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Expression quantitative trait loci

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https://www.readbyqxmd.com/read/29775500/endosperm-sugar-accumulation-caused-by-mutation-of-phs8-isa1-leads-to-pre-harvest-sprouting-in-rice
#1
Lin Du, Fan Xu, Jun Fang, Shaopei Gao, Jiuyou Tang, Shuang Fang, Hongru Wang, Hongning Tong, Fengxia Zhang, Jinfang Chu, Guodong Wang, Chengcai Chu
Pre-harvest sprouting (PHS) is an unfavorable trait in cereal crops which could seriously decrease grain yield and quality. Although some PHS-associated quantitative trait loci (QTL) or genes in cereals have been reported, the molecular mechanism underlying PHS remains largely elusive. Here, we characterized a rice mutant, phs8, which exhibits PHS phenotype accompanied by sugary endosperm. Map-based cloning revealed that PHS8 encodes a starch debranching enzyme named isoamylase1. Mutation in PHS8 resulted in the phytoglycogen breakdown and sugar accumulation in the endosperm...
May 18, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29774565/local-and-systemic-regulation-of-psii-efficiency-in-triticale-infected-by-the-hemibiotrophic-pathogen-microdochium-nivale
#2
Mateusz Dyda, Iwona Wąsek, Mirosław Tyrka, Maria Wędzony, Magdalena Szechyńska-Hebda
Microdochium nivale is a fungal pathogen that causes yield losses of cereals during winter. Cold hardening under light conditions induces genotype-dependent resistance of a plant to infection. We aim to show how photosystem II (PSII) regulation contributes to plant resistance. Using mapping population of triticale doubled haploid lines, three M. nivale strains and different infection assays, we demonstrate that plants that maintain a higher maximum quantum efficiency of PSII show less leaf damage upon infection...
May 17, 2018: Physiologia Plantarum
https://www.readbyqxmd.com/read/29766219/association-study-of-genetic-variants-in-estrogen-metabolic-pathway-genes-and-colorectal-cancer-risk-and-survival
#3
Shuwei Li, Lisheng Xie, Mulong Du, Kaili Xu, Lingjun Zhu, Haiyan Chu, Jinfei Chen, Meilin Wang, Zhengdong Zhang, Dongying Gu
Although studies have investigated the association of genetic variants and the abnormal expression of estrogen-related genes with colorectal cancer risk, the evidence remains inconsistent. We clarified the relationship of genetic variants in estrogen metabolic pathway genes with colorectal cancer risk and survival. A case-control study was performed to assess the association of single-nucleotide polymorphisms (SNPs) in ten candidate genes with colorectal cancer risk in a Chinese population. A logistic regression model and Cox regression model were used to calculate SNP effects on colorectal cancer susceptibility and survival, respectively...
May 16, 2018: Archives of Toxicology
https://www.readbyqxmd.com/read/29763751/integration-of-summary-data-from-gwas-and-eqtl-studies-identified-novel-causal-bmd-genes-with-functional-predictions
#4
Xiang-He Meng, Xiang-Ding Chen, Jonathan Greenbaum, Qin Zeng, Sheng-Lan You, Hong-Mei Xiao, Li-Jun Tan, Hong-Wen Deng
PURPOSE: Osteoporosis is a common global health problem characterized by low bone mineral density (BMD) and increased risk of fracture. Genome-wide association studies (GWAS) have identified >100 genetic loci associated with BMD. However, the functional genes responsible for most associations remain largely unknown. We conducted an innovative summary statistic data-based Mendelian randomization (SMR) analysis to identify novel causal genes associated with BMD and explored their potential functional significance...
