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Efficiently Identifying Significant Associations in Genome-wide Association Studies

Emrah Kostem, Eleazar Eskin
2013 Journal of Computational Biology  
Over the past several years, genome-wide association studies (GWAS) have implicated hundreds of genes in common disease.  ...  We introduce a novel two-stage testing procedure that identifies all of the significant associations more efficiently than testing all the single nucleotide polymorphisms (SNPs).  ...  GRAT, genome-wide rapid association testing; GWAS, genome-wide association studies; SNPs, single nucleotide polymorphisms.  ... 
doi:10.1089/cmb.2013.0087 pmid:24033261 pmcid:PMC3791046 fatcat:c3myrdoorfcrvkr55ppduu2qry

Genome-wide association analysis reveals genetic loci and candidate genes for feeding behavior and eating efficiency in Duroc boars

Rongrong Ding, Jianping Quan, Ming Yang, Xingwang Wang, Enqin Zheng, Huaqiang Yang, Disheng Fu, Yang Yang, Linxue Yang, Zicong Li, Dewu Liu, Gengyuan Cai (+3 others)
2017 PLoS ONE  
Despite the limited sample size, the genome-wide association study was acceptable to detect candidate regions association with feeding behavior and eating efficiency traits in pigs.  ...  Efficiency of feeding is directly related to feeding behavior. In order to identify genomic regions controlling feeding behavior and eating efficiency traits, 338 Duroc boars were used in this study.  ...  Foundation of China (31601912), the Natural Science Foundation of Guangdong Province (2016A030310447), and the Science and Technology Planning Project of Guangdong Province (2015B020231010) supported this study  ... 
doi:10.1371/journal.pone.0183244 pmid:28813538 pmcid:PMC5559094 fatcat:al6dl5cd6neznhun72f7f4tiqe

Identification of Genomic Regions Associated with Concentrations of Milk Fat, Protein, Urea and Efficiency of Crude Protein Utilization in Grazing Dairy Cows

Hewa Bahithige Pavithra Chathurangi Ariyarathne, Martin Correa-Luna, Hugh Thoma Blair, Dorian John Garrick, Nicolas Lopez-Villalobos
2021 Genes  
The objective of this study was to identify genomic regions associated with milk fat percentage (FP), crude protein percentage (CPP), urea concentration (MU) and efficiency of crude protein utilization  ...  Single nucleotide polymorphisms (SNPs) with genome-wide association p-values ≤ 1.11 × 10−6 were considered as putative quantitative trait loci (QTL).  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/genes12030456 pmid:33806889 fatcat:m4rb4k3ibvb7fpgt3dyl5mijcy

Genome-wide association studies for feed intake and efficiency in two laying periods of chickens

Jingwei Yuan, Kehua Wang, Guoqiang Yi, Meng Ma, Taocun Dou, Congjiao Sun, Lu-Jiang Qu, Manman Shen, Liang Qu, Ning Yang
2015 Genetics Selection Evolution  
Univariate, bivariate, and conditional genome-wide association studies (GWAS) were performed with GEMMA, a genome-wide efficient mixed model association algorithm.  ...  In the present study, we used an F 2 chicken population in a genome-wide association study (GWAS) to detect potential genetic variants and candidate genes associated with daily feed intake (FI) and feed  ...  The purpose of our study was to identify genetic variants and candidate genes for feed intake and efficiency in chicken using the genome-wide association approach in an F 2 resource population genotyped  ... 
doi:10.1186/s12711-015-0161-1 pmid:26475174 pmcid:PMC4608132 fatcat:qyy777t3d5hw7kt3j5475zjtfu

Short Communication Genome-wide association with residual body weight gain in Bos indicus cattle

M.H.A. Santana, R.C. Gomes, Y.T. Utsunomiya, H.H.R. Neves, F.J. Novais, M.N. Bonin, H. Fukumasu, J.F. Garcia, P.A. Alexandre, G.A. Oliveira Junior, L.L. Coutinho, J.B.S. Ferraz
2015 Genetics and Molecular Research  
To identify candidate genes and genomic regions associated with residual body weight gain (RWG), we conducted a genome-wide association study (GWAS) with 720 Nellore cattle using the GRAMMAR-Gamma association  ...  We identified 30 significant single nucleotide polymorphisms (SNPs), ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (2): 5229-5233 (2015) especially on chromosomes 2, 8, 12, and 17.  ...  ACKNOWLEDGMENTS Research supported in part by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, #2012/02039-9 and #2013/20571-2).  ... 
doi:10.4238/2015.may.18.14 pmid:26125717 fatcat:c73sxsfiizh5xia5wijke5btge

