scholarly journals De novo genetic variation revealed in somatic sectors of single Arabidopsis plants

F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 5 ◽  
Author(s):  
Marianne T Hopkins ◽  
Aaron M Khalid ◽  
Pei-Chun Chang ◽  
Karen C Vanderhoek ◽  
Dulcie Lai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Reproductive Strategies ◽  
De Novo ◽  
Genomic Information ◽  
Single Nucleotide ◽  
Evolutionary Advantage ◽  
Quantitative Analyses ◽  
Cultivated Species ◽  
Genomic Insertions

Concern over the tremendous loss of genetic diversity among many of our most important crops has prompted major efforts to preserve seed stocks derived from cultivated species and their wild relatives. Arabidopsis thaliana propagates mainly by self-fertilizing, and therefore, like many crop plants, theoretically has a limited potential for producing genetically diverse offspring. Despite this, inbreeding has persisted in Arabidopsis for over a million years suggesting that some underlying adaptive mechanism buffers the deleterious consequences of this reproductive strategy. Using presence-absence molecular markers we demonstrate that single Arabidopsis plants can have multiple genotypes. Sequence analyses reveal single nucleotide changes, loss of sequences and, surprisingly, acquisition of unique genomic insertions. Estimates based on quantitative analyses suggest that these genetically discordant sectors are very small but can have a complex genetic makeup. In ruling out more trivial explanations for these data, our findings raise the possibility that intrinsic drivers of genetic variation are responsible for the targeted sequence changes we detect. Given the evolutionary advantage afforded to populations with greater genetic diversity, we hypothesize that organisms that primarily self-fertilize or propagate clonally counteract the genetic cost of such reproductive strategies by leveraging a cryptic reserve of extra-genomic information.

scholarly journals Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health

2019 ◽  
Vol 6 (4) ◽  
pp. 810-824 ◽  
Author(s):  
Elaine A Ostrander ◽  
Guo-Dong Wang ◽  
Greger Larson ◽  
Bridgett M vonHoldt ◽  
Brian W Davis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Architecture ◽  
Evolutionary History ◽  
De Novo ◽  
Mammalian Species ◽  
Aging Behavior ◽  
Extended Pedigrees ◽  
Geographical Variability ◽  
Whole Genomes

ABSTRACT Dogs are the most phenotypically diverse mammalian species, and they possess more known heritable disorders than any other non-human mammal. Efforts to catalog and characterize genetic variation across well-chosen populations of canines are necessary to advance our understanding of their evolutionary history and genetic architecture. To date, no organized effort has been undertaken to sequence the world's canid populations. The Dog10K Consortium (http://www.dog10kgenomes.org) is an international collaboration of researchers from across the globe who will generate 20× whole genomes from 10 000 canids in 5 years. This effort will capture the genetic diversity that underlies the phenotypic and geographical variability of modern canids worldwide. Breeds, village dogs, niche populations and extended pedigrees are currently being sequenced, and de novo assemblies of multiple canids are being constructed. This unprecedented dataset will address the genetic underpinnings of domestication, breed formation, aging, behavior and morphological variation. More generally, this effort will advance our understanding of human and canine health.

scholarly journals De novo mutations across 1,465 diverse genomes reveal novel mutational insights and reductions in the Amish founder population

2019 ◽  
Author(s):  
Michael D. Kessler ◽  
Douglas P. Loesch ◽  
James A. Perry ◽  
Nancy L. Heard-Costa ◽  
Brian E. Cade ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Mutation Rate ◽  
De Novo ◽  
Population Level ◽  
Mutation Rates ◽  
Founder Population ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Nucleotide Mutation ◽  
Rare Genetic Variation

Abstractde novo Mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) program, we directly estimate and analyze DNM counts, rates, and spectra from 1,465 trios across an array of diverse human populations. Using the resulting call set of 86,865 single nucleotide DNMs, we find a significant positive correlation between local recombination rate and local DNM rate, which together can explain up to 35.5% of the genome-wide variation in population level rare genetic variation from 41K unrelated TOPMed samples. While genome-wide heterozygosity does correlate weakly with DNM count, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, interestingly, we do find significantly fewer DNMs in Amish individuals compared with other Europeans, even after accounting for parental age and sequencing center. Specifically, we find significant reductions in the number of T→C mutations in the Amish, which seems to underpin their overall reduction in DNMs. Finally, we calculate near-zero estimates of narrow sense heritability (h2), which suggest that variation in DNM rate is significantly shaped by non-additive genetic effects and/or the environment, and that a less mutagenic environment may be responsible for the reduced DNM rate in the Amish.SignificanceHere we provide one of the largest and most diverse human de novo mutation (DNM) call sets to date, and use it to quantify the genome-wide relationship between local mutation rate and population-level rare genetic variation. While we demonstrate that the human single nucleotide mutation rate is similar across numerous human ancestries and populations, we also discover a reduced mutation rate in the Amish founder population, which shows that mutation rates can shift rapidly. Finally, we find that variation in mutation rates is not heritable, which suggests that the environment may influence mutation rates more significantly than previously realized.

