Agrifood Research Reports 109

Conventional breeding schemes for dairy cattle are based on phenotypic information obtained from individuals and/or their relatives and progeny testing of the young bull candidates. The genetic model used in the evaluation process of the animals does not assume the underlying genes of the quantitative traits to be known. Knowing the chromosomal areas or actual genes affecting the traits would add more information to be used in the selection decisions which would potentially lead to higher genetic response. The first objective of this study was to map quantitative trait loci (QTL) affecting economically important traits: milk production traits, health traits and fertility traits in the Finnish Ayrshire population. The second objective was to investigate the effects of using QTL information in marker-assisted selection (MAS) on the genetic response and the linkage disequilibrium between the different parts of the genome. Whole genome scans were carried out on a grand-daughter design with 12 half-sib families and a total of 493 sons. Twelve different traits were studied: milk yield, protein yield, protein content, fat yield, fat content, somatic cell score (SCS), mastitis treatments, other veterinary treatments, days open, fertility treatments, non-return rate, and calf mortality. A total of 150 markers were used in all other studies except for fertility traits where 171 markers were used. The average spacing of the markers was 20 cM with 2 to 14 markers per chromosome. Associations between markers and traits were analyzed with multiple marker regression. Chromosomes were analyzed separately and by using QTL on other chromosomes as cofactors. Significance was determined by permutation and genome-wise P-values obtained by Bonferroni correction. The benefits from MAS were investigated by simulation: a conventional progeny testing scheme was compared to a scheme where QTL information was used within families to select among full-sibs in the male path. Two QTL on different chromosomes were modelled. The effects of different starting frequencies of the favourable alleles and different size of the QTL effects were evaluated. In the whole genome scans of milk, health and fertility traits of Finnish Ayrshire a large number of QTL, 48 in total, were detected at 5% or higher chromosome-