Accurate determination of breed origin of alleles in a simulated smallholder crossbred dairy cattle population

Background Accurate assignment of breed origin of alleles at a heterozygote locus may help to introduce a resilient or adaptive haplotype in crossbreeding. In this study, we developed and tested a method to assign breed of origin for individual alleles in crossbred dairy cattle. After generations of mating within and between local breeds as well as the importation of exotic bulls, five rounds of selected crossbred cows were simulated to mimic a dairy breeding programme in the low- and middle-income countries (LMICs). In each round of selection, the alleles of those crossbred animals were phased and assigned to their breed of origin (being either local or exotic). Results Across all core lengths and modes of phasing (with offset or no), the average percentage of alleles correctly assigned a breed origin was 95.76%, with only 1.39% incorrectly assigned and 2.85% missing or unassigned. On consensus, the average percentage of alleles correctly assigned a breed origin was 93.21%, with only 0.46% incorrectly assigned and 6.33% missing or unassigned. This high proportion of alleles correctly assigned a breed origin resulted in a high core-based mean accuracy of 0.99 and a very high consensus-based mean accuracy of 1.00. The algorithm’s assignment yield and accuracy were affected by the choice of threshold levels for the best match of assignments. The threshold level had the opposite effect on assignment yield and assignment accuracy. A less stringent threshold generated higher assignment yields and lower assignment accuracy. Conclusions We developed an algorithm that accurately assigns a breed origin to alleles of crossbred animals designed to represent breeding programmes in the LMICs. The developed algorithm is straightforward in its application and does not require prior knowledge of pedigree, which makes it more relevant and applicable in LMICs breeding programmes. ### Competing Interest Statement RCG and JMH are now employed by Bayer Crop Science. * ADGG : African Dairy Genetic Gains BOA : Breed Origin of Allele CTLGH : Centre for Tropical Livestock Genetics and Health LMICs : Low- and middle-income countries MaCS : Markovian Coalescent Simulator SNP : Single Nucleotide Polymorphism