Polymorphism Discovery Research Articles

Genome Wide SNP Identification in <i>Eucalyptus</i> and its Application for Linkage Mapping and Adventitious Rooting Related QTL Analysis

Eucalyptus is a versatile genus with a particular significance for paper pulp, and it is extensively cultivated in India's marginal lands. Eucalyptus camaldulensis and E. tereticornis are highly preferred due to its optimal pulp yield, excellent fibre quality and good abiotic stress tolerance properties. Marker-assisted selections have played a major role in eucalyptus breeding programs. The use of genotyping-by-sequencing (GBS) approach for a largescale single nucleotide polymorphism (SNP) discovery and genotyping of an inter-specific mapping population, Eucalyptus tereticornis × E. camaldulensis are reported in this study. Reduced representation libraries of 81 F1 progeny were sequenced and number of SNPs considered for linkage analysis was 96,377 single nucleotide substitutions, most of which (54.03%) represented transition events. Totally, 1999 and 4206 SNP markers were mapped to female ( Eucalyptus tereticornis ) and male ( Eucalyptus camaldulensis ) map, respectively. Consensus map consisting of 4844 markers were placed on a linkage map, which spanned 1367.6 cM and had an average of one marker every 0.29 cM corresponding to a physical distance of about 0.66 Mb. The map was utilized to identify six quantitative trait loci (QTLs) associated with adventitious rooting traits of stem cuttings accounting for phenotypic variations ranging from 7.18% to 9.17%. Analysis of the genomic sequence corresponding to six QTLs led to the identification of 201 putative candidate genes and 4 key genes were related to adventitious rooting specific expression. The integrated strategy utilizing the identified QTLs along with the available genome could serve as a platform for candidate gene identification for molecular breeding of eucalypts.

Insights on Genetic Diversity, Population Structure, and Linkage Disequilibrium in Globally Diverse Coconut Accessions Using Genotyping-by-Sequencing.

Genotyping-by-sequencing (GBS) has emerged as a cost-effective approach for genome-wide discovery of single-nucleotide polymorphism (SNP) markers and high-throughput genotyping. In this study, 96 coconut palms, representing 16 accessions from globally diverse origins, were genotyped using the GBS strategy. A total of 10,835 high-quality SNPs, which were identified after stringent filtering, were utilized to assess genetic diversity, population structure, and linkage disequilibrium (LD) analyses. The polymorphism information content (PIC) values of SNPs ranged from 0.1 to 0.4, with a large proportion of SNPs (8633 nos.; 79.7%) having a higher PIC in the range of 0.3-0.4. The genetic diversity analysis revealed the existence of a high level of variation in coconut accessions, with an average expected heterozygosity (He) value of 0.43. Unweighted neighbor-joining phylogenetic tree and Bayesian-based model population structure grouped coconut genotypes into four main clusters. The accessions are generally clustered based on their height (tall or dwarf), with a few accession clusterings based on geographical origins. Investigation of LD pattern in coconut indicated a relatively rapid LD decay with a short range (9 kb). The results obtained in this study will contribute to enhancing the capacity of coconut researchers to utilize genetic diversity for further genetic improvement. In addition, it would open up possibilities for performing genomic studies such as genome-wide association studies and genomic selection to accelerate the efficiency and speed of coconut genetic improvement.

Calorimetric Investigation of Hydrogen-Atom Sublattice Transitions in the Ice VI/XV/XIX Trio.

