scholarly journals Genome-wide characterization of genetic diversity and population structure of Valeriana officinalis L.

2019 ◽  
Author(s):  
Maja Boczkowska ◽  
Katarzyna Bączek ◽  
Olga Kosakowska ◽  
Anna Rucińska ◽  
Wiesław Podyma ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Genomics ◽  
Natural Populations ◽  
Valeriana Officinalis ◽  
Wild Populations ◽  
Genetic Fingerprint ◽  
Genome Wide ◽  
Species Population ◽  
Outcrossing Species

Abstract Background: Valeriana officinalis L. is one of the most important medicinal plant with a mild sedative, nervine, antispasmodic and relaxant effect. Despite a substantial number of studies on this species, population genomics has not yet been analyzed. The main aim of this study was: characterization of genetic variation of natural populations of V. officinalis in Poland and comparison of variation of wild populations and the cultivated form using Next Generation Sequencing based DArTseq technique. We also would like to establish foundations for genetic monitoring of the species in the future and to develop genetic fingerprint profile for samples deposited in gene bank and in natural sites in order to assess the degree of their genetic integrity and population structure preservation in the future.Results: The major and also the most astounding result of our work is the low level of observed heterozygosity of individual plants from natural populations despite the fact that the species is widespread in the studied area. Inbreeding, in naturally outcrossing species such as valerian, decreases the reproductive success. The analysis of the population structure indicated the potential presence of metapopulation in a broad area of Poland and the formation of a distinct gene pool in Bieszczady Mountains. The results also indicate the presence of individuals of the cultivated form in natural populations in the region where the species is cultivated for the needs of the pharmaceutical industry and this could lead to structural and genetic imbalance in wild populations.Conclusions: The DArTseq technology can be applied effectively in genetic studies of V. officinalis. The genetic variability of wild populations is in fact significantly lower than assumed. Individuals from the cultivated population are found in the natural environment and their impact on wild populations should be monitored.

scholarly journals Genome-Wide Diversity Analysis of Valeriana officinalis L. Using DArT-seq Derived SNP Markers

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1346
Author(s):  
Maja Boczkowska ◽  
Katarzyna Bączek ◽  
Olga Kosakowska ◽  
Anna Rucińska ◽  
Wiesław Podyma ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Pool ◽  
Natural Populations ◽  
Snp Markers ◽  
Valeriana Officinalis ◽  
Wild Populations ◽  
Relaxant Effect ◽  
Genome Wide ◽  
Array Technology ◽  
Outcrossing Species

Common valerian (Valeriana officinalis L.) is one of the most important medicinal plants, with a mild sedative, nervine, antispasmodic and relaxant effect. Despite a substantial number of studies on this species, the genetic diversity and population structure have not yet been analyzed. Here, we use a next-generation sequencing-based Diversity Array Technology sequencing (DArT-seq) technique to analyze Polish gene bank accessions that originated from wild populations and cultivars. The major and, also, the most astounding result of our work is the low level of observed heterozygosity of individual plants from natural populations, despite the fact that the species is widespread in the studied area. Inbreeding in naturally outcrossing species such as valerian decreases reproductive success. The analysis of the population structure showed the potential presence of a metapopulation in the central part of Poland and the formation of a distinct gene pool in the Bieszczady Mountains. The results also indicate the presence of the cultivated gene pool within wild populations in the region where the species is cultivated for the needs of the pharmaceutical industry, and this could lead to structural and genetic imbalances in wild populations.

Schistosome genetic diversity: the implications of population structure as detected with microsatellite markers

Parasitology ◽  
2002 ◽  
Vol 125 (7) ◽  
pp. S51-S59 ◽  
Author(s):  
J. CURTIS ◽  
R. E. SORENSEN ◽  
D. J. MINCHELLA
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Molecular Markers ◽  
Microsatellite Markers ◽  
Natural Populations ◽  
Mitochondrial Marker ◽  
Tropical Regions ◽  
Blood Flukes

Blood flukes in the genus Schistosoma are important human parasites in tropical regions. A substantial amount of genetic diversity has been described in populations of these parasites using molecular markers. We first consider the extent of genetic variation found in Schistosoma mansoni and some factors that may be contributing to this variation. Recently, though, attempts have been made to analyze not only the genetic diversity but how that diversity is partitioned within natural populations of schistosomes. Studies with non-allelic molecular markers (e.g. RAPDs and mtVNTRs) have indicated that schistosome populations exhibit varying levels of gene flow among component subpopulations. The recent characterization of microsatellite markers for S. mansoni provided an opportunity to study schistosome population structure within a population of schistosomes from a single Brazilian village using allelic markers. Whereas the detection of population structure depends strongly on the type of analysis with a mitochondrial marker, analyses with a set of seven microsatellite loci consistently revealed moderate genetic differentiation when village boroughs were used to define parasite subpopulations and greater subdivision when human hosts defined subpopulations. Finally, we discuss the implications that such strong population structure might have on schistosome epidemiology.

scholarly journals Genome-wide association, prediction and heritability in bacteria

