Selection signatures associated with adaptation in South African Drakensberger, Nguni, and Tuli beef breeds

Abstract

Climate change is an important consideration for sustainable beef production systems. Sanga cattle (Bos taurus africanus) are a unique genetic resource known for their adaptability to diverse climates. Genomic technologies have allowed opportunities to investigate indigenous cattle at the deoxyribonucleic acid (DNA) and genome level for insight into variation associated with adaptive traits. 1709 cattle, including 1118 Drakensberger (DRB), 377 Nguni (NGI), and 214 Tuli (TUL), were genotyped using the GeneSeek® Genomic Profiler™ 150K bovine SNP panel. 122632 quality-filtered SNPs was used to assess runs of homozygosity (ROH) and runs of heterozygosity (ROHet) within the three cattle populations using the detectRUNS R package (Biscarini et al., 2018) and PLINK v1.90 (Purcell et al., 2007). The study identified selection signatures associated with adaptation within-and-between three breeds based on ROH, ROHet, and FST-based differentiation of SNPs. The mean number of ROH per animal varied across breeds ranging from 36.09 ± 12.82 (NGI) to 51.82 ± 21.01 (DRB), and the mean ROH length per breed ranged between 2.31Mb (NGI) and 3.90Mb (DRB). The smallest length categories i.e., ROH < 4Mb and ROHet < 0.25Mb were most frequent, indicating predominantly historic inbreeding effects for all breeds. The ROH based inbreeding coefficients (FROH) ranged between 0.033 ± 0.024 (NGI) and 0.081 ± 0.046 (DRB). Genes mapped to candidate regions were associated with immunity (ADAMTS12, CYSTM1, WDPCP) and adaptation (LMAN2, TUBB3) in cattle as well as genes previously only reported for immunity in mice and human (EXOC3L1, MYO1G). This study contributes to the understanding of the mechanisms of adaptation, providing information for functional genomic studies and application in genetic evaluation and selection programs.