Ice XIX represents the latest discovery of ice polymorphs and exists in the medium pressure range near 1–2 GPa. Ice XIX is a partially hydrogen-ordered phase, by contrast to its disordered mother phase ice VI, which shares the same oxygen-atom network with ice XIX. Ice XIX differs in terms of the ordering of the hydrogen-atom sublattice, and hence the space group, from its hydrogen-ordered sibling ice XV, which also features the same type of oxygen network. Together, ice VI, XV, and XIX form the only known trio of ice polymorphs, where polymorphic transformations from order to order, order to disorder, and disorder to order are possible, which also compete with each other depending on the thermodynamic path taken and the cooling/heating rates employed. These transitions in the H-sublattice have barely been investigated, so we study here the unique triangular relation in the ice VI/XV/XIX trio based on calorimetry experiments. We reveal the following key features for H-sublattice transitions: (i) upon cooling ice VI, domains of ice XV and XIX develop simultaneously, where pure ice XV forms at ≤0.85 GPa and pure ice XIX forms at ≥1.60 GPa, (ii) ice XIX transforms into ice XV via a transient disordered state, (iii) ice XV recooled at ambient pressure features a complex domain structure, possibly containing an unknown H-ordered polymorph, (iv) recooled ice XV partly transforms back into ice XIX at 1.80 GPa, and (v) partial deuteration slows down domain reordering strongly. These findings not only are of interest in understanding possible hydrogen-ordering and -disordering processes in the interior of icy moons and planets but, more importantly, also provide a challenging benchmark for our understanding and parameterizing many-body interactions in H-bonded networks.

Utilization of Molecular Markers for Rice Breeding

Rice is the staple food for more than half of the world's population. Rice production in 2050 must increase by at least 50% to keep up with the population growth. Efforts to increase rice production continue using various strategies. Breeders apply multiple approaches including application of molecular markers in developing varieties better than the previous ones. Since the discovery of the restriction fragment length polymorphism (RFLP) markers in 1980s and the development of polymerase chain reaction (PCR) method, many types of molecular markers have been developed and applied to various crops including rice. Various molecular approaches to map genetic loci associated with rice superior traits were conducted. The mapped loci are very useful for rice breeding purposes. This paper reports the results of mapping and breeding economically important traits in rice, mainly those related to abiotic stresses, agronomic traits, yield, and yield quality. These included characters of semidwarf stature, aromatic grain, high yield potential, eating quality, higher Zn and Fe grain, more tolerant to abiotic stresses, such as salinity, drought, phosphate deficiency, Al toxicity and Fe toxicity, submergence, as well as early maturity character. The mapped characters can be transferred using marker-assisted backcrossing (MABC) method into cultivated rice genotypes well-adopted by farmers. Several countries including Indonesia have benefited from this breeding method, and Indonesia have released several rice varieties developed through MABC. These include rice varieties such as Code, Angke, Inpari 30, Inpari Blas, Inpari HDB, Bio Patenggang Agritan, and Bioni 63 Ciherang Agritan

Single Nucleotide Polymorphism (SNP) Discovery on Transcriptomes of American Holstein and Pakistanian Cholistani Cows

مطالعه در سطح ترانسکریپتوم می­تواند فاصله بین ژنوتیپ و فنوتیپ را پر نموده و به درک ساز وکارهای تبدیل توالی به عملکرد کمک نمایند. در این مطالعه به منظور کشف چند شکلی­های تک­نوکلئوتیدی (SNP) از داده­های RNA-Seq دو جمعیت گاوهای هلشتاین آمریکا (Bos taurus) و کلیستانی پاکستان (Bos indicus) استفاده شد. کنترل کیفیت و ویرایش داده­ها توسط نرم افزار­های FASTQC و Trimmomatic انجام شد. با همردیفی و مکان­یابی خوانش­های RNA-Seq بر روی ژنوم مرجع گاو با استفاده از نرم افزار TopHat2، ترانسکریپتوم تشکیل شد، سپس با استفاده از بسته نرم­افزاری Samtools­، آنالیز کشف SNP بر روی ترانسکریپتوم صورت گرفت که منجر به شناسایی 50183 و 137954 جایگاه SNP به ترتیب در گاوهای هلشتاین و کلیستانی شد، که 15308 جایگاه مشترک بود. ارتباط مستقیمی بین تعداد SNP­های یافت شده و طول کروموزوم­ها مشاهده نشد. همچنین 12 نوع SNP شناسایی شد که چهار نوع جایگزینی نوکلئوتیدی عامل و هشت نوع جایگزینی نوکلئوتیدی غیر عامل بودند. شایعترین SNP­های شناخته شده، از نوع جایگزینی نوکلئوتیدی عامل بودند، که 6/70­% در نژاد کلیستانی و 6/69­% در نژاد هلشتاین وجود داشت. درمطالعه حاضر 12 نوع SNP شناسایی شد. چهار نوع از SNP­ها، از نوع جایگزینی نوکلئوتیدی عامل وهشت نوع جایگزینی نوکلئوتیدی غیر عامل بودند. شایعترین SNP­های شناخته شده، SNP­های از نوع جایگزینی نوکلئوتیدی عامل بودند، که به ترتیب 6/70­% SNP­ها در نژاد کلیستانی و 6/69­% SNP­ها در نژاد هلشتاین را شامل شد. نسبت جایگزینی نوکلئوتیدی عامل به غیر عامل (Ts/Tv) SNP­ها در نژاد کلیستانی برابر با 4/2 و در نژاد هلشتاین برابر با 3/­2 بود.

