Comparison of mixed-model approaches for association mapping.
Association-mapping methods promise to overcome the limitations of linkage-mapping methods. The main objectives of this study were to (i) evaluate various methods for association mapping in the autogamous species wheat using an empirical data set, (ii) determine a marker-based kinship matrix using a restricted maximum-likelihood (REML) estimate of the probability of two alleles at the same locus being identical in state but not identical by descent, and (iii) compare the results of association-mapping approaches based on adjusted entry means (two-step approaches) with the results of approaches in which the phenotypic data analysis and the association analysis were performed in one step (one-step approaches). On the basis of the phenotypic and genotypic data of 303 soft winter wheat (Triticum aestivum L.) inbreds, various association-mapping methods were evaluated. Spearman's rank correlation between P-values calculated on the basis of one- and two-stage association-mapping methods ranged from 0.63 to 0.93. The mixed-model association-mapping approaches using a kinship matrix estimated by REML are more appropriate for association mapping than the recently proposed QK method with respect to (i) the adherence to the nominal alpha-level and (ii) the adjusted power for detection of quantitative trait loci. Furthermore, we showed that our data set could be analyzed by using two-step approaches of the proposed association-mapping method without substantially increasing the empirical type I error rate in comparison to the corresponding one-step approaches.
Stich
Benjamin
B
Institute for Plant Breeding, Seed Science, and Poulation Genetics, University of Hohenheim, Stuttgart, Germany.
Möhring
Jens
J
Piepho
Hans-Peter
HP
Heckenberger
Martin
M
Buckler
Edward S
ES
Melchinger
Albrecht E
AE
D002874:Chromosome Mapping / Q000379:methods*; D008957:Models, Genetic; D025341:Principal Component Analysis; D040641:Quantitative Trait Loci / Q000235:genetics; D018709:Statistics, Nonparametric; D014908:Triticum / Q000235:genetics*