scholarly journals Development of SNP markers for grain yield screening of Brazilian rice cultivars

2020 ◽  
Vol 55 ◽  
Author(s):  
Gabriel Feresin Pantalião ◽  
Rosana Pereira Vianello ◽  
Luíce Gomes Bueno ◽  
João Antônio Mendonça ◽  
Alexandre Siqueira Guedes Coelho ◽  
...  
Keyword(s):  
Grain Yield ◽  
Field Experiments ◽  
Association Studies ◽  
Snp Markers ◽  
Joint Analysis ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Productive Potential

Abstract: The objective of this work was to identify and validate single-nucleotide polymorphism (SNP) markers related to grain yield in rice (Oryza sativa) core collection. The genome-wide association studies (GWAS) methodology was applied for genotyping of 541 rice accessions by 167,470 SNPs. The grain yield of these accessions was estimated through the joint analysis of nine field experiments carried out in six Brazilian states. Fifteen SNPs were significantly associated with grain yield, and out of the ten SNPs converted to TaqMan assays, four discriminated the most productive accessions. These markers were used for the screening of rice accessions with favorable alleles. The selected accessions were, then, evaluated in field experiments in target environments, in order to select the most productive ones. This screening reduces the number of accessions evaluated experimentally, making it possible to prioritize those with higher productive potential, which allows of the increase of the number of replicates and, consequently, of the experimental accuracy.

scholarly journals Replication of Top Loci From COL4A1/2 Associated With White Matter Hyperintensity Burden in Patients With Ischemic Stroke

Stroke ◽  
2020 ◽  
Vol 51 (12) ◽  
pp. 3751-3755
Author(s):  
Jiang Li ◽  
Vida Abedi ◽  
Ramin Zand ◽  
Christoph J. Griessenauer ◽  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Ischemic Stroke ◽  
Odds Ratio ◽  
Association Studies ◽  
Genome Wide Association ◽  
White Matter Hyperintensity ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide

Background and Purpose: The purpose of this study was to replicate the top loci associated with white matter hyperintensity (WMH) phenotypes identified by large genome-wide association studies and the loci identified from the previous candidate gene studies. Methods: A total of 946 Geisinger MyCode patients with acute ischemic stroke with validated European ancestry and magnetic resonance imaging data were included in this study. Log-transformed WMH volume, as a quantitative trait, was calculated by a fully automated quantification process. The genome-wide association studies was carried out by a linear mixed regression model (GEMMA). A candidate-single nucleotide polymorphism analysis by including known single nucleotide polymorphisms, reported from a meta-analysis and several large GWAS for WMH, was conducted in all cases and binary converted extreme cases. Results: No genome-wide significantly associated variants were identified. In a candidate-single nucleotide polymorphism study, rs9515201 ( COL4A2 ) and rs3744028 ( TRIM65 ), 2 known genetic loci, showed nominal or trend of association with the WMH volume (β=0.13 and P =0.001 for rs9515201; β=0.094 and P =0.094 for rs3744028), and replicated in a subset of extreme cases versus controls (odds ratio=1.78, P =7.74×10 − 4 for rs9515201; odds ratio=1.53, P =0.047 for rs3744028, respectively). MTHFR677 cytosine/thymine (rs1801133) also showed an association with the binary WMH with odds ratio=1.47 for T allele ( P =0.019). Conclusions: Replication of COL4A1/2 associated with WMH reassures that the genetic risk factors for monogenic and polygenic ischemic stroke are shared at gene level.

scholarly journals An Analysis Pipeline for Genome-wide Association Studies

2008 ◽  
Vol 6 ◽  
pp. CIN.S966 ◽  
Author(s):  
Stefan Stefanov ◽  
James Lautenberger ◽  
Bert Gold
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Missing Values ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Population Difference ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
And Control

We developed an efficient pipeline to analyze genome-wide association study single nucleotide polymorphism scan results. Perl scripts were used to convert genotypes called using the BRLMM algorithm into a modified PB format. We computed summary statistics characteristic of our case and control populations including allele counts, missing values, heterozygosity, measures of compliance with Hardy-Weinberg equilibrium, and several population difference statistics. In addition, we computed association tests, including exact tests of association for genotypes, alleles, the Cochran-Armitage linear trend test, and dominant, recessive, and overdominant models at every single nucleotide polymorphism (SNP). In addition, pairwise linkage disequilbrium statistics were elaborated, using the command line version of HaploView, which was possible by writing a reformatting script. Additional Perl scripts permit loading the results into a MySQL database conjoined with a Generic Genome Browser (gbrowse) for comprehensive visualization. This browser incorporates a download feature that provides actual case and control genotypes to users in associated genomic regions. Thus, re-analysis “on the fly” is possible for casual browser users from anywhere on the Internet.

scholarly journals Both variants of A1CF and BAZ1B genes are associated with gout susceptibility: a replication study and meta-analysis in a Japanese population