scholarly journals Genetic variation and identification of single nucleotide polymorphism of insulin-like growth factor- 1 gene in Tilapia guineensis

2020 ◽  
Vol 21 (11) ◽  
Author(s):  
Esther Ukenye ◽  
IWALEWA MEGBOWON ◽  
OLALEKAN OGUNTADE ◽  
TOPE OKETOKI ◽  
OLUWAFEMI AMUSA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Genetic Variation ◽  
Growth Factor ◽  
Coastal Waters ◽  
Growth Traits ◽  
Selection Marker ◽  
Insulin Like Growth Factor ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Abstract. Ukenye E, Megbowon I, Oguntade O, Oketoki T, Amusa O, Usman A, Sokenu B, Adeleke R, Joseph B, Omatah C. 2020. Genetic variation and identification of single nucleotide polymorphism of insulin-like growth factor- 1 gene in Tilapia guineensis Biodiversitas 21: 5317-5321. Tilapia guineensis is an important cichlid species of West African coastal waters with good nutritional, economic, and aquaculture relevance. The knowledge of the genetic basis of variation in growth traits in Tilapia fish is of great importance to support genetic improvement in the context of aquaculture. In this study, regions of the Tilapia guineensis IGF-1 gene were sequenced, aligned and compared across populations to identify single nucleotide polymorphism and genetic diversity among four populations of T. guineensis in South-west Nigerian coastal waters. A total of thirty-four SNPs were identified across the studied populations and were detected in the forward reaction with twenty-two transversions and twelve transitions. Badagry population showed the highest genetic diversity with the highest molecular diversity indices; number of polymorphic sites, pairwise differences, number of segregating sites and nucleotide diversity while the least diverse population was Pepe. Analysis of molecular variance (AMOVA) revealed that genetic variation was mostly within populations. This finding provides more information regarding variation in insulin growth factor I of T. guineensis and will encourage association study for production traits that will inform useful selection marker for breeding program.

scholarly journals Variable opportunities for outcrossing result in hotspots of novel genetic variation in a pathogen metapopulation

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Anna-Liisa Laine ◽  
Benoit Barrès ◽  
Elina Numminen ◽  
Jukka P Siren
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Fungal Pathogen ◽  
Population Genetic ◽  
Reproductive Strategies ◽  
Natural Populations ◽  
Pathogen Population ◽  
To Come ◽  
Pathogen Populations

Many pathogens possess the capacity for sex through outcrossing, despite being able to reproduce also asexually and/or via selfing. Given that sex is assumed to come at a cost, these mixed reproductive strategies typical of pathogens have remained puzzling. While the ecological and evolutionary benefits of outcrossing are theoretically well-supported, support for such benefits in pathogen populations are still scarce. Here, we analyze the epidemiology and genetic structure of natural populations of an obligate fungal pathogen, Podosphaera plantaginis. We find that the opportunities for outcrossing vary spatially. Populations supporting high levels of coinfection –a prerequisite of sex – result in hotspots of novel genetic diversity. Pathogen populations supporting coinfection also have a higher probability of surviving winter. Jointly our results show that outcrossing has direct epidemiological consequences as well as a major impact on pathogen population genetic diversity, thereby providing evidence of ecological and evolutionary benefits of outcrossing in pathogens.

scholarly journals Molecular diversity in Lactucaspeciesusing Isozymes and RAPD Markers

2021 ◽  
Author(s):  
Reda H. Helmy Sammour ◽  
A-Z. A. Mustafa
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Wild Species ◽  
Molecular Basis ◽  
Rapd Markers ◽  
Molecular Diversity ◽  
Breeding Programs ◽  
Primitive Form ◽  
In The Wild ◽  
Cultivated Species

