GWAS & Selection signatures

Genomic prediction of components of heterosis for crosses of cattle breeds and advanced intercross lines of chicken

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Abstract

Heterosis is an extremely important part of genetic systems in livestock, as evidenced by commercial (terminal) crosses in chicken and pig, as well as the establishment of composite lines/breeds in many species. Key components of heterosis are dominance and epistatic effects. Dominance effects are typically positive, due to an increased portfolio of solutions to environmental disturbances due to a higher number of different alleles caused by increased heterozygosity across the genome. Epistatic effects are expected to be negative, due to break-up of established positive interactions of genes within populations. This has been evidenced when crossing high yielding cattle breeds from regions with a history of genetic improvement with local breeds in developing countries. F1 crosses are doing really well in comparison averages of parental breeds, while F2, expected to express half the heterosis based on dominance effects, are doing worse than expected. Traditionally, levels dominance and epistasis have been derived from pedigrees, using various formulae. Genomics provides options of estimating such effects even without pedigrees available. Local ancestry calculation along the chromosomes provides evidence whether the two alleles of a locus of an individual are derived from either breed (i.e. are "breed homozygous" for one breed) of are derived form two breeds ("breed heterozygous"). Calculation of levels of breed difference, dominance and epistatic loss can be derived from these ancestry states.Here, we are presenting results from Swiss Fleckvieh, an advanced cross of Simmental and Holstein Friesian cattle, from recent crosses of Holstein Friesian and local cattle in Ethiopia, and generations 18 and 19 of advanced intercross lines (AIL) of Fayoumi inbred line x Broiler chicken. The study on sperm quality phenotypes of 1,179 Swiss bulls genotyped with a 50k SNP chip gave results according to expectations outlined above. Epistatic loss, when defined as proportion of 100,000 randomly selected pairs of loci showing alternative breed homozygous pairs of alleles, was strong. Results for recent crosses of Holstein Friesian x Ethiopian local breeds, based on 69,915 milk records and 5,300 calving interval records of 4,759 genotyped animals with 38,344 quality controlled SNP indicate strong dominance effects for milk production and calving interval. For heat stressed advanced interline crosses of 839 chickens with phenotypes and 431,399 SNP genotypic data measured for phenotypes including body weight and various blood parameters, significant dominance effects were only found for carbon dioxide partial pressure (PCO2). Significant negative epistatic estimates were observed for body weight, base excess and PCO2, while epistasis was positive for oxygen saturation. Prediction of heterosis effects from genomic data is an effort worth its while and should be done more frequently.

Keywords: 2026

How to Cite:

Sölkner, J., Khayatzadeh, N., Gebreselama, T., Meseret, S., Mrode, R., Gebreyohanes, G., Lamont, S., Van Goor, A., Curik, I. & Gebre, K., (2026) “Genomic prediction of components of heterosis for crosses of cattle breeds and advanced intercross lines of chicken”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286263. doi: https://doi.org/10.31274/wcgalp.23899

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