Variance component model to account for sample structure in genome-wide association studies

Kang, Hyun Min, Sul, Jae Hoon, Service, Susan K, Zaitlen, Noah A, Kong, Sit-yee, Freimer, Nelson B, Sabatti, Chiara, Eskin, Eleazar·2010·Nature Genetics

DOI 10.1038/ng.548

Cited by (1,002)

Items 301–400 of 1,002

Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding
Chunhui Li, Honghui Guan, Xin Jing, Yaoyao Li, Baobao Wang, Xuyang Liu, Xuyang Liu, Dengfeng Zhang, Cheng Liu, Xiaoqing Xie et al. · 2022 · Nature Plants
Identification and Functional Characterization of G6PC2 Coding Variants Influencing Glycemic Traits Define an Effector Transcript at the G6PC2-ABCB11 Locus
Anubha Mahajan, Xueling Sim, Hui Jin Ng, Alisa Knodle Manning, Manuel A. Rivas, Heather M. Highland, Adam E. Locke, Niels Grarup, Hae Kyung Im, Pablo Cingolani et al. · 2015 · PLoS Genetics
A Phi-Class Glutathione S-Transferase Gene for Verticillium Wilt Resistance in Gossypium arboreum Identified in a Genome-Wide Association Study
Qian Gong, Zhaoen Yang, Eryong Chen, Gaofei Sun, Shoupu He, Hamama Islam Butt, Chaojun Zhang, Xueyan Zhang, Zuoren Yang, Xiongming Du et al. · 2017 · Plant and Cell Physiology
GWAS Uncovers Differential Genetic Bases for Drought and Salt Tolerances in Sesame at the Germination Stage
Donghua Li, Komivi Dossa, Yanxin Zhang, Xin Wei, Linhai Wang, Yujuan Zhang, Aili Liu, Rong Zhou, Xiurong Zhang · 2018 · Genes
A guide to genome‐wide association analysis and post‐analytic interrogation
Eric R. Reed, Sara Núñez, David Kulp, Jing Qian, Muredach P. Reilly, Andrea S. Foulkes · 2015 · Statistics in Medicine
Accurate modeling of confounding variation in eQTL studies leads to a great increase in power to detect trans-regulatory effects
Nicolò Fusi, Oliver Stegle, Neil David Lawrence · 2011 · Nature Precedings
Recovering Power in Association Mapping Panels with Variable Levels of Linkage Disequilibrium
Renaud Rincent, Laurence Moreau, Hervé Monod, Estelle Kuhn, Albrecht E. Melchinger, Rosa Ana Malvar Pintos, Jesús Moreno‐González, Stéphane Nicolas, Delphine Madur, Valérie Combes et al. · 2014 · Genetics
GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle
Marc G. Higgins, Claire Fitzsimons, Matthew Charles McClure, Clare McKenna, Stephen B Conroy, David A. Kenny, Mark McGee, Sinéad M. Waters, Derek W. Morris · 2018 · Scientific Reports
ERF4 affects fruit firmness through TPL4 by reducing ethylene production
Yanan Hu, Zhenyun Han, Yaqiang Sun, Shuai Wang, Ting Wang, Yi Wang, Kenong Xu, Xinzhong Zhang, Xuefeng Xu, Zhenhai Han et al. · 2020 · The Plant Journal
LIMIX: genetic analysis of multiple traits
Christoph Lippert, Franceso Paolo Casale, Barbara Rakitsch, Oliver Stegle · 2014 · bioRxiv (Cold Spring Harbor Laboratory)
RAREMETAL: fast and powerful meta-analysis for rare variants
Shuang Feng, Dajiang J. Liu, Xiaowei Zhan, Mary Kate Wing, Gonçalo R. Abecasis · 2014 · Bioinformatics
A random forest approach to capture genetic effects in the presence of population structure
Johannes Stephan, Oliver Stegle, Andreas Beyer · 2015 · Nature Communications
Unraveling a genetic roadmap for improved taste in the domesticated apple
Liao Liao, Weihan Zhang, Bo Zhang, Ting Fang, Xiaofei Wang, Yaming Cai, Collins Otieno Ogutu, Lei Gao, Gang Chen, Xiaoqing Nie et al. · 2021 · Molecular Plant
Common variants in the HLA-DRB1–HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis
Michaela Fakiola, Amy Strange, Heather Jane Cordell, E. Nancy Miller, Matti Pirinen, Zhan Su, Anshuman Mishra, Sanjana Mehrotra, Glória R. Monteiro, Gavin Band et al. · 2013 · Nature Genetics
What can genome‐wide association studies tell us about the evolutionary forces maintaining genetic variation for quantitative traits?
