Genetics underlying phenotypic diversity in South African sheep breeds

Abstract

This study investigates genetic diversity and morphological trait-associated genes in 897 genotyped animals from 14 African sheep breeds. The breeds include Blackhead Persian (BHP), Damara (DAM), Dorper (DOR), Fat-tail (FTT), Karakul (KAR), Meatmaster (MMR), Merino (MER), Namakwa Afrikaner (NAM), Pedi (PED), White Dorper (WDOR), Zulu (ZUL), Ethiopian Menz (EMZ), Ronderib Afrikaner (RDA), and Red Massai (RMA), with the latter three obtained from the WIDDE platform. Results showed lowest genomic heterozygosity in ZUL (0.308) and highest in MER (0.352). PCA analysis based on genome-wide SNPs revealed clustering mostly according to pre-defined populations. Morphological traits were analysed using pairwise FST values and overlapping ROH for tail length, fibre type, coat colour, and horn presence. Coat colour-related genes (ASIP, MC1R, TYRP1) were near regions with the highest FST values. In the horned phenotype population, overlapping ROH was found near the HOXD1 gene, linked to horn development. For hair phenotypes, two keratin-associated genes (KRTAP6–1, LOC101104027), and FGF5, which regulates the hair cycle, were identified. The wool phenotype featured DLX3, related to wool quality. Five genes associated with tail growth were identified in the fat-tailed phenotype populations, including PDGFD, identified in both FST analyses of long and short fat-tailed phenotypes. High differentiation at the BMP2 gene that is linked to tail fat deposition was noted between long fat-tailed and thin-tailed phenotypes. Using SNP genotypes, we clarified the phylogenetic relationships between various indigenous and locally developed sheep breeds and confirmed the conservation of certain genomic areas associated with morphological traits in local populations.

HIGHLIGHTS • Fourteen sheep breeds with diverse phenotypes were investigated using SNP. • PCA analysis revealed clusters based on breed, production, and phenotypic traits. • Key genes were identified for coat colour, tail morphology, and horn types. • Indigenous breeds showed high genetic diversity, contrary to inbreeding concerns. • SNP analysis clarified phylogeny and adaptation in African sheep breeds.