On the mapping of quantitative trait loci at marker and non-marker locations

A - Papers appearing in refereed journals

Walling, G. A., Haley, C. S., Perez-Enciso, M., Thompson, R. and Visscher, P. M. 2002. On the mapping of quantitative trait loci at marker and non-marker locations. Genetics Research. 79 (1), pp. 97-106.

AuthorsWalling, G. A., Haley, C. S., Perez-Enciso, M., Thompson, R. and Visscher, P. M.
Abstract

Previous studies have noted that the estimated positions of a large proportion of mapped quantitative trait loci (QTLs) coincide with marker locations and have suggested that this indicates a bias in the mapping methodology. In this study we predict the expected proportion of QTLs with positions estimated to be at the location of a marker and further examine the problem using simulated data. The results show that the higher proportion of putative QTLs estimated to be at marker positions compared with non-marker positions is an expected consequence of the estimation methods. The study initially focused on a single interval with no QTLs and was extended to include multiple intervals and QTLs of large effect. Further, the study demonstrated that the larger proportion of estimated QTL positions at the location of markers was not unique to linear regression mapping. Maximum likelihood produced similar results, although the accumulation of positional estimates at outermost markers was reduced when regions outside the linkage group were also considered. The bias towards marker positions is greatest under the null hypothesis of no QTLs or when QTL effects are small. This study discusses the impact the findings could have on the calculation of thresholds and confidence intervals produced by bootstrap methods.

Year of Publication2002
JournalGenetics Research
Journal citation79 (1), pp. 97-106
Digital Object Identifier (DOI)doi:10.1017/S0016672301005420
Open accessPublished as non-open access
Funder project or code445
513
Research in statistics relevant to biological processes
Output statusPublished
Publication dates
Print02 Apr 2002
Publication process dates
Accepted13 Sep 2001
Copyright licensePublisher copyright
ISSN0016-6723
PublisherCambridge University Press (CUP)

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