Whole-genome QTL analysis for MAGIC.
Theor Appl Genet
; 127(8): 1753-70, 2014 Aug.
Article
em En
| MEDLINE
| ID: mdl-24927820
ABSTRACT
KEY MESSAGE 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.
Texto completo:
1
Coleções:
01-internacional
Contexto em Saúde:
1_ASSA2030
Base de dados:
MEDLINE
Assunto principal:
Triticum
/
Mapeamento Cromossômico
/
Genoma de Planta
/
Cruzamentos Genéticos
/
Locos de Características Quantitativas
Tipo de estudo:
Health_economic_evaluation
/
Prognostic_studies
Limite:
Animals
Idioma:
En
Revista:
Theor Appl Genet
Ano de publicação:
2014
Tipo de documento:
Article