Determination Of Genetic Diversity Research Articles

Population epigenetics: DNA methylation in the plant omics era.

DNA methylation plays an important role in many biological processes. The mechanisms underlying the establishment and maintenance of DNA methylation are well understood thanks to decades of research using DNA methylation mutants, primarily in Arabidopsis (Arabidopsis thaliana) accession Col-0. Recent genome-wide association studies (GWASs) using the methylomes of natural accessions have uncovered a complex and distinct genetic basis of variation in DNA methylation at the population level. Sequencing following bisulfite treatment has served as an excellent method for quantifying DNA methylation. Unlike studies focusing on specific accessions with reference genomes, population-scale methylome research often requires an additional round of sequencing beyond obtaining genome assemblies or genetic variations from whole-genome sequencing data, which can be cost prohibitive. Here, we provide an overview of recently developed bisulfite-free methods for quantifying methylation and cost-effective approaches for the simultaneous detection of genetic and epigenetic information. We also discuss the plasticity of DNA methylation in a specific Arabidopsis accession, the contribution of DNA methylation to plant adaptation, and the genetic determinants of variation in DNA methylation in natural populations. The recently developed technology and knowledge will greatly benefit future studies in population epigenomes.

A possible circulation of a dominant Dibothriocephalus nihonkaiensis haplotype in Japan revealed by molecular analysis of clinical tapeworm samples.

Human diphyllobothriasis, caused by Dibothriocephalus nihonkaiensis, is prevalent globally, especially in regions where raw fish is consumed. Recent molecular diagnostic techniques have made species identification of tapeworm parasites and the determination of genetic variations among parasite populations possible. However, only a few studies done over a decade ago, have reported on the genetic variation among D. nihonkaiensis in Japan. The present study employed PCR-based mitochondrial DNA analysis to specifically detect D. nihonkaiensis from archived clinical samples, and to determine any genetic variation that may exist among the Japanese broad tapeworms from patients of Kanagawa Prefecture, Japan. Target genes were amplified from DNA extracted from the ethanol- or formaldehyde-fixed samples by PCR. Further sequencing and comparative phylogenetic analyses based on mitochondrial COI and ND1 sequences were also performed. In our results, all PCR-amplified and sequenced samples were identified as D. nihonkaiensis. Analysis of COI sequences revealed two haplotype lineages. However, clustering of almost all COI (and ND1) sample sequences into one of the two haplotype clades, together with reference sequences from different countries worldwide, revealed a common haplotype among D. nihonkaiensis samples in our study. Our results suggest a possible presence of a dominant D. nihonkaiensis haplotype, with a global distribution circulating in Japan. Results from this study have the potential to improve the management of clinical cases and establish robust control measures to reduce the burden of human diphyllobothriasis in Japan.

Determination of Genetic variation among Beauveria bassiana and Metarhizium anisopliae Isolates from Palestine and other Geographic regions using ITS and β-tubulin Sequences, RFLP and ISSR Data

In this work we report the genetic variation of ten isolates of entomopathogenic fungi, four of which were isolated from Palestine while the remaining six were from other geographic regions. The variation was determined using molecular-based techniques including; sequence analysis of β-tubulin (BT) gene, the Internal Transcribed Spacers (ITS) 1 & 2 of the rDNA, Restriction Fragment Length Polymorphism (RFLP), and Inter-Simple Sequence Repeat (ISSR) analysis. The sequencing data of ITS regions confirmed the taxonomic identity of six isolates as Metarhizium anisopliae while the identity of the other four as Beauveria bassiana. These data also revealed that the two Palestinian Beauveria b. isolates are probably new strains since theyshowed 99% homology with the best match sequences reported in the gene bank. The restriction digestion of the ITS2 sequences produced a fingerprint for the PAL-M01 isolate. The ITS and BT sequences were able to distinguish the B-Bot genotype from the other Beauveria b. isolates. In contrast, the ITS could discriminate the three Metarhizium isolates: Ma-7, PAL-M01, and PPRC. Moreover, the ISSR analysis detected high levels of polymorphism among the Beauveria b. (80%) and the Metarhizium a. (90%) isolates. The fact that the PPRC and B-Bot isolates areobviously genetically different from their Metarhizium a. and Beauveria b. counterparts could be attributed to their distant geographic origins. The molecular data obtained in this work can be utilized for specific identification of each ofthese isolates which, would facilitate the local use of these fungi as biocontrol agents. To the best of our knowledge, this is the first study, in Palestine, attempting to discriminate between EPF isolates using advanced molecular techniques.