2021 ◽  
Author(s):  
Sudaraka Mallawaarachchi ◽  
Gerry Tonkin-Hill ◽  
Nicholas J. Croucher ◽  
Paul Turner ◽  
Doug Speed ◽  
...  
Keyword(s):  
Population Structure ◽  
Streptococcus Pneumoniae ◽  
Mixed Models ◽  
Prediction Accuracy ◽  
Human Genetics ◽  
Population Genomics ◽  
Good Control ◽  
Elastic Net ◽  
Genome Wide Association ◽  
Genome Wide

AbstractAdvances in whole-genome genotyping and sequencing have allowed genome-wide analyses of association, prediction and heritability in many organisms. However, the application of such analyses to bacteria is still in its infancy, being limited by difficulties including the plasticity of bacterial genomes and their strong population structure. Here we propose a suite of genome-wide analyses for bacteria that combines methods from human genetics and previous bacterial studies, including linear mixed models, elastic net and LD-score regression. We introduce innovations such as frequency-based allele coding, testing for both insertion/deletion and nucleotide effects and partitioning heritability by genome region. Using a previously-published large cohort study, we analyse three phenotypes of a major human pathogen Streptococcus pneumoniae, including the first analyses of minimum inhibitory concentrations (MIC) for each of two antibiotics, penicillin and ceftriaxone. We show that these are very highly heritable leading to high prediction accuracy, which is explained by many genetic associations identified under good control of population structure effects. In the case of ceftriaxone MIC, these results are surprising because none of the isolates was resistant according to the inhibition zone diameter threshold. We estimate that just over half of the heritability of penicillin MIC is explained by a known drug-resistance region, which also contributes around a quarter of the heritability of ceftriaxone MIC. For the within-host survival phenotype carriage duration, no reliable associations were found but we observed moderate heritability and prediction accuracy, indicating a polygenic trait. While generating important new results for S. pneumoniae, we have critically assessed existing methods and introduced innovations that will be useful for future large-scale population genomics studies to help decipher the genetic architecture of bacterial traits.Author summaryGenome-wide association, prediction and heritability analyses in bacteria are beginning to help unravel the genetic underpinnings of traits such as antimicrobial resistance, virulence, within-host survival and transmissibility. Progress to date is limited by challenges including the effects of strong population structure and variable recombination, and the many gaps in sequence alignments including the absence of entire genes in many isolates. More work is required to critically asses and develop methods for bacterial genomics. We address this task here, using a range of existing methods from bacterial and human genetics, such as linear mixed models, elastic net and LD-score regression. We adapt these methods to introduce new analyses, including separate assessment of gap and nucleotide effects, a new allele coding for association analyses and a method to partition heritability into genome regions. We analyse within-host survival and two antimicrobial response traits of Streptococcus pneumoniae, identifying many novel associations while demonstrating good control of population structure and accurate prediction. We present both new results for an important pathogen and methodological advances that will be useful in guiding future studies in bacterial population genomics.

scholarly journals Genome-wide patterns of population structure and linkage disequilibrium in farmed Nile tilapia (Oreochromis niloticus)

2019 ◽  
Author(s):  
Grazyella M. Yoshida ◽  
Agustín Barria ◽  
Katharina Correa ◽  
Giovanna Cáceres ◽  
Ana Jedlicki ◽  
...  
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Genomic Selection ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Population Genomics ◽  
Association Studies ◽  
Demographic History ◽  
Genome Wide Association Studies ◽  
Genome Wide

AbstractNile tilapia (Oreochromis niloticus) is one of the most produced farmed fish in the world and represents an important source of protein for human consumption. Farmed Nile tilapia populations are increasingly based on genetically improved stocks, which have been established from admixed populations. To date, there is scarce information about the population genomics of farmed Nile tilapia, assessed by dense single nucleotide polymorphism (SNP) panels. The patterns of linkage disequilibrium (LD) may affect the success of genome-wide association studies (GWAS) and genomic selection and can also provide key information about demographic history of farmed Nile tilapia populations. The objectives of this study were to provide further knowledge about the population structure and LD patterns, as well as, estimate the effective population size (Ne) for three farmed Nile tilapia populations, one from Brazil (POP A) and two from Costa Rica (POP B and POP C). A total of 55, 56 and 57 individuals from POP A, POP B and POP C, respectively, were genotyped using a 50K SNP panel selected from a whole-genome sequencing (WGS) experiment. Two principal components explained about 20% of the total variation and clearly discriminated between the three populations. Population genetic structure analysis showed evidence of admixture, especially for POP C. The contemporary Ne values calculated based to LD values, ranged from 71 to 141. No differences were observed in the LD decay among populations, with a rapid decrease of r2 when increasing inter-marker distance. Average r2 between adjacent SNP pairs ranged from 0.03 to 0.18, 0.03 to 0.17 and 0.03 to 0.16 for POP A, POP B and POP C, respectively. Based on the number of independent chromosome segments in the Nile tilapia genome, at least 4.2 K SNP are required for the implementation of GWAS and genomic selection in farmed Nile tilapia populations.