Discovery of a Wurtzite-like Cu2FeSnSe4 Semiconductor Nanocrystal Polymorph and Implications for Related CuFeSe2 Materials.

I2-II-IV-VI4 and I-III-VI2 semiconductor nanocrystals have found applications in photovoltaics and other optoelectronic technologies because of their low toxicity and efficient light absorption into the near-infrared. Herein, we report the discovery of a metastable wurtzite-like polymorph of Cu2FeSnSe4, a member of the I2-II-IV-VI4 family of semiconductors containing only earth-abundant metals. Density functional theory calculations on this metastable polymorph of Cu2FeSnSe4 indicate that it may be a superior semiconductor for solar energy and optoelectronics applications compared to the thermodynamically preferred stannite polymorph, since the former displays a sharper dispersion of energy levels near the conduction band minimum that can enhance electron mobility and suppress hot electron cooling. The experimental optical band gap was measured by the inverse logarithmic derivative method to be direct, in agreement with theory, and in the range of 1.48-1.59 eV. Mechanistic studies reveal that this metastable phase derives from intermediate Cu3Se2 nanocrystals that serve as a structural template for the final hexagonal wurtzite-like product. We compare the chemistry of wurtzite-like Cu2FeSnSe4 to the related CuFeSe2 material system. Our experimental and computational comparisons between Cu2FeSnSe4 and CuFeSe2 help explain both the crystal chemistry of CuFeSe2 that prevents it from forming wurtzite-like polymorphs and the essential role of Sn in stabilizing the metastable structure of Cu2FeSnSe4. This work provides insight into the importance of elemental composition when designing syntheses for metastable materials.

GIDInd: an automated indexing software for grazing-incidence X-ray diffraction data.

Grazing-incidence X-ray diffraction (GIXD) is a widely used technique for the crystallographic characterization of thin films. The identification of a specific phase or the discovery of an unknown polymorph always requires indexing of the associated diffraction pattern. However, despite the importance of this procedure, only a few approaches have been developed so far. Recently, an advanced mathematical framework for indexing of these specific diffraction patterns has been developed. Here, the successful implementation of this framework in the form of an automated indexing software, named GIDInd, is introduced. GIDInd is based on the assumption of a triclinic unit cell with six lattice constants and a distinct contact plane parallel to the substrate surface. Two approaches are chosen: (i) using only diffraction peaks of the GIXD pattern and (ii) combining the GIXD pattern with a specular diffraction peak. In the first approach the six unknown lattice parameters have to be determined by a single fitting procedure, while in the second approach two successive fitting procedures are used with three unknown parameters each. The output unit cells are reduced cells according to approved crystallographic conventions. Unit-cell solutions are additionally numerically optimized. The computational toolkit is compiled in the form of a MATLAB executable and presented within a user-friendly graphical user interface. The program is demonstrated by application on two independent examples of thin organic films.

A new discovery of STAT4 single nucleotide polymorphisms associated with hepatocellular carcinoma risk in Chinese Han population: a case-control study.

