scholarly journals Exploring the genetic basis of chronic periodontitis: a genome-wide association study

2013 ◽  
Vol 22 (11) ◽  
pp. 2312-2324 ◽  
Author(s):  
K. Divaris ◽  
K. L. Monda ◽  
K. E. North ◽  
A. F. Olshan ◽  
L. M. Reynolds ◽  
...  
Keyword(s):  
Association Study ◽  
Chronic Periodontitis ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-Wide Association Study Reveals the Genetic Basis of Chilling Tolerance in Rice at the Reproductive Stage

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1722
Author(s):  
Byeong Yong Jeong ◽  
Yoonjung Lee ◽  
Yebin Kwon ◽  
Jee Hye Kim ◽  
Tae-Ho Ham ◽  
...  
Keyword(s):  
Association Study ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Linkage Disequilibrium Block ◽  
Chilling Tolerance ◽  
Reproductive Stage ◽  
Genome Wide Association ◽  
Matrix Analysis ◽  
Genome Wide ◽  
A Genome

A genome-wide association study (GWAS) was used to investigate the genetic basis of chilling tolerance in a collection of 117 rice accessions, including 26 Korean landraces and 29 weedy rices, at the reproductive stage. To assess chilling tolerance at the early young microspore stage, plants were treated at 12 °C for 5 days, and tolerance was evaluated using seed set fertility. GWAS, together with principal component analysis and kinship matrix analysis, revealed five quantitative trait loci (QTLs) associated with chilling tolerance on chromosomes 3, 6, and 7. The percentage of phenotypic variation explained by the QTLs was 11–19%. The genomic region underlying the QTL on chromosome 3 overlapped with a previously reported QTL associated with spikelet fertility. Subsequent bioinformatic and haplotype analyses suggested three candidate chilling-tolerance genes within the QTL linkage disequilibrium block: Os03g0305700, encoding a protein similar to peptide chain release factor 2; Os06g0495700, encoding a beta tubulin, autoregulation binding-site-domain-containing protein; and Os07g0137800, encoding a protein kinase, core-domain-containing protein. Further analysis of the detected QTLs and the candidate chilling-tolerance genes will facilitate strategies for developing chilling-tolerant rice cultivars in breeding programs.

scholarly journals Genome-Wide Association Study of H/L Traits in Chicken

Animals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 260 ◽  
Author(s):  
Bo Zhu ◽  
Qinghe Li ◽  
Ranran Liu ◽  
Maiqing Zheng ◽  
Jie Wen ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Genetic Basis ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Immune Defense ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

Presently, the heterophil-to-lymphocyte (H/L) ratio is being studied extensively as a disease resistance trait. Through intricate mechanisms to identify and destroy pathogenic microorganisms, heterophils play a pivotal role in the immune defense systems of avian species. To reveal the genetic basis and molecular mechanisms affecting the H/L ratio, phenotypic and H/L data from 1650 white feather chicken broilers were used in performing a genome-wide association study. A self-developed, chicken-specific 55K chip was used for heterophils, lymphocytes, and H/L classification, according to individual genomic DNA profiles. We identified five significant single nucleotide polymorphisms (SNPs) when the genome-wide significance threshold was set to 5% (p < 2.42 × 10−6). A total of 15 SNPs obtained seemingly significant levels (p < 4.84 × 10−5). Gene annotation indicated that CARD11 (Caspase recruitment domain family member 11), BRIX1 (Biogenesis of ribosomes BRX1), and BANP (BTG3 associated nuclear protein) play a role in H/L-associated cell regulation and potentially constitute candidate gene regions for cellular functions dependent on H/L ratios. These results lay the foundation for revealing the genetic basis of disease resistance and future marker-assisted selection for disease resistance.

scholarly journals Heritability and molecular genetic basis of antisaccade eye tracking error rate: A genome-wide association study

2014 ◽  
Vol 51 (12) ◽  
pp. 1272-1284 ◽  
Author(s):  
Uma Vaidyanathan ◽  
Stephen M. Malone ◽  
Jennifer M. Donnelly ◽  
Micah A. Hammer ◽  
Michael B. Miller ◽  
...  
Keyword(s):  
Association Study ◽  
Error Rate ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Molecular Genetic ◽  
Tracking Error ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Molecular Genetic Basis ◽  
A Genome

scholarly journals Genetics of fasting and postprandial metabolite levels are overlapping

2018 ◽  
Vol 50 (4) ◽  
pp. 235-236
Author(s):  
Ruifang Li-Gao ◽  
Renée de Mutsert ◽  
Frits R. Rosendaal ◽  
Ko Willems van Dijk ◽  
Dennis O. Mook-Kanamori
Keyword(s):  
Association Study ◽  
Human Body ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genetic Associations ◽  
Mixed Meal ◽  
Genome Wide ◽  
A Genome ◽  
Metabolite Concentrations

In 2015, a genome-wide association study described 59 independent signals that showed strong associations with 85 fasting metabolite concentrations as measured by the Biocrates AbsoluteIDQ p150 kit. However, the human body resides in a nonfasting state for the greater part of the day, and the genetic basis of postprandial metabolite concentrations remains largely unknown. We systematically examined these previously identified genetic associations in postprandial metabolite concentrations after a mixed meal. Of these 85 metabolites, 23 were identified with significant changes after the meal, for which 38 gene-metabolite associations were analyzed. Of these 38 associations, 31 gene-metabolite associations were replicated with postprandial metabolite concentrations. These data indicate that the genetics of fasting and postprandial metabolite levels are significantly overlapping.

scholarly journals Heritability and molecular-genetic basis of resting EEG activity: A genome-wide association study

