The genomic characterization of the South African Bonsmara using whole-genome sequencing data

Abstract

The South African Bonsmara, a Sanga-derived composite breed, originally developed to be genetically composed of five-eighths Afrikaner (Sanga subspecies) and three-eighths Hereford and Shorthorn, is well-adapted to the diverse South African climate. The breed has an open herd book where females are added based on phenotypic inspection of functional traits, having an unknown base composition of the modern-day Bonsmara. In this study, whole genome sequence (WGS) data of 18 founder animals, and 105 modern-day animals were analysed to assess the within-breed variation, inbreeding and admixture of the Bonsmara and its base breeds. Four Afrikaner (AFR), four Bonsmara (BON), and two Hereford (HFD) animals were sequenced as part of the Beef Genomics Project (BGP), whereas the other eight Hereford founder animals were obtained from the European Nucleotide Archive (ENA) at EMBL-EBI. Furthermore, the whole genome sequence data of the 105 modern-day animals representative of current Bonsmara, Afrikaner and Shorthorn (SHH) herds were added. Following standard quality control, using Plink v2.0, a total of 543 791 and 367 764 autosomal single nucleotide polymorphisms were available for downstream analysis for the founder and modern-day animals, respectively. The average heterozygosity values for the founder animals were highest in the HER (0.580), followed by the BON (0.510) and AFR (0.431), with average inbreeding coefficients (FIS) of -0.572, -0.357 and -0.122 for the HFD, BON and AFR, respectively. The average heterozygosity values for the modern-day animals were highest in the BON (0.379), followed by the AFR (0.329) and the SHH (0.305). Moreover, the inbreeding coefficients for the modern-day animals were 0.154, 0.026 and 0.174 for the AFR, BON and SHH, respectively. Genomic structure analysis indicated that the Bonsmara have the most admixed genome, confirming the development of the breed. The genomic structure analysis also unveiled the ancestry shared between the Bonsmara and certain Afrikaner cattle, confirming infusion used by some breeders. Furthermore, it showed a clear separation between the founder animals and the modern-day animals, despite being from the same breed, with ancestry shared between all of the founders. A comprehensive genomic characterization of the Bonsmara and its base breeds with the use of WGS data will aid in detecting genome-level changes in the historic versus modern genetic composition of the breed over time.