scholarly journals DNA-based genealogy reconstruction of Nebbiolo, Barbera and other ancient grapevine cultivars from northwestern Italy

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Stefano Raimondi ◽  
Giorgio Tumino ◽  
Paola Ruffa ◽  
Paolo Boccacci ◽  
Giorgio Gambino ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Economic Value ◽  
Cultural Value ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Sibling Relations ◽  
Kinship Relations ◽  
History Of ◽  
Wine Region ◽  
Grape Varieties

Abstract Northwestern Italy is a wine region of the world with the highest of reputations, where top quality wines of remarkable economic value are produced from traditional, long-cultivated varieties. Kinship analyses were performed using 32 microsatellite loci and more than 10 K single-nucleotide polymorphism markers on 227 traditional grapes mostly from Northwestern Italy—including those that have been neglected or are threatened. This was done to better understand the genetic grapevine origins and history of this reputable wine producing area, thus enhancing its cultural value and the marketing appeal of its wines. The work revealed a complex network of genetic relationships among varieties, with little contribution of genotypes from other areas. It revealed the major role played by a few ancient grape varieties as parents of numerous offspring, including some that are endangered today. The ancestry of many cultivars is proposed. Among these are Dolcetto, Barbera and Riesling italico. Through the inference of parent–offspring and sibling relations, marker profiles of ungenotyped putative parents were reconstructed, suggesting kinship relations and a possible parentage for Nebbiolo, one of the most ancient wine grapes worldwide. Historic and geographic implications from the resulting kinships are discussed.

scholarly journals Temporal fluctuations of Y-chromosomal variation in Bos taurus

2008 ◽  
Vol 4 (6) ◽  
pp. 752-754 ◽  
Author(s):  
Emma Svensson ◽  
Anders Götherström
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bos Taurus ◽  
Demographic History ◽  
Northern Europe ◽  
Chromosomal Gene ◽  
Chromosomal Variation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Domestic Species ◽  
History Of

Phylogeography has recently become more abundant in studies of demographic history of both wild and domestic species. A single nucleotide polymorphism (SNP) in the intron of the Y-chromosomal gene UTY19 displays a north–south gradient in modern cattle. Support for this geographical distribution of haplogroups has previously also been seen in ancient cattle from Germany. However, when analysing 38 historic remains of domestic bulls and three aurochs from northern Europe for this SNP we found no such association. Instead, we noted extensive amounts of temporal variation that can be attributed to transportation of cattle and late breed formation.

scholarly journals Transmission analysis of a large TB outbreak in London: mathematical modelling study using genomic data

2019 ◽  
Author(s):  
Yuanwei Xu ◽  
Hollie Topliffe ◽  
James Stimson ◽  
Helen R. Stagg ◽  
Ibrahim Abubakar ◽  
...  
Keyword(s):  
Mathematical Modelling ◽  
Disease Transmission ◽  
Machine Learning Techniques ◽  
Reconstruction Method ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Patient Level ◽  
Learning Techniques ◽  
Level Data ◽  
History Of

AbstractOutbreaks of tuberculosis- such as the large isoniazid-resistant outbreak centered on London, United Kingdom, which originated in 1995- provide excellent opportunities to model transmission of this devastating disease. Transmission chains for tuberculosis are notoriously difficult to ascertain, but mathematical modelling approaches, combined with whole-genome sequencing (WGS) data, have strong potential to contribute to transmission analyses. Using such data, we aimed to reconstruct transmission histories for the outbreak using a Bayesian approach, and to use machine learning techniques with patient-level data to identify the key covariates associated with transmission. By using our transmission reconstruction method that accounts for phylogenetic uncertainty, we are able to identify 24 transmission events with reasonable confidence, 11 of which have zero single nucleotide polymorphism (SNP) distance, and as maximum distance of 3. Patient age, alcohol abuse and history of homelessness were found to be the most important predictors of being credible tuberculosis transmitters.

scholarly journals Risk of gout among Taiwanese adults with ALDH-2 rs671 polymorphism according to BMI and alcohol intake

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Yu-Ruey Liu ◽  
Disline Manli Tantoh ◽  
Chuan-Chao Lin ◽  
Chih-Hsuan Hsiao ◽  
Yung-Po Liaw
Keyword(s):  
Alcohol Drinking ◽  
Lower Risk ◽  
Alcohol Intake ◽  
Normal Weight ◽  
Nucleotide Polymorphism ◽  
Aldehyde Dehydrogenase 2 ◽  
Single Nucleotide ◽  
Independent Variables ◽  
History Of ◽  
History Of Cancer

