Whole‑genome QTL analysis for MAGIC
Date
2014
Authors
Verbyla, A.
George, A.
Cavanagh, C.
Verbyla, K.
Editors
Advisors
Journal Title
Journal ISSN
Volume Title
Type:
Journal article
Citation
Theoretical and Applied Genetics, 2014; 127(8):1753-1770
Statement of Responsibility
Arūnas P. Verbyla, Andrew W. George, Colin R. Cavanagh, Klara L. Verbyla
Conference Name
Abstract
An efficient whole genome method of QTL analysis is presented for Multi-parent advanced generation integrated crosses. Multi-parent advanced generation inter-cross (MAGIC) populations have been developed for mice and several plant species and are useful for the genetic dissection of complex traits. The analysis of quantitative trait loci (QTL) in these populations presents some additional challenges compared with traditional mapping approaches. In particular, pedigree and marker information need to be integrated and founder genetic data needs to be incorporated into the analysis. Here, we present a method for QTL analysis that utilizes the probability of inheriting founder alleles across the whole genome simultaneously, either for intervals or markers. The probabilities can be found using three-point or Hidden Markov Model (HMM) methods. This whole-genome approach is evaluated in a simulation study and it is shown to be a powerful method of analysis. The HMM probabilities lead to low rates of false positives and low bias of estimated QTL effect sizes. An implementation of the approach is available as an R package. In addition, we illustrate the approach using a bread wheat MAGIC population.
School/Discipline
Dissertation Note
Provenance
Description
Access Status
Rights
© Springer-Verlag Berlin Heidelberg 2014