as well as simultaneous KI of two reporter genes into different loci with up to 11% efficiency. Additionally, we demonstrate that this method also works in mouse PSCs.

scholarly journals Recombination, variance in genetic relatedness, and selection against introgressed DNA

2019 ◽  
Author(s):  
Carl Veller ◽  
Nathaniel B. Edelman ◽  
Pavitra Muralidhar ◽  
Martin A. Nowak
Keyword(s):  
Gene Flow ◽  
Genetic Relatedness ◽  
Hybrid Vigor ◽  
Recombination Rates ◽  
Deleterious Alleles ◽  
Genome Wide ◽  
Average Proportion ◽  
Positive Correlations ◽  
Genomic Regions ◽  
Hybrid Cross

AbstractThe genomic proportion that two relatives share identically by descent—their genetic relatedness—can vary depending on the patterns of recombination and segregation in their pedigree. Here, we calculate the precise connection between genome-wide genetic shuffling and variance in genetic relatedness. For the relationships of grandparent-grandoffspring and siblings, the variance in genetic relatedness is a simple decreasing function of , the average proportion of locus pairs that recombine in gametogenesis. These formulations explain several recent observations about variance in genetic relatedness. They further allow us to calculate the neutral variance of ancestry among F2s in a hybrid cross, enabling F2-based tests for various kinds of selection, such as Dobzhansky-Muller incompatibilities and hybrid vigor. Our calculations also allow us to characterize how recombination affects the rate at which selection eliminates deleterious introgressed DNA after hybridization—by modulating the variance of introgressed ancestry across individuals. Species with low aggregate recombination rates, like Drosophila, purge introgressed DNA more rapidly and more completely than species with high aggregate recombination rates, like humans. These conclusions also hold for different genomic regions. Within the genomes of several species, positive correlations have been observed between local recombination rate and introgressed ancestry. Our results imply that these correlations can be driven more by recombination’s effect on the purging of deleterious introgressed alleles than its effect in unlinking neutral introgressed alleles from deleterious alleles. In general, our results demonstrate that the aggregate recombination process—as quantified by and analogs—acts as a variable barrier to gene flow between species.

scholarly journals TSABL: Trait Specific Annotation Based Locus Predictor

2021 ◽  
Author(s):  
Kimberly Lorenz ◽  
Christopher S. Thom ◽  
Sanjana Adurty ◽  
Benjamin F. Voight
Keyword(s):  
Blood Cell ◽  
Logistic Regression Model ◽  
Regions Of Interest ◽  
Phenotypic Trait ◽  
Genetic Studies ◽  
Biologically Relevant ◽  
Regulatory Architecture ◽  
Causal Variants ◽  
Genomic Regions ◽  
Trait Groups

AbstractThe majority of GWAS loci fall in the non-coding genome, making causal variants difficult to identify and study. We hypothesized that the regulatory features underlying causal variants are biologically specific, identifiable from data, and that the regulatory architecture that influences one trait is distinct compared to biologically unrelated traits. To better characterize and identify these variants, we used publicly available GWAS loci and genomic annotations to build 17 Trait Specific Annotation Based Locus (TSABL) predictors to identify differences between GWAS loci associated with different phenotypic trait groups. We used a penalized binomial logistic regression model to select trait relevant annotations and tested all models on a holdout set of loci not used for training in any trait. We were able to successfully build models for autoimmune, electrocardiogram, lipid, platelet, red blood cell, and white blood cell trait groups. We used these models both to prioritize variants in existing loci and to identify new genomic regions of interest. We found that TSABL models identified biologically relevant regulatory features, and anticipate their future use to enhance the design and interpretation of genetic studies.

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