Background: Hepatocellular carcinoma (HCC) is a common fatal malignant tumor worldwide. Signal transducer and activator of transcription 4 (STAT4) is HCC susceptibility gene identified by genome-wide association study. The purpose of the present study was to determine the association between four candidate single nucleotide polymorphisms (SNPs) in STAT4 genes and HCC risk in Chinese Han population.Methods: A case–control study was conducted to assess the association between STAT4 SNPs and HCC risk in 1011 Chinese Han population. Agena MassARRAY was used to genotype SNPs. The association between SNPs and HCC susceptibility under different genetic models was evaluated by logistic regression analysis. Multifactorial dimension reduction (MDR) analyzed the interaction of ‘SNP–SNP’ in HCC risk. The difference of clinical characteristics between different genotypes was completed by ANOVA.Results: The results showed that STAT4 rs11889341 was significantly associated with HCC risk under multiple genetic models (homozygote: odds ratio (OR) = 0.60, P=0.033; recessive: OR = 0.63, P=0.028; log-additive: OR = 0.83, P=0.032). The results of subgroup analysis showed that STAT4 rs11889341 is significantly associated with HCC risk with participants who were >55 years, male or smoking. Both STAT4 rs7574865 and rs10174238 were significantly associated with HCC risk among participants who were >55 years, smoking or drinking. STAT4 haplotype (Trs11889341Trs7574865) could reduce the risk of HCC. In addition, rs11889341 and rs7574865 were significantly associated with the level of serum ferritin (SF).Conclusion: STAT4 rs11889341, rs7574865 or rs10174238 is potentially associated with HCC risk in Chinese Han population. In particular, rs11889341 showed outstanding association with HCC risk.

Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS).

Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda® breed, constituting 95% of the country’s population, whereas geese of regional varieties are bred in smaller, conservation flocks. However, a goose’s genetic diversity is inaccurately explored, mainly because the advantages of the most commonly used tools are strongly limited in non-model organisms. One of the most accurate used markers for population genetics is single nucleotide polymorphisms (SNP). A highly efficient strategy for genome-wide SNP detection is genotyping-by-sequencing (GBS), which has been already widely applied in many organisms. This study attempts to use GBS in 12 conservative goose breeds and the White Kołuda® breed maintained in Poland. The GBS method allowed for the detection of 3833 common raw SNPs. Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs. These variants were located within 11 different genes, and one of the most diversified variants was associated with the EDAR gene, which is especially interesting as it participates in the plumage development, which plays a crucial role in goose breeding.

Molecular characterization of Algerian populations of cocksfoot and tall fescue: Ploidy level determination and genetic diversity analysis

AbstractAlgeria is a country rich in phytogenetic resources, especially those of pastoral and forage interest. Unfortunately, few studies have been conducted to characterize Algerian local ecotypes. Recently, advances in next‐generation sequencing technologies have allowed for robust genotyping by sequencing (GBS) for single nucleotide polymorphism (SNP) discovery, making the characterization of plant relationships with complex and unsequenced genomes more feasible. In the present study, we investigate the genetic diversity of cocksfoot and tall fescue ecotypes from different regions in Algeria, using the SNP variation supplied by a GBS analysis. We compared ecotypes to two common cultivars of both species. A total of 787 SNP markers for cocksfoot and 743 for tall fescue were obtained, and the diversity analysis revealed that 88% and 86% of overall variation in cocksfoot and tall fescue, respectively, were within populations rather than among them. Genetic structure analysis revealed a moderate genetic differentiation among accessions with a mean Fst value of 0.127 for cocksfoot and 0.140 for tall fescue, with high gene flow (NmOrchardgrass = 1.723, NmTall fescue = 1.535) and no significant isolation‐by‐distance pattern. A unweighted pair group method with arithmetic mean tree (UPGMA) and principal component analysis revealed the genetic distinctness of populations from cultivars for each species. The flow cytometry analysis confirmed the tetraploid level of cocksfoot and the hexaploid level of all tall fescue entries but one. Although the cocksfoot populations were distinct from the cultivars, the Ruines de djemila population had the broadest base and showed the closest relative relationship to the two cultivars. Similarly, the FE5729 tall fescue population showed the closest relationship to the two tall fescue cultivars.

