scholarly journals Flexible methods for estimating genetic distances from nucleotide data

2014 ◽  
Author(s):  
Simon Joly ◽  
David J Bryant ◽  
Peter J Lockhart
Keyword(s):  
Evolutionary Biology ◽  
Massively Parallel Sequencing ◽  
Allelic Variation ◽  
Gene Dosage ◽  
Genetic Distances ◽  
Distance Measures ◽  
Rate Variation ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Data ◽  
Variance Estimates

With the increasing use of massively parallel sequencing approaches in evolutionary biology, the need for fast and accurate methods suitable to investigate genetic structure and evolutionary history are more important than ever. We propose new distance measures for estimating genetic distances between individuals when allelic variation, gene dosage and recombination could compromise standard approaches. We present four distance measures based on single nucleotide polymorphisms (SNP) and evaluate them against previously published measures using coalescent- based simulations. Simulations were used to test (i) whether the measures give unbiased and accurate distance estimates, (ii) whether they can accurately identify the genomic mixture of hybrid individuals and (iii) whether they give precise (low variance) estimates. The effect of rate variation among genes and recombination was also investigated. The results showed that the SNP-based GENPOFAD distance we propose appears to work well in the widest range of circumstances. It was the most accurate and precise method for estimating genetic distances and is also relatively good at estimating the genomic mixture of hybrid individuals. Our simulations provide benchmarks to compare the performance of different method that estimate genetic distances between organisms.

scholarly journals Genomics of recombination rate variation in temperature-evolved Drosophila melanogaster populations

2020 ◽  
Author(s):  
Ari Winbush ◽  
Nadia D Singh
Keyword(s):  
Drosophila Melanogaster ◽  
Temperature Regime ◽  
Recombination Rate ◽  
Evolutionary Biology ◽  
Genetic Basis ◽  
Rate Variation ◽  
Potential Candidate ◽  
Nucleotide Polymorphisms ◽  
Recombination Rates ◽  
Recombination Rate Variation

Abstract Meiotic recombination is a critical process that ensures proper segregation of chromosome homologues through DNA double strand break repair mechanisms. Rates of recombination are highly variable among various taxa, within species, and within genomes with far-reaching evolutionary and genomic consequences. The genetic basis of recombination rate variation is therefore crucial in the study of evolutionary biology but remains poorly understood. In this study we took advantage of a set of experimental temperature-evolved populations of Drosophila melanogaster with heritable differences in recombination rates depending on the temperature regime in which they evolved. We performed whole genome sequencing and identified several chromosomal regions that appear to be divergent depending on temperature regime. In addition, we identify a set of single nucleotide polymorphisms and associated genes with significant differences in allele frequency when the different temperature populations are compared. Further refinement of these gene candidates emphasizing those expressed in the ovary and associated with DNA binding reveals numerous potential candidate genes such as Hr38, EcR, and mamo responsible for observed differences in recombination rates in these experimental evolution lines thus providing insight into the genetic basis of recombination rate variation.

scholarly journals Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors Canis lupus, German Shepherd Dog, and Different Sheepdogs of European Origin

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 832
Author(s):  
Nina Moravčíková ◽  
Radovan Kasarda ◽  
Radoslav Židek ◽  
Luboš Vostrý ◽  
Hana Vostrá-Vydrová ◽  
...  
Keyword(s):  
Demographic History ◽  
Genome Structure ◽  
Principal Component ◽  
Genetic Distances ◽  
Nucleotide Polymorphisms ◽  
German Shepherd ◽  
German Shepherd Dog ◽  
Genome Wide ◽  
Scale Population ◽  
History Effect

This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the genome of domesticated breeds. The dataset consisted of 131 animals and 143,593 single nucleotide polymorphisms (SNPs). The effects of demographic history on the overall genome structure were determined by screening the distribution of the homozygous segments. The genetic variance distributed within and between groups was quantified by genetic distances, the FST index, and discriminant analysis of principal components. Fine-scale population stratification due to specific morphological and behavioural traits was assessed by principal component and factorial analyses. In the CWD, a demographic history effect was manifested mainly in a high genome-wide proportion of short homozygous segments corresponding to a historical load of inbreeding derived from founders. The observed proportion of long homozygous segments indicated that the inbreeding events shaped the CWD genome relatively recently compared to other groups. Even if there was a significant increase in genetic similarity among wolf-like breeds, they were genetically separated from each other. Moreover, this study showed that the CWD genome carries private alleles that are not found in either wolves or other dog breeds analysed in this study.

