Kinship and network analysis of two South African beef cattle breeds using pedigree and high-density SNP markers

Abstract

Accurate genealogical records are essential in livestock breeding for maintaining genetic diversity, preventing inbreeding, and mapping of economically important traits in beef production. This study aimed to assess parent–offspring relationships within South African Bonsmara and Nguni cattle populations using both traditional pedigree records and genomic data. Hair samples from 119 Nguni and 311 Bonsmara cattle were genotyped using the BovineSNP50 array, and these were imputed to Illumina BovineHD BeadChip using updated SNP coordinates from the assembly genome (ARC—UCSD 1.2). Quality control and data filtering were performed using PLINK v1.9, while relationship inference was conducted using KING v2.2.8 and PLINK v1.9 software for principal component analysis, IBD metrics and Mendelian error-based exclusion. Categories of relatedness through network relationship analysis revealed a predominance of half-sibling relationships in both breeds, with 2317 such relationships identified in Nguni and 1221 in Bonsmara. Inference of parent–offspring pairs showed discrepancies with the recorded pedigrees, with 49 inferred pairs compared to 47 recorded pairs in Nguni, and 62 inferred pairs compared to 75 pairs recorded in Bonsmara. Relationships based on IBD using PLINK with a ‘PI-HAT’ threshold greater than 0.45 revealed unique parent–offspring inferences that differed from those obtained using KING v2.2.8. Phylogenetic network analysis assigned each individual’s genomic origin independent of the pedigree records, supporting the efficiency of SNP data for genetic assignment. These results demonstrated that SNP-based pedigree verification can accurately identify parent–offspring and half-sibling relationships, providing a reliable foundation for recombination analysis and supporting precise trait mapping and informed selection in breeding programs.