The assessment of the genetic improvement of South African composite breeds and their respective foundation breeds

Abstract

South Africa (SA) has a diverse climate that poses potential challenges for future beef production. Different composite breeds that combine the superior growth and beef-producing potential of the European Bos taurus breeds with the adaptive traits of Bos taurus africanus and Bos indicus breeds have been well established over the past century. Even though composite breeds have been used extensively in SA livestock production, research efforts focusing on these breeds have been sparse. The aim of this study was to utilize phenotypic and genotypic data to characterize the genetic status of three SA composite beef breeds (Braford, Santa Gertrudis, and Simbra) in comparison to their selected founder breeds namely, Brahman and Simmentaler. The phenotypic data for the different breeds consisted of pedigree data from the establishment of the herdbook (1957 – 1997) up to 2020. Based on PopReport analysis pedigree completeness (PIC) between composite breeds over six generations was higher than 90% and across breeds PIC in the six-generation depth varied from 24.90% for the Braford to 88.00% for both the Simmentaler and Brahman breed. The average inbreeding coefficient per year was low across all the breeds ranging from 0.011% (Braford) to 0.054% (Simmentaler). The effective population size (Ne) across the breeds varied from 152 in the Santa Gertrudis breed to 750 in the Braford breed respectively. The average genetic change calculated by averaging the estimated breeding values (EBVs) from 2000 to 2020 was investigated for reproduction, growth, and carcass traits. Genetic trends for reproductive trends were favorable in all the breeds varying from -0.088 in days to calving (DC) to +0.020 in scrotal circumference (SC) trait. The Santa Gertrudis breed had a slightly higher birth weight (BW) compared to the Braford and Simbra breeds. Across the breeds, the overall genetic trends for growth traits varied from +0.007 (BW) in the Simmentaler to +0.737 (MCW) in the Simbra breed. Carcass weight (CW) based on real-time ultrasonic records (RTU) across the breeds ranged from 9.80 kg in the Braford breed to 19.12 kg in the Brahman breed in 2020. A total of 5 210 (Illumina® Bovine 7K) and 103 646 (Genomic ProfilerTM Bovine 150K SNP) SNPs after quality control (QC) were available for genomic analysis. Results of the study across the breeds indicated that the Simbra breed had the highest level of genetic diversity (HO = 0.427; 0.413) for both panels and the Brahman had the lowest level of genetic diversity (HO = 0.291; 0.016). Principal component analysis (PCA) and model-based clustering algorithms distinguished the breeds according to their ancestral origin with the Santa Gertrudis animals clustered separate from the other breeds. Admixture analysis revealed that the Simbra is a composite breed composed of 58.1% (Simmentaler) and 26.4% (Brahman) genetic composition. The estimated Ne in the last 12 generations ago across the breeds ranged from 215 (Santa Gertrudis) to 316 (Simmentaler) indicating a higher risk of inbreeding for the Santa Gertrudis if not managed carefully. The results of the study indicated genetic improvement in composite breeds compared to its selected founder breeds over the years, indicating that these breeds have the potential for sustainable beef production in both commercial and non-commercial beef production systems.