GENETIC VARIATION IN RARE AND WIDESPREAD LOMATIUM SPECIES (APIACEAE): A COMPARISON OF AFLP AND SSCP DATA

2001 ◽  
Vol 58 (2) ◽  
pp. 347-356 ◽  
Author(s):  
M. A. GITZENDANNER ◽  
P. S. SOLTIS
Keyword(s):  
Rare Species ◽  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Allelic Variation ◽  
Plant Conservation ◽  
Single Copy ◽  
Small Populations ◽  
Nucleotide Polymorphisms ◽  
Widespread Species ◽  
Low Levels

Plant conservation genetics has been hampered by a lack of markers for studies of levels and patterns of variation in rare species. We investigated the levels of variation in several rare and widespread species of the western North American genus Lomatium Raf. (Apiaceae) using two relatively new molecular markers: AFLPs and single-strand conformation polymorphisms (SSCPs). For each species, approximately 150 AFLP loci have been scored, yielding estimates of species-level percent polymorphic loci in rare species ranging from near zero to over 80%. Levels of AFLP diversity were similar in two of the rare species, L. bradshawii (Rose ex Mathias) Mathas & Constance and L. ochocense Helliwell & Constance, and the widespread species. The third rare species, L. cookii Kagan, which has small populations, has low levels of diversity based on AFLPs. We also examined nucleotide diversity at the single-copy nuclear-DNA locus glyceraldehyde 3-phosphate dehydrogenase (Gap-C). PCR-amplified segments were analysed for allelic variation using SSCPs, and intrapopulational nucleotide polymorphisms were identified in both L. bradshawii and L. cookii. In the 211bp segment of Gap-C analysed, five nucleotide sites were segregating within populations of L. bradshawii and two in L. cookii.

scholarly journals DNA Variation in a Diversity Panel of Tomato Genetic Resources

2021 ◽  
pp. 1-7
Author(s):  
Joanne A. Labate
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Crop Improvement ◽  
Genotyping By Sequencing ◽  
Genetic Distances ◽  
Nucleotide Polymorphisms ◽  
Fresh Market ◽  
Single Nucleotide ◽  
Dna Variation ◽  
Diversity Panel ◽  
Home Gardening

A diversity panel of 190 National Plant Germplasm System (NPGS) tomato (Solanum lycopersicum) accessions was genotyped using genotyping by sequencing. These originated from 31 countries and included fresh market, ornamental, processing, breeders’ lines, landraces, and home gardening types, as well as six different accessions of the economically valuable cultivar San Marzano. Most of the 34,531 discovered single nucleotide polymorphisms were rare and therefore excluded from downstream analyses. A total of 3713 high-quality, mapped single nucleotide polymorphisms that were present in at least two accessions were used to estimate genetic distances and population structure. Results showed that these phenotypically and geographically diverse NPGS tomato accessions were closely related to each other. However, a subset of divergent genotypes was identified that included landraces from primary centers of diversity (South America), secondary centers of diversity (Italy, Taiwan, and France), and genotypes that originated from wild species through 20th century breeding for disease resistance (e.g., ‘VFNT Cherry’). Extreme variant accessions produce cultivated fruit traits in a background that contains many wild or primitive genes. These accessions are promising sources of novel genes for continued crop improvement.

scholarly journals Genetic and epigenetic associations of ANRIL with coronary artery disease and risk factors

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Bayi Xu ◽  
Zhixia Xu ◽  
Yequn Chen ◽  
Nan Lu ◽  
Zhouwu Shu ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Coronary Artery Disease ◽  
Dna Methylation ◽  
Coronary Artery ◽  
Gene Dosage ◽  
Density Lipoprotein ◽  
Nucleotide Polymorphisms ◽  
Coronary Syndrome ◽  
Non Coding Rna ◽  
Artery Disease

