scholarly journals Application of target enrichment sequencing for population genetic analyses of the obligate plant pathogens Pseudoperonospora cubensis and P. humuli in Michigan

2021 ◽  
Author(s):  
Julian Camilo Bello Rodriguez ◽  
Mary Hausbeck ◽  
Monique L Sakalidis
Keyword(s):  
Genetic Variation ◽  
Plant Pathogens ◽  
Target Genes ◽  
Physical Distance ◽  
Genomic Variation ◽  
Genetic Studies ◽  
Additional Tool ◽  
Downy Mildews ◽  
Technological Advances ◽  
Targeted Enrichment

Technological advances in genome sequencing have improved our ability to catalog genomic variation and led to an expansion of the scope and scale of genetic studies. Yet, for agronomically important plant pathogens such as the downy-mildews the scale of genetic studies remains limited. This is, in part, due to the difficulties associated with maintaining obligate pathogens, and the logistical constraints involved in the genotyping of these species. To study the genetic variation of two Pseudoperonospora species (P. cubensis and P. humuli), we describe a targeted enrichment (TE) protocol able to genotype isolates using less than 50 ng of mixed pathogen and plant DNA for library preparation. We enriched 830 target genes across 128 samples and identified 2,514 high-quality SNP variants. We detected significant genetic differentiation (p=0.01) between P. cubensis subpopulations from Cucurbita moschata (clade I) and Cucumis sativus (clade II) in Michigan. No evidence of location-based differentiation was detected within the P. cubensis (clade II) subpopulation. A significant effect of location on the genetic variation of the P. humuli subpopulation was detected in the state (p=0.01). Mantel tests found evidence that the genetic distance among P. humuli samples was associated with the physical distance of the hop yards from which the samples were collected (p=0.005). The differences in the distribution of genetic variation of the P. humuli and P. cubensis subpopulations of Michigan suggest differences in the dispersal of these two species. Our TE protocol provides an additional tool for genotyping obligate pathogens and the execution of new genetic studies

scholarly journals Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kelly B. Klingler ◽  
Joshua P. Jahner ◽  
Thomas L. Parchman ◽  
Chris Ray ◽  
Mary M. Peacock
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Sierra Nevada ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Thermal Sensitivity ◽  
Genomic Variation ◽  
Genome Wide ◽  
A Genome ◽  
American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

scholarly journals The genomics of adaptation

2012 ◽  
Vol 279 (1749) ◽  
pp. 5024-5028 ◽  
Author(s):  
Jacek Radwan ◽  
Wiesław Babik
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Royal Society ◽  
Genetic Basis ◽  
Genomic Data ◽  
Evolutionary Change ◽  
Introductory Article ◽  
Technological Advances ◽  
A Genome ◽  
Genome Level

The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.

scholarly journals Focused Strategies for Defining the Genetic Architecture of Congenital Heart Defects

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 827
Author(s):  
Lisa J. Martin ◽  
D Woodrow Benson
Keyword(s):  
Genetic Variation ◽  
Congenital Heart Defects ◽  
Heart Development ◽  
Genetic Architecture ◽  
Congenital Heart ◽  
Rare Variants ◽  
Heart Defects ◽  
Genetic Origin ◽  
Genetic Studies ◽  
The Ideal

Congenital heart defects (CHD) are malformations present at birth that occur during heart development. Increasing evidence supports a genetic origin of CHD, but in the process important challenges have been identified. This review begins with information about CHD and the importance of detailed phenotyping of study subjects. To facilitate appropriate genetic study design, we review DNA structure, genetic variation in the human genome and tools to identify the genetic variation of interest. Analytic approaches powered for both common and rare variants are assessed. While the ideal outcome of genetic studies is to identify variants that have a causal role, a more realistic goal for genetic analytics is to identify variants in specific genes that influence the occurrence of a phenotype and which provide keys to open biologic doors that inform how the genetic variants modulate heart development. It has never been truer that good genetic studies start with good planning. Continued progress in unraveling the genetic underpinnings of CHD will require multidisciplinary collaboration between geneticists, quantitative scientists, clinicians, and developmental biologists.

scholarly journals Intraspecific genomic variation and local adaptation in a young hybrid species

2019 ◽  
Author(s):  
Angélica Cuevas ◽  
Mark Ravinet ◽  
Glenn-Peter Sætre ◽  
Fabrice Eroukhmanoff
Keyword(s):  
Genetic Variation ◽  
Local Adaptation ◽  
Climatic Variation ◽  
Genomic Variation ◽  
Population Divergence ◽  
Parent Species ◽  
Evolutionary Potential ◽  
Variable Environment ◽  
Hybrid Species ◽  
Species Population