Human Cell ◽  
2021 ◽  
Vol 34 (2) ◽  
pp. 293-299
Author(s):  
Makoto Kawaguchi ◽  
Akiyoshi Nakayama ◽  
Yuka Aoyagi ◽  
Takahiro Nakamura ◽  
Seiko Shimizu ◽  
...  
Keyword(s):  
Japanese Population ◽  
Association Studies ◽  
Meta Analysis ◽  
Elevated Serum ◽  
Common Type ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Replication Studies ◽  
Genome Wide

AbstractGout is a common type of acute arthritis that results from elevated serum uric acid (SUA) levels. Recent genome-wide association studies (GWASs) have revealed several novel single nucleotide polymorphism (SNPs) associated with SUA levels. Of these, rs10821905 of A1CF and rs1178977 of BAZ1B showed the greatest and the second greatest significant effect size for increasing SUA level in the Japanese population, but their association with gout is not clear. We examined their association with gout using 1411 clinically-defined Japanese gout patients and 1285 controls, and meta-analyzed our previous gout GWAS data to investigate any association with gout. Replication studies revealed both SNPs to be significantly associated with gout (P = 0.0366, odds ratio [OR] with 95% confidence interval [CI]: 1.30 [1.02–1.68] for rs10821905 of A1CF, P = 6.49 × 10–3, OR with 95% CI: 1.29 [1.07–1.55] for rs1178977 of BAZ1B). Meta-analysis also revealed a significant association with gout in both SNPs (Pmeta = 3.16 × 10–4, OR with 95% CI: 1.39 [1.17–1.66] for rs10821905 of A1CF, Pmeta = 7.28 × 10–5, OR with 95% CI 1.32 [1.15–1.51] for rs1178977 of BAZ1B). This study shows the first known association between SNPs of A1CF, BAZ1B and clinically-defined gout cases in Japanese. Our results also suggest a shared physiological/pathophysiological background between several populations, including Japanese, for both SUA increase and gout susceptibility. Our findings will not only assist the elucidation of the pathophysiology of gout and hyperuricemia, but also suggest new molecular targets.

scholarly journals Development of Single Nucleotide Polymorphism (SNP) Markers in Tropical Crops

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Yheni Dwiningsih ◽  
Miranti Rahmaningsih ◽  
Jawaher Alkahtani
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Plant Breeding ◽  
Association Studies ◽  
Snp Markers ◽  
Snp Marker ◽  
Marker Genes ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Tropical Crops

Understanding genetic diversity, association studies, evolution analysis, quantitative trait loci, marker-assisted selection and genome-wide association in tropical crops are important for improving plant characteristics in order to increase food sustainability in tropical countries. Single nucleotide polymorphism (SNP) marker is becoming the most popular molecular marker for those studies. By using SNP marker, genes associated with important traits can be identified efficiently compared to the other molecular markers. This review describes about how SNP can be discovered in the plant genomes and the application of SNP in plant breeding, especially in tropical crops such as rice, maize, peas, potato, tomato, cassava, taro, etc.   Keywords: food sustainability, plant breeding, SNP marker, tropical crops

scholarly journals Tumor somatic mutations also existing as germline polymorphisms may help to identify functional SNPs from genome-wide association studies

2020 ◽  
Vol 41 (10) ◽  
pp. 1353-1362
Author(s):  
Ivan P Gorlov ◽  
Xiangjun Xia ◽  
Spiridon Tsavachidis ◽  
Olga Y Gorlova ◽  
Christopher I Amos
Keyword(s):  
Cancer Risk ◽  
Somatic Mutations ◽  
Association Studies ◽  
Selective Advantage ◽  
Joint Analysis ◽  
Genome Wide Association Studies ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Evolutionarily Conserved ◽  
Tumor Somatic Mutations

Abstract We hypothesized that a joint analysis of cancer risk-associated single-nucleotide polymorphism (SNP) and somatic mutations in tumor samples can predict functional and potentially causal SNPs from GWASs. We used mutations reported in the Catalog of Somatic Mutations in Cancer (COSMIC). Confirmed somatic mutations were subdivided into two groups: (1) mutations reported as SNPs, which we call mutational/SNPs and (2) somatic mutations that are not reported as SNPs, which we call mutational/noSNPs. It is generally accepted that the number of times a somatic mutation is reported in COSMIC correlates with its selective advantage to tumors, with more frequently reported mutations being more functional and providing a stronger selective advantage to the tumor cell. We found that mutations reported ≥10 times in COSMIC—frequent mutational/SNPs (fmSNPs) are likely to be functional. We identified 12 cancer risk-associated SNPs reported in the Catalog of published GWASs at least 10 times as confirmed somatic mutations and therefore deemed to be functional. Additionally, we have identified 42 SNPs that are tightly linked (R2 ≥ 0.8) to SNPs reported in the Catalog of published GWASs as cancer risk associated and that are also reported as fmSNPs. As a result, 54 candidate functional/potentially causal cancer risk associated SNPs were identified. We found that fmSNPs are more likely to be located in evolutionarily conserved regions compared with cancer risk associated SNPs that are not fmSNPs. We also found that fmSNPs also underwent positive selection, which can explain why they exist as population polymorphisms.

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