May 12, 2018: Bone
https://www.readbyqxmd.com/read/29761461/bovine-genome-database-tools-for-mining-the-bos-taurus-genome
#5
Darren E Hagen, Deepak R Unni, Aditi Tayal, Gregory W Burns, Christine G Elsik
The Bovine Genome Database (BGD; http://bovinegenome.org ) is a web-accessible resource that supports bovine genomics research by providing genome annotation and data mining tools. BovineMine is a tool within BGD that integrates BGD data, including the genome, genes, precomputed gene expression levels and variant consequences, with external data sources that include quantitative trait loci (QTL), orthologues, Gene Ontology, gene interactions, and pathways. BovineMine enables researchers without programming skills to create custom integrated datasets for use in downstream analyses...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29745274/relationship-of-the-interaction-between-two-quantitative-trait-loci-with-%C3%AE-globin-expression-in-%C3%AE-thalassemia-intermedia-patients
#6
Shiva NickAria, Sezaneh Haghpanah, Mani Ramzi, Mehran Karimi
Globin switching is a significant factor on blood hemoglobin (Hb) level but its molecular mechanisms have not yet been identified, however, several quantitative trait loci (QTL) and polymorphisms involved regions on chromosomes 2p, 6q, 8q and X account for variation in the γ-globin expression level. We studied the effect of interaction between a region on intron six of the TOX gene, chromosome 8q (chr8q) and XmnI locus on the γ-globin promoter, chr11p on γ-globin expression in 150 β-thalassemia intermedia (β-TI) patients, evaluated by statistical interaction analysis...
May 10, 2018: Hemoglobin
https://www.readbyqxmd.com/read/29741584/translating-gwas-in-rheumatic-disease-approaches-to-establishing-mechanism-and-function-for-genetic-associations-with-ankylosing-spondylitis
#7
Julie A Osgood, Julian C Knight
Ankylosing spondylitis (AS) is a highly heritable chronic inflammatory arthritis characterized by osteoproliferation, fusion of affected joints and systemic manifestations. Many disease associations for AS have been reported through genome-wide association studies; however, identifying modulated genes and functional mechanism remains challenging. This review summarizes current genetic associations involving AS and describes strategic approaches for functional follow-up of disease-associated variants. Fine mapping using methods leveraging Bayesian approaches are outlined...
May 5, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29736028/pm20d1-is-a-quantitative-trait-locus-associated-with-alzheimer-s-disease
#8
Jose V Sanchez-Mut, Holger Heyn, Bianca A Silva, Lucie Dixsaut, Paula Garcia-Esparcia, Enrique Vidal, Sergi Sayols, Liliane Glauser, Ana Monteagudo-Sánchez, Jordi Perez-Tur, Isidre Ferrer, David Monk, Bernard Schneider, Manel Esteller, Johannes Gräff
The chances to develop Alzheimer's disease (AD) result from a combination of genetic and non-genetic risk factors 1 , the latter likely being mediated by epigenetic mechanisms 2 . In the past, genome-wide association studies (GWAS) have identified an important number of risk loci associated with AD pathology 3 , but a causal relationship remains difficult to establish. In contrast, locus-specific or epigenome-wide association studies (EWAS) have revealed site-specific epigenetic alterations, which provide mechanistic insights for a particular risk gene but often lack the statistical power of GWAS 4 ...
May 7, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29727689/a-comprehensive-cis-eqtl-analysis-revealed-target-genes-in-breast-cancer-susceptibility-loci-identified-in-genome-wide-association-studies
#9
Xingyi Guo, Weiqiang Lin, Jiandong Bao, Qiuyin Cai, Xiao Pan, Mengqiu Bai, Yuan Yuan, Jiajun Shi, Yaqiong Sun, Mi-Ryung Han, Jing Wang, Qi Liu, Wanqing Wen, Bingshan Li, Jirong Long, Jianghua Chen, Wei Zheng
Genome-wide association studies (GWASs) have identified more than 150 common genetic loci for breast cancer risk. However, the target genes and underlying mechanisms remain largely unknown. We conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using normal or tumor breast transcriptome data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), The Cancer Genome Atlas (TCGA), and the Genotype-Tissue Expression (GTEx) project. We identified a total of 101 genes for 51 lead variants after combing the results of a meta-analysis of METABRIC and TCGA, and the results from GTEx at a Benjamini-Hochberg (BH)-adjusted p < 0...