Emily B. Josephs, John R. Stinchcombe, Stephen Wright · 2017 · New Phytologist
Genome-Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds
Songsong Xu, Lei Gao, Xing-Long Xie, Yanling Ren, Zhiqiang Shen, Feng Wang, Min Shen, Emma Eyϸórsdóttir, Jón Hallsteinn Hallsson, Tatyana Kiseleva et al. · 2018 · Frontiers in Genetics
Genome‐wide association study reveals novel players in defense hormone crosstalk in Arabidopsis
Silvia Proietti, Lotte Caarls, Silvia Coolen, Johan A. van Pelt, Saskia C. M. Van Wees, Corné M. J. Pieterse · 2018 · Plant Cell & Environment
Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies
Stefano Pavan, Chiara Delvento, Luigi M. Ricciardi, Concetta Lotti, Elena Ciani, Nunzio D’Agostino · 2020 · Frontiers in Genetics
CottonMD: a multi-omics database for cotton biological study
Zhiquan Yang, Jing Wang, Yiming Huang, Shengbo Wang, Lulu Wei, Dongxu Liu, Yonglin Weng, Jinhai Xiang, Qiang Zhu, Zhaoen Yang et al. · 2022 · Nucleic Acids Research
Genome‐wide association studies on the phyllosphere microbiome: Embracing complexity in host–microbe interactions
Kathleen R. Beilsmith, Manus P. M. Thoen, Benjamin Brachi, Andrew D. Gloss, Mohammad Haneef Khan, Joy M. Bergelson · 2018 · The Plant Journal
A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data
Amanda J. Lea, Jenny Tung, Xiang Zhou · 2015 · PLoS Genetics
Genome-wide association study of blast resistance in indica rice
Caihong Wang, Yaolong Yang, Xiaoping Yuan, Qun Jie Xu, Yue Feng, Hanyong Yu, Yiping Wang, Xinghua Wei · 2014 · BMC Plant Biology
Genome-wide Association Analyses Reveal the Genetic Basis of Stigma Exsertion in Rice
Hao Zhou, Pingbo Li, Weibo Xie, Saddam Hussain, Yibo Li, Duo Xia, Hu Zhao, Shengyuan Sun, Junxiao Chen, Hong Ye et al. · 2017 · Molecular Plant
Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries
Seyedeh Maryam Zekavat, Sanni Ruotsalainen, Robert E. Handsaker, Maris Alver, Jonathan Bloom, Timothy Poterba, Cotton Seed, Jason Ernst, Mark D. Chaffin, J Engreitz et al. · 2018 · Nature Communications
A Nonsense Mutation in TMEM95 Encoding a Nondescript Transmembrane Protein Causes Idiopathic Male Subfertility in Cattle
Hubert Pausch, Sabine Kölle, Christine Wurmser, Hermann Schwarzenbacher, Reiner Emmerling, Sandra Jansen, Matthias Trottmann, C. Fuerst, Kay‐Uwe Götz, Ruedi Fries · 2014 · PLoS Genetics
TraitCapture: genomic and environment modelling of plant phenomic data
Tim B. Brown, Riyan Cheng, Xavier R. R. Sirault, Tepsuda Rungrat, Kevin Murray, Martin Trtílek, Robert T. Furbank, Murray R. Badger, Barry James Pogson, Justin Borevitz · 2014 · Current Opinion in Plant Biology
High‐density genome‐wide association mapping implicates an F ‐box encoding gene in M edicago truncatula resistance to A phanomyces euteiches
Maxime Bonhomme, Olivier André, Yacine Badis, Joëlle Ronfort, Concetta Burgarella, Nathalie Chantret, Jean‐Marie Prosperi, Roman V. Briskine, Joann Mudge, Frederic Debellé et al. · 2013 · New Phytologist
Height-reducing variants and selection for short stature in Sardinia
Magdalena Żołędziewska, The Understanding Society Scientific Group, Carlo Sidore, Charleston W. K. Chiang, Serena Sanna, Antonella Mulas, Maristella Steri, Fabio Busonero, Joseph H. Marcus, Michele Marongiu et al. · 2015 · Nature Genetics