Characterizing the Impact of Cancer Mutations in DNA Base Editing Enzymes

We have developed a comprehensive approach to find and characterize the impact of cancer mutants on any protein, and have applied it to DNA modification enzymes. This approach is an extension of conventional genome wide-association studies (GWAS). Our approach employs a new method for discovery and statistical validation of single nucleotide polymorphisms (SNPs) on specific genes called HyDn-SNP-S, followed by atomistic simulations via molecular dynamics (MD) and/or quantum mechanics/molecular mechanics (QM/MM) techniques. We will present the details of our mutant discovery and characterization approach, as well as examples of cancer mutations on three different DNA modification enzymes. These examples include a breast cancer mutation on DNA polymerase l, a prostate cancer mutation on the DNA dealkylase ALKBH7, and a lung cancer mutation on the cytidine deaminaseAPOBEC3H. Our simulations provide atomistic details about how these mutations affect the specific protein structure and/or function, which have been further validated by experimental methods.

Association of OLR1 gene polymorphisms with the risk of coronary artery disease: A systematic review and meta-analysis

BackgroundOxidized LDL receptor 1 (OLR1) encodes LOX-1, LOXIN, and OLR1D4 transcript variants. Up-regulation of LOX-1 and down-regulation of LOXIN have an essential role in causing coronary artery disease (CAD). Discovery of risk single nucleotide polymorphisms (SNPs) in OLR1 gene is clinically important as these polymorphisms could be candidate biomarkers of CAD. ObjectivesThe purpose of this study is quantitative evidence synthesis on how OLR1 polymorphisms in the haplotype block impact the risk of CAD. MethodsFirst, a systematic keyword-based search in PubMed, Web of Science, and Scopus was conducted. After data extraction, pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated for OLR1 polymorphisms and CAD. Twelve case-control studies, including 6,238 cases and 15,773 controls, were concluded in the meta-analysis. ResultsOur findings demonstrate significant association of OLR1 polymorphisms in the haplotype block with CAD risk in all genetic models (allelic model: OR = 1.19, 95%CI = 1.06–1.34; additive model: OR = 1.54, 95%CI = 1.16–2.05; recessive model: OR = 1.26, 95%CI = 1.04–1.53; dominant model: OR = 1.28, 95%CI = 1.09–1.51). Subgroup analysis based on the type of polymorphism revealed that rs1050283 (3′UTR*188 C > T) and rs3736235 (IVS4-14 A > G) are more significantly associated with the risk of CAD compared to other polymorphisms in the haplotype block. ConclusionsWe found a significant association between OLR1 polymorphisms in the haplotype block, especially rs1050283 and rs3736235, with CAD. We also suggest that precise determination of disease association with polymorphisms in a haplotype requires investigation of all SNPs rather than a single SNP in that specific haplotype.

