scholarly journals Do Genes Associated with Dyslexia of Chinese Characters Evolve Neutrally?

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 658 ◽  
Author(s):  
Kumiko V. Nishiyama ◽  
Yoko Satta ◽  
Jun Gojobori
Keyword(s):  
Reading Disability ◽  
Reading Ability ◽  
Genetic Basis ◽  
Selective Sweep ◽  
Chinese Characters ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Asian Populations ◽  
Snp Data ◽  
Candidate Target

Dyslexia, or reading disability, is found to have a genetic basis, and several related genes have been reported. We investigated whether natural selection has acted on single nucleotide polymorphisms (SNPs) that were reported to be associated with risk/non-risk for the reading disability of Chinese characters. We applied recently developed 2D SFS-based statistics to SNP data of East Asian populations to examine whether there is any sign of selective sweep. While neutrality was not rejected for most SNPs, significant signs of selection were detected for two linkage disequilibrium (LD) regions containing the reported SNPs of GNPTAB and DCDC2. Furthermore, we searched for a selection target site among the SNPs in these LD regions, because a causal site is not necessarily a reported SNP but could instead be a tightly linked site. In both LD regions, we found candidate target sites, which may have an effect on expression regulation and have been selected, although which genes these SNPs affect remains unknown. Because most people were not engaged in reading until recently, it is unlikely that there has been selective pressure on reading ability itself. Consistent with this, our results suggest a possibility of genetic hitchhiking, whereby alleles of the reported SNPs may have increased in frequency together with the selected target, which could have functions for other genes and traits apart from reading ability.

scholarly journals A Major Genome Region Underlying Artemisinin Resistance in Malaria

Science ◽  
2012 ◽  
Vol 336 (6077) ◽  
pp. 79-82 ◽  
Author(s):  
Ian H. Cheeseman ◽  
Becky A. Miller ◽  
Shalini Nair ◽  
Standwell Nkhoma ◽  
Asako Tan ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Selective Sweep ◽  
Strong Association ◽  
Artemisinin Resistance ◽  
Parasite Clearance ◽  
Nucleotide Polymorphisms ◽  
Two Phase ◽  
Single Nucleotide ◽  
Genome Region ◽  
Major Genome

Evolving resistance to artemisinin-based compounds threatens to derail attempts to control malaria. Resistance has been confirmed in western Cambodia and has recently emerged in western Thailand, but is absent from neighboring Laos. Artemisinin resistance results in reduced parasite clearance rates (CRs) after treatment. We used a two-phase strategy to identify genome region(s) underlying this ongoing selective event. Geographical differentiation and haplotype structure at 6969 polymorphic single-nucleotide polymorphisms (SNPs) in 91 parasites from Cambodia, Thailand, and Laos identified 33 genome regions under strong selection. We screened SNPs and microsatellites within these regions in 715 parasites from Thailand, identifying a selective sweep on chromosome 13 that shows strong association (P = 10−6 to 10−12) with slow CRs, illustrating the efficacy of targeted association for identifying the genetic basis of adaptive traits.

scholarly journals Identification of Genomic Characteristics and Selective Signals in a Du’an Goat Flock

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 994
Author(s):  
Qiuming Chen ◽  
Zihao Wang ◽  
Junli Sun ◽  
Yingfei Huang ◽  
Quratulain Hanif ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Selective Sweep ◽  
Farm Animals ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Adaptive Traits ◽  
Gene Set Enrichment ◽  
Single Nucleotide ◽  
Immune Resistance ◽  
Goat Flock

The Du’an goat is one of the most important farm animals in the Guangxi Autonomous Region of China, but the genetic basis underlying its adaptive traits has still not been investigated. Firstly, in this study, the genomes of 15 Du’an goats from a breeding farm were sequenced (mean depth: 9.50X) to analyze the patterns of genetic variation. A comparable diversity (17.3 million single nucleotide polymorphisms and 2.1 million indels) was observed to be associated with a lower runs of homozygosity-based inbreeding coefficient and smaller effective population size in comparison with other breeds. From selective sweep and gene set enrichment analyses, we revealed selective signals related to adaptive traits, including immune resistance (serpin cluster, INFGR1, TLR2, and immune-related pathways), body size (HMGA2, LCOR, ESR1, and cancer-related pathways) and heat tolerance (MTOR, ABCG2, PDE10A, and purine metabolism pathway). Our findings uncovered the unique diversity at the genomic level and will provide the opportunities for improvement of productivity in the Du’an goat.

