Genomic characterisation of the South African Wagyu populations

Abstract

A genomic characterisation was performed on South African (SA) Wagyu cattle based on pedigree and genomic data. The pedigree-based analysis was performed on records of SA animals between 2000 and 2022, with a minimum of 50% Akaushi (AK: 5 108), Japanese Black (JB: 42 237) and combined Wagyu genetic content (AK and JB combined > 50%; 51 632). The genotypic analysis was performed on the available single nucleotide polymorphism (SNP) genotypes of fullblood and purebred animals. Subtotals of 205 and 439 genotypes were available for the SA Akaushi and Japanese Black Wagyu breeds, while 731 Australian Japanese Black genotypes were made available due to potential genetic linkage between the Japanese Black populations. The genotypes were generated using the Unistel BovineSNP50 v3 BeadChip or Neogen GGP Bovine 100K SNP array. The pedigree-based population analysis was performed using PopReport (Groeneveld et al., 2009). Pedigree completeness, generation interval, average inbreeding and effective population size were evaluated. Pedigree completeness for the SA Wagyu population was low, with an overall completeness of 33.14%. There is a positive trend for an increase in pedigree recording over the past 6 generations. Genotypic analysis with the use of Principal Component analysis (PCA) indicated that the SA Akaushi and Japanese Black populations are two separate populations, and they were treated separately in the subsequent genomic analysis. The population structure investigated with the use of ADMIXTURE (Alexander et al., 2009) supported the results of the PCA. Additionally, genomic parameters indicated a slightly higher genomic variation (He = 0.30) within the SA Japanese Black compared to the Australian subset (He = 0.28). Inbreeding coefficients were negative for the Akaushi and both Japanese Black subsets. The genomic inbreeding (FROH) revealed higher levels of inbreeding in the SA Akaushi population (0.17) in comparison to the Japanese Black populations from SA (0.07) and Australia (0.09), respectively. This study provides a benchmark of the population structure and genomic diversity of the SA Wagyu. It is important to note the distinct genomic difference between the Akaushi and Japanese Black Wagyu and this information can be applied in future genetic management and selection of SA Wagyu.