Haplotype frequencies were estimated using a Bayesian approach implemented with the FBAT software, which carries out a family-based test for association and/or linkage between the haplotype locus and any trait influencing gene. These haplotype frequencies closely agreed with results from a maximum likelihood method implemented via an expectation-maximization (EM) algorithm (Long et al., 1995). Haploview V. 2.0.2 (Whitehead Institute for Biomedical Research, Cambridge, MA) was used to produce LD matrices. Haplotype blocks were reconstructed using the pairs of markers with LD greater than 0.8 (Gabriel et al., 2002).