2014 ◽  
Vol 51 (12) ◽  
pp. 1225-1245 ◽  
Author(s):  
Stephen M. Malone ◽  
Scott J. Burwell ◽  
Uma Vaidyanathan ◽  
Michael B. Miller ◽  
Matt MCGUE ◽  
...  
Keyword(s):  
Association Study ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Molecular Genetic ◽  
Genome Wide Association ◽  
Eeg Activity ◽  
Genome Wide ◽  
Molecular Genetic Basis ◽  
A Genome

scholarly journals High-resolution genome-wide association study pinpoints metal transporter and chelator genes involved in the genetic control of element levels in maize grain

2021 ◽  
Vol 11 (4) ◽  
Author(s):  
Di Wu ◽  
Ryokei Tanaka ◽  
Xiaowei Li ◽  
Guillaume P Ramstein ◽  
Suong Cu ◽  
...  
Keyword(s):  
Association Study ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Prediction Models ◽  
Genome Wide Association ◽  
Metal Transporter ◽  
Metal Chelator ◽  
Genome Wide ◽  
A Genome ◽  
Maize Grain

AbstractDespite its importance to plant function and human health, the genetics underpinning element levels in maize grain remain largely unknown. Through a genome-wide association study in the maize Ames panel of nearly 2,000 inbred lines that was imputed with ∼7.7 million SNP markers, we investigated the genetic basis of natural variation for the concentration of 11 elements in grain. Novel associations were detected for the metal transporter genes rte2 (rotten ear2) and irt1 (iron-regulated transporter1) with boron and nickel, respectively. We also further resolved loci that were previously found to be associated with one or more of five elements (copper, iron, manganese, molybdenum, and/or zinc), with two metal chelator and five metal transporter candidate causal genes identified. The nas5 (nicotianamine synthase5) gene involved in the synthesis of nicotianamine, a metal chelator, was found associated with both zinc and iron and suggests a common genetic basis controlling the accumulation of these two metals in the grain. Furthermore, moderate predictive abilities were obtained for the 11 elemental grain phenotypes with two whole-genome prediction models: Bayesian Ridge Regression (0.33–0.51) and BayesB (0.33–0.53). Of the two models, BayesB, with its greater emphasis on large-effect loci, showed ∼4–10% higher predictive abilities for nickel, molybdenum, and copper. Altogether, our findings contribute to an improved genotype-phenotype map for grain element accumulation in maize.

scholarly journals Genome-wide association study reveals sex-specific genetic architecture of facial attractiveness

2018 ◽  
Author(s):  
Bowen Hu ◽  
Ning Shen ◽  
James J. Li ◽  
Hyunseung Kang ◽  
Jinkuk Hong ◽  
...  
Keyword(s):  
Association Study ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genetic Correlations ◽  
Facial Attractiveness ◽  
Genome Wide Association ◽  
Hormone Synthesis ◽  
Genome Wide ◽  
A Genome

AbstractFacial attractiveness is a complex human trait of great interest in both academia and industry. Literature on sociological and phenotypic factors associated with facial attractiveness is rich, but its genetic basis is poorly understood. In this paper, we conducted a genome-wide association study to discover genetic variants associated with facial attractiveness using 3,928 samples in the Wisconsin Longitudinal Study. We identified two genome-wide significant loci and highlighted a handful of candidate genes, many of which are specifically expressed in human tissues involved in reproduction and hormone synthesis. Additionally, facial attractiveness showed strong and negative genetic correlations with BMI in females and with blood lipids in males. Our analysis also suggested sex-specific selection pressure on variants associated with lower male attractiveness. These results revealed sex-specific genetic architecture of facial attractiveness and provided fundamental new insights into its genetic basis.

scholarly journals A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola

2020 ◽  
Author(s):  
Alkesh Hada ◽  
Tushar K. Dutta ◽  
Nisha Singh ◽  
Vandna Rai ◽  
Nagendra K. Singh ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Wild Rice ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Root Knot Nematode ◽  
Meloidogyne Graminicola ◽  
Genome Wide ◽  
A Genome

Abstract Background: Rice root-knot nematode (RRKN), Meloidogyne graminicola is one of the major biotic constraints in rice-growing countries of Southeast Asia. Host plant resistance is an environmentally-friendly and cost-effective mean to mitigate RRKN damage to rice. Considering the limited availability of genetic resources in the Asian rice (Oryza sativa) cultivars, exploration of novel sources and genetic basis of RRKN resistance is necessary. Results: We screened 272 diverse wild rice accessions (O. nivara, O. rufipogon, O. sativa f. spontanea) to identify genotypes resistant to RRKN. We dissected the genetic basis of RRKN resistance using a genome-wide association study with SNPs (single nucleotide polymorphism) genotyped by 50K “OsSNPnks” genic Affymetrix chip. Population structure analysis revealed that these accessions were stratified into three major sub-populations. Overall, 40 resistant accessions (nematode gall number and multiplication factor/MF < 2) were identified, with 17 novel SNPs being significantly associated with phenotypic traits such as number of galls, egg masses, eggs/egg mass and MF per plant. SNPs were localized to the quantitative trait loci (QTL) on chromosome 1, 2, 3, 4, 6, 10 and 11 harboring the candidate genes including NBS-LRR, Cf2/Cf5 resistance protein, MYB, bZIP, ARF, SCARECROW and WRKY transcription factors. Expression of these identified genes was significantly (P < 0.01) upregulated in RRKN-infected plants compared to mock-inoculated plants at 7 days after inoculation. Conclusion: The identified SNPs enrich the repository of candidate genes for future marker-assisted breeding program to alleviate the damage of RRKN in rice.

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