Allele frequencies for all loci wer

Allele frequencies for all loci were determined directly by counting. Unbiased estimates of gene diversity (expected heterozygosity) with associated standard errors were computed for all locus/population combinations according to Nei (1987). The mean number of alleles per locus (MNA) was also calculated as an index of sample diversity. A size-adjusted MNA value was calculated using 1000 iterations of a resampling method.B. taurus-associated alleles were selected by comparing pooled European breed data with pooled data from all Indian samples. A scaled frequency differential (SFD) was calculated for each allele by the formulawhere PE is the average frequency of the allele in the 11 European breeds and PI is the average frequency in the seven Indian breeds assayed. The higher of these two values is denoted by the denominator. This SFD measure was combined with other criteria to define three categories of PAAs, each a subset of the previous. Initially, zebu alleles were defined as those that are at higher frequency in the Indian population than in the European population, and taurine alleles are the converse. Category I PAAs include both zebu and taurine alleles that have a frequency of greater than 5% in the respective parental population. Alleles with a frequency lower than this were removed from the analysis. Category II PAAs are the subset of category I, which are taurine alleles, that is, those found at higher frequency within B. taurus populations. Category III PAAs are a more stringent selection of taurine-associated alleles and are those found at a frequency of at least 20% in European populations and an SFD of greater than 40%. The average frequencies of categories II and III PAAs were calculated for each breed and these values were used as measures of B. taurus admixture.