Association of RETN and TNFRSF1B polymorphisms with TNF-α inhibitor response in rheumatoid arthritis patients

2020 ◽  
Author(s):  
Nga Thi Trinh ◽  
Hyun Jeong Kim ◽  
Woorim Kim ◽  
Sang Oh Kang ◽  
Kyung Hyun Min ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Disease Activity ◽  
Statistical Significance ◽  
Univariate Analysis ◽  
Multivariable Logistic Regression Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Final Model ◽  
Asian Populations ◽  
Tnf Α

Abstract Background: Despite the improvement from the introduction of tumor necrosis factor inhibitors (TNFi) in the rheumatoid arthritis (RA), TNFi therapy fails for more than 30% or results in a partial response. Thus, we aimed to explore treatment marker by examining the association of single nucleotide polymorphisms (SNPs) with response to TNFi therapy.Method: Genes associated with RA or RA treatment were reviewed and fourteen SNPs with minor allele frequency ≥ 20% in the East Asian populations were selected and analyzed. Data were collected from 105 RA patients. Our primary endpoint was the disease activity score using 28-joint count after six months of treatment (DAS28-6month). The secondary outcomes were the subcomponents of DAS28.Results: A total of 88 patients were included in the final analyses. Among the 14 SNPs analyzed, one SNP showed statistical significance in DAS28-6month: patients with the GG allele of RETN rs1862513 had a 4.7 times higher chance of low disease activity at 6-months than GC or CC-carriers (p = 0.033), as indicated by multivariable logistic regression analysis. Rs3397 was marginally significant in univariate analysis (p=0.059), but was significant in the multivariable model (p=0.041). The final model explained 24.5% (Nagelkerke R2) of the variance in DAS28-6month.Conclusion: Our results demonstrated that, among the genes related to RA, SNPs in RETN and TNFRSF1B were associated with the response of TNFi treatment.

scholarly journals Genetics of Lactose Intolerance: An Updated Review and Online Interactive World Maps of Phenotype and Genotype Frequencies

Nutrients ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2689
Author(s):  
Augusto Anguita-Ruiz ◽  
Concepción M. Aguilera ◽  
Ángel Gil
Keyword(s):  
Genetic Basis ◽  
Human Populations ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genotype Frequencies ◽  
Genetic Mechanisms ◽  
Visualization Tools ◽  
Available Information ◽  
Static World ◽  
Interactive Resources

In humans the ability to digest milk lactose is conferred by a β-galactosidase enzyme called lactase-phlorizin hydrolase (LPH). While in some humans (approximately two-thirds of humankind) the levels of this enzyme decline drastically after the weaning phase (a trait known as lactase non-persistence (LNP)), some other individuals are capable of maintaining high levels of LPH lifelong (lactase persistence (LP)), thus being able to digest milk during adulthood. Both lactase phenotypes in humans present a complex genetic basis and have been widely investigated during the last decades. The distribution of lactase phenotypes and their associated single nucleotide polymorphisms (SNPs) across human populations has also been extensively studied, though not recently reviewed. All available information has always been presented in the form of static world maps or large dimension tables, so that it would benefit from the newly available visualization tools, such as interactive world maps. Taking all this into consideration, the aims of the present review were: (1) to gather and summarize all available information on LNP and LP genetic mechanisms and evolutionary adaptation theories, and (2) to create online interactive world maps, including all LP phenotype and genotype frequency data reported to date. As a result, we have created two online interactive resources, which constitute an upgrade over previously published static world maps, and allow users a personalized data exploration, while at the same time accessing complete reports by population or ethnicity.

scholarly journals Identification of genome-wide single-nucleotide polymorphisms among geographically diverse radish accessions

DNA Research ◽  
2020 ◽  
Vol 27 (1) ◽  
Author(s):  
Hiroto Kobayashi ◽  
Kenta Shirasawa ◽  
Nobuko Fukino ◽  
Hideki Hirakawa ◽  
Takashi Akanuma ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Southeast Asia ◽  
East Asia ◽  
Near East ◽  
Dna Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
South And Southeast Asia ◽  
Snp Data ◽  
Genome Wide