scholarly journals Genome-wide assessment of genetic diversity and population structure in Magnolia odoratissima based on SLAF-Seq

2021 ◽  
Author(s):  
Tao Zhang ◽  
Xue Li ◽  
Shuilian He
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Natural Populations ◽  
Environmental Parameters ◽  
Candidate Snps ◽  
Small Populations ◽  
Nucleotide Polymorphisms ◽  
High Genetic Diversity ◽  
Genome Wide

Abstract Magnolia odoratissima is a highly threatened species with small populations and scattered distribution due to habitat fragmentation and human activity. The species is recognized as a Plant Species with Extremely Small Populations (PSESP) and is endemic to China. In the current study, the population structure and levels of genetic diversity of M. odoratissima in the five remaining natural populations and three cultivated populations were evaluated using single nucleotide polymorphisms (SNPs) derived from Specific-Locus Amplified Fragment Sequencing (SLAF-seq). A total of 180,650 SNP loci were found in seventy M. odoratissima individuals. The genome-wide Nei’s and Shannon’s nucleotide diversity indexes of the total M. odoratissima population were 0.3035 and 0.4695, respectively. The observed heterozygosity (Ho) and expected heterozygosity (He) were 0.1122 and 0.3011. Our results suggest that M. odoratissima has relatively high genetic diversity at the genomic level. FST and AMOVA indicated that high genetic differentiation existed among populations. A phylogenetic neighbor-joining tree, Bayesian model–based clustering and principal components analysis (PCA) all divided the studied M. odoratissima individuals into three distinct clusters. The Treemix analysis showed that there was low gene flow among the natural populations and a certain gene flow from the wild populations to the cultivated population (LS to KIB, and GN to JD). In addition, a total of 36 unique SNPs were detected as being significantly associated with environmental parameters (altitude, temperature and precipitation). These candidate SNPs were found to be involved in multiple pathways including several molecular functions and biological process, suggesting they may play key roles in environmental adaptation. Our results suggested that three distinct evolutionary significant units (ESUs) should be set up to conserve this critically endangered species.

scholarly journals Molecular population genomics: a short history

2010 ◽  
Vol 92 (5-6) ◽  
pp. 397-411 ◽  
Author(s):  
BRIAN CHARLESWORTH
Keyword(s):  
Population Genomics ◽  
Natural Populations ◽  
Molecular Approaches ◽  
Multiple Loci ◽  
Genome Wide ◽  
Wide Variability ◽  
Enzyme Mapping ◽  
The Subject ◽  
Dna Resequencing

SummaryPopulation genomics is the study of the amount and causes of genome-wide variability in natural populations, a topic that has been under discussion since Darwin. This paper first briefly reviews the early development of molecular approaches to the subject: the pioneering unbiased surveys of genetic variability at multiple loci by means of gel electrophoresis and restriction enzyme mapping. The results of surveys of levels of genome-wide variability using DNA resequencing studies are then discussed. Studies of the extent to which variability for different classes of variants (non-synonymous, synonymous and non-coding) are affected by natural selection, or other directional forces such as biased gene conversion, are also described. Finally, the effects of deleterious mutations on population fitness and the possible role of Hill–Robertson interference in shaping patterns of sequence variability are discussed.

scholarly journals The landscape of coadaptation in Vibrio parahaemolyticus

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Yujun Cui ◽  
Chao Yang ◽  
Hongling Qiu ◽  
Hui Wang ◽  
Ruifu Yang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Population Structure ◽  
Vibrio Parahaemolyticus ◽  
Natural Populations ◽  
Bacterial Pathogen ◽  
Ecological Strategies ◽  
Cell Wall Biogenesis ◽  
Genome Wide ◽  
A Genome ◽  
Carbohydrate Transport

Investigating fitness interactions in natural populations remains a considerable challenge. We take advantage of the unique population structure of Vibrio parahaemolyticus, a bacterial pathogen of humans and shrimp, to perform a genome-wide screen for coadapted genetic elements. We identified 90 interaction groups (IGs) involving 1,560 coding genes. 82 IGs are between accessory genes, many of which have functions related to carbohydrate transport and metabolism. Only 8 involve both core and accessory genomes. The largest includes 1,540 SNPs in 82 genes and 338 accessory genome elements, many involved in lateral flagella and cell wall biogenesis. The interactions have a complex hierarchical structure encoding at least four distinct ecological strategies. One strategy involves a divergent profile in multiple genome regions, while the others involve fewer genes and are more plastic. Our results imply that most genetic alliances are ephemeral but that increasingly complex strategies can evolve and eventually cause speciation.

scholarly journals Genome-wide characterization of genetic diversity and population structure in Secale

2014 ◽  
Vol 14 (1) ◽  
pp. 184 ◽  
Author(s):  
Hanna Bolibok-Brągoszewska ◽  
Małgorzata Targońska ◽  
Leszek Bolibok ◽  
Andrzej Kilian ◽  
Monika Rakoczy-Trojanowska
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genome Wide
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