Research
Interval mapping of quantitative trait loci with selective DNA pooling data
-
* Corresponding author: Jack CM Dekkers jdekkers@iastate.edu
1 Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa 50011, USA
2 Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
3 Pioneer Hi-Bred International, Johnston, Iowa 50131, USA
Genetics Selection Evolution 2007, 39:685-709 doi:10.1186/1297-9686-39-6-685
The electronic version of this article is the complete one and can be found online at: http://www.gsejournal.org/content/39/6/685
| Received: | 10 October 2006 |
| Accepted: | 21 May 2007 |
| Published: | 6 December 2007 |
© 2007 INRA, EDP Sciences
Abstract
Selective DNA pooling is an efficient method to identify chromosomal regions that harbor quantitative trait loci (QTL) by comparing marker allele frequencies in pooled DNA from phenotypically extreme individuals. Currently used single marker analysis methods can detect linkage of markers to a QTL but do not provide separate estimates of QTL position and effect, nor do they utilize the joint information from multiple markers. In this study, two interval mapping methods for analysis of selective DNA pooling data were developed and evaluated. One was based on least squares regression (LS-pool) and the other on approximate maximum likelihood (ML-pool). Both methods simultaneously utilize information from multiple markers and multiple families and can be applied to different family structures (half-sib, F2 cross and backcross). The results from these two interval mapping methods were compared with results from single marker analysis by simulation. The results indicate that both LS-pool and ML-pool provided greater power to detect the QTL than single marker analysis. They also provide separate estimates of QTL location and effect. With large family sizes, both LS-pool and ML-pool provided similar power and estimates of QTL location and effect as selective genotyping. With small family sizes, however, the LS-pool method resulted in severely biased estimates of QTL location for distal QTL but this bias was reduced with the ML-pool.
Keywords:
selective DNA pooling; interval mapping; QTLResearch
(To access the full article, please see PDF)