Linkage disequilibrium (LD) was estimated along chicken chromosome 4 (GGA4) in a commercial broiler population. Grandparents (n=119) and the offspring (n=608) of a 3-generation QTL design were typed for 8 microsatellites and 29 SNPs along GGA4. On GGA4 there are at least two QTL regions affecting body weight and bone traits. The traditional estimate of D′ was compared to chi2, which was shown to be more conservative and less erratic than D′. There was considerable LD for closely linked markers (<5 cM) but some closely linked markers showed little LD. It was shown that this variation in LD along GGA4 coincided with the presence of QTL, with higher LD for markers underlying QTL regions. While there is considerable variation in the level of LD along a single chromosome, the increased LD in QTL regions suggests that genome-wide association tests with \textasciitilde10 000 SNPs may prove successful.

D. J de Koning, D. Windsor, D. Morrice, P. M Hocking, Dave W Burt, Chris S Haley

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume , , 21.04, 2006
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