Discovery of single nucleotide polymorphisms in bone morphogenetic protein (

Context Two native goat breeds from Kerala, Malabari and Attappady Black, differ significantly in prolificacy (i.e. no. of kids born/kidding). Prolificacy is an important economic trait and the subject of genetic research showing that bone morphogenetic protein (BMP) genes have a significant effect. Double digest restriction-site associated DNA sequencing (ddRADseq) is a highly efficient and low cost technology for high density discovery of single nucleotide polymorphisms (SNPs), which could serve as predictive markers for animal breeding programs. Aims The study was aimed at discovering SNPs in BMP genes that affect prolificacy, using ddRADseq followed by validation of selected SNP. Methods Blood DNA samples of 10 highly prolific Malabari and 10 less prolific Attappady Black goats were pooled by group and subjected to ddRADseq. SNPs observed in BMP genes were investigated and compared between groups. A validation study was done for the c.614–32789C>T variant in 100 Malabari and 50 Attappady Black goats by using PCR-RFLP. Key results In total, 6333 variants were identified by ddRADseq. Three variants were identified in BMP genes, which included two intronic variants c.614–32789C>T and c.490+6793T>C, in genes BMP6 and BMP5 and a downstream gene variant near the BMPR1B gene. According to ddRADseq data, variants in BMP5 and BMP6 differed in allelic distribution between Malabari and Attappady Black goats. For c.490+6793T>C in BMP5, the CC genotype was predominant in the highly prolific Malabari whereas TC was present in the Attappady Black group. The variant c.614–32789C>T in BMP6 was genotyped as TC in Malabari and CC in Attappady Black goats by ddRADseq. This variant was predicted to have an effect on splicing, according to the tool SplicePort. On the basis of bioinformatics analysis and the role of BMP6 gene in follicular dynamics, the variant in BMP6 was selected for further validation studies. All three genotypes were identified by PCR-RFLP; the C allele was the rare allele in the population with an allele frequency of 0.36. Presence of both alleles C and T and the three genotypes CC, TC and TT in this larger population substantiated the robustness of ddRADseq technique. Conclusions The technique discovered high confidence SNPs, which could be used for further validation and association studies to develop markers for selection of animals and for genetic improvement of this complex trait. Implications Techniques such as ddRADseq provide a large number of SNPs, and investigation of those polymorphisms found across the genome will help to identify new loci affecting traits of interest. This, in turn, will aid in exploring genetically complex traits in a faster and cheaper manner.

A brief summary of human molecular genetic techniques for clinical psychiatrists

Concerted and systematic efforts to understand genetics of human health and disease over the preceding 60 odd years have witnessed remarkable progress. The incremental gains through this journey were enabled by chromosomal analysis, recombinant deoxyribonucleic acid (DNA) techniques, notable discovery of single nucleotide polymorphisms following the Human Genome Project, consequent genome-wide variant-based studies, and now whole genome sequencing with ultimate diagnostic potential. Of note, success in prediction and prevention of chromosomal and single gene disorders comprising ~six to eight per cent each of all genetic disorders have been unprecedented but uncovering genetics of common complex disorders conferring ~60% of the genetic disease burden continues to pose a challenge and await new analytical paradigms - a mix of reductionist and organismal biology together with artificial intelligence and machine learning approaches being the current trend. A brief account of this path of progress in medical genetics and genomic insights along with limitations, to achieve the overarching goals of predictive, preventive, personalised, and participatory medicine is presented in this article.

The unexpected discovery of the ninth polymorph of tolfenamic acid

A new polymorph of tolfenamic acid, form IX, has been crystallised from a simple cooling crystallisation experiment raising the question as to why this polymorph had never been reported before.

Discovery of 20th Ice Polymorphs and Technical Development of High-Pressure Experiment under Electric Field

Discovery of 20th Ice Polymorphs and Technical Development of High-Pressure Experiment under Electric Field

Transcriptome based high-throughput SSRs and SNPs discovery in the medicinal plant Lagenaria siceraria

<i>Lagenaria siceraria</i> (Molina) Standley has unique biological characteristics with high nutritional and medicinal values. It is an important pharmaceutical plant with various biologically active ingredients. Genetic improvement and deeper genomic studies require a rich resource of molecular markers. The application of next-generation sequencing technology, especially for transcriptome profiling, has greatly facilitated high throughput single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) discovery. In this study, we sequenced the transcriptome of three major cultivars of <i>L. siceraria</i> and obtained 64.88 GB of clean data. The assembled high-quality reads were clustered into 89,347 unigenes, which were annotated by non-redundant protein database, Swiss-Port, Eukaryotic Ortholog Groups, Kyoto Encyclopedia of Genes and Genomes, and gene ontology databases. A total of 8,891 SSR and 35,873 SNP markers were predicted from unigenes by MISA and SAM tools, respectively. Characterization of the predicted markers in <i>L. siceraria</i> showed that the SSR and SNP densities were 60 and 243 markers per Mb of genome, respectively, and the estimated ratio of transition to transversion of SNP was 2.016. These markers will be very useful for genetic studies in <i>L. siceraria</i>, especially for the high-density linkage map construction and genome-wide association studies. Further genomic studies based on these results will facilitate the identification of novel genes or alleles of pharmaceutical importance.

