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https://www.readbyqxmd.com/read/28095416/meta-gwas-accuracy-and-power-metagap-calculator-shows-that-hiding-heritability-is-partially-due-to-imperfect-genetic-correlations-across-studies
#1
Ronald de Vlaming, Aysu Okbay, Cornelius A Rietveld, Magnus Johannesson, Patrik K E Magnusson, André G Uitterlinden, Frank J A van Rooij, Albert Hofman, Patrick J F Groenen, A Roy Thurik, Philipp D Koellinger
Large-scale genome-wide association results are typically obtained from a fixed-effects meta-analysis of GWAS summary statistics from multiple studies spanning different regions and/or time periods. This approach averages the estimated effects of genetic variants across studies. In case genetic effects are heterogeneous across studies, the statistical power of a GWAS and the predictive accuracy of polygenic scores are attenuated, contributing to the so-called 'missing heritability'. Here, we describe the online Meta-GWAS Accuracy and Power (MetaGAP) calculator (available at www...
January 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28056267/-association-between-eye-absent-homolog-4-gene-polymorphisms-and-occupational-noise-induced-hearing-loss
#2
Q Y Yang, X R Xu, J Jiao, Y X Zheng, L H He, S F Yu, G Z Gu, G S Chen, W H Zhou, H Wu, Y H Li, H L Zhang, Z R Zhang
Objective: To identify the association between genetic polymorphisms in the eye absent homolog 4 (EYA4) gene and noise-induced hearing loss (NIHL). Method: A nested case control study was conducted based on a cohort of noise-exposed subjects. In total, 292 cases were selected from a steel factory from 6 297 subjects during Jan 1, 2006 to Dec 12, 2015,who had an average hearing threshold of more than 40 dB(A); 584 matched control subjects for each case were designated on the basis of matched criteria including same gender, age (±5 years) and duration of exposure to noise (±2 years)...
January 6, 2017: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
https://www.readbyqxmd.com/read/28056266/-association-between-variations-in-protocadherin-15-gene-and-occupational-noise-induced-hearing-loss
#3
X R Xu, Q Y Yang, J Jiao, Y X Zheng, L H He, S F Yu, G Z Gu, G S Chen, W H Zhou, H Wu, Y H Li, H L Zhang, Z R Zhang
Objective: The aim of this study was to investigate whether genetic variability in the protocadherin 15 (PCDH15) gene may correspond with increased susceptibility to noise-induced hearing loss (NIHL) in a Chinese population. Methods: A nested case-control study was performed that followed a cohort of 7 445 noise-exposed workers in a steel factory of Henan province in China from January 1, 2006 to December 31, 2015. In this study, 394 cases who had an average hearing threshold of more than 40 dB (A) in high frequency were defined as the case group, and 721 controls who had an average hearing threshold of less than 35 dB (A) in high frequency and less than 25 dB (A) in speech frequency were defined as the control group...
January 6, 2017: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
https://www.readbyqxmd.com/read/28055148/genome-wide-association-study-for-13-agronomic-traits-reveals-distribution-of-superior-alleles-in-bread-wheat-from-the-yellow-and-huai-valley-of-china
#4
Congwei Sun, Fuyan Zhang, Xuefang Yan, Xiangfen Zhang, Zhongdong Dong, Dangqun Cui, Feng Chen
Bread wheat is a leading cereal crop worldwide. Limited amount of superior allele loci restricted the progress of molecular improvement in wheat breeding. Here we revealed new allelic variation distribution for 13 yield-related traits in series of genome-wide association studies (GWAS) using the Wheat 90K genotyping assay, characterized in 163 bread wheat cultivars. Agronomic traits were investigated in 14 environments at three locations over three years. After filtering SNP datasets, GWAS using 20,689 high-quality SNPs associated 1,769 significant loci that explained, on average, ~20% of the phenotypic variation, both detected already reported loci and new promising genomic regions...
