A genome-wide association study to identify candidate genes for erectile dysfunction

2020 ◽  
Author(s):  
Elham Kazemi ◽  
Javaad Zargooshi ◽  
Marzieh Kaboudi ◽  
Parviz Heidari ◽  
Danial Kahrizi ◽  
...  
Keyword(s):  
Erectile Dysfunction ◽  
Protein Interactions ◽  
Genome Wide Association Study ◽  
Expression Profiles ◽  
Regulatory Elements ◽  
Local Alignment ◽  
Conserved Motifs ◽  
New Genes ◽  
A Genome ◽  
Ucsc Database

Abstract Erectile dysfunction (ED) can be caused by different diseases and controlled by several genetic networks. In this study, to identify the genes related to ED, the expression profiles of normal and ED samples were investigated by the Gene Expression Omnibus (GEO) database. Seventeen genes were identified as associated genes with ED. The protein and nucleic acid sequences of selected genes were retrieved from the UCSC database. Selected genes were diverse according to their physicochemical properties and functions. Category function revealed that selected genes are involved in pathways related to humans some diseases. Furthermore, based on protein interactions, genes associated with the insulin pathway had the greatest interaction with the studied genes. To identify the common cis-regulatory elements, the promoter site of the selected genes was retrieved from the UCSC database. The Gapped Local Alignment of Motifs tool was used for finding common conserved motifs into the promoter site of selected genes. Besides, INSR protein as an insulin receptor precursor showed a high potential site for posttranslation modifications, including phosphorylation and N-glycosylation. Also, in this study, two Guanine-Cytosine (GC)-rich regions were identified as conserved motifs in the upstream of studied genes which can be involved in regulating the expression of genes associated with ED. Also, the conserved binding site of miR-29-3p that is involved in various cancers was observed in the 3′ untranslated region of genes associated with ED. Our study introduced new genes associated with ED, which can be good candidates for further analyzing related to human ED.

scholarly journals Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation

2018 ◽  
Vol 4 (12) ◽  
pp. eaav8550 ◽  
Author(s):  
Suhn K. Rhie ◽  
Shannon Schreiner ◽  
Heather Witt ◽  
Chris Armoskus ◽  
Fides D. Lay ◽  
...  
Keyword(s):  
Cell Model ◽  
Expression Profiles ◽  
Neuronal Cells ◽  
Three Dimensional ◽  
Gene Expression Profiles ◽  
Regulatory Elements ◽  
A Genome ◽  
Wide Scale ◽  
Cell Model System ◽  
Distal Regulatory Elements

As part of PsychENCODE, we developed a three-dimensional (3D) epigenomic map of primary cultured neuronal cells derived from olfactory neuroepithelium (CNON). We mapped topologically associating domains and high-resolution chromatin interactions using Hi-C and identified regulatory elements using chromatin immunoprecipitation and nucleosome positioning assays. Using epigenomic datasets from biopsies of 63 living individuals, we found that epigenetic marks at distal regulatory elements are more variable than marks at proximal regulatory elements. By integrating genotype and metadata, we identified enhancers that have different levels corresponding to differences in genetic variation, gender, smoking, and schizophrenia. Motif searches revealed that many CNON enhancers are bound by neuronal-related transcription factors. Last, we combined 3D epigenomic maps and gene expression profiles to predict enhancer-target gene interactions on a genome-wide scale. This study not only provides a framework for understanding individual epigenetic variation using a primary cell model system but also contributes valuable data resources for epigenomic studies of neuronal epithelium.

A genome‐wide association study identifies new genes associated with developmental dysplasia of the hip

2019 ◽  
Vol 95 (3) ◽  
pp. 345-355 ◽  
Author(s):  
Wenjin Yan ◽  
Zheng Hao ◽  
Shuyan Tang ◽  
Jin Dai ◽  
Liming Zheng ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Developmental Dysplasia ◽  
Genome Wide Association ◽  
New Genes ◽  
Genome Wide ◽  
A Genome ◽  
Dysplasia Of The Hip

scholarly journals Prioritization of genes associated with the pathogenesis of leukosis in cattle

2019 ◽  
Vol 22 (8) ◽  
pp. 1063-1069 ◽  
Author(s):  
N. S. Yudin ◽  
N. L. Podkolodnyy ◽  
T. A. Agarkova ◽  
E. V. Ignatieva
Keyword(s):  
Protein Interactions ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Mammalian Species ◽  
Genome Wide Association ◽  
Farm Animals ◽  
Genome Wide Association Studies ◽  
Protein Protein Interactions ◽  
Genome Wide ◽  
A Genome