ABSTRACTHybridization increases genetic variation, hence hybrid species may have a strong evolutionary potential once their admixed genomes have stabilized and incompatibilities have been purged. Yet, little is known about how such hybrid lineages evolve at the genomic level following their formation, in particular the characteristics of their adaptive potential, i.e. constraints and facilitations of diversification. Here we investigate how the Italian sparrow (Passer italiae), a homoploid hybrid species, has evolved and locally adapted to its variable environment. Using restriction site-associated DNA sequencing (RAD-seq) on several populations across the Italian peninsula, we evaluate how genomic constraints and novel genetic variation have influenced population divergence and adaptation. We show that population divergence within this hybrid species has evolved in response to climatic variation. As in non-hybrid species, climatic differences may even reduce gene flow between populations, suggesting ongoing local adaptation. We report outlier genes associated with adaptation to climatic variation, known to be involved in beak morphology in other species. Most of the strongly divergent loci among Italian sparrow populations seem not to be differentiated between its parent species, the house and Spanish sparrow. Within the parental species, population divergence has occurred mostly in loci where different alleles segregate in the parent species, unlike in the hybrid, suggesting that novel combinations of parental alleles in the hybrid have not necessarily enhanced its evolutionary potential. Rather, our study suggests that constraints linked to incompatibilities may have restricted the evolution of this admixed genome, both during and after hybrid species formation.

scholarly journals Genetic studies revealed differences between European and North American populations of Calypogeia azurea

2016 ◽  
Vol 42 (1) ◽  
pp. 19-26 ◽  
Author(s):  
Katarzyna Buczkowska ◽  
Alina Bączkiewicz ◽  
Patrycja Gonera
Keyword(s):  
Genetic Variation ◽  
North America ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Oil Bodies ◽  
Genetic Studies ◽  
Isozyme Loci ◽  
The Mean ◽  
Different Parts ◽  
Nei's Genetic Distance

Abstract Calypogeia azurea, a widespread, subboreal-montane liverwort species, is one of a few representatives of the Calypogeia genus that are characterized by the occurrence of blue oil bodies. The aim of the study was to investigate the genetic variation and population structure of C. azurea originating from different parts of its distribution range (Europe and North America). Plants of C. azurea were compared with C. peruviana, another Calypogeia species with blue oil bodies. In general, 339 gametophytes from 15 populations of C. azurea were examined. Total gene diversity (HT) estimated on the basis of nine isozyme loci of C. azurea at the species level was 0.201. The mean Nei’s genetic distance between European populations was equal to 0.083, whereas the mean genetic distance between populations originating from Europe and North America was 0.413. The analysis of molecular variance (AMOVA) showed that 69% of C. azurea genetic variation was distributed among regions (Europe and North America), 15% - among populations within regions, and 16% - within populations. Our study revealed that C. azurea showed genetic diversity within its geographic distribution. All examined samples classified as C. azurea differed in respect of isozyme patterns from C. peruviana.

scholarly journals Temperature-Mediated Plasticity Regulates the Adaptation of Phytophthora infestans to Azoxystrobin Fungicide

2020 ◽  
Vol 12 (3) ◽  
pp. 1188 ◽  
Author(s):  
Yahuza Lurwanu ◽  
Yan-Ping Wang ◽  
Waheed Abdul ◽  
Jiasui Zhan ◽  
Li-Na Yang
Keyword(s):  
Phytophthora Infestans ◽  
Population Differentiation ◽  
Food Production ◽  
Plant Pathogens ◽  
Target Genes ◽  
Common Garden ◽  
Plant Diseases ◽  
Control Effectiveness ◽  
Plant Disease Management ◽  
Simple Sequence