Novel Genes and Genetic Loci Associated With Root Morphological Traits, Phosphorus-Acquisition Efficiency and Phosphorus-Use Efficiency in Chickpea

Mahendar Thudi, Yinglong Chen, Jiayin Pang, Danamma Kalavikatte, Prasad Bajaj, Manish Roorkiwal, Annapurna Chitikineni, Megan H. Ryan, Hans Lambers, Kadambot H. M. Siddique, Rajeev K. Varshney
2021 Frontiers in Plant Science  
The MTAs and novel genes identified in this study can be used to improve P-use efficiency in chickpea.  ...  A genome-wide association mapping approach was used to determine loci and genes associated with root architecture, root traits associated with P-acquisition efficiency and P-use efficiency, and any associated  ...  In legumes, genome-wide association studies (GWAS) are gaining momentum.  ... 
doi:10.3389/fpls.2021.636973 pmid:34122467 pmcid:PMC8192852 fatcat:tyehshmjcjctnow3i7gpggjzrm

Metabolite Genome-Wide Association Study (mGWAS) and Gene-Metabolite Interaction Network Analysis Reveal Potential Biomarkers for Feed Efficiency in Pigs

Xiao Wang, Haja N. Kadarmideen
2020 Metabolites  
This study performed a comprehensive metabolite-based genome-wide association study (GWAS) analysis for pigs with differences in feed efficiency and provided significant metabolites for which there is  ...  In order to achieve these objectives, we firstly conducted a metabolite genome-wide association study (mGWAS) based on mixed linear models and found 152 genome-wide significant SNPs (p-value < 1.06 × 10  ...  Genome-Wide Significant SNP-Related Genes Associated with Metabolites The previous GWAS for Duroc pigs identified two pleiotropic QTLs on chromosome one and seven for feed efficiency [20] .  ... 
doi:10.3390/metabo10050201 pmid:32429265 pmcid:PMC7281523 fatcat:pvyl3foxvbcvnmgscilivwizky

Genome wide association study of body weight and feed efficiency traits in a commercial broiler chicken population, a re-visitation

Wossenie Mebratie, Henry Reyer, Klaus Wimmers, Henk Bovenhuis, Just Jensen
2019 Scientific Reports  
Genome wide association study was conducted using a mixed linear model (MLM) approach that accounted for family structure to identify single nucleotide polymorphisms (SNPs) and candidate genes associated  ...  The SNPs and candidate genes identified in this study provide information on the genetic background of BW and FE traits in broiler chickens and might be used as prior information for genomic selection.  ...  Genome wide association studies (GWAS) are commonly used to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with quantitative traits.  ... 
doi:10.1038/s41598-018-37216-z pmid:30696883 pmcid:PMC6351590 fatcat:r53ivbwejzggldaqg6utoqgnsm

Metabolite genome-wide association study (mGWAS) and gene-metabolite interaction network analysis reveal potential biomarkers for feed efficiency in pigs [article]

Xiao Wang, Haja N Kadarmideen
2020 biorxiv/medrxiv   pre-print
In order to achieve these objectives, we firstly conducted a metabolite genome-wide association study (mGWAS) based on mixed linear models and found 152 genome-wide significant SNPs (P-value < 1.06E-06  ...  Genome-wide significant genetic variants could be then used as potential genetic or biomarkers in breeding programs for feed efficiency.  ...  Genome-Wide Significant SNP-Related Genes Associated with Metabolites The previous GWAS for Duroc pigs identified two pleiotropic QTLs on chromosome one and seven for feed efficiency [20] .  ... 
doi:10.1101/2020.04.11.036939 fatcat:yaurdvgt6ne2pbcqc4t5duprie

Exploring the genetic architecture of feed efficiency traits in chickens

Jorge Augusto Petroli Marchesi, Rafael Keith Ono, Maurício Egídio Cantão, Adriana Mércia Guaratini Ibelli, Jane de Oliveira Peixoto, Gabriel Costa Monteiro Moreira, Thaís Fernanda Godoy, Luiz Lehmann Coutinho, Danísio Prado Munari, Mônica Corrêa Ledur
2021 Scientific Reports  
Therefore, here, a genome-wide association study (GWAS) was conducted to explore candidate genomic regions responsible for Feed Intake (FI), Body Weight Gain (BWG) and Feed Conversion Ratio (FCR) traits  ...  A total of 119 associated SNPs located in 20 chromosomes were identified, where some of them were common in more than one FE trait.  ...  This study was supported by the Bra-  ... 
doi:10.1038/s41598-021-84125-9 pmid:33633287 pmcid:PMC7907133 fatcat:nn4ajl4e3beanpk5apyjbtl4oa

