Maternal lineage effects and genetic diversity in the UK dairy population

Abstract

There is a perceived importance of maternal families among dairy cattle breeders. The aim o f this study was to estimate the magnitude of the component of phenotypic variance attributable to maternal lineage for conformation and production traits in the UK Holstein Friesian dairy cow population. Various population parameters were also estimated.

Advanced statistical methodology including restricted maximum likelihood was used to estimate maternal lineage variance. Production traits at the Langhill dairy herd were analysed to provide insight into feed intake and efficiency traits. Only fat yield had a significant component of phenotypic variance attributable to maternal lineage. In this trait 4% o f the variance was attributable to maternal lineage. Production records of over 50,000 cows from the UK Holstein Friesian population were used to estimate maternal lineage variance with a contemporary data structure. This data structure was used to reduce the average within maternal family nuclear genetic relationship while maintaining the same expected magnitude of maternal lineage variance.

Dairy cattle breeders stress the importance of cow families in breeding for good conformation. To investigate this, type classification records of 32,000 heifers were analysed and maternal lineage variances estimated for all 23 conformation traits. Significance of the maternal lineage component was determined using a likelihood ratio test. Most researchers use an incorrect test when determining the significance level o f a component. An explanation of the correct test is given. Principal component analysis was used to determine the number of independent components accounting for the variance in type traits. This number was then used to establish the significance level of the variance component test statistic. The only type traits to show significant effects were stature, a linear type trait, and body, a composite trait. These traits had maternal lineage variance components of 1.0% and 1.5 % respectively.

Population parameters of the UK Holstein Friesian cow population were estimated. Conservation biology parameters demonstrated that, when 1960 was treated as a pseudo founder generation, only an equivalent of 1% of the founders were responsible for the genomic diversity of the 1997 population. It was shown that the introduction of large numbers o f Holsteins from North America over recent years has reduced the level of inbreeding but at the same time reduced the genetic diversity of the population. It was found that in 1997 one ancestor accounted for 5% of the genome of the UK Holstein Friesian cow population. Average degree of relationship was also shown to be increasing at a rate o f 0.07% per year. It can be hypothesised that in the future the global Holstein Friesian population will show an increase in average inbreeding coefficient and average pairwise degree of relationship.

A theoretical investigation was made of the consequences of incorrect maternal family assignment, through both pedigree errors and the inadequate tracing of pedigrees, on the magnitude of the variance component estimated. This demonstrated that the under­estimation of maternal lineage variance occurs unless complete family information is available and accurately recorded.