May 3, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29725340/genome-wide-association-study-of-cadmium-accumulation-at-the-seedling-stage-in-rapeseed-brassica-napus-l
#10
Lunlin Chen, Heping Wan, Jiali Qian, Jianbin Guo, Chengming Sun, Jing Wen, Bin Yi, Chaozhi Ma, Jinxing Tu, Laiqiang Song, Tingdong Fu, Jinxiong Shen
Cadmium is a potentially toxic heavy metal to human health. Rapeseed ( Brassica napus L.), a vegetable and oilseed crop, might also be a Cd hyperaccumulator, but there is little information on this trait in rapeseed. We evaluated Cd accumulation in different oilseed accessions and employed a genome-wide association study to identify quantitative trait loci (QTLs) related to Cd accumulation. A total of 419 B. napus accessions and inbred lines were genotyped with a 60K Illumina Infinium SNP array of Brassica...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29718103/a-powerful-approach-reveals-numerous-expression-quantitative-trait-haplotypes-in-multiple-tissues
#11
Dingge Ying, Mulin Jun Li, Pak Chung Sham, Miaoxin Li
Motivation: Recently many studies showed single nucleotide polymorphisms (SNPs) affect gene expression and contribute to development of complex traits/diseases in a tissue context-dependent manner. However, little is known about haplotype's influence on gene expression and complex traits, which reflects the interaction effect between SNPs. Results: In the present study, we firstly proposed a regulatory region guided eQTL haplotype association analysis approach, and then systematically investigate the expression quantitative trait loci (eQTL) haplotypes in 20 different tissues by the approach...
April 26, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29706980/a-rad-based-genetic-map-for-anchoring-scaffold-sequences-and-identifying-qtls-in-bitter-gourd-momordica-charantia
#12
Junjie Cui, Shaobo Luo, Yu Niu, Rukui Huang, Qingfang Wen, Jianwen Su, Nansheng Miao, Weiming He, Zhensheng Dong, Jiaowen Cheng, Kailin Hu
Genetic mapping is a basic tool necessary for anchoring assembled scaffold sequences and for identifying QTLs controlling important traits. Though bitter gourd ( Momordica charantia ) is both consumed and used as a medicinal, research on its genomics and genetic mapping is severely limited. Here, we report the construction of a restriction site associated DNA (RAD)-based genetic map for bitter gourd using an F2 mapping population comprising 423 individuals derived from two cultivated inbred lines, the gynoecious line 'K44' and the monoecious line 'Dali-11...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29703961/genetic-variants-in-chemokine-cc-subfamily-genes-influence-hepatitis-c-virus-viral-clearance
#13
Yinan Yao, Ming Yue, Feng Zang, Mei Liu, Haozhi Fan, Lingyun Zhuo, Jingjing Wu, Xueshan Xia, Yue Feng, Peng Huang, Rongbin Yu
Chemokine genes may influence both hepatitis C virus (HCV) spontaneous clearance in acute infection and treatment response in chronic infection. We conducted this study to evaluate whether the genetic variants in several CC family genes influence HCV spontaneous clearance and treatment response. The current research genotyped eight SNPs, including CCR1 rs3733096, rs13096371, CCR5 rs746492, rs1800874, CCL3 rs1130371, CCL5 rs3817656, CCL8 rs1133763, CCL14 rs854625, to explore their associations with HCV spontaneous clearance and response to treatment in two populations...
April 27, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29703947/human-brain-arousal-in-the-resting-state-a-genome-wide-association-study
#14
Philippe Jawinski, Holger Kirsten, Christian Sander, Janek Spada, Christine Ulke, Jue Huang, Ralph Burkhardt, Markus Scholz, Tilman Hensch, Ulrich Hegerl
Arousal affects cognition, emotion, and behavior and has been implicated in the etiology of psychiatric disorders. Although environmental conditions substantially contribute to the level of arousal, stable interindividual characteristics are well-established and a genetic basis has been suggested. Here we investigated the molecular genetics of brain arousal in the resting state by conducting a genome-wide association study (GWAS). We selected N = 1877 participants from the population-based LIFE-Adult cohort...
April 27, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29703142/identification-of-new-loci-involved-in-the-host-susceptibility-to-salmonella-typhimurium-in-collaborative-cross-mice
#15
Jing Zhang, Danielle Malo, Richard Mott, Jean-Jacques Panthier, Xavier Montagutelli, Jean Jaubert
BACKGROUND: Salmonella is a Gram-negative bacterium causing a wide range of clinical syndromes ranging from typhoid fever to diarrheic disease. Non-typhoidal Salmonella (NTS) serovars infect humans and animals, causing important health burden in the world. Susceptibility to salmonellosis varies between individuals under the control of host genes, as demonstrated by the identification of over 20 genetic loci in various mouse crosses. We have investigated the host response to S. Typhimurium infection in 35 Collaborative Cross (CC) strains, a genetic population which involves wild-derived strains that had not been previously assessed...
