Use of lexical analysis to identify positional candidate genes underlying a QTL region.

SUMMARY Candidate genes are being sought for a QTL affecting muscling in the Texel breed of sheep, on Chromosome 2, close to, but centred distally from Myostatin. Using regions of conserved synteny between humans/cattle/sheep, 123 genes were identified within the equivalent human region. In order to rank these candidates, lexical analysis was carried out on abstracts relating to these genes using the WordSmith program. Myostatin was included, as a gene known to effect muscling (a positive control). Through using the WordList, KeyWords and Concord features of this program and using muscle , lean , fat , adipose , hypertrophy , hyperplasia and growth as search words the number of candidate genes was narrowed to 26 including myostatin. Based on these results lexical analysis offers an opportunity to rapidly reduce the number of candidate genes requiring further investigation within a given region. Keywords: Lexical analysis, QTL, muscle INTRODUCTION QTL studies aim to identify markers within a region of DNA accounting for variation seen in a trait caused by an unknown gene variant. In comparison to the human gene map, relatively few genes have been mapped in cattle and even fewer in sheep (O’Brien and Menotti-Raymond, 1999). So although a region of DNA may be identified through QTL work in sheep, it is unlikely that potential candidate genes will be identified using the current sheep gene map. Mapping of sheep/cattle/humans genes shows regions of conserved synteny (groups of genes located together), although rearrangement in their order and exclusions exist (O’Brien and Menotti-Raymond, 1999