Genome-wide Association Study Identifies Shared Risk Loci Common to Two Malignancies in Golden Retrievers
Noriko Tonomura, Ingegerd Elvers, Rachael J. Thomas, Kate Megquier, Jason Turner-Maier, Cédric Howald, Aaron L. Sarver, Ross Swofford, Aric M. Frantz, Daisuke Ito et al. · 2015 · PLoS Genetics
Genome-wide association study identifies loci on 12q24 and 13q32 associated with Tetralogy of Fallot
Heather Jane Cordell, Ana Töpf, Chrysovalanto Mamasoula, Alex Vincent Postma, Jamie Bentham, Diana Zélénika, Simon Charles Heath, Gillian M. Blue, Catherine Cosgrove, Javier T Granados-Riveron et al. · 2013 · Human Molecular Genetics
The genetic architecture of amylose biosynthesis in maize kernel
Changsheng Li, Yongcai Huang, Ruidong Huang, Yongrui Wu, Wenqin Wang · 2017 · Plant Biotechnology Journal
The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog
Matteo Togninalli, Ümit Seren, Dazhe Meng, Joffrey Fitz, Magnus Nordborg, Detlef Weigel, Karsten Michael Borgwardt, Arthur Korte, Dominik G. Grimm · 2017 · Nucleic Acids Research
Identification of CAD candidate genes in GWAS loci and their expression in vascular cells
Ayça Erbilgin, Mete Civelek, Casey E. Romanoski, Calvin Pan, Raffi Hagopian, Judith A. Berliner, Aldons Jake Lusis · 2013 · Journal of Lipid Research
The genetic basis of drought tolerance in the high oil crop Sesamum indicum
Komivi Dossa, Donghua Li, Rong Zhou, Jingyin Yu, Linhai Wang, Yanxin Zhang, Jun You, Aili Liu, Marie Ali Mmadi, Daniel Foncéka et al. · 2019 · Plant Biotechnology Journal
Adaptive diversification of growth allometry in the plant Arabidopsis thaliana
François Vasseur, Moisés Expósito-Alonso, Oscar J. Ayala-Garay, George Wang, B. Enquist, D. Vile, C. Violle, D. Weigel · 2018 · Proceedings of the National Academy of Sciences of the United States of America
Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape
Jiantao Guan, Yaoguang Xu, Yu Yang, Jun Fu, Fei Ren, Jiying Guo, Jianbo Zhao, Quan Jiang, Jianhua Wei, Hua Xie · 2021 · Genome biology
Genome-Wide Association Mapping of Fertility Reduction upon Heat Stress Reveals Developmental Stage-Specific QTLs in Arabidopsis thaliana
Johanna A. Bac-Molenaar, Emilie F. Fradin, Frank F. M. Becker, Juriaan A. Rienstra, J. van der Schoot, Dick Vreugdenhil, Joost J. B. Keurentjes · 2015 · The Plant Cell
Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content
Xiaoqian Wang, Yunlong Pang, Jian Zhang, Zhichao Wu, Kai Chen, Jauhar Ali, Guoyou Ye, Jianlong Xu, Zhikang Li · 2017 · Scientific Reports
A multi-trait meta-analysis with imputed sequence variants reveals twelve QTL for mammary gland morphology in Fleckvieh cattle
Hubert Pausch, Reiner Emmerling, Hermann Schwarzenbacher, Ruedi Fries · 2016 · Genetics Selection Evolution
Integrating Sequence-based GWAS and RNA-Seq Provides Novel Insights into the Genetic Basis of Mastitis and Milk Production in Dairy Cattle
Lingzhao Fang, Goutam Sahana, Guosheng Su, Ying Yu, Shengli Zhang, Mogens Sandø Lund, Peter Sørensen · 2017 · Scientific Reports
Novel Susceptibility Loci for Moyamoya Disease Revealed by a Genome-Wide Association Study
Lian Duan, Ling Wei, Yanghua Tian, Zhengshan Zhang, Panpan Hu, Qiang Wei, Sugang Liu, Jun Zhang, Yuyang Wang, Desheng Li et al. · 2017 · Stroke
Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data
