Abstract
Inbreeding gives rise to continuous lengths of homozygous genotypes called runs of homozygosity (ROH) that occur when identical haplotypes are inherited from both parents. ROHs are enriched for deleterious recessive alleles and can therefore be linked to inbreeding depression, defined as decreased phenotypic performance of the animals. However, not all ROHs within a region are expected to have harmful effects on the trait of interest. We aimed to identify ROHs that unfavourably affect female fertility and milk production traits in the Finnish Ayrshire population. The estimated effect of ROHs with the highest statistical significance varied between parities from 9 to 17 days longer intervals from calving to first insemination, from 13 to 38 days longer intervals from first to last insemination and from 0.3 to 1.0 more insemination per conception. Similarly, for milk production traits ROHs were associated with a reduction of 208 kg for milk yield, 7 kg for protein yield and 16 kg for fat yield. We also found regions where ROHs displayed unfavourable effects across multiple traits. Our findings can be exploited for more efficient control of inbreeding depression, for example by minimizing the occurrence of unfavourable haplotypes as homozygous state in breeding programmes.
Highlights
Inbreeding gives rise to continuous lengths of homozygous genotypes called runs of homozygosity (ROH) that occur when identical haplotypes are inherited from both parents
Inbreeding gives rise to continuous segments of homozygous genotypes known as runs of homozygosity (ROH), which are present in an individual if both parents transmit identical haplotypes to their offspring[6]
A 1% increase in FROH was associated with 1.72 days increase in days open and 20 kg decrease in 205-day milk yield[3], and with 0.4 days longer insemination interval in heifers[5]
Summary
Inbreeding gives rise to continuous lengths of homozygous genotypes called runs of homozygosity (ROH) that occur when identical haplotypes are inherited from both parents. Since the patterns of inbreeding vary throughout the genome[10], identification of genomic regions with associations between ROHs and impaired fertility or milk production traits will allow breeding programmes to balance more efficiently between genetic gain and levels of inbreeding. Pryce et al.[4], Kim et al.[11] and Martikainen et al.[12] reported unfavourable phenotypic effects on reproduction traits for several genomic regions in an ROH in Holstein, Jersey and Finnish Ayrshire cattle, respectively. Howard et al.[13] presented a method to estimate the effect separately for each unique ROH genotype Using this method, Baes et al.[14] were able to identify genotypes within ROHs having unfavourable effects on production, reproduction and health traits in Canadian Dairy cows. For the 305-day milk yield, the animals with the most extreme ROH genotype on chromosome 11 were estimated to produce on average 690 kg less milk than animals without ROH
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