Determination of Genetic Variation and Association Analysis of Yield Contributing Traits for Suitable Selection Criteria in Chickpea

Determination of Genetic Variation and Association Analysis of Yield Contributing Traits for Suitable Selection Criteria in Chickpea

Determination of Genetic Variation Among Beauveria Bassiana and Metarhizium Anisopliae Isolates from Palestine and Other Geographic Regions Using its and Β-Tubulin Sequences, Rflp and Issr Data

Determination of Genetic Variation Among Beauveria Bassiana and Metarhizium Anisopliae Isolates from Palestine and Other Geographic Regions Using its and Β-Tubulin Sequences, Rflp and Issr Data

Determination of Genetic Variation in Some Teff Genotypes Using RAPD Markers

Günümüzde tüketici bilincinin artması sonucu sağlıklı gıda ürünlerine talep her geçen gün artmaktadır. Kimyasal bileşimi ve beslenme özelliklere sahip olan Tef bitkisi, insan beslenmesinde geçmişten beri kullanılan bir bitki olmakla beraber, ülkemizde de alternatif olarak yetiştirilebilecek kaynaklardan biridir. Sağlıklı yaşam açısından son derece önemli bir tahıl olan tef, glutensiz olması nedeniyle de özellikle çölyak hastalarının beslenmesinde önemli yer tutar. Bunun yanında yetişme koşullarının zor olmaması ve hasat süresinin kısa olmasıyla beraber gelecekte kuraklığa kolayca uyum sağlayabileceği düşüncesi tef tahılının değerini her geçen gün arttırmaktadır. Çalışma kapsamında Et 2016 tef bitkisi kullanılarak 19 RAPD markırı ile taranmıştır. İyi amplikon veren 10 tane RAPD primeri ile Tef bitkisinde genetik varyasyon araştırması yapılmıştır. Kullanılan 10 tane RAPD primeri ile PZR sonrası agaroz jel elektroforez yöntemi ile amplikonların ayrıştırılması sağlanarak varlık (1) ve yokluk (0) skorlaması gerçekleştirilmiştir. Elde edilen verilere ile Jaccard benzerlik indeksi kullanılarak temel koordinat analizi ve Bayesian istatistiği ile genotipler arasında dendogram oluşturulmuştur. Yapılan analizler sonucunda genotipler arasındaki genetik varyasyonun düşük olduğu saptanmıştır. Zobel Basic ve Dega Basic genotiplerinde çok az düzeyde farklılık tespit edilmiş olup, daha çok markır ile teyit edilmesi gerekmektedir. Sonuç olarak bu genotipler arasındaki varyasyonun artırılması için farklı yaklaşımlar kullanılarak (mutajenler vb.) varyasyonun artırılması önerilmektedir.

Author Correction: Determinants of genetic variation across eco-evolutionary scales in pinnipeds

Author Correction: Determinants of genetic variation across eco-evolutionary scales in pinnipeds

Determination of genetic variations by using mitochondrial DNA cyt b sequences in populations of Carasobarbus luteus (Cyprinidae)

As the human population increases, freshwater fish has become an important alternative source of protein to meet the need of protein. Especially numerous fish species from the family Cyprinidae are consumed by the people. Among these fish, Carasobarbus luteus (Heckel, 1843) is also one of the most preferred species thanks to its edible flesh as well as its low price. Since it is economically important, there has been the pressure of overfishing and invasive species on the populations of this species, resulting in decrease of the sources day by day. Management and conservation of the species have importance therefore it is need to know its genetic variations in the first place. The present study analyzed sequences of mtDNA cyt b locus and established the genetic variability following the collection of 65 individuals from five different localities in diverse river systems where C. luteus populations naturally inhabit. Sequence analysis revealed 13 polymorphic sites and 5 haplotypes. Birecik was the locality with the highest value in terms of both haplotype diversity and nucleotide diversity, Diyarbakır was the one with the lowest value. Tajima’s D and Fu’s Fs values were found to be statistically insignificant for all the localities. Population genetic diversity of this fish species was found to be low in terms of mtDNA cyt b marker. It is recommended to take measures to stop the loss of genetic diversity and to start conservation studies.

