Genomic analysis improves the control of inbreeding depression on dairy cow fertility

Good fertility of dairy cows impacts the profitability, sustainability and animal welfare of the dairy sector. MSc Katja Martikainen studied in her doctoral dissertation the use of genomic data in the estimation and control of inbreeding depression on female fertility in Finnish Ayrshire cattle. The studies were carried out at the Department of Agricultural Sciences.

Not only is good fertility of dairy cows necessary for milk production, it is also economically important for farmers and impacts the sustainability of the dairy sector. However, poor fertility has been among the most common reasons for culling of dairy cows in Finland in recent years. Fertility traits are sensitive for inbreeding depression, which is defined as impairment in phenotypic performance due to inbreeding. Because inbreeding is unavoidable in closed populations, examining and controlling the harmful effects of inbreeding is important for restraining inbreeding depression.

The overall aim of Martikainen’s thesis was to compare different estimates of inbreeding and to detect genomic regions responsible for inbreeding depression on female fertility traits. The analyses were performed using pedigree and genomic data. The results indicated that pedigree data is insufficient to detect inbreeding depression on fertility. However, statistically significant inbreeding depression was observed when using genomic measures of inbreeding. Dissecting inbreeding to chromosomal segments revealed regions where increased inbreeding was associated with reduced fertility. Examining the genes in the identified regions could provide more insight into the mechanisms of inbreeding depression.

However, not all homozygosity created by inbreeding is detrimental, but some homozygous ROH genotypes (Runs Of Homozygosity) may have neutral or even beneficial effects on the traits of interest. If the effect of each ROH is estimated simultaneously, some detrimental ROHs may not be found, as the effect is diluted by the neutral and favourable ROHs. In this thesis, an analysis of unique ROH genotypes revealed several rare ROHs with large unfavourable effects on fertility. The findings of Katja Martikainen’s thesis can be utilized for more efficient control of inbreeding depression in the Finnish Ayrshire breeding programme by avoiding the matings of the carriers of detrimental ROH haplotypes.

MSc Katja Martikainen will defend her doctoral dissertation entitled "Genomic analysis of inbreeding depression on fertility traits in Finnish Ayrshire cattle" on 25th November 2020 at 13.00 in the Faculty of Agriculture and Forestry, University of Helsinki. The public defense will take place in lecture room B3, Forest Sciences Building, Latokartanonkaari 7. Professor Erling Strandberg from Sveriges lantbruksuniversitet will serve as the opponent and Professor Pekka Uimari as the custos. The dissertation is published in the series Dissertationes Schola Doctoralis Scientiae Circumiectalis, Alimentariae, Biologicae. The dissertation is available via the E-thesis –service.

The public defense can also be followed remotely using the following link: Meeting ID: 68 132 714 795, Password: 831831.

Contact: Katja Martikainen