# Haplotypes affecting stillbirth and fertility in Icelandic Dairy Cattle

## TL;DR

This study identifies specific genetic regions in Icelandic Dairy Cattle linked to increased stillbirths and reduced fertility.

## Contribution

The study discovers 19 haplotypes affecting stillbirth and fertility in Icelandic Dairy Cattle using HHD and GWAS.

## Key findings

- 19 haplotypes significantly impact stillbirth rates or fertility in Icelandic Dairy Cattle.
- Two HHD regions on chromosomes BTA13 and BTA8 are linked to both lower fertility and higher stillbirths.
- No large structural variations were found in HHD regions, suggesting single mutations or small variations.

## Abstract

In the last decades, the rate of stillbirths in the Icelandic Dairy Cattle population has increased. Some of these stillbirths may be caused by recessive lethal mutations segregating in the population. These alleles can be identified by detecting homozygous haplotype deficiency (HHD) in genotyped animals. The aim of this study was to find genomic regions affecting stillbirth and fertility in the Icelandic Dairy Cattle population. We analysed genotypes from 20,557 animals with 35,481 autosomal markers. We identified HHD segments and estimated their effects on stillbirths and insemination failure, measured as non-return rates. We conducted genome-wide association studies (GWAS) for stillbirth and five fertility traits: interval from first to last inseminations, conception rate, number of inseminations, calving interval and infertility. While no GWAS association reached the genome-wide significance threshold, some of the top signals co-located with HHD haplotypes. A total of 19 haplotypes significantly either decreased fertility, or increased incidence of stillbirths, or both. Two HHD regions on BTA13: 43,577,221–59,026,521 and BTA8: 83,276,598–84,472,391 were associated with both lower fertility and higher incidence of stillbirths. We found no evidence of large structural variations in or around the HHD regions, suggesting that these signals are likely due to single loss-of-function mutation or small structural variations. Further research should focus on exploring these regions using whole genome sequence data.

The online version contains supplementary material available at 10.1007/s13353-025-00978-0.