Fungicide is one of the main approaches used in agriculture to manage plant diseases for food production, but their effectiveness can be reduced due to the evolution of plant pathogens. Understanding the genetics and evolutionary processes responsible for the development of fungicide resistance is a key to food production and social sustainability. In this study, we used a common garden experiment to examine the source of genetic variation, natural selection, and temperature contributing to the development of azoxystrobin resistance in Phytophthora infestans and infer sustainable ways of plant disease management in future. We found that plasticity contributed to ~40% of phenotypic variation in azoxystrobin sensitivity while heritability accounted for 16%. Further analysis indicated that overall population differentiation in azoxystrobin sensitivity (QST) was significantly greater than the overall population differentiation in simple sequence repeat (SSR) marker (FST), and the P. infestans isolates demonstrated higher level of azoxystrobin sensitivity at the higher experimental temperature. These results suggest that changes in target gene expression, enzymatic activity, or metabolic rate of P. infestans play a more important role in the adaptation of the pathogen to azoxystrobin resistance than that of mutations in target genes. The development of azoxystrobin resistance in P. infestans is likely driven by diversifying selection for local adaptation, and elevated temperature associated with global warming in the future may increase the effectiveness of using azoxystrobin to manage P. infestans. The sustainable approaches for increasing disease control effectiveness and minimizing the erosion of the fungicide efficacy are proposed.

scholarly journals Genetic variation in arthropod vectors of disease-causing organisms: obstacles and opportunities.

1996 ◽  
Vol 9 (3) ◽  
pp. 301-320 ◽  
Author(s):  
R H Gooding
Keyword(s):  
Genetic Variation ◽  
Temporal Variation ◽  
Biochemical Genetics ◽  
Genetic Structuring ◽  
Genetic Studies ◽  
Arthropod Vectors ◽  
Biochemical Genetic ◽  
Genetic Techniques

An overview of the genetic variation in arthropods that transmit pathogens to vertebrates is presented, emphasizing the genetics of vector-pathogen relationships and the biochemical genetics of vectors. Vector-pathogen interactions are reviewed briefly as a prelude to a discussion of the genetics of susceptibility and refractoriness in vectors. Susceptibility to pathogens is controlled by maternally inherited factors, sex-linked dominant alleles, and dominant and recessive autosomal genes. There is widespread interpopulation (including intercolony) and temporal variation in susceptibility to pathogens. The amount of biochemical genetic variation in vectors is similar to that found in other invertebrates. However, the amount varies widely among species, among populations within species, and temporally within populations. Biochemical genetic studies show that there is considerable genetic structuring of many vectors at the local, regional, and global levels. It is argued that genetic variation in vectors is critical in understanding vector-pathogen interactions and that genetic variation in vectors creates both obstacles to and opportunities for application of genetic techniques to the control of vectors.

Genetic structure of Gahnia radula (Cyperaceae), a key sedge for revegetation

2017 ◽  
Vol 65 (2) ◽  
pp. 128
Author(s):  
Alex Arnold ◽  
Andrea Kodym ◽  
Nancy M. Endersby-Harshman ◽  
John Delpratt ◽  
Ary A. Hoffmann
Keyword(s):  
Genetic Variation ◽  
Adaptive Potential ◽  
Genetic Studies ◽  
Potential Source ◽  
Landscape Processes ◽  
Disturbed Areas ◽  
Eastern Australia ◽  
Genetic Patterns ◽  
Source Populations ◽  
High Level

Genetic studies can help guide effective ecological restoration by identifying potential source populations that contain the genetic variation necessary for adaptive potential, based on past landscape processes. Here we investigate genetic patterns in Gahnia radula (R.Br.) Benth., a sedge from south-eastern Australia that has potential for revegetation of disturbed areas. We developed microsatellite markers for this species and used them to show that it propagates mostly in a clonal manner. Levels of genetic variability differed between populations and the spatial scale of this variability within these populations is identified. A population used in recent restoration efforts and which sets seed has a particularly high level of variability. Recommendations are developed for sourcing material when using this sedge for revegetation.

scholarly journals Significant shared heritability underlies suicide attempt and clinically predicted probability of attempting suicide

2019 ◽  
Vol 25 (10) ◽  
pp. 2422-2430 ◽  
Author(s):  
Douglas M. Ruderfer ◽  
Colin G. Walsh ◽  
Matthew W. Aguirre ◽  
Yosuke Tanigawa ◽  
Jessica D. Ribeiro ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Suicide Attempt ◽  
Genetic Correlation ◽  
Genetic Profile ◽  
Polygenic Risk Score ◽  
Uk Biobank ◽  
Common Genetic Variation ◽  
Genetic Studies ◽  
Patient Reported ◽  
The Uk