Abstract Background Gout stems from both modifiable and genetic sources. We evaluated the risk of gout among Taiwanese adults with aldehyde dehydrogenase-2 (ALDH2) rs671 single nucleotide polymorphism (SNP) according to body mass index (BMI) and alcohol drinking. Methods We obtained information of 9253 individuals having no personal history of cancer from the Taiwan Biobank (2008–2016) and estimated the association between gout and independent variables (e.g., rs671, BMI, and alcohol drinking) using multiple logistic regression. Results Alcohol drinking and abnormal BMI were associated with a higher risk of gout whereas the rs671 GA+AA genotype was associated with a lower risk. The odds ratios (ORs) and 95% confidence intervals (CIs) were 1.297 and 1.098–1.532 for alcohol drinking, 1.550 and 1.368–1.755 for abnormal BMI, and 0.887 and 0.800–0.984 for GA+AA. The interaction between BMI and alcohol on gout was significant for GG (p-value = 0.0102) and GA+AA (p-value = 0.0175). When we stratified genotypes by BMI, alcohol drinking was significantly associated with gout only among individuals with a normal BMI (OR; 95% CI = 1.533; 1.036–2.269 for GG and 2.109; 1.202–3.699 for GA+AA). Concerning the combination of BMI and alcohol drinking among participants stratified by genotypes (reference, GG genotype, normal BMI, and no alcohol drinking), the risk of gout was significantly higher in the following categories: GG, normal BMI, and alcohol drinking (OR, 95% CI = 1.929, 1.385–2.688); GG, abnormal BMI, and no alcohol drinking (OR, 95% CI, = 1.721, 1.442–2.052); GG, abnormal BMI, and alcohol drinking (OR, 95% CI = 1.941, 1.501–2.511); GA+AA, normal BMI, and alcohol drinking (OR, 95% CI = 1.971, 1.167–3.327); GA+AA, abnormal BMI, and no alcohol drinking (OR, 95% CI = 1.498, 1.256–1.586); and GA+AA, abnormal BMI, and alcohol drinking (OR, 95% CI = 1.545, 1.088–2.194). Conclusions Alcohol and abnormal BMI were associated with a higher risk of gout, whereas the rs671 GA+AA genotype was associated with a lower risk. Noteworthy, BMI and alcohol had a significant interaction on gout risk. Stratified analyses revealed that alcohol drinking especially among normal-weight individuals might elevate the risk of gout irrespective of the genotype.

Genetic relationships among fruiting-mei (Prunus mume Sieb. et Zucc.) cultivars evaluated with AFLP and SNP markers

Genome ◽  
2006 ◽  
Vol 49 (10) ◽  
pp. 1256-1264 ◽  
Author(s):  
Jinggui Fang ◽  
Tal Twito ◽  
Zhen Zhang ◽  
ChihCheng T. Chao
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Snp Markers ◽  
Prunus Mume ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The Past ◽  
China And Japan

Genetic relationships among 50 fruiting-mei (Prunus mume Sieb. et Zucc.) cultivars from China and Japan were investigated, using 767 amplified fragment length polymorphism (AFLP) and 103 single nucleotide polymorphism (SNP) markers. The polymorphism among the cultivars was found to be 69.77%, based on EcoR I + Mse I AFLP primer pairs. The sequence alignment of 11 group sequences, derived from 50 samples, yielded 103 SNPs; the total length of genomic sequences was 3683 bp. Among these SNPs, 73 were heterozygous in the loci of different cultivars. The SNP distribution was 58% transition, 40% transversion, and 2% InDels. There was also 1 trinucleotide deletion. AFLP and SNP markers allowed us to evaluate the genetic diversity of these 50 fruiting-mei cultivars. The 2 derived cladograms did display some differences: all cultivars formed 2 subclusters (1A and 1B) in the cladogram based on AFLP polymorphisms, and formed 3 subclusters (2A, 2B, and 2C) in the cladogram based on SNP polymorphisms; and, in the cladogram based on AFLP polymorphisms, most cultivars from the Guangdong to Fujian provinces (G–F) in China, from the Yunnan, Hunan, and Sichuan provinces (Y–S–H) in China, and from Japan grouped in cluster 1A, and 18 (78.26%) of 23 cultivars from Jiangsu to Zhejiang provinces in China (J–Z) grouped in cluster 1B. The results demonstrate that mei cultivars from Japan are clustered with cultivars from China, and support the hypothesis that mei in Japan were introduced from China. Cultivars from the J–Z region of China have more genetic similarities. Cultivars from the G–F and Y–S–H regions have fewer genetic similarities and suggest more germplasm exchanges in the past.

The Culture Memory of the Times — In Urban Redevelopment Should Strengthen the Historical Building Protection

2011 ◽  
Vol 361-363 ◽  
pp. 1166-1169
Author(s):  
Wei Mo ◽  
Yao Qi Wang
Keyword(s):  
Economic Value ◽  
Modern Technology ◽  
Cultural Value ◽  
Space Environment ◽  
Low Carbon ◽  
Historical Building ◽  
Balanced Development ◽  
History Of ◽  
The Times ◽  
Scientific Value