Abstract Understanding of the molecular basis of genetic diversity in Lactucaaccessions is substantial for the management, improvementand efficient uses of Lactuca accessions. Therefore, this workaimed to evaluate molecular diversity among twenty-six accessions of Lactuca species usingisozymes and RAPD analyses. The polymorphic percentages were 87.09%and 100% in isozymes and RAPD analyses respectively, indicating a high genetic variation within and among Lactuca species. The number of alleles were higher in the wild species compared to the cultivated species, reflecting a reduction in the richness of alleles in the cultivated species due to domestication that caused a reduction in genetic diversity to meet the demand for high crop productivity.Isozymes and RAPD clustering dendrogrames: (1) separated,L. sativa accessions in more than one cluster confirming their polyphyletic origin; (2)collected the accessions of L. vimineain one cluster revealed its homogeneity; and (3) divided the accessions of L.saligna in two clusters varied in the number of alleles, particularly “A” form. The corresponding analysis associated the accessions of the wild species based on the alleles “B”of the tested isozymes and the cultivated species on alleles “A” and “C”, suggesting that: (1) allele “B” might be the primitive form of these loci that can tolerate the environmental stresses which prevails in the habitats of the wild species, and (2) “A” and “C” could be the derived forms. These results are of great interest for the management of Lactuca germplasm and for future breeding programs of lettuce.

scholarly journals SNP Marker Discovery in Pima Cotton (Gossypium barbadense L.) Leaf Transcriptomes

2016 ◽  
Vol 9 ◽  
pp. GEI.S40377 ◽  
Author(s):  
Pratibha Kottapalli ◽  
Mauricio Ulloa ◽  
Kameswara Rao Kottapalli ◽  
Paxton Payton ◽  
John Burke
Keyword(s):  
Genetic Diversity ◽  
De Novo ◽  
Gossypium Barbadense ◽  
Snp Markers ◽  
Read Length ◽  
Cdna Libraries ◽  
Average Read Length ◽  
Single Nucleotide ◽  
Pima Cotton ◽  
Cotton Genotypes

The objective of this study was to explore the known narrow genetic diversity and discover single-nucleotide polymorphic (SNP) markers for marker-assisted breeding within Pima cotton ( Gossypium barbadense L.) leaf transcriptomes. cDNA from 25-day plants of three diverse cotton genotypes [Pima S6 (PS6), Pima S7 (PS7), and Pima 3-79 (P3-79)] was sequenced on Illumina sequencing platform. A total of 28.9 million reads (average read length of 138 bp) were generated by sequencing cDNA libraries of these three genotypes. The de novo assembly of reads generated transcriptome sets of 26,369 contigs for PS6, 25,870 contigs for PS7, and 24,796 contigs for P3-79. A Pima leaf reference transcriptome was generated consisting of 42,695 contigs. More than 10,000 single-nucleotide polymorphisms (SNPs) were identified between the genotypes, with 100% SNP frequency and a minimum of eight sequencing reads. The most prevalent SNP substitutions were C–-T and A–-G in these cotton genotypes. The putative SNPs identified can be utilized for characterizing genetic diversity, genotyping, and eventually in Pima cotton breeding through marker-assisted selection.

scholarly journals Single-Nucleotide Polymorphism Markers from De-Novo Assembly of the Pomegranate Transcriptome Reveal Germplasm Genetic Diversity

PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e88998 ◽  
Author(s):  
Ron Ophir ◽  
Amir Sherman ◽  
Mor Rubinstein ◽  
Ravit Eshed ◽  
Michal Sharabi Schwager ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
De Novo Assembly ◽  
De Novo ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Comparison of genetic variation between rare and common congeners of Dipodomys with estimates of contemporary and historical effective population size

2021 ◽  
Author(s):  
Michaela Halsey ◽  
John Stuhler ◽  
Natalia J Bayona-Vasquez ◽  
Roy N Platt ◽  
Jim R Goetze ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Population Fluctuations ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Single Nucleotide ◽  
Demographic Dynamics ◽  
Population Sizes

