Mol Genet Genomics (2007) 277:663–672 DOI 10.1007/s00438-007-0216-2 123 ORIGINAL PAPER Whole-genome linkage disequilibrium screening for complex traits in horses Teruaki Tozaki · Kei-ichi Hirota · Telhisa Hasegawa · Nobushige Ishida · Takashi Tobe Received: 11 December 2006 / Accepted: 25 January 2007 / Published online: 22 February 2007  Springer-Verlag 2007 Abstract The identiWcation of candidate genes for signiWcant traits is crucial. In this study, we developed and tested eVective and systematic methods based on linkage disequilibrium (LD) for the identiWcation of candidate regions for genes with Mendelian inheri- tance and those associated with complex traits. Our approach entailed the combination of primary screen- ing using pooled DNA samples based on TAC, sec- ondary screening using an individual typing method and tertiary screening using a permutation test based on the diVerences in the haplotype frequency between two neighbouring microsatellites. This series of meth- ods was evaluated using horse coat colour traits (chest- nut/non-chestnut) as a simple Mendelian inheritance model. In addition, the methods were evaluated using a complex trait model constructed by mixing samples from chestnut and non-chestnut horses. Using both models, the methods could detect the expected regions for the horse coat colour trait. The results revealed that LD extends up to several centimorgans in horses, indi- cating that whole-genome LD screening in horses could be performed systematically and eYciently by combining the above-mentioned methods. Since genetic maps based on microsatellites have been con- structed for many other species, the approaches pres- ent here could have wide applicability. Keywords Horse · Linkage disequilibrium (LD) · TAC · Pooled DNA · Microsatellite · Haplotype Introduction At present, whole-genome sequence information and many annotated genes are available for many species, including humans and mice, while many signiWcant traits and diseases are also clinically observed. How- ever, because of complex mechanisms such as gene– gene interactions, the relationship between traits and genes is not well established. In this study, we devel- oped eYcient and systematic approaches designed to isolate genes with Mendelian inheritance and complex traits using linkage disequilibrium (LD) screening. Parametric linkage analysis is an extremely eYcient method for the identiWcation of genetic factors exhibit- ing Mendelian inheritance. Many genes from the human genome have been isolated and identiWed as genetic factors that underlie diseases (Funayama et al. 2002; Cader et al. 2003). However, this approach can- not be used for the detection and identiWcation of genetic factors underlying complex diseases that involve several genes and environmental factors. Communicated by S. Hohmann. T. Tozaki (&) · K. Hirota Department of Molecular Genetics, Laboratory of Racing Chemistry (LRC), 1731-2 Tsurutamachi, Utsunomiya, Tochigi 320-0851, Japan e-mail: ttozaki@lrc.or.jp; ttozaki@nyc.odn.ne.jp T. Hasegawa · N. Ishida Equine Research Institute, Japan Racing Association (JRA), 321-4 Tokami-cho, Utsunomiya, Tochigi 320-0856, Japan T. Tobe Department of Medicinal Information, School of Pharmaceutical Sciences, Showa University, 1-5-8, Hatanodai, Shinagawa, Tokyo 142-8555, Japan