scholarly journals The optimal mating distance resulting from heterosis and genetic incompatibility

2018 ◽  
Vol 4 (11) ◽  
pp. eaau5518 ◽  
Author(s):  
Xinzhu Wei ◽  
Jianzhi Zhang
Keyword(s):  
Animal Model ◽  
Genetic Distance ◽  
Polynomial Function ◽  
Genetic Distances ◽  
Quadratic Polynomial ◽  
Model Organisms ◽  
Genetic Incompatibility ◽  
Large Numbers ◽  
Practical Implications

Theory predicts that the fitness of an individual is maximized when the genetic distance between its parents (i.e., mating distance) is neither too small nor too large. However, decades of research have generally failed to validate this prediction or identify the optimal mating distance (OMD). Respectively analyzing large numbers of crosses of fungal, plant, and animal model organisms, we indeed find the hybrid phenotypic value a humped quadratic polynomial function of the mating distance for the vast majority of fitness-related traits examined, with different traits of the same species exhibiting similar OMDs. OMDs are generally slightly greater than the nucleotide diversities of the species concerned but smaller than the observed maximal intraspecific genetic distances. Hence, the benefit of heterosis is at least partially offset by the harm of genetic incompatibility even within species. These results have multiple theoretical and practical implications for speciation, conservation, and agriculture.

scholarly journals Genetic Variation Among Colletotrichum graminicola Isolates from Four Hosts Using Isozyme Analysis

Plant Disease ◽  
2004 ◽  
Vol 88 (4) ◽  
pp. 402-406 ◽  
Author(s):  
B. J. Horvath ◽  
J. M. Vargas
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Geographic Origin ◽  
Creeping Bentgrass ◽  
Genetic Distances ◽  
Colletotrichum Graminicola ◽  
Annual Bluegrass ◽  
Close Relationship ◽  
Host Origin ◽  
Serious Disease

Anthracnose basal rot (ABR) is a serious disease of turfgrasses that is caused by the pathogen Colletotrichum graminicola. The relationships of isolates causing ABR on turfgrasses to those causing disease on important crop hosts (maize, sorghum) remain unresolved. Genetic variation among isolates from annual bluegrass, creeping bentgrass, maize, and sorghum was evaluated based on host origin and geographic origin. Isozymes were used to estimate the genetic variation of the isolates. Five enzyme systems comprising 16 alleles from 5 loci were used. Allele frequencies, genetic distance, and linkage disequilibrium values were calculated for isolates based on both host and geographic origin. Isolates from creeping bentgrass and annual bluegrass were the most closely related based on Nei's genetic distance, while isolates from maize and sorghum were the most distantly related, consistent with their known species-level relationship. Isolates from annual bluegrass and creeping bentgrass had different genetic distances to isolates from both maize and sorghum. Annual bluegrass isolates from different geographic regions had the smallest genetic distance values observed in this study, indicating a very close relationship regardless of geographic origin. Based on these data, it appears that host origin, not geographic origin, plays a more important role in the genetic diversity of these fungi.

MIC-Drop: A platform for large-scale in vivo CRISPR screens

Science ◽  
2021 ◽  
pp. eabi8870
Author(s):  
Saba Parvez ◽  
Chelsea Herdman ◽  
Manu Beerens ◽  
Korak Chakraborti ◽  
Zachary P. Harmer ◽  
...  
Keyword(s):  
Large Scale ◽  
Cultured Cells ◽  
Cardiac Development ◽  
Droplet Microfluidics ◽  
Model Organisms ◽  
Genetic Screens ◽  
Large Numbers ◽  
And Function ◽  
Genome Scale

CRISPR-Cas9 can be scaled up for large-scale screens in cultured cells, but CRISPR screens in animals have been challenging because generating, validating, and keeping track of large numbers of mutant animals is prohibitive. Here, we report Multiplexed Intermixed CRISPR Droplets (MIC-Drop), a platform combining droplet microfluidics, single-needle en masse CRISPR ribonucleoprotein injections, and DNA barcoding to enable large-scale functional genetic screens in zebrafish. The platform can efficiently identify genes responsible for morphological or behavioral phenotypes. In one application, we show MIC-Drop can identify small molecule targets. Furthermore, in a MIC-Drop screen of 188 poorly characterized genes, we discover several genes important for cardiac development and function. With the potential to scale to thousands of genes, MIC-Drop enables genome-scale reverse-genetic screens in model organisms.

