Sequence variation in D-loop mtDNA of cow lineages selected for high and low maternal effects on milk production

The four highest and four lowest cow lineages for milk production were selected from 324 maternal lineages of the Israeli Holstein population. For a single cow from each lineage, the mitochondrial D-loop region was amplified using the polymerase chain reaction and directly sequenced for 719bp. Eighteen polymorphic sites were found of which 17 were substitutions and one was an insertion. Only two alleles were found for each polymorphic site, one of which corresponded to the sequence of Anderson et al. (1982), which was the more frequent allele, in all but two sites. None of the polymorphic sites had an apparent effect on milk production, even though an effect > or = 0.33 phenotypic standard deviations, equivalent to 470 kg milk, could be detected by this experimental design. Furthermore, there was no indication that moderately increasing the sample size would have altered the result, since all rare alleles found in more than a single lineage were found in both the high and low subgroups.