Selection by means of genetic markers is a promising approach to the eradication of infectious diseases in farm animals, especially in the absence of effective methods of treatment and prevention. Bovine leukemia virus (BLV) is spread throughout the world and represents one of the biggest problems for the livestock production and food security in Russia. However, recent genome-wide association studies have shown that sensitivity/resistance to BLV is polygenic. The aim of this study was to create a catalog of cattle genes and genes of other mammalian species involved in the pathogenesis of BLV-induced infection and to perform gene prioritization using bioinformatics methods. Based on manually collected information from a range of open sources, a total of 446 genes were included in the catalog of cattle genes and genes of other mammals involved in the pathogenesis of BLV-induced infection. The following criteria were used to prioritize 446 genes from the catalog: (1) the gene is associated with leukemia according to a genome-wide association study; (2) the gene is associated with leukemia according to a case-control study; (3) the role of the gene in leukemia development has been studied using knockout mice; (4) protein-protein interactions exist between the gene-encoded protein and either viral particles or individual viral proteins; (5) the gene is annotated with Gene Ontology terms that are overrepresented for a given list of genes; (6) the gene participates in biological pathways from the KEGG or REACTOME databases, which are over-represented for a given list of genes; (7) the protein encoded by the gene has a high number of protein-protein interactions with proteins encoded by other genes from the catalog. Based on each criterion, a rank was assigned to each gene. Then the ranks were summarized and an overall rank was determined. Prioritization of 446 candidate genes allowed us to identify 5 genes of interest (TNF,LTB,BOLA-DQA1,BOLA-DRB3,ATF2), which can affect the sensitivity/resistance of cattle to leukemia.

Linkage mapping and genome-wide association reveal candidate genes conferring thermotolerance of seed-set in maize

2019 ◽  
Vol 70 (18) ◽  
pp. 4849-4864 ◽  
Author(s):  
Jingyang Gao ◽  
Songfeng Wang ◽  
Zijian Zhou ◽  
Shiwei Wang ◽  
Chaopei Dong ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Linkage Mapping ◽  
Genome Wide Association Study ◽  
Seed Set ◽  
Crop Yields ◽  
Expression Profiles ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

AbstractIt is predicted that high-temperature stress will increasingly affect crop yields worldwide as a result of climate change. In order to determine the genetic basis of thermotolerance of seed-set in maize under field conditions, we performed mapping of quantitative trait loci (QTLs) in a recombinant inbred line (RIL) population using a collection of 8329 specifically developed high-density single-nucleotide polymorphism (SNP) markers, combined with a genome-wide association study (GWAS) of 261 diverse maize lines using 259 973 SNPs. In total, four QTLs and 17 genes associated with 42 SNPs related to thermotolerance of seed-set were identified. Among them, four candidate genes were found in both linkage mapping and GWAS. Thermotolerance of seed-set was increased significantly in near-isogenic lines (NILs) that incorporated the four candidate genes in a susceptible parent background. The expression profiles of two of the four genes showed that they were induced by high temperatures in the maize tassel in a tolerant parent background. Our results indicate that thermotolerance of maize seed-set is regulated by multiple genes each of which has minor effects, with calcium signaling playing a central role. The genes identified may be exploited in breeding programs to improve seed-set and yield of maize under heat stress.

scholarly journals Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jianping Yu ◽  
Chaolei Liu ◽  
Hai Lin ◽  
Bin Zhang ◽  
Xiaoxia Li ◽  
...  
Keyword(s):  
Association Study ◽  
Transcriptome Analysis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Growth Responses ◽  
Cd Stress ◽  
New Genes ◽  
Genome Wide ◽  
A Genome ◽  
Natural Variations

Abstract Background Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity. Results In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs. Conclusion The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

scholarly journals Mining for Candidate Genes Controlling Secondary Growth of the Carrot Storage Root

2020 ◽  
Vol 21 (12) ◽  
pp. 4263
Author(s):  
Alicja Macko-Podgórni ◽  
Katarzyna Stelmach ◽  
Kornelia Kwolek ◽  
Gabriela Machaj ◽  
Shelby Ellison ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Expression Profiles ◽  
Secondary Growth ◽  
Chromosome 1 ◽  
Phenotypic Variance ◽  
Storage Root ◽  
A Genome ◽  
Elevated Expression ◽  
Edible Roots ◽  
Diverse Groups

Background: Diverse groups of carrot cultivars have been developed to meet consumer demands and industry needs. Varietal groups of the cultivated carrot are defined based on the shape of roots. However, little is known about the genetic basis of root shape determination. Methods: Here, we used 307 carrot plants from 103 open-pollinated cultivars for a genome wide association study to identify genomic regions associated with the storage root morphology. Results: A 180 kb-long region on carrot chromosome 1 explained 10% of the total observed phenotypic variance in the shoulder diameter. Within that region, DcDCAF1 and DcBTAF1 genes were proposed as candidates controlling secondary growth of the carrot storage root. Their expression profiles differed between the cultivated and the wild carrots, likely indicating that their elevated expression was required for the development of edible roots. They also showed higher expression at the secondary root growth stage in cultivars producing thick roots, as compared to those developing thin roots. Conclusions: We provided evidence for a likely involvement of DcDCAF1 and/or DcBTAF1 in the development of the carrot storage root and developed a genotyping assay facilitating the identification of variants in the region on carrot chromosome 1 associated with secondary growth of the carrot root.

scholarly journals The identification of 14 new genes for meat quality traits in chicken using a genome-wide association study

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 458 ◽  
Author(s):  
Yanfa Sun ◽  
Guiping Zhao ◽  
Ranran Liu ◽  
Maiqing Zheng ◽  
Yaodong Hu ◽  
...  
Keyword(s):  
Association Study ◽  
Meat Quality ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Quality Traits ◽  
Meat Quality Traits ◽  
New Genes ◽  
Genome Wide ◽  
A Genome
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