Determination of genetic variation among melon genotypes grown in Aegean Region by morphologic and molecular markers

Determination of genetic variation among melon genotypes grown in Aegean Region by morphologic and molecular markers

Determination of genetic variation within the <i>DYRK2</i> gene and its associations with milk traits in cattle

To speed up the progress of marker-assisted selection (MAS) in cattle breeding, the dual-specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2), cadherin 2 (CDH2), and kinesin family member 1A (KIF1A) genes were chosen based on our pervious genome-wide association study (GWAS) analysis results. DYRK2 is a kinase that may participate in cell growth and/or development; it shows phosphorylation activity toward serine, threonine, and tyrosine fragments of proteins, and it is different from other protein kinases. The CDH2 gene encodes a classic cadherin, which is a member of the cadherin superfamily. The protein encoded by KIF1A is a member of the kinesin family and plays a role in the transportation of membrane organelles along axon microtubules. We detected insertion/deletion (InDel) variation in these three candidate genes in 438 individual cattle (Xinjiang Brown cattle and Wagyu Luxi crossbreed cattle). Only DYRK2-P3-11 bp was polymorphic and genotyped. The polymorphism information content of DYRK2-P3-11 bp was 0.336. Correlation analyses showed that InDel polymorphism was significantly associated with six different milk traits. These findings may aid future analyses of InDel genotypes in cattle breeds, and speed up the progress of MAS in cattle breeding.

Determinants of genetic variation across eco-evolutionary scales in pinnipeds.

The effective size of a population (Ne), which determines its level of neutral variability, is a key evolutionary parameter. Ne can substantially depart from census sizes of present-day breeding populations (NC) as a result of past demographic changes, variation in life-history traits and selection at linked sites. Using genome-wide data we estimated the long-term coalescent Ne for 17 pinniped species represented by 36 population samples (total n = 458 individuals). Ne estimates ranged from 8,936 to 91,178, were highly consistent within (sub)species and showed a strong positive correlation with NC ([Formula: see text] = 0.59; P = 0.0002). Ne/NC ratios were low (mean, 0.31; median, 0.13) and co-varied strongly with demographic history and, to a lesser degree, with species' ecological and life-history variables such as breeding habitat. Residual variation in Ne/NC, after controlling for past demographic fluctuations, contained information about recent population size changes during the Anthropocene. Specifically, species of conservation concern typically had positive residuals indicative of a smaller contemporary NC than would be expected from their long-term Ne. This study highlights the value of comparative population genomic analyses for gauging the evolutionary processes governing genetic variation in natural populations, and provides a framework for identifying populations deserving closer conservation attention.

Determinants of genetic variation across eco-evolutionary scales in pinnipeds

Determinants of genetic variation across eco-evolutionary scales in pinnipeds

Comprehensive Investigation of White Blood Cell and Gene Expression Profiles As Risk Factors for Multiple Myeloma in African Americans

Comprehensive Investigation of White Blood Cell and Gene Expression Profiles As Risk Factors for Multiple Myeloma in African Americans

FRANCISELLA TULARENSIS– REVIEW

Abstract In the early twentieth century, Francisella tularensis was identified as a pathogenic agent of tularaemia, one of the most dangerous zoonoses. Based on its biochemical properties, infective dose and geographical location, four subspecies have been distinguished within the species F. tularensis: the highly infectious F. tularensis subsp. tularensis (type A) occurring mainly in the United States of America, F. tularensis subsp. holarctica (type B) mainly in Europe, F. tularensis subsp. mediasiatica isolated mostly in Asia and F. tularensis subsp. novicida, non-pathogenic to humans. Due to its ability to infect and variable forms of the disease, the etiological agent of tularaemia is classified by the CDC (Centers for Disease Control and Prevention, USA) as a biological warfare agent with a high danger potential (group A). The majority of data describing incidence of tularaemia in Poland is based on serological tests. However, real-time PCR method and MST analysis of F. tularensis highly variable intergenic regions may be also applicable to detection, differentiation and determination of genetic variation among F. tularensis strains. In addition, the above methods could be successfully used in molecular characterization of tularaemia strains from humans and animals isolated in screening research, and during epizootic and epidemic outbreaks. 1. Historical overview. 2. Characteristics and taxonomy of F. tularensis. 3. Morphology. 4. Culture media and conditions. 5. Biochemical properties. 6. Survivability and persistence of F. tularensis. 7. F. tularensis as a biological weapon agent. 8. Tularaemia vaccines. 9. Pathogenicity of F. tularensis. 10. Tularaemia treatment. 11. Laboratory diagnostics of F. tularensis. 12. Summary