Christopher Jon Battey, Peter L. Ralph, Andrew D. Kern · 2020 · Genetics
Efficient computation with a linear mixed model on large-scale data sets with applications to genetic studies
Matti Pirinen, Peter Donnelly, Chris C. A. Spencer · 2013 · The Annals of Applied Statistics
Population structure can inflate SNP-based heritability estimates
Browning, Sharon R., Browning, Brian L. · 2011 · The American Journal of Human Genetics
Inference of Relationships in Population Data Using Identity-by-Descent and Identity-by-State
Eric L. Stevens, Greg Heckenberg, Elisha D. O. Roberson, Joseph D. Baugher, Thomas J. Downey, Jonathan Pevsner · 2011 · PLoS Genetics
Identification of novel genes significantly affecting growth in catfish through GWAS analysis
Ning Li, Tao Zhou, Xin Geng, Yulin Jin, Xiaozhu Wang, Shikai Liu, Xiaoyan Xu, Dongya Gao, Qi Li, Zhanjiang Liu · 2017 · Molecular Genetics and Genomics
Natural variation in HsfA2 pre‐mRNA splicing is associated with changes in thermotolerance during tomato domestication
Yangjie Hu, Anida Mesihović, José M. Jiménez‐Gómez, Sascha Röth, Philipp Gebhardt, Daniela Bublak, Arnaud G. Bovy, Klaus‐Dieter Scharf, Enrico Schleiff, Sotirios Fragkostefanakis · 2019 · New Phytologist
A pangenome reference of wild and cultivated rice
Dongling Guo, Yán Li, Hengyun Lu, Yan Zhao, Nori Kurata, Xinghua Wei, Ahong Wang, Yongchun Wang, Qilin Zhan, Danlin Fan et al. · 2025 · Nature
Sequencing-based genome-wide association study in rice
Bin Han, Xuehui Huang · 2013 · Current Opinion in Plant Biology
Genomewide Association Study of African Children Identifies Association of SCHIP1 and PDE8A with Facial Size and Shape
Joanne B. Cole, Mange Festo Manyama, Emmanuel Kimwaga, Joshua Mathayo, Jacinda R. Larson, Denise K. Liberton, Ken Lukowiak, Tracey M. Ferrara, Sheri L. Riccardi, Mao Li et al. · 2016 · PLoS Genetics
TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data
Huang, Le, Rosen, Jonathan D., Sun, Quan, Chen, Jiawen, Wheeler, Marsha M., Zhou, Ying, Min, Yuan-I, Kooperberg, Charles, Conomos, Matthew P., Stilp, Adrienne M. et al. · 2022 · The American Journal of Human Genetics
Implementation and accuracy of genomic selection
Jeremy F. Taylor · 2013 · Aquaculture
The Triticeae Toolbox: Combining Phenotype and Genotype Data to Advance Small‐Grains Breeding
Victoria C. Blake, Clayton L. Birkett, David E. Matthews, David L. Hane, Peter J. Bradbury, Jean‐Luc Jannink · 2016 · The Plant Genome
Genetic Variation in the Social Environment Contributes to Health and Disease
Amelie Baud, Megan K. Mulligan, Francesco Paolo Casale, Jesse F. Ingels, Casey J. Bohl, Jacques Callebert, Jean‐Marie Launay, Jon P. Krohn, Andrés Legarra, Robert W. Williams et al. · 2017 · PLoS Genetics
The origin of Wx la provides new insights into the improvement of grain quality in rice
Hao Zhou, Duo Xia, Zhao Da, Yànhuá Lǐ, Pingbo Li, Bian Wu, Guanjun Gao, Qinglu Zhang, Gongwei Wang, Jinghua Xiao et al. · 2020 · Journal of Integrative Plant Biology
Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation
Dan Liang, Angela L. Elwell, Nil Aygün, Oleh Krupa, Justin M. Wolter, Felix A. Kyere, Michael J. Lafferty, Kerry E. Cheek, Kenan P. Courtney, Marianna Yusupova et al. · 2021 · Nature Neuroscience
Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet
