Genomic diversity and autozygosity within the SA Drakensberger beef cattle breed

Abstract

The SA Drakensberger, as a Sanga beef breed, is a composite of Bos taurus and Bos indicus subspecies. Variation within admixed genomes will influence downstream applications such as imputation and genomic selection (GS). Being an indigenous breed with unique characteristics, such as the black coat, within-breed selection of the SA Drakensberger has focused on maintaining breed purity, which furthermore predisposes the breed to inbreeding. This study aimed to primarily identify possible patterns of variation in population-specific parameters such as minor allele frequency (MAF) and linkage disequilibrium (LD) that might influence the accuracy of future genomic applications. Second, the study investigated possible patterns of genomic uniformity using runs of homozygosity (ROH) as a measure of inbreeding. Average genome-wide MAF was 0.26 with chromosome-specific MAF ranging from 0.24 (Bos Taurus Autosome; BTA14) to 0.28 (BTA21). The proportion of low-MAF (< 5%) SNPs supported average estimates, ranging from 6.6% for BTA23 to 16.0% for BTA14. The r2 measure of LD was 0.14, 0.17 and 0.22, respectively, when SNPs separated by ≤ 1Mb, ≤ 0.1Mb and ≤ 0.05Mb were considered. LD was generally low, ranging from r2 = 0.11 (BTA28) to r2 = 0.17 (BTA14) for SNPs separated by ≤ 1Mb and r2 = 0.20 extended only up to < 30 kb. LD was weaker between SNP pairs including low-MAF SNPs. The ROH identified were predominantly shorter in length, with more than 50% (54.5%) of ROH falling within the < 4Mb length interval. Consensus ROH segments were identified and the most prevalent of these occurred on BTA14 and was identified in ∼23% of the sampled population. All coefficients of inbreeding indicated low levels of inbreeding, which corresponded to 3% (FPED), 1% (FSNP) and 7% (FROH>1Mb). Correlations of FPED with FSNP and FROH>1Mb were moderate equating to values of ∼0.63 and ∼0.64 (P < 0.001), respectively. Such moderate correlations could be attributed to the incompleteness of pedigree records. The direct impact of MAF, LD and relatedness on the accuracy of within-breed genetic improvement strategies and its accompanying methodologies, such as imputation, may influence how different chromosomes are treated or accounted for in future genomic endeavors.