scholarly journals Effect of population structure corrections on the results of association mapping tests in complex maize diversity panels

2011 ◽  
Vol 122 (6) ◽  
pp. 1149-1160 ◽  
Author(s):  
Sofiane Mezmouk ◽  
Pierre Dubreuil ◽  
Mickaël Bosio ◽  
Laurent Décousset ◽  
Alain Charcosset ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Mapping ◽  
Maize Diversity

scholarly journals Analysis of Population Structure and Association Mapping among Popcorn Inbred Lines using SSR markers

2013 ◽  
Vol 45 (4) ◽  
pp. 358-368 ◽  
Author(s):  
Jin-Sun Jang ◽  
Eun-Ha Chang ◽  
Kyu Jin Sa ◽  
Byeong Wan Kim ◽  
Jong-Hwa Kim ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Mapping ◽  
Ssr Markers ◽  
Inbred Lines

scholarly journals Efficient Control of Population Structure in Model Organism Association Mapping

Genetics ◽  
2008 ◽  
Vol 178 (3) ◽  
pp. 1709-1723 ◽  
Author(s):  
Hyun Min Kang ◽  
Noah A. Zaitlen ◽  
Claire M. Wade ◽  
Andrew Kirby ◽  
David Heckerman ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Mapping ◽  
Model Organism ◽  
Efficient Control

scholarly journals Population structure and association mapping to detect QTL controlling tomato spotted wilt virus resistance in cultivated peanuts

2018 ◽  
Vol 6 (5) ◽  
pp. 516-526 ◽  
Author(s):  
Jing Li ◽  
Yueyi Tang ◽  
Alana L. Jacobson ◽  
Phat M. Dang ◽  
Xiao Li ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Mapping ◽  
Virus Resistance ◽  
Tomato Spotted Wilt Virus ◽  
Tomato Spotted Wilt ◽  
Wilt Virus

Population structure and association mapping of yield contributing agronomic traits in foxtail millet

2014 ◽  
Vol 33 (6) ◽  
pp. 881-893 ◽  
Author(s):  
Sarika Gupta ◽  
Kajal Kumari ◽  
Mehanathan Muthamilarasan ◽  
Swarup Kumar Parida ◽  
Manoj Prasad
Keyword(s):  
Population Structure ◽  
Association Mapping ◽  
Agronomic Traits ◽  
Foxtail Millet

scholarly journals Effect of population structure and kinship relationships on the results of association mapping tests of growth and wood quality traits in four Eucalyptuspopulations

2011 ◽  
Vol 5 (S7) ◽  
Author(s):  
Eduardo Pablo Cappa ◽  
Maria C Martínez ◽  
Martín N Garcia ◽  
Pamela V Villalba ◽  
Susana N Marcucci Poltri
Keyword(s):  
Population Structure ◽  
Association Mapping ◽  
Wood Quality ◽  
Quality Traits

Association mapping of leaf traits, flowering time, and phytate content in Brassica rapa

Genome ◽  
2007 ◽  
Vol 50 (10) ◽  
pp. 963-973 ◽  
Author(s):  
Jianjun Zhao ◽  
Maria-João Paulo ◽  
Diaan Jamar ◽  
Ping Lou ◽  
Fred van Eeuwijk ◽  
...  
Keyword(s):  
Population Structure ◽  
Qtl Mapping ◽  
Association Mapping ◽  
Brassica Rapa ◽  
Morphological Traits ◽  
Genetic Basis ◽  
Leaf Traits ◽  
Structure Association ◽  
Phytate Content ◽  
Trait Associations

Association mapping was used to investigate the genetic basis of variation within Brassica rapa , which is an important vegetable and oil crop. We analyzed the variation of phytate and phosphate levels in seeds and leaves and additional developmental and morphological traits in a set of diverse B. rapa accessions and tested association of these traits with AFLP markers. The analysis of population structure revealed four subgroups in the population. Trait values differed between these subgroups, thus defining associations between population structure and trait values, even for traits such as phytate and phosphate levels. Marker–trait associations were investigated both with and without taking population structure into account. One hundred and seventy markers were found to be associated with the observed traits without correction for population structure. Association analysis with correction for population structure led to the identification of 27 markers, 6 of which had known map positions; 3 of these were confirmed in additional QTL mapping studies.

scholarly journals Multiplex Confounding Factor Correction for Genomic Association Mapping with Squared Sparse Linear Mixed Model

2017 ◽  
Author(s):  
Haohan Wang ◽  
Xiang Liu ◽  
Yunpeng Xiao ◽  
Ming Xu ◽  
Eric P. Xing
Keyword(s):  
Population Structure ◽  
Association Mapping ◽  
Complex Traits ◽  
Association Studies ◽  
Phenotypic Variability ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Confounding Factors ◽  
Genetic Loci ◽  
Genome Wide

AbstractGenome-wide Association Study has presented a promising way to understand the association between human genomes and complex traits. Many simple polymorphic loci have been shown to explain a significant fraction of phenotypic variability. However, challenges remain in the non-triviality of explaining complex traits associated with multifactorial genetic loci, especially considering the confounding factors caused by population structure, family structure, and cryptic relatedness. In this paper, we propose a Squared-LMM (LMM2) model, aiming to jointly correct population and genetic confounding factors. We offer two strategies of utilizing LMM2 for association mapping: 1) It serves as an extension of univariate LMM, which could effectively correct population structure, but consider each SNP in isolation. 2) It is integrated with the multivariate regression model to discover association relationship between complex traits and multifactorial genetic loci. We refer to this second model as sparse Squared-LMM (sLMM2). Further, we extend LMM2/sLMM2 by raising the power of our squared model to the LMMn/sLMMn model. We demonstrate the practical use of our model with synthetic phenotypic variants generated from genetic loci of Arabidopsis Thaliana. The experiment shows that our method achieves a more accurate and significant prediction on the association relationship between traits and loci. We also evaluate our models on collected phenotypes and genotypes with the number of candidate genes that the models could discover. The results suggest the potential and promising usage of our method in genome-wide association studies.

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