Genetic characterization of Mozambican Nguni cattle and their relationship with indigenous populations of South Africa

Abstract

Knowledge of genetic variability among cattle populations is essential to gain insight into the adaptation mechanisms to different environments and to support the conservation of genetic resources. Individuals from Mozambican Nguni (MZ Nguni; n = 119), South African Nguni (SA Nguni; n = 150), South African Tuli (SA Tuli; n = 150), and South African Boran (SA Boran; n = 150) cattle populations were genotyped using the International Dairy and Beef SNP BeadChip version three (IDB) and the GeneSeek Genomic Profiler (GGP 80k) assays, to investigate their levels of genetic diversity and the relationships between these indigenous breeds. Levels of genetic diversity, assessed by expected heterozygosity (He), varied from 0.284 (SA Boran) to 0.324 (SA Tuli). Population structure, as well as principal component analysis (PCA), revealed tight clustering of the two Nguni populations, while the SA Tuli and SA Boran populations diverged, as expected, into two distinct clusters. Little genetic distance (0.031) was observed among MZ Nguni and SA Nguni, while SA Boran (a Zebu breed) was further removed from SA Tuli than from the other Sanga cattle populations. Runs of homozygosity (ROH) analysis revealed low inbreeding rates (with the average FROH per population ranging from 0.003 to 0.006). Short ROH segments (ROH ≤ 5 Mb) were more frequent in all four populations than longer segments, suggesting more ancient inbreeding in these populations. The highest number of ROH (303) was observed in SA Tuli, while the lowest (56) was detected in SA Nguni. Analysis of both Wright's fixation index (FST) and ratio of extended haplotype homozygosity (Rsb) identified a total of 229 differentiated single nucleotide polymorphisms (SNP) to be under selection, in a comparison between the MZ Nguni cattle and South African cattle populations. Highly differentiated SNP (FST ≥ 0.26 or pRsb ≥ 3) indicated genes including KLHL29, ZEB2, LAMC1, MYLK3, and KCNK5 that are implicated in several metabolic processes essential for adaptation and production traits.