Abstract Suicide accounts for nearly 800,000 deaths per year worldwide with rates of both deaths and attempts rising. Family studies have estimated substantial heritability of suicidal behavior; however, collecting the sample sizes necessary for successful genetic studies has remained a challenge. We utilized two different approaches in independent datasets to characterize the contribution of common genetic variation to suicide attempt. The first is a patient reported suicide attempt phenotype asked as part of an online mental health survey taken by a subset of participants (n = 157,366) in the UK Biobank. After quality control, we leveraged a genotyped set of unrelated, white British ancestry participants including 2433 cases and 334,766 controls that included those that did not participate in the survey or were not explicitly asked about attempting suicide. The second leveraged electronic health record (EHR) data from the Vanderbilt University Medical Center (VUMC, 2.8 million patients, 3250 cases) and machine learning to derive probabilities of attempting suicide in 24,546 genotyped patients. We identified significant and comparable heritability estimates of suicide attempt from both the patient reported phenotype in the UK Biobank (h2SNP = 0.035, p = 7.12 × 10−4) and the clinically predicted phenotype from VUMC (h2SNP = 0.046, p = 1.51 × 10−2). A significant genetic overlap was demonstrated between the two measures of suicide attempt in these independent samples through polygenic risk score analysis (t = 4.02, p = 5.75 × 10−5) and genetic correlation (rg = 1.073, SE = 0.36, p = 0.003). Finally, we show significant but incomplete genetic correlation of suicide attempt with insomnia (rg = 0.34–0.81) as well as several psychiatric disorders (rg = 0.26–0.79). This work demonstrates the contribution of common genetic variation to suicide attempt. It points to a genetic underpinning to clinically predicted risk of attempting suicide that is similar to the genetic profile from a patient reported outcome. Lastly, it presents an approach for using EHR data and clinical prediction to generate quantitative measures from binary phenotypes that can improve power for genetic studies.

A Whole Genome Analysis Identifies SLCO1B1 as a Determinant of Methotrexate Pharmacokinetics and Adverse Effects

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 214-214
Author(s):  
Lisa R Trevino ◽  
Noriko Shimasaki ◽  
Wenjian Yang ◽  
John C. Panetta ◽  
Cheng Cheng ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Lymphoblastic Leukemia ◽  
Organic Anion ◽  
Linear Regression Analysis ◽  
Treatment Protocol ◽  
Genomic Variation ◽  
Organic Anion Transporter ◽  
Strong Impact ◽  
Whole Genome Analysis ◽  
Anion Transporter

Abstract Methotrexate is a major component in every treatment protocol for childhood acute lymphoblastic leukemia (ALL). Both beneficial and detrimental effects of methotrexate in ALL have been clearly related to methotrexate plasma pharmacokinetics, which vary substantially among patients. However the genetic basis of such variability remains largely unknown. Herein, we surveyed 600,000 germline single nucleotide polymorphisms (SNPs) to determine how inherited genetic variation affects the disposition of methotrexate among 434 children with ALL who received 3014 courses of methotrexate at 2 to 5 g/m2. Adjusting for age, race, gender and methotrexate regimen, the most significant SNPs associated with methotrexate clearance were annotated to a plausible gene, the organic anion transporter polypeptide, SLCO1B1. The three top SNPs included rs11045879 (P = 1.7 × 10−10), rs4149081 (P = 1.7 × 10−9), and rs2900478 (P = 2.8 × 10−8). Linkage disequilibrium (LD) was observed among these three SLCO1B1 SNPs (r2=1) and with a known functional polymorphism in SLCO1B1, T521C (rs4149056, r2 = 0.86). The top two SLCO1B1 SNPs rs11045879 and rs4149081 were further validated (P = 0.018 and P = 0.017) in an independent cohort of 206 patients with ALL. Additional SNPs annotated to SLCO1B1 were identified and further validated. In a stepwise multiple linear regression analysis, SLCO1B1 genetic variation remained significant and explained clearance variability comparable to that of other non-genetic factors including treatment regimen. SNPs in SLCO1B1 were also associated with methotrexate-related gastrointestinal toxicity (P= 0.03 to 0.0005, odds ratio 8.3 to 16.4). In summary, we have identified a candidate gene, SLCO1B1, which is strongly associated with the pharmacokinetics of methotrexate, an anticancer drug with a low therapeutic index in multiple treatment regimens. Although SLCO1B1 is widely recognized as having a strong impact on the disposition of many drugs in clinical use, based on in vitro data, it was not thought to have a major role in methotrexate transport or disposition. Our study demonstrates proof of principle that genome-wide tools in clinical pharmacologic problems can lead to the discovery of important and novel pharmacogenetic links between inherited genomic variation and drug response in humans.

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