Open access publications in the SLU publication database

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.