Jinfeng Chen, Yang Liu, Minxuan Liu, Wenlei Guo, Yongqiang Wang, Qiang He, Weiyao Chen, Yi Liao, Wei Zhang, Yuanzhu Gao et al. · 2023 · Nature Genetics
Qxpak.5: Old mixed model solutions for new genomics problems
Miguel Pérez-enciso A, I. Misztal · 2011 · BMC Bioinformatics
Identification and Dissection of Four Major QTL Affecting Milk Fat Content in the German Holstein-Friesian Population
Xiaolong Wang, Christine Wurmser, Hubert Pausch, Simone Jung, Friedrich Reinhardt, Jens Tetens, Georg Erwin Thaller, Ruedi Fries · 2012 · PLoS ONE
Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae
Houxiang Kang, Yue Wang, Shasha Peng, Yanli Zhang, Yinghui Xiao, Dan Wang, Shaohong Qu, Zhiqiang Li, Shuangyong Yan, Zhilong Wang et al. · 2015 · Molecular Plant Pathology
Genomic insights into the evolution of Echinochloa species as weed and orphan crop
Dongya Wu, Enhui Shen, Bowen Jiang, Yu Feng, Wei Tang, Sangting Lao, Lei Jia, Hanyang Lin, Lingjuan Xie, Xifang Weng et al. · 2022 · Nature Communications
Natural variation of Dt2 determines branching in soybean
Qianjin Liang, Liyu Chen, Xia Yang, Hui Yang, Shulin Liu, Kun Kou, Lei Fan, Zhifang Zhang, Zongbiao Duan, Yaqin Yuan et al. · 2022 · Nature Communications
Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis
Zhoulin Gu, Junyi Gong, Zhou Zhu, Zhen Li, Qi Feng, Changsheng Wang, Yan Zhao, Qilin Zhan, Congcong Zhou, Ahong Wang et al. · 2023 · Nature Genetics
Using population isolates in genetic association studies
Konstantinos Hatzikotoulas, Arthur Gilly, Eleftheria Zeggini · 2014 · Briefings in Functional Genomics
The adaptive potential of P opulus balsamifera L . to phenology requirements in a warmer global climate
Matthew S. Olson, Nicholas D. Levsen, Raju Y. Soolanayakanahally, Robert D. Guy, William R. Schroeder, Stephen R. Keller, Peter Tiffin · 2012 · Molecular Ecology
The genomic basis of adaptation in plants
Pádraic J. Flood, Angela M. Hancock · 2017 · Current Opinion in Plant Biology
Widespread Allelic Heterogeneity in Complex Traits
Farhad Hormozdiari, Anthony Zhu, Gleb Kichaev, Chelsea J.‐T. Ju, Ayellet V. Segrè, Jong Wha J. Joo, Hyejung Won, Sriram Sankararaman, Bogdan Paşaniuc, Sagiv Shifman et al. · 2017 · The American Journal of Human Genetics
A genome‐wide association study of heat stress‐associated SNP s in catfish
Yulin Jin, Tao Zhou, X. Geng, Shikai Liu, A. Chen, Jun Yao, C. Jiang, Suxu Tan, Baofeng Su, Z. Liu · 2016 · Animal Genetics
Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants
Terhi Iso‐Touru, Goutam Sahana, Bernt Guldbrandtsen, Mogens Sandø Lund, Johanna Vilkki · 2016 · BMC Genetics
Meta-analysis of sequence-based association studies across three cattle breeds reveals 25 QTL for fat and protein percentages in milk at nucleotide resolution
Hubert Pausch, Reiner Emmerling, Birgit Gredler, Ruedi Fries, Hans D. Daetwyler, Michael Edward Goddard · 2017 · BMC Genomics
Structural variation (SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons
Shangkun Jin, Zegang Han, Yan Hu, Zhanfeng Si, Fan Dai, Lu He, Yu Cheng, Yiqian Li, Ting Zhao, Lei Fang et al. · 2023 · Molecular Plant
Rare variants contribute disproportionately to quantitative trait variation in yeast
Joshua S. Bloom, James Boocock, Sebastian Treusch, Meru J. Sadhu, Laura Day, Holly Oates-Barker, Leonid Kruglyak · 2019 · eLife
Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders
the Australian Imaging Biomarkers and Lifestyle study, Nabais, Marta F., the Alzheimer’s Disease Neuroimaging Initiative, Laws, Simon M., Lin, Tian, Vallerga, Costanza L., Armstrong, Nicola J., Blair, Ian P., Kwok, John B., Mather, Karen A. et al. · 2021 · Genome Biology
Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis
Vito M. Butardo, Roslen Anacleto, Sabiha Parween, Irene Samson, Maria Krishna de Guzman, Crisline Mae Alhambra, Gopal Misra, Nese Sreenivasulu · 2016 · PLANT PHYSIOLOGY
Genome-wide association study for grain yield and related traits in elite wheat varieties and advanced lines using SNP markers
Shengxing Wang, Yu-Lei Zhu, Dexin Zhang, Hui Shao, Peng Liu, Jian-Bang Hu, Heng Zhang, Hai-Ping Zhang, Cheng Kuei Chang, Jie Lu et al. · 2017 · PLoS ONE
PLINK: Key Functions for Data Analysis
Susan H. Slifer · 2018 · Current Protocols in Human Genetics
Trichome regulator SlMIXTA‐like directly manipulates primary metabolism in tomato fruit
Shiyu Ying, Min Su, Yu Wu, Lu Zhou, Rao Fu, Yan Li, Hao Guo, Jie Luo, Shouchuang Wang, Yang Zhang · 2019 · Plant Biotechnology Journal
Genotyping-by-sequencing and SNP-arrays are complementary for detecting quantitative trait loci by tagging different haplotypes in association studies
Sandra S. Negro, Emilie Millet, Delphine Madur, Cyril Bauland, Valérie Combes, Claude Welcker, François Tardieu, Alain Charcosset, Stéphane Nicolas · 2019 · BMC Plant Biology
TaTPP‐7A positively feedback regulates grain filling and wheat grain yield through T6P‐SnRK1 signalling pathway and sugar–ABA interaction
Hongxia Liu, Xuemei Si, Zhenyu Wang, Liang-Jing Cao, Lifeng Gao, Xiaolong Zhou, Wenxi Wang, Ke Wang, Chengzhi Jiao, Lei Zhuang et al. · 2023 · Plant Biotechnology Journal
Trends in DNA Methylation with Age Replicate Across Diverse Human Populations
Shyamalika Gopalan, Oana Carja, Maud Fagny, Étienne Patin, Justin W. Myrick, Lisa M. McEwen, Sarah M Mah, Michael Steffen Kobor, Alain Froment, Marcus W. Feldman et al. · 2017 · Genetics
Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley
Liana Nice, Brian Joel Steffenson, Gina Brown‐Guedira, Eduard Akhunov, Chaochih Liu, Thomas J. Y. Kono, Peter Laurent Morrell, Thomas K. Blake, Richard D. Horsley, Kevin P. Smith et al. · 2016 · Genetics
A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits
Feiyang Ji, Qingguo Ma, Wenting Zhang, Jie Liu, Yu Feng, Peng Zhao, Xiaobo Song, Jiaxin Chen, Junpei Zhang, Xin Wei et al. · 2021 · Genome biology
DASH: A Method for Identical-by-Descent Haplotype Mapping Uncovers Association with Recent Variation
Alexander Gusev, Eimear E. Kenny, Jennifer K. Lowe, Jaqueline Salit, Richa Saxena, Sekar Kathiresan, David Altshuler, Jeffrey M. Friedman, Jan L. Breslow, Itsik Pe’er · 2011 · The American Journal of Human Genetics
Genome‐ and transcriptome‐wide association studies reveal the genetic basis and the breeding history of seed glucosinolate content in Brassica napus
Zengdong Tan, Zhaoqi Xie, Lihong Dai, Yuting Zhang, Hu Zhao, Shan Tang, Lili Wan, Xuan Yao, Liang Guo, Dengfeng Hong · 2021 · Plant Biotechnology Journal
False discovery rate control in genome-wide association studies with population structure
Matteo Sesia, Stephen Bates, Emmanuel J. Candès, Jonathan Marchini, Chiara Sabatti · 2021 · Proceedings of the National Academy of Sciences
Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits
Xiaofeng Cai, Xuepeng Sun, Chenxi Xu, Honghe Sun, Xiaoli Wang, Chenhui Ge, Zhonghua Zhang, Quanxi Wang, Zhangjun Fei, Chen Jiao et al. · 2021 · Nature Communications
Perspectives on Human Population Structure at the Cusp of the Sequencing Era
John Novembre, Sohini Ramachandran · 2011 · Annual Review of Genomics and Human Genetics
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1 , ortholog to green revolution dwarf alleles in rice and barley
Luis A. Barboza, Sigi Effgen, Carlos Alonso‐Blanco, Rik Kooke, Joost J. B. Keurentjes, Maarten Koornneef, Rubén Alcázar · 2013 · Proceedings of the National Academy of Sciences
Use of biological priors enhances understanding of genetic architecture and genomic prediction of complex traits within and between dairy cattle breeds
Lingzhao Fang, Goutam Sahana, Peipei Ma, Guosheng Su, Ying Yu, Shengli Zhang, Mogens Sandø Lund, Peter Borgen Sørensen · 2017 · BMC Genomics
Analysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice accessions
Xiuxiu Li, Zhuo Chen, Guomin Zhang, Hongwei Lu, Peng Qin, Ming Qi, Ying Yu, Bingke Jiao, Xianfeng Frank Zhao, Qiang Gao et al. · 2020 · Science China Life Sciences
Estimating FST and kinship for arbitrary population structures
Alejandro Ochoa, John D. Storey · 2021 · PLoS Genetics
Regain flood adaptation in rice through a 14-3-3 protein OsGF14h
Jian Sun, Guangchen Zhang, Zhibo Cui, Ximan Kong, Xiaoyu Yu, Rui Gui, Yuqing Han, Zhuan Li, Hong Lang, Yuchen Hua et al. · 2022 · Nature Communications
Patterns of genomic and phenomic diversity in wine and table grapes
Zoë Migicovsky, Jason Sawler, Kyle M. Gardner, Mallikarjuna K. Aradhya, Bernard Prins, Heidi R. Schwaninger, Carlos D. Bustamante, Edward S. Buckler, Gan‐Yuan Zhong, Patrick J. Brown et al. · 2017 · Horticulture Research
Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon
Padma Nimmakayala, Amnon Levi, Lavanya Abburi, Venkata Lakshmi Abburi, Yan R. Tomason, Thangasamy Saminathan, Venkata Gopinath Vajja, Sridhar Achary Malkaram, Rishi Reddy, Todd C. Wehner et al. · 2014 · BMC Genomics
Cancer classification in the genomic era: five contemporary problems
Qingxuan Song, Sofia Diana Merajver, Jun Z. Li · 2015 · Human Genomics
Genome-Wide Association Study Reveals Multiple Novel QTL Associated with Low Oxygen Tolerance in Hybrid Catfish
Xiaoxiao Zhong, Xiaozhu Wang, Tao Zhou, Yulin Jin, Suxu Tan, J Chen, Xin Geng, Ning Li, Huitong Shi, Qifan Zeng et al. · 2017 · Marine Biotechnology
RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method
Kosuke Hamazaki, Hiroyoshi Iwata · 2020 · PLoS Computational Biology
A Comparison of Association Methods Correcting for Population Stratification in Case–Control Studies
Chengqing Wu, Andrew Thomas DeWan, Josephine J. Hoh, Zuoheng Wang · 2011 · Annals of Human Genetics
Enhancing genomic prediction with genome-wide association studies in multiparental maize populations
Yang Bian, James Brendan Holland · 2017 · Heredity
Leveraging genetically simple traits to identify small-effect variants for complex phenotypes
Kathryn E. Kemper, Mathew D. Littlejohn, Thomas Lopdell, Ben J. Hayes, Louise E. Bennett, Roderick P. W. Williams, Xiuhong Xu, Peter M. Visscher, MJ Carrick, Michael Edward Goddard · 2016 · BMC Genomics