Gene mapping of reproduction traits in dairy cattle

Abstract: In this thesis my aims were to map genes affecting reproduction in cattle and to explore the correlated effect of these genes on yield traits. This knowledge is expected to provide novel insights into the biological processes underlying reproduction traits and to identify individual causal polymorphisms or genetic markers for practical application in marker-assisted and genomic selection strategies. A wide range of female fertility traits has been recorded for cattle indigenous to the Nordic countries. Moreover, the trait definitions have been standardized across these countries and the cattle industry has made its data available for research. The research findings, themselves, highlight the benefit of such a comprehensive data source and increasingly detailed genomic information ranging from relatively few microsatellites to full sequence profiles. In manuscript I, a genome scan was performed using linkage analysis with microsatellite markers in order to identify genomic areas of interest. Twenty-six quantitative trait loci (QTL) affecting female fertility were identified. In manuscript II, the trait fertility treatments were decomposed into sub-traits, four QTL for retained placenta were revealed. These QTLs and additional 24 QTL regions discovered in manuscript I, were analyzed for effects on yield traits. Sixteen of the genomic regions containing QTL for female fertility also harbored QTL for milk production or milk composition traits. Twelve QTL regions with effects on nine different fertility traits did not harbor any QTL for milk production or milk composition traits. When. An association study based on 50k single nucleotide polymorphism (SNP) data indicated significant associations for 4,474 SNPs with eight different female fertility traits in Nordic Holstein. Of these SNPs, 152 were validated in both the Danish Jersey and the Nordic Red breeds, the most significant results were found on Chromosomes1, 4, 9, 11 and 13. Small significant regions on chromosomes 4 and 13 were analyzed by sequencing to further focus the genomic region in which candidate genes and possible causative mutations may be localized. Subsequently, new calving data was added and a validation study was performed, which confirmed 321 of 424 SNPs significantly associated with 14 calving traits. It was determined, however, that the analysis of the new data alone had low power, and an analysis of the full data set was more powerful.

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