Genomic characterisation of two South African composite breeds in comparison to their base breeds
Phillipine Sithole , Este Van Marle-Köster, Simon Lashmar
University of Pretoria, Dept. of Animal Science, South Africa
South Africa (SA) exhibits great agricultural and ecological diversity, including extreme and ever-changing production environments that will necessitate adaptability and efficiency of animal genetic resources in the future. Through complementarity and heterosis, SA composite breeds combine the superior productivity of exotic taurine breeds with the adaptive and maternal traits of indicine and local Sanga breeds. Apart from the predominant composite (e.g., Bonsmara), numerically smaller composite breeds have not been characterised as well (neither on phenotype nor genotype-level) despite their contributions to local beef production. The aim of the study was to perform a genome-wide characterisation of the genetic diversity and population structure of two SA composite breeds, namely the Santa Gertrudis (SGT) and Simbra (SIM), and their base breeds, namely the Brahman (BRA) and Simmentaler (SMM). A total of 684 animals (BRA = 182, SMM = 261, SIM = 172, SGT = 69), genotyped with the Illumina® Bovine LD v.2 SNP genotyping panel (7 421 quality-filtered SNPs), were available. The average minor allele frequency (MAF) ranged from 0.182 (BRA) to 0.332 (SIM). The observed heterozygosity (HO) indicated the highest level of genetic diversity for SIM (HO = 0.432) and the lowest level for BRA (HO = 0.319). The fixation index (FST) values revealed the most genetic differentiation between the BRA and SMM breeds (FST = 0.208). Conversely, the SIM and SMM were the least differentiated (FST = 0.041). Principal component analysis (PCA) and model-based clustering (admixture) distinguished the breeds according to ancestral origin and breed development. PCA clustered all the SGT animals in one cluster separate from the others. At K=2, the taurine and indicine ancestral contributions towards the SIM breed was illustrated and reflected the originally intended composition of the breed (i.e., 5/8 SMM and 3/8 BRA). The estimated effective population sizes (Ne) in the last 12 generations ago ranged from 215 (SGT) to 316 (SMM), indicating a higher risk of inbreeding for SGT if not managed carefully. The results presented an insight into the genome-level diversity present in two smaller composite breeds and will assist in making more informed breed management and selection decisions for future sustainable use.
Keywords: Beef cattle, composite breeds, genetic diversity, SNP panel
Contact Address: Phillipine Sithole , University of Pretoria, Dept. of Animal Science, 538 Grosvenor Street, 0083 Pretoria, South Africa, e-mail: u21771970tuks.co.za