Ampelographic characterization of white grapevine cul-tivars (Vitis vinifera L.) grown in Palestine

2015 ◽  
Vol 3 (1) ◽  
pp. 1-11
Author(s):  
Rezq Basheer-Salimia
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Vitis Vinifera L ◽  
Similarity Matrix ◽  
Breeding Programs ◽  
Local Varieties ◽  
Synonymies And Homonymies

Abstract: In Palestine, grape culture consists of ecotypes and cultivars (also called local varieties), for which a large number of homonymous and synonymous designations exist as well as misnaming of cultivars. The present study is the first report using detailed ampelographic characterizations (39 informative traits) to assess genetic diversity and detect similarities among sixteen accessions collected from putative diverse grape genotypes In general, 30 descriptors presented highly and satisfactory divergent genotypes, whereas the remaining traits showed no or very little ampelographic variation. Based on the similarity matrix and the resulting dendrogram of these ampelographic data, distinguishable genotypes as well as some cases of synonymies and homonymies clearly exist. A synonymy case seemed to be in four genotypes including Jandali-Mfarad, Jan-dali-Mrazraz, Jandali, and Hamadani-Mattar, which indeed showed genetic distances of less than 0.5, sug-gesting their relatedness, and the possibility that they are the same genotype, but with different names. In addition, homonym cases also occur in the following pairs of “Marawi’s, Hamadani’s, and Zaini’s genotypes, in which each pair seems to be two distinctive genotypes. Finally, among the 16 examined genotypes, the Zaini-Baladi genotype tended to show the highest genetic distance values from the others and thus could be potentially incorporated into any further local or regional breeding programs as well as germplasm conservation.

Detection of genetic diversity in rough fescue (Festuca campestris Rydb) populations of southern Alberta and British Columbia, Canada, using RAPD markers

2008 ◽  
Vol 88 (2) ◽  
pp. 307-312
Author(s):  
Zhao Mengli ◽  
Han Bing ◽  
Walter D Willms
Keyword(s):  
Genetic Diversity ◽  
British Columbia ◽  
Genetic Distance ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Distance ◽  
Genetic Distances ◽  
Gene Frequencies ◽  
Southern Alberta ◽  
Potential Adaptation ◽  
Rough Fescue

Mountain rough fescue (Festuca campestris Rydb.) is a tufted native grass in southern Alberta and British Columbia, Canada, and has attracted interest for use in reclamation. However, its seed is often available from only a few localized sources and may not be adapted for areas removed from the collection site. We conducted a study to determine the genetic variability among rough fescue populations to assess its potential adaptation. Thirty plants were collected from each of six populations and analyzed using Random Amplified Polymorphic DNA (RAPD). One population (Kamloops, BC) was separated by several mountain ranges from the five easterly Alberta populations.The Kamloops population was also separated from the Alberta populations by genetic distance in two clusters. Of the total genetic variation present in the data, 21% was found among populations while the remaining (79%) was found within populations. Nei’s genetic distances among populations were related to their geographical distances. Genetic differences among populations appeared to be caused primarily by differences in gene frequencies rather than rare genes. Also, genetic diversity appeared to increase from west to east suggesting that the more easterly populations had greater adaptation potential. We speculate that the more easterly populations are less likely to share genes since the prevailing winds are from the west. Germplasm from the more easterly populations may be used with suitable precautions within Alberta and possibly around Kamloops. Key words: Genetic distance, geographic distance, reclamation, potential adaptation

AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates

Genome ◽  
2003 ◽  
Vol 46 (1) ◽  
pp. 51-58 ◽  
Author(s):  
A Segovia-Lerma ◽  
R G Cantrell ◽  
J M Conway ◽  
I M Ray
Keyword(s):  
Genetic Diversity ◽  
Medicago Sativa ◽  
High Throughput ◽  
Genetic Distances ◽  
Group Method ◽  
Aflp Analysis ◽  
Dna Templates ◽  
Arithmetic Average ◽  
Pair Group ◽  
Large Numbers