Paraoxonase 1 Gene Polymorphism in Patients with Atopic Dermatitis

Atopic dermatitis, commonly called atopic eczema were considered to be a one sort of persistent and backsliding provocative sicknesses of skin with high heterogeneity and heritability. The principle point of this examination was to research the relationship between Paroxonase 1 quality 192Q/R and 55L/M polymorphisms and atopic dermatitis. Subjects and techniques: This was an imminent case-control study included 100 patients experiencing atopic dermatitis (AD) (Group A). Notwithstanding 100 obviously solid people of coordinated age and sex as a benchmark (Group B). Discovery of single nucleotide polymorphism (SNP) for paroxonase 1 quality (192 Q/R and 55 L/M) was finished utilizing explicit preliminaries by a polymerase chain response - based limitation section length polymorphism (PCR-RFLP) test .Results: L allele demonstrated fundamentally higher recurrence in AD patients when contrasted with control gatherings; with danger to grow AD. While 192Q/R RR, RQ+RR genotypes, R allele; 55L/M MM, ML+MM genotypes, M allele had lower recurrence in AD patients when contrasted with control gatherings. End: The QL haplotype was altogether connected with danger of AD. Further examination utilizing the rules and all the more fittingly fueled investigations ought to incredibly improve the trust in the gauge of danger factors and an impact of a specific way to deal with treatment.

Development of SNP-Based Genomic Tools for the Canadian Bison Industry: Parentage Verification and Subspecies Composition.

Genomic technologies have been increasingly applied in livestock production due to their utility in production management and animal genetic improvement. The current project aimed to develop genomic resources for the Canadian bison industry, specifically a parentage verification tool and a subspecies composition tool. Both products stand to help with building and maintaining purebred and crossbred bison populations, and in turn bison conservation and production. The development of this genomic toolkit proceeded in two stages. In the single-nucleotide polymorphism (SNP) discovery and selection stage, raw sequence information from 41 bison samples was analyzed, and approximately 52.5 million candidate biallelic SNPs were discovered from 21 samples with high sequence quality. A set of 19,954 SNPs (2,928 for parentage verification and 17,026 for subspecies composition) were then selected for inclusion on an Axiom myDesign custom array. In the refinement and validation stage, 480 bison were genotyped using the custom SNP panel, and the resulting genotypes were analyzed to further filter SNPs and assess tool performance. In various tests using real and simulated genotypes, the two genomic tools showed excellent performance for their respective tasks. Final SNP sets consisting of 191 SNPs for parentage and 17,018 SNPs for subspecies composition are described. As the first SNP-based genomic toolkit designed for the Canadian bison industry, our results may provide a new opportunity in improving the competitiveness and profitability of the industry in a sustainable manner.

Computational discovery and assessment of non-synonymous single nucleotide polymorphisms from target gene pool associated with Parkinson's disease

Parkinson's disease is a well known neurological disorder across the globe. Even after decades of research, precise knowledge on molecular basis of the disease pathology is still imprecise. However, advancement in experimental and computational techniques have generated high frequency of genomics data which offers a scope to discover effective non synonymous SNPs within PD associated genes. Here, authors have attempted to discovered non-synonymous, deleterious SNPs for the target gene pool with a plausible threat towards PD pathophysiology using dbSNP, SIFT, PredictSNP1 and PredictSNP2 tool. PD related genes list was prepared on the basis of literature evidence and reports from different public repositories such as Gene Cards, GWAS CATALOG, GenAtlas and MalaCards. The present study was identified six novel SNPs such as rs372675589, rs150966634, rs184532476, rs373099722, rs201188374 and rs201555827 for five PD targets (PSMC4, NDUFV1, GSK3B, GPR37 and CUL1). Possibly, all of these six SNPs such as P199H (PSMC4), R386C (NDUFV1), V70I (GSK3B), V399G (GPR37), S424F (GPR37), and L140P (CUL1) in their respective PD targets have remarkable association in the disease pathways. The present observation would provide insights into the complicated structure of PD pathophysiology.