Abstract Background Both DNA genotype and methylation of antisense non-coding RNA in the INK4 locus (ANRIL) have been robustly associated with coronary artery disease (CAD), but the interdependent mechanisms of genotype and methylation remain unclear. Methods Eighteen tag single nucleotide polymorphisms (SNPs) of ANRIL were genotyped in a matched case–control study (cases 503 and controls 503). DNA methylation of ANRIL and the INK4/ARF locus (p14ARF, p15INK4b and p16INK4a) was measured using pyrosequencing in the same set of samples (cases 100 and controls 100). Results Polymorphisms of ANRIL (rs1004638, rs1333048 and rs1333050) were significantly associated with CAD (p < 0.05). The incidence of CAD, multi-vessel disease, and modified Gensini scores demonstrated a strong, direct association with ANRIL gene dosage (p < 0.05). There was no significant association between ANRIL polymorphisms and myocardial infarction/acute coronary syndrome (MI/ACS) (p > 0.05). Methylation levels of ANRIL were similar between the two studied groups (p > 0.05), but were different in the rs1004638 genotype, with AA and AT genotype having a higher level of ANRIL methylation (pos4, p = 0.006; pos8, p = 0.019). Further Spearman analyses indicated that methylation levels of ANRIL were positively associated with systolic blood pressure (pos6, r = 0.248, p = 0.013), diastolic blood pressure (pos3, r = 0.213, p = 0.034; pos6, r = 0.220, p = 0.028), and triglyceride (pos4, r = 0.253, p = 0.013), and negatively associated with high-density lipoprotein cholesterol (pos2, r = − 0.243, p = 0.017). Additionally, we identified 12 transcription factor binding sites (TFBS) within the methylated ANRIL region, and functional annotation indicated these TFBS were associated with basal transcription. Methylation at the INK4/ARF locus was not associated with ANRIL genotype. Conclusions These results indicate that ANRIL genotype (tag SNPs rs1004638, rs1333048 and rs1333050) mainly affects coronary atherosclerosis, but not MI/ACS. There may be allele-related DNA methylation and allele-related binding of transcription factors within the ANRIL promoter.

scholarly journals Allelic variation contributes to bacterial host specificity

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Min Yue ◽  
Xiangan Han ◽  
Leon De Masi ◽  
Chunhong Zhu ◽  
Xun Ma ◽  
...  
Keyword(s):  
Allelic Variation ◽  
Multinomial Logistic Regression ◽  
Gene Gain ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Serovar Typhimurium ◽  
Functional Analyses ◽  
High Degree

Abstract Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

scholarly journals Associations between Oxytocin Receptor Gene Polymorphisms, Empathy towards Animals and Implicit Associations towards Animals

Animals ◽  
2018 ◽  
Vol 8 (8) ◽  
pp. 140 ◽  
Author(s):  
Melanie Connor ◽  
Alistair Lawrence ◽  
Sarah Brown
Keyword(s):  
Social Behaviour ◽  
Allelic Variation ◽  
Receptor Gene ◽  
Oxytocin Receptor ◽  
Implicit Associations ◽  
Nucleotide Polymorphisms ◽  
Psychological Variables ◽  
Oxytocin Receptor Gene ◽  
Receptor Gene Polymorphisms ◽  
Human Social Behaviour

Oxytocin has been well researched in association with psychological variables and is widely accepted as a key modulator of human social behaviour. Previous work indicates involvement of oxytocin receptor gene (OXTR) single nucleotide polymorphisms (SNPs) in human-human empathy, however little is known about associations of OXTR SNPs with empathy and affective reactions of humans towards animals. Five OXTR SNPs previously found to associate with human social behaviour were genotyped in 161 students. Empathy towards animals and implicit associations were evaluated. A General Linear Model was used to investigate the OXTR alleles and allelic combinations along with socio-demographic variables and their influence on empathy towards animals. Empathy towards animals showed a significant association with OXTR SNP rs2254298; homozygous G individuals reported higher levels of empathy towards animals than heterozygous (GA). Our preliminary findings show, for the first time, that between allelic variation in OXTR and animal directed empathy in humans maybe associated, suggesting that OXTRs social behaviour role crosses species boundaries, warranting independent replication.

scholarly journals The Variability of Puroindoline-Encoding Alleles and Their Influence on Grain Hardness in Modern Wheat Cultivars Cultivated in Poland, Breeding Lines and Polish Old Landraces (Triticum aestivum L.)