Improving commercial utilization of perennial Medicago collections requires developing approaches that can rapidly and accurately characterize genetic diversity among large numbers of populations. This study evaluated the potential of using amplified fragment length polymorphism (AFLP) DNA markers, in combination with DNA bulking over multiple genotypes, as a strategy for high-throughput characterization of genetic distances (D) among alfalfa (Medicago sativa L.) accessions. Bulked DNA templates from 30 genotypes within each of nine well-recognized germplasms (African, Chilean, Flemish, Indian, Ladak, Medicago sativa subsp. falcata, Medicago sativa subsp. varia, Peruvian, and Turkistan) were evaluated using 34 primer combinations. A total of 3754 fragments were identified, of which 1541 were polymorphic. The number of polymorphic fragments detected per primer combination ranged from 20 to 85. Pairwise D estimates among the nine germplasms ranged from 0.52 to 1.46 with M. sativa subsp. falcata being the most genetically dissimilar. Unweighted pair-group method arithmetic average (UPGMA) analysis of the marker data produced two main clusters, (i) M. sativa subsp. sativa and M. sativa subsp. varia, and (ii) M. sativa subsp. falcata. Cluster-analysis results and D estimates among the Chilean, Peruvian, Flemish, and M. sativa subsp. varia germplasms supported the hypothesis that Peruvian was more similar to original Spanish introductions into Central and South America than Chilean. Hierarchical arrangement of the nine germplasms was supported by their respective geographic, subspecific, and intersubspecific hybrid origins. Subsets of as few as seven highly informative primer pairs were identified that produced comparable D estimates and similar heirarchical arrangements compared with the complete dataset. The results indicate that use of primer-pair subsets for AFLP analysis of bulk DNA templates could serve as a high-throughput system for accurately characterizing genetic diversity among large numbers of alfalfa populations.Key words: Medicago sativa, DNA bulking, genetic distance.

scholarly journals The Ferret as a Model System for Neocortex Development and Evolution

2021 ◽  
Vol 9 ◽  
Author(s):  
Carlotta Gilardi ◽  
Nereo Kalebic
Keyword(s):  
Animal Model ◽  
Cognitive Abilities ◽  
Genetic Manipulation ◽  
System Development ◽  
Model Organisms ◽  
Cortical Folding ◽  
Technological Advances ◽  
Stem And Progenitor Cells ◽  
Visual System Development

The neocortex is the largest part of the cerebral cortex and a key structure involved in human behavior and cognition. Comparison of neocortex development across mammals reveals that the proliferative capacity of neural stem and progenitor cells and the length of the neurogenic period are essential for regulating neocortex size and complexity, which in turn are thought to be instrumental for the increased cognitive abilities in humans. The domesticated ferret, Mustela putorius furo, is an important animal model in neurodevelopment for its complex postnatal cortical folding, its long period of forebrain development and its accessibility to genetic manipulation in vivo. Here, we discuss the molecular, cellular, and histological features that make this small gyrencephalic carnivore a suitable animal model to study the physiological and pathological mechanisms for the development of an expanded neocortex. We particularly focus on the mechanisms of neural stem cell proliferation, neuronal differentiation, cortical folding, visual system development, and neurodevelopmental pathologies. We further discuss the technological advances that have enabled the genetic manipulation of the ferret in vivo. Finally, we compare the features of neocortex development in the ferret with those of other model organisms.

scholarly journals The Allelic Correlation Structure of Gainj- and Kalam-Speaking People. II. The Genetic Distance Between Population Subdivisions

Genetics ◽  
1987 ◽  
Vol 117 (2) ◽  
pp. 273-283
Author(s):  
Jeffrey C Long ◽  
Peter E Smouse ◽  
James W Wood
Keyword(s):  
Genetic Distance ◽  
Group Size ◽  
Linguistic Diversity ◽  
Genetic Distances ◽  
Demographic Feature ◽  
Distance Methods ◽  
Tribal Populations ◽  
Geographic Differences ◽  
Population Subdivisions ◽  
Theoretical Considerations

ABSTRACT The patterning of allele frequency variability among 18 local groups of Gainj and Kalam speakers of highland Papua New Guinea is investigated using new genetic distance methods. The genetic distances proposed here are obtained by decomposing Sewall Wright's coefficient FST into a set of coefficients corresponding to all pairs of population subdivisions. Two statistical methods are given to estimate these quantities. One method provides estimates weighted by sample sizes, while the other method does not use sample size weighting. Both methods correct for the within-individual and between-individual-within-groups sums of squares. Genetic distances among the Gainj and Kalam subdivisions are analyzed with respect to demographic, geographic, and linguistic variables. We find that a demographic feature, group size, has the greatest demonstrable association with the patterning of genetic distances. The pattern of geographic distances among groups displays a weak congruence with the pattern of genetic distances, and the association of genetic and linguistic diversity is very low. An effect of differences in group size on genetic distances is not surprising, from basic theoretical considerations, but genetic distances have not often been analyzed with respect to these variables in the past. The lack of correspondence between genetic distances and linguistic and geographic differences is an unusual feature that distinguishes the Gainj and Kalam from most other tribal populations.