Abstract Radish (Raphanus sativus L.) is cultivated around the world as a vegetable crop and exhibits diverse morphological and physiological features. DNA polymorphisms are responsible for differences in traits among cultivars. In this study, we determined genome-wide single-nucleotide polymorphisms (SNPs) among geographically diverse radish accessions using the double-digest restriction site-associated DNA sequencing (ddRAD-Seq) method. A total of 52,559 SNPs was identified in a collection of over 500 radish accessions (cultivated and wild) from East Asia, South and Southeast Asia, and the Occident and Near East. In addition, 2,624 SNP sites without missing data (referred to as common SNP sites) were identified among 510 accessions. Genetic diversity analyses, based on the common SNP sites, divided the cultivated radish accessions into four main groups, each derived from four geographical areas (Japan, East Asia, South and Southeast Asia, and the Occident and Near East). Furthermore, we discuss the origin of cultivated radish and its migration from the West to East Asia. SNP data generated in this work will facilitate further genetic studies on the radish breeding and production of DNA markers.

scholarly journals Insight into Gene Polymorphisms Involved in Toll-Like Receptor/Interferon Signalling Pathways for Systemic Lupus Erythematosus in South East Asia

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Hwa Chia Chai ◽  
Kek Heng Chua ◽  
Soo Kun Lim ◽  
Maude Elvira Phipps
Keyword(s):  
Lupus Erythematosus ◽  
Meta Analysis ◽  
Signalling Pathways ◽  
Type I ◽  
Nucleotide Polymorphisms ◽  
Toll Like Receptor ◽  
Single Nucleotide ◽  
Asian Populations ◽  
Interferon Signalling

Polymorphisms in genes involved in toll-like receptor/interferon signalling pathways have been reported previously to be associated with SLE in many populations. This study aimed to investigate the role of seven single nucleotide polymorphisms withinTNFAIP3,STAT4,andIRF5, which are involved in upstream and downstream pathways of type I interferon production, in SLE in the South East Asian populations. Genotyping of 360 Malaysian SLE patients and 430 normal healthy individuals revealed that minor alleles ofSTAT4rs7574865 and rs10168266 were associated with elevated risk of SLE in the Chinese and Malay patients, respectively (P=0.028, odds ratio(OR)=1.42;P=0.035,OR=1.80, respectively). Polymorphisms inTNFAIP3andIRF5did not show significant associations with SLE in any of the ethnicities. Combined analysis of the Malays, Chinese, and Indians for each SNP indicated thatSTAT4rs10168266 was significantly associated with the Malaysian SLE as a whole (P=0.014;OR=1.435). The meta-analysis ofSTAT4rs10168266, which combined the data of other studies and this study, further confirmed its importance as the risk factor for SLE by having pooled OR of 1.559 andPvalue of <0.001.

NIASGBsnp: integration of single nucleotide polymorphism data of rice (Oryzasativa L.) genetic resources

2013 ◽  
Vol 11 (3) ◽  
pp. 221-224
Author(s):  
Masaru Takeya ◽  
Fukuhiro Yamasaki ◽  
Sachiko Hattori ◽  
Kaworu Ebana
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Plant Pathology ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Resources ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Snp Data ◽  
Polymorphism Data

The NIASGBsnp system manages data on single nucleotide polymorphisms (SNPs) of rice (Oryzasativa L.) genetic resources in the National Institute of Agrobiological Science (NIAS) Genebank. NIASGBsnp currently holds data on 768 SNP markers for 301 rice accessions and plans to add the SNP data of active rice accessions in the NIAS Genebank. It can show differences between accessions by graphical genotyping. Passport, characteristics and evaluation data of accessions can be retrieved to allow phenotype to be associated with genotype. NIASGBsnp will support various research purposes such as genomic selection and plant pathology research.

Genetic differences in CYP2C19 single nucleotide polymorphisms among four Asian populations

2001 ◽  
Vol 36 (10) ◽  
pp. 669-672 ◽  
Author(s):  
Sirikan Yamada ◽  
Masahiko Onda ◽  
Shunji Kato ◽  
Noriko Matsuda ◽  
Takeshi Matsuhisa ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Differences ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Asian Populations
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