January 5, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28028632/the-rs3736228-polymorphism-in-the-lrp5-gene-is-associated-with-calcaneal-ultrasound-parameter-but-not-with-body-composition-in-a-cohort-of-young-caucasian-adults
#5
María Correa-Rodríguez, Jacqueline Schmidt-RioValle, Blanca Rueda-Medina
The aim of the present study was to investigate the possible influence of low-density lipoprotein receptor-related protein 5 (LRP5) and sclerostin (SOST) genes as genetic factors contributing to calcaneal quantitative ultrasound (QUS) and body composition variables in a population of young Caucasian adults. The study population comprised a total of 575 individuals (mean age 20.41years; SD 2.36) whose bone mass was assessed through QUS to determine broadband ultrasound attenuation (BUA, dB/MHz). Body composition measurements were performed using a body composition analyser...
December 27, 2016: Journal of Bone and Mineral Metabolism
https://www.readbyqxmd.com/read/28008729/parental-and-child-genetic-contributions-to-obesity-traits-in-early-life-based-on-83-loci-validated-in-adults-the-family-study
#6
A Li, S Robiou-du-Pont, S S Anand, K M Morrison, S D McDonald, S A Atkinson, K K Teo, D Meyre
BACKGROUND: The genetic influence on child obesity has not been fully elucidated. OBJECTIVE: This study investigated the parental and child contributions of 83 adult body mass index (BMI)-associated single-nucleotide polymorphisms (SNPs) to obesity-related traits in children from birth to 5 years old. METHODS: A total of 1402 individuals were genotyped for 83 SNPs. An unweighted genetic risk score (GRS) was generated by the sum of BMI-increasing alleles...
December 23, 2016: Pediatric Obesity
https://www.readbyqxmd.com/read/27997600/exploring-identity-by-descent-segments-and-putative-functions-using-different-foundation-parents-in-maize
#7
Xun Wu, Yongxiang Li, Junjie Fu, Xin Li, Chunhui Li, Dengfeng Zhang, Yunsu Shi, Yanchun Song, Yu Li, Tianyu Wang
Maize foundation parents (FPs) play no-alternative roles in hybrid breeding because they were widely used in the development of new lines and hybrids. The combination of different identity-by-descent (IBD) segments and genes could account for the formation patterns of different FPs, and knowledge of these IBD regions would provide an extensive foundation for the development of new candidate FP lines in future maize breeding. In this paper, a panel of 304 elite lines derived from FPs, i.e., B73, 207, Mo17, and Huangzaosi (HZS), was collected and analyzed using 43,252 single nucleotide polymorphism (SNP) markers...
2016: PloS One
https://www.readbyqxmd.com/read/27994193/association-and-expression-analyses-of-the-ucp2-and-ucp3-gene-polymorphisms-with-body-measurement-and-meat-quality-traits-in-qinchuan-cattle
#8
Yaning Wang, Wucai Yang, Linsheng Gui, Hongbao Wang, Linsen Zan
The uncoupling proteins (UCPs) belong to the mitochondrial inner membrane anion carrier superfamily and play an important role in energy homeostasis. Genetic studies have demonstrated that Ucp2 and Ucp3 gene variants are involved in obesity and metabolic syndrome. The aim of this study was to identify associations between polymorphisms of Ucp2 and Ucp3 genes and economically-important traits in Qinchuan cattle. In the present study, one single-nucleotide polymorphism (SNP) in the 5'UTR region (SNP1:g.C-754G) of the Ucp2 gene was identified by direct sequencing of 441 Qinchuan cattle...
December 2016: Journal of Genetics
https://www.readbyqxmd.com/read/27928975/assessing-causality-in-associations-between-cannabis-use-and-schizophrenia-risk-a-two-sample-mendelian-randomization-study
#9
S H Gage, H J Jones, S Burgess, J Bowden, G Davey Smith, S Zammit, M R Munafò
BACKGROUND: Observational associations between cannabis and schizophrenia are well documented, but ascertaining causation is more challenging. We used Mendelian randomization (MR), utilizing publicly available data as a method for ascertaining causation from observational data. METHOD: We performed bi-directional two-sample MR using summary-level genome-wide data from the International Cannabis Consortium (ICC) and the Psychiatric Genomics Consortium (PGC2). Single nucleotide polymorphisms (SNPs) associated with cannabis initiation (p < 10-5) and schizophrenia (p < 5 × 10-8) were combined using an inverse-variance-weighted fixed-effects approach...
