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

Abstract

Climate change has become a major factor influencing beef production systems. Sanga cattle are a unique genetic resource renowned for their adaptability to diverse climatic conditions. The advent of genomic technologies has allowed opportunities to examine these indigenous cattle at the Deoxyribonucleic acid (DNA) level and may provide insight into genome-level variation associated with adaptive traits. This study aimed to identify signatures of selection within and across the South African Drakensberger (DRB), Nguni (NGI), and Tuli (TUL) populations. A total of 1 706 animals, including 1 117 DRB, 377 NGI, and 214 TUL, were genotyped using GeneSeek® Genomic Profiler™ 150K bovine SNP panel. The R (Biscarini et al., 2018) and PLINK v1.90 (Purcell et al., 2007) analysis tools were used to estimate ROH, ROHet and FST values. A set of 122 632 quality-filtered SNPs were utilized to identify genomic regions under selection based on conserved runs of homozygosity (ROH) and FST-based differentiation of SNPs. The ROH were calculated for various length categories, and a total of 82 871 ROH were identified across all three breeds (mean±standard deviation ROH/animal: DRB=51.82±21.01; NGI=36.09±12.82; TUL=47.94±15.33), with a mean length of 3.90Mb, 2.31Mb and 3.76Mb respectively. The short ROH segments (ROH <4Mb) were most frequent in all breeds. The highest average FROH was observed in DRB (0.081±0.046) followed by TUL (0.074±0.031), while the lowest FROH was found in NGI (0.033±0.024). The estimated mean FST valued between 0.060 (DRB vs NGI & DRB vs TUL), and 0.040 (NGI vs TUL). To identify within-breed selection signatures, genomic regions with the highest frequency for ROH and runs of heterozygosity (ROHet) and observed in more than 20% and 30%, respectively, of the individuals in the population were considered selection signatures. For across-breed selection signatures, regions with FST values falling within the top 0.1% of the empirical FST distribution were considered signatures of positive selection. Annotation of these regions revealed genes which have previously been associated with traits of economic importance such as immunity and adaptation (FKBP4, CTNNA2, MYC, CYSTM1, SRA1, SD14, WDPCP, DTX1, ELMO3, and ADAMTS12), coat colour (MCIR, TUBB3), and reproductive performance (SPARTA33, TCF35, RPS20, CORIN, TXK, NELL2, and TMEM181). Both within-breed (ROH) and across-breed (FST) approaches proved to be useful in identifying genomic regions under selection, and this may contribute to the understanding of the genetic architecture underlying the adaptive traits of local Sanga cattle for sustainable beef production in the future.