Every city has its own history , every nation has its own unique culture . Historical and cultural city as the ancient city of outstanding representative , has important history, culture, art and scientific value . But urban development to the pluralism and urgency of urban construction and historical and cultural heritage protection contradiction . The traditional culture and the modern technology homozygous coexistence , mutual coordination , protect reuse historical building needs government , professional and public unity . The urban culture memory the visual sense except image, and the imagination of space environment around feeling, from ancient to modern, step by step, the change of records of history, environment evolution. So we protection is not isolated cage, but far concept and shall touch, but feel history of memories, and precipitate social function, make it play to bring cultural value and urban economic value, achieve a low carbon cities balanced development.

scholarly journals The Role of Collagen Genetic Discrepancies in Development of Pelvic Organ Prolapse in Women: A Study with Negative Results

2020 ◽  
Vol I (1) ◽  
pp. 12-16
Author(s):  
Hirron Fernando
Keyword(s):  
Pelvic Organ Prolapse ◽  
Meta Analysis ◽  
Pelvic Organ ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The Past ◽  
Negative Results ◽  
Increased Risk ◽  
History Of

Pelvic organ prolapse has a mixed aetiology – hereditary and acquired. During last decade, the role of genetics in POP becomes profoundly obvious. women with a family history of prolapse are at an increased risk of prolapse refractory to treatment. Careful literature review from the past studies reveals that several genetic mutations have been shown to correlate with increased prolapse susceptibility. These mutations can result in disordered collagen metabolism, which weaken the fascial support of the pelvic organs. This prompt us to undertake the above study, look more into genetic discrepancies and pelvic organ prolapse contemporary studies relate to this topic shows that Collagen is playing a major role in pelvic floor supportive structures. However role of single nucleotide polymorphism (SNP) of the COL1A1 or COL3A1 or COL18A1 genes remain controversial relate to pelvic organ prolapse. Some studies and meta-analysis found a strict correlation between these genetic defects and POP.

scholarly journals A systematic review on papers that study on Single Nucleotide Polymorphism that affects coronavirus 2019 severity

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Siyeon Suh ◽  
Sol Lee ◽  
Ho Gym ◽  
Sanghyuk Yoon ◽  
Seunghwan Park ◽  
...  
Keyword(s):  
Clinical Studies ◽  
Time History ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Common Features ◽  
Newcastle Ottawa Scale ◽  
History Of ◽  
Severity Of The Disease ◽  
Ottawa Scale

Abstract Background COVID-19, caused by SARS-CoV-2 has become the most threatening issue to all populations around the world. It is, directly and indirectly, affecting all of us and thus, is an emerging topic dealt in global health. To avoid the infection, various studies have been done and are still ongoing. COVID-19 cases are reported all over the globe, and among the millions of cases, genetic similarity may be seen. The genetical common features seen within confirmed cases may help outline the tendency of infection and degree severity of the disease. Here, we reviewed multiple papers on SNPs related to SARS-CoV-2 infection and analyzed their results. Methods The PubMed databases were searched for papers discussing SNPs associated with SARS-CoV-2 infection and severity. Clinical studies with human patients and statistically showing the relevance of the SNP with virus infection were included. Quality Assessment of all papers was done with Newcastle Ottawa Scale. Results In the analysis, 21 full-text literature out of 2956 screened titles and abstracts, including 63,496 cases, were included. All were human-based clinical studies, some based on certain regions gathered patient data and some based on big databases obtained online. ACE2, TMPRSS2, and IFITM3 are the genes mentioned most frequently that are related to SARS-CoV-2 infection. 20 out of 21 studies mentioned one or more of those genes. The relevant genes according to SNPs were also analyzed. rs12252-C, rs143936283, rs2285666, rs41303171, and rs35803318 are the SNPs that were mentioned at least twice in two different studies. Conclusions We found that ACE2, TMPRSS2, and IFITM3 are the major genes that are involved in SARS-CoV-2 infection. The mentioned SNPs were all related to one or more of the above-mentioned genes. There were discussions on certain SNPs that increased the infection and severity to certain groups more than the others. However, as there is limited follow-up and data due to a shortage of time history of the disease, studies may be limited.

scholarly journals Understanding the genetic relationships between Indonesian bambara groundnut landraces and investigating their origins

Genome ◽  
2020 ◽  
Vol 63 (6) ◽  
pp. 319-327 ◽  
Author(s):  
E.S. Redjeki ◽  
W.K. Ho ◽  
N. Shah ◽  
O.O. Molosiwa ◽  
N.R. Ardiarini ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Bambara Groundnut ◽  
Principal Coordinate Analysis ◽  
Vigna Subterranea ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
And Cluster Analysis ◽  
Simple Sequence

A total of 170 bambara groundnut (Vigna subterranea) accessions were evaluated using both simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers generated using genotyping-by-sequencing (GbS), of which 56 accessions were collected from West and East Java. Principal coordinate analysis (PCoA), population structure, and cluster analysis suggest that the East Java accessions could be a result of the introduction of selected West Java accessions. In addition, the current Indonesian accessions were likely introduced from Southern Africa, which would have produced a very marked founding effect such that these accessions present only a fraction of the genetic variability that exists within this species.

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