Parent-offspring genotyped trios unravelling genomic regions with gametic and genotypic epistatic transmission bias on the cattle genome

Samir Id-Lahoucine; Joaquim Casellas; Filippo Miglior; Flavio S Schenkel; Angela Cánovas

doi:10.3389/fgene.2023.1132796

Parent-offspring genotyped trios unravelling genomic regions with gametic and genotypic epistatic transmission bias on the cattle genome

Front Genet. 2023 Apr 6:14:1132796. doi: 10.3389/fgene.2023.1132796. eCollection 2023.

Authors

Samir Id-Lahoucine¹, Joaquim Casellas², Filippo Miglior¹, Flavio S Schenkel¹, Angela Cánovas¹

Affiliations

¹ Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada.
² Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Barcelona, Spain.

Abstract

Several biological mechanisms affecting the sperm and ova fertility and viability at developmental stages of the reproductive cycle resulted in observable transmission ratio distortion (i.e., deviation from Mendelian expectations). Gene-by-gene interactions (or epistasis) could also potentially cause specific transmission ratio distortion patterns at different loci as unfavorable allelic combinations are under-represented, exhibiting deviation from Mendelian proportions. Here, we aimed to detect pairs of loci with epistatic transmission ratio distortion using 283,817 parent-offspring genotyped trios (sire-dam-offspring) of Holstein cattle. Allelic and genotypic parameterization for epistatic transmission ratio distortion were developed and implemented to scan the whole genome. Different epistatic transmission ratio distortion patterns were observed. Using genotypic models, 7, 19 and 6 pairs of genomic regions were found with decisive evidence with additive-by-additive, additive-by-dominance/dominance-by-additive and dominance-by-dominance effects, respectively. Using the allelic transmission ratio distortion model, more insight was gained in understanding the penetrance of single-locus distortions, revealing 17 pairs of SNPs. Scanning for the depletion of individuals carrying pairs of homozygous genotypes for unlinked loci, revealed 56 pairs of SNPs with recessive epistatic transmission ratio distortion patterns. The maximum number of expected homozygous offspring, with none of them observed, was 23. Finally, in this study, we identified candidate genomic regions harboring epistatic interactions with potential biological implications in economically important traits, such as reproduction.

Keywords: Holstein; allelic and genotypic parameterizations; epistasis; genotyped trios; transmission ratio distortion.

Grants and funding

Authors thank the financial support in main part by Ontario Ministry of Agriculture, Food, and Rural Affairs (OMAFRA; Ontario, Canada), the Ontario Agri-Food Innovation Alliance, Agriculture and Agri-Food Canada, and by the Sustainable Beef and Forage Science Cluster (FDE.13.17) funded by the Canadian Beef Cattle Check-Off, Beef Cattle Research Council (BCRC), Alberta Beef Producers, Alberta Cattle Feeders’ Association, Beef Farmers of Ontario, La Fédération des Productuers de bovins du Québec, and Agriculture and Agri-Food Canada’s Canadian Agricultural Partnership. This study was also supported by NSERC (Natural Sciences and Engineering Research Council).