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1075
Author(s):  
Mateusz Przyborowski ◽  
Sebastian Gasparis ◽  
Maciej Kała ◽  
Wacław Orczyk ◽  
Anna Nadolska-Orczyk
Keyword(s):  
Triticum Aestivum ◽  
System Analysis ◽  
Allelic Variation ◽  
Triticum Aestivum L ◽  
Nucleotide Polymorphisms ◽  
Wheat Cultivars ◽  
Grain Hardness ◽  
Wild Type ◽  
Breeding Lines ◽  
Modern Wheat

Wheat (Triticum aestivum L.) grain hardness is determined mainly by variations in puroindoline genes (Pina-D1 and Pinb-D1), which are located on the short arm of chromosome 5D. This trait has a direct effect on the technological properties of the flour and the final product quality. The objective of the study was to analyze the mutation frequency in both Pin genes and their influence on grain hardness in 118 modern bread wheat cultivars and breeding lines cultivated in Poland, and 80 landraces from Poland. The PCR products containing the Pin gene coding sequences were sequenced by the Sanger method. Based on detected the SNPs (single-nucleotide polymorphisms) we designed CAPS (cleaved amplified polymorphic sequence) markers for the fast screening of Pinb alleles in a large number of genotypes. All analyzed cultivars, breeding lines, and landraces possess the wild-type Pina-D1a allele. Allelic variation was observed within the Pinb gene. The most frequently occurring allele in modern wheat cultivars and breeding lines (over 50%) was Pinb-D1b. The contribution of the remaining alleles (Pinb-D1a, Pinb-D1c, and Pinb-D1d) was much less (approx. 15% each). In landraces, the most frequent allele was Pinb-D1a (over 70%), followed by Pinb-D1b (21% frequency). Pinb-D1c and Pinb-D1g were found in individual varieties. SKCS (single-kernel characterization system) analysis revealed that grain hardness was strictly connected with Pinb gene allelic variation in most tested cultivars. The mean grain hardness values were significantly greater in cultivars with mutant Pinb variants as compared to those with the wild-type Pinb-D1a allele. Based on grain hardness measured by SKCS, we classified the analyzed cultivars and lines into different classes according to a previously proposed classification system.

scholarly journals Identification of Allelic Variation in Drought Responsive Dehydrin Gene Based on Sequence Similarity in Chickpea (Cicer arietinum L.)

2020 ◽  
Vol 11 ◽  
Author(s):  
Tapan Kumar ◽  
Neha Tiwari ◽  
Chellapilla Bharadwaj ◽  
Ashutosh Sarker ◽  
Sneha Priya Reddy Pappula ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Drought Tolerance ◽  
Cicer Arietinum ◽  
Allelic Variation ◽  
Sequence Similarity ◽  
Nucleotide Polymorphisms ◽  
Residual Moisture ◽  
Single Nucleotide ◽  
The World ◽  
Dehydrin Gene

Chickpea (Cicer arietinum L.) is an economically important food legume grown in arid and semi-arid regions of the world. Chickpea is cultivated mainly in the rainfed, residual moisture, and restricted irrigation condition. The crop is always prone to drought stress which is resulting in flower drop, unfilled pods, and is a major yield reducer in many parts of the world. The present study elucidates the association between candidate gene and morpho-physiological traits for the screening of drought tolerance in chickpea. Abiotic stress-responsive gene Dehydrin (DHN) was identified in some of the chickpea genotypes based on the sequence similarity approach to play a major role in drought tolerance. Analysis of variance revealed a significant effect of drought on relative water content, membrane stability index, plant height, and yield traits. The genotypes Pusa1103, Pusa362, and ICC4958 were found most promising genotypes for drought tolerance as they maintained the higher value of osmotic regulations and yield characters. The results were further supported by a sequence similarity approach for the dehydrin gene when analyzed for the presence of single nucleotide polymorphisms (SNPs) and indels. Homozygous indels and single nucleotide polymorphisms were found after the sequencing in some of the selected genotypes.

Classification of STR allelic variation using massively parallel sequencing and assessment of flanking region power

2020 ◽  
Vol 48 ◽  
pp. 102356
Author(s):  
Laurence Devesse ◽  
Lucinda Davenport ◽  
Lisa Borsuk ◽  
Katherine Gettings ◽  
Gabriella Mason-Buck ◽  
...  
Keyword(s):  
Massively Parallel Sequencing ◽  
Allelic Variation ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Flanking Region
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