April 27, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29700068/advances-in-transcriptomics-investigating-cardiovascular-disease-at-unprecedented-resolution
#16
REVIEW
Robert C Wirka, Milos Pjanic, Thomas Quertermous
Whole-genome transcriptional profiling has become a standard genomic approach to investigate biological processes. RNA sequencing (RNAseq) in particular has witnessed myriad applications in genetics and various biomedical fields. RNAseq involves a relatively simple experimental protocol of RNA extraction and cDNA library preparation and, because of decreasing next-generation sequencing cost and lower computational burden for data processing, has obtained a central role in the modern biology. The recent application of RNAseq methodology to single-cell transcriptional profiling has enabled the more precise characterization of cell lineage and cell state genetic profiles...
April 27, 2018: Circulation Research
https://www.readbyqxmd.com/read/29679097/quantitative-trait-loci-qtls-for-water-use-and-crop-production-traits-co-locate-with-major-qtl-for-tolerance-to-water-deficit-in-a-fine-mapping-population-of-pearl-millet-pennisetum-glaucum-l-r-br
#17
Murugesan Tharanya, Jana Kholova, Kaliamoorthy Sivasakthi, Deepmala Seghal, Charles Tom Hash, Basker Raj, Rakesh Kumar Srivastava, Rekha Baddam, Thiyagarajan Thirunalasundari, Rattan Yadav, Vincent Vadez
Four genetic regions associated with water use traits, measured at different levels of plant organization, and with agronomic traits were identified within a previously reported region for terminal water deficit adaptation on linkage group 2. Close linkages between these traits showed the value of phenotyping both for agronomic and secondary traits to better understand plant productive processes. Water saving traits are critical for water stress adaptation of pearl millet, whereas maximizing water use is key to the absence of stress...
April 21, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29672513/rna-seq-reveals-differentially-expressed-genes-affecting-polyunsaturated-fatty-acids-percentage-in-the-huangshan-black-chicken-population
#18
Shaohua Yang, Ying Wang, Lulu Wang, Zhaoyuan Shi, Xiaoqian Ou, Dan Wu, Xinmiao Zhang, Hao Hu, Jia Yuan, Wei Wang, Fuhu Cao, Guoqing Liu
Fatty acids metabolic products determine meat quality in chickens. Identifying genes associated with fatty acids composition could provide valuable information for the complex genetic networks of genes with underlying variations in fatty acids synthesis. RNA sequencing (RNA-Seq) was conducted to explore the chicken transcriptome from the thigh muscle tissue of 6 Huangshan Black Chickens with 3 extremely high and low phenotypic values for percentage of polyunsaturated fatty acids (PUFAs). In total, we obtained 41,139,108-44,901,729 uniquely mapped reads, which covered 74...
2018: PloS One
https://www.readbyqxmd.com/read/29670885/integrative-bioinformatics-approaches-for-identification-of-drug-targets-in-hypertension
#19
Daiane Hemerich, Jessica van Setten, Vinicius Tragante, Folkert W Asselbergs
High blood pressure or hypertension is an established risk factor for a myriad of cardiovascular diseases. Genome-wide association studies have successfully found over nine hundred loci that contribute to blood pressure. However, the mechanisms through which these loci contribute to disease are still relatively undetermined as less than 10% of hypertension-associated variants are located in coding regions. Phenotypic cell-type specificity analyses and expression quantitative trait loci show predominant vascular and cardiac tissue involvement for blood pressure-associated variants...
2018: Frontiers in Cardiovascular Medicine
https://www.readbyqxmd.com/read/29669022/dna-mediated-dimerization-on-a-compact-sequence-signature-controls-enhancer-engagement-and-regulation-by-foxa1
#20
Xuecong Wang, Yogesh Srivastava, Aleksander Jankowski, Vikas Malik, Yuanjie Wei, Ricardo C H Del Rosario, Vlad Cojocaru, Shyam Prabhakar, Ralf Jauch
FOXA1 is a transcription factor capable to bind silenced chromatin to direct context-dependent cell fate conversion. Here, we demonstrate that a compact palindromic DNA element (termed 'DIV' for its diverging half-sites) induces the homodimerization of FOXA1 with strongly positive cooperativity. Alternative structural models are consistent with either an indirect DNA-mediated cooperativity or a direct protein-protein interaction. The cooperative homodimer formation is strictly constrained by precise half-site spacing...
April 14, 2018: Nucleic Acids Research
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