Organisms with low effective population sizes are at greater risk of extinction because of reduced genetic diversity.   Dipodomys elator  is a kangaroo rat that is classified as threatened in Texas and field surveys from the past 50 years indicate that the distribution of this species has decreased. This suggests geographic range reductions that could have caused population fluctuations, potentially impacting effective population size. Conversely, the more common and widespread  D. ordii  is thought to exhibit relative geographic and demographic stability. Genetic variation between  D. elator  and  D. ordii  samples was assessed using 3RAD, a modified restriction site associated sequencing approach. It was hypothesized that  D. elator  would show lower levels of nucleotide diversity, observed heterozygosity, and effective population size when compared to  D. ordii . Also of interest was identifying population structure within contemporary samples of  D. elator  and detecting genetic variation between temporal samples that could indicate demographic dynamics. Up to 61,000 single nucleotide polymorphisms were analyzed. It was determined that genetic variability and effective population size in contemporary  D. elator  populations were lower than that of  D. ordii, that there is only slight, if any, structure within contemporary  D. elator  populations, and there is little genetic differentiation between spatial or temporal historical samples suggesting little change in nuclear genetic diversity over 30 years. Results suggest that genetic diversity of  D. elator  has remained stable despite claims of reduced population size and/or abundance, which may indicate a metapopulation-like system, whose fluctuations might counteract any immediate decrease in fitness.

scholarly journals Genomic outcomes from diverse SNP panels obtained with different de novo building-loci pipelines in a varied species context: Can pipelines be influencing biological interpretations?

2020 ◽  
Author(s):  
Adrian Casanova ◽  
Francesco Maroso ◽  
Andrés Blanco ◽  
Miguel Hermida ◽  
Nestor Rios ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Brown Trout ◽  
Reference Genome ◽  
De Novo ◽  
Manila Clam ◽  
Model Organisms ◽  
Single Nucleotide ◽  
Snp Panels ◽  
Next Generation Sequencing Ngs ◽  
Genome Comparisons

Abstract Background The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. without reference genomes. Here, the performances of two building-loci pipelines, STACKS 2 and Meyer’s 2b-RAD v2.1 pipeline, were compared using a diverse set of aquatic species representing different genomic and/or population structure scenarios. Two bivalve species (Manila clam and common edible cockle) and three fish species (brown trout, silver catfish and small-spotted catshark) were studied. Four SNP panels were evaluated in each species to test both different building-loci pipelines and criteria for SNP selection. Furthermore, for Manila clam and brown trout, a reference genome approach was used as control. Results Despite different outcomes were observed between pipelines and species with the diverse SNP calling and filtering steps tested, no remarkable differences were found on genetic diversity and differentiation within species with the SNP panels obtained with a de novo approach. The main differences were found in brown trout between the de novo and reference genome approaches. Genotyped vs missing data mismatches were the main genotyping difference detected between the two building-loci pipelines or between the de novo and reference genome comparisons. Conclusions Building-loci pipelines seem not to have a substantial influence on population genetics inference. Anyway, we recommend being careful with certain building-loci pipeline parameters and SNP filtering steps, especially when a de novo approach is used. Preliminary trials with subsets of data should be performed for comparison of genetic diversity and differentiation, but always considering the specific goals of the study.

Diversity and genetic structure of cassava landraces and their wild relatives (Manihot spp.) in Colombia revealed by simple sequence repeats

2015 ◽  
Vol 14 (3) ◽  
pp. 200-210 ◽  
Author(s):  
E. Tovar ◽  
J. L. Bocanegra ◽  
C. Villafañe ◽  
L. Fory ◽  
A. Velásquez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Resources ◽  
Wild Relatives ◽  
Targeted Interventions ◽  
Genetic Diversity And Structure ◽  
Baseline Information ◽  
Cultivated Species ◽  
Simple Sequence

Understanding the genetic composition and population structure of plant species at a molecular level is essential for the development of adequate strategies aimed at enhancing the conservation and use of their genetic resources. In addition, such knowledge can help to plan ahead for a scenario under which wild and cultivated species come into contact with their genetically modified (GM) counterpart(s). Using ten simple sequence repeat markers, we genotyped 409 samples pertaining to the species in the Manihot genus known to occur in Colombia, i.e. cassava (Manihot esculenta) and its wild relatives Manihot brachyloba, Manihot carthaginensis and Manihot tristis. High genetic variation was observed in all the species (HE= 0.212–0.603), with cassava showing highest diversity. Most of the genetic variation was found within species populations. Our results suggest that outcrossing events among populations occur much more frequently in M. tristis and M. esculenta, and particularly so in the latter, where the exchange of varieties among local farmers plays a key role in maintaining and introducing new genetic diversity. The occurrence of gene flow within and among populations of Manihot species in Colombia becomes relevant in a biosafety context, where gene flow from GM cassava, if introduced to the country, might have detrimental effects on the structure and dynamics of populations of wild species. The baseline information on the genetic diversity and structure of the four Colombian species that we have presented here provides a first and indispensable step towards the development of targeted interventions necessary to preserve their genetic resources.

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