December 8, 2016: Psychological Medicine
https://www.readbyqxmd.com/read/27924921/birth-weight-and-risk-of-ischemic-heart-disease-a-mendelian-randomization-study
#10
Shiu Lun Au Yeung, Shi Lin Lin, Albert Martin Li, C Mary Schooling
Low birth weight is a risk factor for cardiovascular disease. However, the association could be confounded by many factors. We used Mendelian randomization to clarify the role of birth weight in ischemic heart disease (IHD) and lipids. We used all 7 single nucleotide polymorphisms (SNPs) independently contributing to birth weight at genome wide significance (p < 5 × 10(-8)) in separate sample instrumental variable analysis to estimate the effect of birth weight on IHD using the CARDIoGRAMplusC4D 1000 Genomes based GWAS case (n = 60,801)-control (n = 123,504) study and on lipids using GLGC (n = 188,577)...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27918628/phenotypic-and-genome-wide-association-analysis-of-spike-ethylene-in-diverse-wheat-genotypes-under-heat-stress
#11
Ravi Valluru, Matthew P Reynolds, William J Davies, Sivakumar Sukumaran
The gaseous phytohormone ethylene plays an important role in spike development in wheat (Triticum aestivum). However, the genotypic variation and the genomic regions governing spike ethylene (SET) production in wheat under long-term heat stress remain unexplored. We investigated genotypic variation in the production of SET and its relationship with spike dry weight (SDW) in 130 diverse wheat elite lines and landraces under heat-stressed field conditions. We employed an Illumina iSelect 90K single nucleotide polymorphism (SNP) genotyping array to identify the genetic loci for SET and SDW through a genome-wide association study (GWAS) in a subset of the Wheat Association Mapping Initiative (WAMI) panel...
December 5, 2016: New Phytologist
https://www.readbyqxmd.com/read/27912109/characterization-and-fine-mapping-of-a-novel-premature-leaf-senescence-mutant-yellow-leaf-and-dwarf-1-in-rice
#12
Luchang Deng, Peng Qin, Zhi Liu, Geling Wang, Weilan Chen, Jianhua Tong, Langtao Xiao, Bin Tu, Yuantao Sun, Wei Yan, Hang He, Jun Tan, Xuewei Chen, Yuping Wang, Shigui Li, Bingtian Ma
Leaves are the main organs in which photosynthates are produced. Leaf senescence facilitates the translocation of photosynthates and nutrients from source to sink, which is important for plant development and especially for crop yield. However, the molecular mechanism of leaf senescence is unknown. Here, we identified a mutant, yellow leaf and dwarf 1 (yld1), which exhibited decreased plant height and premature leaf senescence. Nitroblue tetrazolium and diamiobenzidine staining analyses revealed that the concentrations of reactive oxygen species were higher in yld1 leaves than in wild type leaves...
November 22, 2016: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/27902795/genome-wide-association-study-identifies-candidate-loci-underlying-agronomic-traits-in-a-middle-american-diversity-panel-of-common-bean
#13
Samira Mafi Moghaddam, Sujan Mamidi, Juan M Osorno, Rian Lee, Mark Brick, James Kelly, Phillip Miklas, Carlos Urrea, Qijian Song, Perry Cregan, Jane Grimwood, Jeremy Schmutz, Phillip E McClean
Common bean ( L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood. Genome-wide association studies (GWAS) provide an experimental approach to identify genomic regions where important candidate genes are located. A panel of 280 modern bean genotypes from race Mesoamerica, referred to as the Middle American Diversity Panel (MDP), were grown in four US locations, and a GWAS using >150,000 single-nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] ≥ 5%) was conducted for six agronomic traits...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27898815/germplasm-architecture-revealed-through-chromosomal-effects-for-quantitative-traits-in-maize
#14
Rex Bernardo, Addie M Thompson
Germplasm architecture refers to how favorable alleles for a given trait are distributed across the genome in a germplasm collection. Our objective was to assess germplasm architecture for quantitative traits among US maize ( L.) inbreds. A total of 271 inbreds were genotyped at 28,626 single nucleotide polymorphism (SNP) loci and phenotyped for anthesis date, plant height, starch and protein concentration, and resistance to northern corn leaf blight (NCLB, caused by ). Chromosomal effects were calculated as the sum of the trait effects of SNP alleles carried on a specific chromosome by an inbred...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898806/genome-wide-association-study-for-nine-plant-architecture-traits-in-sorghum
#15
Jing Zhao, Maria B Mantilla Perez, Jieyun Hu, Maria G Salas Fernandez
