To the Editor:

In the article "Lab mouse genome isn't simple" by Cathy Holding, it is implied that the (not-so surprising) complex haplotype structure of the mouse genome will hinder the process of gene identification for quantitative traits. It simply isn't true.

The structure of genetic variation in the mouse, as elucidated by Yalcin et al. (PNAS, 101:9734-9739, June 29, 2004), is problematic only for a limited and controversial approach to QTL analysis that is based on exploiting haplotype structure (e.g., Grupe et al., Science, 292:1915-1918, June 8, 2001). This approach is based on the assumption that the mouse genome can be represented as large contiguous blocks with common ancestry. A highly fragmented ancestral structure of the common mouse strains would make this approach untenable.

However, the most widely used methods of QTL analysis (Lander and Botstein, Genetics, 121:185-199, January 1989) make no such assumptions and...

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