Utilisation of marker assisted selection in the New Zealand dairy industry : a thesis presented in partial fulfilment of the requirements for the degree of Master of Agricultural Science in Animal Breeding and Genetics at Massey University

Abstract

The genetic and economic benefits of marker assisted selection (MAS) to the New Zealand dairy industry were evaluated. The genetic marker was assumed to be the additive quantitative trait loci (QTL) itself and thus no recombination existed between the marker and QTL. Three sizes of QTL were evaluated; 0.1, 0.3 and 0.5 genetic standard deviations (σG), at three starting QTL frequencies; 0.01, 0.10 and 0.35. Three MAS strategies were evaluated and compared to the current New Zealand breeding scheme that had no genotypic knowledge of the QTL (control). The economic benefits, for the three MAS strategies, were calculated from the returns of extra milk produced, resultant from superior rates of increase in QTL frequency, less the costs of identifying the QTL linked genetic markers and subsequent genotyping. The size of the QTL had a major effect on the economic viability of the MAS strategies. For a 0.1 σG QTL, the most profitable strategy to utilise the QTL was to ignore it and continue with the current breeding scheme. For a single additive QTL of size 0.3 σG, it had to be at the 0.35 starting frequency for the MAS strategy of progeny testing only homozygous and heterozygous QTL bulls, to be more profitable than the current breeding scheme. This same MAS strategy at the 0.5 σG sized QTL was the most profitable for the range of QTL starting frequencies evaluated. The MAS strategy where only homozygous QTL bulls were progeny tested, was not economically viable for any of the QTL sizes and frequencies. This was due to the reduced selection differential on the cow to bull and bull to bull pathways. The third MAS strategy investigated utilised the current breeding scheme but included knowledge of the QTL genotype for the active cows and bulls. Superior rates of genetic gain were achieved at all QTL sizes and frequencies, but it was only economically profitable for a 0.5 σG QTL with a starting frequency of 0.35. Selection on large QTL with this strategy resulted in short-term genetic gain, but long-term loss. This was due to less selection intensity being applied to the quantitative background, in comparison to the control.