Assessment of Genetic Variability in Sorghum Accessions (<i>Sorghum bicolor</i> L. Moench) at the National Centre for Genetic Resources and Biotechnology, Ibadan, Nigeria

The determination of genetic variation using molecular markers has been found to facilitate the conservation of crops and ensure food security. Genetic diversity among 80 accessions of S. bicolor in the gene bank of National Centre for Genetic Resources and Biotechnology (NACGRAB) Ibadan, was studied using 5 pairs of simple sequence repeat (SSR) markers. The polymorphic information content (PIC) of individual primer ranged from 0.34 to 0.70 with a mean value of 0.54 indicating enough diversity or variability among the accessions studied. The binary matrix obtained from the gel profiles generated a dendrogram which was made up of 4 clusters and one ungrouped accession at 0.66 coefficients of similarity. From the clustering pattern, 7 pairs of accessions were found to be 100% similar. Each similar pairs were subsequently merged together and reduced to a total of 7 accessions. However, it was also observed that the geographical location of collection of accessions did not affect the clustering pattern. The information obtained from this study could serve as the basis for the improvement and breeding programs of Sorghum to achieve food security in the country, and by extension, worldwide. Keywords : Sorghum; Simple Sequence Repeat markers; Genetic variation; Polymorphic Information Content; Coefficient of similarity.

Determination of genetic variations in the genus Dryomys Thomas, 1906 (Rodentia: Gliridae) distributed in Turkey using NADH dehydrogenase 1 (ND1) gene

Genetic diversity and phylogeny of Dryomys nitedula and Dryomys laniger from Turkey was described in the present study by using mitochondrial DNA NADH dehydrogenase 1 gene (ND1). Genetic variation in ND1 gene was determined by two model-based phylogenetic analyses and a network analysis revealed 27 haplotypes of D. nitedula constructing four main lineages (Thrace, Anatolia, North-eastern Anatolia and Şavşat) that have non-overlapping geographic distributions and no shared haplotypes, but on the other hand, three haplotypes were detected in four samples of D. laniger from Turkey. It was determined that nucleotide diversity was low but haplotype diversity was high in D. laniger, whereas, D. nitedula has both high level of haplotype and nucleotide diversity. Characterization of Thrace lineage of D. nitedula with low nucleotide diversity and determination of the total nucleotide diversity of Anatolian lineages (Anatolia + North-eastern Anatolia+Şavşat) to be approximately four times higher than that of Thrace lineage indicated that Anatolia may have served as a refuge for D. nitedula. Divergence times and high level of nucleotide differences between D. nitedula lineages showed that diversification of the lineages may have occurred before and during ice ages in Turkey, thought to be a refuge for post-glacial colonization and biodiversity resource of Europe. Additionally, estimated divergence times and calculated genetic distances yielded compatible results with the previous paleontological and genomic data for the diversification time of two species in the genus.

Population size, center-periphery, and seed dispersers' effects on the genetic diversity and population structure of the Mediterranean relict shrub Cneorum tricoccon.

The effect of population size on population genetic diversity and structure has rarely been studied jointly with other factors such as the position of a population within the species’ distribution range or the presence of mutualistic partners influencing dispersal. Understanding these determining factors for genetic variation is critical for conservation of relict plants that are generally suffering from genetic deterioration. Working with 16 populations of the vulnerable relict shrub Cneorum tricoccon throughout the majority of its western Mediterranean distribution range, and using nine polymorphic microsatellite markers, we examined the effects of periphery (peripheral vs. central), population size (large vs. small), and seed disperser (introduced carnivores vs. endemic lizards) on the genetic diversity and population structure of the species. Contrasting genetic variation (H E: 0.04–0.476) was found across populations. Peripheral populations showed lower genetic diversity, but this was dependent on population size. Large peripheral populations showed high levels of genetic diversity, whereas small central populations were less diverse. Significant isolation by distance was detected, indicating that the effect of long‐distance gene flow is limited relative to that of genetic drift, probably due to high selfing rates (FIS = 0.155–0.887), restricted pollen flow, and ineffective seed dispersal. Bayesian clustering also supported the strong population differentiation and highly fragmented structure. Contrary to expectations, the type of disperser showed no significant effect on either population genetic diversity or structure. Our results challenge the idea of an effect of periphery per se that can be mainly explained by population size, drawing attention to the need of integrative approaches considering different determinants of genetic variation. Furthermore, the very low genetic diversity observed in several small populations and the strong among‐population differentiation highlight the conservation value of large populations throughout the species’ range, particularly in light of climate change and direct human threats.