Genome-wide association studies of cryostability of semen in roosters

2020 Polish journal of veterinary sciences  
Significant SNP associations rs15557972 (p<1.36E-07) on chromosome 10 in the LOXL1 gene and rs15751385 (p<6.10E-06) on chromosome 6 in the intron of the ENSGALG00000052127 gene were identified.  ...  Genome-wide association studies were performed using 33 roosters from four breeds genotyped using Illumina Chicken 60K SNP BeadChip Calculations were performed using PLINK and EMMAX software.  ...  References Du J, Hincke MT, Rose-Martel M, Hennequet-Antier C, Brionne A, Cogburn LA, Nys Y, Gautron J (2015) Identifying specific proteins involved in eggshell membrane Table 1 .  ... 
doi:10.24425/pjvs.2020.134692 pmid:33006861 fatcat:5zlnsycmb5ggzc3kacdcj3oilq

New Insights From Imputed Whole-Genome Sequence-Based Genome-Wide Association Analysis and Transcriptome Analysis: The Genetic Mechanisms Underlying Residual Feed Intake in Chickens

Shaopan Ye, Zi-Tao Chen, Rongrong Zheng, Shuqi Diao, Jinyan Teng, Xiaolong Yuan, Hao Zhang, Zanmou Chen, Xiquan Zhang, Jiaqi Li, Zhe Zhang
2020 Frontiers in Genetics  
In this study, using imputed whole-genome sequencing data, genome-wide association analysis (GWAS) was performed to identify single-nucleotide polymorphisms (SNPs) and genes associated with residual feed  ...  In conclusion, using imputed sequence-based GWAS is an efficient method to identify significant SNPs and candidate genes in chicken.  ...  AUTHOR CONTRIBUTIONS SY, ZZ, and JL conceived the study, designed the project, and helped in preparing the draft. XZ provided the chickens' dataset.  ... 
doi:10.3389/fgene.2020.00243 pmid:32318090 pmcid:PMC7147382 fatcat:vo2y2yfvobch7oxjaphboq7oqa

Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle

Jiyuan Li, Robert Mukiibi, Yining Wang, Graham S. Plastow, Changxi Li
2021 BMC Genomics  
Combining the results of metabolome-genome wide association studies using 10,488,742 imputed SNPs, 40, 66, 15, and 40 unique candidate genes were identified as associated with RFI, DMI, ADG, and MWT (P-value  ...  Results Regression analyses between feed efficiency traits and plasma metabolites in a population of 493 crossbred beef cattle identified 5 (L-valine, lysine, L-tyrosine, L-isoleucine, and L-leucine),  ...  The authors thank Brian Karisa and Michael Vinsky for data collection and thank Yan Meng and Seyed Ali Goldansaz for blood sample processing in the laboratory.  ... 
doi:10.1186/s12864-021-08064-5 pmid:34781903 pmcid:PMC8591823 fatcat:npppxhs2wjdnppefxc32y4mvdi

Genome-wide association and pathway analysis of feed efficiency in pigs reveal candidate genes and pathways for residual feed intake

Duy N. Do, Anders B. Strathe, Tage Ostersen, Sameer D. Pant, Haja N. Kadarmideen
2014 Frontiers in Genetics  
Therefore, the study aimed to identify single nucleotide polymorphisms (SNPs), candidate genes and biological pathways involved in regulating RFI using Genomewide association (GWA) and pathway analyses  ...  Furthermore, our study revealed key genes and genetic variants that control feed efficiency that could potentially be useful for genetic selection of more feed efficient pigs.  ...  ACKNOWLEDGMENTS We would like to thank the Department of Breeding and Genetics of the Danish Pig Research Centre for providing all data for the research reported in this study. Duy N.  ... 
doi:10.3389/fgene.2014.00307 pmid:25250046 pmcid:PMC4159030 fatcat:r4btlcrwxfgnpiigelvifov5ku

Genome-Wide Association Study and QTL Meta-Analysis Identified Novel Genomic Loci Controlling Potassium Use Efficiency and Agronomic Traits in Bread Wheat

Luqman Bin Safdar, Tayyaba Andleeb, Sadia Latif, Muhammad Jawad Umer, Minqiang Tang, Xiang Li, Shengyi Liu, Umar Masood Quraishi
2020 Frontiers in Plant Science  
Genome-wide association studies (GWAS) are widely used to dissect complex traits.  ...  One locus identified in this study (q5B-1) colocalized with an MQTL (MQTL_11 ), while the other ten loci were novel associations.  ...  Genome-wide efficient mixed-model analysis for association studies. Nat.  ... 
doi:10.3389/fpls.2020.00070 pmid:32133017 pmcid:PMC7041172 fatcat:l3w34mophfeqdakvidyke74csm
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