scholarly journals The Theory and Applications of Measuring Broad-Range and Chromosome-Wide Recombination Rate from Allele Frequency Decay around a Selected Locus

2020 ◽  
Vol 37 (12) ◽  
pp. 3654-3671
Author(s):  
Kevin H -C Wei ◽  
Aditya Mantha ◽  
Doris Bachtrog
Keyword(s):  
Genetic Distance ◽  
Allele Frequency ◽  
Recombination Rate ◽  
High Throughput Sequencing ◽  
Genetic Material ◽  
Cost Effective ◽  
Genetic Distances ◽  
Recombination Rates ◽  
Marker Selection ◽  
Cost Effective Approach

Abstract Recombination is the exchange of genetic material between homologous chromosomes via physical crossovers. High-throughput sequencing approaches detect crossovers genome wide to produce recombination rate maps but are difficult to scale as they require large numbers of recombinants individually sequenced. We present a simple and scalable pooled-sequencing approach to experimentally infer near chromosome-wide recombination rates by taking advantage of non-Mendelian allele frequency generated from a fitness differential at a locus under selection. As more crossovers decouple the selected locus from distal loci, the distorted allele frequency attenuates distally toward Mendelian and can be used to estimate the genetic distance. Here, we use marker selection to generate distorted allele frequency and theoretically derive the mathematical relationships between allele frequency attenuation, genetic distance, and recombination rate in marker-selected pools. We implemented nonlinear curve-fitting methods that robustly estimate the allele frequency decay from batch sequencing of pooled individuals and derive chromosome-wide genetic distance and recombination rates. Empirically, we show that marker-selected pools closely recapitulate genetic distances inferred from scoring recombinants. Using this method, we generated novel recombination rate maps of three wild-derived strains of Drosophila melanogaster, which strongly correlate with previous measurements. Moreover, we show that this approach can be extended to estimate chromosome-wide crossover interference with reciprocal marker selection and discuss how it can be applied in the absence of visible markers. Altogether, we find that our method is a simple and cost-effective approach to generate chromosome-wide recombination rate maps requiring only one or two libraries.

scholarly journals AGING INTERVENTIONS GET HUMAN: CAN WE EXTEND HEALTHSPAN?

2019 ◽  
Vol 3 (Supplement_1) ◽  
pp. S811-S811
Author(s):  
Brian Kennedy
Keyword(s):  
Animal Model ◽  
Small Molecules ◽  
Human Health ◽  
Chronic Diseases ◽  
Drug Targeting ◽  
Model Organisms ◽  
Aging Research ◽  
Tor Pathway ◽  
Global Impact ◽  
Tor Kinase

Abstract Understanding biologic aging will afford opportunities for novel interventions to enhance human healthspan. If ageing can be slowed, the effect would be simultaneous protection from many of the chronic diseases. One strategy is to use animal model organisms to find common pathways that modulate ageing and then to seek methods for their human manipulation. The TOR pathway is one point of convergence and a clinically approved drug targeting the TOR kinase, rapamycin, extends murine lifespan and healthspan. Many more small molecules are being added to the list of anti-ageing compounds. Here, I use examples of interventions to conceptualize how agents extending healthspan might improve human health. We are entering a stage in aging research where it is imperative to test ageing interventions in humans and several strategies are contemplated. The potential to directly impact human healthspan is emerging from ageing research and this approach, if successful, will have global impact.

Lessons from Worm Dendritic Patterning

2019 ◽  
Vol 42 (1) ◽  
pp. 365-383 ◽  
Author(s):  
Sharon Inberg ◽  
Anna Meledin ◽  
Veronika Kravtsov ◽  
Yael Iosilevskii ◽  
Meital Oren-Suissa ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Animal Model ◽  
Light And Electron Microscopy ◽  
Dendritic Tree ◽  
Model System ◽  
Model Organisms ◽  
Structural Units ◽  
The Past ◽  
Structural And Functional Properties ◽  
Made In

The structural and functional properties of neurons have intrigued scientists since the pioneering work of Santiago Ramón y Cajal. Since then, emerging cutting-edge technologies, including light and electron microscopy, electrophysiology, biochemistry, optogenetics, and molecular biology, have dramatically increased our understanding of dendritic properties. This advancement was also facilitated by the establishment of different animal model organisms, from flies to mammals. Here we describe the emerging model system of a Caenorhabditis elegans polymodal neuron named PVD, whose dendritic tree follows a stereotypical structure characterized by repeating candelabra-like structural units. In the past decade, progress has been made in understanding PVD's functions, morphogenesis, regeneration, and aging, yet many questions still remain.

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