Comparing Different Statistical Models and Multiple Testing Corrections for Association Mapping in Soybean and Maize

Frontiers in Plant Science
Avjinder S KalerLarry C Purcell

Abstract

Association mapping (AM) is a powerful tool for fine mapping complex trait variation down to nucleotide sequences by exploiting historical recombination events. A major problem in AM is controlling false positives that can arise from population structure and family relatedness. False positives are often controlled by incorporating covariates for structure and kinship in mixed linear models (MLM). These MLM-based methods are single locus models and can introduce false negatives due to over fitting of the model. In this study, eight different statistical models, ranging from single-locus to multilocus, were compared for AM for three traits differing in heritability in two crop species: soybean (Glycine max L.) and maize (Zea mays L.). Soybean and maize were chosen, in part, due to their highly differentiated rate of linkage disequilibrium (LD) decay, which can influence false positive and false negative rates. The fixed and random model circulating probability unification (FarmCPU) performed better than other models based on an analysis of Q-Q plots and on the identification of the known number of quantitative trait loci (QTLs) in a simulated data set. These results indicate that the FarmCPU controls both false positives and fals...Continue Reading

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Citations

Oct 28, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Cloe S PogodaBrent S Hulke
Jan 4, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Manje GowdaBoddupalli M Prasanna
Jan 13, 2021·International Journal of Molecular Sciences·Mengdi LiGuoping Zhang
Dec 5, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·David Sewordor GaikpaThomas Miedaner
Apr 15, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Jacob I MarshDavid Edwards
May 11, 2021·3 Biotech·Kumari ShikhaB Sinha
Aug 11, 2021·Plants·Gunlayarat BhusudsawangKittipat Ukoskit
Sep 7, 2021·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Pushpendra K Gupta
Sep 18, 2021·Frontiers in Plant Science·C Joe MartinKarl Peter Pauls

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Methods Mentioned

BETA
genotyping
PCA

Software Mentioned

mrMLM
FarmCPU
GAPIT
script
FEM
FASTmrEMMA
STRUCTURE
GAPIT R package
R
MLM

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