Candidate genes and molecular markers associated with heat tolerance in colonial Bentgrass.

Elevated temperature is a major abiotic stress limiting the growth of cool-season grasses during the summer months. The objectives of this study were to determine the genetic variation in the expression patterns of selected genes involved in several major metabolic pathways regulating heat tolerance for two genotypes contrasting in heat tolerance to confirm their status as potential candidate genes, and to identify PCR-based markers associated with candidate genes related to heat tolerance in a colonial (Agrostis capillaris L.) x creeping bentgrass (Agrostis stolonifera L.) hybrid backcross population. Plants were subjected to heat stress in controlled-environmental growth chambers for phenotypic evaluation and determination of genetic variation in candidate gene expression. Molecular markers were developed for genes involved in protein degradation (cysteine protease), antioxidant defense (catalase and glutathione-S-transferase), energy metabolism (glyceraldehyde-3-phosphate dehydrogenase), cell expansion (expansin), and stress protection (heat shock proteins HSP26, HSP70, and HSP101). Kruskal-Wallis analysis, a commonly used non-parametric test used to compare population individuals with or without the gene marker, found the physiological traits of chlorophyll content, electrolyte leakage, normalized difference vegetative index, and turf quality were associated with all candidate gene markers with the exception of HSP101. Differential gene expression was frequently found for the tested candidate genes. The development of candidate gene markers for important heat tolerance genes may allow for the development of new cultivars with increased abiotic stress tolerance using marker-assisted selection.

Genetic determinants of variability in warfarin response after the dose-titration phase.

Genetic factors contribute considerably toward variability in warfarin dose requirements and are important in the dose-titration phase; their effects on the stability of anticoagulation later in therapy are not known. Using deidentified electronic medical records linked to a DNA-biobank, we studied 140 African-Americans and 943 European-Americans after the warfarin dose-titration phase. We genotyped 12 single nucleotide polymorphisms in genes (CYP2C9, VKORC1, CYP4F2, GGCX, EPHX1, CALU) associated with altered warfarin dose requirements and tested their associations with international normalized ratio variability (INRVAR) and percent time in therapeutic range in European-Americans and African-Americans. One allele copy of rs2108622 in CYP4F2 was associated with a 15% [95% confidence interval (CI): 1-26, P=0.03] decrease in the median INRVAR in European-Americans. In African-Americans, GGCX variants rs11676382 and rs699664 were associated with 4.16-fold (95% CI: 1.45-11.97, P=0.009) and 1.50-fold (95% CI: 1.07-2.08, P=0.02) changes in the median INRVAR per variant allele copy, respectively; rs11676382 was also significantly associated with a 23.19% (95% CI: 5.89-40.48, P=0.01) decrease in time in therapeutic range. The total variation in INRVAR explained by both clinical factors and rs2108622 was 5.2% for European-Americans. In African-Americans, the inclusion of GGCX variants rs11676382 and rs699664, and the CYP2C9*8 variant rs7900194 explained ∼29% of the variation in INRVAR. The stability of anticoagulation after the warfarin dose-titration phase is differentially affected by variants in CYP4F2 in European-Americans and GGCX loci in African-Americans.

Effective Natural PCR-RFLP Primer Design for SNP Genotyping Using Teaching-Learning-Based Optimization With Elite Strategy

SNP (single nucleotide polymorphism) genotyping is the determination of genetic variations of SNPs between members of a species. In many laboratories, PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) is a usually used biotechnology for SNP genotyping, especially in small-scale basic research studies of complex genetic diseases. PCR-RFLP requires an available restriction enzyme at least for identify a target SNP and an effective primer pair conforms numerous constraints. However, the lots of restriction enzymes, tedious sequence and complicated constraints make the mining of available restriction enzymes and the design of effective primer pairs become a major challenge. In the study, we propose a novel and available CI (Computation Intelligence)-based method called TLBO (teaching-learning-based optimization) and introduce the elite strategy to design effective primer pairs. Three common melting temperature computations are available in the method. REHUNT (Restriction Enzymes HUNTing) is first combined with the method to mine available restriction enzymes. Robust in silico simulations for the GA (genetic algorithm), the PSO (particle swarm optimization), and the method for natural PCR-RFLP primer design in the SLC6A4 gene with two hundred and eighty-eight SNPs had been performed and compared. These methods had been implemented in JAVA and they are freely available at https://sites.google.com/site/yhcheng1981/tlbonpd-elite for users of academic and non-commercial interests.