Using genotypes from Australia’s numerically smaller sheep breeds to expand the genomic reference population

Genetic evaluation of animals with different population ancestry needs to deal with differences in their founder populations or breeds. To accommodate these differences allele frequencies from different genetic groups can be used to correct the genomic relationship matrix to reduce breed and group structure. The majority of the Australian sheep population is comprised of animals originating from 11 major breeds. However, smaller breeds are also used to create crossbred animals for different breeding objectives. To properly include these animals into a multibreed genetic evaluation, the allele frequencies of smaller and often missing breeds need to be included into the allele frequencies of the wider population. This work investigated the use of genotypes from smaller breeds and crossbred populations that are currently not included in the Australian national genetic evaluation (LAMBPLAN) because reference populations for imputation and inclusion in breed adjusted genomic relationship matrices have not been established. Genotypes from 50,999 animals originating from fifteen numerically smaller meat, wool and maternal sheep breeds were combined in a genetic analysis to investigate population structure and diversity within and across breeds and define breed composition. Results are expected to increase the number of animals included in the genetic evaluation and improve prediction accuracy in Australian crossbred populations.