mRMC: A rotating multi-gene pyramiding scheme based on the principle of minimum rotation and maximum complementarity in animals

Abstract Background Gene pyramiding is a breeding process used to combine multiple favorable alleles of target genes from different breeds into a single population. Existing strategies in plants aim to obtain a small number of “ideal individuals” and form inbred lines through asexual reproduction or inbreeding methods. However, animals exhibit distinct features, including sexual reproduction with low reproductive ability and intolerance to inbreeding. These limitations hinder the implementation of existing strategies in animals. Results “Breeding by Design” is a concept that aims to strategically assemble known favorable alleles at major-effect loci of agronomic importance into breeding populations. To accelerate this process of in animals, we proposed a rotating scheme named “mRMC” (Minimum Rotation and Maximum Complementarity) as an effective design for multi-gene pyramiding. The mRMC is designed to match paternal lines with “the least rotation of labels (min-rotation) and the most complementary (max-complementarity)” genotype to form mating pairs. We compared this method with existing schemes in a simulation of breeding animals. The results showed that, to obtain all-target-gene carriers, mRMC reduced the required number of generations by three and one compared with cascading and noncascading pyramiding method, respectively. The average minor allele frequency (MAF) of all gene makers in the population under mRMC was the highest among all the schemes in each generation. The inbreeding level of the mRMC was lower and changed less throughout the entire process than the other pyramiding schemes. Additionally, upon completion of pyramiding, compared with the other two schemes, mRMC reduced the loss of genetic gain by 17.70% and 11.76%, respectively. Conclusions Overall, the proposed mRMC demonstrated clear superiority over existing methods for animal breeding. This strategy will improve breeding schemes and facilitate studies on gene pyramiding in animals.