Novel harmful recessive haplotypes identified for fertility traits in Nordic Holstein cattle

PLoS One. 2013 Dec 20;8(12):e82909. doi: 10.1371/journal.pone.0082909. eCollection 2013.


Using genomic data, lethal recessives may be discovered from haplotypes that are common in the population but never occur in the homozygote state in live animals. This approach only requires genotype data from phenotypically normal (i.e. live) individuals and not from the affected embryos that die. A total of 7,937 Nordic Holstein animals were genotyped with BovineSNP50 BeadChip and haplotypes including 25 consecutive markers were constructed and tested for absence of homozygotes states. We have identified 17 homozygote deficient haplotypes which could be loosely clustered into eight genomic regions harboring possible recessive lethal alleles. Effects of the identified haplotypes were estimated on two fertility traits: non-return rates and calving interval. Out of the eight identified genomic regions, six regions were confirmed as having an effect on fertility. The information can be used to avoid carrier-by-carrier mattings in practical animal breeding. Further, identification of causative genes/polymorphisms responsible for lethal effects will lead to accurate testing of the individuals carrying a lethal allele.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Breeding / statistics & numerical data*
  • Cattle
  • Female
  • Fertility / genetics*
  • Genes, Lethal*
  • Genetic Markers
  • Genotyping Techniques
  • Haplotypes*
  • Heterozygote
  • Homozygote*
  • Male
  • Phenotype
  • Polymorphism, Single Nucleotide


  • Genetic Markers

Grants and funding

This work was performed in the projects ‘Genomic Selection – from function to efficient utilization in cattle breeding’ (grant no. 3412-08-02253), funded by the Danish Directorate for Food, Fisheries and Agri Business, VikingGenetics, Nordic Cattle Genetic Evaluation, and Aarhus University, and ‘DNA based selection to improve disease resistance, fertility, calf survival and production in Danish cattle’ (grant no. 3401-04-00853), funded by the Danish Directorate for Food, Fisheries and Agri Business. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.