Sorghum [ (L) Moench], an important grain and forage crop, is receiving significant attention as a lignocellulosic feedstock because of its water-use efficiency and high biomass yield potential. Because of the advancement of genotyping and sequencing technologies, genome-wide association study (GWAS) has become a routinely used method to investigate the genetic mechanisms underlying natural phenotypic variation. In this study, we performed a GWAS for nine grain and biomass-related plant architecture traits to determine their overall genetic architecture and the specific association of allelic variants in gibberellin (GA) biosynthesis and signaling genes with these phenotypes...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898805/characterization-of-three-rice-multiparent-advanced-generation-intercross-magic-populations-for-quantitative-trait-loci-identification
#16
Lijun Meng, Longbiao Guo, Kimberly Ponce, Xiangqian Zhao, Guoyou Ye
Three new rice ( L.) multiparent advanced generation intercross (MAGIC) populations were developed using eight elite rice varieties from different breeding programs. These three populations were two recombinant inbred line (RIL) populations derived from two 4-way crosses, DC1 and DC2, and one RIL population derived from an 8-way cross. These populations were genotyped using an Illumina Infinium rice 6K SNP chip. The potential of the three MAGIC populations in identifying marker-trait associations was demonstrated using the plant height (PH) and heading date (HD) measured in 2014...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27896743/analysis-of-quantitative-trait-loci
#17
David L Duffy
Although the term quantitative trait locus (QTL) strictly refers merely to a genetic variant that causes changes in a quantitative phenotype such as height, QTL analysis more usually describes techniques used to study oligogenic or polygenic traits where each identified locus contributes a relatively small amount to the genetic determination of the trait, which may be categorical in nature. Originally, too, it would be clear that it covered segregation and genetic linkage analysis, but now genetic association analysis in a genome-wide SNP or sequencing experiment would be the commonest application...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27872629/qtl-analysis-of-spike-morphological-traits-and-plant-height-in-winter-wheat-triticum-aestivum-l-using-a-high-density-snp-and-ssr-based-linkage-map
#18
Huijie Zhai, Zhiyu Feng, Jiang Li, Xinye Liu, Shihe Xiao, Zhongfu Ni, Qixin Sun
Wheat yield can be enhanced by modifying the spike morphology and the plant height. In this study, a population of 191 F9 recombinant inbred lines (RILs) was developed from a cross between two winter cultivars Yumai 8679 and Jing 411. A dense genetic linkage map with 10,816 markers was constructed by incorporating single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker information. Five spike morphological traits and plant height were evaluated under nine environments for the RILs and parental lines, and the number of detected environmentally stable QTLs were 18 and three, respectively...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27846199/height-height-related-snps-and-risk-of-non-melanoma-skin-cancer
#19
Xin Li, Liming Liang, Yen-Chen Anne Feng, Immaculata De Vivo, Edward Giovannucci, Jean Y Tang, Jiali Han
BACKGROUND: Adult height has been associated with risk of several site-specific cancers, including melanoma. However, less attention has been given to non-melanoma skin cancer (NMSC). METHODS: We prospectively examined the risk of squamous cell carcinoma (SCC) and basal cell carcinoma (BCC) in relation to adult height in the Nurses' Health Study (NHS, n=117 863) and the Health Professionals Follow-up Study (HPFS, n=51 111). We also investigated the relationships between height-related genetic markers and risk of BCC and SCC in the genetic data sets of the NHS and HPFS (3898 BCC cases, and 8530 BCC controls; 527 SCC cases, and 8962 SCC controls)...
January 3, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/27829377/range-wide-phenotypic-and-genetic-differentiation-in-wild-sunflower
#20
Edward V McAssey, Jonathan Corbi, John M Burke
BACKGROUND: Divergent phenotypes and genotypes are key signals for identifying the targets of natural selection in locally adapted populations. Here, we used a combination of common garden phenotyping for a variety of growth, plant architecture, and seed traits, along with single-nucleotide polymorphism (SNP) genotyping to characterize range-wide patterns of diversity in 15 populations of wild sunflower (Helianthus annuus L.) sampled along a latitudinal gradient in central North America...
November 10, 2016: BMC Plant Biology
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