Effects of Maternal Lineages Grouped by Mitochondrial Genotypes on Milk Yield and Composition

Maternal lineages grouped by several methods of classification using mitchondrial DNA sequence characteristics were evaluated with animal models. Maternal pedigrees for cattle from a selection experiment begun in 1968 were traced to the earliest female member in the Holstein-Friesian Herd Book, and foundation females were assigned to maternal lineages. Mitochondrial DNA displacement loop sequence data were available for 36 lineages; all cows within lineages were considered to be identical for useful DNA sequence polymorphisms. Maternal lineages were grouped according to base pair substitution at a single locus, clustering based on displacement loop sequences, or genotypes defined by sequence and restriction site differences. Base pair substitution (adenine to guanine) at nucleotide 169 defined two maternal lineage groups that differed significantly for fat yield and percentage and estimated milk energy. Clustering the 36 maternal lineages by using 16 mitochondrial DNA displace- ment loop sequence differences produced 24 groups that significantly influenced fat percentage and energy concentration in milk. Decreasing the number of clustered groups from 24 to 14 produced groups that differed at some polymorphic sites but remained identical for most. The F statistics for 14 groups were larger, but significant outcomes were observed for the same traits. Genotype groups previously defined by sequence and restriction fragment length differences did not have a significant effect on yield or composition of cows in 29 maternal lineages.